title: Individualized Breast Cancer Characterization through Single-Cell Analysis of Tumor and Adjacent Normal Cells.
abstract: There is a need to individualize assays for tumor molecular phenotyping, given variations in the differentiation status of tumor and normal tissues in different patients. To address this, we performed single-cell genomics of breast tumors and adjacent normal cells propagated for a short duration under growth conditions that enable epithelial reprogramming. Cells analyzed were either unselected for a specific subpopulation or phenotypically defined as undifferentiated and highly clonogenic ALDH+/CD49f+/EpCAM+luminal progenitors, which express both basal cell and luminal cell-enriched genes. We analyzed 420 tumor cells and 284 adjacent normal cells for expression of 93 genes that included a PAM50-intrinsic subtype classifier and stemness-related genes. ALDH+/CD49f+/EpCAM+tumor and normal cells clustered differently compared with unselected tumor and normal cells. PAM50 gene-set analyses of ALDH+/CD49f+/EpCAM+populations efficiently identified major and minor clones of tumor cells, with the major clone resembling clinical parameters of the tumor. Similarly, a stemness-associated gene set identified clones with divergent stemness pathway activation within the same tumor. This refined expression profiling technique distinguished genes truly deregulated in cancer from genes that identify cellular precursors of tumors. Collectively, the assays presented here enable more precise identification of cancer-deregulated genes, allow for early identification of therapeutically targetable tumor cell subpopulations, and ultimately provide a refinement of precision therapeutics for cancer treatment.Cancer Res; 77(10); 2759-69. ©2017 AACR.
authors.affiliation: Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana.
authors.forename: Manjushree
authors.initials: M
authors.lastname: Anjanappa
authors.affiliation: Hematology and Oncology Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
authors.forename: Angelo
authors.initials: A
authors.lastname: Cardoso
authors.affiliation: Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.
authors.forename: Lijun
authors.initials: L
authors.lastname: Cheng
authors.affiliation: Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana.
authors.forename: Safa
authors.initials: S
authors.lastname: Mohamad
authors.affiliation: Hematology and Oncology Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
authors.forename: Andrea
authors.initials: A
authors.lastname: Gunawan
authors.affiliation: Hematology and Oncology Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
authors.forename: Susan
authors.initials: S
authors.lastname: Rice
authors.affiliation: Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.
authors.forename: Yan
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.|Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.
authors.forename: Lang
authors.initials: L
authors.lastname: Li
authors.affiliation: Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
authors.forename: George E
authors.initials: GE
authors.lastname: Sandusky
authors.affiliation: Hematology and Oncology Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.|Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana.
authors.forename: Edward F
authors.initials: EF
authors.lastname: Srour
authors.affiliation: Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana. hnakshat@iupui.edu.|Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.|Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana.|VA Roudebush Medical Center, Indianapolis, Indiana.
authors.forename: Harikrishna
authors.initials: H
authors.lastname: Nakshatri
mesh_terms: D014408:Biomarkers, Tumor; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D004847:Epithelial Cells / Q000378:metabolism; D005260:Female; D005434:Flow Cytometry; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods; D006801:Humans; D010641:Phenotype; D057285:Precision Medicine / Q000379:methods; D060888:Real-Time Polymerase Chain Reaction; D059010:Single-Cell Analysis / Q000379:methods
chemical_list: D014408:Biomarkers, Tumor