Journal Article
. 2010 Dec;5(11).
doi: 10.1371/journal.pone.0014002.

In silico ascription of gene expression differences to tumor and stromal cells in a model to study impact on breast cancer outcome

Simen Myhre 1 Hayat Mohammed  Trine Tramm  Jan Alsner  Greg Finak  Morag Park  Jens Overgaard  Anne-Lise Børresen-Dale  Arnoldo Frigessi  Therese Sørlie  
  • PMID: 21124964
  •     36 References
  •     13 citations


Breast tumors consist of several different tissue components. Despite the heterogeneity, most gene expression analyses have traditionally been performed without prior microdissection of the tissue sample. Thus, the gene expression profiles obtained reflect the mRNA contribution from the various tissue components. We utilized histopathological estimations of area fractions of tumor and stromal tissue components in 198 fresh-frozen breast tumor tissue samples for a cell type-associated gene expression analysis associated with distant metastasis. Sets of differentially expressed gene-probes were identified in tumors from patients who developed distant metastasis compared with those who did not, by weighing the contribution from each tumor with the relative content of stromal and tumor epithelial cells in their individual tumor specimen. The analyses were performed under various assumptions of mRNA transcription level from tumor epithelial cells compared with stromal cells. A set of 30 differentially expressed gene-probes was ascribed solely to carcinoma cells. Furthermore, two sets of 38 and five differentially expressed gene-probes were mostly associated to tumor epithelial and stromal cells, respectively. Finally, a set of 26 differentially expressed gene-probes was identified independently of cell type focus. The differentially expressed genes were validated in independent gene expression data from a set of laser capture microdissected invasive ductal carcinomas. We present a method for identifying and ascribing differentially expressed genes to tumor epithelial and/or stromal cells, by utilizing pathologic information and weighted t-statistics. Although a transcriptional contribution from the stromal cell fraction is detectable in microarray experiments performed on bulk tumor, the gene expression differences between the distant metastasis and no distant metastasis group were mostly ascribed to the tumor epithelial cells of the primary breast tumors. However, the gene PIP5K2A was found significantly elevated in stroma cells in distant metastasis group, compared to stroma in no distant metastasis group. These findings were confirmed in gene expression data from the representative compartments from microdissected breast tissue. The method described was also found to be robust to different histopathological procedures.

Molecular portraits of human breast tumours.
C M Perou, T Sørlie, +15 authors, D Botstein.
Nature, 2000 Aug 30; 406(6797). PMID: 10963602
Highly Cited.
Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700/Panther probe-to-gene annotations.
Sebastian Noth, Arndt Benecke, Systems Epigenomics Group.
BMC Bioinformatics, 2005 Dec 24; 6. PMID: 16372901    Free PMC article.
Significance analysis of microarrays applied to the ionizing radiation response.
V G Tusher, R Tibshirani, G Chu.
Proc Natl Acad Sci U S A, 2001 Apr 20; 98(9). PMID: 11309499    Free PMC article.
Highly Cited.
Tumors are unique organs defined by abnormal signaling and context.
D Radisky, C Hagios, M J Bissell.
Semin Cancer Biol, 2001 Apr 27; 11(2). PMID: 11322828
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications.
T Sørlie, C M Perou, +14 authors, A L Børresen-Dale.
Proc Natl Acad Sci U S A, 2001 Sep 13; 98(19). PMID: 11553815    Free PMC article.
Highly Cited.
Gene expression profiling predicts clinical outcome of breast cancer.
Laura J van 't Veer, Hongyue Dai, +13 authors, Stephen H Friend.
Nature, 2002 Feb 02; 415(6871). PMID: 11823860
Highly Cited.
A gene-expression signature as a predictor of survival in breast cancer.
Marc J van de Vijver, Yudong D He, +18 authors, René Bernards.
N Engl J Med, 2002 Dec 20; 347(25). PMID: 12490681
Highly Cited.
The organizing principle: microenvironmental influences in the normal and malignant breast.
Mina J Bissell, Derek C Radisky, +2 authors, Ole W Petersen.
Differentiation, 2002 Dec 21; 70(9-10). PMID: 12492495    Free PMC article.
Highly Cited. Review.
Repeated observation of breast tumor subtypes in independent gene expression data sets.
Therese Sorlie, Robert Tibshirani, +13 authors, David Botstein.
Proc Natl Acad Sci U S A, 2003 Jun 28; 100(14). PMID: 12829800    Free PMC article.
Highly Cited.
In silico dissection of cell-type-associated patterns of gene expression in prostate cancer.
Robert O Stuart, William Wachsman, +12 authors, Dan Mercola.
Proc Natl Acad Sci U S A, 2004 Jan 15; 101(2). PMID: 14722351    Free PMC article.
Adipocyte expression and circulating levels of leptin increase in both gynaecological and breast cancer patients.
L Tessitore, B Vizio, +4 authors, C Benedetto.
Int J Oncol, 2004 May 13; 24(6). PMID: 15138597
The new stereological tools: disector, fractionator, nucleator and point sampled intercepts and their use in pathological research and diagnosis.
H J Gundersen, P Bagger, +7 authors, B Pakkenberg.
APMIS, 1988 Oct 01; 96(10). PMID: 3056461
Highly Cited. Review.
Molecular cloning of an isoform of Doc2 having two C2-like domains.
G Sakaguchi, S Orita, +2 authors, Y Takai.
Biochem Biophys Res Commun, 1995 Dec 26; 217(3). PMID: 8554557
Progesterone regulated expression of flavin-containing monooxygenase 5 by the B-isoform of progesterone receptors: implications for tamoxifen carcinogenicity.
M M Miller, R A James, +3 authors, K B Horwitz.
J Clin Endocrinol Metab, 1997 Sep 01; 82(9). PMID: 9284726
DNA arrays for analysis of gene expression.
M B Eisen, P O Brown.
Methods Enzymol, 1999 Jun 01; 303. PMID: 10349646
Highly Cited.
A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer.
Soonmyung Paik, Steven Shak, +12 authors, Norman Wolmark.
N Engl J Med, 2004 Dec 14; 351(27). PMID: 15591335
Highly Cited.
Analysis of differential gene expression patterns in colon cancer and cancer stroma using microdissected tissues.
Yuko Sugiyama, Buckminster Farrow, +4 authors, B Mark Evers.
Gastroenterology, 2005 Feb 03; 128(2). PMID: 15685558
Semiquantitative evaluation overestimates the degree of steatosis in liver biopsies: a comparison to stereological point counting.
Lennart E Franzén, Mattias Ekstedt, Stergios Kechagias, Lennart Bodin.
Mod Pathol, 2005 May 28; 18(7). PMID: 15920560
Estrogen regulation of the rat anterior pituitary gland proteome.
Charles A Blake, Lewis M Brown, +2 authors, Steve M Helmke.
Exp Biol Med (Maywood), 2005 Dec 13; 230(11). PMID: 16339744
Patterns of cancer incidence, mortality, and prevalence across five continents: defining priorities to reduce cancer disparities in different geographic regions of the world.
Farin Kamangar, Graça M Dores, William F Anderson.
J Clin Oncol, 2006 May 10; 24(14). PMID: 16682732
Highly Cited.
Study of failure pattern among high-risk breast cancer patients with or without postmastectomy radiotherapy in addition to adjuvant systemic therapy: long-term results from the Danish Breast Cancer Cooperative Group DBCG 82 b and c randomized studies.
Danish Breast Cancer Cooperative Group, Hanne M Nielsen, +3 authors, Jens Overgaard.
J Clin Oncol, 2006 Apr 19; 24(15). PMID: 16618947
Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer.
Soonmyung Paik, Gong Tang, +11 authors, Norman Wolmark.
J Clin Oncol, 2006 May 25; 24(23). PMID: 16720680
Highly Cited.
The effect of the stromal component of breast tumours on prediction of clinical outcome using gene expression microarray analysis.
Susan J Cleator, Trevor J Powles, +6 authors, Mitch Dowsett.
Breast Cancer Res, 2006 Jun 23; 8(3). PMID: 16790077    Free PMC article.
Functional studies of the chromosome 3p21.3 candidate tumor suppressor gene BLU/ZMYND10 in nasopharyngeal carcinoma.
Wing Lung Yau, Hong Lok Lung, +6 authors, Maria Li Lung.
Int J Cancer, 2006 Aug 25; 119(12). PMID: 16929489
Multiple genes and factors associated with bipolar disorder converge on growth factor and stress activated kinase pathways controlling translation initiation: implications for oligodendrocyte viability.
C J Carter.
Neurochem Int, 2007 Jan 24; 50(3). PMID: 17239488
Descriptive analysis of estrogen receptor (ER)-negative, progesterone receptor (PR)-negative, and HER2-negative invasive breast cancer, the so-called triple-negative phenotype: a population-based study from the California cancer Registry.
Katrina R Bauer, Monica Brown, +2 authors, Vincent Caggiano.
Cancer, 2007 Mar 28; 109(9). PMID: 17387718
Highly Cited.
Arylamine N-acetyltransferase 1 expression in breast cancer cell lines: a potential marker in estrogen receptor-positive tumors.
Larissa Wakefield, James Robinson, +4 authors, Edith Sim.
Genes Chromosomes Cancer, 2007 Nov 02; 47(2). PMID: 17973251
Development of the 21-gene assay and its application in clinical practice and clinical trials.
Joseph A Sparano, Soonmyung Paik.
J Clin Oncol, 2008 Feb 09; 26(5). PMID: 18258979
Highly Cited. Review.
Expression of leptin and its receptor in female breast cancer in relation with selected apoptotic markers.
Mariusz Koda, Mariola Sulkowska, +2 authors, Stanislaw Sulkowski.
Folia Histochem Cytobiol, 2008 Apr 15; 45 Suppl 1. PMID: 18292831
Inconsistent criteria used in American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer.
Fatima Cardoso, Mahasti Saghatchian, +2 authors, TRANSBIG Consortium Steering Committee.
J Clin Oncol, 2008 Apr 19; 26(12). PMID: 18421063
Stromal gene expression predicts clinical outcome in breast cancer.
Greg Finak, Nicholas Bertos, +9 authors, Morag Park.
Nat Med, 2008 Apr 29; 14(5). PMID: 18438415
Highly Cited.
Estrogen and MYB in breast cancer: potential for new therapies.
Thomas J Gonda, Paul Leo, Robert G Ramsay.
Expert Opin Biol Ther, 2008 May 15; 8(6). PMID: 18476782
Silencing of LRRC49 and THAP10 genes by bidirectional promoter hypermethylation is a frequent event in breast cancer.
Emerson De Souza Santos, Simone A De Bessa, Mario M Netto, Maria A Nagai.
Int J Oncol, 2008 Jun 26; 33(1). PMID: 18575747
A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer.
Pierre Farmer, Hervé Bonnefoi, +18 authors, Mauro Delorenzi.
Nat Med, 2009 Jan 06; 15(1). PMID: 19122658
Highly Cited.
High local recurrence risk is not associated with large survival reduction after postmastectomy radiotherapy in high-risk breast cancer: a subgroup analysis of DBCG 82 b&c.
Marianne Kyndi, Marie Overgaard, +3 authors, Jens Overgaard.
Radiother Oncol, 2008 May 13; 90(1). PMID: 18471914
Characterization of human MAPRE genes and their proteins.
L K Su, Y Qi.
Genomics, 2001 Feb 13; 71(2). PMID: 11161807
Integrative computational biology for cancer research.
Kristen Fortney, Igor Jurisica.
Hum Genet, 2011 Jun 22; 130(4). PMID: 21691773    Free PMC article.
Relationships of ESR1 and XBP1 expression in human breast carcinoma and stromal cells isolated by laser capture microdissection compared to intact breast cancer tissue.
Sarah A Andres, James L Wittliff.
Endocrine, 2011 Aug 23; 40(2). PMID: 21858728
Stromal genes add prognostic information to proliferation and histoclinical markers: a basis for the next generation of breast cancer gene signatures.
Dwain Mefford, Joel Mefford.
PLoS One, 2012 Jun 22; 7(6). PMID: 22719844    Free PMC article.
An "elite hacker": breast tumors exploit the normal microenvironment program to instruct their progression and biological diversity.
Aaron Boudreau, Laura J van't Veer, Mina J Bissell.
Cell Adh Migr, 2012 Aug 07; 6(3). PMID: 22863741    Free PMC article.
Neoplastic and stromal cells contribute to an extracellular matrix gene expression profile defining a breast cancer subtype likely to progress.
Tiziana Triulzi, Patrizia Casalini, +7 authors, Elda Tagliabue.
PLoS One, 2013 Feb 27; 8(2). PMID: 23441215    Free PMC article.
Influence of DNA copy number and mRNA levels on the expression of breast cancer related proteins.
Simen Myhre, Ole-Christian Lingjærde, +8 authors, Therese Sørlie.
Mol Oncol, 2013 Apr 09; 7(3). PMID: 23562353    Free PMC article.
Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment.
Tamasin N Doig, David A Hume, +3 authors, Tom C Freeman.
BMC Genomics, 2013 Jul 13; 14. PMID: 23845084    Free PMC article.
Reliable PCR quantitation of estrogen, progesterone and ERBB2 receptor mRNA from formalin-fixed, paraffin-embedded tissue is independent of prior macro-dissection.
Trine Tramm, Guido Hennig, +5 authors, Jens Overgaard.
Virchows Arch, 2013 Oct 09; 463(6). PMID: 24100522
Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors.
Miriam Ragle Aure, Suvi-Katri Leivonen, +16 authors, Vessela N Kristensen.
Genome Biol, 2013 Nov 22; 14(11). PMID: 24257477    Free PMC article.
Identifying microRNAs regulating B7-H3 in breast cancer: the clinical impact of microRNA-29c.
M K Nygren, C Tekle, +14 authors, S-K Leivonen.
Br J Cancer, 2014 Mar 01; 110(8). PMID: 24577056    Free PMC article.
A targeted knockdown screen of genes coding for phosphoinositide modulators identifies PIP4K2A as required for acute myeloid leukemia cell proliferation and survival.
Julian G Jude, Gary J Spencer, +4 authors, Tim C P Somervaille.
Oncogene, 2014 Apr 01; 34(10). PMID: 24681948    Free PMC article.
Glycan-related gene expression signatures in breast cancer subtypes; relation to survival.
Ivan O Potapenko, Torben Lüders, +7 authors, Vilde D Haakensen.
Mol Oncol, 2015 Feb 07; 9(4). PMID: 25655580    Free PMC article.
Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma.
Luciana Marques Paula, Luis Henrique Ferreira De Moraes, +4 authors, Renata De Azevedo Canevari.
Oncol Lett, 2017 Jan 27; 13(1). PMID: 28123587    Free PMC article.