1
|
Witz A, Dardare J, Betz M, Michel C, Husson M, Gilson P, Merlin JL, Harlé A. Homologous recombination deficiency (HRD) testing landscape: clinical applications and technical validation for routine diagnostics. Biomark Res 2025; 13:31. [PMID: 39985088 PMCID: PMC11846297 DOI: 10.1186/s40364-025-00740-y] [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: 06/24/2024] [Accepted: 02/04/2025] [Indexed: 02/24/2025] Open
Abstract
The use of poly(ADP-ribose) polymerase inhibitors (PARPi) revolutionized the treatment of BRCA-mutated cancers. Identifying patients exhibiting homologous recombination deficiency (HRD) has been proved useful to predict PARPi efficacy. However, obtaining HRD status remains an arduous task due to its evolution over the time. This causes HRD status to become obsolete when obtained from genomic scars, rendering PARPi ineffective for these patients. Only two HRD tests are currently FDA-approved, both based on genomic scars detection and BRCA mutations testing. Nevertheless, new technologies for obtaining an increasingly reliable HRD status continue to evolve. Application of these tests in clinical practice is an additional challenge due to the need for lower costs and shorter time to results delay.In this review, we describe the currently available methods for HRD testing, including the methodologies and corresponding tests for assessing HRD status, and discuss the clinical routine application of these tests and their technical validation.
Collapse
Affiliation(s)
- Andréa Witz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN - Université de Lorraine, Vandoeuvre-lès-Nancy, France.
| | - Julie Dardare
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN - Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Margaux Betz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN - Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Cassandra Michel
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN - Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Marie Husson
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN - Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Pauline Gilson
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN - Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Jean-Louis Merlin
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN - Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Alexandre Harlé
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN - Université de Lorraine, Vandoeuvre-lès-Nancy, France
| |
Collapse
|
2
|
Fink JL, Jaradi B, Stone N, Sanker B, Zhang F, Dobrovic A, Kirschner S, Hadfield J, Kondrashova O, Waring PM. Validation and Performance of Quantitative BRCA1 and RAD51C Promoter Hypermethylation Testing in Breast and Ovarian Cancers. J Mol Diagn 2025; 27:139-153. [PMID: 39675559 DOI: 10.1016/j.jmoldx.2024.11.004] [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: 02/09/2024] [Revised: 09/24/2024] [Accepted: 11/13/2024] [Indexed: 12/17/2024] Open
Abstract
Poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors represent a significant advancement in the treatment of epithelial ovarian cancer, triple-negative breast cancer, pancreatic cancer, and castrate-resistant prostate cancer, and they are poised to improve treatment in an increasing number of other cancer types. PARP inhibitor efficacy as monotherapy has been primarily observed in tumors with deleterious genetic variants in genes involved in the homologous recombination repair pathway. Tumors without these variants have also been shown to respond; notably, those with hypermethylation at all alleles of the BRCA1 or RAD51C promoter can respond to PARP inhibitors. These epigenetic biomarkers therefore represent a patient population that may also benefit from this targeted therapy. However, no robust test has been conducted to identify these biomarkers in routine clinical specimens that is amenable to implementation for decentralized testing. This study describes the analytical and clinical validation of a BRCA1 and RAD51C promoter methylation test that can be run with a single-day library preparation workflow for sequencing on any next-generation sequencing platform. The results show that this test can accurately quantitate the level of promoter methylation at the BRCA1 and RAD51C genes using formalin-fixed, paraffin-embedded samples, even when the extracted DNA is extremely degraded or the input amount is limited. This test increases the precision of diagnostic tests aimed at identifying patients who are likely and unlikely to respond to PARP inhibitor therapy.
Collapse
Affiliation(s)
- J Lynn Fink
- XING Genomic Services, Sinnamon Park, Queensland, Australia.
| | - Binny Jaradi
- XING Genomic Services, Sinnamon Park, Queensland, Australia
| | - Nathan Stone
- XING Genomic Services, Sinnamon Park, Queensland, Australia
| | | | - Fan Zhang
- Beacon Biomarkers Laboratory, University of Melbourne Department of Surgery at Austin Health, Heidelberg, Victoria, Australia
| | - Alexander Dobrovic
- Beacon Biomarkers Laboratory, University of Melbourne Department of Surgery at Austin Health, Heidelberg, Victoria, Australia
| | | | - James Hadfield
- Translational Medicine, AstraZeneca, Cambridge, United Kingdom
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Herston, Queensland, Australia
| | - Paul M Waring
- XING Genomic Services, Sinnamon Park, Queensland, Australia; Translational Medicine, AstraZeneca, Cambridge, United Kingdom
| |
Collapse
|
3
|
Steele EJ, Lindley RA. Deaminase-Driven Reverse Transcription Mutagenesis in Oncogenesis: Critical Analysis of Transcriptional Strand Asymmetries of Single Base Substitution Signatures. Int J Mol Sci 2025; 26:989. [PMID: 39940758 PMCID: PMC11817618 DOI: 10.3390/ijms26030989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 01/05/2025] [Accepted: 01/09/2025] [Indexed: 02/16/2025] Open
Abstract
This paper provides a critical analysis of the molecular mechanisms presently used to explain transcriptional strand asymmetries of single base substitution (SBS) signatures observed in cancer genomes curated at the Catalogue of Somatic Mutations in Cancer (COSMIC) database (Wellcome Trust Sanger Institute). The analysis is based on a deaminase-driven reverse transcriptase (DRT) mutagenesis model of cancer oncogenesis involving both the cytosine (AID/APOBEC) and adenosine (ADAR) mutagenic deaminases. In this analysis we apply what is known, or can reasonably be inferred, of the immunoglobulin somatic hypermutation (Ig SHM) mechanism to the analysis of the transcriptional stand asymmetries of the COSMIC SBS signatures that are observed in cancer genomes. The underlying assumption is that somatic mutations arising in cancer genomes are driven by dysregulated off-target Ig SHM-like mutagenic processes at non-Ig loci. It is reasoned that most SBS signatures whether of "unknown etiology" or assigned-molecular causation, can be readily understood in terms of the DRT-paradigm. These include the major age-related "clock-like" SBS5 signature observed in all cancer genomes sequenced and many other common subset signatures including SBS1, SBS3, SBS2/13, SBS6, SBS12, SBS16, SBS17a/17b, SBS19, SBS21, as well as signatures clearly arising from exogenous causation. We conclude that the DRT-model provides a plausible molecular framework that augments our current understanding of immunogenetic mechanisms driving oncogenesis. It accommodates both what is known about AID/APOBEC and ADAR somatic mutation strand asymmetries and provides a fully integrated understanding into the molecular origins of common COSMIC SBS signatures. The DRT-paradigm thus provides scientists and clinicians with additional molecular insights into the causal links between deaminase-associated genomic signatures and oncogenic processes.
Collapse
Affiliation(s)
- Edward J. Steele
- Melville Analytics Pty Ltd. and Immunomics, Kangaroo Point, Brisbane 4169, Australia
| | - Robyn A. Lindley
- Department Clinical Pathology, Victorian Comprehensive Cancer Centre (VCCC), University of Melbourne, Melbourne 3052, Australia;
| |
Collapse
|
4
|
Durfee C, Bergstrom EN, Díaz-Gay M, Zhou Y, Temiz NA, Ibrahim MA, Nandi SP, Wang Y, Liu X, Steele CD, Proehl J, Vogel RI, Argyris PP, Alexandrov LB, Harris RS. Tobacco smoke carcinogens exacerbate APOBEC mutagenesis and carcinogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.18.633716. [PMID: 39896515 PMCID: PMC11785121 DOI: 10.1101/2025.01.18.633716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
Mutations in somatic cells are inflicted by both extrinsic and intrinsic sources and contribute over time to cancer. Tobacco smoke contains chemical carcinogens that have been causatively implicated with cancers of the lung and head & neck1,2. APOBEC family DNA cytosine deaminases have emerged as endogenous sources of mutation in cancer, with hallmark mutational signatures (SBS2/SBS13) that often co-occur in tumors of tobacco smokers with an equally diagnostic mutational signature (SBS4)3,4. Here we challenge the dogma that mutational processes are thought to occur independently and with additive impact by showing that 4-nitroquinoline 1-oxide (NQO), a model carcinogen for tobacco exposure, sensitizes cells to APOBEC3B (A3B) mutagenesis and leads to synergistic increases in both SBS2 mutation loads and oral carcinomas in vivo. NQO-exposed/A3B-expressing animals exhibit twice as many head & neck lesions as carcinogen-exposed wildtype animals. This increase in carcinogenesis is accompanied by a synergistic increase in mutations from APOBEC signature SBS2, but not from NQO signature SBS4. Interestingly, a large proportion of A3B-catalyzed SBS2 mutations occurs as strand-coordinated pairs within 32 nucleotides of each other in transcribed regions, suggesting a mechanism in which removal of NQO-DNA adducts by nucleotide excision repair exposes short single-stranded DNA tracts to enzymatic deamination. These highly enriched pairs of APOBEC signature mutations are termed didyma (Greek for twins) and are mechanistically distinct from other types of clustered mutation (omikli and kataegis). Computational analyses of lung and head & neck tumor genomes show that both APOBEC mutagenesis and didyma are elevated in cancers from smokers compared to non-smokers. APOBEC signature mutations and didyma are also elevated in normal lung tissues in smokers prior to cancer initiation. Collectively, these results indicate that DNA adducting mutagens in tobacco smoke can amplify DNA damage and mutagenesis by endogenous APOBEC enzymes and, more broadly, suggest that mutational mechanisms can interact synergistically in both cancer initiation and promotion.
Collapse
Affiliation(s)
- Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA, 92093
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA, 92093
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA, 92093
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA, 92093
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA, 92093
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA, 92093
- Digital Genomics Group, Structural Biology Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain, 28029
| | - Yufan Zhou
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Mahmoud A. Ibrahim
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Shuvro P. Nandi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA, 92093
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA, 92093
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA, 92093
| | - Yaxi Wang
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Xingyu Liu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Christopher D. Steele
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA, 92093
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA, 92093
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA, 92093
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Rachel I. Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Department of Obstetrics, Gynecology, and Women’s Health, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Prokopios P. Argyris
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, Ohio, USA, 43210
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA, 92093
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA, 92093
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA, 92093
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| |
Collapse
|
5
|
Kim YN, Gulhan DC, Jin H, Glodzik D, Park PJ. Recent Advances in Genomic Approaches for the Detection of Homologous Recombination Deficiency. Cancer Res Treat 2024; 56:975-990. [PMID: 39026430 PMCID: PMC11491256 DOI: 10.4143/crt.2024.154] [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: 02/15/2024] [Accepted: 07/16/2024] [Indexed: 07/20/2024] Open
Abstract
Accurate detection of homologous recombination deficiency (HRD) in cancer patients is paramount in clinical applications, as HRD confers sensitivity to poly(ADP-ribose) polymerase (PARP) inhibitors. With the advances in genome sequencing technology, mutational profiling on a genome-wide scale has become readily accessible, and our knowledge of the genomic consequences of HRD has been greatly expanded and refined. Here, we review the recent advances in HRD detection methods. We examine the copy number and structural alterations that often accompany the genome instability that results from HRD, describe the advantages of mutational signature-based methods that do not rely on specific gene mutations, and review some of the existing algorithms used for HRD detection. We also discuss the choice of sequencing platforms (panel, exome, or whole-genome) and catalog the HRD detection assays used in key PARP inhibitor trials.
Collapse
Affiliation(s)
- Yoo-Na Kim
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Doga C. Gulhan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Dominik Glodzik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
6
|
Diossy M, Tisza V, Li H, Sahgal P, Zhou J, Sztupinszki Z, Young D, Nousome D, Kuo C, Jiang J, Chen Y, Ebner R, Sesterhenn IA, Moncur JT, Chesnut GT, Petrovics G, Klus GT, Valcz G, Nuzzo PV, Ribli D, Börcsök J, Prosz A, Krzystanek M, Ried T, Szuts D, Rizwan K, Kaochar S, Pathania S, D'Andrea AD, Csabai I, Srivastava S, Freedman ML, Dobi A, Spisak S, Szallasi Z. Frequent CHD1 deletions in prostate cancers of African American men is associated with rapid disease progression. NPJ Precis Oncol 2024; 8:208. [PMID: 39294262 PMCID: PMC11411125 DOI: 10.1038/s41698-024-00705-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 09/11/2024] [Indexed: 09/20/2024] Open
Abstract
We analyzed genomic data from the prostate cancer of African- and European American men to identify differences contributing to racial disparity of outcome. We also performed FISH-based studies of Chromodomain helicase DNA-binding protein 1 (CHD1) loss on prostate cancer tissue microarrays. We created CHD1-deficient prostate cancer cell lines for genomic, drug sensitivity and functional homologous recombination (HR) activity analysis. Subclonal deletion of CHD1 was nearly three times as frequent in prostate tumors of African American than in European American men and it associates with rapid disease progression. CHD1 deletion was not associated with HR deficiency associated mutational signatures or HR deficiency as detected by RAD51 foci formation. This was consistent with the moderate increase of olaparib and talazoparib sensitivity with several CHD1 deficient cell lines showing talazoparib sensitivity in the clinically relevant concentration range. CHD1 loss may contribute to worse disease outcome in African American men.
Collapse
Affiliation(s)
- Miklos Diossy
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Hua Li
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Pranshu Sahgal
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zsofia Sztupinszki
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Denise Young
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Darryl Nousome
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Claire Kuo
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Jiji Jiang
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Yongmei Chen
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | | | | | | | - Gregory T Chesnut
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Gyorgy Petrovics
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Gregory T Klus
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Gabor Valcz
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, 1051, Hungary
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dezso Ribli
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | | | - Aurel Prosz
- Danish Cancer Institute, Copenhagen, Denmark
| | | | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - David Szuts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Kinza Rizwan
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Salma Kaochar
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Shailja Pathania
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA, USA
- Department of Biology, University of Massachusetts, Boston, MA, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Shiv Srivastava
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Biochemistry and Molecular & Cell Biology, Georgetown University School of Medicine, Washington, DC, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Albert Dobi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA.
| | - Sandor Spisak
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- 2nd Department of Pathology and Department of Bioinformatics, Semmelweis University, Budapest, Hungary.
| |
Collapse
|
7
|
Pan JW, Tan ZC, Ng PS, Zabidi MMA, Nur Fatin P, Teo JY, Hasan SN, Islam T, Teoh LY, Jamaris S, See MH, Yip CH, Rajadurai P, Looi LM, Taib NAM, Rueda OM, Caldas C, Chin SF, Lim J, Teo SH. Gene expression signature for predicting homologous recombination deficiency in triple-negative breast cancer. NPJ Breast Cancer 2024; 10:60. [PMID: 39030225 PMCID: PMC11271517 DOI: 10.1038/s41523-024-00671-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 07/10/2024] [Indexed: 07/21/2024] Open
Abstract
Triple-negative breast cancers (TNBCs) are a subset of breast cancers that have remained difficult to treat. A proportion of TNBCs arising in non-carriers of BRCA pathogenic variants have genomic features that are similar to BRCA carriers and may also benefit from PARP inhibitor treatment. Using genomic data from 129 TNBC samples from the Malaysian Breast Cancer (MyBrCa) cohort, we developed a gene expression-based machine learning classifier for homologous recombination deficiency (HRD) in TNBCs. The classifier identified samples with HRD mutational signature at an AUROC of 0.93 in MyBrCa validation datasets and 0.84 in TCGA TNBCs. Additionally, the classifier strongly segregated HRD-associated genomic features in TNBCs from TCGA, METABRIC, and ICGC. Thus, our gene expression classifier may identify triple-negative breast cancer patients with homologous recombination deficiency, suggesting an alternative method to identify individuals who may benefit from treatment with PARP inhibitors or platinum chemotherapy.
Collapse
Affiliation(s)
- Jia-Wern Pan
- Cancer Research Malaysia, Subang Jaya, Malaysia.
| | | | - Pei-Sze Ng
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | | | | | | | | | - Tania Islam
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Li-Ying Teoh
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Suniza Jamaris
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Mee-Hoong See
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | | | - Pathmanathan Rajadurai
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Nur Aishah Mohd Taib
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Oscar M Rueda
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Joanna Lim
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
8
|
Bainbridge LJ, Daigaku Y. Adaptive use of error-prone DNA polymerases provides flexibility in genome replication during tumorigenesis. Cancer Sci 2024; 115:2125-2137. [PMID: 38651239 PMCID: PMC11247608 DOI: 10.1111/cas.16188] [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: 01/11/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Human cells possess many different polymerase enzymes, which collaborate in conducting DNA replication and genome maintenance to ensure faithful duplication of genetic material. Each polymerase performs a specialized role, together providing a balance of accuracy and flexibility to the replication process. Perturbed replication increases the requirement for flexibility to ensure duplication of the entire genome. Flexibility is provided via the use of error-prone polymerases, which maintain the progression of challenged DNA replication at the expense of mutagenesis, an enabling characteristic of cancer. This review describes our recent understanding of mechanisms that alter the usage of polymerases during tumorigenesis and examines the implications of this for cell survival and tumor progression. Although expression levels of polymerases are often misregulated in cancers, this does not necessarily alter polymerase usage since an additional regulatory step may govern the use of these enzymes. We therefore also examine how the regulatory mechanisms of DNA polymerases, such as Rad18-mediated PCNA ubiquitylation, may impact the functionalization of error-prone polymerases to tolerate oncogene-induced replication stress. Crucially, it is becoming increasingly evident that cancer cells utilize error-prone polymerases to sustain ongoing replication in response to oncogenic mutations which inactivate key DNA replication and repair pathways, such as BRCA deficiency. This accelerates mutagenesis and confers chemoresistance, but also presents a dependency that can potentially be exploited by therapeutics.
Collapse
Affiliation(s)
- Lewis J. Bainbridge
- Cancer Genome Dynamics Project, Cancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yasukazu Daigaku
- Cancer Genome Dynamics Project, Cancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
| |
Collapse
|
9
|
Németh E, Szüts D. The mutagenic consequences of defective DNA repair. DNA Repair (Amst) 2024; 139:103694. [PMID: 38788323 DOI: 10.1016/j.dnarep.2024.103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Multiple separate repair mechanisms safeguard the genome against various types of DNA damage, and their failure can increase the rate of spontaneous mutagenesis. The malfunction of distinct repair mechanisms leads to genomic instability through different mutagenic processes. For example, defective mismatch repair causes high base substitution rates and microsatellite instability, whereas homologous recombination deficiency is characteristically associated with deletions and chromosome instability. This review presents a comprehensive collection of all mutagenic phenotypes associated with the loss of each DNA repair mechanism, drawing on data from a variety of model organisms and mutagenesis assays, and placing greatest emphasis on systematic analyses of human cancer datasets. We describe the latest theories on the mechanism of each mutagenic process, often explained by reliance on an alternative repair pathway or the error-prone replication of unrepaired, damaged DNA. Aided by the concept of mutational signatures, the genomic phenotypes can be used in cancer diagnosis to identify defective DNA repair pathways.
Collapse
Affiliation(s)
- Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
| |
Collapse
|
10
|
Vergara X, Manjón AG, de Haas M, Morris B, Schep R, Leemans C, Friskes A, Beijersbergen RL, Sanders MA, Medema RH, van Steensel B. Widespread chromatin context-dependencies of DNA double-strand break repair proteins. Nat Commun 2024; 15:5334. [PMID: 38909016 PMCID: PMC11193718 DOI: 10.1038/s41467-024-49232-x] [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: 02/19/2024] [Accepted: 05/28/2024] [Indexed: 06/24/2024] Open
Abstract
DNA double-strand breaks are repaired by multiple pathways, including non-homologous end-joining (NHEJ) and microhomology-mediated end-joining (MMEJ). The balance of these pathways is dependent on the local chromatin context, but the underlying mechanisms are poorly understood. By combining knockout screening with a dual MMEJ:NHEJ reporter inserted in 19 different chromatin environments, we identified dozens of DNA repair proteins that modulate pathway balance dependent on the local chromatin state. Proteins that favor NHEJ mostly synergize with euchromatin, while proteins that favor MMEJ generally synergize with distinct types of heterochromatin. Examples of the former are BRCA2 and POLL, and of the latter the FANC complex and ATM. Moreover, in a diversity of human cancer types, loss of several of these proteins alters the distribution of pathway-specific mutations between heterochromatin and euchromatin. Together, these results uncover a complex network of proteins that regulate MMEJ:NHEJ balance in a chromatin context-dependent manner.
Collapse
Affiliation(s)
- Xabier Vergara
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Anna G Manjón
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Marcel de Haas
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Ben Morris
- NKI Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ruben Schep
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Christ Leemans
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Anoek Friskes
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Roderick L Beijersbergen
- NKI Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mathijs A Sanders
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.
| |
Collapse
|
11
|
Kong LR, Gupta K, Wu AJ, Perera D, Ivanyi-Nagy R, Ahmed SM, Tan TZ, Tan SLW, Fuddin A, Sundaramoorthy E, Goh GS, Wong RTX, Costa ASH, Oddy C, Wong H, Patro CPK, Kho YS, Huang XZ, Choo J, Shehata M, Lee SC, Goh BC, Frezza C, Pitt JJ, Venkitaraman AR. A glycolytic metabolite bypasses "two-hit" tumor suppression by BRCA2. Cell 2024; 187:2269-2287.e16. [PMID: 38608703 DOI: 10.1016/j.cell.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/01/2024] [Accepted: 03/07/2024] [Indexed: 04/14/2024]
Abstract
Knudson's "two-hit" paradigm posits that carcinogenesis requires inactivation of both copies of an autosomal tumor suppressor gene. Here, we report that the glycolytic metabolite methylglyoxal (MGO) transiently bypasses Knudson's paradigm by inactivating the breast cancer suppressor protein BRCA2 to elicit a cancer-associated, mutational single-base substitution (SBS) signature in nonmalignant mammary cells or patient-derived organoids. Germline monoallelic BRCA2 mutations predispose to these changes. An analogous SBS signature, again without biallelic BRCA2 inactivation, accompanies MGO accumulation and DNA damage in Kras-driven, Brca2-mutant murine pancreatic cancers and human breast cancers. MGO triggers BRCA2 proteolysis, temporarily disabling BRCA2's tumor suppressive functions in DNA repair and replication, causing functional haploinsufficiency. Intermittent MGO exposure incites episodic SBS mutations without permanent BRCA2 inactivation. Thus, a metabolic mechanism wherein MGO-induced BRCA2 haploinsufficiency transiently bypasses Knudson's two-hit requirement could link glycolysis activation by oncogenes, metabolic disorders, or dietary challenges to mutational signatures implicated in cancer evolution.
Collapse
Affiliation(s)
- Li Ren Kong
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Department of Pharmacology, National University of Singapore, Singapore 117600, Singapore
| | - Komal Gupta
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Andy Jialun Wu
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - David Perera
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | | | - Syed Moiz Ahmed
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Shawn Lu-Wen Tan
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Institute of Molecular and Cell Biology (IMCB), A(∗)STAR, Singapore 138673, Singapore
| | | | | | | | | | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Callum Oddy
- Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Hannan Wong
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - C Pawan K Patro
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Yun Suen Kho
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore
| | - Xiao Zi Huang
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore
| | - Joan Choo
- Department of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Mona Shehata
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Soo Chin Lee
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore; Department of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore; Department of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; University of Cologne, 50923 Köln, Germany
| | - Jason J Pitt
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore; Genome Institute of Singapore, A(∗)STAR, Singapore 138673, Singapore
| | - Ashok R Venkitaraman
- Cancer Science Institute of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, Singapore 117599, Singapore; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Institute of Molecular and Cell Biology (IMCB), A(∗)STAR, Singapore 138673, Singapore; Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK; Department of Medicine, National University of Singapore, Singapore 119228, Singapore.
| |
Collapse
|
12
|
Szallasi Z, Diossy M, Tisza V, Li H, Sahgal P, Zhou J, Sztupinszki Z, Young D, Nuosome D, Kuo C, Jiang J, Chen Y, Ebner R, Sesterhenn I, Moncur J, Chesnut G, Petrovics G, T Klus G, Valcz G, Nuzzo P, Ribli D, Börcsök J, Prósz A, Krzystanek M, Ried T, Szüts D, Rizwan K, Kaochar S, Pathania S, D'Andrea A, Csabai I, Srivastava S, Freedman M, Dobi A, Spisak S. Increased frequency of CHD1 deletions in prostate cancers of African American men is associated with rapid disease progression without inducing homologous recombination deficiency. RESEARCH SQUARE 2024:rs.3.rs-3995251. [PMID: 38645014 PMCID: PMC11030533 DOI: 10.21203/rs.3.rs-3995251/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
We analyzed genomic data derived from the prostate cancer of African and European American men in order to identify differences that may contribute to racial disparity of outcome and that could also define novel therapeutic strategies. In addition to analyzing patient derived next generation sequencing data, we performed FISH based confirmatory studies of Chromodomain helicase DNA-binding protein 1 (CHD1) loss on prostate cancer tissue microarrays. We created CRISPR edited, CHD1 deficient prostate cancer cell lines for genomic, drug sensitivity and functional homologous recombination (HR) activity analysis. We found that subclonal deletion of CHD1 is nearly three times as frequent in prostate tumors of African American men than in men of European ancestry and it associates with rapid disease progression. We further showed that CHD1 deletion is not associated with homologous recombination deficiency associated mutational signatures in prostate cancer. In prostate cancer cell line models CHD1 deletion did not induce HR deficiency as detected by RAD51 foci formation assay or mutational signatures, which was consistent with the moderate increase of olaparib sensitivity. CHD1 deficient prostate cancer cells, however, showed higher sensitivity to talazoparib. CHD1 loss may contribute to worse outcome of prostate cancer in African American men. A deeper understanding of the interaction between CHD1 loss and PARP inhibitor sensitivity will be needed to determine the optimal use of targeted agents such as talazoparib in the context of castration resistant prostate cancer.
Collapse
Affiliation(s)
| | | | - Viktoria Tisza
- Institute of Enzymology, Research Centre for Natural Sciences
| | - Hua Li
- Center for Prostate Cancer Research
| | | | - Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Denise Young
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Darryl Nuosome
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Claire Kuo
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Jiji Jiang
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Yongmei Chen
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department Uniformed Services University of the Health Sciences, Bethesda, MD
| | | | | | - Joel Moncur
- Joint Pathology Center, Silver Spring, Maryland, USA
| | - Gregory Chesnut
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Gyorgy Petrovics
- Computational Health Informatics Program, Boston Children's Hospital, USA, Harvard Medical School, Boston, USA
| | | | - Gábor Valcz
- ELKH Translational Extracellular Vesicle Research Group, Budapest, Hungary
| | - Pier Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Dezso Ribli
- Department of Physics of Complex Systems, Eotvos Lorand University, Budapest, Hungary
| | | | | | | | | | - Dávid Szüts
- HUN-REN Research Centre for Natural Sciences
| | - Kinza Rizwan
- Department of Medicine, Baylor College of Medicine, Houston, USA
| | - Salma Kaochar
- Department of Medicine, Baylor College of Medicine, Houston, USA
| | | | | | | | - Shib Srivastava
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Matthew Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Albert Dobi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Sandor Spisak
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network
| |
Collapse
|
13
|
Khandia R, Pandey MK, Garg R, Khan AA, Baklanov I, Alanazi AM, Nepali P, Gurjar P, Choudhary OP. Molecular insights into codon usage analysis of mitochondrial fission and fusion gene: relevance to neurodegenerative diseases. Ann Med Surg (Lond) 2024; 86:1416-1425. [PMID: 38463054 PMCID: PMC10923317 DOI: 10.1097/ms9.0000000000001725] [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: 09/14/2023] [Accepted: 01/05/2024] [Indexed: 03/12/2024] Open
Abstract
Mitochondrial dysfunction is the leading cause of neurodegenerative disorders like Alzheimer's disease and Parkinson's disease. Mitochondria is a highly dynamic organelle continuously undergoing the process of fission and fusion for even distribution of components and maintaining proper shape, number, and bioenergetic functionality. A set of genes governs the process of fission and fusion. OPA1, Mfn1, and Mfn2 govern fusion, while Drp1, Fis1, MIEF1, and MIEF2 genes control fission. Determination of specific molecular patterns of transcripts of these genes revealed the impact of compositional constraints on selecting optimal codons. AGA and CCA codons were over-represented, and CCC, GTC, TTC, GGG, ACG were under-represented in the fusion gene set. In contrast, CTG was over-represented, and GCG, CCG, and TCG were under-represented in the fission gene set. Hydropathicity analysis revealed non-polar protein products of both fission and fusion gene set transcripts. AGA codon repeats are an integral part of translational regulation machinery and present a distinct pattern of over-representation and under-representation in different transcripts within the gene sets, suggestive of selective translational force precisely controlling the occurrence of the codon. Out of six synonymous codons, five synonymous codons encoding for leucine were used differently in both gene sets. Hence, forces regulating the occurrence of AGA and five synonymous leucine-encoding codons suggest translational selection. A correlation of mutational bias with gene expression and codon bias and GRAVY and AROMA signifies the selection pressure in both gene sets, while the correlation of compositional bias with gene expression, codon bias, protein properties, and minimum free energy signifies the presence of compositional constraints. More than 25% of codons of both gene sets showed a significant difference in codon usage. The overall analysis shed light on molecular features of gene sets involved in fission and fusion.
Collapse
Affiliation(s)
| | - Megha Katare Pandey
- Translational Medicine Center, All India Institute of Medical Sciences, Bhopal
| | | | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Igor Baklanov
- Department of Philosophy, North Caucasus Federal University, Stavropol, Russia
| | - Amer M. Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Prakash Nepali
- Government Medical Officer, Bhimad Primary Health Care Center, Government of Nepal, Tanahun, Nepal
| | - Pankaj Gurjar
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Rampura Phul, Bathinda, Punjab, India
| |
Collapse
|
14
|
Tao L, Xia X, Kong S, Wang T, Fan F, Wang W. Natural pentacyclic triterpenoid from Pristimerin sensitizes p53-deficient tumor to PARP inhibitor by ubiquitination of Chk1. Pharmacol Res 2024; 201:107091. [PMID: 38316371 DOI: 10.1016/j.phrs.2024.107091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Inhibition of checkpoint kinase 1 (Chk1) has shown to overcome resistance to poly (ADP-ribose) polymerase (PARP) inhibitors and expand the clinical utility of PARP inhibitors in a broad range of human cancers. Pristimerin, a naturally occurring pentacyclic triterpenoid, has been the focus of intensive studies for its anticancer potential. However, it is not yet known whether low dose of pristimerin can be combined with PARP inhibitors by targeting Chk1 signaling pathway. In this study, we investigated the efficacy, safety and molecular mechanisms of the synergistic effect produced by the combination olaparib and pristimerin in TP53-deficient and BRCA-proficient cell models. As a result, an increased expression of Chk1 was correlated with TP53 mutation, and pristimerin preferentially sensitized p53-defective cells to olaparib. The combination of olaparib and pristimerin resulted in a more pronounced abrogation of DNA synthesis and induction of DNA double-strand breaks (DSBs). Moreover, pristimerin disrupted the constitutional levels of Chk1 and DSB repair activities. Mechanistically, pristimerin promoted K48-linked polyubiquitination and proteasomal degradation of Chk1 while not affecting its kinase domain and activity. Importantly, combinatorial therapy led to a higher rate of tumor growth inhibition without apparent hematological toxicities. In addition, pristimerin suppressed olaparib-induced upregulation of Chk1 and enhanced olaparib-induced DSB marker γΗ2ΑΧ in vivo. Taken together, inhibition of Chk1 by pristimerin has been observed to induce DNA repair deficiency, which may expand the application of olaparib in BRCA-proficient cancers harboring TP53 mutations. Thus, pristimerin can be combined for PARP inhibitor-based therapy.
Collapse
Affiliation(s)
- Li Tao
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Xiangyu Xia
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shujing Kong
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Tingye Wang
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Fangtian Fan
- Anhui Engineering Technology Research Center of Biochemical Pharmaceuticals, School of Pharmacy, Bengbu Medical College, Bengbu, Anhui 233003, China
| | - Weimin Wang
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China; Department of Oncology, Yixing Hospital Affiliated to Medical College of Yangzhou University, Yixing, Jiangsu 214200, China.
| |
Collapse
|
15
|
Póti Á, Szüts D, Vermezovic J. Mutational profile of the regenerative process and de novo genome assembly of the planarian Schmidtea polychroa. Nucleic Acids Res 2024; 52:1779-1792. [PMID: 38180823 PMCID: PMC10899757 DOI: 10.1093/nar/gkad1250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/07/2024] Open
Abstract
Planarians are organisms with a unique capacity to regenerate any part of their body. New tissues are generated in a process that requires many swift cell divisions. How costly is this process to an animal in terms of mutational load remains unknown. Using whole genome sequencing, we defined the mutational profile of the process of regeneration in the planarian species Schmidtea polychroa. We assembled de novo the genome of S. polychroa and analyzed mutations in animals that have undergone regeneration. We observed a threefold increase in the number of mutations and an altered mutational spectrum. High allele frequencies of subclonal mutations in regenerated animals suggested that most of the cells in the regenerated animal were descendants of a small number of stem cells with high expansion potential. We provide, for the first time, the draft genome assembly of S. polychroa, an estimation of the germline mutation rate for a planarian species and the mutational spectrum of the regeneration process of a living organism.
Collapse
Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Jelena Vermezovic
- IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| |
Collapse
|
16
|
Lózsa R, Németh E, Gervai JZ, Márkus BG, Kollarics S, Gyüre Z, Tóth J, Simon F, Szüts D. DNA mismatch repair protects the genome from oxygen-induced replicative mutagenesis. Nucleic Acids Res 2023; 51:11040-11055. [PMID: 37791890 PMCID: PMC10639081 DOI: 10.1093/nar/gkad775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/23/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
DNA mismatch repair (MMR) corrects mismatched DNA bases arising from multiple sources including polymerase errors and base damage. By detecting spontaneous mutagenesis using whole genome sequencing of cultured MMR deficient human cell lines, we show that a primary role of MMR is the repair of oxygen-induced mismatches. We found an approximately twofold higher mutation rate in MSH6 deficient DLD-1 cells or MHL1 deficient HCT116 cells exposed to atmospheric conditions as opposed to mild hypoxia, which correlated with oxidant levels measured using electron paramagnetic resonance spectroscopy. The oxygen-induced mutations were dominated by T to C base substitutions and single T deletions found primarily on the lagging strand. A broad sequence context preference, dependence on replication timing and a lack of transcriptional strand bias further suggested that oxygen-induced mutations arise from polymerase errors rather than oxidative base damage. We defined separate low and high oxygen-specific MMR deficiency mutation signatures common to the two cell lines and showed that the effect of oxygen is observable in MMR deficient cancer genomes, where it best correlates with the contribution of mutation signature SBS21. Our results imply that MMR corrects oxygen-induced genomic mismatches introduced by a replicative process in proliferating cells.
Collapse
Affiliation(s)
- Rita Lózsa
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Judit Z Gervai
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Bence G Márkus
- Stavropoulos Center for Complex Quantum Matter, Department of Physics and Astronomy, University of Notre Dame, Notre Dame, IN 46556, USA
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, H-1525 Budapest, Hungary
- Department of Physics, Institute of Physics, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Sándor Kollarics
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, H-1525 Budapest, Hungary
- Department of Physics, Institute of Physics, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Doctoral School of Molecular Medicine, Semmelweis University, H-1085 Budapest, Hungary
- Turbine Simulated Cell Technologies, H-1027 Budapest, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Ferenc Simon
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, H-1525 Budapest, Hungary
- Department of Physics, Institute of Physics, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| |
Collapse
|
17
|
Lee Y, Moon S, Seok JY, Lee JH, Nam S, Chung YS. Characterization of the genomic alterations in poorly differentiated thyroid cancer. Sci Rep 2023; 13:19154. [PMID: 37932340 PMCID: PMC10628257 DOI: 10.1038/s41598-023-46466-5] [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: 07/26/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023] Open
Abstract
Poorly differentiated thyroid carcinoma (PDTC) is a subtype of thyroid cancer that has a high rate of metastasis or recurrence and a relatively poor prognosis. However, there are few studies that have been conducted on PDTC at the whole protein-coding gene scale. Here, we performed genomic profiling of 15 patients with PDTC originated from follicular thyroid carcinoma using whole exome sequencing and also performed gene functional enrichment analysis of differentially expressed genes (DEGs) for three patients. Further, we investigated genetic variants associated with PDTC progression and the characteristics of clinical pathology. We revealed somatic genomic alterations in the RAF1, MAP2K2, and AKT2 genes that were not reported in previous studies. We confirmed frequent occurrences in the RAS gene in patients with PDTC; the genetic alterations were associated with the RAS-RAF-MEK-ERK/JNK, PI3K-AKT-mTOR signaling pathways, and the cell cycle. DEG analysis showed that immune response was lower in cancer tissues than in normal tissues. Through the association analysis of somatic mutations and the characteristics of clinical pathology from patients with PDTC, the somatic mutations of ABCA12, CLIP1, and ATP13A3 were significantly associated with a vascular invasion phenotype. By providing molecular genetic insight on PDTC, this study may contribute to the discovery of novel therapeutic target candidates.
Collapse
Affiliation(s)
- Yeeun Lee
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Dokjeom-ro 3Beon-gil, 38-13, Namdong-gu, Incheon, 21565, Republic of Korea
| | - SeongRyeol Moon
- A.I. Structural Design Team, Division of Biodrug Analysis, New Drug Development Center, OSONG Medical Innovation Foundation, Cheongju-si, 28160, Chungcheongbuk-do, Korea
| | - Jae Yeon Seok
- Department of Pathology, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin Severance Hospital 363, Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do, 16995, Korea
| | - Joon-Hyop Lee
- Department of Surgery, Gachon University Gil Medical Center, Gachon University College of Medicine, Dokjeom-ro 3Beon-gil, 38-13, Namdong-gu, Incheon, 21565, Republic of Korea
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Dokjeom-ro 3Beon-gil, 38-13, Namdong-gu, Incheon, 21565, Republic of Korea.
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, 21999, Korea.
| | - Yoo Seung Chung
- Department of Surgery, Gachon University Gil Medical Center, Gachon University College of Medicine, Dokjeom-ro 3Beon-gil, 38-13, Namdong-gu, Incheon, 21565, Republic of Korea.
| |
Collapse
|
18
|
Rodriguez-Fos E, Planas-Fèlix M, Burkert M, Puiggròs M, Toedling J, Thiessen N, Blanc E, Szymansky A, Hertwig F, Ishaque N, Beule D, Torrents D, Eggert A, Koche RP, Schwarz RF, Haase K, Schulte JH, Henssen AG. Mutational topography reflects clinical neuroblastoma heterogeneity. CELL GENOMICS 2023; 3:100402. [PMID: 37868040 PMCID: PMC10589636 DOI: 10.1016/j.xgen.2023.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 10/24/2023]
Abstract
Neuroblastoma is a pediatric solid tumor characterized by strong clinical heterogeneity. Although clinical risk-defining genomic alterations exist in neuroblastomas, the mutational processes involved in their generation remain largely unclear. By examining the topography and mutational signatures derived from all variant classes, we identified co-occurring mutational footprints, which we termed mutational scenarios. We demonstrate that clinical neuroblastoma heterogeneity is associated with differences in the mutational processes driving these scenarios, linking risk-defining pathognomonic variants to distinct molecular processes. Whereas high-risk MYCN-amplified neuroblastomas were characterized by signs of replication slippage and stress, homologous recombination-associated signatures defined high-risk non-MYCN-amplified patients. Non-high-risk neuroblastomas were marked by footprints of chromosome mis-segregation and TOP1 mutational activity. Furthermore, analysis of subclonal mutations uncovered differential activity of these processes through neuroblastoma evolution. Thus, clinical heterogeneity of neuroblastoma patients can be linked to differences in the mutational processes that are active in their tumors.
Collapse
Affiliation(s)
- Elias Rodriguez-Fos
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mercè Planas-Fèlix
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Joern Toedling
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nina Thiessen
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Eric Blanc
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Angelika Eggert
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes H. Schulte
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
19
|
Li W, Gao L, Yi X, Shi S, Huang J, Shi L, Zhou X, Wu L, Ying J. Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:962-975. [PMID: 36791952 PMCID: PMC10928375 DOI: 10.1016/j.gpb.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 12/23/2022] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
Defects in genes involved in the DNA damage response cause homologous recombination repair deficiency (HRD). HRD is found in a subgroup of cancer patients for several tumor types, and it has a clinical relevance to cancer prevention and therapies. Accumulating evidence has identified HRD as a biomarker for assessing the therapeutic response of tumor cells to poly(ADP-ribose) polymerase inhibitors and platinum-based chemotherapies. Nevertheless, the biology of HRD is complex, and its applications and the benefits of different HRD biomarker assays are controversial. This is primarily due to inconsistencies in HRD assessments and definitions (gene-level tests, genomic scars, mutational signatures, or a combination of these methods) and difficulties in assessing the contribution of each genomic event. Therefore, we aim to review the biological rationale and clinical evidence of HRD as a biomarker. This review provides a blueprint for the standardization and harmonization of HRD assessments.
Collapse
Affiliation(s)
- Wenbin Li
- 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
| | - Lin Gao
- Geneplus-Shenzhen, Shenzhen 518000, China; Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Yi
- Geneplus-Beijing, Beijing 102206, China
| | | | - Jie Huang
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, 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, Beijing 100021, China
| | - Jianming Ying
- 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.
| |
Collapse
|
20
|
Wu AJ, Perera A, Kularatnarajah L, Korsakova A, Pitt JJ. Mutational signature assignment heterogeneity is widespread and can be addressed by ensemble approaches. Brief Bioinform 2023; 24:bbad331. [PMID: 37742051 PMCID: PMC10518036 DOI: 10.1093/bib/bbad331] [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: 06/11/2023] [Revised: 08/03/2023] [Accepted: 08/27/2023] [Indexed: 09/25/2023] Open
Abstract
Single-base substitution (SBS) mutational signatures have become standard practice in cancer genomics. In lieu of de novo signature extraction, reference signature assignment allows users to estimate the activities of pre-established SBS signatures within individual malignancies. Several tools have been developed for this purpose, each with differing methodologies. However, due to a lack of standardization, there may be inter-tool variability in signature assignment. We deeply characterized three assignment strategies and five SBS signature assignment tools. We observed that assignment strategy choice can significantly influence results and interpretations. Despite varying recommendations by tools, Refit performed best by reducing overfitting and maximizing reconstruction of the original mutational spectra. Even after uniform application of Refit, tools varied remarkably in signature assignments both qualitatively (Jaccard index = 0.38-0.83) and quantitatively (Kendall tau-b = 0.18-0.76). This phenomenon was exacerbated for 'flat' signatures such as the homologous recombination deficiency signature SBS3. An ensemble approach (EnsembleFit), which leverages output from all five tools, increased SBS3 assignment accuracy in BRCA1/2-deficient breast carcinomas. After generating synthetic mutational profiles for thousands of pan-cancer tumors, EnsembleFit reduced signature activity assignment error 15.9-24.7% on average using Catalogue of Somatic Mutations In Cancer and non-standard reference signature sets. We have also released the EnsembleFit web portal (https://www.ensemblefit.pittlabgenomics.com) for users to generate or download ensemble-based SBS signature assignments using any strategy and combination of tools. Overall, we show that signature assignment heterogeneity across tools and strategies is non-negligible and propose a viable, ensemble solution.
Collapse
Affiliation(s)
- Andy J Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- School of Medicine, National University of Singapore, Singapore, Singapore
| | - Akila Perera
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | | | - Anna Korsakova
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| |
Collapse
|
21
|
Gyüre Z, Póti Á, Németh E, Szikriszt B, Lózsa R, Krawczyk M, Richardson AL, Szüts D. Spontaneous mutagenesis in human cells is controlled by REV1-Polymerase ζ and PRIMPOL. Cell Rep 2023; 42:112887. [PMID: 37498746 DOI: 10.1016/j.celrep.2023.112887] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/09/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Translesion DNA synthesis (TLS) facilitates replication over damaged or difficult-to-replicate templates by employing specialized DNA polymerases. We investigate the effect on spontaneous mutagenesis of three main TLS control mechanisms: REV1 and PCNA ubiquitylation that recruit TLS polymerases and PRIMPOL that creates post-replicative gaps. Using whole-genome sequencing of cultured human RPE-1 cell clones, we find that REV1 and Polymerase ζ are wholly responsible for one component of base substitution mutagenesis that resembles homologous recombination deficiency, whereas the remaining component that approximates oxidative mutagenesis is reduced in PRIMPOL-/- cells. Small deletions in short repeats appear in REV1-/-PCNAK164R/K164R double mutants, revealing an alternative TLS mechanism. Also, 500-5,000 bp deletions appear in REV1-/- and REV3L-/- mutants, and chromosomal instability is detectable in REV1-/-PRIMPOL-/- cells. Our results indicate that TLS protects the genome from deletions and large rearrangements at the expense of being responsible for the majority of spontaneous base substitutions.
Collapse
Affiliation(s)
- Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; Doctoral School of Molecular Medicine, Semmelweis University, 1085 Budapest, Hungary; Turbine Simulated Cell Technologies, 1027 Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Rita Lózsa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Michał Krawczyk
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; National Laboratory for Drug Research and Development, 1117 Budapest, Hungary.
| |
Collapse
|
22
|
Maharati A, Samsami Y, Latifi H, Tolue Ghasaban F, Moghbeli M. Role of the long non-coding RNAs in regulation of Gemcitabine response in tumor cells. Cancer Cell Int 2023; 23:168. [PMID: 37580768 PMCID: PMC10426205 DOI: 10.1186/s12935-023-03004-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
Chemotherapy is widely used as one of the first line therapeutic methods in cancer patients. However, chemotherapeutic resistance is one of the most common problems in cancer patients, which leads to the therapeutic failure and tumor relapse. Considering the side effects of chemotherapy drugs in normal tissues, it is required to investigate the molecular mechanisms involved in drug resistance to improve the therapeutic strategies in cancer patients. Long non-coding RNAs (lncRNAs) have pivotal roles in regulation of cellular processes associated with drug resistance. LncRNAs deregulations have been frequently reported in a wide range of chemo-resistant tumors. Gemcitabine (GEM) as a nucleoside analog has a wide therapeutic application in different cancers. However, GEM resistance is considered as a therapeutic challenge. Considering the role of lncRNAs in the occurrence of GEM resistance, in the present review we discussed the molecular mechanisms of lncRNAs in regulation of GEM response among cancer patients. It has been reported that lncRNAs have mainly an oncogenic role as the inducers of GEM resistance through direct or indirect regulation of transcription factors, autophagy, polycomb complex, and signaling pathways such as PI3K/AKT, MAPK, WNT, JAK/STAT, and TGF-β. This review paves the way to present the lncRNAs as non-invasive markers to predict GEM response in cancer patients. Therefore, lncRNAs can be introduced as the efficient markers to reduce the possible chemotherapeutic side effects in GEM resistant cancer patients and define a suitable therapeutic strategy among these patients.
Collapse
Affiliation(s)
- Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yalda Samsami
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hanieh Latifi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Faezeh Tolue Ghasaban
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
23
|
Mazouzi A, Moser SC, Abascal F, van den Broek B, Del Castillo Velasco-Herrera M, van der Heijden I, Hekkelman M, Drenth AP, van der Burg E, Kroese LJ, Jalink K, Adams DJ, Jonkers J, Brummelkamp TR. FIRRM/C1orf112 mediates resolution of homologous recombination intermediates in response to DNA interstrand crosslinks. SCIENCE ADVANCES 2023; 9:eadf4409. [PMID: 37256941 PMCID: PMC10413679 DOI: 10.1126/sciadv.adf4409] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
DNA interstrand crosslinks (ICLs) pose a major obstacle for DNA replication and transcription if left unrepaired. The cellular response to ICLs requires the coordination of various DNA repair mechanisms. Homologous recombination (HR) intermediates generated in response to ICLs, require efficient and timely conversion by structure-selective endonucleases. Our knowledge on the precise coordination of this process remains incomplete. Here, we designed complementary genetic screens to map the machinery involved in the response to ICLs and identified FIRRM/C1orf112 as an indispensable factor in maintaining genome stability. FIRRM deficiency leads to hypersensitivity to ICL-inducing compounds, accumulation of DNA damage during S-G2 phase of the cell cycle, and chromosomal aberrations, and elicits a unique mutational signature previously observed in HR-deficient tumors. In addition, FIRRM is recruited to ICLs, controls MUS81 chromatin loading, and thereby affects resolution of HR intermediates. FIRRM deficiency in mice causes early embryonic lethality and accelerates tumor formation. Thus, FIRRM plays a critical role in the response to ICLs encountered during DNA replication.
Collapse
Affiliation(s)
- Abdelghani Mazouzi
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Amsterdam, Netherlands
| | - Sarah C. Moser
- Oncode Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Bram van den Broek
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, Netherlands
- BioImaging Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Ingrid van der Heijden
- Oncode Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Maarten Hekkelman
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anne Paulien Drenth
- Oncode Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eline van der Burg
- Oncode Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Lona J. Kroese
- Animal Modeling Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Kees Jalink
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - David J. Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Jos Jonkers
- Oncode Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Thijn R. Brummelkamp
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Amsterdam, Netherlands
| |
Collapse
|
24
|
Saar M, Jaal J, Meltsov A, Laasfeld T, Lust H, Kasvandik S, Lavogina D. Exploring the Molecular Players behind the Potentiation of Chemotherapy Effects by Durvalumab in Lung Adenocarcinoma Cell Lines. Pharmaceutics 2023; 15:pharmaceutics15051485. [PMID: 37242727 DOI: 10.3390/pharmaceutics15051485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Immune checkpoint inhibitors are increasingly used in combination with chemotherapy for the treatment of non-small cell lung cancer, yet the success of combination therapies is relatively limited. Thus, more detailed insight regarding the tumor molecular markers that may affect the responsiveness of patients to therapy is required. Here, we set out to explore the proteome of two lung adenocarcinoma cell lines (HCC-44 and A549) treated with cisplatin, pemetrexed, durvalumab, and the corresponding mixtures to establish the differences in post-treatment protein expression that can serve as markers of chemosensitivity or resistance. The mass spectrometry study showed that the addition of durvalumab to the treatment mixture resulted in cell line- and chemotherapeutic agent-dependent responses and confirmed the previously reported involvement of DNA repair machinery in the potentiation of the chemotherapy effect. Further validation using immunofluorescence also indicated that the potentiating effect of durvalumab in the case of cisplatin treatment was dependent on the tumor suppressor RB-1 in the PD-L1 weakly positive cells. In addition, we identified aldehyde dehydrogenase ALDH1A3 as the general putative resistance marker. Further studies in patient biopsy samples will be required to confirm the clinical significance of these findings.
Collapse
Affiliation(s)
- Marika Saar
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, 50406 Tartu, Estonia
- Institute of Pharmacy, University of Tartu, 50411 Tartu, Estonia
- Pharmacy, Tartu University Hospital, 50406 Tartu, Estonia
| | - Jana Jaal
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, 50406 Tartu, Estonia
- Haematology and Oncology Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Alvin Meltsov
- Competence Centre on Health Technologies, 50411 Tartu, Estonia
- Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Tõnis Laasfeld
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia
- Department of Computer Science, University of Tartu, 51009 Tartu, Estonia
| | - Helen Lust
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, 50406 Tartu, Estonia
| | - Sergo Kasvandik
- Proteomics Core Facility, Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Darja Lavogina
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, 50406 Tartu, Estonia
- Competence Centre on Health Technologies, 50411 Tartu, Estonia
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia
| |
Collapse
|
25
|
Pancotti C, Rollo C, Birolo G, Benevenuta S, Fariselli P, Sanavia T. Unravelling the instability of mutational signatures extraction via archetypal analysis. Front Genet 2023; 13:1049501. [PMID: 36685831 PMCID: PMC9846778 DOI: 10.3389/fgene.2022.1049501] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
The high cosine similarity between some single-base substitution mutational signatures and their characteristic flat profiles could suggest the presence of overfitting and mathematical artefacts. The newest version (v3.3) of the signature database available in the Catalogue Of Somatic Mutations In Cancer (COSMIC) provides a collection of 79 mutational signatures, which has more than doubled with respect to previous version (30 profiles available in COSMIC signatures v2), making more critical the associations between signatures and specific mutagenic processes. This study both provides a systematic assessment of the de novo extraction task through simulation scenarios based on the latest version of the COSMIC signatures and highlights, through a novel approach using archetypal analysis, which COSMIC signatures are redundant and more likely to be considered as mathematical artefacts. 29 archetypes were able to reconstruct the profile of all the COSMIC signatures with cosine similarity > 0.8. Interestingly, these archetypes tend to group similar original signatures sharing either the same aetiology or similar biological processes. We believe that these findings will be useful to encourage the development of new de novo extraction methods avoiding the redundancy of information among the signatures while preserving the biological interpretation.
Collapse
|
26
|
Guo JT, Malik F. Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches. Biomolecules 2022; 12:biom12091187. [PMID: 36139026 PMCID: PMC9496475 DOI: 10.3390/biom12091187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022] Open
Abstract
Single-stranded DNA (ssDNA) binding proteins (SSBs) are critical in maintaining genome stability by protecting the transient existence of ssDNA from damage during essential biological processes, such as DNA replication and gene transcription. The single-stranded region of telomeres also requires protection by ssDNA binding proteins from being attacked in case it is wrongly recognized as an anomaly. In addition to their critical roles in genome stability and integrity, it has been demonstrated that ssDNA and SSB-ssDNA interactions play critical roles in transcriptional regulation in all three domains of life and viruses. In this review, we present our current knowledge of the structure and function of SSBs and the structural features for SSB binding specificity. We then discuss the machine learning-based approaches that have been developed for the prediction of SSBs from double-stranded DNA (dsDNA) binding proteins (DSBs).
Collapse
|
27
|
Cresta Morgado P, Mateo J. Clinical implications of homologous recombination repair mutations in prostate cancer. Prostate 2022; 82 Suppl 1:S45-S59. [PMID: 35657156 DOI: 10.1002/pros.24352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 03/28/2022] [Indexed: 11/06/2022]
Abstract
Prostate cancer is a disease with significant interpatient genomics, with a proportion of patients presenting mutations in key homologous recombination repair (HRR) gene aberrations, particularly in late-stage disease. A better understanding of the genomic landscape of prostate cancer and the prognostic and predictive value of HRR mutations could lead to more precise care for prostate cancer patients. BRCA1/2 mutations are associated with a more aggressive disease course and higher risk of developing lethal prostate cancer, but also identify patients who could benefit from directed therapeutic strategies with PARP inhibitors. Other HRR mutations are also frequent but their prognostic and predictive value for prostate cancer patients is less clear. Moreover, a proportion of these mutations are associated with inherited germline defects, being relevant for the patients' risk of second malignancies but also to inform their relatives' risk of cancer through cascade testing. In this manuscript, we review current knowledge of the prognostic and predictive value for different HHR alterations across the different prostate cancer disease states. Additionally, we assess the challenges to implement genomic testing in clinical practice for prostate cancer patients.
Collapse
Affiliation(s)
- Pablo Cresta Morgado
- Medical Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Prostate Cancer Translational Research Group, Barcelona, Spain
| | - Joaquin Mateo
- Medical Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Prostate Cancer Translational Research Group, Barcelona, Spain
| |
Collapse
|
28
|
Feng YL, Liu Q, Chen RD, Liu SC, Huang ZC, Liu KM, Yang XY, Xie AY. DNA nicks induce mutational signatures associated with BRCA1 deficiency. Nat Commun 2022; 13:4285. [PMID: 35879372 PMCID: PMC9314409 DOI: 10.1038/s41467-022-32011-x] [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: 01/26/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Analysis of human cancer genome sequences has revealed specific mutational signatures associated with BRCA1-deficient tumors, but the underlying mechanisms remain poorly understood. Here, we show that one-ended DNA double strand breaks (DSBs) converted from CRISPR/Cas9-induced nicks by DNA replication, not two-ended DSBs, cause more characteristic chromosomal aberrations and micronuclei in Brca1-deficient cells than in wild-type cells. BRCA1 is required for efficient homologous recombination of these nick-converted DSBs and suppresses bias towards long tract gene conversion and tandem duplication (TD) mediated by two-round strand invasion in a replication strand asymmetry. However, aberrant repair of these nick-converted one-ended DSBs, not that of two-ended DSBs in Brca1-deficient cells, generates mutational signatures such as small indels with microhomology (MH) at the junctions, translocations and small MH-mediated TDs, resembling those in BRCA1-deficient tumors. These results suggest a major contribution of DNA nicks to mutational signatures associated with BRCA1 deficiency in cancer and the underlying mechanisms.
Collapse
Affiliation(s)
- Yi-Li Feng
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China. .,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China.
| | - Qian Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - Ruo-Dan Chen
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - Si-Cheng Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - Zhi-Cheng Huang
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - Kun-Ming Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - Xiao-Ying Yang
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China.,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China
| | - An-Yong Xie
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310019, Hangzhou, Zhejiang, P. R. China. .,Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 310029, Hangzhou, Zhejiang, P. R. China.
| |
Collapse
|
29
|
Khandia R, Sharma A, Alqahtani T, Alqahtani AM, Asiri YI, Alqahtani S, Alharbi AM, Kamal MA. Strong Selectional Forces Fine-Tune CpG Content in Genes Involved in Neurological Disorders as Revealed by Codon Usage Patterns. Front Neurosci 2022; 16:887929. [PMID: 35757545 PMCID: PMC9226491 DOI: 10.3389/fnins.2022.887929] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/04/2022] [Indexed: 02/05/2023] Open
Abstract
Neurodegenerative disorders cause irreversible damage to the neurons and adversely affect the quality of life. Protein misfolding and their aggregation in specific parts of the brain, mitochondrial dysfunction, calcium load, proteolytic stress, and oxidative stress are among the causes of neurodegenerative disorders. In addition, altered metabolism has been associated with neurodegeneration as evidenced by reductions in glutamine and alanine in transient global amnesia patients, higher homocysteine-cysteine disulfide, and lower methionine decline in serum urea have been observed in Alzheimer's disease patients. Neurodegeneration thus appears to be a culmination of altered metabolism. The study's objective is to analyze various attributes like composition, physical properties of the protein, and factors like selectional and mutational forces, influencing codon usage preferences in a panel of genes involved directly or indirectly in metabolism and contributing to neurodegeneration. Various parameters, including gene composition, dinucleotide analysis, Relative synonymous codon usage (RSCU), Codon adaptation index (CAI), neutrality and parity plots, and different protein indices, were computed and analyzed to determine the codon usage pattern and factors affecting it. The correlation of intrinsic protein properties such as the grand average of hydropathicity index (GRAVY), isoelectric point, hydrophobicity, and acidic, basic, and neutral amino acid content has been found to influence codon usage. In genes up to 800 amino acids long, the GC3 content was highly variable, while GC12 content was relatively constant. An optimum CpG content is present in genes to maintain a high expression level as required for genes involved in metabolism. Also observed was a low codon usage bias with a higher protein expression level. Compositional parameters and nucleotides at the second position of codons played essential roles in explaining the extent of bias. Overall analysis indicated that the dominance of selection pressure and compositional constraints and mutational forces shape codon usage.
Collapse
Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Anushri Sharma
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Yahya I Asiri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Saud Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Ahmed M Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh.,Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| |
Collapse
|
30
|
Levatić J, Salvadores M, Fuster-Tormo F, Supek F. Mutational signatures are markers of drug sensitivity of cancer cells. Nat Commun 2022; 13:2926. [PMID: 35614096 PMCID: PMC9132939 DOI: 10.1038/s41467-022-30582-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 05/09/2022] [Indexed: 02/06/2023] Open
Abstract
Genomic analyses have revealed mutational footprints associated with DNA maintenance gone awry, or with mutagen exposures. Because cancer therapeutics often target DNA synthesis or repair, we asked if mutational signatures make useful markers of drug sensitivity. We detect mutational signatures in cancer cell line exomes (where matched healthy tissues are not available) by adjusting for the confounding germline mutation spectra across ancestries. We identify robust associations between various mutational signatures and drug activity across cancer cell lines; these are as numerous as associations with established genetic markers such as driver gene alterations. Signatures of prior exposures to DNA damaging agents - including chemotherapy - tend to associate with drug resistance, while signatures of deficiencies in DNA repair tend to predict sensitivity towards particular therapeutics. Replication analyses across independent drug and CRISPR genetic screening data sets reveal hundreds of robust associations, which are provided as a resource for drug repurposing guided by mutational signature markers.
Collapse
Affiliation(s)
- Jurica Levatić
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Marina Salvadores
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Francisco Fuster-Tormo
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
- MDS Group, Josep Carreras Leukaemia Research Institute, Ctra de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010, Barcelona, Spain.
| |
Collapse
|
31
|
Abstract
Analysis of cancer genome sequences reveals new mutational signatures.
Collapse
Affiliation(s)
- Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| |
Collapse
|
32
|
DeWeerd RA, Németh E, Póti Á, Petryk N, Chen CL, Hyrien O, Szüts D, Green AM. Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers. Cell Rep 2022; 38:110555. [PMID: 35320711 PMCID: PMC9283007 DOI: 10.1016/j.celrep.2022.110555] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
Mutational signatures defined by single base substitution (SBS) patterns in cancer have elucidated potential mutagenic processes that contribute to malignancy. Two prevalent mutational patterns in human cancers are attributed to the APOBEC3 cytidine deaminase enzymes. Among the seven human APOBEC3 proteins, APOBEC3A is a potent deaminase and proposed driver of cancer mutagenesis. In this study, we prospectively examine genome-wide aberrations by expressing human APOBEC3A in avian DT40 cells. From whole-genome sequencing, we detect hundreds to thousands of base substitutions per genome. The APOBEC3A signature includes widespread cytidine mutations and a unique insertion-deletion (indel) signature consisting largely of cytidine deletions. This multi-dimensional APOBEC3A signature is prevalent in human cancer genomes. Our data further reveal replication-associated mutations, the rate of stem-loop and clustered mutations, and deamination of methylated cytidines. This comprehensive signature of APOBEC3A mutagenesis is a tool for future studies and a potential biomarker for APOBEC3 activity in cancer.
Collapse
Affiliation(s)
- Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nataliya Petryk
- Epigenetics & Cell Fate UMR7216, CNRS, University of Paris, 35 rue Hélène Brion, 75013 Paris, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75005 Paris, France
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
33
|
Mas-Ponte D, McCullough M, Supek F. Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy. Clin Sci (Lond) 2022; 136:383-404. [PMID: 35274136 PMCID: PMC8919091 DOI: 10.1042/cs20210682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 12/15/2022]
Abstract
Genome sequencing can be used to detect DNA repair failures in tumors and learn about underlying mechanisms. Here, we synthesize findings from genomic studies that examined deficiencies of the DNA mismatch repair (MMR) pathway. The impairment of MMR results in genome-wide hypermutation and in the 'microsatellite instability' (MSI) phenotype-occurrence of indel mutations at short tandem repeat (microsatellite) loci. The MSI status of tumors was traditionally assessed by molecular testing of a selected set of MS loci or by measuring MMR protein expression levels. Today, genomic data can provide a more complete picture of the consequences on genomic instability. Multiple computational studies examined somatic mutation distributions that result from failed DNA repair pathways in tumors. These include analyzing the commonly studied trinucleotide mutational spectra of single-nucleotide variants (SNVs), as well as of other features such as indels, structural variants, mutation clusters and regional mutation rate redistribution. The identified mutation patterns can be used to rigorously measure prevalence of MMR failures across cancer types, and potentially to subcategorize the MMR deficiencies. Diverse data sources, genomic and pre-genomic, from human and from experimental models, suggest there are different ways in which MMR can fail, and/or that the cell-type or genetic background may result in different types of MMR mutational patterns. The spectrum of MMR failures may direct cancer evolution, generating particular sets of driver mutations. Moreover, MMR affects outcomes of therapy by DNA damaging drugs, antimetabolites, nonsense-mediated mRNA decay (NMD) inhibitors, and immunotherapy by promoting either resistance or sensitivity, depending on the type of therapy.
Collapse
Affiliation(s)
- David Mas-Ponte
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Marcel McCullough
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Pg Lluís Companys, 23, Barcelona 08010, Spain
| |
Collapse
|
34
|
Hu PZ, Chen XY, Xiong W, Yang ZJ, Li XR, Deng WZ, Gong LN, Deng H, Yuan LM. A BRCA1 Splice Site Variant Responsible for Familial Ovarian Cancer in a Han-Chinese Family. Curr Med Sci 2022; 42:666-672. [PMID: 35290602 DOI: 10.1007/s11596-022-2527-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 11/30/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Ovarian cancer (OC) is one of the most common and most lethal gynecological malignancies. OC has an age-dependent incidence and occurs more commonly in females older than 50 years old. Most OC patients are diagnosed at an advanced stage and have a poor prognosis. Germline mutations in the BRCA1 DNA repair associated gene (BRCA1) and the BRCA2 DNA repair associated gene (BRCA2) account for 20%-25% of epithelial ovarian cancer (EOC). BRCA1 germline mutations are more common in Chinese EOC patients. METHODS This study reported a three-generation Han-Chinese family containing four EOC patients and a rectal adenocarcinoma patient. Whole-exome sequencing was performed on two EOC patients and an unaffected individual. Variant validation was also performed in all available members by Sanger sequencing. RESULTS A heterozygous splice site variant, c.4358-2A>G in the BRCA1 gene, was identified. Bioinformatic analysis showed that the variant may change the splicing machinery. CONCLUSION The BRCA1 splice site variant, c.4358-2A>G was identified as the likely genetic cause for EOC, and may also be associated with the increased risk of rectal adenocarcinoma in the family. The findings were beneficial for genetic counseling, helpful for cancer prevention in other family members, and may facilitate therapy decision-making in the future to reduce cancer lethality.
Collapse
Affiliation(s)
- Peng-Zhi Hu
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, 410013, China
- Department of Radiology, the Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Xiang-Yu Chen
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Wei Xiong
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
| | - Zhi-Jian Yang
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Xiao-Rong Li
- Department of Gastrointestinal Surgery, the Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Wen-Zhi Deng
- Department of Pathology, the Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Li-Na Gong
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Hao Deng
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, 410013, China
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, 410013, China
- Disease Genome Research Center, Central South University, Changsha, 410013, China
| | - La-Mei Yuan
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, 410013, China.
| |
Collapse
|
35
|
Targeting PARP proteins in acute leukemia: DNA damage response inhibition and therapeutic strategies. J Hematol Oncol 2022; 15:10. [PMID: 35065680 PMCID: PMC8783444 DOI: 10.1186/s13045-022-01228-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
The members of the Poly(ADP‐ribose) polymerase (PARP) superfamily are involved in several biological processes and, in particular, in the DNA damage response (DDR). The most studied members, PARP1, PARP2 and PARP3, act as sensors of DNA damages, in order to activate different intracellular repair pathways, including single-strand repair, homologous recombination, conventional and alternative non-homologous end joining. This review recapitulates the functional role of PARPs in the DDR pathways, also in relationship with the cell cycle phases, which drives our knowledge of the mechanisms of action of PARP inhibitors (PARPi), encompassing inhibition of single-strand breaks and base excision repair, PARP trapping and sensitization to antileukemia immune responses. Several studies have demonstrated a preclinical activity of the current available PARPi, olaparib, rucaparib, niraparib, veliparib and talazoparib, as single agent and/or in combination with cytotoxic, hypomethylating or targeted drugs in acute leukemia, thus encouraging the development of clinical trials. We here summarize the most recent preclinical and clinical findings and discuss the synthetic lethal interactions of PARPi in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). Despite the low frequency of genomic alterations of PARP and other DDR-related genes in acute leukemia, selective vulnerabilities have been reported in several disease subgroups, along with a “BRCAness phenotype.” AML carrying the RUNX1-RUNX1T1 or PML-RARA fusion genes or mutations in signaling genes (FLT3-ITD in combination with TET2 or TET2 and DNMT3A deficiency), cohesin complex members (STAG2), TP53 and BCOR as co-occurring lesions, IDH1/2 and ALL cases expressing the TCF3-HLF chimera or TET1 was highly sensitive to PARPi in preclinical studies. These data, along with the warning coming from the observation of cases of therapy-related myeloid malignancies among patients receiving PARPi for solid tumors treatment, indicate that PARPi represents a promising strategy in a personalized medicine setting. The characterization of the clonal and subclonal genetic background and of the DDR functionality is crucial to select acute leukemia patients that will likely benefit of PARPi-based therapeutic regimens.
Collapse
|
36
|
Shih DJH, Chen MK, Yin J, McGrail DJ, Dai H, Wei R, Zhang J, Zheng WJ, Do KA, Yang L, Hung MC, Lin SY. Exploiting induced vulnerability to overcome PARPi resistance and clonal heterogeneity in BRCA mutant triple-negative inflammatory breast cancer. Am J Cancer Res 2022; 12:337-354. [PMID: 35141022 PMCID: PMC8822293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023] Open
Abstract
Acquired resistance and clonal heterogeneity are critical challenges in cancer treatment, and the lack of effective computational tools hampers the discovery of new treatments to overcome resistance. Using high-throughput transcriptomic databases of compound perturbation profiles, we have developed a bioinformatic strategy for identifying candidate drugs to overcome resistance with combinatorial therapy. We devised this strategy during an investigation into the acquired resistance against PARP inhibitors (PARPi) in a triple-negative inflammatory breast cancer cell line. In this study, we derived multiple PARPi-resistant clones and characterized their transcriptomic adaptations compared to the parental clone. The transcriptomes of the resistant clones showed substantial heterogeneity, highlighting the importance of characterizing multiple clones from the same tumour. Surprisingly, we found that these transcriptomic changes may not actually confer PARPi resistance, but they may nevertheless induce a shared secondary vulnerability. By modeling our data in relation to transcriptomic perturbation profiles of compounds, we uncovered deficiencies in Ras signaling that resulted from transcriptional adaptation to long-term PARPi treatment across multiple resistant clones. Due to these induced deficiencies, we predicted that the resistant clones would be sensitive to pharmacological reinforcement of PARPi-induced transcriptional adaptation. We then experimentally validated this predicted vulnerability that is shared by multiple resistant clones. Our results thus provide a promising paradigm for integrating transcriptomic data with compound perturbation profiles in order to identify drugs that can exploit an induced vulnerability and overcome therapeutic resistance, thus providing another strategy towards precision oncology.
Collapse
Affiliation(s)
- David J H Shih
- Department of Systems Biology, University of Texas MD Anderson Cancer CenterHouston, TX 77030-4009, USA
- School of Biomedical Informatics, University of Texas Health Science Center at HoustonHouston, TX 77030, USA
| | - Mei-Kuang Chen
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer CenterHouston, TX 77030-4009, USA
| | - Jun Yin
- Caris Life SciencesIrving, TX 75039, USA
| | - Daniel J McGrail
- Department of Systems Biology, University of Texas MD Anderson Cancer CenterHouston, TX 77030-4009, USA
| | - Hui Dai
- Department of Systems Biology, University of Texas MD Anderson Cancer CenterHouston, TX 77030-4009, USA
| | - Rongbin Wei
- Department of Systems Biology, University of Texas MD Anderson Cancer CenterHouston, TX 77030-4009, USA
| | - Jing Zhang
- Department of Systems Biology, University of Texas MD Anderson Cancer CenterHouston, TX 77030-4009, USA
| | - Wenjin Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at HoustonHouston, TX 77030, USA
| | - Kim-Anh Do
- Department of Biostatistics, University of Texas MD Anderson Cancer CenterHouston, TX 77030-4009, USA
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer CenterHouston, TX 77030-4009, USA
| | | | - Shiaw-Yih Lin
- Department of Systems Biology, University of Texas MD Anderson Cancer CenterHouston, TX 77030-4009, USA
| |
Collapse
|
37
|
Chen D, Gervai JZ, Póti Á, Németh E, Szeltner Z, Szikriszt B, Gyüre Z, Zámborszky J, Ceccon M, d'Adda di Fagagna F, Szallasi Z, Richardson AL, Szüts D. BRCA1 deficiency specific base substitution mutagenesis is dependent on translesion synthesis and regulated by 53BP1. Nat Commun 2022; 13:226. [PMID: 35017534 PMCID: PMC8752635 DOI: 10.1038/s41467-021-27872-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/15/2021] [Indexed: 12/25/2022] Open
Abstract
Defects in BRCA1, BRCA2 and other genes of the homology-dependent DNA repair (HR) pathway cause an elevated rate of mutagenesis, eliciting specific mutation patterns including COSMIC signature SBS3. Using genome sequencing of knock-out cell lines we show that Y family translesion synthesis (TLS) polymerases contribute to the spontaneous generation of base substitution and short insertion/deletion mutations in BRCA1 deficient cells, and that TLS on DNA adducts is increased in BRCA1 and BRCA2 mutants. The inactivation of 53BP1 in BRCA1 mutant cells markedly reduces TLS-specific mutagenesis, and rescues the deficiency of template switch-mediated gene conversions in the immunoglobulin V locus of BRCA1 mutant chicken DT40 cells. 53BP1 also promotes TLS in human cellular extracts in vitro. Our results show that HR deficiency-specific mutagenesis is largely caused by TLS, and suggest a function for 53BP1 in regulating the choice between TLS and error-free template switching in replicative DNA damage bypass.
Collapse
Affiliation(s)
- Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Judit Z Gervai
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Doctoral School of Molecular Medicine, Semmelweis University, Budapest, H-1085, Hungary
| | - Judit Zámborszky
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Marta Ceccon
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139, Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139, Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP), Boston Children's Hospital and Harvard Medical School, Boston, MA, 02215, USA
- Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, H-1092, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary.
| |
Collapse
|
38
|
OUP accepted manuscript. FEMS Yeast Res 2022; 22:6574410. [DOI: 10.1093/femsyr/foac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/14/2022] Open
|
39
|
Whole-exome sequencing in eccrine porocarcinoma indicates promising therapeutic strategies. Cancer Gene Ther 2022; 29:697-708. [PMID: 34045664 PMCID: PMC9209330 DOI: 10.1038/s41417-021-00347-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/23/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023]
Abstract
Malignant sweat gland tumours are rare, with the most common form being Eccrine porocarcinoma (EP). To investigate the mutational landscape of EP, we performed whole-exome sequencing (WES) on 14 formalin-fixed paraffin-embedded samples of matched primary EP and healthy surrounding tissue. Mutational profiling revealed a high overall median mutation rate. This was attributed to signatures of mutational processes related to ultraviolet (UV) exposure, APOBEC enzyme dysregulation, and defective homologous double-strand break repair. All of these processes cause genomic instability and are implicated in carcinogenesis. Recurrent driving somatic alterations were detected in the EP candidate drivers TP53, FAT2, CACNA1S, and KMT2D. The analyses also identified copy number alterations and recurrent gains and losses in several chromosomal regions including that containing BRCA2, as well as deleterious alterations in multiple HRR components. In accordance with this reduced or even a complete loss of BRCA2 protein expression was detected in 50% of the investigated EP tumours. Our results implicate crucial oncogenic driver pathways and suggest that defective homologous double-strand break repair and the p53 pathway are involved in EP aetiology. Targeting of the p53 axis and PARP inhibition, and/or immunotherapy may represent promising treatment strategies.
Collapse
|
40
|
Taglialatela A, Leuzzi G, Sannino V, Cuella-Martin R, Huang JW, Wu-Baer F, Baer R, Costanzo V, Ciccia A. REV1-Polζ maintains the viability of homologous recombination-deficient cancer cells through mutagenic repair of PRIMPOL-dependent ssDNA gaps. Mol Cell 2021; 81:4008-4025.e7. [PMID: 34508659 PMCID: PMC8500949 DOI: 10.1016/j.molcel.2021.08.016] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 05/29/2021] [Accepted: 08/11/2021] [Indexed: 12/11/2022]
Abstract
BRCA1/2 mutant tumor cells display an elevated mutation burden, the etiology of which remains unclear. Here, we report that these cells accumulate ssDNA gaps and spontaneous mutations during unperturbed DNA replication due to repriming by the DNA primase-polymerase PRIMPOL. Gap accumulation requires the DNA glycosylase SMUG1 and is exacerbated by depletion of the translesion synthesis (TLS) factor RAD18 or inhibition of the error-prone TLS polymerase complex REV1-Polζ by the small molecule JH-RE-06. JH-RE-06 treatment of BRCA1/2-deficient cells results in reduced mutation rates and PRIMPOL- and SMUG1-dependent loss of viability. Through cellular and animal studies, we demonstrate that JH-RE-06 is preferentially toxic toward HR-deficient cancer cells. Furthermore, JH-RE-06 remains effective toward PARP inhibitor (PARPi)-resistant BRCA1 mutant cells and displays additive toxicity with crosslinking agents or PARPi. Collectively, these studies identify a protective and mutagenic role for REV1-Polζ in BRCA1/2 mutant cells and provide the rationale for using REV1-Polζ inhibitors to treat BRCA1/2 mutant tumors.
Collapse
Affiliation(s)
- Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Sannino
- DNA Metabolism Laboratory, IFOM, FIRC Institute for Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Foon Wu-Baer
- Institute for Cancer Genetics, Department of Pathology & Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard Baer
- Institute for Cancer Genetics, Department of Pathology & Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM, FIRC Institute for Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
41
|
Llorens-Agost M, Ensminger M, Le HP, Gawai A, Liu J, Cruz-García A, Bhetawal S, Wood RD, Heyer WD, Löbrich M. POLθ-mediated end joining is restricted by RAD52 and BRCA2 until the onset of mitosis. Nat Cell Biol 2021; 23:1095-1104. [PMID: 34616022 PMCID: PMC8675436 DOI: 10.1038/s41556-021-00764-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/30/2021] [Indexed: 01/25/2023]
Abstract
BRCA2-mutant cells are defective in homologous recombination, making them vulnerable to the inactivation of other pathways for the repair of DNA double-strand breaks (DSBs). This concept can be clinically exploited but is currently limited due to insufficient knowledge about how DSBs are repaired in the absence of BRCA2. We show that DNA polymerase θ (POLθ)-mediated end joining (TMEJ) repairs DSBs arising during the S phase in BRCA2-deficient cells only after the onset of the ensuing mitosis. This process is regulated by RAD52, whose loss causes the premature usage of TMEJ and the formation of chromosomal fusions. Purified RAD52 and BRCA2 proteins both block the DNA polymerase function of POLθ, suggesting a mechanism explaining their synthetic lethal relationships. We propose that the delay of TMEJ until mitosis ensures the conversion of originally one-ended DSBs into two-ended DSBs. Mitotic chromatin condensation might further serve to juxtapose correct break ends and limit chromosomal fusions.
Collapse
Affiliation(s)
- Marta Llorens-Agost
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Michael Ensminger
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Hang Phuong Le
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Anugrah Gawai
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Jie Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Andrés Cruz-García
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Sarita Bhetawal
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany.
| |
Collapse
|
42
|
Wattenberg MM, Reiss KA. Determinants of Homologous Recombination Deficiency in Pancreatic Cancer. Cancers (Basel) 2021; 13:4716. [PMID: 34572943 PMCID: PMC8466888 DOI: 10.3390/cancers13184716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
Pancreatic cancer is a treatment-resistant malignancy associated with high mortality. However, defective homologous recombination (HR), a DNA repair mechanism required for high-fidelity repair of double-strand DNA breaks, is a therapeutic vulnerability. Consistent with this, a subset of patients with pancreatic cancer show unique tumor responsiveness to HR-dependent DNA damage triggered by certain treatments (platinum chemotherapy and PARP inhibitors). While pathogenic mutations in HR genes are a major driver of this sensitivity, another layer of diverse tumor intrinsic and extrinsic factors regulate the HR deficiency (HRD) phenotype. Defining the mechanisms that drive HRD may guide the development of novel strategies and therapeutics to induce treatment sensitivity in non-HRD tumors. Here, we discuss the complexity underlying HRD in pancreatic cancer and highlight implications for identifying and treating this distinct subset of patients.
Collapse
Affiliation(s)
- Max M. Wattenberg
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kim A. Reiss
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
43
|
Giunta S. Decoding human cancer with whole genome sequencing: a review of PCAWG Project studies published in February 2020. Cancer Metastasis Rev 2021; 40:909-924. [PMID: 34097189 PMCID: PMC8180541 DOI: 10.1007/s10555-021-09969-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022]
Abstract
Cancer is underlined by genetic changes. In an unprecedented international effort, the Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) sequenced the tumors of over two thousand five hundred patients across 38 different cancer types, as well as the corresponding healthy tissue, with the aim of identifying genome-wide mutations exclusively found in cancer and uncovering new genetic changes that drive tumor formation. What set this project apart from earlier efforts is the use of whole genome sequencing (WGS) that enabled to explore alterations beyond the coding DNA, into cancer's non-coding genome. WGS of the entire cohort allowed to tease apart driving mutations that initiate and support carcinogenesis from passenger mutations that do not play an overt role in the disease. At least one causative mutation was found in 95% of all cancers, with many tumors showing an average of 5 driver mutations. The PCAWG Project also assessed the transcriptional output altered in cancer and rebuilt the evolutionary history of each tumor showing that initial driver mutations can occur years if not decades prior to a diagnosis. Here, I provide a concise review of the Pan-Cancer Project papers published on February 2020, along with key computational tools and the digital framework generated as part of the project. This represents an historic effort by hundreds of international collaborators, which provides a comprehensive understanding of cancer genetics, with publicly available data and resources representing a treasure trove of information to advance cancer research for years to come.
Collapse
Affiliation(s)
- Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology "Charles Darwin", University of Rome Sapienza, Rome, Italy.
- The Rockefeller University, 1230 York Avenue, New York, NY, USA.
| |
Collapse
|
44
|
Sztupinszki Z, Diossy M, Börcsök J, Prosz A, Cornelius N, Kjeldsen MK, Mirza MR, Szallasi Z. Comparative Assessment of Diagnostic Homologous Recombination Deficiency associated mutational signatures in ovarian cancer. Clin Cancer Res 2021; 27:5681-5687. [PMID: 34380641 DOI: 10.1158/1078-0432.ccr-21-0981] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/08/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Homologous recombination (HR) deficiency is one of the key determinants of PARP inhibitor response in ovarian cancer, and its accurate detection in tumor biopsies is expected to improve the efficacy of this therapy. Since HR deficiency induces a wide array of genomic aberrations, mutational signatures may serve as a companion diagnostic to identify PARP inhibitor responsive cases. METHODS From the TCGA whole exome sequencing data we extracted different types of mutational signature-based HR deficiency measures, such as the HRD score, genome-wide LOH and HRDetect trained on ovarian and breast cancer specific sequencing data. We compared their performance to identify BRCA1/2 deficient cases in the TCGA ovarian cancer cohort and predict survival benefit in platinum treated, BRCA1/2 wild type ovarian cancer. RESULTS We found that the HRD score, which is based on large chromosomal alterations alone, performed similarly well to an ovarian cancer specific HRDetect, which incorporates mutations on a finer scale as well (AUC=0.823 versus AUC=0.837). In an independent cohort these two methods were equally accurate predicting long term survival after platinum treatment (AUC=0.787 versus AUC=0.823). We also found that HRDetect trained on ovarian cancer was more accurate than HRDetect trained on breast cancer data (AUC=0.837 versus AUC=0.795, p=0.0072). CONCLUSION When WES data are available, methods that quantify only large chromosomal alterations such as the HRD score and HRDetect that captures a wider array of HR deficiency induced genomic aberrations are equally efficient identifying HR deficient ovarian cancer cases.
Collapse
Affiliation(s)
| | - Miklos Diossy
- Translational Cancer Genomics, Danish Cancer Society Research Center
| | - Judit Börcsök
- Translational Cancer Genomics, Danish Cancer Society Research Center
| | - Aurel Prosz
- Translational Cancer Genomics, Danish Cancer Society Research Center
| | | | | | | | - Zoltan Szallasi
- Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School
| |
Collapse
|
45
|
Diossy M, Sztupinszki Z, Borcsok J, Krzystanek M, Tisza V, Spisak S, Rusz O, Timar J, Csabai I, Fillinger J, Moldvay J, Pedersen AG, Szuts D, Szallasi Z. A subset of lung cancer cases shows robust signs of homologous recombination deficiency associated genomic mutational signatures. NPJ Precis Oncol 2021; 5:55. [PMID: 34145376 PMCID: PMC8213828 DOI: 10.1038/s41698-021-00199-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/28/2021] [Indexed: 01/14/2023] Open
Abstract
PARP inhibitors are approved for the treatment of solid tumor types that frequently harbor alterations in the key homologous recombination (HR) genes, BRCA1/2. Other tumor types, such as lung cancer, may also be HR deficient, but the frequency of such cases is less well characterized. Specific DNA aberration profiles (mutational signatures) are induced by homologous recombination deficiency (HRD) and their presence can be used to assess the presence or absence of HR deficiency in a given tumor biopsy even in the absence of an observed alteration of an HR gene. We derived various HRD-associated mutational signatures from whole-genome and whole-exome sequencing data in the lung adenocarcinoma and lung squamous carcinoma cases from TCGA, and in a patient of ours with stage IVA lung cancer with exceptionally good response to platinum-based therapy, and in lung cancer cell lines. We found that a subset of the investigated cases, both with and without biallelic loss of BRCA1 or BRCA2, showed robust signs of HR deficiency. The extreme platinum responder case also showed a robust HRD-associated genomic mutational profile. HRD-associated mutational signatures were also associated with PARP inhibitor sensitivity in lung cancer cell lines. Consequently, lung cancer cases with HRD, as identified by diagnostic mutational signatures, may benefit from PARP inhibitor therapy.
Collapse
Affiliation(s)
- Miklos Diossy
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, Kgs. Lyngby, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Judit Borcsok
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Orsolya Rusz
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Jozsef Timar
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Janos Fillinger
- Department of Pathology, National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Judit Moldvay
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
- Department of Tumor Biology, National Korányi Institute of Pulmonology-Semmelweis University, Budapest, Hungary
| | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, Kgs. Lyngby, Denmark
| | - David Szuts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary.
| |
Collapse
|
46
|
Patel J, Baptiste BA, Kim E, Hussain M, Croteau DL, Bohr VA. DNA damage and mitochondria in cancer and aging. Carcinogenesis 2021; 41:1625-1634. [PMID: 33146705 DOI: 10.1093/carcin/bgaa114] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 12/21/2022] Open
Abstract
Age and DNA repair deficiencies are strong risk factors for developing cancer. This is reflected in the comorbidity of cancer with premature aging diseases associated with DNA damage repair deficiencies. Recent research has suggested that DNA damage accumulation, telomere dysfunction and the accompanying mitochondrial dysfunction exacerbate the aging process and may increase the risk of cancer development. Thus, an area of interest in both cancer and aging research is the elucidation of the dynamic crosstalk between the nucleus and the mitochondria. In this review, we discuss current research on aging and cancer with specific focus on the role of mitochondrial dysfunction in cancer and aging as well as how nuclear to mitochondrial DNA damage signaling may be a driving factor in the increased cancer incidence with aging. We suggest that therapeutic interventions aimed at the induction of autophagy and mediation of nuclear to mitochondrial signaling may provide a mechanism for healthier aging and reduced tumorigenesis.
Collapse
Affiliation(s)
- Jaimin Patel
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA
| | - Beverly A Baptiste
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA
| | - Edward Kim
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA
| | - Mansoor Hussain
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA
| |
Collapse
|
47
|
Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair. Cells 2021; 10:cells10051224. [PMID: 34067668 PMCID: PMC8156620 DOI: 10.3390/cells10051224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on Saccharomyces cerevisiae and human tumors. Well-studied organisms include Drosophila melanogaster and Mus musculus, while less genetically tractable species include great apes and long-lived trees. A variety of techniques have been developed to gather mutation rates, either per generation or per cell division. Generational rates are described through whole-organism mutation accumulation experiments and through offspring–parent sequencing, or they have been identified by descent. Rates per somatic cell division have been estimated from cell line mutation accumulation experiments, from systemic variant allele frequencies, and from widely spaced samples with known cell divisions per unit of tissue growth. The latter methods are also used to estimate generational mutation rates for large organisms that lack dedicated germlines, such as trees and hyphal fungi. Mechanistic studies involving genetic manipulation of MMR genes prior to mutation rate determination are thus far confined to yeast, Arabidopsis thaliana, Caenorhabditis elegans, and one chicken cell line. A great deal of work in wild-type organisms has begun to establish a sound baseline, but far more work is needed to uncover the variety of MMR across eukaryotes. Nonetheless, the few MMR studies reported to date indicate that MMR contributes 100-fold or more to genome stability, and they have uncovered insights that would have been impossible to obtain using reporter gene assays.
Collapse
|
48
|
Stok C, Kok Y, van den Tempel N, van Vugt MATM. Shaping the BRCAness mutational landscape by alternative double-strand break repair, replication stress and mitotic aberrancies. Nucleic Acids Res 2021; 49:4239-4257. [PMID: 33744950 PMCID: PMC8096281 DOI: 10.1093/nar/gkab151] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/18/2021] [Accepted: 03/05/2021] [Indexed: 12/16/2022] Open
Abstract
Tumours with mutations in the BRCA1/BRCA2 genes have impaired double-stranded DNA break repair, compromised replication fork protection and increased sensitivity to replication blocking agents, a phenotype collectively known as 'BRCAness'. Tumours with a BRCAness phenotype become dependent on alternative repair pathways that are error-prone and introduce specific patterns of somatic mutations across the genome. The increasing availability of next-generation sequencing data of tumour samples has enabled identification of distinct mutational signatures associated with BRCAness. These signatures reveal that alternative repair pathways, including Polymerase θ-mediated alternative end-joining and RAD52-mediated single strand annealing are active in BRCA1/2-deficient tumours, pointing towards potential therapeutic targets in these tumours. Additionally, insight into the mutations and consequences of unrepaired DNA lesions may also aid in the identification of BRCA-like tumours lacking BRCA1/BRCA2 gene inactivation. This is clinically relevant, as these tumours respond favourably to treatment with DNA-damaging agents, including PARP inhibitors or cisplatin, which have been successfully used to treat patients with BRCA1/2-defective tumours. In this review, we aim to provide insight in the origins of the mutational landscape associated with BRCAness by exploring the molecular biology of alternative DNA repair pathways, which may represent actionable therapeutic targets in in these cells.
Collapse
Affiliation(s)
- Colin Stok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
| | - Yannick P Kok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
| | - Nathalie van den Tempel
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
| |
Collapse
|
49
|
Szikriszt B, Póti Á, Németh E, Kanu N, Swanton C, Szüts D. A comparative analysis of the mutagenicity of platinum-containing chemotherapeutic agents reveals direct and indirect mutagenic mechanisms. Mutagenesis 2021; 36:75-86. [PMID: 33502495 PMCID: PMC8081379 DOI: 10.1093/mutage/geab005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
Platinum-based drugs are a mainstay of cancer chemotherapy. However, their mutagenic effect can increase tumour heterogeneity, contribute to the evolution of treatment resistance and also induce secondary malignancies. We coupled whole genome sequencing with phenotypic investigations on two cell line models to compare the magnitude and examine the mechanism of mutagenicity of cisplatin, carboplatin and oxaliplatin. Cisplatin induced significantly more base substitution mutations than carboplatin or oxaliplatin when used at equitoxic concentrations on human TK6 or chicken DT40 cells, and also induced the highest number of short insertions and deletions. The analysis of base substitution spectra revealed that all three tested platinum drugs elicit both a direct mutagenic effect at purine dinucleotides, and an indirect effect of accelerating endogenous mutagenic processes, whereas the direct mutagenic effect appeared to correlate with the level of DNA damage caused as assessed through histone H2AX phosphorylation and single-cell agarose gel electrophoresis, the indirect mutagenic effects were equal. The different mutagenicity and DNA-damaging effect of equitoxic platinum drug treatments suggest that DNA damage independent mechanisms significantly contribute to their cytotoxicity. Thus, the comparatively high mutagenicity of cisplatin should be taken into account in the design of chemotherapeutic regimens.
Collapse
Affiliation(s)
- Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nnennaya Kanu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| |
Collapse
|
50
|
Xu F, Wu H, Xiong J, Peng T. Long Non-coding RNA DLEU2L Targets miR-210-3p to Suppress Gemcitabine Resistance in Pancreatic Cancer Cells via BRCA2 Regulation. Front Mol Biosci 2021; 8:645365. [PMID: 33968986 PMCID: PMC8100451 DOI: 10.3389/fmolb.2021.645365] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/07/2021] [Indexed: 01/04/2023] Open
Abstract
Gemcitabine (GEM) resistance remains a challenging clinical issue to overcome in chemotherapy against pancreatic cancer. We previously demonstrated that miR-210 derived from pancreatic cancer stem cells enhanced the GEM-resistant properties of pancreatic cancer cells, thus identifying miR-210 as an oncogenic miRNA. Herein, we report the existence of an upstream effector that acts as a competing endogenous RNA (ceRNA) to miR-210. Bioinformatic screening was performed to identify lncRNAs with a binding relationship to miR-210. Overexpression and interference vectors were constructed to demonstrate the effect of ceRNA activity in pancreatic cell behavior, both in vitro and in vivo. DLEU2L (deleted in lymphocytic leukemia 2-like), which is expressed at low levels in pancreatic cancer tissues, was shown to exhibit a binding relationship with miR-210-3p. Overexpression of DLEU2L and silencing of miR-210-3p suppressed the proliferation, migration, and invasion of pancreatic cancer cells while promoting apoptosis. These effects occurred via the inhibition of the Warburg effect (aerobic glycolysis) and AKT/mTOR signaling. In addition, we showed that BRCA2 is a target gene of miR-210-3p, and the downregulation of miR-210-3p by DLEU2L effectively induced an upregulation of BRCA2 via the ceRNA mechanism. In vivo, DLEU2L overexpression and miR-210-3p interference suppressed pancreatic tumor progression, consistent with the results of in vitro studies. The findings of our study establish DLEU2L as a ceRNA to miR-210-3p and reveal the critical role of the DLEU2L/miR-210-3p crosstalk in targeting GEM resistance.
Collapse
Affiliation(s)
- Fei Xu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heshui Wu
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiongxin Xiong
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Peng
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|