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Strand SH, Rivero-Gutiérrez B, Houlahan KE, Seoane JA, King LM, Risom T, Simpson LA, Vennam S, Khan A, Cisneros L, Hardman T, Harmon B, Couch F, Gallagher K, Kilgore M, Wei S, DeMichele A, King T, McAuliffe PF, Nangia J, Lee J, Tseng J, Storniolo AM, Thompson AM, Gupta GP, Burns R, Veis DJ, DeSchryver K, Zhu C, Matusiak M, Wang J, Zhu SX, Tappenden J, Ding DY, Zhang D, Luo J, Jiang S, Varma S, Anderson L, Straub C, Srivastava S, Curtis C, Tibshirani R, Angelo RM, Hall A, Owzar K, Polyak K, Maley C, Marks JR, Colditz GA, Hwang ES, West RB. Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts. Cancer Cell 2022; 40:1521-1536.e7. [PMID: 36400020 PMCID: PMC9772081 DOI: 10.1016/j.ccell.2022.10.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/29/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022]
Abstract
Ductal carcinoma in situ (DCIS) is the most common precursor of invasive breast cancer (IBC), with variable propensity for progression. We perform multiscale, integrated molecular profiling of DCIS with clinical outcomes by analyzing 774 DCIS samples from 542 patients with 7.3 years median follow-up from the Translational Breast Cancer Research Consortium 038 study and the Resource of Archival Breast Tissue cohorts. We identify 812 genes associated with ipsilateral recurrence within 5 years from treatment and develop a classifier that predicts DCIS or IBC recurrence in both cohorts. Pathways associated with recurrence include proliferation, immune response, and metabolism. Distinct stromal expression patterns and immune cell compositions are identified. Our multiscale approach employed in situ methods to generate a spatially resolved atlas of breast precancers, where complementary modalities can be directly compared and correlated with conventional pathology findings, disease states, and clinical outcome.
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MESH Headings
- Humans
- Female
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/metabolism
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Disease Progression
- Breast Neoplasms/pathology
- Biomarkers
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/analysis
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Affiliation(s)
- Siri H Strand
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Belén Rivero-Gutiérrez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathleen E Houlahan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jose A Seoane
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Lorraine M King
- Department of Surgery, Duke University School of Medicine, Durham, NC 27708, USA
| | - Tyler Risom
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lunden A Simpson
- Department of Surgery, Duke University School of Medicine, Durham, NC 27708, USA
| | - Sujay Vennam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aziz Khan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Luis Cisneros
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Timothy Hardman
- Department of Surgery, Duke University School of Medicine, Durham, NC 27708, USA
| | - Bryan Harmon
- Department of Pathology, Montefiore Medical Center, Bronx, NY 10467, USA; TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA
| | - Fergus Couch
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Department of Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Kristalyn Gallagher
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark Kilgore
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Shi Wei
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Angela DeMichele
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tari King
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Breast Oncology Program, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Priscilla F McAuliffe
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Julie Nangia
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston TX 77030, USA
| | - Joanna Lee
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Department of Surgery, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer Tseng
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Department of Surgery, University of Chicago, Chicago, IL 60637, USA
| | - Anna Maria Storniolo
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Alastair M Thompson
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston TX 77030, USA; Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gaorav P Gupta
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robyn Burns
- TBCRC Loco-Regional Working Group, Baltimore, MD 21287, USA; TBCRC, The EMMES Corporation, Rockville, MD 20850, USA
| | - Deborah J Veis
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA; Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Katherine DeSchryver
- Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Chunfang Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Magdalena Matusiak
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jason Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley X Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jen Tappenden
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daisy Yi Ding
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Dadong Zhang
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27708, USA
| | - Jingqin Luo
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shu Jiang
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lauren Anderson
- Department of Surgery, Duke University School of Medicine, Durham, NC 27708, USA
| | - Cody Straub
- Department of Surgery, Duke University School of Medicine, Durham, NC 27708, USA
| | - Sucheta Srivastava
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christina Curtis
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Rob Tibshirani
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Robert Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Allison Hall
- Department of Pathology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Kouros Owzar
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27708, USA; Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, NC 27708, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Carlo Maley
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey R Marks
- Department of Surgery, Duke University School of Medicine, Durham, NC 27708, USA
| | - Graham A Colditz
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - E Shelley Hwang
- Department of Surgery, Duke University School of Medicine, Durham, NC 27708, USA.
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Yue T, Liu X, Zuo S, Zhu J, Li J, Liu Y, Chen S, Wang P. BCL2A1 and CCL18 Are Predictive Biomarkers of Cisplatin Chemotherapy and Immunotherapy in Colon Cancer Patients. Front Cell Dev Biol 2022; 9:799278. [PMID: 35265629 PMCID: PMC8898943 DOI: 10.3389/fcell.2021.799278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Cisplatin enhances the antitumor T cell response, and the combination of PD-L1 blockade produces a synergistic therapeutic effect. However, the clinical correlation between cisplatin and immunotherapy in colon cancer (CC) is unknown. Methods: Using the “pRRophetic” package, we calculated the IC50 of cisplatin. The correlation between cisplatin IC50, cisplatin resistance–related genes (CCL18 and BCL2A1), and immunotherapy were preliminarily verified in TCGA and further validated in independent cohorts (GSE39582 and GSE17538), cisplatin-resistant CC cell line DLD1, and our own clinical specimens. Classification performance was evaluated using the AUC value of the ROC curve. Scores of immune signatures, autophagy, ferroptosis, and stemness were quantified using the ssGSEA algorithm. Results: Based on respective medians of three CC cohorts, patients were divided into high- and low-IC50 groups. Compared with the high IC50 group, the low-IC50 group had significantly higher tumor microenvironment (TME) scores and lower tumor purity. Most co-signaling molecules were upregulated in low IC50 group. CC patients with good immunotherapy efficacy (MSI, dMMR, and more TMB) were more attributable to the low-IC50 group. Among seven shared differentially expressed cisplatin resistance–related genes, CCL18 and BCL2A1 had the best predictive efficacy of the above immunotherapy biomarkers. For wet experimental verification, compared with cisplatin-resistant DLD1, similar to PD-L1, CCL18 and BCL2A1 were significantly upregulated in wild-type DLD1. In our own CC tissues, the mRNA expression of CCL18, BCL2A1, and PD-L1 in dMMR were significantly increased. The high group of CCL18 or BCL2A1 had a higher proportion of MSI, dMMR, and more TMB. IC50, CCL18, BCL2A1, and PD-L1 were closely related to scores of immune-related pathways, immune signatures, autophagy, ferroptosis, and stemness. The microRNA shared by BCL2A1 and PD-L1, hsa-miR-137, were significantly associated with CCL18, BCL2A1, and PD-L1, and downregulated in low-IC50 group. The activity of the TOLL-like receptor signaling pathway affected the sensitivity of CC patients to cisplatin and immunotherapy. For subtype analysis, immune C2, immune C6, HM-indel, HM-SNV, C18, and C20 were equally sensitive to cisplatin chemotherapy and immunotherapy. Conclusions: CC patients sensitive to cisplatin chemotherapy were also sensitive to immunotherapy. CCL18 and BCL2A1 were novel biomarkers for cisplatin and immunotherapy.
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Affiliation(s)
- Taohua Yue
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing, China
| | - Xiangzheng Liu
- Department of Thoracic Surgery, Peking University First Hospital, Peking University, Beijing, China
| | - Shuai Zuo
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing, China
| | - Jing Zhu
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing, China
| | - Jichang Li
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing, China
| | - Yucun Liu
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing, China
| | - Shanwen Chen
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing, China
| | - Pengyuan Wang
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing, China
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Chi C, Ye Y, Chen B, Huang H. Bipartite graph-based approach for clustering of cell lines by gene expression-drug response associations. Bioinformatics 2021; 37:2617-2626. [PMID: 33682877 PMCID: PMC8428606 DOI: 10.1093/bioinformatics/btab143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 02/16/2021] [Accepted: 03/01/2021] [Indexed: 01/29/2023] Open
Abstract
MOTIVATION In pharmacogenomic studies, the biological context of cell lines influences the predictive ability of drug-response models and the discovery of biomarkers. Thus, similar cell lines are often studied together based on prior knowledge of biological annotations. However, this selection approach is not scalable with the number of annotations, and the relationship between gene-drug association patterns and biological context may not be obvious. RESULTS We present a procedure to compare cell lines based on their gene-drug association patterns. Starting with a grouping of cell lines from biological annotation, we model gene-drug association patterns for each group as a bipartite graph between genes and drugs. This is accomplished by applying sparse canonical correlation analysis (SCCA) to extract the gene-drug associations, and using the canonical vectors to construct the edge weights. Then, we introduce a nuclear norm-based dissimilarity measure to compare the bipartite graphs. Accompanying our procedure is a permutation test to evaluate the significance of similarity of cell line groups in terms of gene-drug associations. In the pharmacogenomics datasets CTRP2, GDSC2, and CCLE, hierarchical clustering of carcinoma groups based on this dissimilarity measure uniquely reveals clustering patterns driven by carcinoma subtype rather than primary site. Next, we show that the top associated drugs or genes from SCCA can be used to characterize the clustering patterns of haematopoietic and lymphoid malignancies. Finally, we confirm by simulation that when drug responses are linearly-dependent on expression, our approach is the only one that can effectively infer the true hierarchy compared to existing approaches. AVAILABILITY Bipartite graph-based hierarchical clustering is implemented in R and can be obtained from CRAN: https://CRAN.R-project.org/package=hierBipartite. The source code is available at https://github.com/CalvinTChi/hierBipartite. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Calvin Chi
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Yuting Ye
- Division of Biostatistics, University of California, Berkeley, CA 94720, USA
| | - Bin Chen
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 48912, USA.,Department of Pharmacology and Toxicology, Michigan State University, Grand Rapids, MI 48824, USA
| | - Haiyan Huang
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA
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Bergholtz H, Lien TG, Swanson DM, Frigessi A, Daidone MG, Tost J, Wärnberg F, Sørlie T. Contrasting DCIS and invasive breast cancer by subtype suggests basal-like DCIS as distinct lesions. NPJ Breast Cancer 2020; 6:26. [PMID: 32577501 PMCID: PMC7299965 DOI: 10.1038/s41523-020-0167-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/20/2020] [Indexed: 12/19/2022] Open
Abstract
Ductal carcinoma in situ (DCIS) is a non-invasive type of breast cancer with highly variable potential of becoming invasive and affecting mortality. Currently, many patients with DCIS are overtreated due to the lack of specific biomarkers that distinguish low risk lesions from those with a higher risk of progression. In this study, we analyzed 57 pure DCIS and 313 invasive breast cancers (IBC) from different patients. Three levels of genomic data were obtained; gene expression, DNA methylation, and DNA copy number. We performed subtype stratified analyses and identified key differences between DCIS and IBC that suggest subtype specific progression. Prominent differences were found in tumors of the basal-like subtype: Basal-like DCIS were less proliferative and showed a higher degree of differentiation than basal-like IBC. Also, core basal tumors (characterized by high correlation to the basal-like centroid) were not identified amongst DCIS as opposed to IBC. At the copy number level, basal-like DCIS exhibited fewer copy number aberrations compared with basal-like IBC. An intriguing finding through analysis of the methylome was hypermethylation of multiple protocadherin genes in basal-like IBC compared with basal-like DCIS and normal tissue, possibly caused by long range epigenetic silencing. This points to silencing of cell adhesion-related genes specifically in IBC of the basal-like subtype. Our work confirms that subtype stratification is essential when studying progression from DCIS to IBC, and we provide evidence that basal-like DCIS show less aggressive characteristics and question the assumption that basal-like DCIS is a direct precursor of basal-like invasive breast cancer.
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Affiliation(s)
- Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tonje G. Lien
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - David M. Swanson
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Arnoldo Frigessi
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Maria Grazia Daidone
- Department of Applied Research and Technical development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Fredrik Wärnberg
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Department of Surgery, Uppsala Academic Hospital, Uppsala, Sweden
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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