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The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (CNVs, SNPs) and acquired somatic copy number aberrations (CNAs) were associated with expression in 40% of genes, although the landscape was dominated by cis and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP, and MAP2K4. Unsupervised analysis of paired DNA/RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, ER-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration 0152hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the 0152CNA-devoid sub-group and a Basal-specific chromosome 5 deletion-driven mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic copy number aberrations on the transcriptome.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00010000162 Illumina HT 12 -
EGAD00010000164 Affymetrix SNP 6.0 -
EGAD00010000210 Illumina HT 12 1
EGAD00010000211 Illumina HT 12 -
EGAD00010000212 Illumina HT 12 -
EGAD00010000213 Affymetrix SNP 6.0 -
EGAD00010000214 Affymetrix SNP 6.0 -
EGAD00010000215 Affymetrix SNP 6.0 -
EGAD00010000216 Affymetrix SNP 6.0 -
EGAD00010000217 Affymetrix SNP 6.0 -
Publications Citations
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.
Nature 486: 2012 346-352
Regulation of mRNA expression in breast cancer - a cis-tematic trans-action.
Breast Cancer Res 14: 2012 322
Improving breast cancer survival analysis through competition-based multidimensional modeling.
PLoS Comput Biol 9: 2013 e1003047
The molecular diversity of Luminal A breast tumors.
Breast Cancer Res Treat 141: 2013 409-420
The breast cancer oncogene EMSY represses transcription of antimetastatic microRNA miR-31.
Mol Cell 53: 2014 806-818
Systematic assessment of prognostic gene signatures for breast cancer shows distinct influence of time and ER status.
BMC Cancer 14: 2014 211
Information content and analysis methods for multi-modal high-throughput biomedical data.
Sci Rep 4: 2014 4411
Seven In Absentia Homolog 2 (SIAH2) downregulation is associated with tamoxifen resistance in MCF-7 breast cancer cells.
J Surg Res 190: 2014 203-209
Breast cancer prognosis predicted by nuclear receptor-coregulator networks.
Mol Oncol 8: 2014 998-1013
Hypomethylation of the MMP7 promoter and increased expression of MMP7 distinguishes the basal-like breast cancer subtype from other triple-negative tumors.
Breast Cancer Res Treat 146: 2014 25-40
Validation of the prognostic gene portfolio, ClinicoMolecular Triad Classification, using an independent prospective breast cancer cohort and external patient populations.
Breast Cancer Res 16: 2014 R71
Predicting response and survival in chemotherapy-treated triple-negative breast cancer.
Br J Cancer 111: 2014 1532-1541
Molecular features and survival outcomes of the intrinsic subtypes within HER2-positive breast cancer.
J Natl Cancer Inst 106: 2014 dju152
Cancer progression modeling using static sample data.
Genome Biol 15: 2014 440
Genome-driven integrated classification of breast cancer validated in over 7,500 samples.
Genome Biol 15: 2014 431
Acquired convergence of hormone signaling in breast cancer: ER and PR transition from functionally distinct in normal breast to predictors of metastatic disease.
Oncotarget 5: 2014 8651-8664
Hypoxia promotes stem cell phenotypes and poor prognosis through epigenetic regulation of DICER.
Nat Commun 5: 2014 5203
Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53.
Mol Cancer Res 13: 2015 493-501
A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation.
Breast Cancer Res 17: 2015 4
APOBEC3B expression in breast cancer reflects cellular proliferation, while a deletion polymorphism is associated with immune activation.
Proc Natl Acad Sci U S A 112: 2015 2841-2846
Decreased <i>BECN1</i> mRNA Expression in Human Breast Cancer is Associated with Estrogen Receptor-Negative Subtypes and Poor Prognosis.
EBioMedicine 2: 2015 255-263
Polymorphism at 19q13.41 Predicts Breast Cancer Survival Specifically after Endocrine Therapy.
Clin Cancer Res 21: 2015 4086-4096
MicroRNA profiling of the pubertal mouse mammary gland identifies miR-184 as a candidate breast tumour suppressor gene.
Breast Cancer Res 17: 2015 83
The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set.
PLoS One 10: 2015 e0129711
IDEA: Integrated Drug Expression Analysis-Integration of Gene Expression and Clinical Data for the Identification of Therapeutic Candidates.
CPT Pharmacometrics Syst Pharmacol 4: 2015 415-425
An integrated network platform for contextual prioritization of drugs and pathways.
Mol Biosyst 11: 2015 2850-2859
An ecological measure of immune-cancer colocalization as a prognostic factor for breast cancer.
Breast Cancer Res 17: 2015 131
Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer.
Mol Oncol 10: 2016 179-193
p21-activated kinase group II small compound inhibitor GNE-2861 perturbs estrogen receptor alpha signaling and restores tamoxifen-sensitivity in breast cancer cells.
Oncotarget 6: 2015 43853-43868
Iroquois homeobox 2 suppresses cellular motility and chemokine expression in breast cancer cells.
BMC Cancer 15: 2015 896
Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis.
Genes Dev 29: 2015 2547-2562
YAP enhances the pro-proliferative transcriptional activity of mutant p53 proteins.
EMBO Rep 17: 2016 188-201
Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles.
Nat Commun 7: 2016 10248
Iteratively refining breast cancer intrinsic subtypes in the METABRIC dataset.
BioData Min 9: 2016 2
Microenvironmental Heterogeneity Parallels Breast Cancer Progression: A Histology-Genomic Integration Analysis.
PLoS Med 13: 2016 e1001961
Predicting chemoinsensitivity in breast cancer with 'omics/digital pathology data fusion.
R Soc Open Sci 3: 2016 140501
Oncogenic mTOR signalling recruits myeloid-derived suppressor cells to promote tumour initiation.
Nat Cell Biol 18: 2016 632-644
Germline APOBEC3B deletion is associated with breast cancer risk in an Asian multi-ethnic cohort and with immune cell presentation.
Breast Cancer Res 18: 2016 56
Activation of the orphan receptor GPR55 by lysophosphatidylinositol promotes metastasis in triple-negative breast cancer.
Oncotarget 7: 2016 47565-47575
Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers.
PLoS One 11: 2016 e0158259
Genome-wide association study in East Asians identifies two novel breast cancer susceptibility loci.
Hum Mol Genet 25: 2016 3361-3371
Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia.
Genome Biol 17: 2016 140
Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer.
Breast Cancer Res 18: 2016 70
A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers.
Nat Commun 7: 2016 12222
Association between EZH2 expression, silencing of tumor suppressors and disease outcome in solid tumors.
Cell Cycle 15: 2016 2256-2262
Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer.
Nat Genet 48: 2016 1260-1266
Application of pharmacologically induced transcriptomic profiles to interrogate PI3K-Akt-mTOR pathway activity associated with cancer patient prognosis.
Oncotarget 7: 2016 84142-84154
HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status.
Oncotarget 7: 2016 51012-51026
Comprehensive functional analysis of the tousled-like kinase 2 frequently amplified in aggressive luminal breast cancers.
Nat Commun 7: 2016 12991
Functional redundancy between Apc and Apc2 regulates tissue homeostasis and prevents tumorigenesis in murine mammary epithelium.
Oncogene 36: 2017 1793-1803
Reduced mRNA expression levels of NFE2L2 are associated with poor outcome in breast cancer patients.
BMC Cancer 16: 2016 821
PIM1 kinase regulates cell death, tumor growth and chemotherapy response in triple-negative breast cancer.
Nat Med 22: 2016 1303-1313
Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer.
Genome Med 8: 2016 114
Unique epigenetic gene profiles define human breast cancers with poor prognosis.
Oncotarget 7: 2016 85819-85831
Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome.
PLoS Comput Biol 13: 2017 e1005340
Integrin-β4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells.
Proc Natl Acad Sci U S A 114: 2017 E2337-E2346
A prosurvival DNA damage-induced cytoplasmic interferon response is mediated by end resection factors and is limited by Trex1.
Genes Dev 31: 2017 353-369
Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications.
BMC Med Genomics 10: 2017 16
Basal-like breast cancer: molecular profiles, clinical features and survival outcomes.
BMC Med Genomics 10: 2017 19
Cadherins Associate with Distinct Stem Cell-Related Transcription Factors to Coordinate the Maintenance of Stemness in Triple-Negative Breast Cancer.
Stem Cells Int 2017: 2017 5091541
miR-424(322)/503 is a breast cancer tumor suppressor whose loss promotes resistance to chemotherapy.
Genes Dev 31: 2017 553-566
Regulatory network of GATA3 in pediatric acute lymphoblastic leukemia.
Oncotarget 8: 2017 36040-36053
Transcriptional response profiles of paired tumor-normal samples offer novel perspectives in pan-cancer analysis.
Oncotarget 8: 2017 41334-41347
Predicting Outcomes of Hormone and Chemotherapy in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Study by Biochemically-inspired Machine Learning.
F1000Res 5: 2016 2124
The mutant p53-ID4 complex controls VEGFA isoforms by recruiting lncRNA MALAT1.
EMBO Rep 18: 2017 1331-1351
Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity.
Oncotarget 8: 2017 57121-57133
A role for Tau protein in maintaining ribosomal DNA stability and cytidine deaminase-deficient cell survival.
Nat Commun 8: 2017 693
Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology.
PLoS Genet 13: 2017 e1006945
A novel approach for data integration and disease subtyping.
Genome Res 27: 2017 2025-2039
Transcription factor c-Myb inhibits breast cancer lung metastasis by suppression of tumor cell seeding.
Oncogene 37: 2018 1020-1030
Cancer cell line specific co-factors modulate the FOXM1 cistrome.
Oncotarget 8: 2017 76498-76515
Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer.
Sci Rep 7: 2017 15742
Age, estrogen, and immune response in breast adenocarcinoma and adjacent normal tissue.
Oncoimmunology 6: 2017 e1356142
Immune Checkpoint Molecules on Tumor-Infiltrating Lymphocytes and Their Association with Tertiary Lymphoid Structures in Human Breast Cancer.
Front Immunol 8: 2017 1412
Identification of cancer genes that are independent of dominant proliferation and lineage programs.
Proc Natl Acad Sci U S A 114: 2017 E11276-E11284
Mechanical cues control mutant p53 stability through a mevalonate-RhoA axis.
Nat Cell Biol 20: 2018 28-35
miR-105/93-3p promotes chemoresistance and circulating miR-105/93-3p acts as a diagnostic biomarker for triple negative breast cancer.
Breast Cancer Res 19: 2017 133
Therapeutically targeting tumor microenvironment-mediated drug resistance in estrogen receptor-positive breast cancer.
J Exp Med 215: 2018 895-910
MYC-driven epigenetic reprogramming favors the onset of tumorigenesis by inducing a stem cell-like state.
Nat Commun 9: 2018 1024
Capture Hi-C identifies putative target genes at 33 breast cancer risk loci.
Nat Commun 9: 2018 1028
Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort.
NPJ Breast Cancer 4: 2018 5
Recurrent copy number alterations in young women with breast cancer.
Oncotarget 9: 2018 11541-11558
Applications of Bayesian network models in predicting types of hematological malignancies.
Sci Rep 8: 2018 6951
A Comprehensive cis-eQTL Analysis Revealed Target Genes in Breast Cancer Susceptibility Loci Identified in Genome-wide Association Studies.
Am J Hum Genet 102: 2018 890-903
SIK2 attenuates proliferation and survival of breast cancer cells with simultaneous perturbation of MAPK and PI3K/Akt pathways.
Oncotarget 9: 2018 21876-21892
Cancer Cells Co-opt the Neuronal Redox-Sensing Channel TRPA1 to Promote Oxidative-Stress Tolerance.
Cancer Cell 33: 2018 985-1003.e7
Aerobic Glycolysis Controls Myeloid-Derived Suppressor Cells and Tumor Immunity via a Specific CEBPB Isoform in Triple-Negative Breast Cancer.
Cell Metab 28: 2018 87-103.e6
Identification of highly penetrant Rb-related synthetic lethal interactions in triple negative breast cancer.
Oncogene 37: 2018 5701-5718
Combining Pathway Identification and Breast Cancer Survival Prediction via Screening-Network Methods.
Front Genet 9: 2018 206
SOX4 can redirect TGF-β-mediated SMAD3-transcriptional output in a context-dependent manner to promote tumorigenesis.
Nucleic Acids Res 46: 2018 9578-9590
Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ER<sup>+</sup> breast cancer.
FASEB J 33: 2019 1644-1657
Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity.
Genome Biol 19: 2018 130
A Four-gene Decision Tree Signature Classification of Triple-negative Breast Cancer: Implications for Targeted Therapeutics.
Mol Cancer Ther 18: 2019 204-212
Association Analysis of Somatic Copy Number Alteration Burden With Breast Cancer Survival.
Front Genet 9: 2018 421
Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis.
PLoS Comput Biol 14: 2018 e1006520
Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers.
J Mol Cell Biol 11: 2019 649-664
Tumor mutational burden is a determinant of immune-mediated survival in breast cancer.
Oncoimmunology 7: 2018 e1490854
A comparative study of survival models for breast cancer prognostication revisited: the benefits of multi-gene models.
BMC Bioinformatics 19: 2018 400
An assessment of prognostic immunity markers in breast cancer.
NPJ Breast Cancer 4: 2018 35
Pathway-based subnetworks enable cross-disease biomarker discovery.
Nat Commun 9: 2018 4746
Global transcriptional analysis identifies a novel role for SOX4 in tumor-induced angiogenesis.
Elife 7: 2018 e27706
Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing.
Nat Commun 9: 2018 5150
FOXP1 negatively regulates tumor infiltrating lymphocyte migration in human breast cancer.
EBioMedicine 39: 2019 226-238
Identifying genes with tri-modal association with survival and tumor grade in cancer patients.
BMC Bioinformatics 20: 2019 13
A subgroup of microRNAs defines PTEN-deficient, triple-negative breast cancer patients with poorest prognosis and alterations in RB1, MYC, and Wnt signaling.
Breast Cancer Res 21: 2019 18
pAKT pathway activation is associated with PIK3CA mutations and good prognosis in luminal breast cancer in contrast to p-mTOR pathway activation.
NPJ Breast Cancer 5: 2019 7
The long-term prognostic and predictive capacity of cyclin D1 gene amplification in 2305 breast tumours.
Breast Cancer Res 21: 2019 34
Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups.
Nature 567: 2019 399-404
Genetic mutational status of genes regulating epigenetics: Role of the histone methyltransferase KMT2D in triple negative breast tumors.
PLoS One 14: 2019 e0209134
Inhibition of BRD4 suppresses the malignancy of breast cancer cells via regulation of Snail.
Cell Death Differ 27: 2020 255-268
Chemerin Suppresses Breast Cancer Growth by Recruiting Immune Effector Cells Into the Tumor Microenvironment.
Front Immunol 10: 2019 983
Cooperation between Constitutive and Inducible Chemokines Enables T Cell Engraftment and Immune Attack in Solid Tumors.
Cancer Cell 35: 2019 885-900.e10
LobSig is a multigene predictor of outcome in invasive lobular carcinoma.
NPJ Breast Cancer 5: 2019 18
Landscape of transcriptomic interactions between breast cancer and its microenvironment.
Nat Commun 10: 2019 3116
The phosphatase PPM1A inhibits triple negative breast cancer growth by blocking cell cycle progression.
NPJ Breast Cancer 5: 2019 22
Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types.
NPJ Syst Biol Appl 5: 2019 27
PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer.
Nat Commun 10: 2019 3589
Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome.
Commun Biol 2: 2019 306
High expression of PRKDC promotes breast cancer cell growth via p38 MAPK signaling and is associated with poor survival.
Mol Genet Genomic Med 7: 2019 e908
Bimodal age distribution at diagnosis in breast cancer persists across molecular and genomic classifications.
Breast Cancer Res Treat 179: 2020 185-195
Star-PAP regulates tumor protein D52 through modulating miR-449a/34a in breast cancer.
Biol Open 8: 2019 bio045914
Transcriptional Signature Derived from Murine Tumor-Associated Macrophages Correlates with Poor Outcome in Breast Cancer Patients.
Cell Rep 29: 2019 1221-1235.e5
PathTracer: High-sensitivity detection of differential pathway activity in tumours.
Sci Rep 9: 2019 16332
Human gene expression variability and its dependence on methylation and aging.
BMC Genomics 20: 2019 941
Androgen receptor gene expression in primary breast cancer.
NPJ Breast Cancer 5: 2019 47
A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival.
PLoS Genet 15: 2019 e1008482
miRNA551b-3p Activates an Oncostatin Signaling Module for the Progression of Triple-Negative Breast Cancer.
Cell Rep 29: 2019 4389-4406.e10
Metabolic Profiling Reveals a Dependency of Human Metastatic Breast Cancer on Mitochondrial Serine and One-Carbon Unit Metabolism.
Mol Cancer Res 18: 2020 599-611
Chromosome arm aneuploidies shape tumour evolution and drug response.
Nat Commun 11: 2020 449
Metabolic classification of circulating tumor cells as a biomarker for metastasis and prognosis in breast cancer.
J Transl Med 18: 2020 59
Breast cancer survival and the expression of genes related to alcohol drinking.
PLoS One 15: 2020 e0228957
Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants.
Nat Commun 11: 2020 1217
TGFBR2 mediated phosphorylation of BUB1 at Ser-318 is required for transforming growth factor-β signaling.
Neoplasia 22: 2020 163-178
Pan-cancer systematic identification of lncRNAs associated with cancer prognosis.
PeerJ 8: 2020 e8797
Prediagnostic 25-Hydroxyvitamin D Concentrations in Relation to Tumor Molecular Alterations and Risk of Breast Cancer Recurrence.
Cancer Epidemiol Biomarkers Prev 29: 2020 1253-1263
DNA copy number motifs are strong and independent predictors of survival in breast cancer.
Commun Biol 3: 2020 153
A qualitative transcriptional signature to reclassify histological grade of ER-positive breast cancer patients.
BMC Genomics 21: 2020 283
Stromal Platelet-Derived Growth Factor Receptor-β Signaling Promotes Breast Cancer Metastasis in the Brain.
Cancer Res 81: 2021 606-618
LGR5 in breast cancer and ductal carcinoma in situ: a diagnostic and prognostic biomarker and a therapeutic target.
BMC Cancer 20: 2020 542
The transcriptional repressor BCL11A promotes breast cancer metastasis.
J Biol Chem 295: 2020 11707-11719
Comprehensive characterization of claudin-low breast tumors reflects the impact of the cell-of-origin on cancer evolution.
Nat Commun 11: 2020 3431
Loss of progesterone receptor is associated with distinct tyrosine kinase profiles in breast cancer.
Breast Cancer Res Treat 183: 2020 585-598
Fibrinogen-Like Protein 2 (FGL2) is a Novel Biomarker for Clinical Prediction of Human Breast Cancer.
Med Sci Monit 26: 2020 e923531
A novel single-cell based method for breast cancer prognosis.
PLoS Comput Biol 16: 2020 e1008133
Increased expression of glutamine transporter SNAT2/SLC38A2 promotes glutamine dependence and oxidative stress resistance, and is associated with worse prognosis in triple-negative breast cancer.
Br J Cancer 124: 2021 494-505
CUP-AI-Dx: A tool for inferring cancer tissue of origin and molecular subtype using RNA gene-expression data and artificial intelligence.
EBioMedicine 61: 2020 103030
Differential kynurenine pathway metabolism in highly metastatic aggressive breast cancer subtypes: beyond IDO1-induced immunosuppression.
Breast Cancer Res 22: 2020 113
A tumour suppressive relationship between mineralocorticoid and retinoic acid receptors activates a transcriptional program consistent with a reverse Warburg effect in breast cancer.
Breast Cancer Res 22: 2020 122
Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.
Mol Cell 80: 2020 452-469.e9
A Five-Gene-Pair-Based Prognostic Signature for Predicting the Relapse Risk of Early Stage ER+ Breast Cancer.
Front Genet 11: 2020 566928
Multiomics integrative analysis reveals antagonistic roles of CBX2 and CBX7 in metabolic reprogramming of breast cancer.
Mol Oncol 15: 2021 1450-1465
Coagulation factor V is a marker of tumor-infiltrating immune cells in breast cancer.
Oncoimmunology 9: 2020 1824644
High expression of ACE2 in HER2 subtype of breast cancer is a marker of poor prognosis.
Cancer Treat Res Commun 27: 2021 100321
Up-regulation of L Antigen Family Member 3 Associates With Aggressive Progression of Breast Cancer.
Front Oncol 10: 2020 553628
eTumorMetastasis: A Network-based Algorithm Predicts Clinical Outcomes Using Whole-exome Sequencing Data of Cancer Patients.
Genomics Proteomics Bioinformatics 19: 2021 973-985
Widespread Alternative Splicing Changes in Metastatic Breast Cancer Cells.
Cells 10: 2021 858
SOLTI-1805 TOT-HER3 Study Concept: A Window-of-Opportunity Trial of Patritumab Deruxtecan, a HER3 Directed Antibody Drug Conjugate, in Patients With Early Breast Cancer.
Front Oncol 11: 2021 638482
Genomic features of rapid versus late relapse in triple negative breast cancer.
BMC Cancer 21: 2021 568
Uncovering the roles of microRNAs/lncRNAs in characterising breast cancer subtypes and prognosis.
BMC Bioinformatics 22: 2021 300
IP-10 (CXCL10) Can Trigger Emergence of Dormant Breast Cancer Cells in a Metastatic Liver Microenvironment.
Front Oncol 11: 2021 676135
Differential Regulation of Lacto-/Neolacto- Glycosphingolipid Biosynthesis Pathway Reveals Transcription Factors as Potential Candidates in Triple-Negative Breast Cancer.
Cancers (Basel) 13: 2021 3330
MultiK: an automated tool to determine optimal cluster numbers in single-cell RNA sequencing data.
Genome Biol 22: 2021 232
DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation.
Nat Commun 12: 2021 5406
Genetic variations of DNA bindings of FOXA1 and co-factors in breast cancer susceptibility.
Nat Commun 12: 2021 5318
Breast Cancer Consensus Subtypes: A system for subtyping breast cancer tumors based on gene expression.
NPJ Breast Cancer 7: 2021 136
Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis.
Cell Rep Methods 1: 2021 100050
From Cellular Infiltration Assessment to a Functional Gene Set-Based Prognostic Model for Breast Cancer.
Front Immunol 12: 2021 751530
EGF-SNX3-EGFR axis drives tumor progression and metastasis in triple-negative breast cancers.
Oncogene 41: 2022 220-232
TCOF1 upregulation in triple-negative breast cancer promotes stemness and tumour growth and correlates with poor prognosis.
Br J Cancer 126: 2022 57-71
Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes.
Nat Commun 12: 2021 6276
Detection of subtype-specific breast cancer surface protein biomarkers via a novel transcriptomics approach.
Biosci Rep 41: 2021 BSR20212218
ENTREP/FAM189A2 encodes a new ITCH ubiquitin ligase activator that is downregulated in breast cancer.
EMBO Rep 23: 2022 e51182
oCEM: Automatic detection and analysis of overlapping co-expressed gene modules.
BMC Genomics 23: 2022 39
Tumor-infiltrating exhausted CD8+ T cells dictate reduced survival in premenopausal estrogen receptor-positive breast cancer.
JCI Insight 7: 2022 e153963
A framework to predict the applicability of Oncotype DX, MammaPrint, and E2F4 gene signatures for improving breast cancer prognostic prediction.
Sci Rep 12: 2022 2211
Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.
PLoS One 17: 2022 e0261035
High Expression of G6PD Increases Doxorubicin Resistance in Triple Negative Breast Cancer Cells by Maintaining GSH Level.
Int J Biol Sci 18: 2022 1120-1133
DrGA: cancer driver gene analysis in a simpler manner.
BMC Bioinformatics 23: 2022 86
Tumor cell intrinsic and extrinsic features predict prognosis in estrogen receptor positive breast cancer.
PLoS Comput Biol 18: 2022 e1009495
miR-126 Decreases Proliferation and Mammosphere Formation of MCF-7 and Predicts Prognosis of ER+ Breast Cancer.
Diagnostics (Basel) 12: 2022 745
Survival analysis of pathway activity as a prognostic determinant in breast cancer.
PLoS Comput Biol 18: 2022 e1010020
Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer.
NAR Cancer 4: 2022 zcac008
BDP1 Alterations Correlate with Clinical Outcomes in Breast Cancer.
Cancers (Basel) 14: 2022 1658
Breast tumor microenvironment structures are associated with genomic features and clinical outcome.
Nat Genet 54: 2022 660-669
Computationally repurposing drugs for breast cancer subtypes using a network-based approach.
BMC Bioinformatics 23: 2022 143
Molecular analysis of TCGA breast cancer histologic types.
Cell Genom 1: 2021 100067
Epigenome erosion and SOX10 drive neural crest phenotypic mimicry in triple-negative breast cancer.
NPJ Breast Cancer 8: 2022 57
Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.
Nat Biotechnol 40: 2022 1624-1633
Delineation of Pathogenomic Insights of Breast Cancer in Young Women.
Cells 11: 2022 1927
Combinatorial immunotherapies overcome MYC-driven immune evasion in triple negative breast cancer.
Nat Commun 13: 2022 3671
Differential Private Deep Learning Models for Analyzing Breast Cancer Omics Data.
Front Oncol 12: 2022 879607
Comparative Analysis of Gene Correlation Networks of Breast Cancer Patients Based on Mutations in TP53.
Biomolecules 12: 2022 979
A novel age-related gene expression signature associates with proliferation and disease progression in breast cancer.
Br J Cancer 127: 2022 1865-1875
ABL kinases regulate translation in HER2+ cells through Y-box-binding protein 1 to facilitate colonization of the brain.
Cell Rep 40: 2022 111268
Downregulation of Elovl5 promotes breast cancer metastasis through a lipid-droplet accumulation-mediated induction of TGF-β receptors.
Cell Death Dis 13: 2022 758
RNA-Based Classification of Homologous Recombination Deficiency in Racially Diverse Patients with Breast Cancer.
Cancer Epidemiol Biomarkers Prev 31: 2022 2136-2147
NSMCE2, a novel super-enhancer-regulated gene, is linked to poor prognosis and therapy resistance in breast cancer.
BMC Cancer 22: 2022 1056
Hierarchical Ridge Regression for Incorporating Prior Information in Genomic Studies.
J Data Sci 20: 2022 34-50
Identification of novel genes for triple-negative breast cancer with semiparametric gene-based analysis.
J Appl Stat 50: 2023 691-702
Kindlin-1 regulates IL-6 secretion and modulates the immune environment in breast cancer models.
Elife 12: 2023 e85739
A positive feedback loop driven by fibronectin and IL-1β sustains the inflammatory microenvironment in breast cancer.
Breast Cancer Res 25: 2023 27
Incorporating RNA-based Risk Scores for Genomic Instability to Predict Breast Cancer Recurrence and Immunogenicity in a Diverse Population.
Cancer Res Commun 3: 2023 12-20
A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression.
Nat Cancer 4: 2023 682-698
Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer.
Genome Biol 24: 2023 128
Hypoxia induced responses are reflected in the stromal proteome of breast cancer.
Nat Commun 14: 2023 3724
Dissecting molecular, pathological, and clinical features associated with tumor neural/neuroendocrine heterogeneity.
iScience 26: 2023 106983
SUPREME: multiomics data integration using graph convolutional networks.
NAR Genom Bioinform 5: 2023 lqad063
Tamoxifen Response at Single-Cell Resolution in Estrogen Receptor-Positive Primary Human Breast Tumors.
Clin Cancer Res 29: 2023 4894-4907
An alternatively spliced PD-L1 isoform PD-L1∆3, and PD-L2 expression in breast cancers: implications for eligibility scoring and immunotherapy response.
Cancer Immunol Immunother 72: 2023 4065-4075
Harnessing the value of TCTP in breast cancer treatment resistance: an opportunity for personalized therapy.
Cancer Drug Resist 6: 2023 447-467
Metabolic stratification of human breast tumors reveal subtypes of clinical and therapeutic relevance.
iScience 26: 2023 108059
Mutant p53 sustains serine-glycine synthesis and essential amino acids intake promoting breast cancer growth.
Nat Commun 14: 2023 6777
HSF1 Inhibits Antitumor Immune Activity in Breast Cancer by Suppressing CCL5 to Block CD8+ T-cell Recruitment.
Cancer Res 84: 2024 276-290
MAF amplification licenses ERα through epigenetic remodelling to drive breast cancer metastasis.
Nat Cell Biol 25: 2023 1833-1847
GRB2 is a BECN1 interacting protein that regulates autophagy.
Cell Death Dis 15: 2024 14
Pathway analysis through mutual information.
Bioinformatics 40: 2024 btad776
Cooperative pro-tumorigenic adaptation to oncogenic RAS through epithelial-to-mesenchymal plasticity.
Sci Adv 10: 2024 eadi1736
STING signalling compensates for low tumour mutation burden to drive anti-tumour immunity.
EBioMedicine 101: 2024 105035
MARCH2, a Novel Oncogene-regulated SNAIL E3 Ligase, Suppresses Triple-negative Breast Cancer Metastases.
Cancer Res Commun 4: 2024 946-957
Pathway-based signatures predict patient outcome, chemotherapy benefit and synthetic lethal dependencies in invasive lobular breast cancer.
Br J Cancer 130: 2024 1828-1840
Mutational landscape of HSP family on human breast cancer.
Sci Rep 14: 2024 12471