1
|
Jackson-Spence F, Ackerman C, Jones R, Toms C, Jovaisaite A, Young M, Hussain S, Protheroe A, Birtle A, Chakraborti P, Huddart R, Jagdev S, Bahl A, Sundar S, Crabb S, Powles T, Szabados B. Biomarkers associated with survival in patients with platinum-refractory urothelial carcinoma treated with paclitaxel. Urol Oncol 2024:S1078-1439(24)00491-5. [PMID: 39025719 DOI: 10.1016/j.urolonc.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 05/18/2024] [Accepted: 05/19/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Taxane- based chemotherapy is widely used in patients with platinum- and immunotherapy refractory, metastatic urothelial carcinoma (mUC). Outcomes are poor and biomarkers associated with outcome are lacking. We aim to identify cancer hallmarks associated with survival in patients receiving paclitaxel. METHODS Whole-transcriptome profiles were generated for a subset of patients enrolled in a randomised phase II study investigating paclitaxel and pazopanib in platinum refractory mUC (PLUTO, EudraCT 2011-001841-34). Estimates of gene expression were calculated and input into the Almac proprietary analysis pipeline and signature scores were calculated using ClaraT V3.0.0. Ten key gene signatures were assessed: Immuno-Oncology, Epithelial to Mesenchymal Transition, Angiogenesis, Proliferation, Cell Death, Genome Instability, Energetics, Inflammation, Immortality and Evading Growth. Hazard ratios were calculated using Cox regression model and Kaplan-Meier methods were used to estimate progression free survival (PFS) and overall survival (OS). RESULTS 38 and 45 patients treated with paclitaxel or pazopanib were included. Patients with high genome instability expression treated with paclitaxel had significantly improved survival with a HR of 0.29 (95% CI: 0.14-0.61, p=0.001) and HR 0.34 (95% CI: 0.17-0.69, p=0.003) for PFS and OS, respectively. Similarly, patients with high evading growth suppressor expression treated with paclitaxel had improved PFS and OS with a HR of 0.35 (95% CI: 0.19-0.77, p=0.007) and HR 0.46 (95% CI: 0.23-0.91, p=0.026), respectively. No other gene signatures had significant impact on outcome. In both paclitaxel and pazopanib cohorts, angiogenesis activation was associated with worse PFS and OS, and VEGF targeted therapy did not improve outcomes. CONCLUSION High Genome-instability and Evading-growth suppressor biologies are associated with improved survival in patients with platinum refractory mUC receiving paclitaxel. These may refine mUC risk stratification and guide treatment decision in the future.
Collapse
Affiliation(s)
| | - Charlotte Ackerman
- Department of Genitourinary Oncology, Barts Cancer Institute, QMUL, London, UK
| | - Robert Jones
- Department of Genitourinary Oncology, University of Glasgow, Glasgow, Scotland, UK
| | - Charlotte Toms
- Department of Genitourinary Oncology, Barts Cancer Institute, QMUL, London, UK
| | - Agne Jovaisaite
- Department of Genitourinary Oncology, Barts Cancer Institute, QMUL, London, UK
| | - Matthew Young
- Department of Genitourinary Oncology, Barts Cancer Institute, QMUL, London, UK
| | - Syed Hussain
- Department of Genitourinary Oncology, University of Liverpool, Liverpool, UK
| | - Andrew Protheroe
- Department of Genitourinary Oncology, Churchill Hospital, Oxford, UK
| | - Alison Birtle
- Department of Genitourinary Oncology, Preston Hospital, Preston, UK
| | - Prabir Chakraborti
- Department of Genitourinary Oncology, Derby Hospitals NHS Foundation trust, Derby, UK
| | - Robert Huddart
- Department of Genitourinary Oncology, Institute of Cancer Research, Sutton, UK
| | - Santinder Jagdev
- Department of Genitourinary Oncology, St James's University Hospital, Leeds, UK
| | - Amit Bahl
- Department of Genitourinary Oncology, Bristol Haematology and Oncology Centre, Bristol, UK
| | - Santhanam Sundar
- Department of Genitourinary Oncology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Simon Crabb
- Department of Genitourinary Oncology, University of Southampton, Southampton UK
| | - Thomas Powles
- Department of Genitourinary Oncology, Barts Cancer Institute, QMUL, London, UK.
| | - Bernadett Szabados
- Department of Genitourinary Oncology, Barts Cancer Institute, QMUL, London, UK
| |
Collapse
|
2
|
McGrail DJ, Li Y, Smith RS, Feng B, Dai H, Hu L, Dennehey B, Awasthi S, Mendillo ML, Sood AK, Mills GB, Lin SY, Yi SS, Sahni N. Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins. Cell Rep Med 2023; 4:101255. [PMID: 37909041 PMCID: PMC10694618 DOI: 10.1016/j.xcrm.2023.101255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/02/2022] [Accepted: 09/29/2023] [Indexed: 11/02/2023]
Abstract
Defects in homologous recombination DNA repair (HRD) both predispose to cancer development and produce therapeutic vulnerabilities, making it critical to define the spectrum of genetic events that cause HRD. However, we found that mutations in BRCA1/2 and other canonical HR genes only identified 10%-20% of tumors that display genomic evidence of HRD. Using a networks-based approach, we discovered that over half of putative genes causing HRD originated outside of canonical DNA damage response genes, with a particular enrichment for RNA-binding protein (RBP)-encoding genes. These putative drivers of HRD were experimentally validated, cross-validated in an independent cohort, and enriched in cancer-associated genome-wide association study loci. Mechanistic studies indicate that some RBPs are recruited to sites of DNA damage to facilitate repair, whereas others control the expression of canonical HR genes. Overall, this study greatly expands the repertoire of known drivers of HRD, with implications for basic biology, genetic screening, and therapy stratification.
Collapse
Affiliation(s)
- Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44106, USA; Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA.
| | - Yang Li
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roger S Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Bin Feng
- GSK Oncology Experimental Medicine Unit, Waltham, MA 02451, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Limei Hu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Briana Dennehey
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sharad Awasthi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Cell, Development and Cancer Biology, Knight Cancer Institute, Oregon Health and Sciences University, Portland, OR 97201, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
3
|
Chang SH, Ice RJ, Chen M, Sidorov M, Woo RWL, Rodriguez-Brotons A, Jian D, Kim HK, Kim A, Stone DE, Nazarian A, Oh A, Tranah GJ, Nosrati M, de Semir D, Dar AA, Desprez PY, Kashani-Sabet M, Soroceanu L, McAllister SD. Pan-Cancer Pharmacogenomic Analysis of Patient-Derived Tumor Cells Using Clinically Relevant Drug Exposures. Mol Cancer Ther 2023; 22:1100-1111. [PMID: 37440705 DOI: 10.1158/1535-7163.mct-22-0486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/11/2022] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
As a result of tumor heterogeneity and solid cancers harboring multiple molecular defects, precision medicine platforms in oncology are most effective when both genetic and pharmacologic determinants of a tumor are evaluated. Expandable patient-derived xenograft (PDX) mouse tumor and corresponding PDX culture (PDXC) models recapitulate many of the biological and genetic characteristics of the original patient tumor, allowing for a comprehensive pharmacogenomic analysis. Here, the somatic mutations of 23 matched patient tumor and PDX samples encompassing four cancers were first evaluated using next-generation sequencing (NGS). 19 antitumor agents were evaluated across 78 patient-derived tumor cultures using clinically relevant drug exposures. A binarization threshold sensitivity classification determined in culture (PDXC) was used to identify tumors that best respond to drug in vivo (PDX). Using this sensitivity classification, logic models of DNA mutations were developed for 19 antitumor agents to predict drug response. We determined that the concordance of somatic mutations across patient and corresponding PDX samples increased as variant allele frequency increased. Notable individual PDXC responses to specific drugs, as well as lineage-specific drug responses were identified. Robust responses identified in PDXC were recapitulated in vivo in PDX-bearing mice and logic modeling determined somatic gene mutation(s) defining response to specific antitumor agents. In conclusion, combining NGS of primary patient tumors, high-throughput drug screen using clinically relevant doses, and logic modeling, can provide a platform for understanding response to therapeutic drugs targeting cancer.
Collapse
Affiliation(s)
- Stephen H Chang
- University of California at San Francisco, School of Pharmacy, Department of Clinical Pharmacy, San Francisco, California
| | - Ryan J Ice
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Michelle Chen
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Maxim Sidorov
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Rinette W L Woo
- California Pacific Medical Center Research Institute, San Francisco, California
| | | | - Damon Jian
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Han Kyul Kim
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Angela Kim
- California Pacific Medical Center Research Institute, San Francisco, California
| | - David E Stone
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Ari Nazarian
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Alyssia Oh
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Mehdi Nosrati
- California Pacific Medical Center Research Institute, San Francisco, California
| | - David de Semir
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Altaf A Dar
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Pierre-Yves Desprez
- California Pacific Medical Center Research Institute, San Francisco, California
| | | | - Liliana Soroceanu
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Sean D McAllister
- California Pacific Medical Center Research Institute, San Francisco, California
| |
Collapse
|
4
|
Zhang C, Guo Q, Chen L, Wu Z, Yan XJ, Zou C, Zhang Q, Tan J, Fang T, Rao Q, Li Y, Shen S, Deng M, Wang L, Gao H, Yu J, Li H, Zhang C, Nowsheen S, Kloeber J, Zhao F, Yin P, Teng C, Lin Z, Song K, Yao S, Yao L, Wu L, Zhang Y, Cheng X, Gao Q, Yuan J, Lou Z, Zhang JS. A ribosomal gene panel predicting a novel synthetic lethality in non-BRCAness tumors. Signal Transduct Target Ther 2023; 8:183. [PMID: 37160887 PMCID: PMC10170152 DOI: 10.1038/s41392-023-01401-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/04/2023] [Accepted: 02/27/2023] [Indexed: 05/11/2023] Open
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors are one of the most exciting classes of targeted therapy agents for cancers with homologous recombination (HR) deficiency. However, many patients without apparent HR defects also respond well to PARP inhibitors/cisplatin. The biomarker responsible for this mechanism remains unclear. Here, we identified a set of ribosomal genes that predict response to PARP inhibitors/cisplatin in HR-proficient patients. PARP inhibitor/cisplatin selectively eliminates cells with high expression of the eight genes in the identified panel via DNA damage (ATM) signaling-induced pro-apoptotic ribosomal stress, which along with ATM signaling-induced pro-survival HR repair constitutes a new model to balance the cell fate in response to DNA damage. Therefore, the combined examination of the gene panel along with HR status would allow for more precise predictions of clinical response to PARP inhibitor/cisplatin. The gene panel as an independent biomarker was validated by multiple published clinical datasets, as well as by an ovarian cancer organoids library we established. More importantly, its predictive value was further verified in a cohort of PARP inhibitor-treated ovarian cancer patients with both RNA-seq and WGS data. Furthermore, we identified several marketed drugs capable of upregulating the expression of the genes in the panel without causing HR deficiency in PARP inhibitor/cisplatin-resistant cell lines. These drugs enhance PARP inhibitor/cisplatin sensitivity in both intrinsically resistant organoids and cell lines with acquired resistance. Together, our study identifies a marker gene panel for HR-proficient patients and reveals a broader application of PARP inhibitor/cisplatin in cancer therapy.
Collapse
Affiliation(s)
- Chao Zhang
- Beijing Institute of Basic Medical Sciences, 100850, Beijing, China
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qiang Guo
- School of Pharmaceutical Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Lifeng Chen
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, 310014, Hangzhou, Zhejiang, China
- Department of Gynecology, Zhejiang Provincial People's Hospital, 310014, Hangzhou, Zhejiang, China
| | - Zheming Wu
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xiao-Jian Yan
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang, China
| | - Chengyang Zou
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang, China
| | - Qiuxue Zhang
- Wuhan Kingwise Biotechnology Co., Ltd., 430206, Wuhan, Hubei, China
| | - Jiahong Tan
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Tian Fang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Qunxian Rao
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, Guangdong, China
| | - Yang Li
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, 310006, Hangzhou, Zhejiang, China
| | - Shizhen Shen
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, 310006, Hangzhou, Zhejiang, China
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Somaira Nowsheen
- Department of Dermatology, University of California San Diego, San Diego, CA, 92122, USA
| | - Jake Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Chunbo Teng
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, 150040, Harbin, China
| | - Zhongqiu Lin
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, Guangdong, China
| | - Kun Song
- Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 250012, Jinan, Shandong, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-Sen University, 510080, Guangzhou, Guangdong, China
| | - Liangqing Yao
- Department of Gynecologic Oncology, Obstetrics and Gynecology Hospital of Fudan University, 200090, Shanghai, China
| | - Lingying Wu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yong Zhang
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Xiaodong Cheng
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, 310006, Hangzhou, Zhejiang, China.
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, 310006, Hangzhou, Zhejiang, China.
| | - Qinglei Gao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China.
| | - Jian Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, 200120, Shanghai, China.
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, 200120, Shanghai, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jin-San Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, 324000, Quzhou, Zhejiang, China.
- Medical Research Center, and Key Laboratory of Interventional Pulmonology of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang, China.
| |
Collapse
|
5
|
Clinical Utility of Genomic Tests Evaluating Homologous Recombination Repair Deficiency (HRD) for Treatment Decisions in Early and Metastatic Breast Cancer. Cancers (Basel) 2023; 15:cancers15041299. [PMID: 36831640 PMCID: PMC9954086 DOI: 10.3390/cancers15041299] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/17/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Breast cancer is the most frequently occurring cancer worldwide. With its increasing incidence, it is a major public health problem, with many therapeutic challenges such as precision medicine for personalized treatment. Thanks to next-generation sequencing (NGS), progress in biomedical technologies, and the use of bioinformatics, it is now possible to identify specific molecular alterations in tumor cells-such as homologous recombination deficiencies (HRD)-enabling us to consider using DNA-damaging agents such as platinum salts or PARP inhibitors. Different approaches currently exist to analyze impairment of the homologous recombination pathway, e.g., the search for specific mutations in homologous recombination repair (HRR) genes, such as BRCA1/2; the use of genomic scars or mutational signatures; or the development of functional tests. Nevertheless, the role and value of these different tests in breast cancer treatment decisions remains to be clarified. In this review, we summarize current knowledge on the clinical utility of genomic tests, evaluating HRR deficiency for treatment decisions in early and metastatic breast cancer.
Collapse
|
6
|
Punzón-Jiménez P, Lago V, Domingo S, Simón C, Mas A. Molecular Management of High-Grade Serous Ovarian Carcinoma. Int J Mol Sci 2022; 23:13777. [PMID: 36430255 PMCID: PMC9692799 DOI: 10.3390/ijms232213777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) represents the most common form of epithelial ovarian carcinoma. The absence of specific symptoms leads to late-stage diagnosis, making HGSOC one of the gynecological cancers with the worst prognosis. The cellular origin of HGSOC and the role of reproductive hormones, genetic traits (such as alterations in P53 and DNA-repair mechanisms), chromosomal instability, or dysregulation of crucial signaling pathways have been considered when evaluating prognosis and response to therapy in HGSOC patients. However, the detection of HGSOC is still based on traditional methods such as carbohydrate antigen 125 (CA125) detection and ultrasound, and the combined use of these methods has yet to support significant reductions in overall mortality rates. The current paradigm for HGSOC management has moved towards early diagnosis via the non-invasive detection of molecular markers through liquid biopsies. This review presents an integrated view of the relevant cellular and molecular aspects involved in the etiopathogenesis of HGSOC and brings together studies that consider new horizons for the possible early detection of this gynecological cancer.
Collapse
Affiliation(s)
- Paula Punzón-Jiménez
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
| | - Victor Lago
- Department of Gynecologic Oncology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
- Department of Obstetrics and Gynecology, CEU Cardenal Herrera University, 46115 Valencia, Spain
| | - Santiago Domingo
- Department of Gynecologic Oncology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Universidad de Valencia, 46010 Valencia, Spain
| | - Carlos Simón
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Universidad de Valencia, 46010 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Harvard University, Boston, MA 02215, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aymara Mas
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
| |
Collapse
|
7
|
The Differential Metabolic Signature of Breast Cancer Cellular Response to Olaparib Treatment. Cancers (Basel) 2022; 14:cancers14153661. [PMID: 35954325 PMCID: PMC9367310 DOI: 10.3390/cancers14153661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 01/25/2023] Open
Abstract
Simple Summary Breast cancer remains a leading cause of female cancer related mortality worldwide. Loss of genomic stability and dysregulation of cellular metabolism are well-recognized features of breast cancer, presenting an opportunity to study the drivers of breast cancer progression and resistance to chemotherapy. The overarching goal of this work is to perform combined analysis of DNA damage repair and cellular metabolism in response to olaparib treatment in a panel of breast cancer cell lines. By applying a combined untargeted metabolomics and molecular biology approach, our findings show dysregulation of amino acid metabolism and metabolic reprogramming from glycolysis to amino acid utilization to be a common feature in all breast cancer cell lines examined, some of which are consistent with findings from the analysis of clinical breast cancer tumours. Functional assessment of genetic alterations offers the scope to design new prognostic tools and inform the design of new chemotherapies or drug combinations. Abstract Metabolic reprogramming and genomic instability are key hallmarks of cancer, the combined analysis of which has gained recent popularity. Given the emerging evidence indicating the role of oncometabolites in DNA damage repair and its routine use in breast cancer treatment, it is timely to fingerprint the impact of olaparib treatment in cellular metabolism. Here, we report the biomolecular response of breast cancer cell lines with DNA damage repair defects to olaparib exposure. Following evaluation of olaparib sensitivity in breast cancer cell lines, we immunoprobed DNA double strand break foci and evaluated changes in cellular metabolism at various olaparib treatment doses using untargeted mass spectrometry-based metabolomics analysis. Following identification of altered features, we performed pathway enrichment analysis to measure key metabolic changes occurring in response to olaparib treatment. We show a cell-line-dependent response to olaparib exposure, and an increased susceptibility to DNA damage foci accumulation in triple-negative breast cancer cell lines. Metabolic changes in response to olaparib treatment were cell-line and dose-dependent, where we predominantly observed metabolic reprogramming of glutamine-derived amino acids and lipids metabolism. Our work demonstrates the effectiveness of combining molecular biology and metabolomics studies for the comprehensive characterisation of cell lines with different genetic profiles. Follow-on studies are needed to map the baseline metabolism of breast cancer cells and their unique response to drug treatment. Fused with genomic and transcriptomics data, such readout can be used to identify key oncometabolites and inform the rationale for the design of novel drugs or chemotherapy combinations.
Collapse
|
8
|
McSwain LF, Parwani KK, Shahab SW, Hambardzumyan D, MacDonald TJ, Spangle JM, Kenney AM. Medulloblastoma and the DNA Damage Response. Front Oncol 2022; 12:903830. [PMID: 35747808 PMCID: PMC9209741 DOI: 10.3389/fonc.2022.903830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children with standard of care consisting of surgery, radiation, and chemotherapy. Recent molecular profiling led to the identification of four molecularly distinct MB subgroups – Wingless (WNT), Sonic Hedgehog (SHH), Group 3, and Group 4. Despite genomic MB characterization and subsequent tumor stratification, clinical treatment paradigms are still largely driven by histology, degree of surgical resection, and presence or absence of metastasis rather than molecular profile. Patients usually undergo resection of their tumor followed by craniospinal radiation (CSI) and a 6 month to one-year multi-agent chemotherapeutic regimen. While there is clearly a need for development of targeted agents specific to the molecular alterations of each patient, targeting proteins responsible for DNA damage repair could have a broader impact regardless of molecular subgrouping. DNA damage response (DDR) protein inhibitors have recently emerged as targeted agents with potent activity as monotherapy or in combination in different cancers. Here we discuss the molecular underpinnings of genomic instability in MB and potential avenues for exploitation through DNA damage response inhibition.
Collapse
Affiliation(s)
- Leon F. McSwain
- Department of Pediatrics, Emory University, Atlanta, GA, United States
| | - Kiran K. Parwani
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
- Department of Radiation Oncology, Emory University, Atlanta, GA, United States
| | - Shubin W. Shahab
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
| | - Dolores Hambardzumyan
- Departments of Neurosurgery and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tobey J. MacDonald
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
| | - Jennifer M. Spangle
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
- Department of Radiation Oncology, Emory University, Atlanta, GA, United States
| | - Anna Marie Kenney
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- *Correspondence: Anna Marie Kenney,
| |
Collapse
|
9
|
Schrank TP, Prince AC, Sathe T, Wang X, Liu X, Alzhanov DT, Burtness B, Baldwin AS, Yarbrough WG, Issaeva N. NF-κB over-activation portends improved outcomes in HPV-associated head and neck cancer. Oncotarget 2022; 13:707-722. [PMID: 35634245 PMCID: PMC9131933 DOI: 10.18632/oncotarget.28232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022] Open
Abstract
Evolving understanding of head and neck squamous cell carcinoma (HNSCC) is leading to more specific diagnostic disease classifications. Among HNSCC caused by the human papilloma virus (HPV), tumors harboring defects in TRAF3 or CYLD are associated with improved clinical outcomes and maintenance of episomal HPV. TRAF3 and CYLD are negative regulators of NF-κB and inactivating mutations of either leads to NF-κB overactivity. Here, we developed and validated a gene expression classifier separating HPV+ HNSCCs based on NF-κB activity. As expected, the novel classifier is strongly enriched in NF-κB targets leading us to name it the NF-κB Activity Classifier (NAC). High NF-κB activity correlated with improved survival in two independent cohorts. Using NAC, tumors with high NF-κB activity but lacking defects in TRAF3 or CYLD were identified; thus, while TRAF3 or CYLD gene defects identify the majority of tumors with NF-κB activation, unknown mechanisms leading to NF-kB activity also exist. The NAC correctly classified the functional consequences of two novel CYLD missense mutations. Using a reporter assay, we tested these CYLD mutations revealing that their activity to inhibit NF-kB was equivalent to the wild-type protein. Future applications of the NF-κB Activity Classifier may be to identify HPV+ HNSCC patients with better or worse survival with implications for treatment strategies.
Collapse
Affiliation(s)
- Travis P. Schrank
- Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA
- These authors contributed equally to this work
| | - Andrew C. Prince
- Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA
- These authors contributed equally to this work
| | - Tejas Sathe
- Department of Surgery, Otolaryngology, Yale, New Haven, CT 06519, USA
- Current address: Department of Surgery, Columbia University, New York, NY 10032, USA
| | - Xiaowei Wang
- Department of Pharmacology and Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
- Bioinformatics Core, University of Illinois Cancer Center, Chicago, IL 60612, USA
| | - Xinyi Liu
- Department of Pharmacology and Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
- Bioinformatics Core, University of Illinois Cancer Center, Chicago, IL 60612, USA
| | - Damir T. Alzhanov
- Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA
| | - Barbara Burtness
- Department of Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Albert S. Baldwin
- Department of Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Wendell G. Yarbrough
- Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA
- Lineberger Cancer Center, UNC, Chapel Hill, NC 27599, USA
- Department of Pathology and Laboratory Medicine, UNC, Chapel Hill, NC 27599, USA
- Senior authors
| | - Natalia Issaeva
- Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA
- Lineberger Cancer Center, UNC, Chapel Hill, NC 27599, USA
- Department of Pathology and Laboratory Medicine, UNC, Chapel Hill, NC 27599, USA
- Senior authors
| |
Collapse
|
10
|
Computational Screening of Anti-Cancer Drugs Identifies a New BRCA Independent Gene Expression Signature to Predict Breast Cancer Sensitivity to Cisplatin. Cancers (Basel) 2022; 14:cancers14102404. [PMID: 35626009 PMCID: PMC9139442 DOI: 10.3390/cancers14102404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Using a collection of publicly available drug screening resources, we identified different partners of genes associated with either sensitivity or resistance to 90 anti-cancer therapies. When subsequently applying these signatures to multiple datasets, we found that these predictive models could predict a large range of drug responses in patient samples. In particular, we discovered a new gene signature to identify breast cancer tumors that are likely to respond to cisplatin in the absence of BRCA1 mutations. This work constitutes an important advance to accelerate the application of platinum-based therapies in patient groups that are not routinely treated with these drugs. In the future, this approach may help to guide the choice of drugs based on the molecular profile of the tumors. Abstract The development of therapies that target specific disease subtypes has dramatically improved outcomes for patients with breast cancer. However, survival gains have not been uniform across patients, even within a given molecular subtype. Large collections of publicly available drug screening data matched with transcriptomic measurements have facilitated the development of computational models that predict response to therapy. Here, we generated a series of predictive gene signatures to estimate the sensitivity of breast cancer samples to 90 drugs, comprising FDA-approved drugs or compounds in early development. To achieve this, we used a cell line-based drug screen with matched transcriptomic data to derive in silico models that we validated in large independent datasets obtained from cell lines and patient-derived xenograft (PDX) models. Robust computational signatures were obtained for 28 drugs and used to predict drug efficacy in a set of PDX models. We found that our signature for cisplatin can be used to identify tumors that are likely to respond to this drug, even in absence of the BRCA-1 mutation routinely used to select patients for platinum-based therapies. This clinically relevant observation was confirmed in multiple PDXs. Our study foreshadows an effective delivery approach for precision medicine.
Collapse
|
11
|
Perez J, Twigg CAI, Guan W, Thomas SN. Proteomic Analysis Reveals Low-Dose PARP Inhibitor-Induced Differential Protein Expression in BRCA1-Mutated High-Grade Serous Ovarian Cancer Cells. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:242-250. [PMID: 34958553 PMCID: PMC8824432 DOI: 10.1021/jasms.1c00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 06/14/2023]
Abstract
High-grade serous ovarian cancer (HGSOC) is the most common form of ovarian cancer diagnosed in patients worldwide. Patients with BRCA1/2-mutated HGSOC have benefited from targeted treatments such as poly(ADP-ribose) polymerase inhibitors (PARPi). Despite the initial success of PARPi-based ovarian cancer treatment regimens, approximately 70% of patients with ovarian cancer relapse and the 5-year survival rate remains at 30%. PARPi exhibit variable treatment efficacy and toxicity profiles. Furthermore, the off-target effects of PARP inhibition have not yet been fully elucidated, warranting further study of these classes of molecules in the context of HGSOC treatment. Highly reproducible quantitative mass spectrometry-based proteomic workflows have been developed for the analysis of tumor tissues and cell lines. To detect the off-target effects of PARP inhibition, we conducted a quantitative mass spectrometry-based proteomic analysis of a BRCA1-mutated HGSOC cell line treated with low doses of two PARPi, niraparib and rucaparib. Our goal was to identify PARPi-induced protein signaling pathway alterations toward a more comprehensive elucidation of the mechanism of action of PARPi beyond the DNA damage response pathway. A significant enrichment of nuclear and nucleoplasm proteins that are involved in protein binding was observed in the rucaparib-treated cells. Shared upregulated proteins between niraparib and rucaparib treatment demonstrated RNA II pol promoter-associated pathway enrichment in transcription regulation. Pathway enrichment analyses also revealed off-target effects in the Golgi apparatus and the ER. The results from our mass spectrometry-based proteomic analysis highlights notable off-target effects produced by low-dose treatment of BRCA1-mutated HGSOC cells treated with rucaparib or niraparib.
Collapse
Affiliation(s)
- Jesenia
M. Perez
- Microbiology,
Immunology, and Cancer Biology Graduate Program, University of Minnesota School of Medicine, Minneapolis, Minnesota 55455, United States
| | - Carly A. I. Twigg
- Department
of Laboratory Medicine and Pathology, University
of Minnesota School of Medicine, Minneapolis, Minnesota 55455, United States
| | - Weihua Guan
- Division
of Biostatistics, University of Minnesota
School of Public Health, Minneapolis, Minnesota 55455, United States
| | - Stefani N. Thomas
- Department
of Laboratory Medicine and Pathology, University
of Minnesota School of Medicine, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
12
|
Stolzenburg LR, Ainsworth B, Riley-Gillis B, Pakozdi T, Ammar A, Ellis PA, Wilsbacher JL, Ramathal CY. Transcriptomics reveals in vivo efficacy of PARP inhibitor combinatorial synergy with platinum-based chemotherapy in human non-small cell lung carcinoma models. Oncotarget 2022; 13:1-12. [PMID: 35018214 PMCID: PMC8729805 DOI: 10.18632/oncotarget.28162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 12/05/2022] Open
Abstract
Inhibitors of poly(ADP)-ribose polymerase (PARP) exploit defective DNA repair pathways existing in several forms of cancer, such as those with BRCA mutations, and have proven clinical efficacy as chemosensitizers. However, platinum-based chemopotentiation by PARP inhibitors (PARPi), particularly for non-small cell lung cancer (NSCLC), has only been confirmed in a few preclinical models and the molecular mechanisms that drive PARPi combinatorial synergy with chemotherapeutics remains poorly defined. To better understand these mechanisms, we characterized cisplatin and veliparib efficacy in A549 and Calu6 NSCLC in vivo tumor xenograft models and observed combinatorial synergy in the Calu6 model. Transcriptome-wide analysis of xenografts revealed several differentially expressed genes (DEGs) between untreated and cisplatin + veliparib-treated groups, which were unique from genes identified in either of the single-agent treatment arms. Particularly at 10- and 21-days post-treatment, these DEGs were enriched within pathways involved in DNA damage repair, cell cycle regulation, and senescence. Furthermore, TGF-β- and integrin-related pathways were enriched in the combination treatment arm, while pathways involved in cholesterol metabolism were identified at earlier time points in both the combination and cisplatin-only groups. These data advance the biological underpinnings of PARPi combined with platinum-based chemotherapy and provides additional insight into the diverse sensitivity of NSCLC models.
Collapse
Affiliation(s)
- Lindsay R Stolzenburg
- AbbVie Inc., North Chicago, IL 60064, USA.,These authors contributed equally to this work
| | - Barrett Ainsworth
- AbbVie Inc., North Chicago, IL 60064, USA.,These authors contributed equally to this work
| | | | | | | | | | | | | |
Collapse
|
13
|
Sankaranarayanan RA, Peil J, Vogg ATJ, Bolm C, Terhorst S, Classen A, Bauwens M, Maurer J, Mottaghy F, Morgenroth A. Auger Emitter Conjugated PARP Inhibitor for Therapy in Triple Negative Breast Cancers: A Comparative In-Vitro Study. Cancers (Basel) 2022; 14:cancers14010230. [PMID: 35008392 PMCID: PMC8750932 DOI: 10.3390/cancers14010230] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer, with a high recurrence rate. Since treatment of BRCAmut TNBC patients with PARP inhibitor (PARPi), targeting the nuclear protein PARP1, shows varied responses, its therapeutic efficacy is currently evaluated in combination with chemotherapy. Auger emitters (AEs) are radionuclides that can cause DNA damage when delivered close to the DNA. Due to the nuclear location of PARP1, radiolabelling of PARPi with AEs provide an efficient nuclear delivery mechanism. This study shows the radiosynthesis of an AE radiolabelled PARPi ([125I]-PARPi-01) and its therapeutic effect as monotherapy or in combination with chemotherapeutics in a panel of TNBC cell lines. We found that [125I]-PARPi-01 efficiently induces DNA damage with therapeutic effect irrespective of BRCA mutation. All responsive cell lines have homologous recombination deficiency. Short pretreatment with doxorubicin significantly reduces clonogenic survival of both responsive and resistant cell lines. Abstract PARP1 inhibitors (PARPi) are currently approved for BRCAmut metastatic breast cancer, but they have shown limited response in triple negative breast cancer (TNBC) patients. Combination of an Auger emitter with PARPis enables PARP inhibition and DNA strand break induction simultaneously. This will enhance cytotoxicity and additionally allow a theranostic approach. This study presents the radiosynthesis of the Auger emitter [125I] coupled olaparib derivative: [125I]-PARPi-01, and its therapeutic evaluation in a panel of TNBC cell lines. Specificity was tested by a blocking assay. DNA strand break induction was analysed by γH2AX immunofluorescence staining. Cell cycle analysis and apoptosis assays were studied using flow cytometry in TNBC cell lines (BRCAwt/mut). Anchorage independent growth potential was evaluated using soft agar assay. [125I]-PARPi-01 showed PARP1-specificity and higher cytotoxicity than olaparib in TNBC cell lines irrespective of BRCA their status. Cell lines harbouring DNA repair deficiency showed response to [125I]-PARPi-01 monotherapy. Combined treatment with Dox-NP further enhanced therapeutic efficiency in metastatic resistant BRCAwt cell lines. The clonogenic survival was significantly reduced after treatment with [125I]-PARPi-01 in all TNBC lines investigated. Therapeutic efficacy was further enhanced after combined treatment with chemotherapeutics. [125I]-PARPi-01 is a promising radiotherapeutic agent for low radiation dosages, and mono/combined therapies of TNBC.
Collapse
Affiliation(s)
- Ramya Ambur Sankaranarayanan
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (R.A.S.); (J.P.); (A.T.J.V.); (M.B.); (F.M.)
| | - Jennifer Peil
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (R.A.S.); (J.P.); (A.T.J.V.); (M.B.); (F.M.)
| | - Andreas T. J. Vogg
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (R.A.S.); (J.P.); (A.T.J.V.); (M.B.); (F.M.)
| | - Carsten Bolm
- Institute of Organic Chemistry, RWTH Aachen University, 52056 Aachen, Germany; (C.B.); (S.T.); (A.C.)
| | - Steven Terhorst
- Institute of Organic Chemistry, RWTH Aachen University, 52056 Aachen, Germany; (C.B.); (S.T.); (A.C.)
| | - Arno Classen
- Institute of Organic Chemistry, RWTH Aachen University, 52056 Aachen, Germany; (C.B.); (S.T.); (A.C.)
| | - Matthias Bauwens
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (R.A.S.); (J.P.); (A.T.J.V.); (M.B.); (F.M.)
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center (MUMC+), 6229HX Maastricht, The Netherlands
- School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229HX Maastricht, The Netherlands
| | - Jochen Maurer
- Department of Molecular Gynecology, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany;
| | - Felix Mottaghy
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (R.A.S.); (J.P.); (A.T.J.V.); (M.B.); (F.M.)
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center (MUMC+), 6229HX Maastricht, The Netherlands
| | - Agnieszka Morgenroth
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (R.A.S.); (J.P.); (A.T.J.V.); (M.B.); (F.M.)
- Correspondence:
| |
Collapse
|
14
|
Federico L, McGrail DJ, Bentebibel SE, Haymaker C, Ravelli A, Forget MA, Karpinets T, Jiang P, Reuben A, Negrao MV, Li J, Khairullah R, Zhang J, Weissferdt A, Vaporciyan AA, Antonoff MB, Walsh G, Lin SY, Futreal A, Wistuba I, Roth J, Byers LA, Gaudreau PO, Uraoka N, Cruz AF, Dejima H, Lazcano RN, Solis LM, Parra ER, Lee JJ, Swisher S, Cascone T, Heymach JV, Zhang J, Sepesi B, Gibbons DL, Bernatchez C. Distinct tumor-infiltrating lymphocyte landscapes are associated with clinical outcomes in localized non-small-cell lung cancer. Ann Oncol 2022; 33:42-56. [PMID: 34653632 PMCID: PMC10019222 DOI: 10.1016/j.annonc.2021.09.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/11/2021] [Accepted: 09/30/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Despite the importance of tumor-infiltrating T lymphocytes (TILs) in cancer biology, the relationship between TIL phenotypes and their prognostic relevance for localized non-small-cell lung cancer (NSCLC) has not been well established. PATIENTS AND METHODS Fresh tumor and normal adjacent tissue was prospectively collected from 150 patients with localized NSCLC. Tissue was comprehensively characterized by high-dimensional flow cytometry of TILs integrated with immunogenomic data from multiplex immunofluorescence, T-cell receptor sequencing, exome sequencing, RNA sequencing, targeted proteomics, and clinicopathologic features. RESULTS While neither the magnitude of TIL infiltration nor specific TIL subsets were significantly prognostic alone, the integration of high-dimensional flow cytometry data identified two major immunotypes (IM1 and IM2) that were predictive of recurrence-free survival independent of clinical characteristics. IM2 was associated with poor prognosis and characterized by the presence of proliferating TILs expressing cluster of differentiation 103, programmed cell death protein 1, T-cell immunoglobulin and mucin-domain containing protein 3, and inducible T-cell costimulator. Conversely, IM1 was associated with good prognosis and differentiated by an abundance of CD8+ T cells expressing cytolytic enzymes, CD4+ T cells lacking the expression of inhibitory receptors, and increased levels of B-cell infiltrates and tertiary lymphoid structures. While increased B-cell infiltration was associated with good prognosis, the best prognosis was observed in patients with tumors exhibiting high levels of both B cells and T cells. These findings were validated in patient tumors from The Cancer Genome Atlas. CONCLUSIONS Our study suggests that although the number of infiltrating T cells is not associated with patient survival, the nature of the infiltrating T cells, resolved in distinct TIL immunotypes, is prognostically relevant in NSCLC and may inform therapeutic approaches to clinical care.
Collapse
Affiliation(s)
- L Federico
- Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S-E Bentebibel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Ravelli
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M-A Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - P Jiang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Khairullah
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Weissferdt
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - G Walsh
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S-Y Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - L A Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - P-O Gaudreau
- Department of Oncology, Queens' University and the Canadian Cancer Trials Group, Kingston, Canada
| | - N Uraoka
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A F Cruz
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Dejima
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R N Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - L M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J J Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - B Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - D L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - C Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
| |
Collapse
|
15
|
Martincuks A, Song J, Kohut A, Zhang C, Li YJ, Zhao Q, Mak E, Rodriguez-Rodriguez L, Yu H, Cristea M. PARP Inhibition Activates STAT3 in Both Tumor and Immune Cells Underlying Therapy Resistance and Immunosuppression In Ovarian Cancer. Front Oncol 2021; 11:724104. [PMID: 34956861 PMCID: PMC8693573 DOI: 10.3389/fonc.2021.724104] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Despite the promising activity of poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) in many cancer types with defects in the DNA damage response the majority of the treated patients acquire PARPi resistance and succumb to their diseases. Consequently, there is an urgent need to identify the mechanisms of PARPi resistance. Here, we show that PARPi treatment promotes STAT3 activation in ovarian cancer cells, tumor-associated immune cells and fibroblasts, resulting in PARPi resistance and immunosuppression. Comparison of ovarian cancer patient-matched tumor biopsies before and after PARPi therapy revealed that STAT3 activity was significantly higher in tumor cells and tumor-associated immune cells and fibroblasts post PARPi treatment. Moreover, one-time PARPi treatment activated STAT3 both in tumor cells as well as diverse immune subsets and fibroblasts. PARPi-treated immune cells exhibited decreased expression of immunostimulatory interferon (IFN)-γ and Granzyme B while increasing immunosuppressive cytokine IL-10. Finally, we demonstrate that the acquisition of PARPi resistance in ovarian cancer cells was accompanied by increased STAT3 activity. Ablating STAT3 inhibited PARPi-resistant ovarian tumor cell growth and/or restored PARPi sensitivity. Therefore, our study has identified a critical mechanism intrinsic to PARPi that promotes resistance to PARPi and induces immunosuppression during PARPi treatment by activating STAT3 in tumor cells and tumor-associated immune cells/fibroblasts.
Collapse
Affiliation(s)
- Antons Martincuks
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center (COH), Duarte, CA, United States
| | - Jieun Song
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center (COH), Duarte, CA, United States
| | - Adrian Kohut
- Department of Surgery, Division of Gynecologic Oncology, City of Hope National Medical Center (COH), Duarte, CA, United States
| | - Chunyan Zhang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center (COH), Duarte, CA, United States
| | - Yi-Jia Li
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center (COH), Duarte, CA, United States
| | - Qianqian Zhao
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center (COH), Duarte, CA, United States
| | - Edward Mak
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center (COH), Duarte, CA, United States
| | - Lorna Rodriguez-Rodriguez
- Department of Surgery, Division of Gynecologic Oncology, City of Hope National Medical Center (COH), Duarte, CA, United States
| | - Hua Yu
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center (COH), Duarte, CA, United States
| | - Mihaela Cristea
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center (COH), Duarte, CA, United States
| |
Collapse
|
16
|
Shah MA, Cunningham D, Metges JP, Van Cutsem E, Wainberg Z, Elboudwarej E, Lin KW, Turner S, Zavodovskaya M, Inzunza D, Liu J, Patterson SD, Zhou J, He J, Thai D, Bhargava P, Brachmann CB, Cantenacci DVT. Randomized, open-label, phase 2 study of andecaliximab plus nivolumab versus nivolumab alone in advanced gastric cancer identifies biomarkers associated with survival. J Immunother Cancer 2021; 9:jitc-2021-003580. [PMID: 34893523 PMCID: PMC8666898 DOI: 10.1136/jitc-2021-003580] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 12/13/2022] Open
Abstract
Background Matrix metalloproteinase-9 (MMP9) selectively cleaves extracellular matrix proteins contributing to tumor growth and an immunosuppressive microenvironment. This study evaluated andecaliximab (ADX), an inhibitor of MMP9, in combination with nivolumab (NIVO), for the treatment of advanced gastric cancer. Methods Phase 2, open-label, randomized multicenter study evaluating the efficacy, safety, and pharmacodynamics of ADX+NIVO versus NIVO in patients with pretreated metastatic gastric or gastroesophageal junction (GEJ) adenocarcinoma. The primary endpoint was objective response rate (ORR). Secondary endpoints included progression-free survival (PFS), overall survival (OS), and adverse events (AEs). We explored the correlation of efficacy outcomes with biomarkers. Results 144 patients were randomized; 141 were treated: 81% white, 69% male, median age was 61 years in the ADX+NIVO group and 62 years in the NIVO-alone group. The ORR was 10% (95% CI 4 to 19) in the ADX+NIVO group and 7% (95% CI 2 to 16) in the NIVO-alone group (OR: 1.5 (95% CI 0.4 to 6.1; p=0.8)). There was no response or survival benefit associated with adding ADX. AE rates were comparable in both treatment groups; the most common AEs were fatigue, decreased appetite, nausea, and vomiting. Programmed cell death ligand 1, interferon-γ (IFN), and intratumoral CD8+ cell density were not associated with treatment response or survival. The gene signature most correlated with shorter survival was the epithelial-to-mesenchymal gene signature; high transforming growth factor (TGF)-β fibrosis score was negatively associated with OS (p=0.036). Gene expression analysis of baseline tumors comparing long-(1+ years) and short-term (<1 year) survivors showed that GRB7 was associated with survival beyond 1 year. Human epidermal growth factor receptor 2 (HER2)-positive disease was associated with significantly longer survival (p=0.0077). Median tumor mutation burden (TMB) was 2.01; patients with TMB ≥median had longer survival (p=0.0025) and improved PFS (p=0.016). Based on a model accounting for TMB, TGF-β fibrosis, and HER2, TMB was the main driver of survival in this patient population. Conclusion Combination of ADX+NIVO had a favorable safety profile but did not improve efficacy compared with NIVO alone in patients with pretreated metastatic gastric or GEJ adenocarcinoma. HER2 positivity, higher TMB or GRB7, and lower TGF-β were associated with improved outcomes. Trial registration number NCT02864381 or GS-US-296–-2013.
Collapse
Affiliation(s)
- Manish A Shah
- Medicine, Weill Cornell Medicine, New York, New York, USA .,Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
| | - David Cunningham
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, Sutton and London Hospital, Sutton, UK
| | | | - Eric Van Cutsem
- Division Head of Digestive Oncology, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Zev Wainberg
- Gastrointestinal Medical Oncology, University of California Los Angeles School of Medicine, Los Angeles, California, USA
| | | | - Kai-Wen Lin
- Gilead Sciences, Inc, Foster City, California, USA
| | - Scott Turner
- Gilead Sciences, Inc, Foster City, California, USA
| | | | | | - Jinfeng Liu
- Gilead Sciences, Inc, Foster City, California, USA
| | | | - Jingzhu Zhou
- Gilead Sciences, Inc, Foster City, California, USA
| | - Jing He
- Gilead Sciences, Inc, Foster City, California, USA
| | - Dung Thai
- Gilead Sciences, Inc, Foster City, California, USA
| | | | | | - Daniel V T Cantenacci
- Biological Sciences Division, University of Chicago Medical Center, Chicago, Illinois, USA
| |
Collapse
|
17
|
Yordanova M, Hubert A, Hassan S. Expanding the Use of PARP Inhibitors as Monotherapy and in Combination in Triple-Negative Breast Cancer. Pharmaceuticals (Basel) 2021; 14:1270. [PMID: 34959671 PMCID: PMC8709256 DOI: 10.3390/ph14121270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, and is known to be associated with a poor prognosis and limited therapeutic options. Poly (ADP-ribose) polymerase inhibitors (PARPi) are targeted therapeutics that have demonstrated efficacy as monotherapy in metastatic BRCA-mutant (BRCAMUT) TNBC patients. Improved efficacy of PARPi has been demonstrated in BRCAMUT breast cancer patients who have either received fewer lines of chemotherapy or in chemotherapy-naïve patients in the metastatic, adjuvant, and neoadjuvant settings. Moreover, recent trials in smaller cohorts have identified anti-tumor activity of PARPi in TNBC patients, regardless of BRCA-mutation status. While there have been concerns regarding the efficacy and toxicity of the use of PARPi in combination with chemotherapy, these challenges can be mitigated with careful attention to PARPi dosing strategies. To better identify a patient subpopulation that will best respond to PARPi, several genomic biomarkers of homologous recombination deficiency have been tested. However, gene expression signatures associated with PARPi response can integrate different pathways in addition to homologous recombination deficiency and can be implemented in the clinic more readily. Taken together, PARPi have great potential for use in TNBC patients beyond BRCAMUT status, both as a single-agent and in combination.
Collapse
Affiliation(s)
- Mariya Yordanova
- Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
| | - Audrey Hubert
- Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3T5, Canada;
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), l’Institut de Cancer de Montreal, Montreal, QC H2X 0A9, Canada
| | - Saima Hassan
- Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3T5, Canada;
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), l’Institut de Cancer de Montreal, Montreal, QC H2X 0A9, Canada
- Division of Surgical Oncology, Department of Surgery, Centre Hospitalier de l’Université de Montréal (CHUM), Montreal, QC H2X 0C1, Canada
| |
Collapse
|
18
|
McGrail DJ, Pilié PG, Dai H, Lam TNA, Liang Y, Voorwerk L, Kok M, Zhang XHF, Rosen JM, Heimberger AB, Peterson CB, Jonasch E, Lin SY. Replication stress response defects are associated with response to immune checkpoint blockade in nonhypermutated cancers. Sci Transl Med 2021; 13:eabe6201. [PMID: 34705519 DOI: 10.1126/scitranslmed.abe6201] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick G Pilié
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Truong Nguyen Anh Lam
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yulong Liang
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leonie Voorwerk
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Marleen Kok
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.,Department of Medical Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Xiang H-F Zhang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.,McNair Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy B Heimberger
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.,Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Christine B Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
19
|
Berlow NE. Probabilistic Boolean Modeling of Pre-clinical Tumor Models for Biomarker Identification in Cancer Drug Development. Curr Protoc 2021; 1:e269. [PMID: 34661991 DOI: 10.1002/cpz1.269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
As high-throughput sequencing experiments become more widely used in pre-clinical and clinical settings, pharmacogenetic and pharmacogenomic biomarker development plays an increasingly important role in oncology drug development pipelines and programs. Consequently, computer-based learning approaches have entered into use at multiple stages in pre-clinical and clinical pipelines. However, few approaches are available to identify interpretable and implementable biomarkers of response early in the drug development process when only small pre-clinical data packages are available. To address the need for early-stage biomarker development using pre-clinical tumor models, we have adapted the previously published Probabilistic Target Inhibitor Map (PTIM) platform to the challenge of biomarker hypothesis development, and denoted this approach the Probabilistic Target Map-Biomarker (PTM-Biomarker). In this article, we detail the history and design philosophy of PTM-Biomarker, and present two case studies using the biomarker discovery tool to illustrate its utility in guiding cancer drug development. © 2021 Wiley Periodicals LLC.
Collapse
|
20
|
A Gene Expression Signature to Predict Nucleotide Excision Repair Defects and Novel Therapeutic Approaches. Int J Mol Sci 2021; 22:ijms22095008. [PMID: 34066883 PMCID: PMC8125907 DOI: 10.3390/ijms22095008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022] Open
Abstract
Nucleotide excision repair (NER) resolves DNA adducts, such as those caused by ultraviolet light. Deficient NER (dNER) results in a higher mutation rate that can predispose to cancer development and premature ageing phenotypes. Here, we used isogenic dNER model cell lines to establish a gene expression signature that can accurately predict functional NER capacity in both cell lines and patient samples. Critically, none of the identified NER deficient cell lines harbored mutations in any NER genes, suggesting that the prevalence of NER defects may currently be underestimated. Identification of compounds that induce the dNER gene expression signature led to the discovery that NER can be functionally impaired by GSK3 inhibition, leading to synergy when combined with cisplatin treatment. Furthermore, we predicted and validated multiple novel drugs that are synthetically lethal with NER defects using the dNER gene signature as a drug discovery platform. Taken together, our work provides a dynamic predictor of NER function that may be applied for therapeutic stratification as well as development of novel biological insights in human tumors.
Collapse
|
21
|
Precision oncology for breast cancer through clinical trials. Clin Exp Metastasis 2021; 39:71-78. [PMID: 33950412 DOI: 10.1007/s10585-021-10092-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/22/2021] [Indexed: 12/26/2022]
Abstract
Precision treatment for breast cancers has made several notable advances in recent decades, but challenges of tumor heterogeneity, drug resistance, and aggressive recurrence and metastases remain. To meet and overcome these challenges, we must refine our understanding of breast subtypes and treatment biomarkers according to the knowledge afforded across the spectrum of 'omics assays. A critical aspect of harnessing this knowledge into actionable biomarkers for treatment decision relies on our ability to integrate knowledge across data types and leverage our insight in evidence-based clinical trials. We review recent advances in cutting-edge clinical trials for precision treatment of breast cancer, including chemotherapies, targeted therapies, immunotherapies, and combination therapies. We comment on promising future areas of development for this exciting point in precision breast cancer research.
Collapse
|
22
|
Alay A, Cordero D, Hijazo-Pechero S, Aliagas E, Lopez-Doriga A, Marín R, Palmero R, Llatjós R, Escobar I, Ramos R, Padrones S, Moreno V, Nadal E, Solé X. Integrative transcriptome analysis of malignant pleural mesothelioma reveals a clinically relevant immune-based classification. J Immunother Cancer 2021; 9:jitc-2020-001601. [PMID: 33632900 PMCID: PMC7908918 DOI: 10.1136/jitc-2020-001601] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 12/24/2022] Open
Abstract
Background Malignant pleural mesothelioma (MPM) is a rare and aggressive neoplasia affecting the lung mesothelium. Immune checkpoint inhibitors (ICI) in MPM have not been extremely successful, likely due to poor identification of suitable candidate patients for the therapy. We aimed to identify cellular immune fractions associated with clinical outcome and classify patients with MPM based on their immune contexture. For each defined group, we sought for molecular specificities that could help further define our MPM classification at the genomic and transcriptomic level, as well as identify differential therapeutic strategies based on transcriptional signatures predictive of drug response. Methods The abundance of 20 immune cell fractions in 516 MPM samples from 7 gene expression datasets was inferred using gene set variation analysis. Identification of clinically relevant fractions was performed with Cox proportional-hazards models adjusted for age, stage, sex, and tumor histology. Immune-based groups were defined based on the identified fractions. Results T-helper 2 (TH2) and cytotoxic T (TC) cells were found to be consistently associated with overall survival. Three immune clusters (IG) were subsequently defined based on TH2 and TC immune infiltration levels: IG1 (54.5%) was characterized by high TH2 and low TC levels, IG2 (37%) had either low or high levels of both fractions, and IG3 (8.5%) was defined by low TH2 and high TC levels. IG1 and IG3 groups were associated with worse and better overall survival, respectively. While no differential genomic alterations were identified among immune groups, at the transcriptional level, IG1 samples showed upregulation of proliferation signatures, while IG3 samples presented upregulation of immune and inflammation-related pathways. Finally, the integration of gene expression with functional signatures of drug response showed that IG3 patients might be more likely to respond to ICI. Conclusions This study identifies a novel immune-based signature with potential clinical relevance based on TH2 and TC levels, unveiling a fraction of patients with MPM with better prognosis and who might benefit from immune-based therapies. Molecular specificities of the different groups might be used to tailor specific potential therapies in the future.
Collapse
Affiliation(s)
- Ania Alay
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO)-Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - David Cordero
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO)-Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Biomedical Research Centre Network for Epidemiology & Public Health (CIBERESP), Madrid, Comunidad de Madrid, Spain
| | - Sara Hijazo-Pechero
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO)-Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Elisabet Aliagas
- Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Adriana Lopez-Doriga
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO)-Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Biomedical Research Centre Network for Epidemiology & Public Health (CIBERESP), Madrid, Comunidad de Madrid, Spain
| | - Raúl Marín
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO)-Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ramón Palmero
- Department of Medical Oncology, Catalan Institute of Oncology (ICO)-Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Roger Llatjós
- Department of Pathology, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ignacio Escobar
- Department of Thoracic Surgery, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ricard Ramos
- Department of Thoracic Surgery, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Susana Padrones
- Department of Respiratory Medicine, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Víctor Moreno
- Biomedical Research Centre Network for Epidemiology & Public Health (CIBERESP), Madrid, Comunidad de Madrid, Spain.,Oncology Data Analytics Program, Catalan Institute of Oncology (ICO)-Bellvitge Biomedical Research Institute (IDIBELL)-University of Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ernest Nadal
- Department of Medical Oncology, Catalan Institute of Oncology (ICO)-Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Solé
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO)-Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain .,Biomedical Research Centre Network for Epidemiology & Public Health (CIBERESP), Madrid, Comunidad de Madrid, Spain
| |
Collapse
|
23
|
Chiappa M, Guffanti F, Bertoni F, Colombo I, Damia G. Overcoming PARPi resistance: Preclinical and clinical evidence in ovarian cancer. Drug Resist Updat 2021; 55:100744. [PMID: 33551306 DOI: 10.1016/j.drup.2021.100744] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
Ovarian cancer is the fifth cause of cancer-related deaths in women with high grade serous carcinoma (HGSOC) representing the most common histological subtype. Approximately 50 % of HGSOC are characterized by deficiency in homologous recombination (HR), one of the main cellular pathways to repair DNA double strand breaks and one of the well-described mechanisms is the loss of function of the BRCA1 or BRCA2 genes. Inhibition of the poly-ADP-ribose polymerase (PARP) is synthetic lethal with HR deficiency and the use of PARP inhibitors (PARPi) has significantly improved the outcome of patients with HGSOC with a greater benefit in patients with BRCA1/2 deficient tumors. However, intrinsic or acquired resistance to PARPi inevitably occurs in most HGSOC patients. Distinct heterogeneous mechanisms underlying the resistance to PARPi have been described, including a decrease in intracellular drug levels due to upregulation of multidrug efflux pumps, loss of expression/inactivating mutations in the PARP1 protein, restoration of HR and the protection of the replicative fork. Deciphering the molecular mechanisms of resistance to PARPi is of paramount importance towards the development of new treatment strategies and/or novel pharmacological agents to overcome this chemoresistance and optimize the treatment regimen for individual HGSOC patients. The current review summarizes the mechanisms underlying the resistance to PARPi, the available preclinical and clinical data on new combination treatment strategies (with chemotherapy, anti-angiogenic agents and immune checkpoint inhibitors) as well as agents under investigation which target the DNA damage response.
Collapse
Affiliation(s)
- M Chiappa
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - F Guffanti
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - F Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland; Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | - I Colombo
- Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland.
| | - G Damia
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy.
| |
Collapse
|
24
|
Caracciolo D, Scionti F, Juli G, Altomare E, Golino G, Todoerti K, Grillone K, Riillo C, Arbitrio M, Iannone M, Morelli E, Amodio N, Di Martino MT, Rossi M, Neri A, Tagliaferri P, Tassone P. Exploiting MYC-induced PARPness to target genomic instability in multiple myeloma. Haematologica 2021; 106:185-195. [PMID: 32079692 PMCID: PMC7776341 DOI: 10.3324/haematol.2019.240713] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/17/2020] [Indexed: 11/09/2022] Open
Abstract
Multiple Myeloma (MM) is a hematologic malignancy strongly characterized by genomic instability, which promotes disease progression and drug resistance. Since we previously demonstrated that LIG3-dependent repair is involved in the genomic instability, drug resistance and survival of MM cells, we here investigated the biological relevance of PARP1, a driver component of Alternative-Non Homologous End Joining (Alt-NHEJ) pathway, in MM. We found a significant correlation between higher PARP1 mRNA expression and poor prognosis of MM patients. PARP1 knockdown or its pharmacological inhibition by Olaparib impaired MM cells viability in vitro and was effective against in vivo xenografts of human MM. Anti-proliferative effects induced by PARP1-inhibition were correlated to increase of DNA double-strand breaks, activation of DNA Damage Response (DDR) and finally apoptosis. Importantly, by comparing a gene expression signature of PARP inhibitors (PARPi) sensitivity to our plasma cell dyscrasia (PC) gene expression profiling (GEP), we identified a subset of MM patients which could benefit from PARP inhibitors. In particular, Gene Set Enrichment Analysis (GSEA) suggested that high MYC expression correlates to PARPi sensitivity in MM. Indeed, we identified MYC as promoter of PARP1-mediated repair in MM and, consistently, we demonstrate that cytotoxic effects induced by PARP inhibition are mostly detectable on MYC-proficient MM cells. Taken together, our findings indicate that MYC-driven MM cells are addicted to PARP1 Alt-NHEJ repair, which represents therefore a druggable target in this still incurable disease.
Collapse
Affiliation(s)
- Daniele Caracciolo
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | - Francesca Scionti
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro
| | - Giada Juli
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro
| | - Emanuela Altomare
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro
| | - Gaetanina Golino
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro
| | - Katia Todoerti
- University of Milan, Fondazione Cà Granda IRCCS Policlinico, Milan
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro
| | - Caterina Riillo
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | | | | | - Eugenio Morelli
- Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute,Boston, USA
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | | | - Marco Rossi
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro
| | - Antonino Neri
- University of Milan, Fondazione Cà Granda IRCCS Policlinico, Milan
| | | | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro
| |
Collapse
|
25
|
McIntosh MT, Koganti S, Boatwright JL, Li X, Spadaro SV, Brantly AC, Ayers JB, Perez RD, Burton EM, Burgula S, MacCarthy T, Bhaduri-McIntosh S. STAT3 imparts BRCAness by impairing homologous recombination repair in Epstein-Barr virus-transformed B lymphocytes. PLoS Pathog 2020; 16:e1008849. [PMID: 33002095 PMCID: PMC7529304 DOI: 10.1371/journal.ppat.1008849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/31/2020] [Indexed: 12/30/2022] Open
Abstract
Epstein-Barr virus (EBV) causes lymphomas and epithelial cell cancers. Though generally silent in B lymphocytes, this widely prevalent virus can cause endemic Burkitt lymphoma and post-transplant lymphoproliferative disorders/lymphomas in immunocompromised hosts. By learning how EBV breaches barriers to cell proliferation, we hope to undermine those strategies to treat EBV lymphomas and potentially other cancers. We had previously found that EBV, through activation of cellular STAT3 prevents phosphorylation of Chk1, and thereby, suppresses activation of the intra-S phase cell-cycle checkpoint, a potent barrier to oncogene-driven proliferation. This observation prompted us to examine the consequences on DNA repair since homologous recombination repair, the most error-free form, requires phosphoChk1. We now report that the defect in Chk1 phosphorylation also curtails RAD51 nucleation, and thereby, homologous recombination repair of DNA double strand breaks. The resulting reliance on error-prone microhomology-mediated end-joining (MMEJ) repair makes EBV-transformed cells susceptible to PARP inhibition and simultaneous accrual of genome-wide deletions and insertions resulting from synthesis-dependent MMEJ. Analysis of transcriptomic and drug susceptibility data from hundreds of cancer lines reveals a STAT3-dependent gene-set predictive of susceptibility of cancers to synthetic lethal PARP inhibition. These findings i) demonstrate how the tumor virus EBV re-shapes cellular DNA repair, ii) provide the first genome-wide evidence for insertions resulting from MMEJ in human cells, and iii) expand the range of cancers (EBV-related and -unrelated) that are likely to respond to synthetic lethal inhibitors given the high prevalence of cancers with constitutively active STAT3.
Collapse
Affiliation(s)
- Michael T. McIntosh
- Child Health Research Institute, Department of Pediatrics, University of Florida, Gainesville, FL, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, United States of America
- * E-mail: (MTM); (SBM)
| | - Siva Koganti
- Division of Infectious Diseases, Department of Pediatrics, Stony Brook University, Stony Brook, NY, United States of America
| | - J. Lucas Boatwright
- Bioinformatics Core Facility, University of Florida, Gainesville, FL, United States of America
| | - Xiaofan Li
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL, United States of America
| | - Salvatore V. Spadaro
- Division of Infectious Diseases, Department of Pediatrics, Stony Brook University, Stony Brook, NY, United States of America
| | - Alexis C. Brantly
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL, United States of America
| | - Jasmine B. Ayers
- Division of Infectious Diseases, Department of Pediatrics, Stony Brook University, Stony Brook, NY, United States of America
| | - Ramon D. Perez
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, United States of America
| | - Eric M. Burton
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL, United States of America
| | - Sandeepta Burgula
- Division of Infectious Diseases, Department of Pediatrics, Stony Brook University, Stony Brook, NY, United States of America
| | - Thomas MacCarthy
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, United States of America
| | - Sumita Bhaduri-McIntosh
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, United States of America
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL, United States of America
- * E-mail: (MTM); (SBM)
| |
Collapse
|
26
|
Le Page C, Amuzu S, Rahimi K, Gotlieb W, Ragoussis J, Tonin PN. Lessons learned from understanding chemotherapy resistance in epithelial tubo-ovarian carcinoma from BRCA1and BRCA2mutation carriers. Semin Cancer Biol 2020; 77:110-126. [PMID: 32827632 DOI: 10.1016/j.semcancer.2020.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
BRCA1 and BRCA2 are multi-functional proteins and key factors for maintaining genomic stability through their roles in DNA double strand break repair by homologous recombination, rescuing stalled or damaged DNA replication forks, and regulation of cell cycle DNA damage checkpoints. Impairment of any of these critical roles results in genomic instability, a phenotypic hallmark of many cancers including breast and epithelial ovarian carcinomas (EOC). Damaging, usually loss of function germline and somatic variants in BRCA1 and BRCA2, are important drivers of the development, progression, and management of high-grade serous tubo-ovarian carcinoma (HGSOC). However, mutations in these genes render patients particularly sensitive to platinum-based chemotherapy, and to the more innovative targeted therapies with poly-(ADP-ribose) polymerase inhibitors (PARPis) that are targeted to BRCA1/BRCA2 mutation carriers. Here, we reviewed the literature on the responsiveness of BRCA1/2-associated HGSOC to platinum-based chemotherapy and PARPis, and propose mechanisms underlying the frequent development of resistance to these therapeutic agents.
Collapse
Affiliation(s)
- Cécile Le Page
- McGill Research Institute of the McGill University Health Center, Montreal, QC, Canada.
| | - Setor Amuzu
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kurosh Rahimi
- Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Walter Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University, Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
| |
Collapse
|
27
|
Smeby J, Kryeziu K, Berg KCG, Eilertsen IA, Eide PW, Johannessen B, Guren MG, Nesbakken A, Bruun J, Lothe RA, Sveen A. Molecular correlates of sensitivity to PARP inhibition beyond homologous recombination deficiency in pre-clinical models of colorectal cancer point to wild-type TP53 activity. EBioMedicine 2020; 59:102923. [PMID: 32799124 PMCID: PMC7452640 DOI: 10.1016/j.ebiom.2020.102923] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/01/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND PARP inhibitors are active in various tumour types beyond BRCA-mutant cancers, but their activity and molecular correlates in colorectal cancer (CRC) are not well studied. METHODS Mutations and genome-wide mutational patterns associated with homologous recombination deficiency (HRD) were investigated in 255 primary CRCs with whole-exome sequencing and/or DNA copy number data. Efficacy of five PARP inhibitors and their molecular correlates were evaluated in 93 CRC cell lines partly annotated with mutational-, DNA copy number-, and/or gene expression profiles. Post-treatment gene expression profiling and specific protein expression analyses were performed in two pairs of PARP inhibitor sensitive and resistant cell lines. FINDINGS A subset of microsatellite stable (MSS) CRCs had truncating mutations in homologous recombination-related genes, but these were not associated with genomic signatures of HRD. Eight CRC cell lines (9%) were sensitive to PARP inhibition, but sensitivity was not predicted by HRD-related genomic and transcriptomic signatures. In contrast, drug sensitivity in MSS cell lines was strongly associated with TP53 wild-type status (odds ratio 15.7, p = 0.023) and TP53-related expression signatures. Increased downstream TP53 activity was among the primary response mechanisms, and TP53 inhibition antagonized the effect of PARP inhibitors. Wild-type TP53-mediated suppression of RAD51 was identified as a possible mechanism of action for sensitivity to PARP inhibition. INTERPRETATION PARP inhibitors are active in a subset of CRC cell lines and preserved TP53 function may increase the likelihood of response.
Collapse
Affiliation(s)
- Jørgen Smeby
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway;; K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Department of Oncology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kushtrim Kryeziu
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway;; K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway;; K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway;; K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway;; K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway;; K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marianne G Guren
- K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Gastroenterological Surgery, Oslo University Hospital, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway;; K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway;; K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway;; K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| |
Collapse
|
28
|
Pasculli B, Barbano R, Fontana A, Biagini T, Di Viesti MP, Rendina M, Valori VM, Morritti M, Bravaccini S, Ravaioli S, Maiello E, Graziano P, Murgo R, Copetti M, Mazza T, Fazio VM, Esteller M, Parrella P. Hsa-miR-155-5p Up-Regulation in Breast Cancer and Its Relevance for Treatment With Poly[ADP-Ribose] Polymerase 1 (PARP-1) Inhibitors. Front Oncol 2020; 10:1415. [PMID: 32903519 PMCID: PMC7435065 DOI: 10.3389/fonc.2020.01415] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/06/2020] [Indexed: 01/12/2023] Open
Abstract
miR-155-5p is a well-known oncogenic microRNA, showing frequent overexpression in human malignancies, including breast cancer. Here, we show that high miR-155-5p levels are associated with unfavorable prognostic factors in two independent breast cancer cohorts (CSS cohort, n = 283; and TCGA-BRCA dataset, n = 1,095). Consistently, miR-155-5p results as differentially expressed in the breast cancer subgroups identified by the surrogate molecular classification in the CSS cohort and the PAM50 classifier in TCGA-BRCA dataset, with the TNBC and HER2-amplified tumors carrying the highest levels. Since the analysis of TCGA-BC dataset also demonstrated a significant association between miR-155-5p levels and the presence of mutations in homologous recombination (HR) genes, we hypothesized that miR-155-5p might affect cell response to the PARP-1 inhibitor Olaparib. As expected, miR-155-5p ectopic overexpression followed by Olaparib administration resulted in a greater reduction of cell viability as compared to Olaparib administration alone, suggesting that miR-155-5p might induce a synthetic lethal effect in cancer cells when coupled with PARP-1-inhibition. Overall, our data point to a role of miR-155-5p in homologous recombination deficiency and suggest miR-155-5p might be useful in predicting response to PARP1 inhibitors in the clinical setting.
Collapse
Affiliation(s)
- Barbara Pasculli
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Laboratorio di Oncologia, San Giovanni Rotondo, Italy
| | - Raffaela Barbano
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Laboratorio di Oncologia, San Giovanni Rotondo, Italy
| | - Andrea Fontana
- Fondazione IRCCS Casa Sollievo Della Sofferenza, UO di Biostatistica, San Giovanni Rotondo, Italy
| | - Tommaso Biagini
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Laboratory of Bioinformatics Unit, San Giovanni Rotondo, Italy
| | - Maria Pia Di Viesti
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Laboratorio di Oncologia, San Giovanni Rotondo, Italy
| | - Michelina Rendina
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Laboratorio di Oncologia, San Giovanni Rotondo, Italy
| | - Vanna Maria Valori
- Fondazione IRCCS Casa Sollievo Della Sofferenza, UO di Oncologia, San Giovanni Rotondo, Italy
| | - Maria Morritti
- Fondazione IRCCS Casa Sollievo Della Sofferenza, UO di Oncologia, San Giovanni Rotondo, Italy
| | - Sara Bravaccini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Biosciences Laboratory, Meldola, Italy
| | - Sara Ravaioli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Biosciences Laboratory, Meldola, Italy
| | - Evaristo Maiello
- Fondazione IRCCS Casa Sollievo Della Sofferenza, UO di Oncologia, San Giovanni Rotondo, Italy
| | - Paolo Graziano
- Fondazione IRCCS Casa Sollievo Della Sofferenza, UO di Anatomia Patologica, San Giovanni Rotondo, Italy
| | - Roberto Murgo
- Fondazione IRCCS Casa Sollievo Della Sofferenza, UO di Chirurgia Senologica, San Giovanni Rotondo, Italy
| | - Massimiliano Copetti
- Fondazione IRCCS Casa Sollievo Della Sofferenza, UO di Biostatistica, San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Laboratory of Bioinformatics Unit, San Giovanni Rotondo, Italy
| | - Vito Michele Fazio
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Laboratorio di Oncologia, San Giovanni Rotondo, Italy
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Paola Parrella
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Laboratorio di Oncologia, San Giovanni Rotondo, Italy
| |
Collapse
|
29
|
Keung MY, Wu Y, Badar F, Vadgama JV. Response of Breast Cancer Cells to PARP Inhibitors Is Independent of BRCA Status. J Clin Med 2020; 9:jcm9040940. [PMID: 32235451 PMCID: PMC7231148 DOI: 10.3390/jcm9040940] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPi) have proven to be beneficial to patients with metastatic breast cancer with BRCA1/2 (BReast CAncer type 1 and type 2 genes) mutations. However, certain PARPi in pre-clinical studies have been shown to inhibit cell growth and promote the death of breast cancer cells lacking mutations in BRCA1/2. Here, we examined the inhibitory potency of 13 different PARPi in 12 breast cancer cell lines with and without BRCA-mutations using cell viability assays. The results showed that 5 of the 8 triple-negative breast cancer (TNBC) cell lines were susceptible to PARPi regardless of the BRCA-status. The estrogen receptor (ER) negative/ human epidermal growth factor receptor 2 (HER2) positive (ER-/HER2+) cells, SKBR3 and JIMT1, showed high sensitivity to Talazoparib. Especially JIMT1, which is known to be resistant to trastuzumab, was responsive to Talazoparib at 0.002 µM. Niraparib, Olaparib, and Rucaparib also demonstrated effective inhibitory potency in both advanced TNBC and ER-/HER2+ cells with and without BRCA-mutations. In contrast, a BRCA-mutant TNBC line, HCC1937, was less sensitive to Talazoparib, Niraparib, Rucaparib, and not responsive to Olaparib. Other PARPi such as UPF1069, NU1025, AZD2461, and PJ34HCl also showed potent inhibitory activity in specific breast cancer cells. Our data suggest that the benefit of PARPi therapy in breast cancer is beyond the BRCA-mutations, and equally effective on metastatic TNBC and ER-/HER2+ breast cancers.
Collapse
Affiliation(s)
- Man Yee Keung
- Division of Cancer Research and Training, Charles R. Drew University of Medicine and Science, Los Angeles, CA 90059, USA; (M.Y.K.); (F.B.)
| | - Yanyuan Wu
- Division of Cancer Research and Training, Charles R. Drew University of Medicine and Science, Los Angeles, CA 90059, USA; (M.Y.K.); (F.B.)
- David Geffen UCLA School of Medicine, Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Correspondence: (Y.W.); (J.V.V.)
| | - Francesca Badar
- Division of Cancer Research and Training, Charles R. Drew University of Medicine and Science, Los Angeles, CA 90059, USA; (M.Y.K.); (F.B.)
| | - Jaydutt V. Vadgama
- Division of Cancer Research and Training, Charles R. Drew University of Medicine and Science, Los Angeles, CA 90059, USA; (M.Y.K.); (F.B.)
- David Geffen UCLA School of Medicine, Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Correspondence: (Y.W.); (J.V.V.)
| |
Collapse
|
30
|
McGrail DJ, Garnett J, Yin J, Dai H, Shih DJH, Lam TNA, Li Y, Sun C, Li Y, Schmandt R, Wu JY, Hu L, Liang Y, Peng G, Jonasch E, Menter D, Yates MS, Kopetz S, Lu KH, Broaddus R, Mills GB, Sahni N, Lin SY. Proteome Instability Is a Therapeutic Vulnerability in Mismatch Repair-Deficient Cancer. Cancer Cell 2020; 37:371-386.e12. [PMID: 32109374 PMCID: PMC7337255 DOI: 10.1016/j.ccell.2020.01.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 11/22/2019] [Accepted: 01/30/2020] [Indexed: 12/30/2022]
Abstract
Deficient DNA mismatch repair (dMMR) induces a hypermutator phenotype that can lead to tumorigenesis; however, the functional impact of the high mutation burden resulting from this phenotype remains poorly explored. Here, we demonstrate that dMMR-induced destabilizing mutations lead to proteome instability in dMMR tumors, resulting in an abundance of misfolded protein aggregates. To compensate, dMMR cells utilize a Nedd8-mediated degradation pathway to facilitate clearance of misfolded proteins. Blockade of this Nedd8 clearance pathway with MLN4924 causes accumulation of misfolded protein aggregates, ultimately inducing immunogenic cell death in dMMR cancer cells. To leverage this immunogenic cell death, we combined MLN4924 treatment with PD1 inhibition and found the combination was synergistic, significantly improving efficacy over either treatment alone.
Collapse
Affiliation(s)
- Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Jeannine Garnett
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jun Yin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David J H Shih
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Truong Nguyen Anh Lam
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chaoyang Sun
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rosemarie Schmandt
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ji Yuan Wu
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Limei Hu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yulong Liang
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Melinda S Yates
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Karen H Lu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Russell Broaddus
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
31
|
Santiago-O’Farrill JM, Weroha SJ, Hou X, Oberg AL, Heinzen EP, Maurer MJ, Pang L, Rask P, Amaravadi RK, Becker SE, Romero I, Rubió MJ, Matias-Guiu X, Santacana M, Llombart-Cussac A, Poveda A, Lu Z, Bast RC. Poly(adenosine diphosphate ribose) polymerase inhibitors induce autophagy-mediated drug resistance in ovarian cancer cells, xenografts, and patient-derived xenograft models. Cancer 2020; 126:894-907. [PMID: 31714594 PMCID: PMC6992526 DOI: 10.1002/cncr.32600] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/07/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Poly(adenosine diphosphate ribose) polymerase (PARP) inhibitors exhibit promising activity against ovarian cancers, but their efficacy can be limited by acquired drug resistance. This study explores the role of autophagy in regulating the sensitivity of ovarian cancer cells to PARP inhibitors. METHODS Induction of autophagy was detected by punctate LC3 fluorescence staining, LC3I to LC3II conversion on Western blot analysis, and electron microscopy. Enhanced growth inhibition and apoptosis were observed when PARP inhibitors were used with hydroxychloroquine, chloroquine (CQ), or LYS05 to block the hydrolysis of proteins and lipids in autophagosomes or with small interfering RNA against ATG5 or ATG7 to prevent the formation of autophagosomes. The preclinical efficacy of the combination of CQ and olaparib was evaluated with a patient-derived xenograft (PDX) and the OVCAR8 human ovarian cancer cell line. RESULTS Four PARP inhibitors (olaparib, niraparib, rucaparib, and talazoparib) induced autophagy in a panel of ovarian cancer cells. Inhibition of autophagy with CQ enhanced the sensitivity of ovarian cancer cells to PARP inhibitors. In vivo, olaparib and CQ produced additive growth inhibition in OVCAR8 xenografts and a PDX. Olaparib inhibited PARP activity, and this led to increased reactive oxygen species (ROS) and an accumulation of γ-H2AX. Inhibition of autophagy also increased ROS and γ-H2AX and enhanced the effect of olaparib on both entities. Treatment with olaparib increased phosphorylation of ATM and PTEN while decreasing the phosphorylation of AKT and mTOR and inducing autophagy. CONCLUSIONS PARP inhibitor-induced autophagy provides an adaptive mechanism of resistance to PARP inhibitors in cancer cells with wild-type BRCA, and a combination of PARP inhibitors with CQ or other autophagy inhibitors could improve outcomes for patients with ovarian cancer.
Collapse
Affiliation(s)
| | | | - Xiaonan Hou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Ann L. Oberg
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ethan P. Heinzen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Matthew J. Maurer
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Lan Pang
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Philip Rask
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ravi K. Amaravadi
- Department of Medicine, Abramson Cancer Center, University of Pennsylvania, Philadelphia, USA
| | - Sarah E. Becker
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ignacio Romero
- Instituto Valenciano de Oncología, Valencia, Spain
- MedSIR, Barcelona, Spain
| | - M. Jesús Rubió
- Hospital Universitario Reina Sofía de Córdoba, Córdoba, Spain
- MedSIR, Barcelona, Spain
| | - X. Matias-Guiu
- Hospital U Arnau de Vilanova de Lleida, IRBLLEIDA, University of Lleida, CIBERONC
- MedSIR, Barcelona, Spain
| | - Maria Santacana
- Hospital U Arnau de Vilanova de Lleida, IRBLLEIDA, University of Lleida, CIBERONC
- MedSIR, Barcelona, Spain
| | | | - Andrés Poveda
- Instituto Valenciano de Oncología, Valencia, Spain
- MedSIR, Barcelona, Spain
| | - Zhen Lu
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Robert C. Bast
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
32
|
Abstract
In this review, Slade provides an overview of the molecular mechanisms and cellular consequences of PARP and PARG inhibition. The author also highlights the clinical performance of four PARP inhibitors used in cancer therapy (olaparib, rucaparib, niraparib, and talazoparib) and discusses the predictive biomarkers of inhibitor sensitivity and mechanisms of resistance as well as the means of overcoming them through combination therapy. Oxidative and replication stress underlie genomic instability of cancer cells. Amplifying genomic instability through radiotherapy and chemotherapy has been a powerful but nonselective means of killing cancer cells. Precision medicine has revolutionized cancer therapy by putting forth the concept of selective targeting of cancer cells. Poly(ADP-ribose) polymerase (PARP) inhibitors represent a successful example of precision medicine as the first drugs targeting DNA damage response to have entered the clinic. PARP inhibitors act through synthetic lethality with mutations in DNA repair genes and were approved for the treatment of BRCA mutated ovarian and breast cancer. PARP inhibitors destabilize replication forks through PARP DNA entrapment and induce cell death through replication stress-induced mitotic catastrophe. Inhibitors of poly(ADP-ribose) glycohydrolase (PARG) exploit and exacerbate replication deficiencies of cancer cells and may complement PARP inhibitors in targeting a broad range of cancer types with different sources of genomic instability. Here I provide an overview of the molecular mechanisms and cellular consequences of PARP and PARG inhibition. I highlight clinical performance of four PARP inhibitors used in cancer therapy (olaparib, rucaparib, niraparib, and talazoparib) and discuss the predictive biomarkers of inhibitor sensitivity, mechanisms of resistance as well as the means of overcoming them through combination therapy.
Collapse
Affiliation(s)
- Dea Slade
- Department of Biochemistry, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, 1030 Vienna, Austria
| |
Collapse
|
33
|
Tamhankar A, Tamhankar T. Hereditary Breast and Ovarian Cancer Syndrome (BRCA) Gene: Concept, Pathways, Therapeutics, and Future. Indian J Med Paediatr Oncol 2020. [DOI: 10.4103/ijmpo.ijmpo_172_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
AbstractHereditary breast and ovarian cancers are most commonly caused by mutations in BRCA1 and 2 genes. These are autosomal dominant mutations with high penetrance into subsequent generations. Affected individuals have deficiency in DNA repair mechanisms such as double strand DNA breaks (DSB) and non-homologous end joining (NHEJ). These tumors are peculiar due to early age of onset, typical histology such as triple negative breast cancers and high grade serous ovarian cancers and exquisite sensitivity to platinum analogues. These patients usually have better survival as compared to their wild type counterparts. Incidence of these mutations is rising due to better awareness about them amongst oncologists and patient population. Various genomic assays are available to detect germline and somatic BRCA mutations. Newer therapeutic frontiers like PARP inhibition have opened up due to better understanding of various mutations and their impact on subsequent pathways. Further studies are required to explore possibility of direct BRCA inhibition which may be useful in treatment of other solid organ cancers as well. This review focuses on understanding the pathophysiology of BRCA mutations, various pathways associated with the same, chemosensitivity patterns amongst affected cancer cells, targeted therapeutic opportunities and potential future developments in this field. We collected data from various published electronic records on google and have no conflicts of interest to be declared.
Collapse
Affiliation(s)
- Anup Tamhankar
- Deartment of Surgical Oncology, Deenanath Mangeshkar Hospital, Pune, Maharashtra, India
| | | |
Collapse
|
34
|
Jalili V, Afgan E, Taylor J, Goecks J. Cloud bursting galaxy: federated identity and access management. Bioinformatics 2020; 36:1-9. [PMID: 31197310 PMCID: PMC6956780 DOI: 10.1093/bioinformatics/btz472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/29/2019] [Accepted: 06/05/2019] [Indexed: 12/02/2022] Open
Abstract
MOTIVATION Large biomedical datasets, such as those from genomics and imaging, are increasingly being stored on commercial and institutional cloud computing platforms. This is because cloud-scale computing resources, from robust backup to high-speed data transfer to scalable compute and storage, are needed to make these large datasets usable. However, one challenge for large-scale biomedical data on the cloud is providing secure access, especially when datasets are distributed across platforms. While there are open Web protocols for secure authentication and authorization, these protocols are not in wide use in bioinformatics and are difficult to use for even technologically sophisticated users. RESULTS We have developed a generic and extensible approach for securely accessing biomedical datasets distributed across cloud computing platforms. Our approach combines OpenID Connect and OAuth2, best-practice Web protocols for authentication and authorization, together with Galaxy (https://galaxyproject.org), a web-based computational workbench used by thousands of scientists across the world. With our enhanced version of Galaxy, users can access and analyze data distributed across multiple cloud computing providers without any special knowledge of access/authorization protocols. Our approach does not require users to share permanent credentials (e.g. username, password, API key), instead relying on automatically generated temporary tokens that refresh as needed. Our approach is generalizable to most identity providers and cloud computing platforms. To the best of our knowledge, Galaxy is the only computational workbench where users can access biomedical datasets across multiple cloud computing platforms using best-practice Web security approaches and thereby minimize risks of unauthorized data access and credential use. AVAILABILITY AND IMPLEMENTATION Freely available for academic and commercial use under the open-source Academic Free License (https://opensource.org/licenses/AFL-3.0) from the following Github repositories: https://github.com/galaxyproject/galaxy and https://github.com/galaxyproject/cloudauthz.
Collapse
Affiliation(s)
- Vahid Jalili
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Enis Afgan
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - James Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jeremy Goecks
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| |
Collapse
|
35
|
McGrail DJ, Lin CCJ, Dai H, Mo W, Li Y, Stephan C, Davies P, Lu Z, Mills GB, Lee JS, Lin SY. Defective Replication Stress Response Is Inherently Linked to the Cancer Stem Cell Phenotype. Cell Rep 2019; 23:2095-2106. [PMID: 29768207 DOI: 10.1016/j.celrep.2018.04.068] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 01/04/2018] [Accepted: 02/12/2018] [Indexed: 01/05/2023] Open
Abstract
Extensive spontaneous DNA damage from oncogene-induced replication stress is ubiquitous in precancerous lesions. While this damage induces differentiation, senescence, or apoptosis in normal cells, defects in DNA replication stress response (RSR) allow cells to continue proliferating, ultimately leading to early tumorigenesis. Using systems-level approaches, we developed a replication stress response defect gene signature that predicted risk of cancer development from hyperplastic lesions. Intriguingly, we found that replication stress response defects rewire non-malignant cells into a cancer stem cell (CSC)-like state, and analysis of CSCs indicated that they inherently harbor replication stress response defects. High-throughput drug screening to elucidate molecules required for survival of replication stress response defective cells identified a dependence on MEK/ERK signaling. Inhibition of this signaling cascade restored oncogene-induced senescence through a p53-independent MDM2/p21 axis. Moreover, MEK/ERK inhibition also depleted CSC populations. Together, these findings provide insights into the role of replication stress response defects in CSCs and an actionable pathway for therapeutic targeting.
Collapse
Affiliation(s)
- Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Curtis Chun-Jen Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Mo
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Clifford Stephan
- The Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Peter Davies
- The Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Zhimin Lu
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
36
|
Bertelsen B, Tuxen IV, Yde CW, Gabrielaite M, Torp MH, Kinalis S, Oestrup O, Rohrberg K, Spangaard I, Santoni-Rugiu E, Wadt K, Mau-Sorensen M, Lassen U, Nielsen FC. High frequency of pathogenic germline variants within homologous recombination repair in patients with advanced cancer. NPJ Genom Med 2019; 4:13. [PMID: 31263571 PMCID: PMC6588611 DOI: 10.1038/s41525-019-0087-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/15/2019] [Indexed: 12/31/2022] Open
Abstract
Genomic screening of cancer patients for predisposing variants is traditionally based on age at onset, family history and type of cancer. Whereas the clinical guidelines have proven efficient in identifying families exhibiting classical attributes of hereditary cancer, the frequency of patients with alternative presentations is unclear. We identified and characterized germline variants in 636 patients with advanced solid cancer using whole exome sequencing. Pathogenic and likely pathogenic germline variants among 168 genes associated with hereditary cancer were considered. These variants were identified in 17.8% of the patients and within a wide range of cancer types. In particular, patients with mesothelioma, ovarian cancer, cervical cancer, urothelial cancer, and cancer of unknown primary origin displayed high frequencies of pathogenic variants. Variants were predominantly found in DNA-repair pathways and about half were within genes involved in homologous recombination repair. Twenty-two BRCA1 and BRCA2 germline variants were identified in 12 different cancer types, of which 10 (45%) were not previously identified in these patients based on the current clinical guidelines. Loss of heterozygosity and somatic second hits were identified in several of the affected genes, supporting possible causality for cancer development. A potential treatment target based on the pathogenic germline variant could be suggested in 25 patients (4%). The study demonstrates a high frequency of pathogenic germline variants in the homologous recombination pathway in patients with advanced solid cancers. We infer that genetic screening in this group of patients may reveal high-risk families and identify patients with potential PARP inhibitor sensitive tumors.
Collapse
Affiliation(s)
| | - Ida Viller Tuxen
- 2The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | | | | | | | - Savvas Kinalis
- 1Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Olga Oestrup
- 1Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Kristoffer Rohrberg
- 2The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | - Iben Spangaard
- 2The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | | | - Karin Wadt
- 4Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Morten Mau-Sorensen
- 2The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | - Ulrik Lassen
- 2The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen, Denmark
| | | |
Collapse
|
37
|
High-Grade Serous Ovarian Cancer: Basic Sciences, Clinical and Therapeutic Standpoints. Int J Mol Sci 2019. [PMID: 30813239 DOI: 10.3390/ijms20040952] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Among a litany of malignancies affecting the female reproductive tract, that of the ovary is the most frequently fatal. Moreover, while the steady pace of scientific discovery has fuelled recent ameliorations in the outcomes of many other cancers, the rates of mortality for ovarian cancer have been stagnant since around 1980. Yet despite the grim outlook, progress is being made towards better understanding the fundamental biology of this disease and how its biology in turn influences clinical behaviour. It has long been evident that ovarian cancer is not a unitary disease but rather a multiplicity of distinct malignancies that share a common anatomical site upon presentation. Of these, the high-grade serous subtype predominates in the clinical setting and is responsible for a disproportionate share of the fatalities from all forms of ovarian cancer. This review aims to provide a detailed overview of the clinical-pathological features of ovarian cancer with a particular focus on the high-grade serous subtype. Along with a description of the relevant clinical aspects of this disease, including novel trends in treatment strategies, this text will inform the reader of recent updates to the scientific literature regarding the origin, aetiology and molecular-genetic basis of high-grade serous ovarian cancer (HGSOC).
Collapse
|
38
|
High-Grade Serous Ovarian Cancer: Basic Sciences, Clinical and Therapeutic Standpoints. Int J Mol Sci 2019. [PMID: 30813239 DOI: 10.3390/ijms20040952]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Among a litany of malignancies affecting the female reproductive tract, that of the ovary is the most frequently fatal. Moreover, while the steady pace of scientific discovery has fuelled recent ameliorations in the outcomes of many other cancers, the rates of mortality for ovarian cancer have been stagnant since around 1980. Yet despite the grim outlook, progress is being made towards better understanding the fundamental biology of this disease and how its biology in turn influences clinical behaviour. It has long been evident that ovarian cancer is not a unitary disease but rather a multiplicity of distinct malignancies that share a common anatomical site upon presentation. Of these, the high-grade serous subtype predominates in the clinical setting and is responsible for a disproportionate share of the fatalities from all forms of ovarian cancer. This review aims to provide a detailed overview of the clinical-pathological features of ovarian cancer with a particular focus on the high-grade serous subtype. Along with a description of the relevant clinical aspects of this disease, including novel trends in treatment strategies, this text will inform the reader of recent updates to the scientific literature regarding the origin, aetiology and molecular-genetic basis of high-grade serous ovarian cancer (HGSOC).
Collapse
|
39
|
High-Grade Serous Ovarian Cancer: Basic Sciences, Clinical and Therapeutic Standpoints. Int J Mol Sci 2019; 20:ijms20040952. [PMID: 30813239 PMCID: PMC6412907 DOI: 10.3390/ijms20040952] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 02/07/2023] Open
Abstract
Among a litany of malignancies affecting the female reproductive tract, that of the ovary is the most frequently fatal. Moreover, while the steady pace of scientific discovery has fuelled recent ameliorations in the outcomes of many other cancers, the rates of mortality for ovarian cancer have been stagnant since around 1980. Yet despite the grim outlook, progress is being made towards better understanding the fundamental biology of this disease and how its biology in turn influences clinical behaviour. It has long been evident that ovarian cancer is not a unitary disease but rather a multiplicity of distinct malignancies that share a common anatomical site upon presentation. Of these, the high-grade serous subtype predominates in the clinical setting and is responsible for a disproportionate share of the fatalities from all forms of ovarian cancer. This review aims to provide a detailed overview of the clinical-pathological features of ovarian cancer with a particular focus on the high-grade serous subtype. Along with a description of the relevant clinical aspects of this disease, including novel trends in treatment strategies, this text will inform the reader of recent updates to the scientific literature regarding the origin, aetiology and molecular-genetic basis of high-grade serous ovarian cancer (HGSOC).
Collapse
|
40
|
Pilié PG, Tang C, Mills GB, Yap TA. State-of-the-art strategies for targeting the DNA damage response in cancer. Nat Rev Clin Oncol 2019; 16:81-104. [PMID: 30356138 PMCID: PMC8327299 DOI: 10.1038/s41571-018-0114-z] [Citation(s) in RCA: 677] [Impact Index Per Article: 135.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genomic instability is a key hallmark of cancer that arises owing to defects in the DNA damage response (DDR) and/or increased replication stress. These alterations promote the clonal evolution of cancer cells via the accumulation of driver aberrations, including gene copy-number changes, rearrangements and mutations; however, these same defects also create vulnerabilities that are relatively specific to cancer cells, which could potentially be exploited to increase the therapeutic index of anticancer treatments and thereby improve patient outcomes. The discovery that BRCA-mutant cancer cells are exquisitely sensitive to inhibition of poly(ADP-ribose) polymerase has ushered in a new era of research on biomarker-driven synthetic lethal treatment strategies for different cancers. The therapeutic landscape of antitumour agents targeting the DDR has rapidly expanded to include inhibitors of other key mediators of DNA repair and replication, such as ATM, ATR, CHK1 and CHK2, DNA-PK and WEE1. Efforts to optimize these therapies are ongoing across a range of cancers, involving the development of predictive biomarker assays of responsiveness (beyond BRCA mutations), assessment of the mechanisms underlying intrinsic and acquired resistance, and evaluation of rational, tolerable combinations with standard-of-care treatments (such as chemotherapeutics and radiation), novel molecularly targeted agents and immune-checkpoint inhibitors. In this Review, we discuss the current status of anticancer therapies targeting the DDR.
Collapse
Affiliation(s)
- Patrick G Pilié
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad Tang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy A Yap
- Department of Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
41
|
Gobin M, Nazarov PV, Warta R, Timmer M, Reifenberger G, Felsberg J, Vallar L, Chalmers AJ, Herold-Mende CC, Goldbrunner R, Niclou SP, Van Dyck E. A DNA Repair and Cell-Cycle Gene Expression Signature in Primary and Recurrent Glioblastoma: Prognostic Value and Clinical Implications. Cancer Res 2019; 79:1226-1238. [PMID: 30674534 DOI: 10.1158/0008-5472.can-18-2076] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/26/2018] [Accepted: 01/16/2019] [Indexed: 11/16/2022]
Abstract
Inevitable tumor recurrence and a poor median survival are frustrating reminders of the inefficacy of our current standard of care for patients with newly diagnosed glioblastoma (GBM), which includes surgery followed by radiotherapy and chemotherapy with the DNA alkylating agent temozolomide. Because resistance to genotoxic damage is achieved mainly through execution of the DNA damage response (DDR) and DNA repair pathways, knowledge of the changes in DNA repair and cell-cycle gene expression that occur during tumor development might help identify new targets and improve treatment. Here, we performed a gene expression analysis targeting components of the DNA repair and cell-cycle machineries in cohorts of paired tumor samples (i.e., biopsies from the same patient obtained at the time of primary tumor operation and at recurrence) from patients treated with radiotherapy or radiotherapy plus temozolomide. We identified and validated a 27-gene signature that resulted in the classification of GBM specimens into three groups, two of which displayed inverse expression profiles. Each group contained primary and recurrent samples, and the tumor at relapse frequently displayed a gene expression profile different from that of the matched primary biopsy. Within the groups that exhibited opposing gene expression profiles, the expression pattern of the gene signature at relapse was linked to progression-free survival. We provide experimental evidence that our signature exposes group-specific vulnerabilities against genotoxicants and inhibitors of the cell cycle and DDR, with the prospect of personalized therapeutic strategies.Significance: These findings suggest that classification of GBM tumors based on a DNA repair and cell-cycle gene expression signature exposes vulnerabilities to standard-of-care therapies and offers the potential for personalized therapeutic strategies.
Collapse
Affiliation(s)
- Matthieu Gobin
- NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.,Faculty of Science, Technology and Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Petr V Nazarov
- Proteome and Genome Research Unit, LIH, Luxembourg, Luxembourg
| | - Rolf Warta
- Department of Neurosurgery, University Clinic Heidelberg, Heidelberg, Germany
| | - Marco Timmer
- Neurosurgery Centre, University Clinic Cologne, Cologne, Germany
| | | | | | - Laurent Vallar
- Proteome and Genome Research Unit, LIH, Luxembourg, Luxembourg
| | - Anthony J Chalmers
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Eric Van Dyck
- NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.
| |
Collapse
|
42
|
Zhao C, Takahashi N, Rajan A. Sleep better on combination therapy: SLFN11 predicts response to veliparib and temozolomide in recurrent small cell lung cancer. Transl Lung Cancer Res 2018; 7:S308-S311. [PMID: 30705842 DOI: 10.21037/tlcr.2018.12.11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chen Zhao
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nobuyuki Takahashi
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arun Rajan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
43
|
Jiang Y, Dai H, Li Y, Yin J, Guo S, Lin SY, McGrail DJ. PARP inhibitors synergize with gemcitabine by potentiating DNA damage in non-small-cell lung cancer. Int J Cancer 2018; 144:1092-1103. [PMID: 30152517 DOI: 10.1002/ijc.31770] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/28/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022]
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors have demonstrated great promise in the treatment of patients with deficiencies in homologous recombination (HR) DNA repair, such as those with loss of BRCA1 or BRCA2 function. However, emerging studies suggest that PARP inhibition can also target HR-competent cancers, such as non-small-cell lung cancer (NSCLC), and that the therapeutic effect of PARP inhibition may be improved by combination with chemotherapy agents. In our study, it was found that PARP inhibitors talazoparib (BMN-673) and olaparib (AZD-2281) both had synergistic activity with the common first-line chemotherapeutic gemcitabine in a panel of lung cancer cell lines. Furthermore, the combination demonstrated significant in vivo antitumor activity in an H23 xenograft model of NSCLC compared to either agent as monotherapy. This synergism occurred without loss of HR repair efficiency. Instead, the combination induced synergistic single-strand DNA breaks, leading to accumulation of toxic double-strand DNA lesions in vitro and in vivo. Our study elucidates the underlying mechanisms of synergistic activity of PARP inhibitors and gemcitabine, providing a strong motivation to pursue this combination as an improved therapeutic regimen.
Collapse
Affiliation(s)
- Yu Jiang
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Respiratory Medicine, The University-Town Hospital of Chongqing Medical University, Chongqing, China
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yang Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jun Yin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shuliang Guo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| |
Collapse
|
44
|
Wang X, Tan Y, Cao X, Kim JA, Chen T, Hu Y, Wexler M, Wang X. Epigenetic activation of HORMAD1 in basal-like breast cancer: role in Rucaparib sensitivity. Oncotarget 2018; 9:30115-30127. [PMID: 30046392 PMCID: PMC6059019 DOI: 10.18632/oncotarget.25728] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 06/22/2018] [Indexed: 12/27/2022] Open
Abstract
Basal-like breast cancer (BLBC) is an aggressive breast cancer subtype with features similar to the basal cells surrounding the mammary ducts. Treatment of patients with BLBC has been challenging due to the lack of well-defined molecular targets. Due to the clinical and pathological similarities of BLBC with BRCA-deficient breast cancers, the effectiveness of Poly (ADP-ribose) polymerase inhibitors (PARPi) has been tested in early phase clinical trials for patients with advanced BLBC, with limited clinical responses. Recently, it was reported that HORMAD1 overexpression sensitizes BLBC to HR-targeting agents by suppressing homologous recombination. Our independent analysis suggests that HORMAD1 is aberrantly overexpressed in about 80% of BLBC, and its expression in normal tissues is restricted to testis. Our experimental data suggests that HORMAD1 overexpression correlates with focal hypomethylation in BLBC. On the other hand, investigation of the Genomics of Drug Sensitivity in Cancer dataset revealed significantly reduced sensitivity of HORMAD1-overexpressing BLBC cell lines to Rucaparib, a commonly used PARPi. To further assess the role of HORMAD1 in PARPi sensitivity, we generated three HORMAD1-overexpressing xenograft models using the HORMAD1-low BLBC cell lines HCC1954, HCC1806, and BT20; we then subjected these xenograft models to Rucaparib treatment. Ectopic expression of HORMAD1 enhances tumor formations in two of these models, and significantly reduces sensitivity to Rucaparib in the HCC1954 model. Taken together, our data suggest that epigenetic activation of HORMAD1 by hypomethylation in BLBC may endow reduced sensitivity to Rucaparib treatment in some tumor models.
Collapse
Affiliation(s)
- Xian Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh, PA 15232, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ying Tan
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xixi Cao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jin Ah Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tianmeng Chen
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh, PA 15232, USA
| | - Yiheng Hu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh, PA 15232, USA
| | - Matthew Wexler
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh, PA 15232, USA
| | - Xiaosong Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh, PA 15232, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
45
|
PATRI, a Genomics Data Integration Tool for Biomarker Discovery. BIOMED RESEARCH INTERNATIONAL 2018; 2018:2012078. [PMID: 30065933 PMCID: PMC6051285 DOI: 10.1155/2018/2012078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/29/2018] [Indexed: 12/31/2022]
Abstract
The availability of genomic datasets in association with clinical, phenotypic, and drug sensitivity information represents an invaluable source for potential therapeutic applications, supporting the identification of new drug sensitivity biomarkers and pharmacological targets. Drug discovery and precision oncology can largely benefit from the integration of treatment molecular discriminants obtained from cell line models and clinical tumor samples; however this task demands comprehensive analysis approaches for the discovery of underlying data connections. Here we introduce PATRI (Platform for the Analysis of TRanslational Integrated data), a standalone tool accessible through a user-friendly graphical interface, conceived for the identification of treatment sensitivity biomarkers from user-provided genomics data, associated with information on sample characteristics. PATRI streamlines a translational analysis workflow: first, baseline genomics signatures are statistically identified, differentiating treatment sensitive from resistant preclinical models; then, these signatures are used for the prediction of treatment sensitivity in clinical samples, via random forest categorization of clinical genomics datasets and statistical evaluation of the relative phenotypic features. The same workflow can also be applied across distinct clinical datasets. The ease of use of the PATRI tool is illustrated with validation analysis examples, performed with sensitivity data for drug treatments with known molecular discriminants.
Collapse
|
46
|
BRCA1/2 testing: therapeutic implications for breast cancer management. Br J Cancer 2018; 119:141-152. [PMID: 29867226 PMCID: PMC6048046 DOI: 10.1038/s41416-018-0127-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 04/10/2018] [Accepted: 04/24/2018] [Indexed: 12/15/2022] Open
Abstract
Testing for germline BRCA1/2 mutations has an established predictive role in breast cancer risk assessment. More recently, studies have also identified BRCA1/2 status as clinically relevant in the selection of therapy for patients already diagnosed with breast cancer. Emerging breast and ovarian cancer research indicate that BRCA status predicts responsiveness to platinum-based chemotherapy, as well as to inhibitors of poly(ADP-ribose) polymerase (PARP), owing to the ability of these interventions to inhibit DNA repair pathways. BRCA1/2 mutation testing thus has important and expanding roles in treatment planning for subsets of patients with breast cancer. Recent studies have demonstrated different activity of platinum salts in BRCA-mutated compared with non-BRCA-mutated breast cancer. Furthermore, phase II/III studies of single-agent PARP inhibitors (PARPi) have shown encouraging progression-free survival results in patients with BRCA1/2-mutated breast cancer, which led to the recent approval of olaparib, the first PARPi to be approved in breast cancer. Determining BRCA1/2 mutation status in this breast cancer subgroup could potentially expand treatment options beyond the current standard of taxane and anthracycline-based chemotherapy. Although attempts have been made to develop scoring systems that measure defects in homologous recombination repair pathways to predict response to platinum or PARPi, none have yet made it into clinical use. In this review, we summarise the recent and ongoing preclinical and clinical studies on the treatment of BRCA-associated breast cancer, and discuss efforts to identify other breast cancer patients who may be responsive to therapies effective in BRCA mutation carriers, including platinum-containing chemotherapy and PARPi.
Collapse
|
47
|
McGrail DJ, Federico L, Li Y, Dai H, Lu Y, Mills GB, Yi S, Lin SY, Sahni N. Multi-omics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers. Nat Commun 2018; 9:1317. [PMID: 29615613 PMCID: PMC5882811 DOI: 10.1038/s41467-018-03730-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 03/05/2018] [Indexed: 12/20/2022] Open
Abstract
To realize the full potential of immunotherapy, it is critical to understand the drivers of tumor infiltration by immune cells. Previous studies have linked immune infiltration with tumor neoantigen levels, but the broad applicability of this concept remains unknown. Here, we find that while this observation is true across cancers characterized by recurrent mutations, it does not hold for cancers driven by recurrent copy number alterations, such as breast and pancreatic tumors. To understand immune invasion in these cancers, we developed an integrative multi-omics framework, identifying the DNA damage response protein ATM as a driver of cytokine production leading to increased immune infiltration. This prediction was validated in numerous orthogonal datasets, as well as experimentally in vitro and in vivo by cytokine release and immune cell migration. These findings demonstrate diverse drivers of immune cell infiltration across cancer lineages and may facilitate the clinical adaption of immunotherapies across diverse malignancies.
Collapse
Affiliation(s)
- Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lorenzo Federico
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Song Yi
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| |
Collapse
|
48
|
Vanderstichele A, Busschaert P, Olbrecht S, Lambrechts D, Vergote I. Genomic signatures as predictive biomarkers of homologous recombination deficiency in ovarian cancer. Eur J Cancer 2017; 86:5-14. [PMID: 28950147 DOI: 10.1016/j.ejca.2017.08.029] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 12/22/2022]
Abstract
DNA repair deficiency is a common hallmark of many cancers and is increasingly recognised as a target for cancer therapeutics. Selecting patients for these treatments requires a functional assessment of multiple redundant DNA repair pathways. With the advent of whole-genome sequencing of cancer genomes, it is increasingly recognised that multiple signatures of mutational and chromosomal alterations can be correlated with specific DNA repair defects. The clinical relevance of this approach is underlined by the use of poly-(ADP-ribose) polymerase inhibitors (PARPi) in homologous recombination (HR) deficient high-grade serous ovarian cancers. Beyond deleterious mutations in HR-related genes such as BRCA1/2, it is recognised that HR deficiency endows ovarian cancers with specific signatures of base substitutions and structural chromosomal variation. Multiple metrics quantifying loss-of-heterozygosity (LOH) events were proposed and implemented in trials with PARPi. However, it was shown that some of the HR-deficient cases, i.e. CDK12-mutated tumours, were not associated with high LOH-based scores, but with distinct patterns of genomic alterations such as tandem duplication. Therefore, more complex signatures of structural genomic variation were identified and quantified. Ultimately, optimal prediction models for treatments targeting DNA repair will need to integrate multiples of these genomic signatures and will also need to assess multiple resistance mechanisms such as genomic reversion events that partially or fully re-activate DNA repair.
Collapse
Affiliation(s)
- Adriaan Vanderstichele
- Department of Gynaecology and Obstetrics, University Hospitals Leuven, Belgium; Division of Gynaecological Oncology, Leuven Cancer Institute, KU Leuven, Leuven, Belgium.
| | - Pieter Busschaert
- Department of Gynaecology and Obstetrics, University Hospitals Leuven, Belgium; Division of Gynaecological Oncology, Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Siel Olbrecht
- Department of Gynaecology and Obstetrics, University Hospitals Leuven, Belgium; Division of Gynaecological Oncology, Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Ignace Vergote
- Department of Gynaecology and Obstetrics, University Hospitals Leuven, Belgium; Division of Gynaecological Oncology, Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| |
Collapse
|