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Jeddi F, Faghfuri E, Mehranfar S, Soozangar N. The common bisulfite-conversion-based techniques to analyze DNA methylation in human cancers. Cancer Cell Int 2024; 24:240. [PMID: 38982390 PMCID: PMC11234524 DOI: 10.1186/s12935-024-03405-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024] Open
Abstract
DNA methylation is an important molecular modification that plays a key role in the expression of cancer genes. Evaluation of epigenetic changes, hypomethylation and hypermethylation, in specific genes are applied for cancer diagnosis. Numerous studies have concentrated on describing DNA methylation patterns as biomarkers for cancer diagnosis monitoring and predicting response to cancer therapy. Various techniques for detecting DNA methylation status in cancers are based on sodium bisulfite treatment. According to the application of these methods in research and clinical studies, they have a number of advantages and disadvantages. The current review highlights sodium bisulfite treatment-based techniques, as well as, the advantages, drawbacks, and applications of these methods in the evaluation of human cancers.
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Affiliation(s)
- Farhad Jeddi
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Elnaz Faghfuri
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sahar Mehranfar
- Department of Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Narges Soozangar
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
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2
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Piscitelli JM, Witte SJ, Sakinejad YS, Manhart CM. The Mlh1-Pms1 endonuclease uses ATP to preserve DNA discontinuities as strand discrimination signals to facilitate mismatch repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598860. [PMID: 38915520 PMCID: PMC11195183 DOI: 10.1101/2024.06.13.598860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
In eukaryotic post-replicative mismatch repair, MutS homologs (MSH) detect mismatches and recruit MLH complexes to nick the newly replicated DNA strand upon activation by the replication processivity clamp, PCNA. This incision enables mismatch removal and DNA repair. Biasing MLH endonuclease activity to the newly replicated DNA strand is crucial for repair. In reconstituted in vitro assays, PCNA is loaded at pre-existing discontinuities and orients the major MLH endonuclease Mlh1-Pms1/MLH1-PMS2 (yeast/human) to nick the discontinuous strand. In vivo, newly replicated DNA transiently contains discontinuities which are critical for efficient mismatch repair. How these discontinuities are preserved as strand discrimination signals during the window of time where mismatch repair occurs is unknown. Here, we demonstrate that yeast Mlh1-Pms1 uses ATP binding to recognize DNA discontinuities. This complex does not efficiently interact with PCNA, which partially suppresses ATPase activity, and prevents dissociation from the discontinuity. These data suggest that in addition to initiating mismatch repair by nicking newly replicated DNA, Mlh1-Pms1 protects strand discrimination signals, aiding in maintaining its own strand discrimination signposts. Our findings also highlight the significance of Mlh1-Pms1's ATPase activity for inducing DNA dissociation, as mutant proteins deficient in this function become immobilized on DNA post-incision, explaining in vivo phenotypes.
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Affiliation(s)
| | - Scott J. Witte
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Yasmine S. Sakinejad
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Carol M. Manhart
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA
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3
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Fendler NL, Ly J, Welp L, Urlaub H, Vos SM. Identification and characterization of a human MORC2 DNA binding region that is required for gene silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597643. [PMID: 38895295 PMCID: PMC11185635 DOI: 10.1101/2024.06.05.597643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The eukaryotic microrchidia (MORC) protein family are DNA gyrase, Hsp90, histidine kinase, MutL (GHKL)-type ATPases involved in gene expression regulation and chromatin compaction. The molecular mechanisms underlying these activities are incompletely understood. Here we studied the full-length human MORC2 protein biochemically. We identified a DNA binding site in the C-terminus of the protein, and we observe that this region is heavily phosphorylated in cells. Phosphorylation of MORC2 reduces its affinity for DNA and appears to exclude the protein from the nucleus. We observe that DNA binding by MORC2 reduces its ATPase activity and that MORC2 can topologically entrap multiple DNA substrates between its N-terminal GHKL and C-terminal coiled coil 3 dimerization domains. Finally, we observe that the MORC2 C-terminal DNA binding region is required for gene silencing in cells. Together, our data provide a model to understand how MORC2 engages with DNA substrates to mediate gene silencing.
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Affiliation(s)
- Nikole L. Fendler
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139
| | - Jimmy Ly
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139
| | - Luisa Welp
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics Group, University Medical Center Göttingen, Department of Clinical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics Group, University Medical Center Göttingen, Department of Clinical Chemistry, Göttingen, Germany
| | - Seychelle M. Vos
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139
- Howard Hughes Medical Institute
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4
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Provasek VE, Bacolla A, Rangaswamy S, Mitra J, Kodavati M, Yusuf IO, Malojirao VH, Vasquez V, Britz GW, Li GM, Xu Z, Mitra S, Garruto RM, Tainer JA, Hegde ML. RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594552. [PMID: 38798341 PMCID: PMC11118483 DOI: 10.1101/2024.05.16.594552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
TDP43 is an RNA/DNA binding protein increasingly recognized for its role in neurodegenerative conditions including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). As characterized by its aberrant nuclear export and cytoplasmic aggregation, TDP43 proteinopathy is a hallmark feature in over 95% of ALS/FTD cases, leading to the formation of detrimental cytosolic aggregates and a reduction in nuclear functionality within neurons. Building on our prior work linking TDP43 proteinopathy to the accumulation of DNA double-strand breaks (DSBs) in neurons, the present investigation uncovers a novel regulatory relationship between TDP43 and DNA mismatch repair (MMR) gene expressions. Here, we show that TDP43 depletion or overexpression directly affects the expression of key MMR genes. Alterations include MLH1, MSH2, MSH3, MSH6, and PMS2 levels across various primary cell lines, independent of their proliferative status. Our results specifically establish that TDP43 selectively influences the expression of MLH1 and MSH6 by influencing their alternative transcript splicing patterns and stability. We furthermore find aberrant MMR gene expression is linked to TDP43 proteinopathy in two distinct ALS mouse models and post-mortem brain and spinal cord tissues of ALS patients. Notably, MMR depletion resulted in the partial rescue of TDP43 proteinopathy-induced DNA damage and signaling. Moreover, bioinformatics analysis of the TCGA cancer database reveals significant associations between TDP43 expression, MMR gene expression, and mutational burden across multiple cancers. Collectively, our findings implicate TDP43 as a critical regulator of the MMR pathway and unveil its broad impact on the etiology of both neurodegenerative and neoplastic pathologies.
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Affiliation(s)
- Vincent E Provasek
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- School of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Suganya Rangaswamy
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Joy Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Manohar Kodavati
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Issa O Yusuf
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Vikas H Malojirao
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Velmarini Vasquez
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Gavin W Britz
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Neurosurgery and Department of Neuroscience, Weill Cornell Medical College, New York, NY 10065, USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zuoshang Xu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Sankar Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Ralph M Garruto
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902
| | - John A Tainer
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Muralidhar L Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Neuroscience, Weill Cornell Medical College, New York, NY 10065, USA
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5
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Sun X, Liu L, Wu C, Li X, Guo J, Zhang J, Guan J, Wang N, Gu L, Yang XW, Li GM. Mutant huntingtin protein induces MLH1 degradation, DNA hyperexcision, and cGAS-STING-dependent apoptosis. Proc Natl Acad Sci U S A 2024; 121:e2313652121. [PMID: 38498709 PMCID: PMC10990133 DOI: 10.1073/pnas.2313652121] [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: 08/18/2023] [Accepted: 01/27/2024] [Indexed: 03/20/2024] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the huntingtin (HTT) gene. The repeat-expanded HTT encodes a mutated HTT (mHTT), which is known to induce DNA double-strand breaks (DSBs), activation of the cGAS-STING pathway, and apoptosis in HD. However, the mechanism by which mHTT triggers these events is unknown. Here, we show that HTT interacts with both exonuclease 1 (Exo1) and MutLα (MLH1-PMS2), a negative regulator of Exo1. While the HTT-Exo1 interaction suppresses the Exo1-catalyzed DNA end resection during DSB repair, the HTT-MutLα interaction functions to stabilize MLH1. However, mHTT displays a significantly reduced interaction with Exo1 or MutLα, thereby losing the ability to regulate Exo1. Thus, cells expressing mHTT exhibit rapid MLH1 degradation and hyperactive DNA excision, which causes severe DNA damage and cytosolic DNA accumulation. This activates the cGAS-STING pathway to mediate apoptosis. Therefore, we have identified unique functions for both HTT and mHTT in modulating DNA repair and the cGAS-STING pathway-mediated apoptosis by interacting with MLH1. Our work elucidates the mechanism by which mHTT causes HD.
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Affiliation(s)
- Xiao Sun
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
- The Ministry of Education Key Laboratory of Reproductive Genetics, Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou310006, China
| | - Lu Liu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Chao Wu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Xueying Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jinzhen Guo
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Junqiu Zhang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Junhong Guan
- Cui-ying Experimental Center, Lanzhou University Second Hospital, Lanzhou730030, China
| | - Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human behavior, University of California, Los Angeles, CA90095
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Liya Gu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - X. Willian Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human behavior, University of California, Los Angeles, CA90095
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
- Institute for Cancer Research, Chinese Institutes for Medical Research, Beijing100069, China
- School of Basic Medical Sciences, Capital Medical University, Beijing100069, China
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6
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Waters KL, Spratt DE. New Discoveries on Protein Recruitment and Regulation during the Early Stages of the DNA Damage Response Pathways. Int J Mol Sci 2024; 25:1676. [PMID: 38338953 PMCID: PMC10855619 DOI: 10.3390/ijms25031676] [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: 12/19/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
Maintaining genomic stability and properly repairing damaged DNA is essential to staying healthy and preserving cellular homeostasis. The five major pathways involved in repairing eukaryotic DNA include base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), non-homologous end joining (NHEJ), and homologous recombination (HR). When these pathways do not properly repair damaged DNA, genomic stability is compromised and can contribute to diseases such as cancer. It is essential that the causes of DNA damage and the consequent repair pathways are fully understood, yet the initial recruitment and regulation of DNA damage response proteins remains unclear. In this review, the causes of DNA damage, the various mechanisms of DNA damage repair, and the current research regarding the early steps of each major pathway were investigated.
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Affiliation(s)
| | - Donald E. Spratt
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA;
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7
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Zhang L, Zhang W, Mu Y, Hu H, Dong K, Wen X, Ye Z, Sun Q, Yan B, Mao Z, Xiao X. Ultrasensitive and Quantitative DNA Methylation Detection Method Based on the MutS Protein. Anal Chem 2023; 95:18828-18835. [PMID: 38078896 DOI: 10.1021/acs.analchem.3c04013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
DNA methylation is closely related to cancer. It is generally accepted that DNA methylation detection is crucial in cancer diagnosis, prognosis, and treatment monitoring. Therefore, there is an urgent demand for developing a simple, rapid, highly sensitive, and highly specific methylation detection method to detect DNA methylation at specific sites quantitatively. In this work, we introduce a DNA methylation detection method based on MutS and methylation-specific PCR, named MutS-based methylation-specific PCR (MB-MSP), which has the advantages of simplicity, speed, high specificity, sensitivity, and broad applicability. Utilizing the MutS's ability to bind mismatched base pairs, we inhibit not only the amplification of unmethylated DNA but also nonspecific primer amplification. We achieved a detection sensitivity of 0.5% for the methylated genes of ACP1, CLEC11A, and SEPT9 by MB-MSP. It has a good linear relationship and a detection time of only 1.5 h. To validate the feasibility of the MB-MSP method in clinical application, we conducted methylation detection on plasma-circulating tumor DNA samples from 10 liver cancer patients and 5 healthy people, achieving a 100% accuracy rate. In conclusion, MB-MSP, as a novel and reliable DNA methylation detection tool, holds significant application value and potential for advancing early cancer diagnosis.
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Affiliation(s)
- Lei Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Yaoqin Mu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Hao Hu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Xu Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Zhengxin Ye
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
| | - Qiangqiang Sun
- Wuhan Yujian Biotechnology, Co. Ltd., Wuhan 430000, P.R. China
| | - Bei Yan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
- Ningxia Human Sperm Bank, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, P.R. China
| | - Zenghui Mao
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha 410007, P.R. China
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, P.R. China
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha 410007, P.R. China
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8
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Li J, Wang H, Yang W. Tandem MutSβ binding to long extruded DNA trinucleotide repeats underpins pathogenic expansions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571350. [PMID: 38168405 PMCID: PMC10760016 DOI: 10.1101/2023.12.12.571350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Expansion of trinucleotide repeats causes Huntington's disease, Fragile X syndrome and over twenty other monogenic disorders1. How mismatch repair protein MutSβ and large repeats of CNG (N=A, T, C or G) cooperate to drive the expansion is poorly understood. Contrary to expectations, we find that MutSβ prefers to bind the stem of an extruded (CNG) hairpin rather than the hairpin end or hairpin-duplex junction. Structural analyses reveal that in the presence of MutSβ, CNG repeats with N:N mismatches adopt a B form-like pseudo-duplex, with one or two CNG repeats slipped out forming uneven bubbles that partly mimic insertion-deletion loops of mismatched DNA2. When the extruded hairpin exceeds 40-45 repeats, it can be bound by three or more MutSβ molecules, which are resistant to ATP-dependent dissociation. We envision that such MutSβ-CNG complexes recruit MutLγ endonuclease to nick DNA and initiate the repeat expansion process3,4. To develop drugs against the expansion diseases, we have identified lead compounds that prevent MutSβ binding to CNG repeats but not to mismatched DNA.
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Affiliation(s)
- Jun Li
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892
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9
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Guan J, Li GM. DNA mismatch repair in cancer immunotherapy. NAR Cancer 2023; 5:zcad031. [PMID: 37325548 PMCID: PMC10262306 DOI: 10.1093/narcan/zcad031] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/08/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023] Open
Abstract
Tumors defective in DNA mismatch repair (dMMR) exhibit microsatellite instability (MSI). Currently, patients with dMMR tumors are benefitted from anti-PD-1/PDL1-based immune checkpoint inhibitor (ICI) therapy. Over the past several years, great progress has been made in understanding the mechanisms by which dMMR tumors respond to ICI, including the identification of mutator phenotype-generated neoantigens, cytosolic DNA-mediated activation of the cGAS-STING pathway, type-I interferon signaling and high tumor-infiltration of lymphocytes in dMMR tumors. Although ICI therapy shows great clinical benefits, ∼50% of dMMR tumors are eventually not responsive. Here we review the discovery, development and molecular basis of dMMR-mediated immunotherapy, as well as tumor resistant problems and potential therapeutic interventions to overcome the resistance.
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Affiliation(s)
- Junhong Guan
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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10
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Phadte AS, Bhatia M, Ebert H, Abdullah H, Elrazaq EA, Komolov KE, Pluciennik A. FAN1 removes triplet repeat extrusions via a PCNA- and RFC-dependent mechanism. Proc Natl Acad Sci U S A 2023; 120:e2302103120. [PMID: 37549289 PMCID: PMC10438374 DOI: 10.1073/pnas.2302103120] [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: 02/06/2023] [Accepted: 06/22/2023] [Indexed: 08/09/2023] Open
Abstract
Human genome-wide association studies have identified FAN1 and several DNA mismatch repair (MMR) genes as modifiers of Huntington's disease age of onset. In animal models, FAN1 prevents somatic expansion of CAG triplet repeats, whereas MMR proteins promote this process. To understand the molecular basis of these opposing effects, we evaluated FAN1 nuclease function on DNA extrahelical extrusions that represent key intermediates in triplet repeat expansion. Here, we describe a strand-directed, extrusion-provoked nuclease function of FAN1 that is activated by RFC, PCNA, and ATP at physiological ionic strength. Activation of FAN1 in this manner results in DNA cleavage in the vicinity of triplet repeat extrahelical extrusions thereby leading to their removal in human cell extracts. The role of PCNA and RFC is to confer strand directionality to the FAN1 nuclease, and this reaction requires a physical interaction between PCNA and FAN1. Using cell extracts, we show that FAN1-dependent CAG extrusion removal relies on a very short patch excision-repair mechanism that competes with MutSβ-dependent MMR which is characterized by longer excision tracts. These results provide a mechanistic basis for the role of FAN1 in preventing repeat expansion and could explain the antagonistic effects of MMR and FAN1 in disease onset/progression.
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Affiliation(s)
- Ashutosh S. Phadte
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Mayuri Bhatia
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Hope Ebert
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Haaris Abdullah
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Essam Abed Elrazaq
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Konstantin E. Komolov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Anna Pluciennik
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
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11
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Wolf K, Kosinski J, Gibson TJ, Wesch N, Dötsch V, Genuardi M, Cordisco EL, Zeuzem S, Brieger A, Plotz G. A conserved motif in the disordered linker of human MLH1 is vital for DNA mismatch repair and its function is diminished by a cancer family mutation. Nucleic Acids Res 2023; 51:6307-6320. [PMID: 37224528 PMCID: PMC10325900 DOI: 10.1093/nar/gkad418] [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: 12/12/2022] [Revised: 04/26/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
DNA mismatch repair (MMR) is essential for correction of DNA replication errors. Germline mutations of the human MMR gene MLH1 are the major cause of Lynch syndrome, a heritable cancer predisposition. In the MLH1 protein, a non-conserved, intrinsically disordered region connects two conserved, catalytically active structured domains of MLH1. This region has as yet been regarded as a flexible spacer, and missense alterations in this region have been considered non-pathogenic. However, we have identified and investigated a small motif (ConMot) in this linker which is conserved in eukaryotes. Deletion of the ConMot or scrambling of the motif abolished mismatch repair activity. A mutation from a cancer family within the motif (p.Arg385Pro) also inactivated MMR, suggesting that ConMot alterations can be causative for Lynch syndrome. Intriguingly, the mismatch repair defect of the ConMot variants could be restored by addition of a ConMot peptide containing the deleted sequence. This is the first instance of a DNA mismatch repair defect conferred by a mutation that can be overcome by addition of a small molecule. Based on the experimental data and AlphaFold2 predictions, we suggest that the ConMot may bind close to the C-terminal MLH1-PMS2 endonuclease and modulate its activation during the MMR process.
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Affiliation(s)
- Karla Wolf
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Centre for Structural Systems Biology (CSSB), Hamburg, 22607, Germany
| | - Toby J Gibson
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, 69117, Germany
| | - Nicole Wesch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, 60438, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, 60438, Germany
| | - Maurizio Genuardi
- UOC Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome00168, Italy
| | - Emanuela Lucci Cordisco
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome00168, Italy
| | - Stefan Zeuzem
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Angela Brieger
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Guido Plotz
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
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12
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Kavun A, Veselovsky E, Lebedeva A, Belova E, Kuznetsova O, Yakushina V, Grigoreva T, Mileyko V, Fedyanin M, Ivanov M. Microsatellite Instability: A Review of Molecular Epidemiology and Implications for Immune Checkpoint Inhibitor Therapy. Cancers (Basel) 2023; 15:cancers15082288. [PMID: 37190216 DOI: 10.3390/cancers15082288] [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: 03/01/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Microsatellite instability (MSI) is one of the most important molecular characteristics of a tumor, which occurs among various tumor types. In this review article, we examine the molecular characteristics of MSI tumors, both sporadic and Lynch-associated. We also overview the risks of developing hereditary forms of cancer and potential mechanisms of tumor development in patients with Lynch syndrome. Additionally, we summarize the results of major clinical studies on the efficacy of immune checkpoint inhibitors for MSI tumors and discuss the predictive role of MSI in the context of chemotherapy and checkpoint inhibitors. Finally, we briefly discuss some of the underlying mechanisms causing therapy resistance in patients treated with immune checkpoint inhibitors.
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Affiliation(s)
| | - Egor Veselovsky
- OncoAtlas LLC, 119049 Moscow, Russia
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 119334 Moscow, Russia
| | | | - Ekaterina Belova
- OncoAtlas LLC, 119049 Moscow, Russia
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olesya Kuznetsova
- OncoAtlas LLC, 119049 Moscow, Russia
- N.N. Blokhin Russian Cancer Research Center, 115478 Moscow, Russia
| | - Valentina Yakushina
- OncoAtlas LLC, 119049 Moscow, Russia
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Tatiana Grigoreva
- OncoAtlas LLC, 119049 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Mikhail Fedyanin
- N.N. Blokhin Russian Cancer Research Center, 115478 Moscow, Russia
- State Budgetary Institution of Health Care of the City of Moscow "Moscow Multidisciplinary Clinical Center" "Kommunarka" of the Department of Health of the City of Moscow, 142770 Moscow, Russia
- Federal State Budgetary Institution "National Medical and Surgical Center named after N.I. Pirogov" of the Ministry of Health of the Russian Federation, 105203 Moscow, Russia
| | - Maxim Ivanov
- OncoAtlas LLC, 119049 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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13
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Xu Y, Nowsheen S, Deng M. DNA Repair Deficiency Regulates Immunity Response in Cancers: Molecular Mechanism and Approaches for Combining Immunotherapy. Cancers (Basel) 2023; 15:cancers15051619. [PMID: 36900418 PMCID: PMC10000854 DOI: 10.3390/cancers15051619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/26/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023] Open
Abstract
Defects in DNA repair pathways can lead to genomic instability in multiple tumor types, which contributes to tumor immunogenicity. Inhibition of DNA damage response (DDR) has been reported to increase tumor susceptibility to anticancer immunotherapy. However, the interplay between DDR and the immune signaling pathways remains unclear. In this review, we will discuss how a deficiency in DDR affects anti-tumor immunity, highlighting the cGAS-STING axis as an important link. We will also review the clinical trials that combine DDR inhibition and immune-oncology treatments. A better understanding of these pathways will help exploit cancer immunotherapy and DDR pathways to improve treatment outcomes for various cancers.
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Affiliation(s)
- Yi Xu
- State Key Laboratory of Molecular Oncology and Department of Radiation 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
| | - Somaira Nowsheen
- Department of Dermatology, University of California San Diego, San Diego, CA 92122, USA
- Correspondence: (S.N.); (M.D.)
| | - Min Deng
- State Key Laboratory of Molecular Oncology and Department of Radiation 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
- Correspondence: (S.N.); (M.D.)
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14
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Szurman-Zubrzycka M, Jędrzejek P, Szarejko I. How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants. Int J Mol Sci 2023; 24:ijms24032404. [PMID: 36768727 PMCID: PMC9916837 DOI: 10.3390/ijms24032404] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
DNA damage is induced by many factors, some of which naturally occur in the environment. Because of their sessile nature, plants are especially exposed to unfavorable conditions causing DNA damage. In response to this damage, the DDR (DNA damage response) pathway is activated. This pathway is highly conserved between eukaryotes; however, there are some plant-specific DDR elements, such as SOG1-a transcription factor that is a central DDR regulator in plants. In general, DDR signaling activates transcriptional and epigenetic regulators that orchestrate the cell cycle arrest and DNA repair mechanisms upon DNA damage. The cell cycle halts to give the cell time to repair damaged DNA before replication. If the repair is successful, the cell cycle is reactivated. However, if the DNA repair mechanisms fail and DNA lesions accumulate, the cell enters the apoptotic pathway. Thereby the proper maintenance of DDR is crucial for plants to survive. It is particularly important for agronomically important species because exposure to environmental stresses causing DNA damage leads to growth inhibition and yield reduction. Thereby, gaining knowledge regarding the DDR pathway in crops may have a huge agronomic impact-it may be useful in breeding new cultivars more tolerant to such stresses. In this review, we characterize different genotoxic agents and their mode of action, describe DDR activation and signaling and summarize DNA repair mechanisms in plants.
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15
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Trost H, Merkell A, Lopezcolorado FW, Stark J. Resolution of sequence divergence for repeat-mediated deletions shows a polarity that is mediated by MLH1. Nucleic Acids Res 2023; 51:650-667. [PMID: 36620890 PMCID: PMC9881173 DOI: 10.1093/nar/gkac1240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/07/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
Repeat-mediated deletions (RMDs) are a type of chromosomal rearrangement between two homologous sequences that causes loss of the sequence between the repeats, along with one of the repeats. Sequence divergence between repeats suppresses RMDs; the mechanisms of such suppression and of resolution of the sequence divergence remains poorly understood. We identified RMD regulators using a set of reporter assays in mouse cells that test two key parameters: repeat sequence divergence and the distances between one repeat and the initiating chromosomal break. We found that the mismatch repair factor MLH1 suppresses RMDs with sequence divergence in the same pathway as MSH2 and MSH6, and which is dependent on residues in MLH1 and its binding partner PMS2 that are important for nuclease activity. Additionally, we found that the resolution of sequence divergence in the RMD product has a specific polarity, where divergent bases that are proximal to the chromosomal break end are preferentially removed. Moreover, we found that the domain of MLH1 that forms part of the MLH1-PMS2 endonuclease is important for polarity of resolution of sequence divergence. We also identified distinctions between MLH1 versus TOP3α in regulation of RMDs. We suggest that MLH1 suppresses RMDs with sequence divergence, while also promoting directional resolution of sequence divergence in the RMD product.
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Affiliation(s)
- Hannah Trost
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Arianna Merkell
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Jeremy M Stark
- To whom correspondence should be addressed. Tel: +1 626 218-6346; Fax: +1 626 218 8892;
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16
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Britton BM, London JA, Martin-Lopez J, Jones ND, Liu J, Lee JB, Fishel R. Exploiting the distinctive properties of the bacterial and human MutS homolog sliding clamps on mismatched DNA. J Biol Chem 2022; 298:102505. [PMID: 36126773 PMCID: PMC9597889 DOI: 10.1016/j.jbc.2022.102505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 12/30/2022] Open
Abstract
MutS homologs (MSHs) are highly conserved core components of DNA mismatch repair. Mismatch recognition provokes ATP-binding by MSH proteins that drives a conformational transition from a short-lived lesion-searching clamp to an extremely stable sliding clamp on the DNA. Here, we have expanded on previous bulk biochemical studies to examine the stability, lifetime, and kinetics of bacterial and human MSH sliding clamps on mismatched DNA using surface plasmon resonance and single-molecule analysis of fluorescently labeled proteins. We found that ATP-bound MSH complexes bound to blocked-end or very long mismatched DNAs were extremely stable over a range of ionic conditions. These observations underpinned the development of a high-throughput Förster resonance energy transfer system that specifically detects the formation of MSH sliding clamps on mismatched DNA. The Förster resonance energy transfer system is capable of distinguishing between HsMSH2-HsMSH3 and HsMSH2-HsMSH6 and appears suitable for chemical inhibitor screens. Taken together, our results provide additional insight into MSH sliding clamps as well as methods to distinguish their functions in mismatch repair.
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Affiliation(s)
- Brooke M Britton
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - James A London
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Juana Martin-Lopez
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Nathan D Jones
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jiaquan Liu
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Korea; Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Korea
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA.
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17
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The mismatch recognition protein MutSα promotes nascent strand degradation at stalled replication forks. Proc Natl Acad Sci U S A 2022; 119:e2201738119. [PMID: 36161943 PMCID: PMC9546528 DOI: 10.1073/pnas.2201738119] [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] [Indexed: 11/20/2022] Open
Abstract
DNA mismatch repair (MMR) is well known for its role in maintaining replication fidelity by correcting mispairs generated during replication. Here, we identify an unusual MMR function to promote genome instability in the replication stress response. Under replication stress, binding of the mismatch recognition protein MutSα to replication forks blocks the loading of fork protection factors FANCD2 and BRCA1 to replication forks and promotes the recruitment of exonuclease MRE11 onto DNA to nascent strand degradation. This MutSα-dependent MRE11-catalyzed DNA degradation causes DNA breaks and chromosome abnormalities, contributing to an ultramutator phenotype. Mismatch repair (MMR) is a replication-coupled DNA repair mechanism and plays multiple roles at the replication fork. The well-established MMR functions include correcting misincorporated nucleotides that have escaped the proofreading activity of DNA polymerases, recognizing nonmismatched DNA adducts, and triggering a DNA damage response. In an attempt to determine whether MMR regulates replication progression in cells expressing an ultramutable DNA polymerase ɛ (Polɛ), carrying a proline-to-arginine substitution at amino acid 286 (Polɛ-P286R), we identified an unusual MMR function in response to hydroxyurea (HU)-induced replication stress. Polɛ-P286R cells treated with hydroxyurea exhibit increased MRE11-catalyzed nascent strand degradation. This degradation by MRE11 depends on the mismatch recognition protein MutSα and its binding to stalled replication forks. Increased MutSα binding at replication forks is also associated with decreased loading of replication fork protection factors FANCD2 and BRCA1, suggesting blockage of these fork protection factors from loading to replication forks by MutSα. We find that the MutSα-dependent MRE11-catalyzed fork degradation induces DNA breaks and various chromosome abnormalities. Therefore, unlike the well-known MMR functions of ensuring replication fidelity, the newly identified MMR activity of promoting genome instability may also play a role in cancer avoidance by eliminating rogue cells.
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18
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Yang XW, Han XP, Han C, London J, Fishel R, Liu J. MutS functions as a clamp loader by positioning MutL on the DNA during mismatch repair. Nat Commun 2022; 13:5808. [PMID: 36192430 PMCID: PMC9530208 DOI: 10.1038/s41467-022-33479-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/20/2022] [Indexed: 11/20/2022] Open
Abstract
Highly conserved MutS and MutL homologs operate as protein dimers in mismatch repair (MMR). MutS recognizes mismatched nucleotides forming ATP-bound sliding clamps, which subsequently load MutL sliding clamps that coordinate MMR excision. Several MMR models envision static MutS-MutL complexes bound to mismatched DNA via a positively charged cleft (PCC) located on the MutL N-terminal domains (NTD). We show MutL-DNA binding is undetectable in physiological conditions. Instead, MutS sliding clamps exploit the PCC to position a MutL NTD on the DNA backbone, likely enabling diffusion-mediated wrapping of the remaining MutL domains around the DNA. The resulting MutL sliding clamp enhances MutH endonuclease and UvrD helicase activities on the DNA, which also engage the PCC during strand-specific incision/excision. These MutS clamp-loader progressions are significantly different from the replication clamp-loaders that attach the polymerase processivity factors β-clamp/PCNA to DNA, highlighting the breadth of mechanisms for stably linking crucial genome maintenance proteins onto DNA.
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Affiliation(s)
- Xiao-Wen Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Xiao-Peng Han
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Chong Han
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - James London
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA.
- The Molecular Carcinogenesis and Chemoprevention Program, The James Comprehensive Cancer Center, Columbus, OH, 43210, USA.
| | - Jiaquan Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
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19
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Arrey G, Keating ST, Regenberg B. A unifying model for extrachromosomal circular DNA load in eukaryotic cells. Semin Cell Dev Biol 2022; 128:40-50. [PMID: 35292190 DOI: 10.1016/j.semcdb.2022.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023]
Abstract
Extrachromosomal circular DNA (eccDNA) with exons and whole genes are common features of eukaryotic cells. Work from especially tumours and the yeast Saccharomyces cerevisiae has revealed that eccDNA can provide large selective advantages and disadvantages. Besides the phenotypic effect due to expression of an eccDNA fragment, eccDNA is different from other mutations in that it is released from 1:1 segregation during cell division. This means that eccDNA can quickly change copy number, pickup secondary mutations and reintegrate into a chromosome to establish substantial genetic variation that could not have evolved via canonical mechanisms. We propose a unifying 5-factor model for conceptualizing the eccDNA load of a eukaryotic cell, emphasizing formation, replication, segregation, selection and elimination. We suggest that the magnitude of these sequential events and their interactions determine the copy number of eccDNA in mitotically dividing cells. We believe that our model will provide a coherent framework for eccDNA research, to understand its biology and the factors that can be manipulated to modulate eccDNA load in eukaryotic cells.
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Affiliation(s)
- Gerard Arrey
- Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Samuel T Keating
- Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Regenberg
- Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark.
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20
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Interplay between H3K36me3, methyltransferase SETD2, and mismatch recognition protein MutSα facilitates processing of oxidative DNA damage in human cells. J Biol Chem 2022; 298:102102. [PMID: 35667440 PMCID: PMC9241034 DOI: 10.1016/j.jbc.2022.102102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/21/2022] Open
Abstract
Oxidative DNA damage contributes to aging and the pathogenesis of numerous human diseases including cancer. 8-hydroxyguanine (8-oxoG) is the major product of oxidative DNA lesions. Although OGG1-mediated base excision repair is the primary mechanism for 8-oxoG removal, DNA mismatch repair has also been implicated in processing oxidative DNA damage. However, the mechanism of the latter is not fully understood. Here, we treated human cells defective in various 8-oxoG repair factors with H2O2 and performed biochemical, live cell imaging, and chromatin immunoprecipitation sequencing analyses to determine their response to the treatment. We show that the mismatch repair processing of oxidative DNA damage involves cohesive interactions between mismatch recognition protein MutSα, histone mark H3K36me3, and H3K36 trimethyltransferase SETD2, which activates the ATM DNA damage signaling pathway. We found that cells depleted of MutSα or SETD2 accumulate 8-oxoG adducts and fail to trigger H2O2-induced ATM activation. Furthermore, we show that SETD2 physically interacts with both MutSα and ATM, which suggests a role for SETD2 in transducing DNA damage signals from lesion-bound MutSα to ATM. Consistently, MutSα and SETD2 are highly coenriched at oxidative damage sites. The data presented here support a model wherein MutSα, SETD2, ATM, and H3K36me3 constitute a positive feedback loop to help cells cope with oxidative DNA damage.
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21
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The nuclease activity of DNA2 promotes exonuclease 1-independent mismatch repair. J Biol Chem 2022; 298:101831. [PMID: 35300981 PMCID: PMC9036127 DOI: 10.1016/j.jbc.2022.101831] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/03/2022] Open
Abstract
The DNA mismatch repair (MMR) system is a major DNA repair system that corrects DNA replication errors. In eukaryotes, the MMR system functions via mechanisms both dependent on and independent of exonuclease 1 (EXO1), an enzyme that has multiple roles in DNA metabolism. Although the mechanism of EXO1-dependent MMR is well understood, less is known about EXO1-independent MMR. Here, we provide genetic and biochemical evidence that the DNA2 nuclease/helicase has a role in EXO1-independent MMR. Biochemical reactions reconstituted with purified human proteins demonstrated that the nuclease activity of DNA2 promotes an EXO1-independent MMR reaction via a mismatch excision-independent mechanism that involves DNA polymerase δ. We show that DNA polymerase ε is not able to replace DNA polymerase δ in the DNA2-promoted MMR reaction. Unlike its nuclease activity, the helicase activity of DNA2 is dispensable for the ability of the protein to enhance the MMR reaction. Further examination established that DNA2 acts in the EXO1-independent MMR reaction by increasing the strand-displacement activity of DNA polymerase δ. These data reveal a mechanism for EXO1-independent mismatch repair.
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22
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Chan KY, Li X, Ortega J, Gu L, Li GM. DNA polymerase θ promotes CAG•CTG repeat expansions in Huntington's disease via insertion sequences of its catalytic domain. J Biol Chem 2021; 297:101144. [PMID: 34473992 PMCID: PMC8463855 DOI: 10.1016/j.jbc.2021.101144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/04/2022] Open
Abstract
Huntington's disease (HD), a neurodegenerative disease characterized by progressive dementia, psychiatric problems, and chorea, is known to be caused by CAG repeat expansions in the HD gene HTT. However, the mechanism of this pathology is not fully understood. The translesion DNA polymerase θ (Polθ) carries a large insertion sequence in its catalytic domain, which has been shown to allow DNA loop-outs in the primer strand. As a result of high levels of oxidative DNA damage in neural cells and Polθ's subsequent involvement in base excision repair of oxidative DNA damage, we hypothesized that Polθ contributes to CAG repeat expansion while repairing oxidative damage within HTT. Here, we performed Polθ-catalyzed in vitro DNA synthesis using various CAG•CTG repeat DNA substrates that are similar to base excision repair intermediates. We show that Polθ efficiently extends (CAG)n•(CTG)n hairpin primers, resulting in hairpin retention and repeat expansion. Polθ also triggers repeat expansions to pass the threshold for HD when the DNA template contains 35 repeats upward. Strikingly, Polθ depleted of the catalytic insertion fails to induce repeat expansions regardless of primers and templates used, indicating that the insertion sequence is responsible for Polθ's error-causing activity. In addition, the level of chromatin-bound Polθ in HD cells is significantly higher than in non-HD cells and exactly correlates with the degree of CAG repeat expansion, implying Polθ's involvement in triplet repeat instability. Therefore, we have identified Polθ as a potent factor that promotes CAG•CTG repeat expansions in HD and other neurodegenerative disorders.
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Affiliation(s)
- Kara Y Chan
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Xueying Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Janice Ortega
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Liya Gu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky, USA.
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23
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Abstract
The pathogenic consequences of 369 unique human HsMLH1 missense variants has been hampered by the lack of a detailed function in mismatch repair (MMR). Here single-molecule images show that HsMSH2-HsMSH6 provides a platform for HsMLH1-HsPMS2 to form a stable sliding clamp on mismatched DNA. The mechanics of sliding clamp progression solves a significant operational puzzle in MMR and provides explicit predictions for the distribution of clinically relevant HsMLH1 missense mutations.
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24
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Fuchs RP, Isogawa A, Paulo JA, Onizuka K, Takahashi T, Amunugama R, Duxin JP, Fujii S. Crosstalk between repair pathways elicits double-strand breaks in alkylated DNA and implications for the action of temozolomide. eLife 2021; 10:e69544. [PMID: 34236314 PMCID: PMC8289412 DOI: 10.7554/elife.69544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Temozolomide (TMZ), a DNA methylating agent, is the primary chemotherapeutic drug used in glioblastoma treatment. TMZ induces mostly N-alkylation adducts (N7-methylguanine and N3-methyladenine) and some O6-methylguanine (O6mG) adducts. Current models propose that during DNA replication, thymine is incorporated across from O6mG, promoting a futile cycle of mismatch repair (MMR) that leads to DNA double-strand breaks (DSBs). To revisit the mechanism of O6mG processing, we reacted plasmid DNA with N-methyl-N-nitrosourea (MNU), a temozolomide mimic, and incubated it in Xenopus egg-derived extracts. We have shown that in this system, MMR proteins are enriched on MNU-treated DNA and we observed robust, MMR-dependent, repair synthesis. Our evidence also suggests that MMR, initiated at O6mG:C sites, is strongly stimulated in cis by repair processing of other lesions, such as N-alkylation adducts. Importantly, MNU-treated plasmids display DSBs in extracts, the frequency of which increases linearly with the square of alkylation dose. We suggest that DSBs result from two independent repair processes, one involving MMR at O6mG:C sites and the other involving base excision repair acting at a nearby N-alkylation adduct. We propose a new, replication-independent mechanism of action of TMZ, which operates in addition to the well-studied cell cycle-dependent mode of action.
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Affiliation(s)
- Robert P Fuchs
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Asako Isogawa
- Cancer Research Center of Marseille, UMR7258, CNRSMarseilleFrance
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku UniversitySendaiJapan
| | | | - Ravindra Amunugama
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Julien P Duxin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Shingo Fujii
- Cancer Research Center of Marseille, UMR7258, CNRSMarseilleFrance
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25
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Microsatellite Instability in Colorectal Cancers: Carcinogenesis, Neo-Antigens, Immuno-Resistance and Emerging Therapies. Cancers (Basel) 2021; 13:cancers13123063. [PMID: 34205397 PMCID: PMC8235567 DOI: 10.3390/cancers13123063] [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: 05/06/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary A deficient mismatch repair system (dMMR) results in microsatellite instability (MSI). The MSI status of a tumor predicts the response to immune checkpoint inhibitors (ICI) that are now approved in patients with dMMR/MSI metastatic colorectal cancers. In addition to the mechanisms through which MSI can activate the immune system via particular neo-antigens, this review reports the clinical and pre-clinical strategies being developed in the case of resistance to ICI, including emerging therapies and new biomarkers. Abstract A defect in the DNA repair system through a deficient mismatch repair system (dMMR) leads to microsatellite instability (MSI). Microsatellites are located in both coding and non-coding sequences and dMMR/MSI tumors are associated with a high mutation burden. Some of these mutations occur in coding sequences and lead to the production of neo-antigens able to trigger an anti-tumoral immune response. This explains why non-metastatic MSI tumors are associated with high immune infiltrates and good prognosis. Metastatic MSI tumors result from tumor escape to the immune system and are associated with poor prognosis and chemoresistance. Consequently, immune checkpoint inhibitors (ICI) are highly effective and have recently been approved in dMMR/MSI metastatic colorectal cancers (mCRC). Nevertheless, some patients with dMMR/MSI mCRC have primary or secondary resistance to ICI. This review details carcinogenesis and the mechanisms through which MSI can activate the immune system. After which, we discuss mechanistic hypotheses in an attempt to explain primary and secondary resistances to ICI and emerging strategies being developed to overcome this phenomenon by targeting other immune checkpoints or through vaccination and modification of microbiota.
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