1
|
Fragkos M, Choleza M, Papadopoulou P. The Role of γH2AX in Replication Stress-induced Carcinogenesis: Possible Links and Recent Developments. CANCER DIAGNOSIS & PROGNOSIS 2023; 3:639-648. [PMID: 37927801 PMCID: PMC10619570 DOI: 10.21873/cdp.10266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023]
Abstract
Cancer is a condition characterized by genomic instability and gross chromosomal aberrations. The inability of the cell to timely and efficiently complete its replication cycle before entering mitosis is one of the most common causes of DNA damage and carcinogenesis. Phosphorylation of histone 2AX (H2AX) on S139 (γH2AX) is an indispensable step in the response to DNA damage, as it is required for the assembly of repair factors at the sites of damage. γH2AX is also a marker of DNA replication stress, mainly due to fork collapse that often follows prolonged replication stalling or repair of arrested forks, which involves the generation of DNA breaks. Although the role of γH2AX in the repair of DNA breaks has been well defined, the function of γH2AX in replicative stress remains unclear. In this review, we present the recent advances in the field of replication stress, and highlight a novel function for γH2AX that is independent of its role in the response to DNA damage. We discuss studies that support a role for γΗ2ΑΧ early in the response to replicative stress, which does not involve the repair of DNA breaks. We also highlight recent data proposing that γH2AX acts as a chromatin remodeling component, implicated in the efficient resolution of stalled replication forks. Understanding the mechanism by which γH2AX enables cellular recovery after replication stress will allow identification of novel cancer biomarkers, as well as new targets for cancer therapies.
Collapse
Affiliation(s)
- Michalis Fragkos
- Department of Science and Mathematics, Deree-The American College of Greece, Athens, Greece
| | - Maria Choleza
- Department of Science and Mathematics, Deree-The American College of Greece, Athens, Greece
| | - Paraskevi Papadopoulou
- Department of Science and Mathematics, Deree-The American College of Greece, Athens, Greece
| |
Collapse
|
2
|
Gupta N, Yakhou L, Albert JR, Azogui A, Ferry L, Kirsh O, Miura F, Battault S, Yamaguchi K, Laisné M, Domrane C, Bonhomme F, Sarkar A, Delagrange M, Ducos B, Cristofari G, Ito T, Greenberg MVC, Defossez PA. A genome-wide screen reveals new regulators of the 2-cell-like cell state. Nat Struct Mol Biol 2023; 30:1105-1118. [PMID: 37488355 DOI: 10.1038/s41594-023-01038-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/19/2023] [Indexed: 07/26/2023]
Abstract
In mammals, only the zygote and blastomeres of the early embryo are totipotent. This totipotency is mirrored in vitro by mouse '2-cell-like cells' (2CLCs), which appear at low frequency in cultures of embryonic stem cells (ESCs). Because totipotency is not completely understood, we carried out a genome-wide CRISPR knockout screen in mouse ESCs, searching for mutants that reactivate the expression of Dazl, a gene expressed in 2CLCs. Here we report the identification of four mutants that reactivate Dazl and a broader 2-cell-like signature: the E3 ubiquitin ligase adaptor SPOP, the Zinc-Finger transcription factor ZBTB14, MCM3AP, a component of the RNA processing complex TREX-2, and the lysine demethylase KDM5C. All four factors function upstream of DPPA2 and DUX, but not via p53. In addition, SPOP binds DPPA2, and KDM5C interacts with ncPRC1.6 and inhibits 2CLC gene expression in a catalytic-independent manner. These results extend our knowledge of totipotency, a key phase of organismal life.
Collapse
Affiliation(s)
- Nikhil Gupta
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France.
- Joint AZ CRUK Functional Genomics Centre, The Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
| | - Lounis Yakhou
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | | | - Anaelle Azogui
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Laure Ferry
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Olivier Kirsh
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, Japan
| | - Sarah Battault
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Kosuke Yamaguchi
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Marthe Laisné
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Cécilia Domrane
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Frédéric Bonhomme
- Epigenetic Chemical Biology, UMR3523, Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Arpita Sarkar
- IRCAN, Université Côte d'Azur, Inserm, CNRS, Nice, France
| | - Marine Delagrange
- High Throughput qPCR Facility, Institut de Biologie de l'École Normale Supérieure (IBENS), Laboratoire de Physique de l'ENS CNRS UMR8023, PSL Research University, Paris, France
| | - Bertrand Ducos
- High Throughput qPCR Facility, Institut de Biologie de l'École Normale Supérieure (IBENS), Laboratoire de Physique de l'ENS CNRS UMR8023, PSL Research University, Paris, France
| | | | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, Japan
| | | | | |
Collapse
|
3
|
Wang L, Wang B, Wu C, Wang J, Sun M. Autism Spectrum Disorder: Neurodevelopmental Risk Factors, Biological Mechanism, and Precision Therapy. Int J Mol Sci 2023; 24:ijms24031819. [PMID: 36768153 PMCID: PMC9915249 DOI: 10.3390/ijms24031819] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous, behaviorally defined neurodevelopmental disorder. Over the past two decades, the prevalence of autism spectrum disorders has progressively increased, however, no clear diagnostic markers and specifically targeted medications for autism have emerged. As a result, neurobehavioral abnormalities, neurobiological alterations in ASD, and the development of novel ASD pharmacological therapy necessitate multidisciplinary collaboration. In this review, we discuss the development of multiple animal models of ASD to contribute to the disease mechanisms of ASD, as well as new studies from multiple disciplines to assess the behavioral pathology of ASD. In addition, we summarize and highlight the mechanistic advances regarding gene transcription, RNA and non-coding RNA translation, abnormal synaptic signaling pathways, epigenetic post-translational modifications, brain-gut axis, immune inflammation and neural loop abnormalities in autism to provide a theoretical basis for the next step of precision therapy. Furthermore, we review existing autism therapy tactics and limits and present challenges and opportunities for translating multidisciplinary knowledge of ASD into clinical practice.
Collapse
|
4
|
Miao Y, Mu L, Chen Y, Tang X, Wang J, Quan W, Mi D. Construction and Validation of a Protein-associated Prognostic Model for Gastrointestinal Cancer. Comb Chem High Throughput Screen 2023; 26:191-206. [PMID: 35430986 DOI: 10.2174/1386207325666220414105743] [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: 10/15/2021] [Revised: 02/05/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022]
Abstract
Background Gastrointestinal cancer (GIC) is a prevalent and lethal malignant tumor. It is obligatory to investigate innovative biomarkers for the diagnosis and prognosis. Proteins play a crucial role in regulating the occurrence and progression of GIC. However, the prognostic value of proteins is unclear in GIC. OBJECTIVE This paper aims to identify the hub prognosis-related proteins (PAPs) and construct a prognosis model for GIC patients for clinical application. METHODS Protein expression data of GIC was obtained from The Cancer Proteome Atlas (TCPA) and downloaded the clinicopathological data from The Cancer Genome Atlas database (TCGA). Besides, hub proteins were filtrated via univariate and multivariate Cox regression analysis. Moreover, survival analysis and nomogram were used to predict overall survival (OS). We used the calibration curves to assess the consistency of predictive and actual survival rates. The consistency index (C-index) was used to evaluate the prognostic ability of the predictive model. Furthermore, functional enrichment analysis and protein co-expression of PAPs were used to explore their roles in GIC. RESULTS Finally, a prognosis model was conducted based on ten PAPs (CYCLIND1, DVL3, NCADHERIN, SYK, ANNEXIN VII, CD20, CMET, RB, TFRC, and PREX1). The risk score calculated by the model was an independent prognostic predictor. Compared with the high-risk subgroup, the low-risk subgroup had better OS. In the TCGA cohort, the area under the curve value of the receiver operating characteristic curve of the prognostic model was 0.692. The expression of proteins and risk score had a significant association with the clinicopathological characteristics of GIC. Besides, a nomogram based on GIC clinicopathological features and risk scores could properly predict the OS of individual GIC patients. The C-index is 0.71 in the TCGA cohort and 0.73 in the GEO cohort. CONCLUSION The results indicate that the risk score is an independent prognostic biomarker and is related to the malignant clinical features of GIC patients. Besides, several PAPs associated with the survival and clinicopathological characteristics of GIC might be potential biomarkers for GIC diagnosis and treatment.
Collapse
Affiliation(s)
- Yandong Miao
- The First Clinical Medical College, Lanzhou University, Lanzhou City, 730000, China
- Gansu Academy of Traditional Chinese Medicine, Lanzhou, 730000, China
| | - Linjie Mu
- The First Clinical Medical College, Lanzhou University, Lanzhou City, 730000, China
- The First Affiliated Hospital of Kunming Medical University, Kunming, 650000, China
| | - Yonggang Chen
- The Second Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Xiaolong Tang
- The First Clinical Medical College, Lanzhou University, Lanzhou City, 730000, China
| | - Jiangtao Wang
- The First Clinical Medical College, Lanzhou University, Lanzhou City, 730000, China
| | - Wuxia Quan
- Qingyang People's Hospital, Qingyang City, Gansu Province, P.R. China
| | - Denghai Mi
- The First Clinical Medical College, Lanzhou University, Lanzhou City, 730000, China
- Gansu Academy of Traditional Chinese Medicine, Lanzhou, 730000, China
| |
Collapse
|
5
|
Zeng X, Zhao F, Cui G, Zhang Y, Deshpande RA, Chen Y, Deng M, Kloeber JA, Shi Y, Zhou Q, Zhang C, Hou J, Kim W, Tu X, Yan Y, Xu Z, Chen L, Gao H, Guo G, Liu J, Zhu Q, Cao Y, Huang J, Wu Z, Zhu S, Yin P, Luo K, Mer G, Paull TT, Yuan J, Tao K, Lou Z. METTL16 antagonizes MRE11-mediated DNA end resection and confers synthetic lethality to PARP inhibition in pancreatic ductal adenocarcinoma. NATURE CANCER 2022; 3:1088-1104. [PMID: 36138131 DOI: 10.1038/s43018-022-00429-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/26/2022] [Indexed: 06/16/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers. Characterization of genetic alterations will improve our understanding and therapies for this disease. Here, we report that PDAC with elevated expression of METTL16, one of the 'writers' of RNA N6-methyladenosine modification, may benefit from poly-(ADP-ribose)-polymerase inhibitor (PARPi) treatment. Mechanistically, METTL16 interacts with MRE11 through RNA and this interaction inhibits MRE11's exonuclease activity in a methyltransferase-independent manner, thereby repressing DNA end resection. Upon DNA damage, ATM phosphorylates METTL16 resulting in a conformational change and autoinhibition of its RNA binding. This dissociates the METTL16-RNA-MRE11 complex and releases inhibition of MRE11. Concordantly, PDAC cells with high METTL16 expression show increased sensitivity to PARPi, especially when combined with gemcitabine. Thus, our findings reveal a role for METTL16 in homologous recombination repair and suggest that a combination of PARPi with gemcitabine could be an effective treatment strategy for PDAC with elevated METTL16 expression.
Collapse
Affiliation(s)
- Xiangyu Zeng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Yong Zhang
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Yuping Chen
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- 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, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, USA
| | - Yu Shi
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Chao Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jing Hou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Wootae Kim
- Soonchunhyang Institute of Med-bio Science (SIMS), Soonchunhyang University, Cheonan-si, Republic of Korea
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Yuanliang Yan
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Lifeng Chen
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Center for Reproductive Medicine, Department of Gynecology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaqi Liu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yueyu Cao
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Zheming Wu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Shouhai Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Jian Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China.
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
6
|
Potential Methods of Targeting Cellular Aging Hallmarks to Reverse Osteoarthritic Phenotype of Chondrocytes. BIOLOGY 2022; 11:biology11070996. [PMID: 36101377 PMCID: PMC9312132 DOI: 10.3390/biology11070996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/12/2022] [Accepted: 06/20/2022] [Indexed: 01/15/2023]
Abstract
Osteoarthritis (OA) is a chronic degenerative joint disease that causes pain, physical disability, and life quality impairment. The pathophysiology of OA remains largely unclear, and currently no FDA-approved disease-modifying OA drugs (DMOADs) are available. As has been acknowledged, aging is the primary independent risk factor for OA, but the mechanisms underlying such a connection are not fully understood. In this review, we first revisit the changes in OA chondrocytes from the perspective of cellular hallmarks of aging. It is concluded that OA chondrocytes share many alterations similar to cellular aging. Next, based on the findings from studies on other cell types and diseases, we propose methods that can potentially reverse osteoarthritic phenotype of chondrocytes back to a healthier state. Lastly, current challenges and future perspectives are summarized.
Collapse
|
7
|
The Molecular Landscape of Medulloblastoma in Teenagers and Young Adults. Cancers (Basel) 2022; 14:cancers14010251. [PMID: 35008416 PMCID: PMC8750554 DOI: 10.3390/cancers14010251] [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: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 02/01/2023] Open
Abstract
Medulloblastoma (MB) is a childhood malignant brain tumour but also occurs in teenagers and young adults (TYA). Considering that MB is heterogeneous, this study aimed to define the molecular landscape of MBs in TYAs. We collated more than 2000 MB samples that included 287 TYA patients (13-24 years). We performed computational analyses consisting of genome-wide methylation and transcriptomic profiles and developed a prognostics model for the TYAs with MB. We identified that TYAs predominantly comprised of Group 4 (40%) and Sonic Hedgehog (SHH)-activated (33%) tumours, with Wingless-type (WNT, 17%) and Group 3 (10%) being less common. TYAs with SHH tumours displayed significantly more gene expression alterations, whereas no gene was detected in the Group 4 tumours. Across MB subgroups, we identified unique and shared sets of TYA-specific differentially methylated probes and DNA-binding motifs. Finally, a 22-gene signature stratified TYA patients into high- and low-risk groups, and the prognostic significance of these risk groups persisted in multivariable regression models (P = 0.001). This study is an important step toward delineating the molecular landscape of TYAs with MB. The emergence of novel genes and pathways may provide a basis for improved clinical management of TYA with MB.
Collapse
|
8
|
Wang RS, Lembo AJ, Kaptchuk TJ, Cheng V, Nee J, Iturrino J, Rao M, Loscalzo J, Silvester JA, Hall KT. Genomic Effects Associated With Response to Placebo Treatment in a Randomized Trial of Irritable Bowel Syndrome. FRONTIERS IN PAIN RESEARCH 2022; 2:775386. [PMID: 35295415 PMCID: PMC8915627 DOI: 10.3389/fpain.2021.775386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Background and Aims: Irritable bowel syndrome (IBS), a functional pain disorder of gut-brain interactions, is characterized by a high placebo response in randomized clinical trials (RCTs). Catechol-O-methyltransferase (COMT) rs4680, which encodes high-activity (val) or low-activity (met) enzyme variants, was previously associated with placebo response to sham-acupuncture in an IBS RCT. Examining COMT effects and identifying novel genomic factors that influence response to placebo pills is critical to identifying underlying mechanisms and predicting and managing placebos in RCTs. Methods: Participants with IBS (N = 188) were randomized to three placebo-related interventions, namely, double-blind placebo (DBP), open-label placebo (OLP), or simply trial enrollment without placebo treatment [no placebo (i.e., no pill) treatment control (NPC)], for 6 weeks. COMT rs4680, gene-set, and genome-wide suggestive (p < 10-5) loci effects on irritable bowel symptom severity score (IBS-SSS) across all participants were examined. Results: Participants with IBS homozygous for rs4680 met (met/met) had the greatest improvement across all arms, with significantly greater improvement compared to val/val in DBP (beta (SE), -89.4 (42.3); p = 0.04). Twelve genome-wide suggestive loci formed a gene regulatory network highly connected to EGR1, a transcription factor involved in placebo-related processes of learning, memory, and response to stress and reward. EGR1 gene expression in peripheral blood mononuclear cells (PBMC) was significantly reduced at the endpoint across all treatment arms (log fold-change, -0.15; p = 0.02). Gene-set enrichment analysis returned three genome-wide significant ontology terms (GO:0032968, GO:0070934, and GO:0070937) linked to transcription regulation and GO:0003918 associated with DNA topoisomerase regulation. Conclusion: These results suggest common molecular mechanisms in response to varying forms of placebo that may inform personalized IBS treatment and placebo response prediction. Clinical Trial Registration: ClinicalTrials.gov, Identifier: NCT0280224.
Collapse
Affiliation(s)
- Rui-Sheng Wang
- Department of Medicine, Brigham Women's Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Anthony J. Lembo
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Ted J. Kaptchuk
- Program in Placebo Studies, Beth Israel Deaconess Medical Center, Boston, MA, United States
- Department of General Medicine Primary Care, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Vivian Cheng
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Judy Nee
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Johanna Iturrino
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Meenakshi Rao
- Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Joseph Loscalzo
- Department of Medicine, Brigham Women's Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Jocelyn A. Silvester
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, United States
- Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
- Celiac Disease Program, Boston Children's Hospital, Boston, MA, United States
| | - Kathryn T. Hall
- Department of Medicine, Brigham Women's Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Program in Placebo Studies, Beth Israel Deaconess Medical Center, Boston, MA, United States
| |
Collapse
|
9
|
Raj K, Szladovits B, Haghani A, Zoller JA, Li CZ, Black P, Maddox D, Robeck TR, Horvath S. Epigenetic clock and methylation studies in cats. GeroScience 2021; 43:2363-2378. [PMID: 34463900 PMCID: PMC8599556 DOI: 10.1007/s11357-021-00445-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/17/2021] [Indexed: 12/21/2022] Open
Abstract
Human DNA methylation profiles have been used successfully to develop highly accurate biomarkers of aging ("epigenetic clocks"). Although these human epigenetic clocks are not immediately applicable to all species of the animal kingdom, the principles underpinning them appear to be conserved even in animals that are evolutionarily far removed from humans. This is exemplified by recent development of epigenetic clocks for mice and other mammalian species. Here, we describe epigenetic clocks for the domestic cat (Felis catus), based on methylation profiles of CpGs with flanking DNA sequences that are highly conserved between multiple mammalian species. Methylation levels of these CpGs are measured using a custom-designed Infinium array (HorvathMammalMethylChip40). From these, we present 3 epigenetic clocks for cats; of which, one applies only to blood samples from cats, while the remaining two dual-species human-cat clocks apply both to cats and humans. We demonstrate that these domestic cat clocks also lead to high age correlations in cheetahs, tigers, and lions. It is expected that these epigenetic clocks for cats possess the potential to be further developed for monitoring feline health as well as being used for identifying and validating anti-aging interventions.
Collapse
Affiliation(s)
- Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Balazs Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, 695 Charles E. Young Drive South, Los Angeles, CA 90095 USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
| | | | | | - Todd R. Robeck
- Corporate Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, 695 Charles E. Young Drive South, Los Angeles, CA 90095 USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
| |
Collapse
|
10
|
Ju MK, Shin KJ, Lee JR, Khim KW, A Lee E, Ra JS, Kim BG, Jo HS, Yoon JH, Kim TM, Myung K, Choi JH, Kim H, Chae YC. NSMF promotes the replication stress-induced DNA damage response for genome maintenance. Nucleic Acids Res 2021; 49:5605-5622. [PMID: 33963872 PMCID: PMC8191778 DOI: 10.1093/nar/gkab311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/14/2022] Open
Abstract
Proper activation of DNA repair pathways in response to DNA replication stress is critical for maintaining genomic integrity. Due to the complex nature of the replication fork (RF), problems at the RF require multiple proteins, some of which remain unidentified, for resolution. In this study, we identified the N-methyl-D-aspartate receptor synaptonuclear signaling and neuronal migration factor (NSMF) as a key replication stress response factor that is important for ataxia telangiectasia and Rad3-related protein (ATR) activation. NSMF localizes rapidly to stalled RFs and acts as a scaffold to modulate replication protein A (RPA) complex formation with cell division cycle 5-like (CDC5L) and ATR/ATR-interacting protein (ATRIP). Depletion of NSMF compromised phosphorylation and ubiquitination of RPA2 and the ATR signaling cascade, resulting in genomic instability at RFs under DNA replication stress. Consistently, NSMF knockout mice exhibited increased genomic instability and hypersensitivity to genotoxic stress. NSMF deficiency in human and mouse cells also caused increased chromosomal instability. Collectively, these findings demonstrate that NSMF regulates the ATR pathway and the replication stress response network for genome maintenance and cell survival.
Collapse
Affiliation(s)
- Min Kyung Ju
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyeong Jin Shin
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Joo Rak Lee
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Keon Woo Khim
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Eun A Lee
- Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea
| | - Han-Seul Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Tae Moon Kim
- Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jang Hyun Choi
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hongtae Kim
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.,Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea
| | - Young Chan Chae
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| |
Collapse
|
11
|
DNA methylation predicts age and provides insight into exceptional longevity of bats. Nat Commun 2021; 12:1615. [PMID: 33712580 PMCID: PMC7955057 DOI: 10.1038/s41467-021-21900-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/08/2021] [Indexed: 01/31/2023] Open
Abstract
Exceptionally long-lived species, including many bats, rarely show overt signs of aging, making it difficult to determine why species differ in lifespan. Here, we use DNA methylation (DNAm) profiles from 712 known-age bats, representing 26 species, to identify epigenetic changes associated with age and longevity. We demonstrate that DNAm accurately predicts chronological age. Across species, longevity is negatively associated with the rate of DNAm change at age-associated sites. Furthermore, analysis of several bat genomes reveals that hypermethylated age- and longevity-associated sites are disproportionately located in promoter regions of key transcription factors (TF) and enriched for histone and chromatin features associated with transcriptional regulation. Predicted TF binding site motifs and enrichment analyses indicate that age-related methylation change is influenced by developmental processes, while longevity-related DNAm change is associated with innate immunity or tumorigenesis genes, suggesting that bat longevity results from augmented immune response and cancer suppression.
Collapse
|
12
|
Activation of DNA damage response signaling in mammalian cells by ionizing radiation. Free Radic Res 2021; 55:581-594. [PMID: 33455476 DOI: 10.1080/10715762.2021.1876853] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cellular responses to DNA damage are fundamental to preserve genomic integrity during various endogenous and exogenous stresses. Following radiation therapy and chemotherapy, this DNA damage response (DDR) also determines development of carcinogenesis and therapeutic outcome. In humans, DNA damage activates a robust network of signal transduction cascades, driven primarily through phosphorylation events. These responses primarily involve two key non-redundant signal transducing proteins of phosphatidylinositol 3-kinase-like (PIKK) family - ATR and ATM, and their downstream kinases (hChk1 and hChk2). They further phosphorylate effectors proteins such as p53, Cdc25A and Cdc25C which function either to activate the DNA damage checkpoints and cell death mechanisms, or DNA repair pathways. Identification of molecular pathways that determine signaling after DNA damage and trigger DNA repair in response to differing types of DNA lesions allows for a far better understanding of the consequences of radiation and chemotherapy on normal and tumor cells. Here we highlight the network of DNA damage response pathways that are activated after treatment with different types of radiation. Further, we discuss regulation of cell cycle checkpoint and DNA repair processes in the context of DDR in response to radiation.
Collapse
|
13
|
Yan Y, Xu Z, Huang J, Guo G, Gao M, Kim W, Zeng X, Kloeber JA, Zhu Q, Zhao F, Luo K, Lou Z. The deubiquitinase USP36 Regulates DNA replication stress and confers therapeutic resistance through PrimPol stabilization. Nucleic Acids Res 2021; 48:12711-12726. [PMID: 33237263 PMCID: PMC7736794 DOI: 10.1093/nar/gkaa1090] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
PrimPol has been recently identified as a DNA damage tolerant polymerase that plays an important role in replication stress response. However, the regulatory mechanisms of PrimPol are not well defined. In this study, we identify that the deubiquitinase USP36 interferes with degradation of PrimPol to regulate the replication stress response. Mechanistically, USP36 is deubiquitinated following DNA replication stress, which in turn facilitates its upregulation and interaction with PrimPol. USP36 deubiquitinates K29-linked polyubiquitination of PrimPol and increases its protein stability. Depletion of USP36 results in replication stress-related defects and elevates cell sensitivity to DNA-damage agents, such as cisplatin and olaparib. Moreover, USP36 expression positively correlates with the level of PrimPol protein and poor prognosis in patient samples. These findings indicate that the regulation of PrimPol K29-linked ubiquitination by USP36 plays a critical role in DNA replication stress and chemotherapy response.
Collapse
Affiliation(s)
- Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhijie Xu
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Wootae Kim
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiangyu Zeng
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA.,Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN 55905, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
14
|
PARP Inhibition Increases the Reliance on ATR/CHK1 Checkpoint Signaling Leading to Synthetic Lethality-An Alternative Treatment Strategy for Epithelial Ovarian Cancer Cells Independent from HR Effectiveness. Int J Mol Sci 2020; 21:ijms21249715. [PMID: 33352723 PMCID: PMC7766831 DOI: 10.3390/ijms21249715] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
Poly (ADP-ribose) polymerase inhibitor (PARPi, olaparib) impairs the repair of DNA single-strand breaks (SSBs), resulting in double-strand breaks (DSBs) that cannot be repaired efficiently in homologous recombination repair (HRR)-deficient cancers such as BRCA1/2-mutant cancers, leading to synthetic lethality. Despite the efficacy of olaparib in the treatment of BRCA1/2 deficient tumors, PARPi resistance is common. We hypothesized that the combination of olaparib with anticancer agents that disrupt HRR by targeting ataxia telangiectasia and Rad3-related protein (ATR) or checkpoint kinase 1 (CHK1) may be an effective strategy to reverse ovarian cancer resistance to olaparib. Here, we evaluated the effect of olaparib, the ATR inhibitor AZD6738, and the CHK1 inhibitor MK8776 alone and in combination on cell survival, colony formation, replication stress response (RSR) protein expression, DNA damage, and apoptotic changes in BRCA2 mutated (PEO-1) and HRR-proficient BRCA wild-type (SKOV-3 and OV-90) cells. Combined treatment caused the accumulation of DNA DSBs. PARP expression was associated with sensitivity to olaparib or inhibitors of RSR. Synergistic effects were weaker when olaparib was combined with CHK1i and occurred regardless of the BRCA2 status of tumor cells. Because PARPi increases the reliance on ATR/CHK1 for genome stability, the combination of PARPi with ATR inhibition suppressed ovarian cancer cell growth independently of the efficacy of HRR. The present results were obtained at sub-lethal doses, suggesting the potential of these inhibitors as monotherapy as well as in combination with olaparib.
Collapse
|
15
|
Mognato M, Burdak-Rothkamm S, Rothkamm K. Interplay between DNA replication stress, chromatin dynamics and DNA-damage response for the maintenance of genome stability. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108346. [PMID: 34083038 DOI: 10.1016/j.mrrev.2020.108346] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
DNA replication stress is a major source of DNA damage, including double-stranded breaks that promote DNA damage response (DDR) signaling. Inefficient repair of such lesions can affect genome integrity. During DNA replication different factors act on chromatin remodeling in a coordinated way. While recent studies have highlighted individual molecular mechanisms of interaction, less is known about the orchestration of chromatin changes under replication stress. In this review we attempt to explore the complex relationship between DNA replication stress, DDR and genome integrity in mammalian cells, taking into account the role of chromatin disposition as an important modulator of DNA repair. Recent data on chromatin restoration and epigenetic re-establishment after DNA replication stress are reviewed.
Collapse
Affiliation(s)
| | - Susanne Burdak-Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
| | - Kai Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
| |
Collapse
|