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Rai SK, Du W, Zhang J, Yu H, Deng Y, Fei P. Somatic gene mutations involved in DNA damage response/Fanconi anemia signaling are tissue- and cell-type specific in human solid tumors. Front Med (Lausanne) 2024; 11:1462810. [PMID: 39421870 PMCID: PMC11483370 DOI: 10.3389/fmed.2024.1462810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 08/28/2024] [Indexed: 10/19/2024] Open
Abstract
With significant advancements in the study of DNA Damage Response (DDR) and Fanconi Anemia (FA) signaling, we previously introduced the term "FA signaling" to encompass "all signaling transductions involving one or more FA proteins." This network has now evolved into the largest cellular defense network, integrating over 30 key players, including ATM, ATR, BLM, HRR6, RAD18, FANCA, FANCB, FANCC, BRCA2, FANCD2, FANCE, FANCF, FANCG, FANCI, BRIP1, FANCL, FANCM, PALB2, RAD51C, SLX4, ERCC4, RAD51, BRCA1, UBE2T, XRCC2, MAD2L2, RFWD3, FAAP20, FAAP24, FAAP100, and CENPX. This system responds to both endogenous and exogenous cellular insults. However, the mutational signatures associated with this defense mechanism in non-FA human cancers have not been extensively explored. In this study, we report that different types of human cancers are characterized by distinct somatically mutated genes related to DDR/FA signaling, each accompanied by a unique spectrum of potential driver mutations. For example, in pan-cancer samples, ATM emerges as the most frequently mutated gene (5%) among the 31 genes analyzed, with the highest number of potential driver mutations (1714), followed by BRCA2 (4% with 970 putative driver mutations). However, this pattern is not universal across specific cancer types. For example, FANCT is the most frequently mutated gene in breast (14%) and liver (4%) cancers. In addition, the alteration frequency of DDR/FA signaling due to these mutations exceeds 70% in a subtype of prostate cancer, with each subtype of brain, breast, lung, and prostate cancers displaying distinct patterns of gene alteration frequency. Furthermore, these gene alteration patterns significantly impact patient survival and disease-free periods. Collectively, our findings not only enhance our understanding of cancer development and progression but also have significant implications for cancer patient care and prognosis, particularly in the development of effective therapeutic strategies.
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Affiliation(s)
- Sudhir Kumar Rai
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, United States
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Wei Du
- Division of Malignant Hematology and Medical Oncology, University of Pittsburgh School of Medicine, UPMC Hillma Cancer Center, Pittsburgh, PA, United States
| | - Jun Zhang
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Arizona Campus, Phoenix, AZ, United States
| | - Herbert Yu
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, United States
| | - Youping Deng
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, United States
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Peiwen Fei
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, United States
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Li J, Jia Z, Dong L, Cao H, Huang Y, Xu H, Xie Z, Jiang Y, Wang X, Liu J. DNA damage response in breast cancer and its significant role in guiding novel precise therapies. Biomark Res 2024; 12:111. [PMID: 39334297 PMCID: PMC11437670 DOI: 10.1186/s40364-024-00653-2] [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: 09/05/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
DNA damage response (DDR) deficiency has been one of the emerging targets in treating breast cancer in recent years. On the one hand, DDR coordinates cell cycle and signal transduction, whose dysfunction may lead to cell apoptosis, genomic instability, and tumor development. Conversely, DDR deficiency is an intrinsic feature of tumors that underlies their response to treatments that inflict DNA damage. In this review, we systematically explore various mechanisms of DDR, the rationale and research advances in DDR-targeted drugs in breast cancer, and discuss the challenges in its clinical applications. Notably, poly (ADP-ribose) polymerase (PARP) inhibitors have demonstrated favorable efficacy and safety in breast cancer with high homogenous recombination deficiency (HRD) status in a series of clinical trials. Moreover, several studies on novel DDR-related molecules are actively exploring to target tumors that become resistant to PARP inhibition. Before further clinical application of new regimens or drugs, novel and standardized biomarkers are needed to develop for accurately characterizing the benefit population and predicting efficacy. Despite the promising efficacy of DDR-related treatments, challenges of off-target toxicity and drug resistance need to be addressed. Strategies to overcome drug resistance await further exploration on DDR mechanisms, and combined targeted drugs or immunotherapy will hopefully provide more precise or combined strategies and expand potential responsive populations.
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Affiliation(s)
- Jiayi Li
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Ziqi Jia
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Dong
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Heng Cao
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yansong Huang
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Hengyi Xu
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhixuan Xie
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Yiwen Jiang
- School of Clinical Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Xiang Wang
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jiaqi Liu
- Department of Breast Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Bigos KJA, Quiles CG, Lunj S, Smith DJ, Krause M, Troost EGC, West CM, Hoskin P, Choudhury A. Tumour response to hypoxia: understanding the hypoxic tumour microenvironment to improve treatment outcome in solid tumours. Front Oncol 2024; 14:1331355. [PMID: 38352889 PMCID: PMC10861654 DOI: 10.3389/fonc.2024.1331355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024] Open
Abstract
Hypoxia is a common feature of solid tumours affecting their biology and response to therapy. One of the main transcription factors activated by hypoxia is hypoxia-inducible factor (HIF), which regulates the expression of genes involved in various aspects of tumourigenesis including proliferative capacity, angiogenesis, immune evasion, metabolic reprogramming, extracellular matrix (ECM) remodelling, and cell migration. This can negatively impact patient outcomes by inducing therapeutic resistance. The importance of hypoxia is clearly demonstrated by continued research into finding clinically relevant hypoxia biomarkers, and hypoxia-targeting therapies. One of the problems is the lack of clinically applicable methods of hypoxia detection, and lack of standardisation. Additionally, a lot of the methods of detecting hypoxia do not take into consideration the complexity of the hypoxic tumour microenvironment (TME). Therefore, this needs further elucidation as approximately 50% of solid tumours are hypoxic. The ECM is important component of the hypoxic TME, and is developed by both cancer associated fibroblasts (CAFs) and tumour cells. However, it is important to distinguish the different roles to develop both biomarkers and novel compounds. Fibronectin (FN), collagen (COL) and hyaluronic acid (HA) are important components of the ECM that create ECM fibres. These fibres are crosslinked by specific enzymes including lysyl oxidase (LOX) which regulates the stiffness of tumours and induces fibrosis. This is partially regulated by HIFs. The review highlights the importance of understanding the role of matrix stiffness in different solid tumours as current data shows contradictory results on the impact on therapeutic resistance. The review also indicates that further research is needed into identifying different CAF subtypes and their exact roles; with some showing pro-tumorigenic capacity and others having anti-tumorigenic roles. This has made it difficult to fully elucidate the role of CAFs within the TME. However, it is clear that this is an important area of research that requires unravelling as current strategies to target CAFs have resulted in worsened prognosis. The role of immune cells within the tumour microenvironment is also discussed as hypoxia has been associated with modulating immune cells to create an anti-tumorigenic environment. Which has led to the development of immunotherapies including PD-L1. These hypoxia-induced changes can confer resistance to conventional therapies, such as chemotherapy, radiotherapy, and immunotherapy. This review summarizes the current knowledge on the impact of hypoxia on the TME and its implications for therapy resistance. It also discusses the potential of hypoxia biomarkers as prognostic and predictive indictors of treatment response, as well as the challenges and opportunities of targeting hypoxia in clinical trials.
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Affiliation(s)
- Kamilla JA. Bigos
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Conrado G. Quiles
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Sapna Lunj
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Danielle J. Smith
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Mechthild Krause
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- OncoRay – National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- Translational Radiooncology and Clinical Radiotherapy, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
- Translational Radiooncology and Clinical Radiotherapy and Image-guided High Precision Radiotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Translational Radiooncology and Clinical Radiotherapy and Image-guided High Precision Radiotherapy, Helmholtz Association / Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- School of Medicine, Technische Universitat Dresden, Dresden, Germany
| | - Esther GC. Troost
- OncoRay – National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
- Translational Radiooncology and Clinical Radiotherapy and Image-guided High Precision Radiotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Translational Radiooncology and Clinical Radiotherapy and Image-guided High Precision Radiotherapy, Helmholtz Association / Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- School of Medicine, Technische Universitat Dresden, Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Institute of Radiooncology – OncoRay, Helmholtz-Zentrum Dresden-Rossendorf, Rossendorf, Germany
| | - Catharine M. West
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, United Kingdom
| | - Peter Hoskin
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- Mount Vernon Cancer Centre, Northwood, United Kingdom
| | - Ananya Choudhury
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- Christie Hospital NHS Foundation Trust, Manchester, Germany
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Magadeeva S, Qian X, Korff N, Flörkemeier I, Hedemann N, Rogmans C, Forster M, Arnold N, Maass N, Bauerschlag DO, Weimer JP. Assessing the Phenotype of a Homologous Recombination Deficiency Using High Resolution Array-Based Comparative Genome Hybridization in Ovarian Cancer. Int J Mol Sci 2023; 24:17467. [PMID: 38139296 PMCID: PMC10743768 DOI: 10.3390/ijms242417467] [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: 10/27/2023] [Revised: 12/05/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
Ovarian cancer (OC) cells with homologous recombination deficiency (HRD) accumulate genomic scars (LST, TAI, and LOH) over a value of 42 in sum. PARP inhibitors can treat OC with HRD. The detection of HRD can be done directly by imaging these genomic scars, or indirectly by detecting mutations in the genes involved in HR. We show that HRD detection is also possible using high-resolution aCGH. A total of 30 OCs were analyzed retrospectively with high-resolution arrays as a test set and 19 OCs prospectively as a validation set. Mutation analysis was performed by HBOC TruRisk V2 panel to detect HR-relevant mutations. CNVs were clustered with respect to the involved HR genes versus the OC cases. In prospective validation, the HRD status determined by aCGH was compared with external HRD assessments. Two BRCA mutation carriers did not have HRD. OC could approximately differentiate into two groups with characteristic CNV patterns with different survival rates. Mutation frequencies have a linear regression on the HRD score. Mutations in individual HR-relevant genes do not always indicate HRD. This may depend on the mutation frequency in tumor cells. The aCGH shows the genomic scars of an HRD inexpensively and directly.
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Affiliation(s)
- Svetlana Magadeeva
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Xueqian Qian
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Nadine Korff
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Inken Flörkemeier
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Nina Hedemann
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Christoph Rogmans
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Nicolai Maass
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Dirk O. Bauerschlag
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Jörg P. Weimer
- Department of Gynaecology and Obstetrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
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