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Yang JH, Hayano M, Griffin PT, Amorim JA, Bonkowski MS, Apostolides JK, Salfati EL, Blanchette M, Munding EM, Bhakta M, Chew YC, Guo W, Yang X, Maybury-Lewis S, Tian X, Ross JM, Coppotelli G, Meer MV, Rogers-Hammond R, Vera DL, Lu YR, Pippin JW, Creswell ML, Dou Z, Xu C, Mitchell SJ, Das A, O'Connell BL, Thakur S, Kane AE, Su Q, Mohri Y, Nishimura EK, Schaevitz L, Garg N, Balta AM, Rego MA, Gregory-Ksander M, Jakobs TC, Zhong L, Wakimoto H, El Andari J, Grimm D, Mostoslavsky R, Wagers AJ, Tsubota K, Bonasera SJ, Palmeira CM, Seidman JG, Seidman CE, Wolf NS, Kreiling JA, Sedivy JM, Murphy GF, Green RE, Garcia BA, Berger SL, Oberdoerffer P, Shankland SJ, Gladyshev VN, Ksander BR, Pfenning AR, Rajman LA, Sinclair DA. Loss of epigenetic information as a cause of mammalian aging. Cell 2023; 186:305-326.e27. [PMID: 36638792 PMCID: PMC10166133 DOI: 10.1016/j.cell.2022.12.027] [Citation(s) in RCA: 203] [Impact Index Per Article: 203.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 08/09/2022] [Accepted: 12/15/2022] [Indexed: 01/13/2023]
Abstract
All living things experience an increase in entropy, manifested as a loss of genetic and epigenetic information. In yeast, epigenetic information is lost over time due to the relocalization of chromatin-modifying proteins to DNA breaks, causing cells to lose their identity, a hallmark of yeast aging. Using a system called "ICE" (inducible changes to the epigenome), we find that the act of faithful DNA repair advances aging at physiological, cognitive, and molecular levels, including erosion of the epigenetic landscape, cellular exdifferentiation, senescence, and advancement of the DNA methylation clock, which can be reversed by OSK-mediated rejuvenation. These data are consistent with the information theory of aging, which states that a loss of epigenetic information is a reversible cause of aging.
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Affiliation(s)
- Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA.
| | - Motoshi Hayano
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Ophthalmology, Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Patrick T Griffin
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - João A Amorim
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Michael S Bonkowski
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - John K Apostolides
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Elias L Salfati
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | | | | | - Mital Bhakta
- Cantata/Dovetail Genomics, Scotts Valley, CA, USA
| | | | - Wei Guo
- Zymo Research Corporation, Irvine, CA, USA
| | | | - Sun Maybury-Lewis
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Xiao Tian
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Jaime M Ross
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Giuseppe Coppotelli
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Margarita V Meer
- Department of Medicine, Brigham and Women's Hospital, HMS, Boston, MA, USA
| | - Ryan Rogers-Hammond
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Daniel L Vera
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Yuancheng Ryan Lu
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Jeffrey W Pippin
- Division of Nephrology, University of Washington, Seattle, WA, USA
| | - Michael L Creswell
- Division of Nephrology, University of Washington, Seattle, WA, USA; Georgetown University School of Medicine, Washington, DC, USA
| | - Zhixun Dou
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Caiyue Xu
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Abhirup Das
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Pharmacology, UNSW, Sydney, NSW, Australia
| | | | - Sachin Thakur
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Alice E Kane
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Qiao Su
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yasuaki Mohri
- Department of Stem Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Emi K Nishimura
- Department of Stem Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Neha Garg
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Ana-Maria Balta
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Meghan A Rego
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | | | - Tatjana C Jakobs
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, HMS, Boston, MA, USA
| | - Lei Zhong
- The Massachusetts General Hospital Cancer Center, HMS, Boston, MA, USA
| | | | - Jihad El Andari
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, University of Heidelberg, BioQuant, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, University of Heidelberg, BioQuant, Heidelberg, Germany
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, HMS, Boston, MA, USA
| | - Amy J Wagers
- Paul F. Glenn Center for Biology of Aging Research, Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Joslin Diabetes Center, Boston, MA, USA
| | - Kazuo Tsubota
- Department of Ophthalmology, Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Stephen J Bonasera
- Division of Geriatrics, University of Nebraska Medical Center, Durham Research Center II, Omaha, NE, USA
| | - Carlos M Palmeira
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | | | | | - Norman S Wolf
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Jill A Kreiling
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - George F Murphy
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Richard E Green
- Department of Biomolecular Engineering, UCSC, Santa Cruz, CA, USA
| | - Benjamin A Garcia
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Vadim N Gladyshev
- Department of Medicine, Brigham and Women's Hospital, HMS, Boston, MA, USA
| | - Bruce R Ksander
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, HMS, Boston, MA, USA
| | - Andreas R Pfenning
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Luis A Rajman
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - David A Sinclair
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA.
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Tang S, Gökbağ B, Fan K, Shao S, Huo Y, Wu X, Cheng L, Li L. Synthetic lethal gene pairs: Experimental approaches and predictive models. Front Genet 2022; 13:961611. [PMID: 36531238 PMCID: PMC9751344 DOI: 10.3389/fgene.2022.961611] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/07/2022] [Indexed: 03/27/2024] Open
Abstract
Synthetic lethality (SL) refers to a genetic interaction in which the simultaneous perturbation of two genes leads to cell or organism death, whereas viability is maintained when only one of the pair is altered. The experimental exploration of these pairs and predictive modeling in computational biology contribute to our understanding of cancer biology and the development of cancer therapies. We extensively reviewed experimental technologies, public data sources, and predictive models in the study of synthetic lethal gene pairs and herein detail biological assumptions, experimental data, statistical models, and computational schemes of various predictive models, speculate regarding their influence on individual sample- and population-based synthetic lethal interactions, discuss the pros and cons of existing SL data and models, and highlight potential research directions in SL discovery.
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Affiliation(s)
- Shan Tang
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Birkan Gökbağ
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Kunjie Fan
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Shuai Shao
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Yang Huo
- Indiana University, Bloomington, IN, United States
| | - Xue Wu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Lijun Cheng
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
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Merabet S, Carnesecchi J. Hox dosage and morphological diversification during development and evolution. Semin Cell Dev Biol 2022:S1084-9521(22)00360-3. [PMID: 36481343 DOI: 10.1016/j.semcdb.2022.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/15/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Hox genes encode for evolutionary conserved transcription factors that have long fascinated biologists since the observation of the first homeotic transformations in flies. Hox genes are developmental architects that instruct the formation of various and precise morphologies along the body axes in cnidarian and bilaterian species. In contrast to these highly specific developmental functions, Hox genes encode for proteins that display poorly selective DNA-binding properties in vitro. This "Hox paradox" has been partially solved with the discovery of the TALE-class cofactors, which interact with all Hox members and form versatile Hox/TALE protein complexes on DNA. Here, we describe the role of the Hox dosage as an additional molecular strategy contributing to further resolve the Hox paradox. We present several cases where the Hox dosage is involved in the formation of different morphologies in invertebrates and vertebrates, with a particular emphasis on flight appendages in insects. We also discuss how the Hox dosage could be interpreted in different types of target enhancers within the nuclear environment in vivo. Altogether our survey underlines the Hox dosage as a key mechanism for shaping Hox molecular function during development and evolution.
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Feltes BC, Menck CFM. Current state of knowledge of human DNA polymerase eta protein structure and disease-causing mutations. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108436. [PMID: 35952573 DOI: 10.1016/j.mrrev.2022.108436] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/29/2022] [Accepted: 07/31/2022] [Indexed: 01/01/2023]
Abstract
POLη, encoded by the POLH gene, is a crucial protein for replicating damaged DNA and the most studied specialized translesion synthesis polymerases. Mutations in POLη are associated with cancer and the human syndrome xeroderma pigmentosum variant, which is characterized by extreme photosensitivity and an increased likelihood of developing skin cancers. The myriad of structural information about POLη is vast, covering dozens of different mutants, numerous crucial residues, domains, and posttranslational modifications that are essential for protein function within cells. Since POLη is key vital enzyme for cell survival, and mutations in this protein are related to aggressive diseases, understanding its structure is crucial for biomedical sciences, primarily due to its similarities with other Y-family polymerases and its potential as a targeted therapy-drug for tumors. This work provides an up-to-date review on structural aspects of the human POLη: from basic knowledge about critical residues and protein domains to its mutant variants, posttranslational modifications, and our current understanding of therapeutic molecules that target POLη. Thus, this review provides lessons about POLη's structure and gathers critical discussions and hypotheses that may contribute to understanding this protein's vital roles within the cells.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS Brazil; Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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Wang C, Liu B, Chen M, Ning J, Lu X, Wang C. Mutations in Growth-Related Genes Induced by EMS Treatment in Scallops. Front Genet 2022; 13:879844. [PMID: 35559043 PMCID: PMC9086186 DOI: 10.3389/fgene.2022.879844] [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: 02/20/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The goal of genetic breeding is to select variants with mutations that are related to expected traits, such as fast growth. Artificial induction has been widely used to obtain strains with more mutations for further selection. Ethylmethylsulfone (EMS) is one of the most commonly used chemical mutagens in plant and microorganism breeding. However, the application of EMS mutagenesis in shellfish has not been reported. The aim of this study is to evaluate the potential use of EMS as a mutagen in scallop breeding, especially in characterization of mutations in growth-related genes. Results: Our results indicated that hatching of about 50% of fertilized eggs was blocked by treatment with 20 mM EMS for 3 h and the resulted larvae developed normally into adult stages. We then evaluated the mutagenic effects of EMS by sequencing the genomes of 4 adult scallops from the control group and 12 from the treatment group at 8 months after fertilization. On average, after removing shared types of mutations, there were 1,151,380 ± 258,188 SNPs (Single Nucleotide Polymorphisms) and 229,256 ± 51,714 InDels (insertion-deletion) in each animal in the EMS treatment group, while there were only134841 ± 10,115 SNPs and 42,605 ± 5,136 InDels in the control group. The average mutation rate in the genome of the EMS treatment group (0.0137 ± 0.0013%) was about 9 times that of the control group (0.0015 ± 0.0002%). GO (Gene Ontology) annotation and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses revealed that mutations induced by EMS occurred evenly in most biological processes, cellular components and functions, as well in most pathways. However, significant lower percentage of mutations were found in the exonic region, in non-synonymous or Stopgain/Stoploss SNPs and in coding domains, suggesting apparent DNA repair or selection during grow-out stage. Analyses of the growth-related genes with mutations indicated that mutations in MFS (Major Facilitator Superfamily) and Tubulin were only found in the large-sized group (Five largest scallops: Treated-1, Treated-2, Treated-3, Treated-4, and Treated-5) and Homeobox and Socs (Suppressor of cytokine signaling) only in the small group (Two smallest scallops: Treated-11 and Treated-12). These results suggested that these genes may be involved in the regulation of growth in these animals, although further verification is certainly warranted. Conclusion: Treatment of fertilized eggs with 20 mM EMS for 3 h induced 9 times more mutations in scallop genomes. We found that mutations in MFS and Tubulin may be related to fast growth in the large-sized group and those mutations in Homeobox and SOCs may be involved in the slow growth in the small-sized scallops. EMS can be used to accelerate selection of economically important traits in molluscs.
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Affiliation(s)
- Caihui Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Bo Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Min Chen
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Junhao Ning
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xia Lu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Chunde Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
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Rajagopal T, Seshachalam A, Rathnam KK, Talluri S, Venkatabalasubramanian S, Dunna NR. Homologous recombination DNA repair gene RAD51, XRCC2 & XRCC3 polymorphisms and breast cancer risk in South Indian women. PLoS One 2022; 17:e0259761. [PMID: 35061678 PMCID: PMC8782413 DOI: 10.1371/journal.pone.0259761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/26/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Homologous recombination repair (HRR) accurately repairs the DNA double-strand breaks (DSBs) and is crucial for genome stability. Genetic polymorphisms in crucial HRR pathway genes might affect genome stability and promote tumorigenesis. Up to our knowledge, the present study is the first to investigate the impact of HRR gene polymorphisms on BC development in South Indian women. The present population-based case-control study investigated the association of polymorphisms in three key HRR genes (XRCC2-Arg188His, XRCC3-Thr241Met and RAD51-G135C) with BC risk. MATERIALS AND METHODS Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used for genotyping the HRR variants in 491 BC cases and 493 healthy women. RESULTS We observed that the XRCC3 Met allele was significantly associated with BC risk [OR:1.27 (95% CI: 1.02-1.60); p = 0.035]. In addition, the homozygous mutant (C/C) genotype of RAD51 G135C variant conferred 2.19 fold elevated risk of BC [OR: 2.19 (95% CI: 1.06-4.54); p = 0.034]. Stratified analysis of HRR variants and BC clinicopathological features revealed that the XRCC3-Thr241Met and RAD51-G135C variants are associated with BC progression. Combined SNP analysis revealed that the individuals with RAD51-C/C, XRCC2-Arg/Arg, and XRCC3-Thr/Thr genotype combination have three-fold increased BC risk. CONCLUSION The present study imparts additional evidence that genetic variants in crucial HRR pathway genes might play a pivotal role in modulating BC risk in South Indian women.
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Affiliation(s)
- Taruna Rajagopal
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA–Deemed University, Thanjavur, India
| | - Arun Seshachalam
- Department of Medical and Paediatric Oncology, Dr.G.V.N Cancer Institute, Singarathope, Trichy, India
| | - Krishna Kumar Rathnam
- Department of Hemato Oncology–Medical Oncology and Bone Marrow Transplantation, Meenakshi Mission Hospital & Research Centre, Madurai, India
| | - Srikanth Talluri
- Dana Farber Cancer Institute, Boston, MA, United States of America
- Veterans Administration Boston Healthcare System, West Roxbury, MA, United States of America
| | | | - Nageswara Rao Dunna
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA–Deemed University, Thanjavur, India
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Feltes BC. Revisiting the structural features of the xeroderma pigmentosum proteins: Focus on mutations and knowledge gaps. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108416. [PMID: 35690419 DOI: 10.1016/j.mrrev.2022.108416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
The nucleotide excision repair pathway is a broadly studied DNA repair mechanism because impairments of its key players, the xeroderma pigmentosum proteins (XPA to XPG), are associated with multiple hereditary diseases. Due to the massive number of novel mutations reported for these proteins and new structural data published every year, proper categorization and discussion of relevant observations is needed to organize this extensive inflow of knowledge. This review aims to revisit the structural data of all XP proteins while updating it with the information developed in of the past six years. Discussions and interpretations of mutation outcomes, mechanisms of action, and knowledge gaps regarding their structures are provided, as well as new perspectives based on recent research.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Feltes BC. Every protagonist has a sidekick: Structural aspects of human xeroderma pigmentosum-binding proteins in nucleotide excision repair. Protein Sci 2021; 30:2187-2205. [PMID: 34420242 DOI: 10.1002/pro.4173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022]
Abstract
The seven xeroderma pigmentosum proteins (XPps), XPA-XPG, coordinate the nucleotide excision repair (NER) pathway, promoting the excision of DNA lesions caused by exposition to ionizing radiation, majorly from ultraviolet light. Significant efforts are made to investigate NER since mutations in any of the seven XPps may cause the xeroderma pigmentosum and trichothiodystrophy diseases. However, these proteins collaborate with other pivotal players in all known NER steps to accurately exert their purposes. Therefore, in the old and ever-evolving field of DNA repair, it is imperative to reexamine and describe their structures to understand NER properly. This work provides an up-to-date review of the protein structural aspects of the closest partners that directly interact and influence XPps: RAD23B, CETN2, DDB1, RPA (RPA70, 32, and 14), p8 (GTF2H5), and ERCC1. Structurally and functionally vital domains, regions, and critical residues are reexamined, providing structural lessons and perspectives about these indispensable proteins in the NER and other DNA repair pathways. By gathering all data related to the major human xeroderma pigmentosum-interacting proteins, this review will aid newcomers on the subject and guide structural and functional future studies.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D. Proteogenomic Characterization of Endometrial Carcinoma. Cell 2020; 180:729-748.e26. [PMID: 32059776 PMCID: PMC7233456 DOI: 10.1016/j.cell.2020.01.026] [Citation(s) in RCA: 264] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
Abstract
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. An extensive genome-wide acetylation survey yielded insights into regulatory mechanisms linking Wnt signaling and histone acetylation. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, identify new molecular associations of potential mechanistic significance in the development of endometrial cancers, and suggest novel approaches for identifying potential therapeutic targets.
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Affiliation(s)
- Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily A Kawaler
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Daniel Cui Zhou
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lili Blumenberg
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Alla Karpova
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shankha Satpathy
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Yige Wu
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhi Li
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Song Cao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Matthew A Wyczalkowski
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hua Zhou
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Qingsong Gao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sunantha Sethuraman
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - David Heiman
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karsten Krug
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl Clauser
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramani Kothadia
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yosef Maruvka
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Amanda E Oliphant
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Emily L Hoskins
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Samuel L Pugh
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Sean J I Beecroft
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - David W Adams
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jonathan C Jarman
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Andy Kong
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Steven Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrzej Czekański
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Marcin Jędryka
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Rafał Matkowski
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; University Hospital of Lord's Transfiguration, 60-569 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Mutch
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine Fuh
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Deborah DeLair
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Noble
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew L Anderson
- College of Medicine Obstetrics & Gynecology, University of South Florida Health, Tampa, FL 33620, USA
| | - Douglas A Levine
- Gynecologic Oncology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kelly V Ruggles
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - David Fenyö
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
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10
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Liu Q, Gao J, Zhao C, Guo Y, Wang S, Shen F, Xing X, Luo Y. To control or to be controlled? Dual roles of CDK2 in DNA damage and DNA damage response. DNA Repair (Amst) 2019; 85:102702. [PMID: 31731257 DOI: 10.1016/j.dnarep.2019.102702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 09/09/2019] [Accepted: 09/13/2019] [Indexed: 02/04/2023]
Abstract
CDK2 (cyclin-dependent kinase 2), a member of the CDK family, has been shown to play a role in many cellular activities including cell cycle progression, apoptosis and senescence. Recently, accumulating evidence indicates that CDK2 is involved in DNA damage and DNA repair response (DDR). When DNA is damaged by internal or external genotoxic stresses, CDK2 activity is required for proper DNA repair in vivo and in vitro, whereas inactivation of CDK2 by siRNA techniques or by inhibitors could result in DNA damage and stimulate DDR. Hence, CDK2 seems to play dual roles in DNA damage and DDR. On one aspect, it is activated and stimulates DDR to repair DNA damage when DNA damage occurs; on the other hand, its inactivation directly leads to DNA damage and evokes DDR. Here, we describe the roles of CDK2 in DNA damage and DDR, and discuss the potential application of CDK2 inhibitors as anti-cancer agents.
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Affiliation(s)
- Qi Liu
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Science, China Medical University, Shenyang, Liaoning Province, PR China
| | - Jinlan Gao
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Science, China Medical University, Shenyang, Liaoning Province, PR China
| | - Chenyang Zhao
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Science, China Medical University, Shenyang, Liaoning Province, PR China
| | - Yingying Guo
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Science, China Medical University, Shenyang, Liaoning Province, PR China
| | - Shiquan Wang
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Science, China Medical University, Shenyang, Liaoning Province, PR China
| | - Fei Shen
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Science, China Medical University, Shenyang, Liaoning Province, PR China
| | - Xuesha Xing
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Science, China Medical University, Shenyang, Liaoning Province, PR China
| | - Yang Luo
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Science, China Medical University, Shenyang, Liaoning Province, PR China.
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