1
|
Taylor BC, Sun X, Gonzalez-Ericsson PI, Sanchez V, Sanders ME, Wescott EC, Opalenik SR, Hanna A, Chou ST, Van Kaer L, Gomez H, Isaacs C, Ballinger TJ, Santa-Maria CA, Shah PD, Dees EC, Lehmann BD, Abramson VG, Pietenpol JA, Balko JM. NKG2A Is a Therapeutic Vulnerability in Immunotherapy Resistant MHC-I Heterogeneous Triple-Negative Breast Cancer. Cancer Discov 2024; 14:290-307. [PMID: 37791898 PMCID: PMC10850946 DOI: 10.1158/2159-8290.cd-23-0519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/21/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
Despite the success of immune checkpoint inhibition (ICI) in treating cancer, patients with triple-negative breast cancer (TNBC) often develop resistance to therapy, and the underlying mechanisms are unclear. MHC-I expression is essential for antigen presentation and T-cell-directed immunotherapy responses. This study demonstrates that TNBC patients display intratumor heterogeneity in regional MHC-I expression. In murine models, loss of MHC-I negates antitumor immunity and ICI response, whereas intratumor MHC-I heterogeneity leads to increased infiltration of natural killer (NK) cells in an IFNγ-dependent manner. Using spatial technologies, MHC-I heterogeneity is associated with clinical resistance to anti-programmed death (PD) L1 therapy and increased NK:T-cell ratios in human breast tumors. MHC-I heterogeneous tumors require NKG2A to suppress NK-cell function. Combining anti-NKG2A and anti-PD-L1 therapies restores complete response in heterogeneous MHC-I murine models, dependent on the presence of activated, tumor-infiltrating NK and CD8+ T cells. These results suggest that similar strategies may enhance patient benefit in clinical trials. SIGNIFICANCE Clinical resistance to immunotherapy is common in breast cancer, and many patients will likely require combination therapy to maximize immunotherapeutic benefit. This study demonstrates that heterogeneous MHC-I expression drives resistance to anti-PD-L1 therapy and exposes NKG2A on NK cells as a target to overcome resistance. This article is featured in Selected Articles from This Issue, p. 201.
Collapse
Affiliation(s)
| | - Xiaopeng Sun
- Cancer Biology Program, Vanderbilt University, Nashville, Tennessee
| | - Paula I. Gonzalez-Ericsson
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Violeta Sanchez
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Melinda E. Sanders
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Elizabeth C. Wescott
- Department of Pathology, Microbiology, and Immunology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Susan R. Opalenik
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ann Hanna
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shu-Ting Chou
- Cancer Biology Program, Vanderbilt University, Nashville, Tennessee
| | - Luc Van Kaer
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pathology, Microbiology, and Immunology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Henry Gomez
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplásicas, Lima, Perú
| | - Claudine Isaacs
- Division of Hematology-Oncology, Department of Medicine, Georgetown University, Washington, District of Columbia
| | - Tarah J. Ballinger
- Division of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Payal D. Shah
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elizabeth C. Dees
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Brian D. Lehmann
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Vandana G. Abramson
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jennifer A. Pietenpol
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Justin M. Balko
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pathology, Microbiology, and Immunology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| |
Collapse
|
2
|
Bhat-Nakshatri P, Khatpe AS, Chen D, Batic K, Mang H, Herodotou C, McGuire PC, Xuei X, Erdogan C, Gao H, Liu Y, Sandusky G, Storniolo AM, Nakshatri H. Signaling Pathway Alterations Driven by BRCA1 and BRCA2 Germline Mutations are Sufficient to Initiate Breast Tumorigenesis by the PIK3CAH1047R Oncogene. Cancer Res Commun 2024; 4:38-54. [PMID: 38059556 PMCID: PMC10774565 DOI: 10.1158/2767-9764.crc-23-0330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
Single-cell transcriptomics studies have begun to identify breast epithelial cell and stromal cell specific transcriptome differences between BRCA1/2 mutation carriers and non-carriers. We generated a single-cell transcriptome atlas of breast tissues from BRCA1, BRCA2 mutation carriers and compared this single-cell atlas of mutation carriers with our previously described single-cell breast atlas of healthy non-carriers. We observed that BRCA1 but not BRCA2 mutations altered the ratio between basal (basal-myoepithelial), luminal progenitor (luminal adaptive secretory precursor, LASP), and mature luminal (luminal hormone sensing) cells in breast tissues. A unique subcluster of cells within LASP cells is underrepresented in case of BRCA1 and BRCA2 mutation carriers compared with non-carriers. Both BRCA1 and BRCA2 mutations specifically altered transcriptomes in epithelial cells which are an integral part of NFκB, LARP1, and MYC signaling. Signaling pathway alterations in epithelial cells unique to BRCA1 mutations included STAT3, BRD4, SMARCA4, HIF2A/EPAS1, and Inhibin A signaling. BRCA2 mutations were associated with upregulation of IL6, PDK1, FOXO3, and TNFSF11 signaling. These signaling pathway alterations are sufficient to alter sensitivity of BRCA1/BRCA2-mutant breast epithelial cells to transformation as epithelial cells from BRCA1 mutation carriers overexpressing hTERT + PIK3CAH1047R generated adenocarcinomas, whereas similarly modified mutant BRCA2 cells generated basal carcinomas in NSG mice. Thus, our studies provide a high-resolution transcriptome atlas of breast epithelial cells of BRCA1 and BRCA2 mutation carriers and reveal their susceptibility to PIK3CA mutation-driven transformation. SIGNIFICANCE This study provides a single-cell atlas of breast tissues of BRCA1/2 mutation carriers and demonstrates that aberrant signaling due to BRCA1/2 mutations is sufficient to initiate breast cancer by mutant PIK3CA.
Collapse
Affiliation(s)
| | - Aditi S. Khatpe
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Duojiao Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Katie Batic
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Henry Mang
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Patrick C. McGuire
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Xiaoling Xuei
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Cihat Erdogan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - George Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Anna Maria Storniolo
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Harikrishna Nakshatri
- Department of Surgery, 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
| |
Collapse
|
3
|
Nishida J, Cristea S, Bodapati S, Puleo J, Bai G, Patel A, Hughes M, Snow C, Borges V, Ruddy KJ, Collins LC, Feeney AM, Slowik K, Bossuyt V, Dillon D, Lin NU, Partridge AH, Michor F, Polyak K. Peripheral blood TCR clonotype diversity as an age-associated marker of breast cancer progression. Proc Natl Acad Sci U S A 2023; 120:e2316763120. [PMID: 38011567 DOI: 10.1073/pnas.2316763120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/27/2023] [Indexed: 11/29/2023] Open
Abstract
Immune escape is a prerequisite for tumor growth. We previously described a decline in intratumor activated cytotoxic T cells and T cell receptor (TCR) clonotype diversity in invasive breast carcinomas compared to ductal carcinoma in situ (DCIS), implying a central role of decreasing T cell responses in tumor progression. To determine potential associations between peripheral immunity and breast tumor progression, here, we assessed the peripheral blood TCR clonotype of 485 breast cancer patients diagnosed with either DCIS or de novo stage IV disease at younger (<45) or older (≥45) age. TCR clonotype diversity was significantly lower in older compared to younger breast cancer patients regardless of tumor stage at diagnosis. In the younger age group, TCR-α clonotype diversity was lower in patients diagnosed with de novo stage IV breast cancer compared to those diagnosed with DCIS. In the older age group, DCIS patients with higher TCR-α clonotype diversity were more likely to have a recurrence compared to those with lower diversity. Whole blood transcriptome profiles were distinct depending on the TCR-α Chao1 diversity score. There were more CD8+ T cells and a more active immune environment in DCIS tumors of young patients with higher peripheral blood TCR-α Chao1 diversity than in those with lower diversity. These results provide insights into the role that host immunity plays in breast cancer development across different age groups.
Collapse
MESH Headings
- Humans
- Aged
- Female
- Breast Neoplasms/pathology
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- CD8-Positive T-Lymphocytes/pathology
- Biomarkers, Tumor/genetics
- Receptors, Antigen, T-Cell/genetics
- Neoplastic Processes
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Carcinoma, Ductal, Breast/pathology
Collapse
Affiliation(s)
- Jun Nishida
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Julieann Puleo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Gali Bai
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Ashka Patel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Melissa Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Craig Snow
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Virginia Borges
- Medicine-Medical Oncology, University of Colorado Comprehensive Cancer Center, Aurora, CO 80045
| | - Kathryn J Ruddy
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN 55905
| | - Laura C Collins
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02115
| | - Anne-Marie Feeney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Kara Slowik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02138
| | - Veerle Bossuyt
- Mass General Pathology, Massachusetts General Hospital, Boston, MA 02114
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Ann H Partridge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115
- The Broad Institute of MIT and Harvard, Cambridge, MA 02138
- The Ludwig Center at Harvard, Boston, MA 02115
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
- Mass General Pathology, Massachusetts General Hospital, Boston, MA 02114
- The Ludwig Center at Harvard, Boston, MA 02115
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215
| |
Collapse
|
4
|
Alečković M, Li Z, Zhou N, Qiu X, Lulseged B, Foidart P, Huang XY, Garza K, Shu S, Kesten N, Li R, Lim K, Garrido-Castro AC, Guerriero JL, Qi J, Long HW, Polyak K. Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer. Mol Cancer Ther 2023; 22:1304-1318. [PMID: 37676980 PMCID: PMC10618734 DOI: 10.1158/1535-7163.mct-23-0303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/05/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023]
Abstract
Immune checkpoint inhibition combined with chemotherapy is currently approved as first-line treatment for patients with advanced PD-L1-positive triple-negative breast cancer (TNBC). However, a significant proportion of metastatic TNBC is PD-L1-negative and, in this population, chemotherapy alone largely remains the standard-of-care and novel therapeutic strategies are needed to improve clinical outcomes. Here, we describe a triple combination of anti-PD-L1 immune checkpoint blockade, epigenetic modulation thorough bromodomain and extra-terminal (BET) bromodomain inhibition (BBDI), and chemotherapy with paclitaxel that effectively inhibits both primary and metastatic tumor growth in two different syngeneic murine models of TNBC. Detailed cellular and molecular profiling of tumors from single and combination treatment arms revealed increased T- and B-cell infiltration and macrophage reprogramming from MHCIIlow to a MHCIIhigh phenotype in mice treated with triple combination. Triple combination also had a major impact on gene expression and chromatin profiles shifting cells to a more immunogenic and senescent state. Our results provide strong preclinical evidence to justify clinical testing of BBDI, paclitaxel, and immune checkpoint blockade combination.
Collapse
Affiliation(s)
- Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Ningxuan Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Bethlehem Lulseged
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Pierre Foidart
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Xiao-Yun Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kodie Garza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Nikolas Kesten
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Ana C. Garrido-Castro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jennifer L. Guerriero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Surgery, Division of Breast Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Henry W. Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
5
|
Gou X, Kim BJ, Anurag M, Lei JT, Young MN, Holt MV, Fandino D, Vollert CT, Singh P, Alzubi MA, Malovannaya A, Dobrolecki LE, Lewis MT, Li S, Foulds CE, Ellis MJ. Kinome Reprogramming Is a Targetable Vulnerability in ESR1 Fusion-Driven Breast Cancer. Cancer Res 2023; 83:3237-3251. [PMID: 37071495 PMCID: PMC10543968 DOI: 10.1158/0008-5472.can-22-3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/20/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023]
Abstract
Transcriptionally active ESR1 fusions (ESR1-TAF) are a potent cause of breast cancer endocrine therapy (ET) resistance. ESR1-TAFs are not directly druggable because the C-terminal estrogen/anti-estrogen-binding domain is replaced with translocated in-frame partner gene sequences that confer constitutive transactivation. To discover alternative treatments, a mass spectrometry (MS)-based kinase inhibitor pulldown assay (KIPA) was deployed to identify druggable kinases that are upregulated by diverse ESR1-TAFs. Subsequent explorations of drug sensitivity validated RET kinase as a common therapeutic vulnerability despite remarkable ESR1-TAF C-terminal sequence and structural diversity. Organoids and xenografts from a pan-ET-resistant patient-derived xenograft model that harbors the ESR1-e6>YAP1 TAF were concordantly inhibited by the selective RET inhibitor pralsetinib to a similar extent as the CDK4/6 inhibitor palbociclib. Together, these findings provide preclinical rationale for clinical evaluation of RET inhibition for the treatment of ESR1-TAF-driven ET-resistant breast cancer. SIGNIFICANCE Kinome analysis of ESR1 translocated and mutated breast tumors using drug bead-based mass spectrometry followed by drug-sensitivity studies nominates RET as a therapeutic target. See related commentary by Wu and Subbiah, p. 3159.
Collapse
Affiliation(s)
- Xuxu Gou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston Texas
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Beom-Jun Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jonathan T. Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Meggie N. Young
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Matthew V. Holt
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Diana Fandino
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Craig T. Vollert
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Employee of Adrienne Helis Malvin Medical Research Foundation, New Orleans, Los Angeles
| | - Purba Singh
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Mohammad A. Alzubi
- Employee of Adrienne Helis Malvin Medical Research Foundation, New Orleans, Los Angeles
| | - Anna Malovannaya
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Lacey E. Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Michael T. Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Radiology, Baylor College of Medicine, Houston, Texas
| | - Shunqiang Li
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Charles E. Foulds
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Matthew J. Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
6
|
Dashzeveg NK, Jia Y, Zhang Y, Gerratana L, Patel P, Shajahan A, Dandar T, Ramos EK, Almubarak HF, Adorno-Cruz V, Taftaf R, Schuster EJ, Scholten D, Sokolowski MT, Reduzzi C, El-Shennawy L, Hoffmann AD, Manai M, Zhang Q, D'Amico P, Azadi P, Colley KJ, Platanias LC, Shah AN, Gradishar WJ, Cristofanilli M, Muller WA, Cobb BA, Liu H. Dynamic Glycoprotein Hyposialylation Promotes Chemotherapy Evasion and Metastatic Seeding of Quiescent Circulating Tumor Cell Clusters in Breast Cancer. Cancer Discov 2023; 13:2050-2071. [PMID: 37272843 PMCID: PMC10481132 DOI: 10.1158/2159-8290.cd-22-0644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 04/14/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Most circulating tumor cells (CTC) are detected as single cells, whereas a small proportion of CTCs in multicellular clusters with stemness properties possess 20- to 100-times higher metastatic propensity than the single cells. Here we report that CTC dynamics in both singles and clusters in response to therapies predict overall survival for breast cancer. Chemotherapy-evasive CTC clusters are relatively quiescent with a specific loss of ST6GAL1-catalyzed α2,6-sialylation in glycoproteins. Dynamic hyposialylation in CTCs or deficiency of ST6GAL1 promotes cluster formation for metastatic seeding and enables cellular quiescence to evade paclitaxel treatment in breast cancer. Glycoproteomic analysis reveals newly identified protein substrates of ST6GAL1, such as adhesion or stemness markers PODXL, ICAM1, ECE1, ALCAM1, CD97, and CD44, contributing to CTC clustering (aggregation) and metastatic seeding. As a proof of concept, neutralizing antibodies against one newly identified contributor, PODXL, inhibit CTC cluster formation and lung metastasis associated with paclitaxel treatment for triple-negative breast cancer. SIGNIFICANCE This study discovers that dynamic loss of terminal sialylation in glycoproteins of CTC clusters contributes to the fate of cellular dormancy, advantageous evasion to chemotherapy, and enhanced metastatic seeding. It identifies PODXL as a glycoprotein substrate of ST6GAL1 and a candidate target to counter chemoevasion-associated metastasis of quiescent tumor cells. This article is featured in Selected Articles from This Issue, p. 1949.
Collapse
Affiliation(s)
- Nurmaa K. Dashzeveg
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yuzhi Jia
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Youbin Zhang
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lorenzo Gerratana
- Department of Medicinal Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Priyam Patel
- Quantitative Data Science Core, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Asif Shajahan
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Tsogbadrakh Dandar
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Erika K. Ramos
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Hannah F. Almubarak
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Valery Adorno-Cruz
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rokana Taftaf
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Emma J. Schuster
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David Scholten
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Michael T. Sokolowski
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Carolina Reduzzi
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Division of Hematology-Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Lamiaa El-Shennawy
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Andrew D. Hoffmann
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Maroua Manai
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Qiang Zhang
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Paolo D'Amico
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Karen J. Colley
- Department of Biochemistry and Molecular Genetics, University of Illinois Chicago, Chicago, Illinois
| | - Leonidas C. Platanias
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ami N. Shah
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - William J. Gradishar
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Massimo Cristofanilli
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Division of Hematology-Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - William A. Muller
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Brian A. Cobb
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Huiping Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| |
Collapse
|
7
|
Lulic-Kuryllo T, Leonardis JM, Momoh AO, Lipps DB. Assessing shoulder muscle stretch reflexes following breast cancer treatment and postmastectomy breast reconstruction. J Neurophysiol 2023; 129:914-926. [PMID: 36947887 PMCID: PMC10110716 DOI: 10.1152/jn.00081.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
Muscle stiffness is altered following postmastectomy breast reconstruction and breast cancer treatment. The exact mechanisms underlying these alterations are unknown; however, muscle stretch reflexes may play a role. This work examined short- (SLR) and long-latency (LLR) shoulder muscle stretch reflexes in breast cancer survivors. Forty-nine patients who had undergone postmastectomy breast reconstruction, 17 who had undergone chemoradiation, and 18 healthy, age-matched controls were enrolled. Muscle activity was recorded from the clavicular and sternocostal regions of the pectoralis major and anterior, middle, and posterior deltoids during vertical ab/adduction or horizontal flex/extension perturbations while participants maintained minimal torques. SLR and LLR were quantified for each muscle. Our major finding was that following postmastectomy breast reconstruction, SLR and LLR are impaired in the clavicular region of the pectoralis major. Individuals who had chemoradiation had impaired stretch reflexes in the clavicular and sternocostal region of the pectoralis major, anterior, middle, and posterior deltoid. These findings indicate that breast cancer treatments alter the regulation of shoulder muscle stretch reflexes and may be associated with surgical or nonsurgical damage to the pectoral fascia, muscle spindles, and/or sensory Ia afferents.NEW & NOTEWORTHY Shoulder muscle stretch reflexes may be impacted following postmastectomy breast reconstruction and chemoradiation. Here, we examined short- and long-latency shoulder muscle stretch reflexes in two experiments following common breast reconstruction procedures and chemoradiation. We show impairments in pectoralis major stretch reflexes following postmastectomy breast reconstruction and pectoralis major and deltoid muscle stretch reflexes following chemoradiation. These findings indicate that breast cancer treatments alter the regulation of shoulder muscle stretch reflexes.
Collapse
Affiliation(s)
- Tea Lulic-Kuryllo
- School of Kinesiology, University of Michigan, Ann Arbor, Michigan, United States
| | - Joshua M Leonardis
- College of Applied Health Sciences, University of Illinois, Urbana-Champaign, Illinois, United States
| | - Adeyiza O Momoh
- Section of Plastic Surgery, University of Michigan, Ann Arbor, Michigan, United States
| | - David B Lipps
- School of Kinesiology, University of Michigan, Ann Arbor, Michigan, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States
| |
Collapse
|
8
|
Yamamoto A, Huang Y, Krajina BA, McBirney M, Doak AE, Qu S, Wang CL, Haffner MC, Cheung KJ. Metastasis from the tumor interior and necrotic core formation are regulated by breast cancer-derived angiopoietin-like 7. Proc Natl Acad Sci U S A 2023; 120:e2214888120. [PMID: 36853945 PMCID: PMC10013750 DOI: 10.1073/pnas.2214888120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/06/2023] [Indexed: 03/01/2023] Open
Abstract
Necrosis in the tumor interior is a common feature of aggressive cancers that is associated with poor clinical prognosis and the development of metastasis. How the necrotic core promotes metastasis remains unclear. Here, we report that emergence of necrosis inside the tumor is correlated temporally with increased tumor dissemination in a rat breast cancer model and in human breast cancer patients. By performing spatially focused transcriptional profiling, we identified angiopoietin-like 7 (Angptl7) as a tumor-specific factor localized to the perinecrotic zone. Functional studies showed that Angptl7 loss normalizes central necrosis, perinecrotic dilated vessels, metastasis, and reduces circulating tumor cell counts to nearly zero. Mechanistically, Angptl7 promotes vascular permeability and supports vascular remodeling in the perinecrotic zone. Taken together, these findings show that breast tumors actively produce factors controlling central necrosis formation and metastatic dissemination from the tumor core.
Collapse
Affiliation(s)
- Ami Yamamoto
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA98195
| | - Yin Huang
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Brad A. Krajina
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Margaux McBirney
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Andrea E. Doak
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA98195
| | - Sixuan Qu
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Carolyn L. Wang
- Department of Radiology, University of Washington School of Medicine, Seattle, WA98195
| | - Michael C. Haffner
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98109
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Kevin J. Cheung
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| |
Collapse
|
9
|
McClure MB, Kogure Y, Ansari-Pour N, Saito Y, Chao HH, Shepherd J, Tabata M, Olopade OI, Wedge DC, Hoadley KA, Perou CM, Kataoka K. Landscape of Genetic Alterations Underlying Hallmark Signature Changes in Cancer Reveals TP53 Aneuploidy-driven Metabolic Reprogramming. Cancer Res Commun 2023; 3:281-296. [PMID: 36860655 PMCID: PMC9973382 DOI: 10.1158/2767-9764.crc-22-0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 10/08/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
The hallmark signatures based on gene expression capture core cancer processes. Through a pan-cancer analysis, we describe the overview of hallmark signatures across tumor types/subtypes and reveal significant relationships between these signatures and genetic alterations. TP53 mutation exerts diverse changes, including increased proliferation and glycolysis, which are closely mimicked by widespread copy-number alterations. Hallmark signature and copy-number clustering identify a cluster of squamous tumors and basal-like breast and bladder cancers with elevated proliferation signatures, frequent TP53 mutation, and high aneuploidy. In these basal-like/squamous TP53-mutated tumors, a specific and consistent spectrum of copy-number alterations is preferentially selected prior to whole-genome duplication. Within Trp53-null breast cancer mouse models, these copy-number alterations spontaneously occur and recapitulate the hallmark signature changes observed in the human condition. Together, our analysis reveals intertumor and intratumor heterogeneity of the hallmark signatures, uncovering an oncogenic program induced by TP53 mutation and select aneuploidy events to drive a worsened prognosis. Significance Our data demonstrate that TP53 mutation and a resultant selected pattern of aneuploidies cause an aggressive transcriptional program including upregulation of glycolysis signature with prognostic implications. Importantly, basal-like breast cancer demonstrates genetic and/or phenotypic changes closely related to squamous tumors including 5q deletion that reveal alterations that could offer therapeutic options across tumor types regardless of tissue of origin.
Collapse
Affiliation(s)
- Marni B. McClure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Naser Ansari-Pour
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Hann-Hsiang Chao
- Department of Radiation Oncology, Richmond VA Medical Center, Richmond, Virginia
- Department of Radiation Oncology, Virginia Commonwealth University, Richmond, Virginia
| | - Jonathan Shepherd
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Olufunmilayo I. Olopade
- Center for Clinical Cancer Genetics & Global Health, University of Chicago School of Medicine, The University of Chicago, Chicago, Illinois
| | - David C. Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, United Kingdom
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| |
Collapse
|
10
|
Hamilton AM, Van Alsten SC, Gao X, Nsonwu-Farley J, Calhoun BC, Love MI, Troester MA, Hoadley KA. Incorporating RNA-based Risk Scores for Genomic Instability to Predict Breast Cancer Recurrence and Immunogenicity in a Diverse Population. Cancer Res Commun 2023; 3:12-20. [PMID: 36968228 PMCID: PMC10035450 DOI: 10.1158/2767-9764.crc-22-0267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/26/2022] [Accepted: 12/19/2022] [Indexed: 04/12/2023]
Abstract
Markers of genomic instability, including TP53 status and homologous recombination deficiency (HRD), are candidate biomarkers of immunogenicity and immune-mediated survival, but little is known about the distribution of these markers in large, population-based cohorts of racially diverse patients with breast cancer. In prior clinical trials, DNA-based approaches have been emphasized, but recent data suggest that RNA-based assessment can capture pathway differences conveniently and may be streamlined with other RNA-based genomic risk scores. Thus, we used RNA expression to study genomic instability (HRD and TP53 pathways) in context of the breast cancer immune microenvironment in three datasets (total n = 4,892), including 1,942 samples from the Carolina Breast Cancer Study, a population-based study that oversampled Black (n = 1,026) and younger women (n = 1,032). Across all studies, 36.9% of estrogen receptor (ER)-positive and 92.6% of ER-negative breast cancer had presence of at least one genomic instability signature. TP53 and HRD status were significantly associated with immune expression in both ER-positive and ER-negative breast cancer. RNA-based genomic instability signatures were associated with higher PD-L1, CD8 T-cell marker, and global and multimarker immune cell expression. Among tumors with genomic instability signatures, adaptive immune response was associated with improved recurrence-free survival regardless of ER status, highlighting genomic instability as a candidate marker for predicting immunotherapy response. Leveraging a convenient, integrated RNA-based approach, this analysis shows that genomic instability interacts with immune response, an important target in breast cancer overall and in Black women who experience higher frequency of TP53 and HR deficiency. Significance Despite promising advances in breast cancer immunotherapy, predictive biomarkers that are valid across diverse populations and breast cancer subtypes are needed. Genomic instability signatures can be coordinated with other RNA-based scores to define immunogenic breast cancers and may have value in stratifying immunotherapy trial participants.
Collapse
Affiliation(s)
- Alina M. Hamilton
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sarah C. Van Alsten
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Xiaohua Gao
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joseph Nsonwu-Farley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Benjamin C. Calhoun
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Melissa A. Troester
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Katherine A. Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| |
Collapse
|
11
|
Walens A, Van Alsten SC, Olsson LT, Smith MA, Lockhart A, Gao X, Hamilton AM, Kirk EL, Love MI, Gupta GP, Perou CM, Vaziri C, Hoadley KA, Troester MA. RNA-Based Classification of Homologous Recombination Deficiency in Racially Diverse Patients with Breast Cancer. Cancer Epidemiol Biomarkers Prev 2022; 31:2136-2147. [PMID: 36129803 PMCID: PMC9720427 DOI: 10.1158/1055-9965.epi-22-0590] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/03/2022] [Accepted: 09/14/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Aberrant expression of DNA repair pathways such as homologous recombination (HR) can lead to DNA repair imbalance, genomic instability, and altered chemotherapy response. DNA repair imbalance may predict prognosis, but variation in DNA repair in diverse cohorts of breast cancer patients is understudied. METHODS To identify RNA-based patterns of DNA repair expression, we performed unsupervised clustering on 51 DNA repair-related genes in the Cancer Genome Atlas Breast Cancer [TCGA BRCA (n = 1,094)] and Carolina Breast Cancer Study [CBCS (n = 1,461)]. Using published DNA-based HR deficiency (HRD) scores (high-HRD ≥ 42) from TCGA, we trained an RNA-based supervised classifier. Unsupervised and supervised HRD classifiers were evaluated in association with demographics, tumor characteristics, and clinical outcomes. RESULTS : Unsupervised clustering on DNA repair genes identified four clusters of breast tumors, with one group having high expression of HR genes. Approximately 39.7% of CBCS and 29.3% of TCGA breast tumors had this unsupervised high-HRD (U-HRD) profile. A supervised HRD classifier (S-HRD) trained on TCGA had 84% sensitivity and 73% specificity to detect HRD-high samples. Both U-HRD and S-HRD tumors in CBCS had higher frequency of TP53 mutant-like status (45% and 41% enrichment) and basal-like subtype (63% and 58% enrichment). S-HRD high was more common among black patients. Among chemotherapy-treated participants, recurrence was associated with S-HRD high (HR: 2.38, 95% confidence interval = 1.50-3.78). CONCLUSIONS HRD is associated with poor prognosis and enriched in the tumors of black women. IMPACT RNA-level indicators of HRD are predictive of breast cancer outcomes in diverse populations.
Collapse
Affiliation(s)
- Andrea Walens
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Sarah C. Van Alsten
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Linnea T. Olsson
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Markia A. Smith
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Alex Lockhart
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Xiaohua Gao
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Alina M. Hamilton
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Erin L. Kirk
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gaorav P. Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Melissa A. Troester
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| |
Collapse
|
12
|
Fackler MJ, Tulac S, Venkatesan N, Aslam AJ, de Guzman T, Mercado-Rodriguez C, Cope LM, Downs BM, Vali AH, Ding W, Lehman J, Denbow R, Reynolds J, Buckley ME, Visvanathan K, Umbricht CB, Wolff AC, Stearns V, Bates M, Lai EW, Sukumar S. Development of an automated liquid biopsy assay for methylated markers in advanced breast cancer. Cancer Res Commun 2022; 2:391-401. [PMID: 36046124 PMCID: PMC9426415 DOI: 10.1158/2767-9764.crc-22-0133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/03/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022]
Abstract
Current molecular liquid biopsy assays to detect recurrence or monitor response to treatment require sophisticated technology, highly trained personnel, and a turnaround time of weeks. We describe the development and technical validation of an automated Liquid Biopsy for Breast Cancer Methylation (LBx-BCM) prototype, a DNA methylation detection cartridge assay that is simple to perform and quantitatively detects nine methylated markers within 4.5 h. LBx-BCM demonstrated high interassay reproducibility when analyzing exogenous methylated DNA (75-300 DNA copies) spiked into plasma (Coefficient of Variation, CV = 7.1 - 10.9%) and serum (CV = 19.1 - 36.1%). It also demonstrated high interuser reproducibility (Spearman r = 0.887, P < 0.0001) when samples of metastatic breast cancer (MBC, N = 11) and normal control (N = 4) were evaluated independently by two users. Analyses of interplatform reproducibility indicated very high concordance between LBx-BCM and the reference assay, cMethDNA, among 66 paired plasma samples (MBC N = 40, controls N = 26; Spearman r = 0.891; 95% CI = 0.825 - 0.933, P< 0.0001). LBx-BCM achieved a ROC AUC = 0.909 (95% CI = 0.836 - 0.982), 83% sensitivity and 92% specificity; cMethDNA achieved a ROC AUC = 0.896 (95% CI = 0.817 - 0.974), 83% sensitivity and 92% specificity in test set samples. The automated LBx-BCM cartridge prototype is fast, with performance levels equivalent to the highly sensitive, manual cMethDNA method. Future prospective clinical studies will evaluate LBx-BCM detection sensitivity and its ability to monitor therapeutic response during treatment for advanced breast cancer.
Collapse
Affiliation(s)
- Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | | | | | | | - Leslie M. Cope
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bradley M. Downs
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Abdul Hussain Vali
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wanjun Ding
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Jennifer Lehman
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rita Denbow
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeffrey Reynolds
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Morgan E. Buckley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kala Visvanathan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Antonio C. Wolff
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vered Stearns
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
13
|
Axelrod ML, Wang Y, Xu Y, Sun X, Bejan CA, Gonzalez-Ericsson PI, Nunnery S, Bergman RE, Donaldson J, Guerrero-Zotano AL, Massa C, Seliger B, Sanders M, Mayer IA, Balko JM. Peripheral Blood Monocyte Abundance Predicts Outcomes in Patients with Breast Cancer. Cancer Res Commun 2022; 2:286-292. [PMID: 36304942 PMCID: PMC9604512 DOI: 10.1158/2767-9764.crc-22-0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/02/2022] [Accepted: 04/21/2022] [Indexed: 04/27/2023]
Abstract
Biomarkers of response are needed in breast cancer to stratify patients to appropriate therapies and avoid unnecessary toxicity. We used peripheral blood gene expression and cell type abundance to identify biomarkers of response and recurrence in neoadjuvant chemotherapy treated breast cancer patients. We identified a signature of interferon and complement response that was higher in the blood of patients with pathologic complete response. This signature was preferentially expressed by monocytes in single cell RNA sequencing. Monocytes are routinely measured clinically, enabling examination of clinically measured monocytes in multiple independent cohorts. We found that peripheral monocytes were higher in patients with good outcomes in four cohorts of breast cancer patients. Blood gene expression and cell type abundance biomarkers may be useful for prognostication in breast cancer. Significance Biomarkers are needed in breast cancer to identify patients at risk for recurrence. Blood is an attractive site for biomarker identification due to the relative ease of longitudinal sampling. Our study suggests that blood-based gene expression and cell type abundance biomarkers may have clinical utility in breast cancer.
Collapse
Affiliation(s)
- Margaret L. Axelrod
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yu Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiaopeng Sun
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cosmin A. Bejan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Sara Nunnery
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Riley E. Bergman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joshua Donaldson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Chiara Massa
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Melinda Sanders
- Breast Cancer Research Program, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ingrid A. Mayer
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Breast Cancer Research Program, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Justin M. Balko
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Breast Cancer Research Program, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| |
Collapse
|
14
|
Gao Y, Kabotyanski EB, Shepherd JH, Villegas E, Acosta D, Hamor C, Sun T, Montmeyor-Garcia C, He X, Dobrolecki LE, Westbrook TF, Lewis MT, Hilsenbeck SG, Zhang XHF, Perou CM, Rosen JM. Tumor suppressor PLK2 may serve as a biomarker in triple-negative breast cancer for improved response to PLK1 therapeutics. Cancer Res Commun 2021; 1:178-193. [PMID: 35156101 PMCID: PMC8827906 DOI: 10.1158/2767-9764.crc-21-0106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Polo-like kinase (PLK) family members play important roles in cell cycle regulation. The founding member PLK1 is oncogenic and preclinically validated as a cancer therapeutic target. Paradoxically, frequent loss of chromosome 5q11-35 which includes PLK2 is observed in basal-like breast cancer. In this study, we found that PLK2 was tumor suppressive in breast cancer, preferentially in basal-like and triple-negative breast cancer (TNBC) subtypes. Knockdown of PLK1 rescued phenotypes induced by PLK2-loss both in vitro and in vivo. We also demonstrated that PLK2 directly interacted with PLK1 at prometaphase through the kinase but not the polo-box domains of PLK2, suggesting PLK2 functioned at least partially through the interaction with PLK1. Furthermore, an improved treatment response was seen in both Plk2-deleted/low mouse preclinical and PDX TNBC models using the PLK1 inhibitor volasertib alone or in combination with carboplatin. Re-expression of PLK2 in an inducible PLK2-null mouse model reduced the therapeutic efficacy of volasertib. In summary, this study delineates the effects of chromosome 5q loss in TNBC that includes PLK2, the relationship between PLK2 and PLK1, and how this may render PLK2-deleted/low tumors more sensitive to PLK1 inhibition in combination with chemotherapy.
Collapse
Affiliation(s)
- Yang Gao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Elena B. Kabotyanski
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | | | | | - Deanna Acosta
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Clark Hamor
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Tingting Sun
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | | | - Xiaping He
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lacey E. Dobrolecki
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Thomas F. Westbrook
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Michael T. Lewis
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Susan G. Hilsenbeck
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Xiang H.-F. Zhang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- McNair Medical Institute, Baylor College of Medicine, Houston, Texas
| | - Charles M. Perou
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffrey M. Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Corresponding Author: Jeffrey M. Rosen, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030. Phone: 832-215-9503; E-mail:
| |
Collapse
|
15
|
Uretmen Kagiali ZC, Sanal E, Karayel Ö, Polat AN, Saatci Ö, Ersan PG, Trappe K, Renard BY, Önder TT, Tuncbag N, Şahin Ö, Ozlu N. Systems-level Analysis Reveals Multiple Modulators of Epithelial-mesenchymal Transition and Identifies DNAJB4 and CD81 as Novel Metastasis Inducers in Breast Cancer. Mol Cell Proteomics 2019; 18:1756-1771. [PMID: 31221721 PMCID: PMC6731077 DOI: 10.1074/mcp.ra119.001446] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/21/2019] [Indexed: 01/01/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is driven by complex signaling events that induce dramatic biochemical and morphological changes whereby epithelial cells are converted into cancer cells. However, the underlying molecular mechanisms remain elusive. Here, we used mass spectrometry based quantitative proteomics approach to systematically analyze the post-translational biochemical changes that drive differentiation of human mammary epithelial (HMLE) cells into mesenchymal. We identified 314 proteins out of more than 6,000 unique proteins and 871 phosphopeptides out of more than 7,000 unique phosphopeptides as differentially regulated. We found that phosphoproteome is more unstable and prone to changes during EMT compared with the proteome and multiple alterations at proteome level are not thoroughly represented by transcriptional data highlighting the necessity of proteome level analysis. We discovered cell state specific signaling pathways, such as Hippo, sphingolipid signaling, and unfolded protein response (UPR) by modeling the networks of regulated proteins and potential kinase-substrate groups. We identified two novel factors for EMT whose expression increased on EMT induction: DnaJ heat shock protein family (Hsp40) member B4 (DNAJB4) and cluster of differentiation 81 (CD81). Suppression of DNAJB4 or CD81 in mesenchymal breast cancer cells resulted in decreased cell migration in vitro and led to reduced primary tumor growth, extravasation, and lung metastasis in vivo Overall, we performed the global proteomic and phosphoproteomic analyses of EMT, identified and validated new mRNA and/or protein level modulators of EMT. This work also provides a unique platform and resource for future studies focusing on metastasis and drug resistance.
Collapse
Affiliation(s)
| | - Erdem Sanal
- ‡Department of Molecular Biology and Genetics, Koç University, 34450 Istanbul, Turkey
| | - Özge Karayel
- ‡Department of Molecular Biology and Genetics, Koç University, 34450 Istanbul, Turkey
| | - Ayse Nur Polat
- ‡Department of Molecular Biology and Genetics, Koç University, 34450 Istanbul, Turkey
| | - Özge Saatci
- §Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208
| | - Pelin Gülizar Ersan
- ¶Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800 Ankara, Turkey
| | - Kathrin Trappe
- ‖Bioinformatics Unit (MF1), Robert Koch Institute, 13353 Berlin, Germany
| | - Bernhard Y Renard
- ‖Bioinformatics Unit (MF1), Robert Koch Institute, 13353 Berlin, Germany
| | - Tamer T Önder
- **Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey; ‡‡School of Medicine, Koç University, 34450 Istanbul, Turkey
| | - Nurcan Tuncbag
- §§Graduate School of Informatics, Department of Health Informatics, METU, 06800 Ankara, Turkey; ¶¶Cancer Systems Biology Laboratory (CanSyL), METU, 06800 Ankara, Turkey
| | - Özgür Şahin
- §Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208; ¶Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800 Ankara, Turkey
| | - Nurhan Ozlu
- ‡Department of Molecular Biology and Genetics, Koç University, 34450 Istanbul, Turkey; **Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey.
| |
Collapse
|
16
|
Song X, Ji J, Gleason KJ, Yang F, Martignetti JA, Chen LS, Wang P. Insights into Impact of DNA Copy Number Alteration and Methylation on the Proteogenomic Landscape of Human Ovarian Cancer via a Multi-omics Integrative Analysis. Mol Cell Proteomics 2019; 18:S52-S65. [PMID: 31227599 PMCID: PMC6692782 DOI: 10.1074/mcp.ra118.001220] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 06/19/2019] [Indexed: 12/19/2022] Open
Abstract
In this work, we propose iProFun, an integrative analysis tool to screen for proteogenomic functional traits perturbed by DNA copy number alterations (CNAs) and DNA methylations. The goal is to characterize functional consequences of DNA copy number and methylation alterations in tumors and to facilitate screening for cancer drivers contributing to tumor initiation and progression. Specifically, we consider three functional molecular quantitative traits: mRNA expression levels, global protein abundances, and phosphoprotein abundances. We aim to identify those genes whose CNAs and/or DNA methylations have cis-associations with either some or all three types of molecular traits. Compared with analyzing each molecular trait separately, the joint modeling of multi-omics data enjoys several benefits: iProFun experienced enhanced power for detecting significant cis-associations shared across different omics data types, and it also achieved better accuracy in inferring cis-associations unique to certain type(s) of molecular trait(s). For example, unique associations of CNAs/methylations to global/phospho protein abundances may imply posttranslational regulations.We applied iProFun to ovarian high-grade serous carcinoma tumor data from The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium and identified CNAs and methylations of 500 and 121 genes, respectively, affecting the cis-functional molecular quantitative traits of the corresponding genes. We observed substantial power gain via the joint analysis of iProFun. For example, iProFun identified 117 genes whose CNAs were associated with phosphoprotein abundances by leveraging mRNA expression levels and global protein abundances. By comparison, analyses based on phosphoprotein data alone identified none. A network analysis of these 117 genes revealed the known oncogene AKT1 as a key hub node interacting with many of the rest. In addition, iProFun identified one gene, BIN2, whose DNA methylation has cis-associations with its mRNA expression, global protein, and phosphoprotein abundances. These and other genes identified by iProFun could serve as potential drug targets for ovarian cancer.
Collapse
Affiliation(s)
- Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kevin J Gleason
- Department of Public Health Sciences, The University of Chicago, Chicago, IL
| | - Fan Yang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Anschutz Medical Campus, Aurora, CO
| | - John A Martignetti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lin S Chen
- Department of Public Health Sciences, The University of Chicago, Chicago, IL.
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY.
| |
Collapse
|