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Oberholster L, Mathias A, Perriot S, Blaser E, Canales M, Jones S, Culebras L, Gimenez M, Kaynor GC, Sapozhnik A, Richetin K, Goelz S, Du Pasquier R. Comprehensive proteomic analysis of JC polyomavirus-infected human astrocytes and their extracellular vesicles. Microbiol Spectr 2023; 11:e0275123. [PMID: 37815349 PMCID: PMC10714778 DOI: 10.1128/spectrum.02751-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/24/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE Progressive multifocal leukoencephalopathy is a crimpling demyelinating disease of the central nervous system caused by JC polyomavirus (JCPyV). Much about JCPyV propagation in the brain remains obscure because of a lack of proper animal models to study the virus in the context of the disease, thus hampering efforts toward the development of new antiviral strategies. Here, having established a robust and representative model of JCPyV infection in human-induced pluripotent stem cell-derived astrocytes, we are able to fully characterize the effect of JCPyV on the biology of the cells and show that the proteomic signature observed for JCPyV-infected astrocytes is extended to extracellular vesicles (EVs). These data suggest that astrocyte-derived EVs found in body fluids might serve as a rich source of information relevant to JCPyV infection in the brain, opening avenues toward better understanding the pathogenesis of the virus and, ultimately, the identification of new antiviral targets.
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Affiliation(s)
- Larise Oberholster
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Amandine Mathias
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Sylvain Perriot
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Emma Blaser
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Mathieu Canales
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Samuel Jones
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Lucas Culebras
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Department of Psychiatry, Center for Psychiatric Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Marie Gimenez
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | | | - Alexey Sapozhnik
- Laboratory for Ultrafast Microscopy and Electron Scattering (LUMES), Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Kevin Richetin
- Department of Psychiatry, Center for Psychiatric Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Susan Goelz
- MS&SI, Biogen, Cambridge, Massachusetts, USA
- Department of Neurology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Renaud Du Pasquier
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Service of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
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2
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Lavi ES, Lin ZP, Ratner ES. Gene expression of non-homologous end-joining pathways in the prognosis of ovarian cancer. iScience 2023; 26:107934. [PMID: 37810216 PMCID: PMC10558711 DOI: 10.1016/j.isci.2023.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/04/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Ovarian cancer is the deadliest gynecologic malignancy in women, with a 46% five-year overall survival rate. The objective of the study was to investigate the effects of non-homologous end-joining (NHEJ) genes on clinical outcomes of ovarian cancer patients. To determine if these genes act as prognostic biomarkers of mortality and disease progression, the expression profiles of 48 NHEJ-associated genes were analyzed using an array of statistical and machine learning techniques: logistic regression models, decision trees, naive-Bayes, two sample t-tests, support vector machines, hierarchical clustering, principal component analysis, and neural networks. In this process, the correlation of genes with patient survival and disease progression and recurrence was noted. Also, multiple features from the gene set were found to have significant predictive capabilities. APTX, BRCA1, PAXX, LIG1, and TP53 were identified as most important out of all the candidate genes for predicting clinical outcomes of ovarian cancer patients.
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Affiliation(s)
- Ethan S. Lavi
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Z. Ping Lin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Elena S. Ratner
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
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3
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Ferragut Cardoso AP, Banerjee M, Nail AN, Lykoudi A, States JC. miRNA dysregulation is an emerging modulator of genomic instability. Semin Cancer Biol 2021; 76:120-131. [PMID: 33979676 PMCID: PMC8576067 DOI: 10.1016/j.semcancer.2021.05.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022]
Abstract
Genomic instability consists of a range of genetic alterations within the genome that contributes to tumor heterogeneity and drug resistance. It is a well-established characteristic of most cancer cells. Genome instability induction results from defects in DNA damage surveillance mechanisms, mitotic checkpoints and DNA repair machinery. Accumulation of genetic alterations ultimately sets cells towards malignant transformation. Recent studies suggest that miRNAs are key players in mediating genome instability. miRNAs are a class of small RNAs expressed in most somatic tissues and are part of the epigenome. Importantly, in many cancers, miRNA expression is dysregulated. Consequently, this review examines the role of miRNA dysregulation as a causal step for induction of genome instability and subsequent carcinogenesis. We focus specifically on mechanistic studies assessing miRNA(s) and specific subtypes of genome instability or known modes of genome instability. In addition, we provide insight on the existing knowledge gaps within the field and possible ways to address them.
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Affiliation(s)
- Ana P Ferragut Cardoso
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Mayukh Banerjee
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Alexandra N Nail
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Angeliki Lykoudi
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - J Christopher States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA.
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4
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Leukocyte Telomere Length Is Not Reduced in Children and Adults with Cystic Fibrosis but Associates with Clinical Characteristics-A Cross-Sectional Study. J Clin Med 2021; 10:jcm10040590. [PMID: 33557298 PMCID: PMC7915028 DOI: 10.3390/jcm10040590] [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: 12/16/2020] [Revised: 01/23/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022] Open
Abstract
We hypothezied that telomere length is considerably altered in cystic fibrosis (CF) patients compared to healthy subjects (HS), and that leukocyte telomere length variation reflects the severity of CF. Relative telomere length (RTL) was assessed by qPCR in 70 children aged 5-10 (34 CF; 36 HS) and 114 adults aged 18-45 (53 CF; 61 HS). Telomere length was similar in CF and HS (median (interquartile range): 0.799 (0.686-0.950) vs. 0.831 (0.707-0.986); p = 0.5283) both in children and adults. In adults, women had longer telomeres than men (0.805 (0.715-0.931) vs. 0.703 (0.574-0.790); p = 0.0002). Patients treated with inhaled corticosteroids had a shorter RTL compared to those without steroid therapy (0.765 (0.664-0.910) vs. 0.943 (0.813-1.191); p = 0.0007) and this finding remained significant after adjusting for gender, age, BMI, and child/adult status (p = 0.0003). Shorter telomeres were independently associated with the presence of comorbidities (0.763 (0.643-0.905) vs. 0.950 (0.783-1.130); p = 0.0006) and antibiotic treatment at the moment of blood sampling (0.762 (0.648-0.908) vs. 0.832 (0.748-1.129); p = 0.0172). RTL correlated with number of multiple-day hospitalizations (rho = -0.251; p = 0.0239), as well as number of hospitalization days (rho = -0.279; p = 0.0113). Leukocyte RTL in children and adults with CF was not shorter than in healthy controls, and did not seem to have any potential as a predictor of CF survival. However, it inversely associated with the investigated clinical characteristics.
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Functional interplay between the oxidative stress response and DNA damage checkpoint signaling for genome maintenance in aerobic organisms. J Microbiol 2019; 58:81-91. [DOI: 10.1007/s12275-020-9520-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 12/13/2022]
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Lanz MC, Dibitetto D, Smolka MB. DNA damage kinase signaling: checkpoint and repair at 30 years. EMBO J 2019; 38:e101801. [PMID: 31393028 PMCID: PMC6745504 DOI: 10.15252/embj.2019101801] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 07/03/2019] [Accepted: 07/24/2019] [Indexed: 12/27/2022] Open
Abstract
From bacteria to mammalian cells, damaged DNA is sensed and targeted by DNA repair pathways. In eukaryotes, kinases play a central role in coordinating the DNA damage response. DNA damage signaling kinases were identified over two decades ago and linked to the cell cycle checkpoint concept proposed by Weinert and Hartwell in 1988. Connections between the DNA damage signaling kinases and DNA repair were scant at first, and the initial perception was that the importance of these kinases for genome integrity was largely an indirect effect of their roles in checkpoints, DNA replication, and transcription. As more substrates of DNA damage signaling kinases were identified, it became clear that they directly regulate a wide range of DNA repair factors. Here, we review our current understanding of DNA damage signaling kinases, delineating the key substrates in budding yeast and humans. We trace the progress of the field in the last 30 years and discuss our current understanding of the major substrate regulatory mechanisms involved in checkpoint responses and DNA repair.
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Affiliation(s)
- Michael Charles Lanz
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Diego Dibitetto
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
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7
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Wang J, Peng X, Chen C, Ning X, Peng S, Li T, Liu S, Hong B, Zhou J, Ma K, Cai L, Gong K. Intra-Familial Phenotypic Heterogeneity and Telomere Abnormality in von Hippel- Lindau Disease: Implications for Personalized Surveillance Plan and Pathogenesis of VHL-Associated Tumors. Front Genet 2019; 10:358. [PMID: 31068970 PMCID: PMC6491623 DOI: 10.3389/fgene.2019.00358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/03/2019] [Indexed: 01/10/2023] Open
Abstract
von Hippel-Lindau (VHL) disease is a hereditary cancer syndrome with poor survival. The current recommendations have proposed uniform surveillance strategies for all patients, neglecting the obvious phenotypic varieties. In this study, we aim to confirm the phenotypic heterogeneity in VHL disease and the underlying mechanism. A total of 151 parent-child pairs were enrolled for genetic anticipation analysis, and 77 sibling pairs for birth order effect analysis. Four statistical methods were used to compare the onset age of patients among different generations and different birth orders. The results showed that the average onset age was 18.9 years earlier in children than in their parents, which was statistically significant in all of the four statistical methods. Furthermore, the first-born siblings were affected 8.3 years later than the other ones among the maternal patients. Telomere shortening was confirmed to be associated with genetic anticipation in VHL families, while it failed to explain the birth order effect. Moreover, no significant difference was observed for overall survival between parents and children (p = 0.834) and between first-born patients and the other siblings (p = 0.390). This study provides definitive evidence and possible mechanisms of intra-familial phenotypic heterogeneity in VHL families, which is helpful to the update of surveillance guidelines.
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Affiliation(s)
- Jiangyi Wang
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiang Peng
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Cen Chen
- School of Statistics, Renmin University, Beijing, China
| | - Xianghui Ning
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuanghe Peng
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Teng Li
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Department of Urology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Shengjie Liu
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Department of Urology, Beijing Hospital, Beijing, China
| | - Baoan Hong
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China
| | - Jingcheng Zhou
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China
| | - Kaifang Ma
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China
| | - Lin Cai
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China
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8
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Lukaszewicz A, Lange J, Keeney S, Jasin M. Control of meiotic double-strand-break formation by ATM: local and global views. Cell Cycle 2018; 17:1155-1172. [PMID: 29963942 PMCID: PMC6110601 DOI: 10.1080/15384101.2018.1464847] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/19/2018] [Accepted: 04/08/2018] [Indexed: 10/28/2022] Open
Abstract
DNA double-strand breaks (DSBs) generated by the SPO11 protein initiate meiotic recombination, an essential process for successful chromosome segregation during gametogenesis. The activity of SPO11 is controlled by multiple factors and regulatory mechanisms, such that the number of DSBs is limited and DSBs form at distinct positions in the genome and at the right time. Loss of this control can affect genome integrity or cause meiotic arrest by mechanisms that are not fully understood. Here we focus on the DSB-responsive kinase ATM and its functions in regulating meiotic DSB numbers and distribution. We review the recently discovered roles of ATM in this context, discuss their evolutionary conservation, and examine future research perspectives.
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Affiliation(s)
- Agnieszka Lukaszewicz
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julian Lange
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Kedziora S, Gali VK, Wilson RHC, Clark KRM, Nieduszynski CA, Hiraga SI, Donaldson AD. Rif1 acts through Protein Phosphatase 1 but independent of replication timing to suppress telomere extension in budding yeast. Nucleic Acids Res 2018; 46:3993-4003. [PMID: 29529242 PMCID: PMC5934629 DOI: 10.1093/nar/gky132] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 02/09/2018] [Accepted: 02/23/2018] [Indexed: 12/24/2022] Open
Abstract
The Rif1 protein negatively regulates telomeric TG repeat length in the budding yeast Saccharomyces cerevisiae, but how it prevents telomere over-extension is unknown. Rif1 was recently shown to control DNA replication by acting as a Protein Phosphatase 1 (PP1)-targeting subunit. Therefore, we investigated whether Rif1 controls telomere length by targeting PP1 activity. We find that a Rif1 mutant defective for PP1 interaction causes a long-telomere phenotype, similar to that of rif1Δ cells. Tethering PP1 at a specific telomere partially substitutes for Rif1 in limiting TG repeat length, confirming the importance of PP1 in telomere length control. Ablating Rif1-PP1 interaction is known to cause precocious activation of telomere-proximal replication origins and aberrantly early telomere replication. However, we find that Rif1 still limits telomere length even if late replication is forced through deletion of nearby replication origins, indicating that Rif1 can control telomere length independent of replication timing. Moreover we find that, even at a de novo telomere created after DNA synthesis during a mitotic block, Rif1-PP1 interaction is required to suppress telomere lengthening and prevent inappropriate recruitment of Tel1 kinase. Overall, our results show that Rif1 controls telomere length by recruiting PP1 to directly suppress telomerase-mediated TG repeat lengthening.
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Affiliation(s)
- Sylwia Kedziora
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Vamsi K Gali
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Rosemary HC Wilson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Kate RM Clark
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Conrad A Nieduszynski
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Shin-ichiro Hiraga
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Anne D Donaldson
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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10
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Bordignon V, Di Domenico EG, Trento E, D'Agosto G, Cavallo I, Pontone M, Pimpinelli F, Mariani L, Ensoli F. How Human Papillomavirus Replication and Immune Evasion Strategies Take Advantage of the Host DNA Damage Repair Machinery. Viruses 2017; 9:v9120390. [PMID: 29257060 PMCID: PMC5744164 DOI: 10.3390/v9120390] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/11/2022] Open
Abstract
The DNA damage response (DDR) is a complex signalling network activated when DNA is altered by intrinsic or extrinsic agents. DDR plays important roles in genome stability and cell cycle regulation, as well as in tumour transformation. Viruses have evolved successful life cycle strategies in order to ensure a chronic persistence in the host, virtually avoiding systemic sequelae and death. This process promotes the periodic shedding of large amounts of infectious particles to maintain a virus reservoir in individual hosts, while allowing virus spreading within the community. To achieve such a successful lifestyle, the human papilloma virus (HPV) needs to escape the host defence systems. The key to understanding how this is achieved is in the virus replication process that provides by itself an evasion mechanism by inhibiting and delaying the host immune response against the viral infection. Numerous studies have demonstrated that HPV exploits both the ataxia-telangiectasia mutated (ATM) and ataxia-telangiectasia and rad3-related (ATR) DDR pathways to replicate its genome and maintain a persistent infection by downregulating the innate and cell-mediated immunity. This review outlines how HPV interacts with the ATM- and ATR-dependent DDR machinery during the viral life cycle to create an environment favourable to viral replication, and how the interaction with the signal transducers and activators of transcription (STAT) protein family and the deregulation of the Janus kinase (JAK)-STAT pathways may impact the expression of interferon-inducible genes and the innate immune responses.
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Affiliation(s)
- Valentina Bordignon
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Enea Gino Di Domenico
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Elisabetta Trento
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Giovanna D'Agosto
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Ilaria Cavallo
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Martina Pontone
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Fulvia Pimpinelli
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Luciano Mariani
- HPV Unit, Department of Gynaecologic Oncology, National Cancer Institute Regina Elena, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
| | - Fabrizio Ensoli
- Clinical Pathology and Microbiology Unit, San Gallicano Dermatology Institute, IRCCS, IFO, Via Elio Chianesi 53, 00144 Rome, Italy.
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11
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Sheng J, Zhao J, Xu Q, Wang L, Zhang W, Zhang Y. Bioinformatics analysis of SRSF1-controlled gene networks in colorectal cancer. Oncol Lett 2017; 14:5393-5399. [PMID: 29113173 PMCID: PMC5656040 DOI: 10.3892/ol.2017.6900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/15/2017] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer is the third most common type of cancer and the fourth leading cause of cancer-associated mortality worldwide. Serine/arginine-rich splicing factor 1 (SRSF1) is a well-characterized oncogenic factor that promotes tumorigenesis by controlling a number of alternative splicing events. However, there is limited network analysis, from a global aspect, to study the effect of SRSF1 on colorectal cancer. In the present study, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of available gene regulation data from The Cancer Genome Atlas database revealed the enriched functions and signaling pathways of SRSF1. Subsequently, Oncomine analysis was performed, which demonstrated that SRSF1 was upregulated in a number of types of colon cancer. From overlapping the analysis of 2,678 SRSF1-related genes and 3,625 colorectal cancer genes in GeneCards, 468 genes were identified as SRSF1-related colorectal cancer genes. The GO results revealed that these overlapped genes were primarily enriched in metabolic processes, response to DNA damage, regulation of the cell cycle and a number of additional biological processes. KEGG pathway analysis revealed that SRSF1-related colorectal cancer genes were associated with the cell cycle, deregulated signaling pathways associated with cancer progression and colorectal cancer signaling pathways. In addition, the Search Tool for the Retrieval of Interacting Genes/Proteins database and Cytoscape analysis demonstrated that 468 SRSF1-related colorectal cancer genes exhibit potential interaction networks in which these genes were enriched in DNA metabolic processes, cell cycle regulation and regulation of apoptosis. The results of the present study suggested that SRSF1 exhibited an increased degree of interaction with key molecules, including NUF2 NDC80 kinetochore complex component, kinesin family member 2C, structural maintenance of chromosomes 3, ATM serine/threonine kinase, BRCA1 DNA repair associated, protein kinase DNA-activated catalytic polypeptide, heat shock protein 90 alpha family class A member 1, ras homolog family member A, and phosphatase and tensin homolog. Collectively, the bioinformatics analysis of the present study indicated that SRSF1 may have key functions in the progression and development of colorectal cancer.
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Affiliation(s)
- Junxiu Sheng
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China.,Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Qiuhong Xu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Linlin Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Yang Zhang
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
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12
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Di Domenico EG, Cavallo I, Pontone M, Toma L, Ensoli F. Biofilm Producing Salmonella Typhi: Chronic Colonization and Development of Gallbladder Cancer. Int J Mol Sci 2017; 18:ijms18091887. [PMID: 28858232 PMCID: PMC5618536 DOI: 10.3390/ijms18091887] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 01/05/2023] Open
Abstract
Salmonella enterica subspecies enterica serovar Typhi is the aetiological agent of typhoid or enteric fever. In a subset of individuals, S. Typhi colonizes the gallbladder causing an asymptomatic chronic infection. Nonetheless, these asymptomatic carriers provide a reservoir for further spreading of the disease. Epidemiological studies performed in regions where S. Typhi is endemic, revealed that the majority of chronically infected carriers also harbour gallstones, which in turn, have been indicated as a primary predisposing factor for the onset of gallbladder cancer (GC). It is now well recognised, that S. Typhi produces a typhoid toxin with a carcinogenic potential, that induces DNA damage and cell cycle alterations in intoxicated cells. In addition, biofilm production by S. Typhi may represent a key factor for the promotion of a persistent infection in the gallbladder, thus sustaining a chronic local inflammatory response and exposing the epithelium to repeated damage caused by carcinogenic toxins. This review aims to highlight the putative connection between the chronic colonization by highly pathogenic strains of S. Typhi capable of combining biofilm and toxin production and the onset of GC. Considering the high risk of GC associated with the asymptomatic carrier status, the rapid identification and profiling of biofilm production by S. Typhi strains would be key for effective therapeutic management and cancer prevention.
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Affiliation(s)
- Enea Gino Di Domenico
- Clinical Pathology and Microbiology, San Gallicano Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00144 Rome, Italy.
| | - Ilaria Cavallo
- Clinical Pathology and Microbiology, San Gallicano Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00144 Rome, Italy.
| | - Martina Pontone
- Clinical Pathology and Microbiology, San Gallicano Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00144 Rome, Italy.
| | - Luigi Toma
- Infectious Disease Consultant, Regina Elena National Cancer Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00144 Rome, Italy.
| | - Fabrizio Ensoli
- Clinical Pathology and Microbiology, San Gallicano Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00144 Rome, Italy.
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13
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Khoronenkova SV. Mechanisms of Non-canonical Activation of Ataxia Telangiectasia Mutated. BIOCHEMISTRY (MOSCOW) 2017; 81:1669-1675. [PMID: 28260489 DOI: 10.1134/s0006297916130058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
ATM is a master regulator of the cellular response to DNA damage. The classical mechanism of ATM activation involves its monomerization in response to DNA double-strand breaks, resulting in ATM-dependent phosphorylation of more than a thousand substrates required for cell cycle progression, DNA repair, and apoptosis. Here, new experimental evidence for non-canonical mechanisms of ATM activation in response to stimuli distinct from DNA double-strand breaks is discussed. It includes cytoskeletal changes, chromatin modifications, RNA-DNA hybrids, and DNA single-strand breaks. Noncanonical ATM activation may be important for the pathology of the multisystemic disease Ataxia Telangiectasia.
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Affiliation(s)
- S V Khoronenkova
- University of Cambridge, Department of Biochemistry, Cambridge, CB2 1GA, UK.
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14
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Ratnaparkhe M, Hlevnjak M, Kolb T, Jauch A, Maass KK, Devens F, Rode A, Hovestadt V, Korshunov A, Pastorczak A, Mlynarski W, Sungalee S, Korbel J, Hoell J, Fischer U, Milde T, Kramm C, Nathrath M, Chrzanowska K, Tausch E, Takagi M, Taga T, Constantini S, Loeffen J, Meijerink J, Zielen S, Gohring G, Schlegelberger B, Maass E, Siebert R, Kunz J, Kulozik AE, Worst B, Jones DT, Pfister SM, Zapatka M, Lichter P, Ernst A. Genomic profiling of Acute lymphoblastic leukemia in ataxia telangiectasia patients reveals tight link between ATM mutations and chromothripsis. Leukemia 2017; 31:2048-2056. [PMID: 28196983 DOI: 10.1038/leu.2017.55] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 01/17/2017] [Accepted: 02/02/2017] [Indexed: 12/28/2022]
Abstract
Recent developments in sequencing technologies led to the discovery of a novel form of genomic instability, termed chromothripsis. This catastrophic genomic event, involved in tumorigenesis, is characterized by tens to hundreds of simultaneously acquired locally clustered rearrangements on one chromosome. We hypothesized that leukemias developing in individuals with Ataxia Telangiectasia, who are born with two mutated copies of the ATM gene, an essential guardian of genome stability, would show a higher prevalence of chromothripsis due to the associated defect in DNA double-strand break repair. Using whole-genome sequencing, fluorescence in situ hybridization and RNA sequencing, we characterized the genomic landscape of Acute Lymphoblastic Leukemia (ALL) arising in patients with Ataxia Telangiectasia. We detected a high frequency of chromothriptic events in these tumors, specifically on acrocentric chromosomes, as compared with tumors from individuals with other types of DNA repair syndromes (27 cases total, 10 with Ataxia Telangiectasia). Our data suggest that the genomic landscape of Ataxia Telangiectasia ALL is clearly distinct from that of sporadic ALL. Mechanistically, short telomeres and compromised DNA damage response in cells of Ataxia Telangiectasia patients may be linked with frequent chromothripsis. Furthermore, we show that ATM loss is associated with increased chromothripsis prevalence in additional tumor entities.
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Affiliation(s)
- M Ratnaparkhe
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Hlevnjak
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - T Kolb
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - A Jauch
- Institute of Human Genetics, University Heidelberg, Heidelberg, Germany
| | - K K Maass
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - F Devens
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - A Rode
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - V Hovestadt
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - A Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), and Department of Neuropathology University Hospital, Heidelberg, Germany
| | - A Pastorczak
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - W Mlynarski
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - S Sungalee
- EMBL Heidelberg, Genome Biology, Heidelberg, Germany
| | - J Korbel
- EMBL Heidelberg, Genome Biology, Heidelberg, Germany
| | - J Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - U Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, Medical Faculty, Düsseldorf, Germany
| | - T Milde
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
| | - C Kramm
- Department of Pediatric Oncology, University of Halle, Halle, Germany.,Division of Pediatric Hematology and Oncology, Goettingen, Germany
| | - M Nathrath
- Clinical Cooperation Group Osteosarcoma, Pediatric Oncology Center, Department of Pediatrics, Technical University Munich, Munich, Germany.,Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - K Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - E Tausch
- Department of Internal Medicine III, University of Ulm, Germany
| | - M Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - T Taga
- Department of Pediatrics, Shiga University of Medical Science, Otsu, Japan
| | - S Constantini
- Department of Pediatric Neurosurgery, Dana Children's Hospital, Tel-Aviv Medical Center, Tel-Aviv University, Tel Aviv, Israel
| | - J Loeffen
- Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - J Meijerink
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - S Zielen
- Department of Paediatric Pulmonology, Allergy and Cystic Fibrosis, Children's Hospital, Goethe-University, Frankfurt, Germany
| | - G Gohring
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - B Schlegelberger
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - E Maass
- Olgahospital Stuttgart, Children's Hospital, Klinikum Stuttgart, Stuttgart, Germany
| | - R Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany
| | - J Kunz
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
| | - A E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
| | - B Worst
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - D T Jones
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - S M Pfister
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Zapatka
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P Lichter
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - A Ernst
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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15
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Di Domenico EG, Toma L, Bordignon V, Trento E, D'Agosto G, Cordiali-Fei P, Ensoli F. Activation of DNA Damage Response Induced by the Kaposi's Sarcoma-Associated Herpes Virus. Int J Mol Sci 2016; 17:ijms17060854. [PMID: 27258263 PMCID: PMC4926388 DOI: 10.3390/ijms17060854] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/23/2016] [Accepted: 05/27/2016] [Indexed: 01/24/2023] Open
Abstract
The human herpes virus 8 (HHV-8), also known as Kaposi sarcoma-associated herpes virus (KSHV), can infect endothelial cells often leading to cell transformation and to the development of tumors, namely Kaposi’s sarcoma (KS), primary effusion lymphoma (PEL), and the plasmablastic variant of multicentric Castleman’s disease. KSHV is prevalent in areas such as sub-Saharan Africa and the Mediterranean region presenting distinct genotypes, which appear to be associated with differences in disease manifestation, according to geographical areas. In infected cells, KSHV persists in a latent episomal form. However, in a limited number of cells, it undergoes spontaneous lytic reactivation to ensure the production of new virions. During both the latent and the lytic cycle, KSHV is programmed to express genes which selectively modulate the DNA damage response (DDR) through the activation of the ataxia telangiectasia mutated (ATM) pathway and by phosphorylating factors associated with the DDR, including the major tumor suppressor protein p53 tumor suppressor p53. This review will focus on the interplay between the KSHV and the DDR response pathway throughout the viral lifecycle, exploring the putative molecular mechanism/s that may contribute to malignant transformation of host cells.
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Affiliation(s)
- Enea Gino Di Domenico
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Luigi Toma
- Infectious Disease Consultant, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Valentina Bordignon
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Elisabetta Trento
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Giovanna D'Agosto
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Paola Cordiali-Fei
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Fabrizio Ensoli
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
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16
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Gu Y, Yu C, Miao L, Wang L, Xu C, Xue W, Du J, Yuan H, Dai J, Jin G, Hu Z, Ma H, Shen H. Telomere length, genetic variants and risk of squamous cell carcinoma of the head and neck in Southeast Chinese. Sci Rep 2016; 6:20675. [PMID: 26857734 PMCID: PMC4746643 DOI: 10.1038/srep20675] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/21/2015] [Indexed: 11/09/2022] Open
Abstract
Telomere dysfunction participates in malignant transformation and tumorigenesis. Previous studies have explored the associations between telomere length (TL) and cancer susceptibility; however, the findings are inconclusive. The associations between genetic variants and TL have been verified by quite a few genome-wide association studies (GWAS). Yet, to date, there was no published study on the relationship between TL, related genetic variants and susceptibility to squamous cell carcinoma of the head and neck (SCCHN) in Chinese. Hence, we detected relative telomere length (RTL) by using quantitative PCR and genotyped seven selected single nucleotide polymorphisms by TaqMan allelic discrimination assay in 510 SCCHN cases and 913 controls in southeast Chinese. The results showed that RTL was significantly associated with SCCHN risk [(adjusted odds ratio (OR) = 1.19, 95% confidence interval (CI) = 1.08–1.32, P = 0.001]. Furthermore, among seven selected SNPs, only G allele of rs2736100 related to RTL in Caucasians was significantly associated with both the decreased RTL (P = 0.002) and the increased susceptibility to SCCHN in Chinese (additive model: adjusted OR = 1.17, 95%CI = 1.00–1.38, P = 0.049). These findings provide evidence that shortened TL is a risk factor for SCCHN, and genetic variants can contribute to both TL and the susceptibility to SCCHN in southeast Chinese population.
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Affiliation(s)
- Yayun Gu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Chengxiao Yu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Limin Miao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, China
| | - Lihua Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Chongquan Xu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Wenjie Xue
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jiangbo Du
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Hua Yuan
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing 210029, China
| | - Juncheng Dai
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Guangfu Jin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Zhibin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongxia Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongbing Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
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17
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The ATM- and ATR-related SCD domain is over-represented in proteins involved in nervous system development. Sci Rep 2016; 6:19050. [PMID: 26743489 PMCID: PMC4705472 DOI: 10.1038/srep19050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/02/2015] [Indexed: 12/16/2022] Open
Abstract
ATM and ATR are cellular kinases with a well-characterized role in the DNA-damage response. Although the complete set of ATM/ATR targets is unknown, they often contain clusters of S/TQ motifs that constitute an SCD domain. In this study, we identified putative ATM/ATR targets that have a conserved SCD domain across vertebrates. Using this approach, we have identified novel putative ATM/ATR targets in pathways known to be under direct control of these kinases. Our analysis has also unveiled significant enrichment of SCD-containing proteins in cellular pathways, such as vesicle trafficking and actin cytoskeleton, where a regulating role for ATM/ATR is either unknown or poorly understood, hinting at a much broader and overarching role for these kinases in the cell. Of particular note is the overrepresentation of conserved SCD-containing proteins involved in pathways related to neural development. This finding suggests that ATM/ATR could be directly involved in controlling this process, which may be linked to the adverse neurological effects observed in patients with mutations in ATM.
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18
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ATM rs189037 (G > A) polymorphism and risk of lung cancer and head and neck cancer: A meta-analysis. Meta Gene 2015; 6:42-8. [PMID: 26504743 PMCID: PMC4564396 DOI: 10.1016/j.mgene.2015.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/12/2015] [Indexed: 11/30/2022] Open
Abstract
A number of different epidemiological studies have measured the association between the risk of different cancers and polymorphism at promoter region of 5′ untranslated region (5′-UTR) of the Ataxia-telangiectasia mutated (ATM) gene. However the results were contentious rather than conclusive. The current study was aimed at evaluating the association between the SNP (rs189037 G>A) and the risk of head and neck cancer and lung cancer by conducting a meta-analysis. A total of 9 case–control studies were considered for this quantitative analysis. Stats Direct Statistical software (version 2.7.2) was used to evaluate the crude odds ratio (OR) with their 95% confidence interval (CI). The dominant model (GG vs. GA + AA) showed no heterogeneity and the fixed effects pooled OR was found to be significant (OR = 1.14, 95% CI = 1.05–1.25) at p = 0.003. The pooled OR for fixed effects of heterozygote and homozygote mutant allele (GA vs. AA) model was significant (OR = 1.17, 95% CI = 1.04–1.30, p = 0.006) and no heterogeneity was observed for this model. The current meta-analysis manifested that ATM rs189037 G>A genetic polymorphism may contribute increased risk of head and neck and lung cancer. Moreover, the AA mutant allele was found to be related significantly with the prognosis of lung cancer and head and neck cancer.
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