Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

Elham Azizi ¹, Ambrose J Carr ², George Plitas ³, Andrew E Cornish ¹, Catherine Konopacki ⁴, Sandhya Prabhakaran ¹, Juozas Nainys ⁵, Kenmin Wu ⁶, Vaidotas Kiseliovas ⁷, Manu Setty ¹, Kristy Choi ⁸, Rachel M Fromme ⁹, Phuong Dao ¹, Peter T McKenney ¹⁰, Ruby C Wasti ¹¹, Krishna Kadaveru ¹¹, Linas Mazutis ¹, Alexander Y Rudensky ¹², Dana Pe'er ¹³

Affiliations

¹ Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
² Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Biological Sciences, Columbia University, New York, NY, USA.
³ Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Breast Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
⁴ Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
⁵ Department of Biological Sciences, Columbia University, New York, NY, USA; Sector of Microtechnologies, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.
⁶ Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
⁷ Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Sector of Microtechnologies, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.
⁸ Department of Biological Sciences, Columbia University, New York, NY, USA.
⁹ Breast Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
¹⁰ Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA.
¹¹ Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA.
¹² Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: rudenska@mskcc.org.
¹³ Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: peerd@mskcc.org.

PMID: 29961579
40 References
531 citations

Abstract

Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We profiled 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph nodes, using single-cell RNA-seq. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. Despite significant similarity between normal and tumor tissue-resident immune cells, we observed continuous phenotypic expansions specific to the tumor microenvironment. Analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data from 27,000 additional T cells revealed the combinatorial impact of TCR utilization on phenotypic diversity. Our results support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer. Our results have important implications for characterizing tumor-infiltrating immune cells.

Keywords: Bayesian modeling; T cell activation; TCR utilization; breast cancer; single-cell RNA-seq; tumor microenvironment; tumor-infiltrating immune cells.

Other Links

Free PMC article
Full text on Cell

References
Cited By

References
The cellular and molecular origin of tumor-associated macrophages. Ruth A Franklin, Will Liao, +5 authors, Ming O Li. less Science, 2014 May 09; 344(6186). PMID: 24812208 Free PMC article. Highly Cited.
The role of myeloid cells in cancer therapies. Camilla Engblom, Christina Pfirschke, Mikael J Pittet. Nat Rev Cancer, 2016 Jun 25; 16(7). PMID: 27339708 Highly Cited. Review.
viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. El-ad David Amir, Kara L Davis, +7 authors, Dana Pe'er. less Nat Biotechnol, 2013 May 21; 31(6). PMID: 23685480 Free PMC article. Highly Cited.
Regulatory T cells in cancer immunotherapy. Atsushi Tanaka, Shimon Sakaguchi. Cell Res, 2016 Dec 21; 27(1). PMID: 27995907 Free PMC article. Highly Cited. Review.
The M1 and M2 paradigm of macrophage activation: time for reassessment. Fernando O Martinez, Siamon Gordon. F1000Prime Rep, 2014 Mar 29; 6. PMID: 24669294 Free PMC article. Highly Cited. Review.
Near-optimal probabilistic RNA-seq quantification. Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol, 2016 Apr 05; 34(5). PMID: 27043002 Highly Cited.
Hypoxia, inflammation, and the tumor microenvironment in metastatic disease. Elizabeth C Finger, Amato J Giaccia. Cancer Metastasis Rev, 2010 Apr 16; 29(2). PMID: 20393783 Free PMC article. Highly Cited. Review.
Treg cells expressing the coinhibitory molecule TIGIT selectively inhibit proinflammatory Th1 and Th17 cell responses. Nicole Joller, Ester Lozano, +13 authors, Vijay K Kuchroo. less Immunity, 2014 Apr 22; 40(4). PMID: 24745333 Free PMC article. Highly Cited.
An Immune Atlas of Clear Cell Renal Cell Carcinoma. Stéphane Chevrier, Jacob Harrison Levine, +14 authors, Bernd Bodenmiller. less Cell, 2017 May 06; 169(4). PMID: 28475899 Free PMC article. Highly Cited.
Relevance of tumor-infiltrating lymphocytes in breast cancer. Sathana Dushyanthen, Paul A Beavis, +5 authors, Sherene Loi. less BMC Med, 2015 Aug 25; 13. PMID: 26300242 Free PMC article. Highly Cited. Review.
Neoantigen landscape dynamics during human melanoma-T cell interactions. Els M E Verdegaal, Noel F C C de Miranda, +11 authors, Sjoerd H van der Burg. less Nature, 2016 Jun 29; 536(7614). PMID: 27350335 Highly Cited.
Between-region genetic divergence reflects the mode and tempo of tumor evolution. Ruping Sun, Zheng Hu, +6 authors, Christina Curtis. less Nat Genet, 2017 Jun 06; 49(7). PMID: 28581503 Free PMC article. Highly Cited.
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Itay Tirosh, Benjamin Izar, +34 authors, Levi A Garraway. less Science, 2016 Apr 29; 352(6282). PMID: 27124452 Free PMC article. Highly Cited.
Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing. Chunhong Zheng, Liangtao Zheng, +13 authors, Zemin Zhang. less Cell, 2017 Jun 18; 169(7). PMID: 28622514 Highly Cited.
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Yasin Şenbabaoğlu, Ron S Gejman, +26 authors, A Ari Hakimi. less Genome Biol, 2016 Nov 20; 17(1). PMID: 27855702 Free PMC article. Highly Cited.
Diffusion maps for high-dimensional single-cell analysis of differentiation data. Laleh Haghverdi, Florian Buettner, Fabian J Theis. Bioinformatics, 2015 May 24; 31(18). PMID: 26002886 Highly Cited.
Regulatory T cells: mechanisms of differentiation and function. Steven Z Josefowicz, Li-Fan Lu, Alexander Y Rudensky. Annu Rev Immunol, 2012 Jan 10; 30. PMID: 22224781 Free PMC article. Highly Cited. Review.
Immune checkpoint blockade: a common denominator approach to cancer therapy. Suzanne L Topalian, Charles G Drake, Drew M Pardoll. Cancer Cell, 2015 Apr 11; 27(4). PMID: 25858804 Free PMC article. Highly Cited. Review.
Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient. Alejandro Jiménez-Sánchez, Danish Memon, +16 authors, Martin L Miller. less Cell, 2017 Aug 26; 170(5). PMID: 28841418 Free PMC article. Highly Cited.
Positive regulation of immune cell function and inflammatory responses by phosphatase PAC-1. Kate L Jeffrey, Tilman Brummer, +10 authors, Charles R Mackay. less Nat Immunol, 2006 Feb 14; 7(3). PMID: 16474395
Single-cell barcoding and sequencing using droplet microfluidics. Rapolas Zilionis, Juozas Nainys, +4 authors, Linas Mazutis. less Nat Protoc, 2016 Dec 09; 12(1). PMID: 27929523 Highly Cited.
Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer. George Plitas, Catherine Konopacki, +5 authors, Alexander Y Rudensky. less Immunity, 2016 Nov 17; 45(5). PMID: 27851913 Free PMC article. Highly Cited.
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity. Jellert T Gaublomme, Nir Yosef, +10 authors, Aviv Regev. less Cell, 2015 Nov 27; 163(6). PMID: 26607794 Free PMC article. Highly Cited.
Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Noa Novershtern, Aravind Subramanian, +22 authors, Benjamin L Ebert. less Cell, 2011 Jan 19; 144(2). PMID: 21241896 Free PMC article. Highly Cited.
Hallmarks of Tissue-Resident Lymphocytes. Xiying Fan, Alexander Y Rudensky. Cell, 2016 Mar 12; 164(6). PMID: 26967286 Free PMC article. Highly Cited. Review.
Overcoming T cell exhaustion in infection and cancer. Kristen E Pauken, E John Wherry. Trends Immunol, 2015 Mar 24; 36(4). PMID: 25797516 Free PMC article. Highly Cited. Review.
Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses. Yonit Lavin, Soma Kobayashi, +26 authors, Miriam Merad. less Cell, 2017 May 06; 169(4). PMID: 28475900 Free PMC article. Highly Cited.
Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data. Sandhya Prabhakaran, Elham Azizi, Ambrose Carr, Dana Pe'er. JMLR Workshop Conf Proc, 2016 Jan 01; 48. PMID: 29928470 Free PMC article.
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. Bo Li, Colin N Dewey. BMC Bioinformatics, 2011 Aug 06; 12. PMID: 21816040 Free PMC article. Highly Cited.
Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps. R R Coifman, S Lafon, +4 authors, S W Zucker. less Proc Natl Acad Sci U S A, 2005 May 19; 102(21). PMID: 15899970 Free PMC article. Highly Cited.
Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Jacob H Levine, Erin F Simonds, +13 authors, Garry P Nolan. less Cell, 2015 Jun 23; 162(1). PMID: 26095251 Free PMC article. Highly Cited.
Chromatin states define tumour-specific T cell dysfunction and reprogramming. Mary Philip, Lauren Fairchild, +11 authors, Andrea Schietinger. less Nature, 2017 May 18; 545(7655). PMID: 28514453 Free PMC article. Highly Cited.
Molecular and cellular insights into T cell exhaustion. E John Wherry, Makoto Kurachi. Nat Rev Immunol, 2015 Jul 25; 15(8). PMID: 26205583 Free PMC article. Highly Cited. Review.
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Diego Adhemar Jaitin, Ephraim Kenigsberg, +8 authors, Ido Amit. less Science, 2014 Feb 18; 343(6172). PMID: 24531970 Free PMC article. Highly Cited.
Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Lucy R Yates, Moritz Gerstung, +35 authors, Peter J Campbell. less Nat Med, 2015 Jun 23; 21(7). PMID: 26099045 Free PMC article. Highly Cited.
A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. Meromit Singer, Chao Wang, +16 authors, Ana C Anderson. less Cell, 2016 Sep 10; 166(6). PMID: 27610572 Free PMC article. Highly Cited.
Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment. Sören Müller, Gary Kohanbash, +13 authors, Aaron Diaz. less Genome Biol, 2017 Dec 22; 18(1). PMID: 29262845 Free PMC article. Highly Cited.
Tumor-associated macrophages as a paradigm of macrophage plasticity, diversity, and polarization: lessons and open questions. Alberto Mantovani, Massimo Locati. Arterioscler Thromb Vasc Biol, 2013 Jun 15; 33(7). PMID: 23766387 Highly Cited.
The development and maintenance of resident macrophages. Elisa Gomez Perdiguero, Frederic Geissmann. Nat Immunol, 2015 Dec 19; 17(1). PMID: 26681456 Free PMC article. Highly Cited. Review.
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Allon M Klein, Linas Mazutis, +6 authors, Marc W Kirschner. less Cell, 2015 May 23; 161(5). PMID: 26000487 Free PMC article. Highly Cited.

Citedby
Tissue-Resident Lymphocytes Across Innate and Adaptive Lineages. Chun Chou, Ming O Li. Front Immunol, 2018 Oct 10; 9. PMID: 30298068 Free PMC article. Review.
Role of Hypoxic Stress in Regulating Tumor Immunogenicity, Resistance and Plasticity. Stéphane Terry, Rania Faouzi Zaarour, +6 authors, Salem Chouaib. less Int J Mol Sci, 2018 Oct 12; 19(10). PMID: 30301213 Free PMC article. Review.
Multi-Omics Profiling of the Tumor Microenvironment: Paving the Way to Precision Immuno-Oncology. Francesca Finotello, Federica Eduati. Front Oncol, 2018 Oct 23; 8. PMID: 30345255 Free PMC article. Review.
CD49b defines functionally mature Treg cells that survey skin and vascular tissues. Xiying Fan, Bruno Moltedo, +7 authors, Alexander Y Rudensky. less J Exp Med, 2018 Oct 26; 215(11). PMID: 30355617 Free PMC article.
Learning time-varying information flow from single-cell epithelial to mesenchymal transition data. Smita Krishnaswamy, Nevena Zivanovic, +2 authors, Roshan Sharma, Dana Pe'er, Bernd Bodenmiller. less PLoS One, 2018 Oct 30; 13(10). PMID: 30372433 Free PMC article.
CD4+ Memory T Cells at Home in the Tissue: Mechanisms for Health and Disease. David Schreiner, Carolyn G King. Front Immunol, 2018 Nov 06; 9. PMID: 30386342 Free PMC article. Review.
Single-Cell Transcriptomics in Cancer Immunobiology: The Future of Precision Oncology. Fatima Valdes-Mora, Kristina Handler, +4 authors, David Gallego-Ortega. less Front Immunol, 2018 Nov 30; 9. PMID: 30483257 Free PMC article. Review.
Non-hematopoietic Control of Peripheral Tissue T Cell Responses: Implications for Solid Tumors. Ryan S Lane, Amanda W Lund. Front Immunol, 2018 Dec 01; 9. PMID: 30498499 Free PMC article. Review.
Understanding tumor ecosystems by single-cell sequencing: promises and limitations. Xianwen Ren, Boxi Kang, Zemin Zhang. Genome Biol, 2018 Dec 05; 19(1). PMID: 30509292 Free PMC article. Review.
The molecular landscape of glioma in patients with Neurofibromatosis 1. Fulvio D'Angelo, Michele Ceccarelli, +44 authors, Antonio Iavarone. less Nat Med, 2018 Dec 12; 25(1). PMID: 30531922 Free PMC article. Highly Cited.
Brain Theranostics and Radiotheranostics: Exosomes and Graphenes In Vivo as Novel Brain Theranostics. Minseok Suh, Dong Soo Lee. Nucl Med Mol Imaging, 2018 Dec 13; 52(6). PMID: 30538772 Free PMC article. Review.
Monocyte heterogeneity and functions in cancer. Claire E Olingy, Huy Q Dinh, Catherine C Hedrick. J Leukoc Biol, 2019 Feb 19; 106(2). PMID: 30776148 Free PMC article. Highly Cited. Review.
Revolutionizing immunology with single-cell RNA sequencing. Haide Chen, Fang Ye, Guoji Guo. Cell Mol Immunol, 2019 Feb 24; 16(3). PMID: 30796351 Free PMC article. Review.
Recent Advances Targeting CCR5 for Cancer and Its Role in Immuno-Oncology. Xuanmao Jiao, Omar Nawab, +4 authors, Richard G Pestell. less Cancer Res, 2019 Jul 12; 79(19). PMID: 31292161 Free PMC article. Highly Cited. Review.
Inflammation and Cancer: Triggers, Mechanisms, and Consequences. Florian R Greten, Sergei I Grivennikov. Immunity, 2019 Jul 18; 51(1). PMID: 31315034 Free PMC article. Highly Cited. Review.
Differential Variation Analysis Enables Detection of Tumor Heterogeneity Using Single-Cell RNA-Sequencing Data. Emily F Davis-Marcisak, Thomas D Sherman, +9 authors, Elana J Fertig. less Cancer Res, 2019 Jul 25; 79(19). PMID: 31337651 Free PMC article.
LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data. Changlin Wan, Wennan Chang, +8 authors, Chi Zhang. less Nucleic Acids Res, 2019 Aug 03; 47(18). PMID: 31372654 Free PMC article.
Resident memory CD8+ T cells within cancer islands mediate survival in breast cancer patients. Colt A Egelston, Christian Avalos, +18 authors, Peter P Lee. less JCI Insight, 2019 Aug 30; 4(19). PMID: 31465302 Free PMC article.
In vivo effects of mutant RHOA on tumor formation in an orthotopic inoculation model. Takashi Nishizawa, Kiyotaka Nakano, +7 authors, Masami Suzuki. less Oncol Rep, 2019 Sep 06; 42(5). PMID: 31485674 Free PMC article.
Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation. Aaron D Viny, Robert L Bowman, +18 authors, Ross L Levine. less Cell Stem Cell, 2019 Sep 10; 25(5). PMID: 31495782 Free PMC article.
cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes. Erica A K DePasquale, Daniel Schnell, +7 authors, Nathan Salomonis. less Nucleic Acids Res, 2019 Sep 19; 47(21). PMID: 31529053 Free PMC article.
Unraveling Heterogeneity in Epithelial Cell Fates of the Mammary Gland and Breast Cancer. Alexandr Samocha, Hanna Doh, Kai Kessenbrock, Jeroen P Roose. Cancers (Basel), 2019 Sep 27; 11(10). PMID: 31554261 Free PMC article. Review.
Tumor-Derived Thymic Stromal Lymphopoietin Expands Bone Marrow B-cell Precursors in Circulation to Support Metastasis. Emeline Ragonnaud, Kanako Moritoh, +10 authors, Arya Biragyn. less Cancer Res, 2019 Oct 03; 79(22). PMID: 31575547 Free PMC article.
Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer. Lichun Ma, Maria O Hernandez, +13 authors, Xin Wei Wang. less Cancer Cell, 2019 Oct 08; 36(4). PMID: 31588021 Free PMC article.
MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions. Yael Baran, Akhiad Bercovich, +7 authors, Amos Tanay. less Genome Biol, 2019 Oct 13; 20(1). PMID: 31604482 Free PMC article. Highly Cited.
Breast Cancer Stem Cells as Drivers of Tumor Chemoresistance, Dormancy and Relapse: New Challenges and Therapeutic Opportunities. Maria Laura De Angelis, Federica Francescangeli, Ann Zeuner. Cancers (Basel), 2019 Oct 18; 11(10). PMID: 31619007 Free PMC article. Review.
Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses. Ciara H O'Flanagan, Kieran R Campbell, +20 authors, Samuel Aparicio. less Genome Biol, 2019 Oct 19; 20(1). PMID: 31623682 Free PMC article.
Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease. Peter A Szabo, Hanna Mendes Levitin, +9 authors, Peter A Sims. less Nat Commun, 2019 Oct 19; 10(1). PMID: 31624246 Free PMC article.
Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity. Chrysothemis C Brown, Herman Gudjonson, +9 authors, Alexander Y Rudensky. less Cell, 2019 Nov 02; 179(4). PMID: 31668803 Free PMC article. Highly Cited.
Novel and Alternative Targets Against Breast Cancer Stemness to Combat Chemoresistance. Sangita Sridharan, Cory M Howard, +4 authors, Dayanidhi Raman. less Front Oncol, 2019 Nov 05; 9. PMID: 31681564 Free PMC article. Review.
Digitaldlsorter: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data. Carlos Torroja, Fatima Sanchez-Cabo. Front Genet, 2019 Nov 12; 10. PMID: 31708961 Free PMC article.
Fast, sensitive and accurate integration of single-cell data with Harmony. Ilya Korsunsky, Nghia Millard, +7 authors, Soumya Raychaudhuri. less Nat Methods, 2019 Nov 20; 16(12). PMID: 31740819 Free PMC article. Highly Cited.
The Transcription Factor Bhlhe40 Programs Mitochondrial Regulation of Resident CD8+ T Cell Fitness and Functionality. Chaofan Li, Bibo Zhu, +18 authors, Jie Sun. less Immunity, 2019 Sep 19; 51(3). PMID: 31533057 Free PMC article. Highly Cited.
Siglecs, Novel Immunotherapy Targets, Potentially Enhance The Effectiveness of Existing Immune Checkpoint Inhibitors in Glioma Immunotherapy. Guan-Zhang Li, Ke-Nan Zhang, +12 authors, Wei Zhang. less Onco Targets Ther, 2019 Dec 11; 12. PMID: 31819511 Free PMC article.
More than one antibody of individual B cells revealed by single-cell immune profiling. Zhan Shi, Qingyang Zhang, +17 authors, Xiaoyan Qiu. less Cell Discov, 2019 Dec 17; 5. PMID: 31839985 Free PMC article.
Biomarker for personalized immunotherapy. Si-Yang Liu, Yi-Long Wu. Transl Lung Cancer Res, 2019 Dec 21; 8(Suppl 3). PMID: 31857954 Free PMC article. Review.
LXR-inverse agonism stimulates immune-mediated tumor destruction by enhancing CD8 T-cell activity in triple negative breast cancer. Katherine J Carpenter, Aurore-Cecile Valfort, +8 authors, Colin A Flaveny. less Sci Rep, 2019 Dec 22; 9(1). PMID: 31863071 Free PMC article.
Balancing STAT Activity as a Therapeutic Strategy. Kelsey L Polak, Noah M Chernosky, +2 authors, Jacob M Smigiel, Ilaria Tamagno, Mark W Jackson. less Cancers (Basel), 2019 Nov 07; 11(11). PMID: 31684144 Free PMC article. Review.
Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells. Assaf Magen, Jia Nie, +7 authors, Rémy Bosselut. less Cell Rep, 2019 Dec 05; 29(10). PMID: 31801070 Free PMC article.
M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data. Yu Zhang, Changlin Wan, +6 authors, Chi Zhang. less BMC Bioinformatics, 2019 Dec 22; 20(Suppl 24). PMID: 31861972 Free PMC article.
Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma. Junya Peng, Bao-Fa Sun, +20 authors, Wenming Wu. less Cell Res, 2019 Jul 06; 29(9). PMID: 31273297 Free PMC article. Highly Cited.
Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity. Mikhail Binnewies, Adriana M Mujal, +15 authors, Matthew F Krummel. less Cell, 2019 Apr 09; 177(3). PMID: 30955881 Free PMC article. Highly Cited.
Single-cell sequencing and its applications in head and neck cancer. Zongtai Qi, Thomas Barrett, +2 authors, Anuraag S Parikh, Itay Tirosh, Sidharth V Puram. less Oral Oncol, 2019 Nov 07; 99. PMID: 31689639 Free PMC article. Review.
Benchmarking principal component analysis for large-scale single-cell RNA-sequencing. Koki Tsuyuzaki, Hiroyuki Sato, Kenta Sato, Itoshi Nikaido. Genome Biol, 2020 Jan 21; 21(1). PMID: 31955711 Free PMC article.
The Adaptive and Innate Immune Cell Landscape of Uterine Leiomyosarcomas. Marco Manzoni, Maddalena M Bolognesi, +5 authors, Giorgio Cattoretti. less Sci Rep, 2020 Jan 22; 10(1). PMID: 31959856 Free PMC article.
Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. Christopher A Jackson, Dayanne M Castro, +2 authors, David Gresham. less Elife, 2020 Jan 28; 9. PMID: 31985403 Free PMC article.
'Omics Approaches to Explore the Breast Cancer Landscape. Joseph Parsons, Chiara Francavilla. Front Cell Dev Biol, 2020 Feb 11; 7. PMID: 32039208 Free PMC article. Review.
Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Ashley M Laughney, Jing Hu, +16 authors, Joan Massagué. less Nat Med, 2020 Feb 12; 26(2). PMID: 32042191 Free PMC article.
Adult Human Glioblastomas Harbor Radial Glia-like Cells. Rong Wang, Roshan Sharma, +15 authors, Viviane Tabar. less Stem Cell Reports, 2020 Feb 01; 14(2). PMID: 32004492 Free PMC article.
Very rapid cloning, expression and identifying specificity of T-cell receptors for T-cell engineering. Shan Zong, Tiejuan Mi, +7 authors, Hiroki Torikai. less PLoS One, 2020 Feb 11; 15(2). PMID: 32040512 Free PMC article.
CD163+ tumor-associated macrophage accumulation in breast cancer patients reflects both local differentiation signals and systemic skewing of monocytes. Rodrigo Nalio Ramos, Céline Rodriguez, +15 authors, Nathalie Bendriss-Vermare. less Clin Transl Immunology, 2020 Feb 23; 9(2). PMID: 32082570 Free PMC article.
Single-Cell Expression Variability Implies Cell Function. Daniel Osorio, Xue Yu, +5 authors, James J Cai. less Cells, 2019 Dec 22; 9(1). PMID: 31861624 Free PMC article.
Tracing tumorigenesis in a solid tumor model at single-cell resolution. Samantha D Praktiknjo, Benedikt Obermayer, +7 authors, Nikolaus Rajewsky. less Nat Commun, 2020 Feb 23; 11(1). PMID: 32080185 Free PMC article.
High-dimensional immune-profiling in cancer: implications for immunotherapy. Samuel Chuah, Valerie Chew. J Immunother Cancer, 2020 Feb 09; 8(1). PMID: 32034066 Free PMC article. Review.
Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry. Karolyn A Oetjen, Katherine E Lindblad, +6 authors, Christopher S Hourigan. less JCI Insight, 2018 Dec 07; 3(23). PMID: 30518681 Free PMC article.
Organoid Modeling of the Tumor Immune Microenvironment. James T Neal, Xingnan Li, +31 authors, Calvin J Kuo. less Cell, 2018 Dec 15; 175(7). PMID: 30550791 Free PMC article. Highly Cited.
Revolutionizing Cancer Immunology: The Power of Next-Generation Sequencing Technologies. Meromit Singer, Ana C Anderson. Cancer Immunol Res, 2019 Feb 03; 7(2). PMID: 30709909 Free PMC article. Review.
Single-Cell Profiling of Cutaneous T-Cell Lymphoma Reveals Underlying Heterogeneity Associated with Disease Progression. Nicholas Borcherding, Andrew P Voigt, +3 authors, Ali Jabbari. less Clin Cancer Res, 2019 Feb 06; 25(10). PMID: 30718356 Free PMC article.
MicroRNA-155 coordinates the immunological landscape within murine melanoma and correlates with immunity in human cancers. H Atakan Ekiz, Thomas B Huffaker, +4 authors, Ryan M O'Connell. less JCI Insight, 2019 Feb 06; 4(6). PMID: 30721153 Free PMC article.
Dissecting CLL through high-dimensional single-cell technologies. Satyen H Gohil, Catherine J Wu. Blood, 2019 Feb 08; 133(13). PMID: 30728142 Free PMC article. Review.
Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions. Maria Gutierrez-Arcelus, Nikola Teslovich, +10 authors, Patrick J Brennan. less Nat Commun, 2019 Feb 10; 10(1). PMID: 30737409 Free PMC article. Highly Cited.
Reactive oxygen species modulate macrophage immunosuppressive phenotype through the up-regulation of PD-L1. Cecilia Roux, Soode Moghadas Jafari, +14 authors, Chiara Gorrini. less Proc Natl Acad Sci U S A, 2019 Feb 17; 116(10). PMID: 30770442 Free PMC article.
Quantifying in situ adaptive immune cell cognate interactions in humans. Vladimir M Liarski, Adam Sibley, +7 authors, Marcus R Clark. less Nat Immunol, 2019 Feb 20; 20(4). PMID: 30778242 Free PMC article.
Negative Co-stimulation Constrains T Cell Differentiation by Imposing Boundaries on Possible Cell States. Spencer C Wei, Roshan Sharma, +8 authors, James P Allison. less Immunity, 2019 Mar 31; 50(4). PMID: 30926234 Free PMC article.
The emergent landscape of the mouse gut endoderm at single-cell resolution. Sonja Nowotschin, Manu Setty, +11 authors, Dana Pe'er. less Nature, 2019 Apr 09; 569(7756). PMID: 30959515 Free PMC article. Highly Cited.
Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry. Sabine Amon, Fabienne Meier-Abt, +4 authors, Ruedi Aebersold. less Mol Cell Proteomics, 2019 Apr 13; 18(7). PMID: 30975897 Free PMC article.
A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer. Johanna Wagner, Maria Anna Rapsomaniki, +15 authors, Bernd Bodenmiller. less Cell, 2019 Apr 16; 177(5). PMID: 30982598 Free PMC article. Highly Cited.
Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. Eleni P Mimitou, Anthony Cheng, +11 authors, Peter Smibert. less Nat Methods, 2019 Apr 24; 16(5). PMID: 31011186 Free PMC article. Highly Cited.
Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood. Yi Zhao, Xiao Li, +20 authors, Xiao Liu. less Gigascience, 2019 May 03; 8(5). PMID: 31049560 Free PMC article.
The B-side of Cancer Immunity: The Underrated Tune. Anne Largeot, Giulia Pagano, +2 authors, Susanne Gonder, Etienne Moussay, Jerome Paggetti. less Cells, 2019 May 16; 8(5). PMID: 31086070 Free PMC article. Review.
Current best practices in single-cell RNA-seq analysis: a tutorial. Malte D Luecken, Fabian J Theis. Mol Syst Biol, 2019 Jun 21; 15(6). PMID: 31217225 Free PMC article. Highly Cited. Review.
Mutual editing of alternative splicing between breast cancer cells and macrophages. Wanbao Ding, Dongdong Li, +7 authors, Lei Deng. less Oncol Rep, 2019 Jun 25; 42(2). PMID: 31233192 Free PMC article.
De novo prediction of cell-type complexity in single-cell RNA-seq and tumor microenvironments. Jun Woo, Boris J Winterhoff, +2 authors, Timothy K Starr, Constantin Aliferis, Jinhua Wang. less Life Sci Alliance, 2019 Jul 04; 2(4). PMID: 31266885 Free PMC article.
Joint analysis of heterogeneous single-cell RNA-seq dataset collections. Nikolas Barkas, Viktor Petukhov, +4 authors, Peter V Kharchenko. less Nat Methods, 2019 Jul 17; 16(8). PMID: 31308548 Free PMC article.
High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes. Mandeep Singh, Ghamdan Al-Eryani, +11 authors, Alexander Swarbrick. less Nat Commun, 2019 Jul 18; 10(1). PMID: 31311926 Free PMC article.
The Unmixing Problem: A Guide to Applying Single-Cell RNA Sequencing to Bone. Matthew B Greenblatt, Noriaki Ono, +2 authors, Ugur M Ayturk, Shawon Debnath, Sarfaraz Lalani. less J Bone Miner Res, 2019 Jul 25; 34(7). PMID: 31336008 Free PMC article. Review.
Bioinspired lipoproteins-mediated photothermia remodels tumor stroma to improve cancer cell accessibility of second nanoparticles. Tao Tan, Haiyan Hu, +6 authors, Yaping Li. less Nat Commun, 2019 Jul 28; 10(1). PMID: 31346166 Free PMC article.
Computational approaches for characterizing the tumor immune microenvironment. Candace C Liu, Chloé B Steen, Aaron M Newman. Immunology, 2019 Jul 28; 158(2). PMID: 31347163 Free PMC article. Review.
Clonal replacement of tumor-specific T cells following PD-1 blockade. Kathryn E Yost, Ansuman T Satpathy, +13 authors, Howard Y Chang. less Nat Med, 2019 Jul 31; 25(8). PMID: 31359002 Free PMC article. Highly Cited.
Multimodal single-cell approaches shed light on T cell heterogeneity. Aparna Nathan, Yuriy Baglaenko, +2 authors, Chamith Y Fonseka, Jessica I Beynor, Soumya Raychaudhuri. less Curr Opin Immunol, 2019 Aug 21; 61. PMID: 31430664 Free PMC article. Review.
Single-cell profiling guided combinatorial immunotherapy for fast-evolving CDK4/6 inhibitor-resistant HER2-positive breast cancer. Qingfei Wang, Ian H Guldner, +4 authors, Siyuan Zhang. less Nat Commun, 2019 Aug 25; 10(1). PMID: 31444334 Free PMC article.
Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy. Jerome C Martin, Christie Chang, +28 authors, Ephraim Kenigsberg. less Cell, 2019 Sep 03; 178(6). PMID: 31474370 Free PMC article. Highly Cited.
Controlling the Phenotype of Tumor-Infiltrating Macrophages via the PHD-HIF Axis Inhibits Tumor Growth in a Mouse Model. Shunji Nishide, Shinji Matsunaga, +9 authors, Shuhei Tomita. less iScience, 2019 Sep 14; 19. PMID: 31518902 Free PMC article.
Functional interpretation of single cell similarity maps. David DeTomaso, Matthew G Jones, +3 authors, Nir Yosef. less Nat Commun, 2019 Sep 29; 10(1). PMID: 31558714 Free PMC article.
Application of single-cell RNA sequencing methodologies in understanding haematopoiesis and immunology. Anna M Ranzoni, Paulina M Strzelecka, Ana Cvejic. Essays Biochem, 2019 Jun 13; 63(2). PMID: 31186287 Free PMC article. Review.
JAK/STAT inhibition in macrophages promotes therapeutic resistance by inducing expression of protumorigenic factors. Emily A Irey, Chelsea M Lassiter, +9 authors, Kathryn L Schwertfeger. less Proc Natl Acad Sci U S A, 2019 May 31; 116(25). PMID: 31147469 Free PMC article.
Transcriptional Signature Derived from Murine Tumor-Associated Macrophages Correlates with Poor Outcome in Breast Cancer Patients. Sander Tuit, Camilla Salvagno, +7 authors, Joachim L Schultze. less Cell Rep, 2019 Oct 31; 29(5). PMID: 31665635 Free PMC article.
Tumor-Associated Macrophages: Recent Insights and Therapies. Jiawei Zhou, Ziwei Tang, +3 authors, Siyang Gao, Chunyu Li, Yiting Feng, Xikun Zhou. less Front Oncol, 2020 Mar 13; 10. PMID: 32161718 Free PMC article. Review.
Fragment Enrichment of Circulating Tumor DNA With Low-Frequency Mutations. Xiaojun Liu, Jidong Lang, +18 authors, Geng Tian. less Front Genet, 2020 Mar 18; 11. PMID: 32180799 Free PMC article.
The single-cell eQTLGen consortium. Mgp van der Wijst, D H de Vries, +13 authors, L Franke. less Elife, 2020 Mar 10; 9. PMID: 32149610 Free PMC article.
FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells. Noudjoud Attaf, Iñaki Cervera-Marzal, +4 authors, Pierre Milpied. less Front Immunol, 2020 Mar 21; 11. PMID: 32194545 Free PMC article.
Immune and Stroma Related Genes in Breast Cancer: A Comprehensive Analysis of Tumor Microenvironment Based on the Cancer Genome Atlas (TCGA) Database. Ming Xu, Yu Li, +5 authors, Pengfei Yi. less Front Med (Lausanne), 2020 Mar 21; 7. PMID: 32195260 Free PMC article.
Enhanced Lipid Accumulation and Metabolism Are Required for the Differentiation and Activation of Tumor-Associated Macrophages. Pan Su, Qiang Wang, +5 authors, Qing Yi. less Cancer Res, 2020 Feb 06; 80(7). PMID: 32015091 Free PMC article.
Targeting the Interplay between Epithelial-to-Mesenchymal-Transition and the Immune System for Effective Immunotherapy. Rama Soundararajan, Jared J Fradette, +18 authors, Sendurai A Mani. less Cancers (Basel), 2019 May 30; 11(5). PMID: 31137625 Free PMC article. Review.
Single-Cell Approaches to Profile the Response to Immune Checkpoint Inhibitors. Lara Gibellini, Sara De Biasi, +5 authors, Andrea Cossarizza. less Front Immunol, 2020 Apr 09; 11. PMID: 32265933 Free PMC article. Review.
Preferential Infiltration of Unique Vγ9Jγ2-Vδ2 T Cells Into Glioblastoma Multiforme. Mijeong Lee, Chanho Park, +8 authors, Tae Jin Kim. less Front Immunol, 2019 Apr 11; 10. PMID: 30967876 Free PMC article.
Unfolding innate mechanisms in the cancer microenvironment: The emerging role of the mesenchyme. Vasiliki Koliaraki, Ana Henriques, Alejandro Prados, George Kollias. J Exp Med, 2020 Feb 12; 217(4). PMID: 32044979 Free PMC article. Review.
In vivo Differentiation of Human Monocytes. Alice Coillard, Elodie Segura. Front Immunol, 2019 Aug 29; 10. PMID: 31456804 Free PMC article. Review.
Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq. Qianqian Song, Gregory A Hawkins, +17 authors, Wei Zhang. less Cancer Med, 2019 Apr 30; 8(6). PMID: 31033233 Free PMC article.
Tuning the Tumor Myeloid Microenvironment to Fight Cancer. Nadine S Jahchan, Adriana M Mujal, +4 authors, Matthew F Krummel. less Front Immunol, 2019 Aug 14; 10. PMID: 31402908 Free PMC article. Review.
Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma. Sangeeta Goswami, Thomas Walle, +17 authors, Padmanee Sharma. less Nat Med, 2019 Dec 25; 26(1). PMID: 31873309 Free PMC article.
RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis. Shuqiang Li, Jing Sun, +10 authors, Kenneth J Livak. less Nat Protoc, 2019 Jul 26; 14(8). PMID: 31341290 Free PMC article.
CHIT1 at Diagnosis Reflects Long-Term Multiple Sclerosis Disease Activity. Emanuela Oldoni, Ide Smets, +6 authors, An Goris. less Ann Neurol, 2020 Jan 31; 87(4). PMID: 31997416 Free PMC article.
CD4+ teff cell heterogeneity: the perspective from single-cell transcriptomics. David Zemmour, Evgeny Kiner, Christophe Benoist. Curr Opin Immunol, 2020 Apr 08; 63. PMID: 32259715 Free PMC article. Review.
Highly parallel and efficient single cell mRNA sequencing with paired picoliter chambers. Mingxia Zhang, Yuan Zou, +9 authors, Chaoyong Yang. less Nat Commun, 2020 May 02; 11(1). PMID: 32355211 Free PMC article.
Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer. Anthony R Cillo, Cornelius H L Kürten, +13 authors, Dario A A Vignali. less Immunity, 2020 Jan 12; 52(1). PMID: 31924475 Free PMC article.
Breast cancer-derived exosomes transmit lncRNA SNHG16 to induce CD73+γδ1 Treg cells. Chao Ni, Qing-Qing Fang, +9 authors, Jian Huang. less Signal Transduct Target Ther, 2020 Apr 30; 5(1). PMID: 32345959 Free PMC article.
Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics. Hamad Alshetaiwi, Nicholas Pervolarakis, +10 authors, Kai Kessenbrock. less Sci Immunol, 2020 Feb 23; 5(44). PMID: 32086381 Free PMC article.
Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma. Nayoung Kim, Hong Kwan Kim, +18 authors, Hae-Ock Lee. less Nat Commun, 2020 May 10; 11(1). PMID: 32385277 Free PMC article.
Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line. Yapeng Su, Melissa E Ko, +20 authors, James R Heath. less Nat Commun, 2020 May 13; 11(1). PMID: 32393797 Free PMC article.
Massively parallel interrogation and mining of natively paired human TCRαβ repertoires. Matthew J Spindler, Ayla L Nelson, +11 authors, David S Johnson. less Nat Biotechnol, 2020 May 13; 38(5). PMID: 32393905 Free PMC article.
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. Gregor Sturm, Francesca Finotello, +5 authors, Tatsiana Aneichyk. less Bioinformatics, 2019 Sep 13; 35(14). PMID: 31510660 Free PMC article. Highly Cited.
A guide to cancer immunotherapy: from T cell basic science to clinical practice. Alex D Waldman, Jill M Fritz, Michael J Lenardo. Nat Rev Immunol, 2020 May 21; 20(11). PMID: 32433532 Free PMC article. Review.
Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma. Hanjie Li, Anne M van der Leun, +15 authors, Ido Amit. less Cell, 2019 Jan 01; 176(4). PMID: 30595452 Free PMC article. Highly Cited.
The Tumor Microenvironment in the Response to Immune Checkpoint Blockade Therapies. Florent Petitprez, Maxime Meylan, +2 authors, Wolf H Fridman. less Front Immunol, 2020 May 28; 11. PMID: 32457745 Free PMC article. Review.
Tracking the immune response with single-cell genomics. Kathryn E Yost, Howard Y Chang, Ansuman T Satpathy. Vaccine, 2019 Dec 21; 38(28). PMID: 31859202 Free PMC article.
2DImpute: imputation in single-cell RNA-seq data from correlations in two dimensions. Kaiyi Zhu, Dimitris Anastassiou. Bioinformatics, 2020 Feb 29; 36(11). PMID: 32108864 Free PMC article.
Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data. Antonio Federico, Angela Serra, +17 authors, Dario Greco. less Nanomaterials (Basel), 2020 May 14; 10(5). PMID: 32397130 Free PMC article. Review.
Thioholgamide A, a New Anti-Proliferative Anti-Tumor Agent, Modulates Macrophage Polarization and Metabolism. Charlotte Dahlem, Wei Xiong Siow, +9 authors, Alexandra K Kiemer. less Cancers (Basel), 2020 May 23; 12(5). PMID: 32438733 Free PMC article.
Poincaré maps for analyzing complex hierarchies in single-cell data. Anna Klimovskaia, David Lopez-Paz, Léon Bottou, Maximilian Nickel. Nat Commun, 2020 Jun 13; 11(1). PMID: 32528075 Free PMC article.
Prostate cancer research: The next generation; report from the 2019 Coffey-Holden Prostate Cancer Academy Meeting. Andrea K Miyahira, Adam Sharp, +8 authors, Howard R Soule. less Prostate, 2019 Dec 12; 80(2). PMID: 31825540 Free PMC article. Review.
Ligand-receptor interaction atlas within and between tumor cells and T cells in lung adenocarcinoma. Zhencong Chen, Xiaodong Yang, +12 authors, Lijie Tan. less Int J Biol Sci, 2020 Jun 19; 16(12). PMID: 32549766 Free PMC article.
Rapid non-uniform adaptation to conformation-specific KRAS(G12C) inhibition. Jenny Y Xue, Yulei Zhao, +9 authors, Piro Lito. less Nature, 2020 Jan 10; 577(7790). PMID: 31915379 Free PMC article.
Heme oxygenase-1 orchestrates the immunosuppressive program of tumor-associated macrophages. Emmanuelle Alaluf, Benoît Vokaer, +8 authors, Stanislas Goriely. less JCI Insight, 2020 May 06; 5(11). PMID: 32369450 Free PMC article.
Single-cell immune landscape of human atherosclerotic plaques. Dawn M Fernandez, Adeeb H Rahman, +22 authors, Chiara Giannarelli. less Nat Med, 2019 Oct 09; 25(10). PMID: 31591603 Free PMC article. Highly Cited.
Single-cell transcriptome and antigen-immunoglobin analysis reveals the diversity of B cells in non-small cell lung cancer. Jian Chen, Yun Tan, +16 authors, Peng Zhang. less Genome Biol, 2020 Jun 26; 21(1). PMID: 32580738 Free PMC article.
Unravelling the heterogeneity and dynamic relationships of tumor-infiltrating T cells by single-cell RNA sequencing analysis. Xin Yu, Lei Zhang, +2 authors, Ashutosh Chaudhry, Aaron S Rapaport, Wenjun Ouyang. less J Leukoc Biol, 2020 Apr 10; 107(6). PMID: 32272497 Free PMC article. Review.
Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF. Meenakshi Venkatasubramanian, Kashish Chetal, +2 authors, Daniel J Schnell, Gowtham Atluri, Nathan Salomonis. less Bioinformatics, 2020 Mar 25; 36(12). PMID: 32207533 Free PMC article.
Predictors of Neoadjuvant Chemotherapy Response in Breast Cancer: A Review. Weilin Xu, Xiu Chen, +3 authors, Fei Deng, Jian Zhang, Wei Zhang, Jinhai Tang. less Onco Targets Ther, 2020 Jul 02; 13. PMID: 32606799 Free PMC article. Review.
Immune profiling of pediatric solid tumors. Rachael L Terry, Deborah Meyran, +4 authors, Paul J Neeson. less J Clin Invest, 2020 Jun 17; 130(7). PMID: 32538896 Free PMC article. Review.
Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms. Austin N Southard-Smith, Alan J Simmons, +14 authors, Ken S Lau. less BMC Genomics, 2020 Jul 04; 21(1). PMID: 32616006 Free PMC article.
Early precursors and molecular determinants of tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing. Nadia S Kurd, Zhaoren He, +15 authors, John T Chang. less Sci Immunol, 2020 May 18; 5(47). PMID: 32414833 Free PMC article.
Extensive Remodeling of the Immune Microenvironment in B Cell Acute Lymphoblastic Leukemia. Matthew T Witkowski, Igor Dolgalev, +24 authors, Iannis Aifantis. less Cancer Cell, 2020 May 30; 37(6). PMID: 32470390 Free PMC article.
L1CAM defines the regenerative origin of metastasis-initiating cells in colorectal cancer. Karuna Ganesh, Harihar Basnet, +18 authors, Joan Massagué. less Nat Cancer, 2020 Jul 14; 1(1). PMID: 32656539 Free PMC article.
Identification of non-cancer cells from cancer transcriptomic data. Michele Bortolomeazzi, Mohamed Reda Keddar, Francesca D Ciccarelli, Lorena Benedetti. Biochim Biophys Acta Gene Regul Mech, 2019 Oct 28; 1863(6). PMID: 31654804 Free PMC article. Review.
Cancer systems immunology. Nathan E Reticker-Flynn, Edgar G Engleman. Elife, 2020 Jul 14; 9. PMID: 32657757 Free PMC article. Review.
Trajectory and Functional Analysis of PD-1high CD4+CD8+ T Cells in Hepatocellular Carcinoma by Single-Cell Cytometry and Transcriptome Sequencing. Bo Zheng, Dongfang Wang, +15 authors, Lei Chen. less Adv Sci (Weinh), 2020 Jul 17; 7(13). PMID: 32670760 Free PMC article.
Dissecting the Tumor-Immune Landscape in Chimeric Antigen Receptor T-cell Therapy: Key Challenges and Opportunities for a Systems Immunology Approach. Gregory M Chen, Andrew Azzam, +3 authors, Kai Tan. less Clin Cancer Res, 2020 Mar 05; 26(14). PMID: 32127393 Free PMC article. Review.
Precision Detection Technology: Equipping Precision Oncology with Wings. Rilan Bai, Zheng Lv, +5 authors, Jiuwei Cui. less J Oncol, 2020 Jul 23; 2020. PMID: 32695166 Free PMC article. Review.
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Orit Rozenblatt-Rosen, Aviv Regev, +35 authors, Human Tumor Atlas Network. less Cell, 2020 Apr 18; 181(2). PMID: 32302568 Free PMC article. Review.
Monocyte-derived APCs are central to the response of PD1 checkpoint blockade and provide a therapeutic target for combination therapy. Sjoerd T T Schetters, Ernesto Rodriguez, +5 authors, Yvette Van Kooyk. less J Immunother Cancer, 2020 Jul 22; 8(2). PMID: 32690667 Free PMC article.
Circulating immune cell phenotype dynamics reflect the strength of tumor-immune cell interactions in patients during immunotherapy. Jason I Griffiths, Pierre Wallet, +13 authors, Andrea H Bild. less Proc Natl Acad Sci U S A, 2020 Jun 24; 117(27). PMID: 32571915 Free PMC article.
M1hot tumor-associated macrophages boost tissue-resident memory T cells infiltration and survival in human lung cancer. Eva M Garrido-Martin, Toby W P Mellows, +13 authors, Tilman Sanchez-Elsner. less J Immunother Cancer, 2020 Jul 24; 8(2). PMID: 32699181 Free PMC article.
Single-Cell Profiling and SCOPE-Seq Reveal Lineage Dynamics of Adult Ventricular-Subventricular Zone Neurogenesis and NOTUM as a Key Regulator. Dogukan Mizrak, N Sumru Bayin, +8 authors, Peter A Sims. less Cell Rep, 2020 Jun 25; 31(12). PMID: 32579931 Free PMC article.
Imaging Mass Spectrometry Reveals Tumor Metabolic Heterogeneity. Yang Zhang, Christelle Guillermier, +9 authors, Matthew L Steinhauser. less iScience, 2020 Jul 28; 23(8). PMID: 32712466 Free PMC article.
The expanding landscape of inflammatory cells affecting cancer therapy. Ralph Weissleder, Mikael J Pittet. Nat Biomed Eng, 2020 Mar 24; 4(5). PMID: 32203281 Free PMC article. Review.
A transcriptomic map of murine and human alopecia areata. Nicholas Borcherding, Sydney B Crotts, +3 authors, Ali Jabbari. less JCI Insight, 2020 May 27; 5(13). PMID: 32453712 Free PMC article.
Demystifying "drop-outs" in single-cell UMI data. Tae Hyun Kim, Xiang Zhou, Mengjie Chen. Genome Biol, 2020 Aug 09; 21(1). PMID: 32762710 Free PMC article.
Single-cell RNA sequencing in breast cancer: Understanding tumor heterogeneity and paving roads to individualized therapy. Shuning Ding, Xiaosong Chen, Kunwei Shen. Cancer Commun (Lond), 2020 Jul 13; 40(8). PMID: 32654419 Free PMC article. Review.
The history and advances in cancer immunotherapy: understanding the characteristics of tumor-infiltrating immune cells and their therapeutic implications. Yuanyuan Zhang, Zemin Zhang. Cell Mol Immunol, 2020 Jul 03; 17(8). PMID: 32612154 Free PMC article. Review.
The Application of Single-Cell RNA Sequencing in Vaccinology. Andrés Noé, Tamsin N Cargill, +2 authors, Eleanor Barnes. less J Immunol Res, 2020 Aug 18; 2020. PMID: 32802896 Free PMC article. Review.
CD8+ T cell states in human cancer: insights from single-cell analysis. Anne M van der Leun, Daniela S Thommen, Ton N Schumacher. Nat Rev Cancer, 2020 Feb 07; 20(4). PMID: 32024970 Free PMC article. Review.
Immune Landscape in Tumor Microenvironment: Implications for Biomarker Development and Immunotherapy. Karim Pérez-Romero, Ramón M Rodríguez, +2 authors, Daniel H Lopez. less Int J Mol Sci, 2020 Aug 06; 21(15). PMID: 32752264 Free PMC article. Review.
A Rosetta Stone for Breast Cancer: Prognostic Value and Dynamic Regulation of Neutrophil in Tumor Microenvironment. Wei Zhang, Yimin Shen, +6 authors, Chao Ni. less Front Immunol, 2020 Aug 28; 11. PMID: 32849640 Free PMC article. Review.
Systems biology approaches to measure and model phenotypic heterogeneity in cancer. Aaron S Meyer, Laura M Heiser. Curr Opin Syst Biol, 2020 Aug 31; 17. PMID: 32864511 Free PMC article.
Myeloid signature reveals immune contexture and predicts the prognosis of hepatocellular carcinoma. Chong Wu, Jie Lin, +17 authors, Limin Zheng. less J Clin Invest, 2020 Jun 05; 130(9). PMID: 32497024 Free PMC article.
Environmental Carcinogenesis at the Single-Cell Level. Gregory Chang, Kohei Saeki, Hitomi Mori, Shiuan Chen. Cancer Epidemiol Biomarkers Prev, 2020 Mar 07; 29(10). PMID: 32132147 Free PMC article.
Single-Cell Ssequencing in Cancer: Recent Applications to Immunogenomics and Multi-omics Tools. Michael C Sierant, Jungmin Choi. Genomics Inform, 2019 Jan 03; 16(4). PMID: 30602078 Free PMC article.
Vascular-endothelial response to IDH1 mutant fibrosarcoma secretome and metabolite: implications on cancer microenvironment. Maiya J Mao, Donna E Leonardi. Am J Cancer Res, 2019 Feb 14; 9(1). PMID: 30755816 Free PMC article.
Tumor derived EDIL3 modulates the expansion and osteoclastogenesis of myeloid derived suppressor cells in murine breast cancer model. Zhang Kun, Gao Xin, +5 authors, Xiao Jianru. less J Bone Oncol, 2019 May 22; 16. PMID: 31110935 Free PMC article.
Extensive exploration of T cell heterogeneity in cancers by single cell sequencing. Xiaofang Wang, Yangqiu Li. Chin J Cancer Res, 2019 Jun 04; 31(2). PMID: 31156311 Free PMC article.
Targeting the Tumor Microenvironment in Renal Cell Cancer Biology and Therapy. Isabel Heidegger, Andreas Pircher, Renate Pichler. Front Oncol, 2019 Jul 02; 9. PMID: 31259150 Free PMC article. Review.
The single-cell sequencing: new developments and medical applications. Xiaoning Tang, Yongmei Huang, +2 authors, Jinli Lei, Hui Luo, Xiao Zhu. less Cell Biosci, 2019 Aug 09; 9. PMID: 31391919 Free PMC article. Review.
Divide and conquer: A perspective on biochips for single-cell and rare-molecule analysis by next-generation sequencing. A C Lee, Y Lee, D Lee, S Kwon. APL Bioeng, 2019 Aug 23; 3(2). PMID: 31431936 Free PMC article.
Exploiting Manipulated Small Extracellular Vesicles to Subvert Immunosuppression at the Tumor Microenvironment through Mannose Receptor/CD206 Targeting. Maria Luisa Fiani, Valeria Barreca, +3 authors, Maurizio Federico. less Int J Mol Sci, 2020 Sep 04; 21(17). PMID: 32878276 Free PMC article. Review.
Tumor-Promoting Ly-6G+ SiglecFhigh Cells Are Mature and Long-Lived Neutrophils. Christina Pfirschke, Camilla Engblom, +11 authors, Mikael J Pittet. less Cell Rep, 2020 Sep 24; 32(12). PMID: 32966785 Free PMC article.
Targeting STAT3 in Cancer Immunotherapy. Sailan Zou, Qiyu Tong, +3 authors, Bowen Liu, Wei Huang, Yan Tian, Xianghui Fu. less Mol Cancer, 2020 Sep 26; 19(1). PMID: 32972405 Free PMC article. Review.
A single-cell survey of cellular hierarchy in acute myeloid leukemia. Junqing Wu, Yanyu Xiao, +31 authors, Guoji Guo. less J Hematol Oncol, 2020 Sep 27; 13(1). PMID: 32977829 Free PMC article.
Analyzing One Cell at a TIME: Analysis of Myeloid Cell Contributions in the Tumor Immune Microenvironment. Vitaliy Davidov, Garrett Jensen, +2 authors, Sunny Mai, Shu-Hsia Chen, Ping-Ying Pan. less Front Immunol, 2020 Sep 29; 11. PMID: 32983100 Free PMC article. Review.
TCR sequencing paired with massively parallel 3' RNA-seq reveals clonotypic T cell signatures. Ang A Tu, Todd M Gierahn, +6 authors, J Christopher Love. less Nat Immunol, 2019 Nov 21; 20(12). PMID: 31745340 Free PMC article.
Human Tregs at the materno-fetal interface show site-specific adaptation reminiscent of tumor Tregs. Judith Wienke, Laura Brouwers, +5 authors, Femke van Wijk. less JCI Insight, 2020 Aug 19; 5(18). PMID: 32809975 Free PMC article.
Characterization of cell fate probabilities in single-cell data with Palantir. Manu Setty, Vaidotas Kiseliovas, +3 authors, Dana Pe'er. less Nat Biotechnol, 2019 Mar 23; 37(4). PMID: 30899105 Free PMC article. Highly Cited.
A gene expression signature of TREM2hi macrophages and γδ T cells predicts immunotherapy response. Donghai Xiong, Yian Wang, Ming You. Nat Commun, 2020 Oct 10; 11(1). PMID: 33033253 Free PMC article.
A semi-automatic cell type annotation method for single-cell RNA sequencing dataset. Wan Kim, Sung Min Yoon, Sangsoo Kim. Genomics Inform, 2020 Oct 06; 18(3). PMID: 33017870 Free PMC article.
Diverse Macrophage Populations Contribute to the Inflammatory Microenvironment in Premalignant Lesions During Localized Invasion. Ayman M Ibrahim, Matthew A Moss, +5 authors, Heather L Machado. less Front Oncol, 2020 Oct 20; 10. PMID: 33072601 Free PMC article.
Cathepsin Inhibition Modulates Metabolism and Polarization of Tumor-Associated Macrophages. Diana Oelschlaegel, Tommy Weiss Sadan, +5 authors, Patrick Michl. less Cancers (Basel), 2020 Sep 16; 12(9). PMID: 32927704 Free PMC article.
Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives. Geyang Luo, Qian Gao, Shuye Zhang, Bo Yan. Comput Struct Biotechnol J, 2020 Oct 28; 18. PMID: 33106757 Free PMC article. Review.
Emerging Roles of Single-Cell Multi-Omics in Studying Developmental Temporal Patterning. Andrea Lopes, Elia Magrinelli, Ludovic Telley. Int J Mol Sci, 2020 Oct 15; 21(20). PMID: 33050604 Free PMC article. Review.
Immunotherapy for Ovarian Cancer: Adjuvant, Combination, and Neoadjuvant. Chang Yang, Bai-Rong Xia, +3 authors, Wei-Lin Jin. less Front Immunol, 2020 Oct 31; 11. PMID: 33123161 Free PMC article. Review.
Heterogeneity and fate choice: T cell exhaustion in cancer and chronic infections. Mary Philip, Andrea Schietinger. Curr Opin Immunol, 2019 Jun 11; 58. PMID: 31181510 Free PMC article. Highly Cited. Review.
Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma. Lindsay M LaFave, Vinay K Kartha, +15 authors, Tyler Jacks. less Cancer Cell, 2020 Jul 25; 38(2). PMID: 32707078 Free PMC article.
Progress and applications of mass cytometry in sketching immune landscapes. Ting Zhang, Antony R Warden, Yiyang Li, Xianting Ding. Clin Transl Med, 2020 Nov 03; 10(6). PMID: 33135337 Free PMC article. Review.
Cancer-associated hypersialylated MUC1 drives the differentiation of human monocytes into macrophages with a pathogenic phenotype. Richard Beatson, Rosalind Graham, +13 authors, Joy M Burchell. less Commun Biol, 2020 Nov 06; 3(1). PMID: 33149188 Free PMC article.
Spectacle: An interactive resource for ocular single-cell RNA sequencing data analysis. Andrew P Voigt, S Scott Whitmore, +5 authors, Todd E Scheetz. less Exp Eye Res, 2020 Sep 11; 200. PMID: 32910939 Free PMC article.
A map of tumor-host interactions in glioma at single-cell resolution. Francesca Pia Caruso, Luciano Garofano, +13 authors, Michele Ceccarelli. less Gigascience, 2020 Nov 07; 9(10). PMID: 33155039 Free PMC article.
Tumor-infiltrating TNFRSF9+ CD8+ T cells define different subsets of clear cell renal cell carcinoma with prognosis and immunotherapeutic response. Yaohui Li, Zewei Wang, +15 authors, Jiejie Xu. less Oncoimmunology, 2020 Nov 13; 9(1). PMID: 33178496 Free PMC article.
Adoptive Cell Therapy in Breast Cancer: A Current Perspective of Next-Generation Medicine. Jesús Fuentes-Antrás, Kissy Guevara-Hoyer, +4 authors, Alberto Ocaña. less Front Oncol, 2020 Nov 17; 10. PMID: 33194771 Free PMC article. Review.
A Random Matrix Theory Approach to Denoise Single-Cell Data. Luis Aparicio, Mykola Bordyuh, Andrew J Blumberg, Raul Rabadan. Patterns (N Y), 2020 Nov 19; 1(3). PMID: 33205104 Free PMC article.
Osteopontin: A Key Regulator of Tumor Progression and Immunomodulation. Hannah R Moorman, Dakota Poschel, +3 authors, Kebin Liu. less Cancers (Basel), 2020 Nov 19; 12(11). PMID: 33203146 Free PMC article. Review.
The evolving landscape of predictive biomarkers in immuno-oncology with a focus on spatial technologies. Habib Sadeghi Rad, Sajad Razavi Bazaz, +4 authors, Arutha Kulasinghe. less Clin Transl Immunology, 2020 Dec 01; 9(11). PMID: 33251010 Free PMC article. Review.
Cancer research in the era of immunogenomics. Yochai Wolf, Yardena Samuels. ESMO Open, 2019 Jan 10; 3(7). PMID: 30622743 Free PMC article. Review.
Emerging approaches to study cell-cell interactions in tumor microenvironment. Nao Nishida-Aoki, Taranjit S Gujral. Oncotarget, 2019 Feb 19; 10(7). PMID: 30774780 Free PMC article. Review.
Immune contexture defined by single cell technology for prognosis prediction and immunotherapy guidance in cancer. Tong Wu, Xuan Wu, Hong-Yang Wang, Lei Chen. Cancer Commun (Lond), 2019 Apr 20; 39(1). PMID: 30999966 Free PMC article. Review.
Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data. Savvas Kinalis, Finn Cilius Nielsen, Ole Winther, Frederik Otzen Bagger. BMC Bioinformatics, 2019 Jul 10; 20(1). PMID: 31286861 Free PMC article.
bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data. Wenhao Tang, François Bertaux, +4 authors, Vahid Shahrezaei. less Bioinformatics, 2019 Oct 05; 36(4). PMID: 31584606 Free PMC article.
Breathing fresh air into respiratory research with single-cell RNA sequencing. Michael J Alexander, G R Scott Budinger, Paul A Reyfman. Eur Respir Rev, 2020 Jul 06; 29(156). PMID: 32620586 Free PMC article. Review.
TCGA and ESTIMATE data mining to identify potential prognostic biomarkers in HCC patients. Guolin He, Shunjun Fu, +12 authors, Yi Gao. less Aging (Albany NY), 2020 Nov 13; 12(21). PMID: 33177245 Free PMC article.
DSAVE: Detection of misclassified cells in single-cell RNA-Seq data. Johan Gustafsson, Jonathan Robinson, +3 authors, Jens Nielsen. less PLoS One, 2020 Dec 04; 15(12). PMID: 33270740 Free PMC article.
RNA sequencing: new technologies and applications in cancer research. Mingye Hong, Shuang Tao, +6 authors, Hua Zhang. less J Hematol Oncol, 2020 Dec 06; 13(1). PMID: 33276803 Free PMC article. Review.
Immune suppressive landscape in the human esophageal squamous cell carcinoma microenvironment. Yingxia Zheng, Zheyi Chen, +16 authors, Lisong Shen. less Nat Commun, 2020 Dec 10; 11(1). PMID: 33293583 Free PMC article.
Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression. Guohe Song, Yang Shi, +20 authors, Qiang Gao. less Cell Discov, 2020 Dec 11; 6(1). PMID: 33298893 Free PMC article.
Methodological Advancements for Investigating Intra-tumoral Heterogeneity in Breast Cancer at the Bench and Bedside. Mokryun Baek, Jeffrey T Chang, Gloria V Echeverria. J Mammary Gland Biol Neoplasia, 2020 Dec 11; 25(4). PMID: 33300087 Free PMC article.
Lung Cancer Survival in Patients With Autoimmune Disease. Saya Jacob, Kian Rahbari, +8 authors, Victoria Villaflor. less JAMA Netw Open, 2020 Dec 15; 3(12). PMID: 33315114 Free PMC article.
Applications of Single-Cell Omics to Dissect Tumor Microenvironment. Tingting Guo, Weimin Li, Xuyu Cai. Front Genet, 2020 Dec 18; 11. PMID: 33329692 Free PMC article. Review.
Molecularly targeted photothermal ablation improves tumor specificity and immune modulation in a rat model of hepatocellular carcinoma. Nina M Muñoz, Crystal Dupuis, +8 authors, Rahul A Sheth. less Commun Biol, 2020 Dec 19; 3(1). PMID: 33335270 Free PMC article.
A single cell atlas of the human liver tumor microenvironment. Hassan Massalha, Keren Bahar Halpern, +9 authors, Shalev Itzkovitz. less Mol Syst Biol, 2020 Dec 18; 16(12). PMID: 33332768 Free PMC article.
Tumor-Associated Neutrophils and Macrophages-Heterogenous but Not Chaotic. Ling Wu, Xiang H-F Zhang. Front Immunol, 2020 Dec 22; 11. PMID: 33343560 Free PMC article. Review.
The G protein coupled receptor CCR5 in cancer. Chandan Upadhyaya, Xuanmao Jiao, +3 authors, Richard G Pestell. less Adv Cancer Res, 2020 Feb 25; 145. PMID: 32089164 Free PMC article. Review.
Single-Cell RNA Sequencing of a Postmenopausal Normal Breast Tissue Identifies Multiple Cell Types That Contribute to Breast Cancer. Sen Peng, Lora L Hebert, Jennifer M Eschbacher, Suwon Kim. Cancers (Basel), 2020 Dec 10; 12(12). PMID: 33291647 Free PMC article.
The Tumor Microenvironment as a Driving Force of Breast Cancer Stem Cell Plasticity. Flavia Fico, Albert Santamaria-Martínez. Cancers (Basel), 2020 Dec 30; 12(12). PMID: 33371274 Free PMC article. Review.
The Role of Immune Cells in Breast Tissue and Immunotherapy for the Treatment of Breast Cancer. Stephanie L Goff, David N Danforth. Clin Breast Cancer, 2020 Sep 08; 21(1). PMID: 32893093 Free PMC article. Review.
Single-cell profiling of the human decidual immune microenvironment in patients with recurrent pregnancy loss. Chuang Guo, Pengfei Cai, +17 authors, Kun Qu. less Cell Discov, 2021 Jan 05; 7(1). PMID: 33390590 Free PMC article.
Data denoising with transfer learning in single-cell transcriptomics. Jingshu Wang, Divyansh Agarwal, +4 authors, Nancy R Zhang. less Nat Methods, 2019 Sep 01; 16(9). PMID: 31471617 Free PMC article.
The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution. Qing Liang, Yudi Hu, +8 authors, Kejia Wang. less Front Immunol, 2021 Jan 05; 11. PMID: 33391261 Free PMC article.
Metabolic regulatory crosstalk between tumor microenvironment and tumor-associated macrophages. Degao Chen, Xiaomei Zhang, Zhongjun Li, Bo Zhu. Theranostics, 2021 Jan 05; 11(3). PMID: 33391518 Free PMC article. Review.
Single-cell transcriptome profiling of the vaginal wall in women with severe anterior vaginal prolapse. Yaqian Li, Qing-Yang Zhang, +9 authors, Lan Zhu. less Nat Commun, 2021 Jan 06; 12(1). PMID: 33397933 Free PMC article.
Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma. Ruiping Wang, Minghao Dang, +29 authors, Linghua Wang. less Nat Med, 2021 Jan 06; 27(1). PMID: 33398161 Free PMC article.
Tumor-promoting macrophages prevail in malignant ascites of advanced gastric cancer. Hye Hyeon Eum, Minsuk Kwon, +9 authors, Woong-Yang Park. less Exp Mol Med, 2020 Dec 06; 52(12). PMID: 33277616 Free PMC article.
Human cutaneous neurofibroma matrisome revealed by single-cell RNA sequencing. Jean-Philippe Brosseau, Adwait A Sathe, +4 authors, Lu Q Le. less Acta Neuropathol Commun, 2021 Jan 09; 9(1). PMID: 33413690 Free PMC article.
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. Dongqing Sun, Jin Wang, +13 authors, Chenfei Wang. less Nucleic Acids Res, 2020 Nov 13; 49(D1). PMID: 33179754 Free PMC article.
DeepImmuno: Deep learning-empowered prediction and generation of immunogenic peptides for T cell immunity. Guangyuan Li, Balaji Iyer, +2 authors, V B Surya Prasath, Yizhao Ni, Nathan Salomonis. less bioRxiv, 2021 Jan 06;. PMID: 33398286 Free PMC article.
Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics. Ze Zhang, Danyi Xiong, +2 authors, Xinlei Wang, Hongyu Liu, Tao Wang. less Nat Methods, 2021 Jan 08; 18(1). PMID: 33408405 Free PMC article.
Tumour heterogeneity and the evolutionary trade-offs of cancer. Jean Hausser, Uri Alon. Nat Rev Cancer, 2020 Feb 26; 20(4). PMID: 32094544 Review.
Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma. Yu-Pei Chen, Jian-Hua Yin, +28 authors, Jun Ma. less Cell Res, 2020 Jul 21; 30(11). PMID: 32686767 Free PMC article.
Single-cell transcriptomic analysis defines the interplay between tumor cells, viral infection, and the microenvironment in nasopharyngeal carcinoma. Shanzhao Jin, Ruoyan Li, +26 authors, Mu-Sheng Zeng. less Cell Res, 2020 Sep 10; 30(11). PMID: 32901110 Free PMC article.
Single-cell RNA sequencing reveals heterogeneous tumor and immune cell populations in early-stage lung adenocarcinomas harboring EGFR mutations. Di He, Di Wang, +5 authors, Guoping Fan. less Oncogene, 2020 Nov 05; 40(2). PMID: 33144684 Free PMC article.
Leaving no one behind: tracing every human thymocyte by single-cell RNA-sequencing. Yujun Deng, Hong Chen, +3 authors, Yang Zeng, Keyue Wang, Huiyuan Zhang, Hongbo Hu. less Semin Immunopathol, 2021 Jan 16; 43(1). PMID: 33449155 Review.
Regulatory T Cells Support Breast Cancer Progression by Opposing IFN-γ-Dependent Functional Reprogramming of Myeloid Cells. Nicholas M Clark, Leandro M Martinez, +5 authors, Paula D Bos. less Cell Rep, 2020 Dec 10; 33(10). PMID: 33296659 Free PMC article.
Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes. Evgeny Kiner, Elijah Willie, +10 authors, Immunological Genome Project Consortium. less Nat Immunol, 2021 Jan 20; 22(2). PMID: 33462454 Free PMC article.
Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to human prostate cancer progression. Sujun Chen, Guanghui Zhu, +30 authors, Shancheng Ren. less Nat Cell Biol, 2021 Jan 10; 23(1). PMID: 33420488
Immune Checkpoint Profiles in Luminal B Breast Cancer (Alliance). Meenakshi Anurag, Mayanne Zhu, +10 authors, Matthew J Ellis. less J Natl Cancer Inst, 2019 Oct 31; 112(7). PMID: 31665365 Free PMC article.
Cancer cells deploy lipocalin-2 to collect limiting iron in leptomeningeal metastasis. Yudan Chi, Jan Remsik, +11 authors, Adrienne Boire. less Science, 2020 Jul 18; 369(6501). PMID: 32675368 Free PMC article.
Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis. Saige L Pompura, Allon Wagner, +4 authors, David A Hafler. less J Clin Invest, 2020 Nov 11; 131(2). PMID: 33170805 Free PMC article.
Leronlimab, a humanized monoclonal antibody to CCR5, blocks breast cancer cellular metastasis and enhances cell death induced by DNA damaging chemotherapy. Xuanmao Jiao, Min Wang, +6 authors, Richard G Pestell. less Breast Cancer Res, 2021 Jan 25; 23(1). PMID: 33485378 Free PMC article.
A High-Dimensional Window into the Micro-Environment of Triple Negative Breast Cancer. Iris Nederlof, Hugo M Horlings, Christina Curtis, Marleen Kok. Cancers (Basel), 2021 Jan 21; 13(2). PMID: 33467084 Free PMC article. Review.
Mapping the immune environment in clear cell renal carcinoma by single-cell genomics. Nicholas Borcherding, Ajaykumar Vishwakarma, +7 authors, Weizhou Zhang. less Commun Biol, 2021 Jan 29; 4(1). PMID: 33504936 Free PMC article.
Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution. Yang Liu, Shuai He, +18 authors, Jin-Xin Bei. less Nat Commun, 2021 Feb 04; 12(1). PMID: 33531485 Free PMC article.
Immune crosstalk in cancer progression and metastatic spread: a complex conversation. Hannah Garner, Karin E de Visser. Nat Rev Immunol, 2020 Feb 07; 20(8). PMID: 32024984 Review.
Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans. Miri Gordin, Hagit Philip, +8 authors, Sol Efroni. less PLoS Comput Biol, 2021 Jan 20; 17(1). PMID: 33465095 Free PMC article.
Quantification of Immune Variables from Liquid Biopsy in Breast Cancer Patients Links Vδ2+ γδ T Cell Alterations with Lymph Node Invasion. Stéphane Fattori, Laurent Gorvel, +21 authors, Daniel Olive. less Cancers (Basel), 2021 Jan 29; 13(3). PMID: 33503843 Free PMC article.
Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer's disease. Sudha R Guttikonda, Lisa Sikkema, +12 authors, Lorenz Studer. less Nat Neurosci, 2021 Feb 10; 24(3). PMID: 33558694 Free PMC article.
Monocyte Regulation in Homeostasis and Malignancy. Amy Robinson, Claudia Z Han, Christopher K Glass, Jeffrey W Pollard. Trends Immunol, 2021 Jan 16; 42(2). PMID: 33446416 Free PMC article. Review.
Intratumoral heterogeneity in cancer progression and response to immunotherapy. Ilio Vitale, Efrat Shema, Sherene Loi, Lorenzo Galluzzi. Nat Med, 2021 Feb 13; 27(2). PMID: 33574607 Review.
Single-cell RNA-seq dissects the intratumoral heterogeneity of triple-negative breast cancer based on gene regulatory networks. Shunheng Zhou, Yu-E Huang, +5 authors, Wei Jiang. less Mol Ther Nucleic Acids, 2021 Feb 13; 23. PMID: 33575114 Free PMC article.
Single-cell RNA-sequencing analyses identify heterogeneity of CD8+ T cell subpopulations and novel therapy targets in melanoma. Weiwei Deng, Yubo Ma, +9 authors, Ruoyu Li. less Mol Ther Oncolytics, 2021 Feb 13; 20. PMID: 33575475 Free PMC article.
Decoding the multicellular ecosystem of lung adenocarcinoma manifested as pulmonary subsolid nodules by single-cell RNA sequencing. Xudong Xing, Fan Yang, +5 authors, Jun Wang. less Sci Adv, 2021 Feb 12; 7(5). PMID: 33571124 Free PMC article.
Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer. Xi Yang, Quan Qi, +6 authors, Shuwen Han. less Front Immunol, 2021 Feb 16; 11. PMID: 33584715 Free PMC article.
Spatiotemporal analysis of human intestinal development at single-cell resolution. David Fawkner-Corbett, Agne Antanaviciute, +11 authors, Alison Simmons. less Cell, 2021 Jan 07; 184(3). PMID: 33406409 Free PMC article.
The current landscape of single-cell transcriptomics for cancer immunotherapy. Puneeth Guruprasad, Yong Gu Lee, Ki Hyun Kim, Marco Ruella. J Exp Med, 2021 Feb 19; 218(1). PMID: 33601414 Free PMC article. Review.
Advancing Cancer Research and Medicine with Single-Cell Genomics. Bora Lim, Yiyun Lin, Nicholas Navin. Cancer Cell, 2020 Apr 15; 37(4). PMID: 32289270 Free PMC article. Review.
Progress and Clinical Application of Single-Cell Transcriptional Sequencing Technology in Cancer Research. Jian Liu, Tianmin Xu, +2 authors, Yuemei Jin, Bingyu Huang, Yan Zhang. less Front Oncol, 2021 Feb 23; 10. PMID: 33614479 Free PMC article. Review.
Lipid signalling enforces functional specialization of Treg cells in tumours. Seon Ah Lim, Jun Wei, +9 authors, Hongbo Chi. less Nature, 2021 Feb 26; 591(7849). PMID: 33627871 Free PMC article.
Single-Cell Gene Network Analysis and Transcriptional Landscape of MYCN-Amplified Neuroblastoma Cell Lines. Daniele Mercatelli, Nicola Balboni, +4 authors, Federico Manuel Giorgi. less Biomolecules, 2021 Feb 03; 11(2). PMID: 33525507 Free PMC article.
Tumor-associated myeloid cells: diversity and therapeutic targeting. Alberto Mantovani, Federica Marchesi, +2 authors, Sebastien Jaillon, Cecilia Garlanda, Paola Allavena. less Cell Mol Immunol, 2021 Jan 22; 18(3). PMID: 33473192 Free PMC article. Review.
CD25-Treg-depleting antibodies preserving IL-2 signaling on effector T cells enhance effector activation and antitumor immunity. Isabelle Solomon, Maria Amann, +29 authors, Sergio A Quezada. less Nat Cancer, 2021 Mar 02; 1(12). PMID: 33644766 Free PMC article.
High-Throughput Automated Single-Cell Imaging Analysis Reveals Dynamics of Glioblastoma Stem Cell Population During State Transition. Anastasia P Chumakova, Masahiro Hitomi, Erik P Sulman, Justin D Lathia. Cytometry A, 2019 Feb 08; 95(3). PMID: 30729665 Free PMC article.
Influence of injection technique, drug formulation and tumor microenvironment on intratumoral immunotherapy delivery and efficacy. Nina M Muñoz, Malea Williams, +15 authors, Rahul A Sheth. less J Immunother Cancer, 2021 Feb 17; 9(2). PMID: 33589526 Free PMC article.
Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer. Christen A Khella, Gaurav A Mehta, Rushabh N Mehta, Michael L Gatza. J Pers Med, 2021 Mar 07; 11(2). PMID: 33669749 Free PMC article. Review.
Circulating clonally expanded T cells reflect functions of tumor-infiltrating T cells. Liliana E Lucca, Pierre-Paul Axisa, +10 authors, David A Hafler. less J Exp Med, 2021 Mar 03; 218(4). PMID: 33651881 Free PMC article.
Exosome-mediated communication between tumor cells and tumor-associated macrophages: implications for tumor microenvironment. Chen Han, Cong Zhang, Hengxiao Wang, Lianmei Zhao. Oncoimmunology, 2021 Mar 09; 10(1). PMID: 33680573 Free PMC article. Review.
Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer. Amélie Cachot, Mariia Bilous, +22 authors, Camilla Jandus. less Sci Adv, 2021 Feb 28; 7(9). PMID: 33637530 Free PMC article.
Single-cell transcriptome analysis revealed the heterogeneity and microenvironment of gastrointestinal stromal tumors. Xiaofan Mao, Xuezhu Yang, +7 authors, Wei Luo. less Cancer Sci, 2021 Jan 05; 112(3). PMID: 33393143 Free PMC article.
CXCL9-expressing tumor-associated macrophages: new players in the fight against cancer. Paola Marie Marcovecchio, Graham Thomas, Shahram Salek-Ardakani. J Immunother Cancer, 2021 Feb 28; 9(2). PMID: 33637602 Free PMC article. Review.
Multi-Omics Data Analysis of Gene Expressions and Alterations, Cancer-Associated Fibroblast and Immune Infiltrations, Reveals the Onco-Immune Prognostic Relevance of STAT3/CDK2/4/6 in Human Malignancies. Bashir Lawal, Li-Ching Lin, +4 authors, Ching-Liang Ho. less Cancers (Basel), 2021 Mar 07; 13(5). PMID: 33668805 Free PMC article.
Osteopontin Blockade Immunotherapy Increases Cytotoxic T Lymphocyte Lytic Activity and Suppresses Colon Tumor Progression. John D Klement, Dakota B Poschel, +4 authors, Kebin Liu. less Cancers (Basel), 2021 Mar 07; 13(5). PMID: 33670921 Free PMC article.
Single-Cell Profiling to Explore Immunological Heterogeneity of Tumor Microenvironment in Breast Cancer. Xiao Yuan, Jinxi Wang, +2 authors, Yixuan Huang, Dangang Shangguan, Peng Zhang. less Front Immunol, 2021 Mar 16; 12. PMID: 33717201 Free PMC article. Review.
Macrophages and Extracellular Matrix in Breast Cancer: Partners in Crime or Protective Allies? Claire Deligne, Kim S Midwood. Front Oncol, 2021 Mar 16; 11. PMID: 33718177 Free PMC article. Review.
Leveraging Single-Cell Approaches in Cancer Precision Medicine. Aritro Nath, Andrea H Bild. Trends Cancer, 2021 Feb 11; 7(4). PMID: 33563578 Free PMC article. Review.
Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy. Satyen H Gohil, J Bryan Iorgulescu, +2 authors, David A Braun, Derin B Keskin, Kenneth J Livak. less Nat Rev Clin Oncol, 2020 Dec 06; 18(4). PMID: 33277626 Free PMC article. Review.
Allele-specific expression: applications in cancer and technical considerations. Carla Daniela Robles-Espinoza, Pejman Mohammadi, Ximena Bonilla, Maria Gutierrez-Arcelus. Curr Opin Genet Dev, 2021 Jan 01; 66. PMID: 33383480 Free PMC article. Review.
Remodeling of Stromal Cells and Immune Landscape in Microenvironment During Tumor Progression. Leena Arora, Durba Pal. Front Oncol, 2021 Mar 26; 11. PMID: 33763348 Free PMC article. Review.
Robust integration of multiple single-cell RNA sequencing datasets using a single reference space. Yang Liu, Tao Wang, Bin Zhou, Deyou Zheng. Nat Biotechnol, 2021 Mar 27; 39(7). PMID: 33767393 Free PMC article.
Immune cell profiling of the cerebrospinal fluid enables the characterization of the brain metastasis microenvironment. Carlota Rubio-Perez, Ester Planas-Rigol, +20 authors, Joan Seoane. less Nat Commun, 2021 Mar 10; 12(1). PMID: 33686071 Free PMC article.
The architectural design of CD8+ T cell responses in acute and chronic infection: Parallel structures with divergent fates. H Kay Chung, Bryan McDonald, Susan M Kaech. J Exp Med, 2021 Mar 24; 218(4). PMID: 33755719 Free PMC article. Review.
Radiotherapy as an immune checkpoint blockade combination strategy for hepatocellular carcinoma. Byung Min Lee, Jinsil Seong. World J Gastroenterol, 2021 Mar 30; 27(10). PMID: 33776363 Free PMC article. Review.
Landscape and dynamics of single tumor and immune cells in early and advanced-stage lung adenocarcinoma. Zhencong Chen, Yiwei Huang, +12 authors, Lijie Tan. less Clin Transl Med, 2021 Mar 31; 11(3). PMID: 33783985 Free PMC article.
Differences in Tumor Immune Microenvironment in Metastatic Sites of Breast Cancer. Hyunjong Lee, Kwon Joong Na, Hongyoon Choi. Front Oncol, 2021 Apr 06; 11. PMID: 33816302 Free PMC article.
Phenotyping of immune and endometrial epithelial cells in endometrial carcinomas revealed by single-cell RNA sequencing. Yu-E Guo, Yiran Li, +6 authors, Qin Yan. less Aging (Albany NY), 2021 Jan 12; 13(5). PMID: 33429363 Free PMC article.
Leptin and Cancer: Updated Functional Roles in Carcinogenesis, Therapeutic Niches, and Developments. Tsung-Chieh Lin, Michael Hsiao. Int J Mol Sci, 2021 Apr 04; 22(6). PMID: 33799880 Free PMC article. Review.
Mutations in BRCA1 and BRCA2 differentially affect the tumor microenvironment and response to checkpoint blockade immunotherapy. Robert M Samstein, Chirag Krishna, +25 authors, Nadeem Riaz. less Nat Cancer, 2021 Apr 10; 1(12). PMID: 33834176 Free PMC article.
Systemic immunity in cancer. Kamir J Hiam-Galvez, Breanna M Allen, Matthew H Spitzer. Nat Rev Cancer, 2021 Apr 11; 21(6). PMID: 33837297 Free PMC article. Review.
Atlas of breast cancer infiltrated B-lymphocytes revealed by paired single-cell RNA-sequencing and antigen receptor profiling. Qingtao Hu, Yu Hong, +10 authors, Yu Zhang. less Nat Commun, 2021 Apr 14; 12(1). PMID: 33846305 Free PMC article.
Predicting recognition between T cell receptors and epitopes with TCRGP. Emmi Jokinen, Jani Huuhtanen, +2 authors, Satu Mustjoki, Markus Heinonen, Harri Lähdesmäki. less PLoS Comput Biol, 2021 Mar 26; 17(3). PMID: 33764977 Free PMC article.
Immunotherapy for Hepatocellular Carcinoma: Current Limits and Prospects. Cheng Zhong, Yirun Li, +5 authors, Hui Lin. less Front Oncol, 2021 Apr 16; 11. PMID: 33854960 Free PMC article. Review.
Interaction Networks Converging on Immunosuppressive Roles of Granzyme B: Special Niches Within the Tumor Microenvironment. Weinan Wang, Rui Zou, +4 authors, Zhidong Qiu. less Front Immunol, 2021 Apr 20; 12. PMID: 33868318 Free PMC article. Review.
Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench. Ruben Chazarra-Gil, Stijn van Dongen, Vladimir Yu Kiselev, Martin Hemberg. Nucleic Acids Res, 2021 Feb 02; 49(7). PMID: 33524142 Free PMC article.
Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells. Michael Delacher, Malte Simon, +26 authors, Markus Feuerer. less Immunity, 2021 Apr 01; 54(4). PMID: 33789089 Free PMC article.
Single-cell RNA-seq reveals dynamic change in tumor microenvironment during pancreatic ductal adenocarcinoma malignant progression. Kai Chen, Qi Wang, +5 authors, Yinmo Yang. less EBioMedicine, 2021 Apr 06; 66. PMID: 33819739 Free PMC article.
Comprehensive description of the current breast cancer microenvironment advancements via single-cell analysis. Xueqi Yan, Yinghong Xie, +10 authors, Yongmei Yin. less J Exp Clin Cancer Res, 2021 Apr 29; 40(1). PMID: 33906694 Free PMC article. Review.
TNFR2: Role in Cancer Immunology and Immunotherapy. Yang Yang, Md Sahidul Islam, Yuanjia Hu, Xin Chen. Immunotargets Ther, 2021 Apr 29; 10. PMID: 33907692 Free PMC article. Review.
Single-cell transcriptomics in cancer: computational challenges and opportunities. Jean Fan, Kamil Slowikowski, Fan Zhang. Exp Mol Med, 2020 Sep 16; 52(9). PMID: 32929226 Free PMC article. Review.
Tumor microenvironment as a therapeutic target in cancer. Yi Xiao, Dihua Yu. Pharmacol Ther, 2020 Dec 02; 221. PMID: 33259885 Free PMC article. Review.
Functional Roles of SPINK1 in Cancers. Tsung-Chieh Lin. Int J Mol Sci, 2021 May 01; 22(8). PMID: 33916984 Free PMC article. Review.
Recruitment and Expansion of Tregs Cells in the Tumor Environment-How to Target Them? Justine Cinier, Margaux Hubert, +5 authors, Christine Ménétrier-Caux. less Cancers (Basel), 2021 May 01; 13(8). PMID: 33924428 Free PMC article. Review.
STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets. Dev Bhatt, Boxi Kang, +13 authors, Wenjun Ouyang. less J Exp Med, 2021 Apr 27; 218(6). PMID: 33900375 Free PMC article.
Single-Cell TCR Sequencing Reveals the Dynamics of T Cell Repertoire Profiling During Pneumocystis Infection. Hu-Qin Yang, Yi-Shan Wang, Kan Zhai, Zhao-Hui Tong. Front Microbiol, 2021 May 08; 12. PMID: 33959105 Free PMC article.
Knockout of immunotherapy prognostic marker genes eliminates the effect of the anti-PD-1 treatment. Naixue Yang, Fansen Ji, +4 authors, Xun Lan. less NPJ Precis Oncol, 2021 May 09; 5(1). PMID: 33963274 Free PMC article.
DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing. Arjun Bhattacharya, Alina M Hamilton, Melissa A Troester, Michael I Love. Nucleic Acids Res, 2021 Feb 02; 49(8). PMID: 33524140 Free PMC article.
Prognostic analysis of tumor mutation burden and immune infiltration in hepatocellular carcinoma based on TCGA data. Shaoqing Liu, Qianjie Tang, +8 authors, Xu He. less Aging (Albany NY), 2021 Apr 07; 13(8). PMID: 33820866 Free PMC article.
What are the applications of single-cell RNA sequencing in cancer research: a systematic review. Lvyuan Li, Fang Xiong, +15 authors, Can Guo. less J Exp Clin Cancer Res, 2021 May 13; 40(1). PMID: 33975628 Free PMC article. Systematic Review.
Single cell RNA sequencing for breast cancer: present and future. Lili Ren, Junyi Li, +8 authors, Jing Tang. less Cell Death Discov, 2021 May 16; 7(1). PMID: 33990550 Free PMC article. Review.
Interpretation of T cell states from single-cell transcriptomics data using reference atlases. Massimo Andreatta, Jesus Corria-Osorio, +3 authors, Santiago J Carmona. less Nat Commun, 2021 May 22; 12(1). PMID: 34017005 Free PMC article.
Clonally expanded EOMES+ Tr1-like cells in primary and metastatic tumors are associated with disease progression. Raoul J P Bonnal, Grazisa Rossetti, +43 authors, Massimiliano Pagani. less Nat Immunol, 2021 May 22; 22(6). PMID: 34017124
Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. David A Braun, Kelly Street, +32 authors, Catherine J Wu. less Cancer Cell, 2021 Mar 13; 39(5). PMID: 33711273 Free PMC article.
Delineating the heterogeneity of matrix-directed differentiation toward soft and stiff tissue lineages via single-cell profiling. Shlomi Brielle, Danny Bavli, +6 authors, Amnon Buxboim. less Proc Natl Acad Sci U S A, 2021 May 05; 118(19). PMID: 33941688 Free PMC article.
DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Guangyuan Li, Balaji Iyer, +2 authors, V B Surya Prasath, Yizhao Ni, Nathan Salomonis. less Brief Bioinform, 2021 May 20; 22(6). PMID: 34009266 Free PMC article.
Developing neoantigen-targeted T cell-based treatments for solid tumors. Tori N Yamamoto, Rigel J Kishton, Nicholas P Restifo. Nat Med, 2019 Oct 09; 25(10). PMID: 31591590 Highly Cited. Review.
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes. Marc Elosua-Bayes, Paula Nieto, +2 authors, Elisabetta Mereu, Ivo Gut, Holger Heyn. less Nucleic Acids Res, 2021 Feb 06; 49(9). PMID: 33544846 Free PMC article.
[Research Progress of Single Cell Sequencing in Lung Cancer]. Mengjun Yu, Jinjing Tan, Jinghui Wang. Zhongguo Fei Ai Za Zhi, 2021 Apr 30; 24(4). PMID: 33910276 Free PMC article. Review.
Mechanisms of Macrophage Plasticity in the Tumor Environment: Manipulating Activation State to Improve Outcomes. Tiffany Davia Ricketts, Nestor Prieto-Dominguez, Pramod Sreerama Gowda, Eric Ubil. Front Immunol, 2021 May 25; 12. PMID: 34025653 Free PMC article. Review.
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. Zoe A Clarke, Tallulah S Andrews, +4 authors, Gary D Bader. less Nat Protoc, 2021 May 26; 16(6). PMID: 34031612 Review.
Robust Carbonated Structural Color Barcodes with Ultralow Ontology Fluorescence as Biomimic Culture Platform. Panmiao Liu, Zhongde Mu, +6 authors, Fuyin Zheng. less Research (Wash D C), 2021 May 27; 2021. PMID: 34036265 Free PMC article.
Single-cell transcriptomics: a novel precision medicine technique in nephrology. Jisoo Kim, Jihwan Park. Korean J Intern Med, 2020 Oct 21; 36(3). PMID: 33076636 Free PMC article. Review.
Mammary gland development from a single cell 'omics view. Alecia-Jane Twigger, Walid T Khaled. Semin Cell Dev Biol, 2021 Apr 04; 114. PMID: 33810979 Free PMC article. Review.
Claudin-Low Breast Cancer Inflammatory Signatures Support Polarization of M1-Like Macrophages with Protumoral Activity. Mayra Cecilia Suárez-Arriaga, Alfonso Méndez-Tenorio, Vadim Pérez-Koldenkova, Ezequiel M Fuentes-Pananá. Cancers (Basel), 2021 Jun 03; 13(9). PMID: 34067089 Free PMC article.
Exosomes in Breast Cancer - Mechanisms of Action and Clinical Potential. Tiantong Liu, Jagmohan Hooda, +3 authors, Adrian V Lee. less Mol Cancer Res, 2021 Feb 26; 19(6). PMID: 33627501 Free PMC article. Review.
T cell stemness and dysfunction in tumors are triggered by a common mechanism. Suman Kumar Vodnala, Robert Eil, +16 authors, Nicholas P Restifo. less Science, 2019 Mar 30; 363(6434). PMID: 30923193 Free PMC article. Highly Cited.
A single-cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast. Bhupinder Pal, Yunshun Chen, +14 authors, Jane E Visvader. less EMBO J, 2021 May 06; 40(11). PMID: 33950524 Free PMC article.
Tumor-infiltrating B cells as a favorable prognostic biomarker in breast cancer: a systematic review and meta-analysis. You Qin, Fei Peng, +4 authors, Yu Hu. less Cancer Cell Int, 2021 Jun 14; 21(1). PMID: 34118931 Free PMC article. Review.
The Immunology of Hormone Receptor Positive Breast Cancer. Jonathan Goldberg, Ricardo G Pastorello, +9 authors, Jennifer L Guerriero. less Front Immunol, 2021 Jun 18; 12. PMID: 34135901 Free PMC article. Review.
Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges. Jiajia Liu, Zhiwei Fan, Weiling Zhao, Xiaobo Zhou. Front Genet, 2021 Jun 18; 12. PMID: 34135939 Free PMC article. Review.
The triumphs and limitations of computational methods for scRNA-seq. Peter V Kharchenko. Nat Methods, 2021 Jun 23; 18(7). PMID: 34155396 Review.
scGCN is a graph convolutional networks algorithm for knowledge transfer in single cell omics. Qianqian Song, Jing Su, Wei Zhang. Nat Commun, 2021 Jun 24; 12(1). PMID: 34158507 Free PMC article.
Single-cell transcriptomic analysis reveals disparate effector differentiation pathways in human Treg compartment. Yuechen Luo, Changlu Xu, +18 authors, Xiaoming Feng. less Nat Commun, 2021 Jun 25; 12(1). PMID: 34162888 Free PMC article.
Single-Cell TCR and Transcriptome Analysis: An Indispensable Tool for Studying T-Cell Biology and Cancer Immunotherapy. Anna Pasetto, Yong-Chen Lu. Front Immunol, 2021 Jun 25; 12. PMID: 34163487 Free PMC article. Review.
Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response. Yuping Zhang, Sathiya P Narayanan, +16 authors, Arul M Chinnaiyan. less Proc Natl Acad Sci U S A, 2021 Jun 09; 118(24). PMID: 34099557 Free PMC article.
Applications of Single-Cell Omics in Tumor Immunology. Junwei Liu, Saisi Qu, +5 authors, Weiwei Yin. less Front Immunol, 2021 Jun 29; 12. PMID: 34177965 Free PMC article. Review.
Unsupervised logic-based mechanism inference for network-driven biological processes. Martina Prugger, Lukas Einkemmer, +3 authors, Carlos F Lopez. less PLoS Comput Biol, 2021 Jun 03; 17(6). PMID: 34077417 Free PMC article.
A Literature-Derived Knowledge Graph Augments the Interpretation of Single Cell RNA-seq Datasets. Deeksha Doddahonnaiah, Patrick J Lenehan, +11 authors, Venky Soundararajan. less Genes (Basel), 2021 Jul 03; 12(6). PMID: 34200671 Free PMC article.
Myeloid-Specific Acly Deletion Alters Macrophage Phenotype In Vitro and In Vivo without Affecting Tumor Growth. Kyra E de Goede, Sanne G S Verberk, +5 authors, Jan Van den Bossche. less Cancers (Basel), 2021 Jul 03; 13(12). PMID: 34205266 Free PMC article.
Dissecting the single-cell transcriptome network underlying esophagus non-malignant tissues and esophageal squamous cell carcinoma. Zhencong Chen, Mengnan Zhao, +11 authors, Lijie Tan. less EBioMedicine, 2021 Jul 01; 69. PMID: 34192657 Free PMC article.
CD8+ T cell differentiation and dysfunction in cancer. Mary Philip, Andrea Schietinger. Nat Rev Immunol, 2021 Jul 14; 22(4). PMID: 34253904 Review.
New technology on the horizon: Fast analytical screening technique FNA (FAST-FNA) enables rapid, multiplex biomarker analysis in head and neck cancers. Sara I Pai, William C Faquin, +2 authors, Peter M Sadow, Mikael J Pittet, Ralph Weissleder. less Cancer Cytopathol, 2020 Aug 26; 128(11). PMID: 32841527 Free PMC article. Review.
Bulk and single-cell transcriptome profiling reveal the metabolic heterogeneity in human breast cancers. Tian-Jian Yu, Ding Ma, +6 authors, Gen-Hong Di. less Mol Ther, 2021 Mar 08; 29(7). PMID: 33677091 Free PMC article.
Specialized Pro-Resolving Mediators Mitigate Cancer-Related Inflammation: Role of Tumor-Associated Macrophages and Therapeutic Opportunities. Margot Lavy, Vanessa Gauttier, +2 authors, Christophe Blanquart. less Front Immunol, 2021 Jul 20; 12. PMID: 34276698 Free PMC article. Review.
Multi-Omics Analysis Showed the Clinical Value of Gene Signatures of C1QC+ and SPP1+ TAMs in Cervical Cancer. Xiong Li, Qinghua Zhang, Gang Chen, Danfeng Luo. Front Immunol, 2021 Jul 24; 12. PMID: 34295336 Free PMC article.
C5aR1-positive neutrophils promote breast cancer glycolysis through WTAP-dependent m6A methylation of ENO1. Baochi Ou, Yuan Liu, +3 authors, Xiaowei Yang, Xiaojun Xu, Yunwen Yan, Jingjie Zhang. less Cell Death Dis, 2021 Jul 28; 12(8). PMID: 34312368 Free PMC article.
High-throughput and single-cell T cell receptor sequencing technologies. Joy A Pai, Ansuman T Satpathy. Nat Methods, 2021 Jul 21; 18(8). PMID: 34282327 Review.
Myeloid Cell-associated Resistance to PD-1/PD-L1 Blockade in Urothelial Cancer Revealed Through Bulk and Single-cell RNA Sequencing. Li Wang, John P Sfakianos, +18 authors, Matthew D Galsky. less Clin Cancer Res, 2021 Apr 11; 27(15). PMID: 33837006 Free PMC article.
Single-Cell Transcriptome Profiling Simulation Reveals the Impact of Sequencing Parameters and Algorithms on Clustering. Yunhe Liu, Aoshen Wu, +3 authors, Xueqing Peng, Xiaona Liu, Gang Liu, Lei Liu. less Life (Basel), 2021 Aug 07; 11(7). PMID: 34357088 Free PMC article.
A Combination of GM-CSF and Released Factors from Gamma-Irradiated Tumor Cells Enhances the Differentiation of Macrophages from Bone Marrow Cells and Their Antigen-Presenting Function and Polarization to Type 1. Lichao Chen, Shoji Imamichi, +6 authors, Mitsuko Masutani. less Medicines (Basel), 2021 Aug 07; 8(7). PMID: 34357151 Free PMC article.
Endogenous and Therapeutic Estrogens: Maestro Conductors of the Microenvironment of ER+ Breast Cancers. Linda A Schuler, Fern E Murdoch. Cancers (Basel), 2021 Aug 08; 13(15). PMID: 34359625 Free PMC article. Review.
Single-Cell Transcriptomics Reveals the Complexity of the Tumor Microenvironment of Treatment-Naive Osteosarcoma. Yun Liu, Wenyu Feng, +22 authors, Zengnan Mo. less Front Oncol, 2021 Aug 10; 11. PMID: 34367994 Free PMC article.
Interleukin-2 inducible T-cell kinase: a potential prognostic biomarker and tumor microenvironment remodeling indicator for hepatocellular carcinoma. Binhua Pan, Modan Yang, +7 authors, Xiao Xu. less Aging (Albany NY), 2021 Jul 21; 13(14). PMID: 34282055 Free PMC article.
The Promise of Personalized TCR-Based Cellular Immunotherapy for Cancer Patients. Marion Arnaud, Sara Bobisse, Johanna Chiffelle, Alexandre Harari. Front Immunol, 2021 Aug 17; 12. PMID: 34394096 Free PMC article. Review.
Cancer biology deciphered by single-cell transcriptomic sequencing. Yanmeng Li, Jianshi Jin, Fan Bai. Protein Cell, 2021 Aug 19; 13(3). PMID: 34405376 Free PMC article. Review.
Tumor-Infiltrating B Lymphocyte Profiling Identifies IgG-Biased, Clonally Expanded Prognostic Phenotypes in Triple-Negative Breast Cancer. Robert J Harris, Anthony Cheung, +24 authors, Sophia N Karagiannis. less Cancer Res, 2021 Jul 06; 81(16). PMID: 34224371 Free PMC article.
Cell-autonomous inflammation of BRCA1-deficient ovarian cancers drives both tumor-intrinsic immunoreactivity and immune resistance via STING. Marine Bruand, David Barras, +32 authors, George Coukos. less Cell Rep, 2021 Jul 22; 36(3). PMID: 34289354 Free PMC article.
Single-cell evaluation reveals shifts in the tumor-immune niches that shape and maintain aggressive lesions in the breast. Vidya C Sinha, Amanda L Rinkenbaugh, +9 authors, Helen Piwnica-Worms. less Nat Commun, 2021 Aug 20; 12(1). PMID: 34408137 Free PMC article.
MultiK: an automated tool to determine optimal cluster numbers in single-cell RNA sequencing data. Siyao Liu, Aatish Thennavan, +2 authors, Joseph P Garay, J S Marron, Charles M Perou. less Genome Biol, 2021 Aug 21; 22(1). PMID: 34412669 Free PMC article.
Technological advances in cancer immunity: from immunogenomics to single-cell analysis and artificial intelligence. Ying Xu, Guan-Hua Su, +3 authors, Ding Ma, Yi Xiao, Zhi-Ming Shao, Yi-Zhou Jiang. less Signal Transduct Target Ther, 2021 Aug 22; 6(1). PMID: 34417437 Free PMC article. Review.
Multi-Parameter Quantitative Imaging of Tumor Microenvironments Reveals Perivascular Immune Niches Associated With Anti-Tumor Immunity. Caleb R Stoltzfus, Ramya Sivakumar, +8 authors, Michael Y Gerner. less Front Immunol, 2021 Aug 24; 12. PMID: 34421928 Free PMC article.
Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA). Stefan A Schattgen, Kate Guion, +5 authors, Philip Bradley. less Nat Biotechnol, 2021 Aug 25; 40(1). PMID: 34426704 Free PMC article.
A clinically applicable integrative molecular classification of meningiomas. Farshad Nassiri, Jeff Liu, +23 authors, Gelareh Zadeh. less Nature, 2021 Aug 27; 597(7874). PMID: 34433969
m6A RNA Methylation Regulator YTHDF1 Correlated With Immune Microenvironment Predicts Clinical Outcomes and Therapeutic Efficacy in Breast Cancer. Ying Hu, Qinwen Pan, +6 authors, Jun Jiang. less Front Med (Lausanne), 2021 Aug 27; 8. PMID: 34434939 Free PMC article.
Tumor Microenvironment in Breast Cancer-Updates on Therapeutic Implications and Pathologic Assessment. Joshua J Li, Julia Y Tsang, Gary M Tse. Cancers (Basel), 2021 Aug 28; 13(16). PMID: 34439387 Free PMC article. Review.
From bench to bedside: Single-cell analysis for cancer immunotherapy. Emily F Davis-Marcisak, Atul Deshpande, +5 authors, Luciane T Kagohara. less Cancer Cell, 2021 Jul 31; 39(8). PMID: 34329587 Free PMC article. Review.
Head and neck squamous cell carcinoma cell lines have an immunomodulatory effect on macrophages independent of hypoxia and toll-like receptor 9. Tamiko Ishizu, Dominik Eichin, +5 authors, Johanna M Tuomela. less BMC Cancer, 2021 Sep 05; 21(1). PMID: 34479492 Free PMC article.
Seeing the forest and the tree: TILs and PD-L1 as immune biomarkers. Peter Savas, Roberto Salgado, Sherene Loi. Breast Cancer Res Treat, 2021 Sep 07; 189(3). PMID: 34487294 Review.
Comprehensive Analysis of RUNX and TGF-β Mediated Regulation of Immune Cell Infiltration in Breast Cancer. Liang Gao, Fangfang Zhou. Front Cell Dev Biol, 2021 Sep 07; 9. PMID: 34485309 Free PMC article.
A single-cell atlas of liver metastases of colorectal cancer reveals reprogramming of the tumor microenvironment in response to preoperative chemotherapy. Li-Heng Che, Jing-Wen Liu, +14 authors, Jian-Ming Li. less Cell Discov, 2021 Sep 08; 7(1). PMID: 34489408 Free PMC article.
A single-cell and spatially resolved atlas of human breast cancers. Sunny Z Wu, Ghamdan Al-Eryani, +37 authors, Alexander Swarbrick. less Nat Genet, 2021 Sep 09; 53(9). PMID: 34493872 Free PMC article.
Single-Cell RNA Sequencing Reveals the Migration of Osteoclasts in Giant Cell Tumor of Bone. Wenyu Feng, Mingwei He, +11 authors, Qingjun Wei. less Front Oncol, 2021 Sep 11; 11. PMID: 34504794 Free PMC article.
Chemokines and the immune response to cancer. Aleksandra J Ozga, Melvyn T Chow, Andrew D Luster. Immunity, 2021 Apr 12; 54(5). PMID: 33838745 Free PMC article. Review.
Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging. Daria Lazic, Florian Kromp, +13 authors, Sabine Taschner-Mandl. less Cancers (Basel), 2021 Sep 11; 13(17). PMID: 34503120 Free PMC article.
Pro-Oncogenic c-Met/EGFR, Biomarker Signatures of the Tumor Microenvironment are Clinical and Therapy Response Prognosticators in Colorectal Cancer, and Therapeutic Targets of 3-Phenyl-2H-benzo[e][1,3]-Oxazine-2,4(3H)-Dione Derivatives. Bashir Lawal, Yu-Chi Wang, Alexander T H Wu, Hsu-Shan Huang. Front Pharmacol, 2021 Sep 14; 12. PMID: 34512327 Free PMC article.
Schrödinger's T Cells: Molecular Insights Into Stemness and Exhaustion. Nancy M Gonzalez, Dawei Zou, Andy Gu, Wenhao Chen. Front Immunol, 2021 Sep 14; 12. PMID: 34512656 Free PMC article. Review.
Single-cell profiling of infiltrating B cells and tertiary lymphoid structures in the TME of gastric adenocarcinomas. Lizhou Jia, Tengqi Wang, +8 authors, Haishi Qiao. less Oncoimmunology, 2021 Sep 14; 10(1). PMID: 34513317 Free PMC article.
SCISSOR™: a single-cell inferred site-specific omics resource for tumor microenvironment association study. Xiang Cui, Fei Qin, +2 authors, Xuanxuan Yu, Feifei Xiao, Guoshuai Cai. less NAR Cancer, 2021 Sep 14; 3(3). PMID: 34514416 Free PMC article.
Loss of polycomb repressive complex 1 activity and chromosomal instability drive uveal melanoma progression. Mathieu F Bakhoum, Jasmine H Francis, +11 authors, Ashley M Laughney. less Nat Commun, 2021 Sep 15; 12(1). PMID: 34518527 Free PMC article.
Tumor-Infiltrating Neutrophils and Non-Classical Monocytes May Be Potential Therapeutic Targets for HER2negative Gastric Cancer. Juhee Jeong, Duk Ki Kim, +5 authors, Keehoon Jung. less Immune Netw, 2021 Sep 16; 21(4). PMID: 34522444 Free PMC article.
A unified atlas of CD8 T cell dysfunctional states in cancer and infection. Yuri Pritykin, Joris van der Veeken, +6 authors, Christina S Leslie. less Mol Cell, 2021 Apr 24; 81(11). PMID: 33891860 Free PMC article.
Single-cell profiling defines the prognostic benefit of CD39high tissue resident memory CD8+ T cells in luminal-like breast cancer. Agnese Losurdo, Caterina Scirgolea, +13 authors, Enrico Lugli. less Commun Biol, 2021 Sep 24; 4(1). PMID: 34552178 Free PMC article.
Single-Cell Applications of Next-Generation Sequencing. Naishitha Anaparthy, Yu-Jui Ho, +2 authors, Luciano Martelotto, Molly Hammell, James Hicks. less Cold Spring Harb Perspect Med, 2019 Jan 09; 9(10). PMID: 30617056 Free PMC article. Review.
Multimodel preclinical platform predicts clinical response of melanoma to immunotherapy. Eva Pérez-Guijarro, Howard H Yang, +22 authors, Glenn Merlino. less Nat Med, 2020 Apr 15; 26(5). PMID: 32284588 Free PMC article.
Bringing Macrophages to the Frontline against Cancer: Current Immunotherapies Targeting Macrophages. Mariana Reis-Sobreiro, Afonso Teixeira da Mota, Carolina Jardim, Karine Serre. Cells, 2021 Sep 29; 10(9). PMID: 34572013 Free PMC article. Review.
3D Cancer Models: Depicting Cellular Crosstalk within the Tumour Microenvironment. Teresa Franchi-Mendes, Rodrigo Eduardo, Giacomo Domenici, Catarina Brito. Cancers (Basel), 2021 Sep 29; 13(18). PMID: 34572836 Free PMC article. Review.
CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells. Myung-Chul Kim, Nicholas Borcherding, +32 authors, Weizhou Zhang. less Nat Commun, 2021 Oct 03; 12(1). PMID: 34599187 Free PMC article.
Type 2 dendritic cells mediate control of cytotoxic T cell resistant tumors. Stephen Iwanowycz, Soo Ngoi, +6 authors, Bei Liu. less JCI Insight, 2021 Jul 21; 6(17). PMID: 34283809 Free PMC article.
A single-cell tumor immune atlas for precision oncology. Paula Nieto, Marc Elosua-Bayes, +23 authors, Holger Heyn. less Genome Res, 2021 Sep 23; 31(10). PMID: 34548323 Free PMC article.
Systematic tissue collection during clinical breast biopsy is feasible, safe and enables high-content translational analyses. Siang-Boon Koh, Brian N Dontchos, +15 authors, Laura M Spring. less NPJ Precis Oncol, 2021 Sep 23; 5(1). PMID: 34548623 Free PMC article.
Classification of Estrogen Receptor-Positive Breast Cancer Based on Immunogenomic Profiling and Validation at Single-Cell Resolution. Xianxiong Ma, Hengyu Chen, +4 authors, Lei Li. less Front Cell Dev Biol, 2021 Oct 09; 9. PMID: 34621742 Free PMC article.
Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq. Ying Yao, Łukasz Wyrozżemski, +2 authors, Knut E A Lundin, Geir Kjetil Sandve, Shuo-Wang Qiao. less PLoS One, 2021 Oct 08; 16(10). PMID: 34618841 Free PMC article.
The Multifaceted Role of Regulatory T Cells in Breast Cancer. Kevin Kos, Karin E de Visser. Annu Rev Cancer Biol, 2021 Oct 12; 5. PMID: 34632244 Free PMC article.
Single-Cell RNA-Seq of T Cells in B-ALL Patients Reveals an Exhausted Subset with Remarkable Heterogeneity. Xiaofang Wang, Yanjuan Chen, +8 authors, Yangqiu Li. less Adv Sci (Weinh), 2021 Aug 09; 8(19). PMID: 34365737 Free PMC article.
Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions. Alma Andersson, Ludvig Larsson, +10 authors, Joakim Lundeberg. less Nat Commun, 2021 Oct 16; 12(1). PMID: 34650042 Free PMC article.
Evolution of the Tumor Microenvironment toward Immune-Suppressive Seclusion during Brain Metastasis of Breast Cancer: Implications for Targeted Therapy. Myung-Giun Noh, Sung Sun Kim, +9 authors, Kyung-Hwa Lee. less Cancers (Basel), 2021 Oct 14; 13(19). PMID: 34638378 Free PMC article.
Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy. Hussein A Abbas, Dapeng Hao, +31 authors, Andrew Futreal. less Nat Commun, 2021 Oct 20; 12(1). PMID: 34663807 Free PMC article.
Atlas of clinically distinct cell states and ecosystems across human solid tumors. Bogdan A Luca, Chloé B Steen, +10 authors, Aaron M Newman. less Cell, 2021 Oct 02; 184(21). PMID: 34597583 Free PMC article.
Microdissection of the Bulk Transcriptome at Single-Cell Resolution Reveals Clinical Significance and Myeloid Cells Heterogeneity in Lung Adenocarcinoma. Hao Wu, Jiale Qin, +2 authors, Qiang Zhao, Lu Lu, Chen Li. less Front Immunol, 2021 Oct 19; 12. PMID: 34659209 Free PMC article.
Characterizing Intercellular Communication of Pan-Cancer Reveals SPP1+ Tumor-Associated Macrophage Expanded in Hypoxia and Promoting Cancer Malignancy Through Single-Cell RNA-Seq Data. Jinfen Wei, Zixi Chen, +4 authors, Hongli Du. less Front Cell Dev Biol, 2021 Oct 23; 9. PMID: 34676217 Free PMC article.
Single-cell transcriptomics reveal the heterogeneity and dynamic of cancer stem-like cells during breast tumor progression. Guojuan Jiang, Juchuanli Tu, +6 authors, Suling Liu. less Cell Death Dis, 2021 Oct 23; 12(11). PMID: 34675206 Free PMC article.
High-Dimensional Single-Cell Transcriptomics in Melanoma and Cancer Immunotherapy. Camelia Quek, Xinyu Bai, +2 authors, Georgina V Long, Richard A Scolyer, James S Wilmott. less Genes (Basel), 2021 Oct 24; 12(10). PMID: 34681023 Free PMC article. Review.
Nature vs. Nurture: The Two Opposing Behaviors of Cytotoxic T Lymphocytes in the Tumor Microenvironment. Nagaja Capitani, Laura Patrussi, Cosima T Baldari. Int J Mol Sci, 2021 Oct 24; 22(20). PMID: 34681881 Free PMC article. Review.
Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data. Xuan Liu, Sara J C Gosline, +5 authors, Jeffrey T Chang. less Brief Bioinform, 2021 Mar 09; 22(5). PMID: 33681983 Free PMC article.
From Cellular Infiltration Assessment to a Functional Gene Set-Based Prognostic Model for Breast Cancer. Huamei Li, Yiting Huang, +5 authors, Hongde Liu. less Front Immunol, 2021 Oct 26; 12. PMID: 34691065 Free PMC article.
Single-cell sequencing reveals antitumor characteristics of intratumoral immune cells in old mice. Cangang Zhang, Lei Lei, +14 authors, Baojun Zhang. less J Immunother Cancer, 2021 Oct 14; 9(10). PMID: 34642245 Free PMC article.
Daily caloric restriction limits tumor growth more effectively than caloric cycling regardless of dietary composition. Laura C D Pomatto-Watson, Monica Bodogai, +16 authors, Rafael de Cabo. less Nat Commun, 2021 Oct 29; 12(1). PMID: 34707136 Free PMC article.
Integrating single cell sequencing with a spatial quantitative systems pharmacology model spQSP for personalized prediction of triple-negative breast cancer immunotherapy response. Shuming Zhang, Chang Gong, +5 authors, Elana J Fertig. less Immunoinformatics (Amst), 2021 Oct 29; 1-2. PMID: 34708216 Free PMC article.
Phased differentiation of γδ T and T CD8 tumor-infiltrating lymphocytes revealed by single-cell transcriptomics of human cancers. Juan-Pablo Cerapio, Marion Perrier, +15 authors, Jean-Jacques Fournie. less Oncoimmunology, 2021 Nov 02; 10(1). PMID: 34721945 Free PMC article.
Application of Single-Cell Multi-Omics in Dissecting Cancer Cell Plasticity and Tumor Heterogeneity. Deshen Pan, Deshui Jia. Front Mol Biosci, 2021 Nov 02; 8. PMID: 34722635 Free PMC article. Review.
Postpartum breast cancer has a distinct molecular profile that predicts poor outcomes. Sonali Jindal, Nathan D Pennock, +9 authors, Pepper Schedin. less Nat Commun, 2021 Nov 05; 12(1). PMID: 34732713 Free PMC article.
Ductal Macrophages Predominate in the Immune Landscape of the Lactating Mammary Gland. Chervin Hassel, Blandine Gausserès, Laurence Guzylack-Piriou, Gilles Foucras. Front Immunol, 2021 Nov 09; 12. PMID: 34745127 Free PMC article.
The Single-Cell Sequencing: A Dazzling Light Shining on the Dark Corner of Cancer. Jing Li, Nan Yu, +2 authors, Xin Li, Mengna Cui, Qie Guo. less Front Oncol, 2021 Nov 09; 11. PMID: 34745998 Free PMC article. Review.
Treatment landscape of triple-negative breast cancer - expanded options, evolving needs. Giampaolo Bianchini, Carmine De Angelis, Luca Licata, Luca Gianni. Nat Rev Clin Oncol, 2021 Nov 11; 19(2). PMID: 34754128 Review.
The microenvironment of DLBCL is characterized by noncanonical macrophages recruited by tumor-derived CCL5. Benoît Manfroi, Maria De Grandis, +7 authors, Bertrand Huard. less Blood Adv, 2021 Sep 14; 5(21). PMID: 34516642 Free PMC article.
Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment. Youmna Kfoury, Ninib Baryawno, +16 authors, as part of the Boston Bone Metastases Consortium. less Cancer Cell, 2021 Nov 02; 39(11). PMID: 34719426 Free PMC article.
Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data. Duanchen Sun, Xiangnan Guan, +9 authors, Zheng Xia. less Nat Biotechnol, 2021 Nov 13; 40(4). PMID: 34764492 Free PMC article.
Maximizing the Utility of Transcriptomics Data in Inflammatory Skin Diseases. Jingni Wu, Zhixiao Fang, +3 authors, Teng Liu, Wei Hu, Yangjun Wu, Shengli Li. less Front Immunol, 2021 Nov 16; 12. PMID: 34777377 Free PMC article. Review.
Single-Cell Proteomic Analysis Dissects the Complexity of Tumor Microenvironment in Muscle Invasive Bladder Cancer. Chao Feng, Xi Wang, +10 authors, Zengnan Mo. less Cancers (Basel), 2021 Nov 14; 13(21). PMID: 34771607 Free PMC article.
Dynamic regulatory networks of T cell trajectory dissect transcriptional control of T cell state transition. Min Yan, Jing Hu, +9 authors, Xia Li. less Mol Ther Nucleic Acids, 2021 Nov 18; 26. PMID: 34786214 Free PMC article.
Single-cell analysis of diverse immune phenotypes in malignant pleural effusion. Zhong-Yin Huang, Ming-Ming Shao, +9 authors, Huan-Zhong Shi. less Nat Commun, 2021 Nov 20; 12(1). PMID: 34795282 Free PMC article.
Cross Talk Between Macrophages and Cancer Cells in the Bone Metastatic Environment. Lena Batoon, Laurie K McCauley. Front Endocrinol (Lausanne), 2021 Nov 23; 12. PMID: 34803925 Free PMC article. Review.
Single-Cell Transcriptomic Analysis Revealed a Critical Role of SPP1/CD44-Mediated Crosstalk Between Macrophages and Cancer Cells in Glioma. Cong He, Luoyan Sheng, +5 authors, Deshui Jia. less Front Cell Dev Biol, 2021 Nov 23; 9. PMID: 34805184 Free PMC article.
Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2. Xiliang Wang, Yao He, +2 authors, Qiming Zhang, Xianwen Ren, Zemin Zhang. less Genomics Proteomics Bioinformatics, 2021 Mar 05; 19(2). PMID: 33662621 Free PMC article.
scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-cell Datasets. Qianqian Song, Jing Su, Lance D Miller, Wei Zhang. Genomics Proteomics Bioinformatics, 2020 Dec 29; 19(2). PMID: 33359676 Free PMC article.
Interrogation of the microenvironmental landscape in spinal ependymomas reveals dual functions of tumor-associated macrophages. Qianqian Zhang, Sijin Cheng, +14 authors, Xiaoqun Wang. less Nat Commun, 2021 Nov 27; 12(1). PMID: 34824203 Free PMC article.
Single-Cell Analysis Using Machine Learning Techniques and Its Application to Medical Research. Ken Asada, Ken Takasawa, +8 authors, Ryuji Hamamoto. less Biomedicines, 2021 Nov 28; 9(11). PMID: 34829742 Free PMC article. Review.
Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer. Joseph M Chan, Álvaro Quintanal-Villalonga, +31 authors, Charles M Rudin. less Cancer Cell, 2021 Oct 16; 39(11). PMID: 34653364 Free PMC article.
Redefining intestinal immunity with single-cell transcriptomics. Kylie Renee James, Rasa Elmentaite, Sarah Amalia Teichmann, Georgina Louise Hold. Mucosal Immunol, 2021 Dec 02;. PMID: 34848830 Free PMC article. Review.
A Novel Immune and Stroma Related Prognostic Marker for Invasive Breast Cancer in Tumor Microenvironment: A TCGA Based Study. Yizhou Huang, Lizhi Chen, +4 authors, Lili Zhang. less Front Endocrinol (Lausanne), 2021 Dec 07; 12. PMID: 34867821 Free PMC article.
Research Progress on the Role of Regulatory T Cell in Tumor Microenvironment in the Treatment of Breast Cancer. Jianyu Liu, Xueying Wang, +3 authors, Yuhan Deng, Xin Yu, Hongbin Wang, Zhigao Li. less Front Oncol, 2021 Dec 07; 11. PMID: 34868991 Free PMC article. Review.
Non-genetic determinants of malignant clonal fitness at single-cell resolution. Katie A Fennell, Dane Vassiliadis, +15 authors, Mark A Dawson. less Nature, 2021 Dec 10; 601(7891). PMID: 34880496
Research advances and new challenges in overcoming triple-negative breast cancer. Yu Zong, Mark Pegram. Cancer Drug Resist, 2021 Dec 11; 4(3). PMID: 34888495 Free PMC article.
In situ functional cell phenotyping reveals microdomain networks in colorectal cancer recurrence. Samantha A Furman, Andrew M Stern, +3 authors, S Chakra Chennubhotla. less Cell Rep Methods, 2021 Dec 11; 1(5). PMID: 34888541 Free PMC article.
Application and prospects of single cell sequencing in tumors. Ruo Han Huang, Le Xin Wang, Jing He, Wen Gao. Biomark Res, 2021 Dec 14; 9(1). PMID: 34895349 Free PMC article. Review.
Epigenetic loss of heterogeneity from low to high grade localized prostate tumours. Sebnem Ece Eksi, Alex Chitsazan, +5 authors, Andrew C Adey. less Nat Commun, 2021 Dec 17; 12(1). PMID: 34911933 Free PMC article.
Integrated single-cell transcriptome analysis reveals heterogeneity of esophageal squamous cell carcinoma microenvironment. Huy Q Dinh, Feng Pan, +18 authors, En-Min Li. less Nat Commun, 2021 Dec 19; 12(1). PMID: 34921160 Free PMC article.
Subclonal heterogeneity and evolution in breast cancer. Ioanna Mavrommati, Flora Johnson, Gloria V Echeverria, Rachael Natrajan. NPJ Breast Cancer, 2021 Dec 23; 7(1). PMID: 34934048 Free PMC article. Review.
TMB and TCR Are Correlated Indicators Predictive of the Efficacy of Neoadjuvant Chemotherapy in Breast Cancer. Hongling Liang, Jia Huang, +17 authors, Jianqing Huang. less Front Oncol, 2021 Dec 25; 11. PMID: 34950580 Free PMC article.
Single-Cell Transcriptome Analysis Reveals RGS1 as a New Marker and Promoting Factor for T-Cell Exhaustion in Multiple Cancers. Yunmeng Bai, Meiling Hu, +2 authors, Zixi Chen, Jinfen Wei, Hongli Du. less Front Immunol, 2021 Dec 28; 12. PMID: 34956194 Free PMC article.
Myeloid Immune Cells CARrying a New Weapon Against Cancer. Rodrigo Nalio Ramos, Samuel Campanelli Freitas Couto, +5 authors, Vanderson Rocha. less Front Cell Dev Biol, 2022 Jan 04; 9. PMID: 34977027 Free PMC article. Review.
JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Nadia M Davidson, Ying Chen, +5 authors, Alicia Oshlack. less Genome Biol, 2022 Jan 08; 23(1). PMID: 34991664 Free PMC article.
Clinical Trials with Biologic Primary Endpoints in Immuno-oncology: Concepts and Usage. James Isaacs, Aaron C Tan, +6 authors, Mustafa Khasraw. less Clin Cancer Res, 2021 Jul 28; 28(1). PMID: 34312214 Free PMC article. Review.
Landscape of cancer-associated fibroblasts identifies the secreted biglycan as a protumor and immunosuppressive factor in triple-negative breast cancer. Shaoquan Zheng, Yutian Zou, +10 authors, Xiaoming Xie. less Oncoimmunology, 2022 Jan 11; 11(1). PMID: 35003899 Free PMC article.
(Pro)renin Receptor Inhibition Reduces Plasma Cholesterol and Triglycerides but Does Not Attenuate Atherosclerosis in Atherosclerotic Mice. Dien Ye, Xiaofei Yang, +14 authors, Xifeng Lu. less Front Cardiovasc Med, 2022 Jan 11; 8. PMID: 35004870 Free PMC article.
Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states. Hanbing Song, Hannah N W Weinstein, +12 authors, Franklin W Huang. less Nat Commun, 2022 Jan 12; 13(1). PMID: 35013146 Free PMC article.
Breast cancer metastasis: immune profiling of lymph nodes reveals exhaustion of effector T cells and immunosuppression. Inga Hansine Rye, Kanutte Huse, +9 authors, Hege G Russnes. less Mol Oncol, 2021 Jun 25; 16(1). PMID: 34165864 Free PMC article.
TCR signal strength defines distinct mechanisms of T cell dysfunction and cancer evasion. Mojdeh Shakiba, Paul Zumbo, +19 authors, Andrea Schietinger. less J Exp Med, 2021 Dec 23; 219(2). PMID: 34935874 Free PMC article.
Harnessing Antitumor CD4+ T Cells for Cancer Immunotherapy. Myriam Ben Khelil, Yann Godet, +3 authors, Romain Loyon. less Cancers (Basel), 2022 Jan 12; 14(1). PMID: 35008422 Free PMC article. Review.
Breast cancer heterogeneity through the lens of single-cell analysis and spatial pathologies. Na Zhao, Jeffrey M Rosen. Semin Cancer Biol, 2021 Jul 19; 82. PMID: 34274486 Free PMC article. Review.
Spatial immune heterogeneity of hypoxia-induced exhausted features in high-grade glioma. A-Reum Kim, Seong Jin Choi, +9 authors, Eui-Cheol Shin. less Oncoimmunology, 2022 Jan 18; 11(1). PMID: 35036078 Free PMC article.
Deep learning tackles single-cell analysis-a survey of deep learning for scRNA-seq analysis. Mario Flores, Zhentao Liu, +10 authors, Yufei Huang. less Brief Bioinform, 2021 Dec 21; 23(1). PMID: 34929734 Free PMC article.
SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging. Qinhuan Luo, Yongzhen Yu, Xun Lan. Brief Bioinform, 2021 Dec 29; 23(1). PMID: 34962260 Free PMC article.
Radiomics Assessment of the Tumor Immune Microenvironment to Predict Outcomes in Breast Cancer. Xiaorui Han, Wuteng Cao, Lei Wu, Changhong Liang. Front Immunol, 2022 Jan 21; 12. PMID: 35046937 Free PMC article.
Macrophages play a role in inflammatory transformation of colorectal cancer. Lu Lu, Yu-Jing Liu, +3 authors, Pei-Qiu Cheng, Dan Hu, Han-Chen Xu, Guang Ji. less World J Gastrointest Oncol, 2022 Jan 25; 13(12). PMID: 35070038 Free PMC article. Review.
Prognostic implications of N6-methyladenosine RNA regulators in breast cancer. Jiaojiao Tai, Linbang Wang, +2 authors, Hao Guo, Ziqiang Yan, Jingkun Liu. less Sci Rep, 2022 Jan 26; 12(1). PMID: 35075167 Free PMC article.
Evolution and Diversity of Immune Responses during Acute HIV Infection. Samuel W Kazer, Bruce D Walker, Alex K Shalek. Immunity, 2020 Nov 19; 53(5). PMID: 33207216 Free PMC article. Review.
Subversion of infiltrating prostate macrophages to a mixed immunosuppressive tumor-associated macrophage phenotype. Clovis Boibessot, Oscar Molina, +10 authors, Paul Toren. less Clin Transl Med, 2022 Jan 26; 12(1). PMID: 35075795 Free PMC article.
DNA Damage Repair in Brain Tumor Immunotherapy. Shihong Zhao, Boya Xu, +4 authors, Xiangqi Meng. less Front Immunol, 2022 Feb 01; 12. PMID: 35095931 Free PMC article. Review.
Dissecting the heterogeneity of the microenvironment in primary and recurrent nasopharyngeal carcinomas using single-cell RNA sequencing. Wen-Sa Peng, Xin Zhou, +9 authors, Chao-Su Hu. less Oncoimmunology, 2022 Feb 01; 11(1). PMID: 35096485 Free PMC article.
Cytotoxic CD4+ T cells in cancer: Expanding the immune effector toolbox. David Y Oh, Lawrence Fong. Immunity, 2021 Dec 16; 54(12). PMID: 34910940 Free PMC article. Review.
A novel prognostic model based on single-cell RNA sequencing data for hepatocellular carcinoma. Juan Lu, Yanfei Chen, +3 authors, Xiaoqian Zhang, Jing Guo, Kaijin Xu, Lanjuan Li. less Cancer Cell Int, 2022 Jan 27; 22(1). PMID: 35078458 Free PMC article.
ADRB2 is a potential protective gene in breast cancer by regulating tumor immune microenvironment. Xiang Wei, Liang Chen, +3 authors, Aiming Yang, Zhaoyu Lv, Meng Xiong, Chengxiang Shan. less Transl Cancer Res, 2022 Feb 05; 10(12). PMID: 35116377 Free PMC article.
Understanding and overcoming tumor heterogeneity in metastatic breast cancer treatment. Nida Pasha, Nicholas C Turner. Nat Cancer, 2022 Feb 06; 2(7). PMID: 35121946 Review.
Examining heterogeneity of stromal cells in tumor microenvironment based on pan-cancer single-cell RNA sequencing data. Wenhui Wang, Li Wang, Junjun She, Jun Zhu. Cancer Biol Med, 2021 Aug 17;. PMID: 34398535 Free PMC article. Review.
FRMC: a fast and robust method for the imputation of scRNA-seq data. Honglong Wu, Xuebin Wang, +2 authors, Mengtian Chu, Ruizhi Xiang, Ke Zhou. less RNA Biol, 2021 Aug 31; 18(sup1). PMID: 34459719 Free PMC article.
Quiescent human glioblastoma cancer stem cells drive tumor initiation, expansion, and recurrence following chemotherapy. Xuanhua P Xie, Dan R Laks, +8 authors, Luis F Parada. less Dev Cell, 2022 Jan 12; 57(1). PMID: 35016005 Free PMC article.
Transcriptional changes in the mammary gland during lactation revealed by single cell sequencing of cells from human milk. Alecia-Jane Twigger, Lisa K Engelbrecht, +6 authors, Walid T Khaled. less Nat Commun, 2022 Jan 30; 13(1). PMID: 35091553 Free PMC article.
Allosteric inhibition reveals SHP2-mediated tumor immunosuppression in colon cancer by single-cell transcriptomics. Jian Gao, Zhigui Wu, +10 authors, Yang Sun. less Acta Pharm Sin B, 2022 Feb 08; 12(1). PMID: 35127377 Free PMC article.
BAF Complexes and the Glucocorticoid Receptor in Breast Cancers. Nicholas Dietrich, Jackson A Hoffman, Trevor K Archer. Curr Opin Endocr Metab Res, 2020 Dec 01; 15. PMID: 35128145 Free PMC article.
PD-L1+CD8+ T cells enrichment in lung cancer exerted regulatory function and tumor-promoting tolerance. Yingxia Zheng, Li Han, +10 authors, Lisong Shen. less iScience, 2022 Feb 12; 25(2). PMID: 35146396 Free PMC article.
Urine Single-Cell RNA Sequencing in Focal Segmental Glomerulosclerosis Reveals Inflammatory Signatures. Khun Zaw Latt, Jurgen Heymann, +24 authors, Jeffrey B Kopp. less Kidney Int Rep, 2022 Feb 15; 7(2). PMID: 35155868 Free PMC article.
Polypharmacologic Reprogramming of Tumor-Associated Macrophages toward an Inflammatory Phenotype. Nao Nishida-Aoki, Taranjit S Gujral. Cancer Res, 2021 Dec 15; 82(3). PMID: 34903600 Free PMC article.
Repertoire analyses reveal T cell antigen receptor sequence features that influence T cell fate. Kaitlyn A Lagattuta, Joyce B Kang, +6 authors, Soumya Raychaudhuri. less Nat Immunol, 2022 Feb 19; 23(3). PMID: 35177831 Free PMC article.
CCR8-targeted specific depletion of clonally expanded Treg cells in tumor tissues evokes potent tumor immunity with long-lasting memory. Yujiro Kidani, Wataru Nogami, +39 authors, Shimon Sakaguchi. less Proc Natl Acad Sci U S A, 2022 Feb 11; 119(7). PMID: 35140181 Free PMC article.
Evolution and Targeting of Myeloid Suppressor Cells in Cancer: A Translational Perspective. Augusto Bleve, Francesca Maria Consonni, +2 authors, Chiara Porta, Valentina Garlatti, Antonio Sica. less Cancers (Basel), 2022 Feb 16; 14(3). PMID: 35158779 Free PMC article. Review.
Single-Cell Sequencing: Current Applications in Precision Onco-Genomics and Cancer Therapeutics. Lisa Maria Mustachio, Jason Roszik. Cancers (Basel), 2022 Feb 16; 14(3). PMID: 35158925 Free PMC article. Review.
Modeling Progression of Single Cell Populations Through the Cell Cycle as a Sequence of Switches. Andrei Zinovyev, Michail Sadovsky, +5 authors, Alexander N Gorban. less Front Mol Biosci, 2022 Feb 19; 8. PMID: 35178429 Free PMC article.
Cellular architecture of human brain metastases. Hugo Gonzalez, Wenbin Mei, +13 authors, Zena Werb. less Cell, 2022 Jan 23; 185(4). PMID: 35063085 Free PMC article.
Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation. Jaikumar Duraiswamy, Riccardo Turrini, +33 authors, George Coukos. less Cancer Cell, 2021 Nov 06; 39(12). PMID: 34739845 Free PMC article.
Discovering dominant tumor immune archetypes in a pan-cancer census. Alexis J Combes, Bushra Samad, +35 authors, Matthew F Krummel. less Cell, 2021 Dec 29; 185(1). PMID: 34963056 Free PMC article.
SENP3 loss promotes M2 macrophage polarization and breast cancer progression. Ming Xiao, Qi Bian, +4 authors, Jie Yang. less Mol Oncol, 2021 May 02; 16(4). PMID: 33932085 Free PMC article.
Preclinical PET Imaging of Granzyme B Shows Promotion of Immunological Response Following Combination Paclitaxel and Immune Checkpoint Inhibition in Triple Negative Breast Cancer. Tiara S Napier, Chanelle L Hunter, +2 authors, Patrick N Song, Benjamin M Larimer, Anna G Sorace. less Pharmaceutics, 2022 Feb 27; 14(2). PMID: 35214172 Free PMC article.
Single-cell transcriptomic profiling unravels the adenoma-initiation role of protein tyrosine kinases during colorectal tumorigenesis. Xiaobo Zheng, Jinen Song, +17 authors, Hubing Shi. less Signal Transduct Target Ther, 2022 Mar 01; 7(1). PMID: 35221332 Free PMC article.
Assessing Tumor-Infiltrating Lymphocytes in Breast Cancer: A Proposal for Combining Immunohistochemistry and Gene Expression Analysis to Refine Scoring. Hanne Locy, Stefaan Verhulst, +9 authors, Karine Breckpot. less Front Immunol, 2022 Mar 01; 13. PMID: 35222378 Free PMC article.
scDPN for High-throughput Single-cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence. Liang Wu, Miaomiao Jiang, +9 authors, Shiping Liu. less Genomics Proteomics Bioinformatics, 2021 Jul 20; 19(3). PMID: 34280548 Free PMC article.
Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity. Haitao Luo, Dechao Bu, +9 authors, Furong Li. less Genomics Proteomics Bioinformatics, 2021 Jul 21; 19(3). PMID: 34284134 Free PMC article.
Lipid-Laden Macrophages and Inflammation in Atherosclerosis and Cancer: An Integrative View. Miriam Lee-Rueckert, Jani Lappalainen, Petri T Kovanen, Joan Carles Escola-Gil. Front Cardiovasc Med, 2022 Mar 04; 9. PMID: 35237673 Free PMC article. Review.
Single-cell transcriptomics links malignant T cells to the tumor immune landscape in cutaneous T cell lymphoma. Xiangjun Liu, Shanzhao Jin, +25 authors, Yang Wang. less Nat Commun, 2022 Mar 05; 13(1). PMID: 35241665 Free PMC article.
scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data. Wei Vivian Li, Yanzeng Li. Genomics Proteomics Bioinformatics, 2021 Jul 13; 19(3). PMID: 34252628 Free PMC article.
APOBEC3F expression in triple-negative breast cancer is associated with tumor microenvironment infiltration and activation of cancer immunity and improved survival. Rongrong Wu, Masanori Oshi, +7 authors, Kazuaki Takabe. less Am J Cancer Res, 2022 Mar 10; 12(2). PMID: 35261799 Free PMC article.
Single-Cell Transcriptome Comparison of Bladder Cancer Reveals Its Ecosystem. Yongxiang Luo, Tao Tao, +2 authors, Ran Tao, Guixiao Huang, Song Wu. less Front Oncol, 2022 Mar 11; 12. PMID: 35265520 Free PMC article.
Metastatic Tumor Cell-Specific FABP7 Promotes NSCLC Metastasis via Inhibiting β-Catenin Degradation. Qiaorui Bai, Xia Yang, +6 authors, Yi Yang. less Cells, 2022 Mar 11; 11(5). PMID: 35269427 Free PMC article.
Beyond Immunosuppression: The Multifaceted Functions of Tumor-Promoting Myeloid Cells in Breast Cancers. Céline Blaye, Thomas Boyer, +2 authors, Florent Peyraud, Charlotte Domblides, Nicolas Larmonier. less Front Immunol, 2022 Mar 22; 13. PMID: 35309358 Free PMC article. Review.
scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data. Kun Qian, Shiwei Fu, Hongwei Li, Wei Vivian Li. Genome Biol, 2022 Mar 23; 23(1). PMID: 35313930 Free PMC article.
The interaction of CD4+ helper T cells with dendritic cells shapes the tumor microenvironment and immune checkpoint blockade response. Merav Cohen, Amir Giladi, +16 authors, Ido Amit. less Nat Cancer, 2022 Mar 05; 3(3). PMID: 35241835
Single-cell transcriptomic analysis suggests two molecularly subtypes of intrahepatic cholangiocarcinoma. Guohe Song, Yang Shi, +24 authors, Qiang Gao. less Nat Commun, 2022 Mar 30; 13(1). PMID: 35347134 Free PMC article.
4-1BBL-containing leukemic extracellular vesicles promote immunosuppressive effector regulatory T cells. Julian Swatler, Laura Turos-Korgul, +16 authors, Katarzyna Piwocka. less Blood Adv, 2022 Feb 08; 6(6). PMID: 35130345 Free PMC article.
Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data. Rui Hong, Yusuke Koga, +11 authors, Joshua D Campbell. less Nat Commun, 2022 Apr 01; 13(1). PMID: 35354805 Free PMC article.
Clinical relevance of tumour-associated macrophages. Mikael J Pittet, Olivier Michielin, Denis Migliorini. Nat Rev Clin Oncol, 2022 Apr 01; 19(6). PMID: 35354979 Review.
Integrated Analysis Highlights the Immunosuppressive Role of TREM2+ Macrophages in Hepatocellular Carcinoma. Lisha Zhou, Meiling Wang, +6 authors, Lianghai Wang. less Front Immunol, 2022 Apr 02; 13. PMID: 35359989 Free PMC article.
Single-cell and spatial analysis reveal interaction of FAP+ fibroblasts and SPP1+ macrophages in colorectal cancer. Jingjing Qi, Hongxiang Sun, +18 authors, Bing Su. less Nat Commun, 2022 Apr 03; 13(1). PMID: 35365629 Free PMC article.
Radiotherapy orchestrates natural killer cell dependent antitumor immune responses through CXCL8. Thomas Walle, Joscha A Kraske, +29 authors, Peter E Huber. less Sci Adv, 2022 Mar 24; 8(12). PMID: 35319989 Free PMC article.
Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer. Adriana M Mujal, Alexis J Combes, +12 authors, Matthew F Krummel. less Cancer Immunol Res, 2022 Feb 20; 10(4). PMID: 35181780 Free PMC article.
Single-cell RNA sequencing technologies and applications: A brief overview. Dragomirka Jovic, Xue Liang, +3 authors, Hua Zeng, Lin Lin, Fengping Xu, Yonglun Luo. less Clin Transl Med, 2022 Mar 31; 12(3). PMID: 35352511 Free PMC article. Review.
Tumour-infiltrating B cells: immunological mechanisms, clinical impact and therapeutic opportunities. Céline M Laumont, Allyson C Banville, +2 authors, Mara Gilardi, Daniel P Hollern, Brad H Nelson. less Nat Rev Cancer, 2022 Apr 09;. PMID: 35393541 Review.
Concurrent delivery of immune checkpoint blockade modulates T cell dynamics to enhance neoantigen vaccine-generated antitumor immunity. Longchao Liu, Jiahui Chen, +6 authors, Bo Li. less Nat Cancer, 2022 Apr 09; 3(4). PMID: 35393580 Free PMC article.
Immortalization and functional screening of natively paired human T cell receptor repertoires. Ahmed S Fahad, Cheng-Yu Chung, +14 authors, Brandon J DeKosky. less Protein Eng Des Sel, 2022 Feb 18; 35. PMID: 35174859 Free PMC article.
Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders. Yuge Wang, Hongyu Zhao. PLoS Comput Biol, 2022 Apr 02; 18(4). PMID: 35363784 Free PMC article.
Single-Cell Transcriptional Profiling Reveals Signatures of Helper, Effector, and Regulatory MAIT Cells during Homeostasis and Activation. Charles Kyriakos Vorkas, Chirag Krishna, +5 authors, Michael S Glickman. less J Immunol, 2022 Feb 13; 208(5). PMID: 35149530 Free PMC article.
Stress-glucocorticoid-TSC22D3 axis compromises therapy-induced antitumor immunity. Heng Yang, Lin Xia, +24 authors, Yuting Ma. less Nat Med, 2019 Sep 11; 25(9). PMID: 31501614
Next-generation computational tools for interrogating cancer immunity. Francesca Finotello, Dietmar Rieder, Hubert Hackl, Zlatko Trajanoski. Nat Rev Genet, 2019 Sep 14; 20(12). PMID: 31515541 Review.
Single-cell atlas of colonic CD8+ T cells in ulcerative colitis. Daniele Corridoni, Agne Antanaviciute, +17 authors, Alison Simmons. less Nat Med, 2020 Aug 05; 26(9). PMID: 32747828
Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Esther Danenberg, Helen Bardwell, +10 authors, H Raza Ali. less Nat Genet, 2022 Apr 20; 54(5). PMID: 35437329 Free PMC article.
Evaluation of glucocorticoid-induced TNF receptor (GITR) expression in breast cancer and across multiple tumor types. Mayanne M T Zhu, Samantha Burugu, +5 authors, Torsten O Nielsen. less Mod Pathol, 2020 May 01; 33(9). PMID: 32350416
Programme of self-reactive innate-like T cell-mediated cancer immunity. Chun Chou, Xian Zhang, +22 authors, Ming O Li. less Nature, 2022 Apr 22; 605(7908). PMID: 35444279
Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Pavan Bachireddy, Elham Azizi, +19 authors, Catherine J Wu. less Cell Rep, 2021 Nov 11; 37(6). PMID: 34758319 Free PMC article.
Heterogeneity of the tumor immune microenvironment and its clinical relevance. Qingzhu Jia, Aoyun Wang, +2 authors, Yixiao Yuan, Bo Zhu, Haixia Long. less Exp Hematol Oncol, 2022 Apr 25; 11(1). PMID: 35461288 Free PMC article. Review.
Perivascular tenascin C triggers sequential activation of macrophages and endothelial cells to generate a pro-metastatic vascular niche in the lungs. Tsunaki Hongu, Maren Pein, +11 authors, Thordur Oskarsson. less Nat Cancer, 2022 Apr 27; 3(4). PMID: 35469015 Free PMC article.
Double-jeopardy: scRNA-seq doublet/multiplet detection using multi-omic profiling. Bo Sun, Emmanuel Bugarin-Estrada, +3 authors, Rachael Jennifer Mary Bashford-Rogers. less Cell Rep Methods, 2021 Jul 20; 1(1). PMID: 34278374 Free PMC article.
Single-cell RNA sequencing coupled to TCR profiling of large granular lymphocyte leukemia T cells. Shouguo Gao, Zhijie Wu, +10 authors, Neal S Young. less Nat Commun, 2022 Apr 13; 13(1). PMID: 35411048 Free PMC article.
Metabolism drives macrophage heterogeneity in the tumor microenvironment. Shasha Li, Jiali Yu, +13 authors, Weiping Zou. less Cell Rep, 2022 Apr 07; 39(1). PMID: 35385733 Free PMC article.
Tumor-Associated Regulatory T Cells in Non-Small-Cell Lung Cancer: Current Advances and Future Perspectives. Jiaqi Liang, Guoshu Bi, +3 authors, Guangyao Shan, Xing Jin, Yunyi Bian, Qun Wang. less J Immunol Res, 2022 May 03; 2022. PMID: 35497874 Free PMC article. Review.
A T cell resilience model associated with response to immunotherapy in multiple tumor types. Yu Zhang, Vu Trang, +14 authors, Peng Jiang. less Nat Med, 2022 May 03;. PMID: 35501486
High-throughput single-сell sequencing in cancer research. Qingzhu Jia, Han Chu, +2 authors, Zheng Jin, Haixia Long, Bo Zhu. less Signal Transduct Target Ther, 2022 May 04; 7(1). PMID: 35504878 Free PMC article. Review.
Tumor microenvironment heterogeneity an important mediator of prostate cancer progression and therapeutic resistance. Rongbin Ge, Zongwei Wang, Liang Cheng. NPJ Precis Oncol, 2022 May 05; 6(1). PMID: 35508696 Free PMC article. Review.
DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data. Livnat Jerby-Arnon, Aviv Regev. Nat Biotechnol, 2022 May 06;. PMID: 35513526
miR-6077 promotes cisplatin/pemetrexed resistance in lung adenocarcinoma via CDKN1A/cell cycle arrest and KEAP1/ferroptosis pathways. Guoshu Bi, Jiaqi Liang, +11 authors, Lijie Tan. less Mol Ther Nucleic Acids, 2022 May 05; 28. PMID: 35505963 Free PMC article.
Mapping Breast Cancer Microenvironment Through Single-Cell Omics. Zhenya Tan, Chen Kan, +4 authors, Hong Zheng. less Front Immunol, 2022 May 07; 13. PMID: 35514975 Free PMC article. Review.
Single-cell characterization of malignant phenotypes and microenvironment alteration in retinoblastoma. Cheng Wu, Jiaqi Yang, +7 authors, Zhi Xie. less Cell Death Dis, 2022 May 07; 13(5). PMID: 35523772 Free PMC article.
Single-cell sequencing: a promising approach for uncovering the mechanisms of tumor metastasis. Yingying Han, Dan Wang, +4 authors, Chunlin Ou. less J Hematol Oncol, 2022 May 14; 15(1). PMID: 35549970 Free PMC article. Review.
MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets. Xintao Qiu, Nadia Boufaied, +32 authors, David P Labbé. less Nat Commun, 2022 May 14; 13(1). PMID: 35562350 Free PMC article.
Dissecting Intra-Tumoral Changes Following Immune Checkpoint Blockades in Intrahepatic Cholangiocarcinoma via Single-Cell Analysis. Bao-Ye Sun, Cheng Zhou, +8 authors, Shuang-Jian Qiu. less Front Immunol, 2022 May 14; 13. PMID: 35558087 Free PMC article.
Updated Functional Roles of NAMPT in Carcinogenesis and Therapeutic Niches. Tsung-Chieh Lin. Cancers (Basel), 2022 May 15; 14(9). PMID: 35565188 Free PMC article. Review.
The Era of Cytotoxic CD4 T Cells. Mara Cenerenti, Margaux Saillard, Pedro Romero, Camilla Jandus. Front Immunol, 2022 May 17; 13. PMID: 35572552 Free PMC article. Review.
Single-Cell Sequencing and Its Applications in Liver Cancer. Binle Tian, Qi Li. Front Oncol, 2022 May 17; 12. PMID: 35574365 Free PMC article. Review.
Modeling zero inflation is not necessary for spatial transcriptomics. Peiyao Zhao, Jiaqiang Zhu, Ying Ma, Xiang Zhou. Genome Biol, 2022 May 19; 23(1). PMID: 35585605 Free PMC article.
hECA: The cell-centric assembly of a cell atlas. Sijie Chen, Yanting Luo, +23 authors, Xuegong Zhang. less iScience, 2022 May 24; 25(5). PMID: 35602947 Free PMC article.
Identification of CD4+ Conventional T Cells-Related lncRNA Signature to Improve the Prediction of Prognosis and Immunotherapy Response in Breast Cancer. Shipeng Ning, Jianbin Wu, +3 authors, You Pan, Kun Qiao, Lei Li, Qinghua Huang. less Front Immunol, 2022 May 24; 13. PMID: 35603183 Free PMC article.
Epigenetic regulation of T cell exhaustion. Julia A Belk, Bence Daniel, Ansuman T Satpathy. Nat Immunol, 2022 May 28; 23(6). PMID: 35624210 Review.

BioKDE: Biomedical Knowledge Discovery Engine

Abstract

Other Links