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Xing Z, Guo G, Pan X, Xu L, Guo C, An R. The Association Between hMLH1 and hMSH2 Polymorphisms and Renal Tumors in Northeastern China. Genet Test Mol Biomarkers 2019; 23:573-579. [PMID: 31373852 DOI: 10.1089/gtmb.2019.0011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: Although hMLH1 and hMSH2 are closely associated with the development and drug resistance of multiple types of tumors, their role in renal tumors remains unclear. This study was designed to examine the relationship between renal tumor development and polymorphisms in the hMLH1 and hMSH2 genes. Methods: The study included 180 patients with renal tumors that were confirmed by pathological examination and 199 healthy controls. The clinical and pathological stages of the tumor samples were determined, and DNA was extracted from the peripheral blood of the subjects. Polymorphisms in the hMLH1 and hMSH2 loci were identified using the 1000 genomes database and the multiplex ligase detection method. Correlation analyses was performed using single nucleotide polymorphism tests. Results: 88.9% (160/180) of the tumor specimens were identified as clear cell renal cell carcinoma (CCRC) and 89.4% (161/180) were stage I carcinomas. Three hMLH1 and nine hMSH2 polymorphic sites were identified, and the frequency of the AA genotype of the hMSH2 rs2303424 variant was found to be significantly higher in the renal tumor group (odds ratio [OR] = 1.37, 95% confidence interval [CI]: 1.02-1.86) in the additive model (p = 0.029), the recessive model (p = 0.005), and codominant model (p = 0.02). Multiple testing corrections were performed and the differences between the clear cell carcinoma and control samples remained significant. Compared with the controls, the distribution of the GG genotype of the hMSH2 rs11886591 locus was significantly higher in the clear cell carcinoma group (OR = 0.80, 95% CI: 0.59-1.10, p = 0.04) after multiple testing corrections in the dominant model. Conclusion: The AA genotype at the rs2303424 locus and GG genotype at rs11886591 locus of the DNA repair gene hMSH2 were closely associated with the development of renal tumors. Further studies are needed on larger cohorts to confirm this correlation.
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Affiliation(s)
- Zhaohui Xing
- 1Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guiying Guo
- 1Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinling Pan
- 2Department of Biomedical Sciences Laboratory, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, China
| | - Lidan Xu
- 3Department of Genetics, Harbin Medical University, Harbin, China
| | - Chaopu Guo
- 4Department of Surgery, Traditional Chinese Medicine Hospital of Yanggu, Liaocheng, China
| | - Ruihua An
- 1Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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Microsatellite instability in mismatch repair and tumor suppressor genes and their expression profiling provide important targets for the development of biomarkers in gastric cancer. Gene 2019; 710:48-58. [DOI: 10.1016/j.gene.2019.05.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/13/2019] [Accepted: 05/25/2019] [Indexed: 12/24/2022]
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Thyroid Cancer: The Quest for Genetic Susceptibility Involving DNA Repair Genes. Genes (Basel) 2019; 10:genes10080586. [PMID: 31374908 PMCID: PMC6722859 DOI: 10.3390/genes10080586] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/10/2019] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
The incidence of thyroid cancer (TC), particularly well-differentiated forms (DTC), has been rising and remains the highest among endocrine malignancies. Although ionizing radiation (IR) is well established on DTC aetiology, other environmental and genetic factors may also be involved. DNA repair single nucleotide polymorphisms (SNPs) could be among the former, helping in explaining the high incidence. To further clarify the role of DNA repair SNPs in DTC susceptibility, we analyzed 36 SNPs in 27 DNA repair genes in a population of 106 DTCs and corresponding controls with the aim of interpreting joint data from previously studied isolated SNPs in DNA repair genes. Significant associations with DTC susceptibility were observed for XRCC3 rs861539, XPC rs2228001, CCNH rs2230641, MSH6 rs1042821 and ERCC5 rs2227869 and for a haplotype block on chromosome 5q. From 595 SNP-SNP combinations tested and 114 showing relevance, 15 significant SNP combinations (p < 0.01) were detected on paired SNP analysis, most of which involving CCNH rs2230641 and mismatch repair variants. Overall, a gene-dosage effect between the number of risk genotypes and DTC predisposition was observed. In spite of the volume of data presented, new studies are sought to provide an interpretability of the role of SNPs in DNA repair genes and their combinations in DTC susceptibility.
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Mazian MA, Suenaga N, Ishii T, Hayashi A, Shiomi Y, Nishitani H. A DNA-binding domain in the C-terminal region of Cdt2 enhances the DNA synthesis-coupled CRL4Cdt2 ubiquitin ligase activity for Cdt1. J Biochem 2019; 165:505-516. [PMID: 30649446 DOI: 10.1093/jb/mvz001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
The Cullin-RING ubiquitin ligase CRL4Cdt2 maintains genome integrity by mediating the cell cycle- and DNA damage-dependent degradation of proteins such as Cdt1, p21 and Set8. Human Cdt2 has two regions, a conserved N-terminal seven WD40 repeat region and a less conserved C-terminal region. Here, we showed that the N-terminal region is sufficient for complex formation with CRL4, but the C-terminal region is required for the full ubiquitin ligase activity. UV irradiation-induced polyubiquitination and degradation of Cdt1 were impaired in Cdt2 (N-terminus only)-expressing cells. Deletion and mutation analysis identified a domain in the C-terminal region that increased ubiquitination activity and displayed DNA-binding activity. The identified domain mediated binding to double-stranded DNA and showed higher affinity binding to single-stranded DNA. As the ligase activity of CRL4Cdt2 depends on proliferating cell nuclear antigen (PCNA) loading onto DNA, the present results suggest that the DNA-binding domain facilitates the CRL4Cdt2-mediated recognition and ubiquitination of substrates bound to PCNA on chromatin.
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Affiliation(s)
- Muadz Ahmad Mazian
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
| | - Naohiro Suenaga
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
| | - Takashi Ishii
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
| | - Akiyo Hayashi
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
| | - Yasushi Shiomi
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
| | - Hideo Nishitani
- Graduate School of Life Science, University of Hyogo, Kamigori, Akogun Hyogo, Japan
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Liu Y, Wang M, Chen Q, Zheng Q, Li G, Cheng Q, Liu S, Ye S. A novel heterozygous large deletion of MSH6 gene in a Chinese family with Lynch syndrome. Gene 2019; 704:103-112. [PMID: 30974197 DOI: 10.1016/j.gene.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 03/19/2019] [Accepted: 04/02/2019] [Indexed: 12/27/2022]
Abstract
Lynch syndrome (LS) is a common cancer syndrome that is inherited in an autosomal dominant manner. Its pathogenesis is thought to be closely related to germline mutations of mismatch repair (MMR) genes such as the MLH1, MSH2, PMS2 and MSH6 genes. This study identifies a Chinese family with LS clinically diagnosed according to the Amsterdam II criteria. In these patients, immuno-histochemical staining showed negative MSH6 expressions but positive MLH1, MSH2, and PMS2 expressions. In order to further explore the molecular biology of this LS family, we used targeted next-generation sequencing (NGS) and Multiplex ligation dependent probe amplification (MLPA) to identify the mutation and verify the authenticity of the mutation in 15 family members. For NGS, two panels have been used, one is of MLH1, MSH2, PMS2 and MSH6 genes, the other one is of 139 cancer genetic susceptibility genes. And for the large deletions/duplications can also be identified by NGS panel, an adjusted data analysis strategy of NGS has been used. As a result, we identified a novel heterozygous large deletion in MSH6 gene that was found to be co-segregated among affected family members. This deletion results in the loss of a 3246 bp-sized fragment in MSH6 gene exons 5-9 which represents the coding regions of the MSH6 ATPase domain. This novel mutation has yet to be documented in the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) database. This mutation resulted in MSH6 protein losing gene mismatch repair function, and further caused the microsatellite instable. We speculate that this mutation may significantly impact MMR function through impaired ATP domain function. Theoretically, this proband would likely benefit from PD-1 immune check-point blockade therapy, but conversely, we observed that tumors appeared to rapidly progress after 4 sessions of anti-PD-1 treatment. Further studies to validate the effectiveness of anti-PD-1 treatments in carriers of this mutation are necessary.
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Affiliation(s)
- Yuanyuan Liu
- Department of Biobank, Hubei Cancer Hospital, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Wuhan, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Hubei Province, 116 Zuodaoquan South Road, Wuhan, Hubei, China
| | - Mingwei Wang
- Department of Pathology, Hubei Cancer Hospital, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Wuhan, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Hubei Province, 116 Zuodaoquan South Road, Wuhan, Hubei, China
| | - Qiongrong Chen
- Department of Pathology, Zhongnan Hospital, 169 Donghu Road, Wuhan, Hubei, China
| | - Qiaosong Zheng
- Beijing Genetron Health Co., Ltd, Changping, Beijing, China
| | - Guangyu Li
- Beijing Genetron Health Co., Ltd, Changping, Beijing, China
| | - Qian Cheng
- Department of Gastrointestinal Surgery, Hubei Cancer Hospital, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Wuhan, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Hubei Province, 116 Zuodaoquan South Road, Wuhan, Hubei, China
| | - Sanhe Liu
- Department of Gastrointestinal Surgery, Hubei Cancer Hospital, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Wuhan, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Hubei Province, 116 Zuodaoquan South Road, Wuhan, Hubei, China
| | - Shengwei Ye
- Department of Gastrointestinal Surgery, Hubei Cancer Hospital, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Wuhan, 116 Zuodaoquan South Road, Wuhan, Hubei, China; Colorectal Cancer Clinical Research Center of Hubei Province, 116 Zuodaoquan South Road, Wuhan, Hubei, China.
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Liu J, Zheng B, Li Y, Yuan Y, Xing C. Genetic Polymorphisms of DNA Repair Pathways in Sporadic Colorectal Carcinogenesis. J Cancer 2019; 10:1417-1433. [PMID: 31031852 PMCID: PMC6485219 DOI: 10.7150/jca.28406] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/12/2019] [Indexed: 12/20/2022] Open
Abstract
DNA repair systems play a critical role in maintaining the integrity and stability of the genome, which mainly include base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR) and double-strand break repair (DSBR). The polymorphisms in different DNA repair genes that are mainly represented by single-nucleotide polymorphisms (SNPs) can potentially modulate the individual DNA repair capacity and therefore exert an impact on individual genetic susceptibility to cancer. Sporadic colorectal cancer arises from the colorectum without known contribution from germline causes or significant family history of cancer or inflammatory bowel disease. In recent years, emerging studies have investigated the association between polymorphisms of DNA repair system genes and sporadic CRC. Here, we review recent insights into the polymorphisms of DNA repair pathway genes, not only individual gene polymorphism but also gene-gene and gene-environment interactions, in sporadic colorectal carcinogenesis.
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Affiliation(s)
- Jingwei Liu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Bowen Zheng
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Ying Li
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Chengzhong Xing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
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Li Y, Yao M, Wu T, Zhang L, Wang Y, Chen L, Fu G, Weng X, Wang J. Loss of hypermethylated in cancer 1 (HIC1) promotes lung cancer progression. Cell Signal 2019; 53:162-169. [DOI: 10.1016/j.cellsig.2018.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 11/25/2022]
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Indraccolo S, Lombardi G, Fassan M, Pasqualini L, Giunco S, Marcato R, Gasparini A, Candiotto C, Nalio S, Fiduccia P, Fanelli GN, Pambuku A, Della Puppa A, D'Avella D, Bonaldi L, Gardiman MP, Bertorelle R, De Rossi A, Zagonel V. Genetic, Epigenetic, and Immunologic Profiling of MMR-Deficient Relapsed Glioblastoma. Clin Cancer Res 2018; 25:1828-1837. [PMID: 30514778 DOI: 10.1158/1078-0432.ccr-18-1892] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/25/2018] [Accepted: 11/28/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE In-depth characterization of recurrent glioblastoma (rGBM) might contribute to a better understanding of the mechanisms behind tumor progression and enable rGBM treatment with targeted drugs.Experimental Design: In this study, GBM samples were collected at diagnosis and recurrence from adult patients treated with Stupp protocol. Expression of mismatch repair (MMR) proteins was evaluated by IHC, followed by whole exome sequencing (WES) of tumor samples showing loss of MSH6 reactivity. Established genetic, epigenetic, and immunologic markers were assessed by standard methods and correlated with loss of MMR proteins and patient survival. RESULTS Expression of MMR proteins was partially or completely lost in 25.9% rGBM samples. Specifically, 12 samples showed partial or total MSH6 expression reduction. Conversely, 96.4% of GBM samples at diagnosis expressed MMR markers. WES disclosed lack of variants in MMR genes in primary samples, whereas two MSH6-negative rGBM samples shared a c.3438+1G>A* splicing MSH6 variant with a potential loss of function effect. MSH6-negative rGBM specimens had high tumor mutational burden (TMB), but no microsatellite instability. In contrast, GBM samples with partial loss of MMR proteins disclosed low TMB. MMR-deficient rGBM showed significant telomere shortening and MGMT methylation and are characterized by highly heterogeneous MHC class I expression. CONCLUSIONS Multilevel profiling of MMR-deficient rGBM uncovered hypermutated genotype uncoupled from enriched expression of immune-related markers. Assessment of MHC class I expression and TMB should be included in protocols aiming to identify rGBM patients potentially eligible for treatment with drugs targeting immune-checkpoint inhibitors.
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Affiliation(s)
- Stefano Indraccolo
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy.
| | - Giuseppe Lombardi
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padova, Padova, Italy
| | - Lorenza Pasqualini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Silvia Giunco
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Raffaella Marcato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Alessandra Gasparini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Cinzia Candiotto
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Silvia Nalio
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Pasquale Fiduccia
- Clinical Trials and Biostatistics Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Giuseppe Nicolò Fanelli
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padova, Padova, Italy
| | - Ardi Pambuku
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | | | - Domenico D'Avella
- Neurosurgery, Department of Neurosciences DNS, University Hospital of Padova, Padova, Italy
| | - Laura Bonaldi
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Marina Paola Gardiman
- Surgical Pathology and Cytopathology Unit, University Hospital of Padova, Padova, Italy
| | - Roberta Bertorelle
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
| | - Anita De Rossi
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy.,Department of Surgery, Oncology and Gastroenterology (DISCOG), University of Padova, Padova, Italy
| | - Vittorina Zagonel
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV -IRCCS, Padova, Italy
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Weßbecher IM, Brieger A. Phosphorylation meets DNA mismatch repair. DNA Repair (Amst) 2018; 72:107-114. [PMID: 30249411 DOI: 10.1016/j.dnarep.2018.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022]
Abstract
DNA mismatch repair (MMR) is a highly conserved process and ensures the removal of mispaired DNA bases and insertion-deletion loops right after replication. For this, a MutSα or MutSβ protein complex recognizes the DNA damage, MutLα nicks the erroneous strand, exonuclease 1 removes the wrong nucleotides, DNA polymerase δ refills the gap and DNA ligase I joins the fragments to seal the nicks and complete the repair process. The failure to accomplish these functions is associated with higher mutation rates and may lead to cancer, which highlights the importance of MMR by the maintenance of genomic stability. The post-replicative MMR implies that involved proteins are regulated at several levels, including posttranslational modifications (PTMs). Phosphorylation is one of the most common and major PTMs. Suitable with its regulatory force phosphorylation was shown to influence MMR factors thereby adjusting eukaryotic MMR activity. In this review, we summarized the current knowledge of the role of phosphorylation of MMR process involved proteins and their functional relevance.
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Affiliation(s)
| | - Angela Brieger
- Medical Clinic I, Biomedical Research Laboratory, Goethe-University, Frankfurt a.M., Germany.
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60
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Hahne JC, Valeri N. Non-Coding RNAs and Resistance to Anticancer Drugs in Gastrointestinal Tumors. Front Oncol 2018; 8:226. [PMID: 29967761 PMCID: PMC6015885 DOI: 10.3389/fonc.2018.00226] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/31/2018] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNAs are important regulators of gene expression and transcription. It is well established that impaired non-coding RNA expression especially the one of long non-coding RNAs and microRNAs is involved in a number of pathological conditions including cancer. Non-coding RNAs are responsible for the development of resistance to anticancer treatments as they regulate drug resistance-related genes, affect intracellular drug concentrations, induce alternative signaling pathways, alter drug efficiency via blocking cell cycle regulation, and DNA damage response. Furthermore, they can prevent therapeutic-induced cell death and promote epithelial-mesenchymal transition (EMT) and elicit non-cell autonomous mechanisms of resistance. In this review, we summarize the role of non-coding RNAs for different mechanisms resulting in drug resistance (e.g., drug transport, drug metabolism, cell cycle regulation, regulation of apoptotic pathways, cancer stem cells, and EMT) in the context of gastrointestinal cancers.
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Affiliation(s)
- Jens C. Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Department of Medicine, The Royal Marsden NHS Trust, London, United Kingdom
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Bhattacharjee P, Sanyal T, Bhattacharjee S, Bhattacharjee P. Epigenetic alteration of mismatch repair genes in the population chronically exposed to arsenic in West Bengal, India. ENVIRONMENTAL RESEARCH 2018; 163:289-296. [PMID: 29499398 DOI: 10.1016/j.envres.2018.01.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/04/2018] [Accepted: 01/06/2018] [Indexed: 06/08/2023]
Abstract
INTRODUCTION Arsenic exposure and its adverse health outcome, including the association with cancer risk are well established from several studies across the globe. The present study aims to analyze the epigenetic regulation of key mismatch repair (MMR) genes in the arsenic-exposed population. METHOD A case-control study was conducted involving two hundred twenty four (N=224) arsenic exposed [with skin lesion (WSL=110) and without skin lesion (WOSL=114)] and one hundred and two (N=102) unexposed individuals. The methylation status of key MMR genes i.e. MLH1, MSH2, and PMS2 were analyzed using methylation-specific PCR (MSP). The gene expression was studied by qRTPCR. The expression of H3K36me3, which was earlier reported to be an important regulator of MMR pathway, was assessed using ELISA. RESULTS Arsenic-exposed individuals showed significant promoter hypermethylation (p < 0.0001) of MLH1 and MSH2 compared to those unexposed with consequent down-regulation in their gene expression [MLH1 (p=0.001) and MSH2 (p<0.05)]. However, no significant association was found in expression and methylation of PMS2 with arsenic exposure. We found significant down-regulation of H3K36me3 in the arsenic-exposed group, most significantly in the WSL group (p<0.0001). The expression of SETD2, the methyltransferase of an H3K36me3 moiety was found to be unaltered in arsenic exposure, suggesting the involvement of other regulatory factors yet to be identified. DISCUSSION In summary, the epigenetic repression of DNA damage repair genes due to promoter hypermethylation of MLH1 and MSH2 and inefficient recruitment of MMR complex at the site of DNA damage owing to the reduced level of H3K36me3 impairs the mismatch repair pathway that might render the arsenic-exposed individuals more susceptible towards DNA damage and associated cancer risk.
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Affiliation(s)
- Pritha Bhattacharjee
- Department of Zoology, University of Calcutta, Kolkata 700019, India; Department of Environmental Science, University of Calcutta, Kolkata 700019, India
| | - Tamalika Sanyal
- Department of Zoology, University of Calcutta, Kolkata 700019, India; Department of Environmental Science, University of Calcutta, Kolkata 700019, India
| | | | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India.
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Bologna-Molina R, Pereira-Prado V, Sánchez-Romero C, Tapia-Repetto G, Soria S, Hernandez M, Gónzalez-Gónzalez R, Molina-Frechero M, Mikami T. Expression of hMLH1 and hMSH2 proteins in ameloblastomas and tooth germs. Med Oral Patol Oral Cir Bucal 2018; 23:e126-e131. [PMID: 29476681 PMCID: PMC5911352 DOI: 10.4317/medoral.22210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/09/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Mismatch repair proteins (MMRPs) are a group of nuclear enzymes that participate in the repair of base mismatches that occur during DNA replication in all proliferating cells. The most studied MMRPs are hMSH2 and hMLH1, which are known to be highly expressed in normal tissues. A loss of MMRPs leads to the accumulation of DNA replication errors in proliferating cells. Ki-67 is a biomarker regarded to be the gold-standard tool for determining cell proliferation by immunohistochemical methods. The aim of this study was to investigate the immunohistochemical expression of hMLH1, hMSH2 and Ki-67 proteins in ameloblastomas and tooth germs, to contribute to the understanding of the development of this odontogenic neoplasm. MATERIAL AND METHODS Immunohistochemical assays to determine the presence of proteins hMSH2, hMLH1 and Ki-67 were performed in 80 ameloblastomas (40 solid and 40 unicystic) and five tooth germs. RESULTS Unicystic ameloblastomas showed higher MMRP expression (hMLH1: 62.5 ± 43.4; hMSH2: 83.3 ± 47.8) than did solid ameloblastomas (hMLH1: 59.4 ± 13.5; hMSH2: 75.8 ± 40.2). Additionally, the cell proliferation index assessed by Ki-67 was inversely proportional to the expression of MMRP. Comparison between tooth germs and ameloblastoma revealed significantly higher expression of hMLH1, hMSH2 and Ki-67 in tooth germs (p=0.02). CONCLUSIONS The differences of MMRP and Ki-67 immunoexpression between ameloblastomas and tooth germ suggest that alterations in the MMRP mechanisms could participate in the biological behavior of ameloblastomas.
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Affiliation(s)
- R Bologna-Molina
- School of Dentistry, Molecular Pathology Area, Universidad de la República, Las Heras 1925, Montevideo, Uruguay,
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Santos LS, Silva SN, Gil OM, Ferreira TC, Limbert E, Rueff J. Mismatch repair single nucleotide polymorphisms and thyroid cancer susceptibility. Oncol Lett 2018; 15:6715-6726. [PMID: 29616133 DOI: 10.3892/ol.2018.8103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/14/2017] [Indexed: 12/16/2022] Open
Abstract
Thyroid cancer (TC) is the most common endocrine malignancy and its incidence continues to rise worldwide. Ionizing radiation exposure is the best established etiological factor. Heritability is high; however, despite valuable contribution from recent genome-wide association studies, the current understanding of genetic susceptibility to TC remains limited. Several studies suggest that altered function or expression of the DNA mismatch repair (MMR) system may contribute to TC pathogenesis. Therefore, the present study aimed to evaluate the potential role of a panel of MMR single nucleotide polymorphisms (SNPs) on the individual susceptibility to well-differentiated TC (DTC). A case-control study was performed involving 106 DTC patients and 212 age- and gender-matched controls, who were all Caucasian Portuguese. Six SNPs present in distinct MMR genes (MLH1 rs1799977, MSH3 rs26279, MSH4 rs5745325, PMS1 rs5742933, MLH3 rs175080 and MSH6 rs1042821) were genotyped through TaqMan® assays and genotype-associated risk estimates were calculated. An increased risk was observed in MSH6 rs1042821 variant homozygotes [adjusted odds ratio (OR)=3.42, 95% CI: 1.04-11.24, P=0.04, under the co-dominant model; adjusted OR=3.84, 95% CI: 1.18-12.44, P=0.03, under the recessive model]. The association was especially evident for the follicular histotype and female sex. The association was also apparent when MSH6 was analysed in combination with other MMR SNPs such as MSH3 rs26279. Interestingly, two other SNP combinations, both containing the MSH6 heterozygous genotype, were associated with a risk reduction, suggesting a protective effect for these genotype combinations. These data support the idea that MMR SNPs such as MSH6 rs1042821, alone or in combination, may contribute to DTC susceptibility. This is coherent with the limited evidence available. Nevertheless, further studies are needed to validate these findings and to establish the usefulness of these SNPs as genetic susceptibility biomarkers for DTC so that, in the near future, cancer prevention policies may be optimized under a personalized medicine perspective.
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Affiliation(s)
- Luís S Santos
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal.,Centre for Interdisciplinary Research in Health (CIIS), Health Sciences Institute (ICS), Universidade Católica Portuguesa, 3504-505 Viseu, Portugal
| | - Susana N Silva
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal
| | - Octávia M Gil
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal.,Center for Nuclear Sciences and Technologies (CTN), Instituto Superior Técnico, Universidade de Lisboa, 2695-066 Bobadela LRS, Portugal
| | - Teresa C Ferreira
- Department of Nuclear Medicine, Instituto Português de Oncologia de Lisboa, 1099-023 Lisboa, Portugal
| | - Edward Limbert
- Department of Nuclear Medicine, Instituto Português de Oncologia de Lisboa, 1099-023 Lisboa, Portugal
| | - José Rueff
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal
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64
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Evensen NA, Madhusoodhan PP, Meyer J, Saliba J, Chowdhury A, Araten DJ, Nersting J, Bhatla T, Vincent TL, Teachey D, Hunger SP, Yang J, Schmiegelow K, Carroll WL. MSH6 haploinsufficiency at relapse contributes to the development of thiopurine resistance in pediatric B-lymphoblastic leukemia. Haematologica 2018; 103:830-839. [PMID: 29449434 PMCID: PMC5927991 DOI: 10.3324/haematol.2017.176362] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/02/2018] [Indexed: 01/10/2023] Open
Abstract
Survival of children with relapsed acute lymphoblastic leukemia is poor, and understanding mechanisms underlying resistance is essential to developing new therapy. Relapse-specific heterozygous deletions in MSH6, a crucial part of DNA mismatch repair, are frequently detected. Our aim was to determine whether MSH6 deletion results in a hypermutator phenotype associated with generation of secondary mutations involved in drug resistance, or if it leads to a failure to initiate apoptosis directly in response to chemotherapeutic agents. We knocked down MSH6 in mismatch repair proficient cell lines (697 and UOCB1) and showed significant increases in IC50s to 6-thioguanine and 6-mercaptopurine (697: 26- and 9-fold; UOCB1: 5- and 8-fold) in vitro, as well as increased resistance to 6-mercaptopurine treatment in vivo. No shift in IC50 was observed in deficient cells (Reh and RS4;11). 697 MSH6 knockdown resulted in increased DNA thioguanine nucleotide levels compared to non-targeted cells (3070 vs. 1722 fmol/μg DNA) with no difference observed in mismatch repair deficient cells. Loss of MSH6 did not give rise to microsatellite instability in cell lines or clinical samples, nor did it significantly increase mutation rate, but rather resulted in a defect in cell cycle arrest upon thiopurine exposure. MSH6 knockdown cells showed minimal activation of checkpoint regulator CHK1, γH2AX (DNA damage marker) and p53 levels upon treatment with thiopurines, consistent with intrinsic chemoresistance due to failure to recognize thioguanine nucleotide mismatching and initiate mismatch repair. Aberrant MSH6 adds to the list of alterations/mutations associated with acquired resistance to purine analogs emphasizing the importance of thiopurine therapy.
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Affiliation(s)
- Nikki A Evensen
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - P Pallavi Madhusoodhan
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - Julia Meyer
- Huntsman Cancer Institute, University of Utah Medical Center, Salt Lake City, USA
| | - Jason Saliba
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - Ashfiyah Chowdhury
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - David J Araten
- Department of Medicine, Perlmutter Cancer Center, NYU-Langone Medical Center, New York NY, USA
| | - Jacob Nersting
- Department of Pediatrics and Adolescent Medicine, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Teena Bhatla
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - Tiffaney L Vincent
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
| | - David Teachey
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
| | - Stephen P Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
| | - Jun Yang
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - William L Carroll
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
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65
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Sun Q, Pei C, Li Q, Dong T, Dong Y, Xing W, Zhou P, Gong Y, Zhen Z, Gao Y, Xiao Y, Su J, Ren H. Up-regulation of MSH6 is associated with temozolomide resistance in human glioblastoma. Biochem Biophys Res Commun 2018; 496:1040-1046. [PMID: 29366782 DOI: 10.1016/j.bbrc.2018.01.093] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 01/13/2018] [Indexed: 01/13/2023]
Abstract
The impact of DNA mismatch repair (MMR) on resistance to temozolomide (TMZ) therapy in patients with glioblastoma (GBM) is recently reported but the mechanisms are not understood. We aim to analyze the correlation between MMR function and the acquired TMZ resistance in GBM using both relevant clinical samples and TMZ resistant cells. First we found increased expression of MSH6, one of key components of MMR, in recurrent GBM patients' samples who underwent TMZ chemotherapy, comparing with those matched samples collected at the time of diagnosis. Using the cellular models of acquired resistance to TMZ, we further confirmed the up-regulation of MSH6 in TMZ resistant cells. Moreover, a TCGA dataset contains a large cohort of GBM clinical samples with or without TMZ treatment reinforced the increased expression of MSH6 and other MMR genes after long-term TMZ chemotherapy, which may resulted in MMR dysfunction and acquired TMZ resistance. Our results suggest that increased expression of MSH6, or other MMR, may be a new mechanism contributing to the acquired resistance during TMZ therapy; and may serve as an indicator to the resistance in GBM.
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Affiliation(s)
- Quanye Sun
- Department of Immunology, Harbin Medical University, Harbin 150081, China; Immunity & Infection Key Laboratory of Heilongjiang Province, Harbin 150081, China
| | - Chunying Pei
- Department of Immunology, Harbin Medical University, Harbin 150081, China; Immunity & Infection Key Laboratory of Heilongjiang Province, Harbin 150081, China
| | - Qiuyuan Li
- Fundamental Medicine Institute, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Tianxiu Dong
- Department of Abdominal Ultrasound, The 1st Affiliated Hospital to Harbin Medical University, Harbin 150081, China
| | - Yucui Dong
- Department of Immunology, Harbin Medical University, Harbin 150081, China; Immunity & Infection Key Laboratory of Heilongjiang Province, Harbin 150081, China
| | - Wenjing Xing
- Department of Immunology, Harbin Medical University, Harbin 150081, China; Immunity & Infection Key Laboratory of Heilongjiang Province, Harbin 150081, China
| | - Peng Zhou
- Department of Neurosurgery, The 4th Hospital Affiliated to Harbin Medical University, Harbin 150081, China
| | - Yujiao Gong
- Department of Immunology, Harbin Medical University, Harbin 150081, China; Immunity & Infection Key Laboratory of Heilongjiang Province, Harbin 150081, China
| | - Ziqi Zhen
- Department of Immunology, Harbin Medical University, Harbin 150081, China; Immunity & Infection Key Laboratory of Heilongjiang Province, Harbin 150081, China
| | - Yifan Gao
- Department of Immunology, Harbin Medical University, Harbin 150081, China; Immunity & Infection Key Laboratory of Heilongjiang Province, Harbin 150081, China
| | - Yun Xiao
- Department of Bioinformatics, College of Bioinformatics and Technology, Harbin Medical University, Harbin 150081, China.
| | - Jun Su
- Department of Neurosurgery, The 3rd Hospital Affiliated to Harbin Medical University, Harbin 150086, China.
| | - Huan Ren
- Department of Immunology, Harbin Medical University, Harbin 150081, China; Immunity & Infection Key Laboratory of Heilongjiang Province, Harbin 150081, China.
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66
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Melvin RL, Xiao J, Godwin RC, Berenhaut KS, Salsbury FR. Visualizing correlated motion with HDBSCAN clustering. Protein Sci 2018; 27:62-75. [PMID: 28799290 PMCID: PMC5734272 DOI: 10.1002/pro.3268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 12/22/2022]
Abstract
Correlated motion analysis provides a method for understanding communication between and dynamic similarities of biopolymer residues and domains. The typical equal-time correlation matrices-frequently visualized with pseudo-colorings or heat maps-quickly convey large regions of highly correlated motion but hide more subtle similarities of motion. Here we propose a complementary method for visualizing correlations within proteins (or general biopolymers) that quickly conveys intuition about which residues have a similar dynamic behavior. For grouping residues, we use the recently developed non-parametric clustering algorithm HDBSCAN. Although the method we propose here can be used to group residues using correlation as a similarity matrix-the most straightforward and intuitive method-it can also be used to more generally determine groups of residues which have similar dynamic properties. We term these latter groups "Dynamic Domains", as they are based not on spatial closeness but rather closeness in the column space of a correlation matrix. We provide examples of this method across three human proteins of varying size and function-the Nf-Kappa-Beta essential modulator, the clotting promoter Thrombin and the mismatch repair protein (dimer) complex MutS-alpha. Although the examples presented here are from all-atom molecular dynamics simulations, this visualization technique can also be used on correlations matrices built from any ensembles of conformations from experiment or computation.
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Affiliation(s)
- Ryan L. Melvin
- Department of PhysicsWake Forest UniversityWinston SalemNorth Carolina
- Department of Mathematics and StatisticsWake Forest UniversityWinston‐SalemNorth Carolina27109
| | - Jiajie Xiao
- Department of PhysicsWake Forest UniversityWinston SalemNorth Carolina
- Department of Computer ScienceWake Forest UniversityWinston‐SalemNorth Carolina27109
| | - Ryan C. Godwin
- Department of PhysicsWake Forest UniversityWinston SalemNorth Carolina
| | - Kenneth S. Berenhaut
- Department of Mathematics and StatisticsWake Forest UniversityWinston‐SalemNorth Carolina27109
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67
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Santamaría PG, Floristán A, Fontanals-Cirera B, Vázquez-Naharro A, Santos V, Morales S, Yuste L, Peinado H, García-Gómez A, Portillo F, Hernando E, Cano A. Lysyl oxidase-like 3 is required for melanoma cell survival by maintaining genomic stability. Cell Death Differ 2017; 25:935-950. [PMID: 29229995 PMCID: PMC5907912 DOI: 10.1038/s41418-017-0030-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 10/09/2017] [Accepted: 10/31/2017] [Indexed: 01/07/2023] Open
Abstract
Lysyl oxidase-like 3 (LOXL3) is a member of the lysyl oxidase family comprising multifunctional enzymes with depicted roles in extracellular matrix maturation, tumorigenesis, and metastasis. In silico expression analyses followed by experimental validation in a comprehensive cohort of human cell lines revealed a significant upregulation of LOXL3 in human melanoma. We show that LOXL3 silencing impairs cell proliferation and triggers apoptosis in various melanoma cell lines. Further supporting a pro-oncogenic role in melanoma, LOXL3 favors tumor growth in vivo and cooperates with oncogenic BRAF in melanocyte transformation. Upon LOXL3 depletion, melanoma cells display a faulty DNA damage response (DDR), characterized by ATM checkpoint activation and inefficient ATR activation leading to the accumulation of double-strand breaks (DSBs) and aberrant mitosis. Consistent with these findings, LOXL3 binds to proteins involved in the maintenance of genome integrity, in particular BRCA2 and MSH2, whose levels dramatically decrease upon LOXL3 depletion. Moreover, LOXL3 is required for efficient DSB repair in melanoma cells. Our results reveal an unexpected role for LOXL3 in the control of genome stability and melanoma progression, exposing its potential as a novel therapeutic target in malignant melanoma, a very aggressive condition yet in need for more effective treatment options.
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Affiliation(s)
- Patricia G Santamaría
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Arzobispo Morcillo 4, 28029, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Alfredo Floristán
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Arzobispo Morcillo 4, 28029, Madrid, Spain
| | - Bárbara Fontanals-Cirera
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Alberto Vázquez-Naharro
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Arzobispo Morcillo 4, 28029, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Vanesa Santos
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Arzobispo Morcillo 4, 28029, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Saleta Morales
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Arzobispo Morcillo 4, 28029, Madrid, Spain
| | - Lourdes Yuste
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Arzobispo Morcillo 4, 28029, Madrid, Spain
| | - Héctor Peinado
- Microenvironment and Metastasis Laboratory, Department of Molecular Oncology, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Antonio García-Gómez
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Francisco Portillo
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Arzobispo Morcillo 4, 28029, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Eva Hernando
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Amparo Cano
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Arzobispo Morcillo 4, 28029, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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68
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Spampinato CP. Protecting DNA from errors and damage: an overview of DNA repair mechanisms in plants compared to mammals. Cell Mol Life Sci 2017; 74:1693-1709. [PMID: 27999897 PMCID: PMC11107726 DOI: 10.1007/s00018-016-2436-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/10/2023]
Abstract
The genome integrity of all organisms is constantly threatened by replication errors and DNA damage arising from endogenous and exogenous sources. Such base pair anomalies must be accurately repaired to prevent mutagenesis and/or lethality. Thus, it is not surprising that cells have evolved multiple and partially overlapping DNA repair pathways to correct specific types of DNA errors and lesions. Great progress in unraveling these repair mechanisms at the molecular level has been made by several talented researchers, among them Tomas Lindahl, Aziz Sancar, and Paul Modrich, all three Nobel laureates in Chemistry for 2015. Much of this knowledge comes from studies performed in bacteria, yeast, and mammals and has impacted research in plant systems. Two plant features should be mentioned. Plants differ from higher eukaryotes in that they lack a reserve germline and cannot avoid environmental stresses. Therefore, plants have evolved different strategies to sustain genome fidelity through generations and continuous exposure to genotoxic stresses. These strategies include the presence of unique or multiple paralogous genes with partially overlapping DNA repair activities. Yet, in spite (or because) of these differences, plants, especially Arabidopsis thaliana, can be used as a model organism for functional studies. Some advantages of this model system are worth mentioning: short life cycle, availability of both homozygous and heterozygous lines for many genes, plant transformation techniques, tissue culture methods and reporter systems for gene expression and function studies. Here, I provide a current understanding of DNA repair genes in plants, with a special focus on A. thaliana. It is expected that this review will be a valuable resource for future functional studies in the DNA repair field, both in plants and animals.
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Affiliation(s)
- Claudia P Spampinato
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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69
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Melvin RL, Thompson WG, Godwin RC, Gmeiner WH, Salsbury FR. MutS α's Multi-Domain Allosteric Response to Three DNA Damage Types Revealed by Machine Learning. FRONTIERS IN PHYSICS 2017; 5:10. [PMID: 31938712 PMCID: PMC6959842 DOI: 10.3389/fphy.2017.00010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
MutSα is a key component in the mismatch repair (MMR) pathway. This protein is responsible for initiating the signaling pathways for DNA repair or cell death. Herein we investigate this heterodimer's post-recognition, post-binding response to three types of DNA damage involving cytotoxic, anti-cancer agents-carboplatin, cisplatin, and FdU. Through a combination of supervised and unsupervised machine learning techniques along with more traditional structural and kinetic analysis applied to all-atom molecular dynamics (MD) calculations, we predict that MutSα has a distinct response to each of the three damage types. Via a binary classification tree (a supervised machine learning technique), we identify key hydrogen bond motifs unique to each type of damage and suggest residues for experimental mutation studies. Through a combination of a recently developed clustering (unsupervised learning) algorithm, RMSF calculations, PCA, and correlated motions we predict that each type of damage causes MutSα to explore a specific region of conformation space. Detailed analysis suggests a short range effect for carboplatin-primarily altering the structures and kinetics of residues within 10 angstroms of the damaged DNA-and distinct longer-range effects for cisplatin and FdU. In our simulations, we also observe that a key phenylalanine residue-known to stack with a mismatched or unmatched bases in MMR-stacks with the base complementary to the damaged base in 88.61% of MD frames containing carboplatinated DNA. Similarly, this Phe71 stacks with the base complementary to damage in 91.73% of frames with cisplatinated DNA. This residue, however, stacks with the damaged base itself in 62.18% of trajectory frames with FdU-substituted DNA and has no stacking interaction at all in 30.72% of these frames. Each drug investigated here induces a unique perturbation in the MutSα complex, indicating the possibility of a distinct signaling event and specific repair or death pathway (or set of pathways) for a given type of damage.
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Affiliation(s)
- Ryan L. Melvin
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - William G. Thompson
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - Ryan C. Godwin
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - William H. Gmeiner
- Gmeiner Laboratory, Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Freddie R. Salsbury
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
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70
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Nagel S, Pommerenke C, Meyer C, Kaufmann M, MacLeod RAF, Drexler HG. Identification of a tumor suppressor network in T-cell leukemia. Leuk Lymphoma 2017; 58:2196–2207. [PMID: 28142295 DOI: 10.1080/10428194.2017.1283029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To identify novel cancer-related genes targeted by copy number alterations, we performed genomic profiling of T-cell acute lymphoblastic leukemia (T-ALL) cell lines. In 3/8, we identified a shared deletion at chromosomal position 2p16.3-p21. Within the minimally deleted region, we recognized several candidate tumor suppressor (TS) genes, including FBXO11 and FOXN2. An additional deletion at chromosome 14q23.2-q32.11 included FOXN3, highlighting this class of FOX genes as potential TS. Quantitative expression analyses of FBXO11, FOXN2, and FOXN3 confirmed reduced transcript levels in the identified cell lines. Moreover, reduced expression of these genes was also observed in about 7% of T-ALL patients, showing their clinical relevance in this malignancy. Bioinformatic analyses revealed concurrent reduction of FOXN2 and/or FOXN3 together with homeobox gene ZHX1. Consistently, experiments demonstrated that both FOXN2 and FOXN3 directly activated transcription of ZHX1. Taken together, we identified novel TS genes forming a regulatory network in T-cell development and leukemogenesis.
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Affiliation(s)
- Stefan Nagel
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Claudia Pommerenke
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Corinna Meyer
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Maren Kaufmann
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Roderick A F MacLeod
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
| | - Hans G Drexler
- a Department of Human and Animal Cell Lines , Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
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71
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Sigley J, Jarzen J, Scarpinato K, Guthold M, Pu T, Nelli D, Low J, Bonin K. Diffusion and Binding of Mismatch Repair Protein, MSH2, in Breast Cancer Cells at Different Stages of Neoplastic Transformation. PLoS One 2017; 12:e0170414. [PMID: 28125613 PMCID: PMC5268495 DOI: 10.1371/journal.pone.0170414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/04/2017] [Indexed: 12/19/2022] Open
Abstract
The interior of cells is a highly complex medium, containing numerous organelles, a matrix of different fibers and a viscous, aqueous fluid of proteins and small molecules. The interior of cells is also a highly dynamic medium, in which many components move, either by active transport or passive diffusion. The mobility and localization of proteins inside cells can provide important insights into protein function and also general cellular properties, such as viscosity. Neoplastic transformation affects numerous cellular properties, and our goal was to investigate the diffusional and binding behavior of the important mismatch repair (MMR) protein MSH2 in live human cells at various stages of neoplastic transformation. Toward this end, noncancerous, immortal, tumorigenic, and metastatic mammary epithelial cells were transfected with EGFP and EGFP-tagged MSH2. MSH2 forms two MMR proteins (MutSα and MutSβ) and we assume MSH2 is in the complex MutSα, though our results are similar in either case. Unlike the MutS complexes that bind to nuclear DNA, EGFP diffuses freely. EGFP and MutSα-EGFP diffusion coefficients were determined in the cytoplasm and nucleus of each cell type using fluorescence recovery after photobleaching. Diffusion coefficients were 14-24 μm2/s for EGFP and 3-7 μm2/s for MutSα-EGFP. EGFP diffusion increased in going from noncancerous to immortal cells, indicating a decrease in viscosity, with smaller changes in subsequent stages. MutSα produces an effective diffusion coefficient that, coupled with the free EGFP diffusion measurements, can be used to extract a pure diffusion coefficient and a pseudo-equilibrium constant K*. The MutSα nuclear K* increased sixfold in the first stage of cancer and then decreased in the more advanced stages. The ratio of nuclear to cytoplasmic K*for MutSα increased almost two orders of magnitude in going from noncancerous to immortal cells, suggesting that this quantity may be a sensitive metric for recognizing the onset of cancer.
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Affiliation(s)
- Justin Sigley
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - John Jarzen
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Karin Scarpinato
- OVPR, University of Miami, Miami, Florida, United States of America
| | - Martin Guthold
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Tracey Pu
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Daniel Nelli
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Josiah Low
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Keith Bonin
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States of America
- * E-mail:
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Lin PH, Kuo WH, Huang AC, Lu YS, Lin CH, Kuo SH, Wang MY, Liu CY, Cheng FTF, Yeh MH, Li HY, Yang YH, Hsu YH, Fan SC, Li LY, Yu SL, Chang KJ, Chen PL, Ni YH, Huang CS. Multiple gene sequencing for risk assessment in patients with early-onset or familial breast cancer. Oncotarget 2016; 7:8310-20. [PMID: 26824983 PMCID: PMC4884994 DOI: 10.18632/oncotarget.7027] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/01/2016] [Indexed: 12/31/2022] Open
Abstract
Since BRCA mutations are only responsible for 10–20% of cases of breast cancer in patients with early-onset or a family history and since next-generation sequencing technology allows the simultaneous sequencing of a large number of target genes, testing for multiple cancer-predisposing genes is now being considered, but its significance in clinical practice remains unclear. We then developed a sequencing panel containing 68 genes that had cancer risk association for patients with early-onset or familial breast cancer. A total of 133 patients were enrolled and 30 (22.6%) were found to carry germline deleterious mutations, 9 in BRCA1, 11 in BRCA2, 2 in RAD50, 2 in TP53 and one each in ATM, BRIP1, FANCI, MSH2, MUTYH, and RAD51C. Triple-negative breast cancer (TNBC) was associated with the highest mutation rate (45.5%, p = 0.025). Seven of the 9 BRCA1 mutations and the single FANCI mutation were in the TNBC group; 9 of the 11 BRCA2, 1 of the 2 RAD50 as well as BRIP1, MSH2, MUTYH, and RAD51C mutations were in the hormone receptor (HR)(+)Her2(−) group, and the other RAD50, ATM, and TP53 mutations were in the HR(+)Her2(+) group. Mutation carriers were considered as high-risk to develop malignancy and advised to receive cancer screening. Screening protocols of non-BRCA genes were based on their biologic functions; for example, patients carrying RAD51C mutation received a screening protocol similar to that for BRCA, since BRCA and RAD51C are both involved in homologous recombination. In conclusion, we consider that multiple gene sequencing in cancer risk assessment is clinically valuable.
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Affiliation(s)
- Po-Han Lin
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan.,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Hung Kuo
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Ai-Chu Huang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Shen Lu
- Department of Medical Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ching-Hung Lin
- Department of Medical Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Hsin Kuo
- Department of Medical Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Yu Liu
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | | | - Ming-Hsin Yeh
- Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Huei-Ying Li
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Hsuan Yang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Hua Hsu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Sheng-Chih Fan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Long-Yuan Li
- Graduate Institute of Cancer Biology, China Medical University, Taichung, Taiwan
| | - Sung-Liang Yu
- Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
| | - King-Jen Chang
- Department of Surgery, Cheng Ching Hospital, Taichung, Taiwan
| | - Pei-Lung Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Hsuan Ni
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
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73
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Li H, An J, Wu M, Zheng Q, Gui X, Li T, Pu H, Lu D. LncRNA HOTAIR promotes human liver cancer stem cell malignant growth through downregulation of SETD2. Oncotarget 2016; 6:27847-64. [PMID: 26172293 PMCID: PMC4695030 DOI: 10.18632/oncotarget.4443] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 06/19/2015] [Indexed: 02/02/2023] Open
Abstract
Long non-coding RNA HOTAIR predicts negative tumor prognosis and exhibits oncogenic activity. Herein, we demonstrate HOTAIR promotes human liver cancer stem cell malignant growth through downregulation of SETD2. Mechanistically, HOTAIR reduces the recuritment of the CREB, P300, RNA polII onto the SETD2 promoter region that inhibits SETD2 expression and its phosphorylation. Thereby, the SETD2 binding capacity to substrate histone H3 is weakened, triggering a reduction of trimethylation on histone H3 thirty-sixth lysine, and thereby the H3K36me3–hMSH2-hMSH6-SKP2 complex is also decreased. Strikingly, the complex occupancy on chromosome is depressed, preventing from mismatch DNA repair. While reducing the degradation capacity of Skp2 for aging histone H3 bound to damaged DNA, the aging histone repair is impaired. Furthermore, that the damaged DNA escaped to repair can causes microsatellite instability(MSI) and abnormal expression of cell cycle related genes that may trigger the hepatocarcinogenesis. This study provides evidence for HOTAIR to promote tumorigenesis via downregulating SETD2 in liver cancer stem cells.
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Affiliation(s)
- Haiyan Li
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jiahui An
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Mengying Wu
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Qidi Zheng
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Xin Gui
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Tianming Li
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Hu Pu
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Dongdong Lu
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
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74
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Fesler A, Xu X, Zheng X, Li X, Jiang J, Russo JJ, Ju J. Identification of miR-215 mediated targets/pathways via translational immunoprecipitation expression analysis (TrIP-chip). Oncotarget 2016; 6:24463-73. [PMID: 26287603 PMCID: PMC4695198 DOI: 10.18632/oncotarget.4425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/31/2015] [Indexed: 01/28/2023] Open
Abstract
Steady state mRNA expression profiling can identify the majority of miRNA targets. However, some translationally repressed miRNA targets are missed and thus not considered for functional validation. Therefore, analysis of mRNA translation can enhance miRNA target identification for functional studies. We have applied a unique approach to identify miRNA targets in a small number of cells. Actively translating mRNAs are associated with polyribosomes and newly synthesized peptide chains are associated with molecular chaperones such as HSP70s. Affinity capture beads were used to capture HSP70 chaperones associated with polyribosome complexes. The isolated actively translating mRNAs were used for high throughput expression profiling analysis. miR-215 is an important miRNA in colorectal cancer and loss of miR-215 is significantly associated with prognosis of this disease. miR-215 suppresses the expression of several key targets. We utilized the affinity capture approach to isolate miR-215 mediated mRNA target transcripts. This approach provides a unique way to identify targets regulated by non-coding RNAs and RNA binding proteins from a small number of cells.
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Affiliation(s)
- Andrew Fesler
- Department of Pathology, Stony Brook University, School of Medicine, Stony Brook, NY, USA
| | - Xiao Xu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiao Zheng
- The Third Affiliated Hospital, Soochow University, China
| | - Xiaodong Li
- The Third Affiliated Hospital, Soochow University, China
| | - Jingting Jiang
- The Third Affiliated Hospital, Soochow University, China
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Jingfang Ju
- Department of Pathology, Stony Brook University, School of Medicine, Stony Brook, NY, USA
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75
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Clinicopathologic Features and Germline Sequence Variants in Young Patients (≤40 Years Old) With Pancreatic Ductal Adenocarcinoma. Pancreas 2016; 45:1056-61. [PMID: 26692440 DOI: 10.1097/mpa.0000000000000574] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVES The median age of patients with pancreatic ductal adenocarcinoma (PDAC) is approximately 70 years, and PDAC rarely affects individuals younger than 40 years. Here, we investigated clinicopathologic features and genetic background of PDAC occurring in young patients (age ≤ 40 years) to determine whether any difference exists in comparison with those of older patients (>40 years). METHODS We reviewed 908 patients with pathologically proven PDAC for clinicopathologic characteristics. In addition, we performed targeted sequencing of germline variants for 49 genes that are associated with a hereditary predisposition for cancer in 9 young patients with available DNA. RESULTS Among the 908 patients, a total of 17 were diagnosed at age younger than 40 years. There were no significant differences between young and old groups in terms of sex, smoking history, tumor location, Union for International Cancer Control stage, family histories of any cancer and PDAC in first-degree relatives, and medical history of other cancer. Targeted sequencing analysis demonstrated no definite "pathogenic" variants. CONCLUSIONS The clinicopathologic features in young patients were generally similar to those in older patients. The rarity of family history of PDAC and the sequencing analysis for germline variants suggest that hereditary factors might have a weak, if any, relationship with early-onset PDAC.
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76
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Wang H, He L, Song J, Cui W, Zhang Y, Jia C, Francis D, Rogers HJ, Sun L, Tai P, Hui X, Yang Y, Liu W. Cadmium-induced genomic instability in Arabidopsis: Molecular toxicological biomarkers for early diagnosis of cadmium stress. CHEMOSPHERE 2016; 150:258-265. [PMID: 26907594 DOI: 10.1016/j.chemosphere.2016.02.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 01/26/2016] [Accepted: 02/09/2016] [Indexed: 05/11/2023]
Abstract
Microsatellite instability (MSI) analysis, random-amplified polymorphic DNA (RAPD), and methylation-sensitive arbitrarily primed PCR (MSAP-PCR) are methods to evaluate the toxicity of environmental pollutants in stress-treated plants and human cancer cells. Here, we evaluate these techniques to screen for genetic and epigenetic alterations of Arabidopsis plantlets exposed to 0-5.0 mg L(-1) cadmium (Cd) for 15 d. There was a substantial increase in RAPD polymorphism of 24.5, and in genomic methylation polymorphism of 30.5-34.5 at CpG and of 14.5-20 at CHG sites under Cd stress of 5.0 mg L(-1) by RAPD and of 0.25-5.0 mg L(-1) by MSAP-PCR, respectively. However, only a tiny increase of 1.5 loci by RAPD occurred under Cd stress of 4.0 mg L(-1), and an additional high dose (8.0 mg L(-1)) resulted in one repeat by MSI analysis. MSAP-PCR detected the most significant epigenetic modifications in plantlets exposed to Cd stress, and the patterns of hypermethylation and polymorphisms were consistent with inverted U-shaped dose responses. The presence of genomic methylation polymorphism in Cd-treated seedlings, prior to the onset of RAPD polymorphism, MSI and obvious growth effects, suggests that these altered DNA methylation loci are the most sensitive biomarkers for early diagnosis and risk assessment of genotoxic effects of Cd pollution in ecotoxicology.
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Affiliation(s)
- Hetong Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China; Department of Basic Medicine, He University, Shenyang 110163, PR China
| | - Lei He
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China; Environmental Science College, Liao University, Shenyang 110036, PR China
| | - Jie Song
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China; Environmental Science College, Liao University, Shenyang 110036, PR China
| | - Weina Cui
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China; Shanghai Institute of Technology, Shanghai 201418, PR China
| | - Yanzhao Zhang
- Life Science Department, Luoyang Normal University, Luoyang 471022, PR China
| | - Chunyun Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China
| | - Dennis Francis
- Key Laboratory of Eco-restoration, Shenyang University, Shenyang 11044, PR China
| | - Hilary J Rogers
- Cardiff University, School of Biosciences, Cardiff CF10 33TL, UK
| | - Lizong Sun
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China
| | - Peidong Tai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China
| | - Xiujuan Hui
- Shanghai Institute of Technology, Shanghai 201418, PR China
| | - Yuesuo Yang
- Key Laboratory of Eco-restoration, Shenyang University, Shenyang 11044, PR China
| | - Wan Liu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China.
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Wagner VP, Webber LP, Salvadori G, Meurer L, Fonseca FP, Castilho RM, Squarize CH, Vargas PA, Martins MD. Overexpression of MutSα Complex Proteins Predicts Poor Prognosis in Oral Squamous Cell Carcinoma. Medicine (Baltimore) 2016; 95:e3725. [PMID: 27258499 PMCID: PMC4900707 DOI: 10.1097/md.0000000000003725] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The DNA mismatch repair (MMR) system is responsible for the detection and correction of errors created during DNA replication, thereby avoiding the incorporation of mutations in dividing cells. The prognostic value of alterations in MMR system has not previously been analyzed in oral squamous cell carcinoma (OSCC).The study comprised 115 cases of OSCC diagnosed between 1996 and 2010. The specimens collected were constructed into tissue microarray blocks. Immunohistochemical staining for MutSα complex proteins hMSH2 and hMSH6 was performed. The slides were subsequently scanned into high-resolution images, and nuclear staining of hMSH2 and hMSH6 was analyzed using the Nuclear V9 algorithm. Univariable and multivariable Cox proportional hazard regression models were performed to evaluate the prognostic value of hMSH2 and hMSH6 in OSCC.All cases in the present cohort were positive for hMSH2 and hMSH6 and a direct correlation was found between the expression of the proteins (P < 0.05). The mean number of positive cells for hMSH2 and hMSH6 was 64.44 ± 15.21 and 31.46 ± 22.38, respectively. These values were used as cutoff points to determine high protein expression. Cases with high expression of both proteins simultaneously were classified as having high MutSα complex expression. In the multivariable analysis, high expression of the MutSα complex was an independent prognostic factor for poor overall survival (hazard ratio: 2.75, P = 0.02).This study provides a first insight of the prognostic value of alterations in MMR system in OSCC. We found that MutSα complex may constitute a molecular marker for the poor prognosis of OSCC.
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Affiliation(s)
- Vivian Petersen Wagner
- From the Department of Oral Pathology, School of Dentistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (VPW, LPW, MDM); Experimental Pathology Unit, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil (VPW, LPW, LM, MDM); Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Norway (GS); Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil (FPF, PAV); and Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan, School of Dentistry, Ann Arbor, MI (RMC, CHS)
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Quantitative proteomic analysis of anticancer drug RH1 resistance in liver carcinoma. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:219-32. [DOI: 10.1016/j.bbapap.2015.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/26/2015] [Accepted: 11/16/2015] [Indexed: 01/18/2023]
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79
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Crouse GF. Non-canonical actions of mismatch repair. DNA Repair (Amst) 2016; 38:102-109. [PMID: 26698648 PMCID: PMC4740236 DOI: 10.1016/j.dnarep.2015.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 09/06/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022]
Abstract
At the heart of the mismatch repair (MMR) system are proteins that recognize mismatches in DNA. Such mismatches can be mispairs involving normal or damaged bases or insertion/deletion loops due to strand misalignment. When such mispairs are generated during replication or recombination, MMR will direct removal of an incorrectly paired base or block recombination between nonidentical sequences. However, when mispairs are recognized outside the context of replication, proper strand discrimination between old and new DNA is lost, and MMR can act randomly and mutagenically on mispaired DNA. Such non-canonical actions of MMR are important in somatic hypermutation and class switch recombination, expansion of triplet repeats, and potentially in mutations arising in nondividing cells. MMR involvement in damage recognition and signaling is complex, with the end result likely dependent on the amount of DNA damage in a cell.
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Affiliation(s)
- Gray F Crouse
- Department of Biology, Emory University, Atlanta, GA 30322, USA.
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80
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Peña-Diaz J, Rasmussen LJ. Approaches to diagnose DNA mismatch repair gene defects in cancer. DNA Repair (Amst) 2015; 38:147-154. [PMID: 26708048 DOI: 10.1016/j.dnarep.2015.11.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 08/12/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022]
Abstract
The DNA repair pathway mismatch repair (MMR) is responsible for the recognition and correction of DNA biosynthetic errors caused by inaccurate nucleotide incorporation during replication. Faulty MMR leads to failure to address the mispairs or insertion deletion loops (IDLs) left behind by the replicative polymerases and results in increased mutation load at the genome. The realization that defective MMR leads to a hypermutation phenotype and increased risk of tumorigenesis highlights the relevance of this pathway for human disease. The association of MMR defects with increased risk of cancer development was first observed in colorectal cancer patients that carried inactivating germline mutations in MMR genes and the disease was named as hereditary non-polyposis colorectal cancer (HNPCC). Currently, a growing list of cancers is found to be MMR defective and HNPCC has been renamed Lynch syndrome (LS) partly to include the associated risk of developing extra-colonic cancers. In addition, a number of non-hereditary, mostly epigenetic, alterations of MMR genes have been described in sporadic tumors. Besides conferring a strong cancer predisposition, genetic or epigenetic inactivation of MMR genes also renders cells resistant to some chemotherapeutic agents. Therefore, diagnosis of MMR deficiency has important implications for the management of the patients, the surveillance of their relatives in the case of LS and for the choice of treatment. Some of the alterations found in MMR genes have already been well defined and their pathogenicity assessed. Despite this substantial wealth of knowledge, the effects of a large number of alterations remain uncharacterized (variants of uncertain significance, VUSs). The advent of personalized genomics is likely to increase the list of VUSs found in MMR genes and anticipates the need of diagnostic tools for rapid assessment of their pathogenicity. This review describes current tools and future strategies for addressing the relevance of MMR gene alterations in human disease.
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Affiliation(s)
- Javier Peña-Diaz
- Center for Healthy Aging, Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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81
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Ding N, Bonham EM, Hannon BE, Amick TR, Baylin SB, O'Hagan HM. Mismatch repair proteins recruit DNA methyltransferase 1 to sites of oxidative DNA damage. J Mol Cell Biol 2015; 8:244-54. [PMID: 26186941 DOI: 10.1093/jmcb/mjv050] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 06/08/2015] [Indexed: 12/11/2022] Open
Abstract
At sites of chronic inflammation, epithelial cells are exposed to high levels of reactive oxygen species and undergo cancer-associated DNA methylation changes, suggesting that inflammation may initiate epigenetic alterations. Previously, we demonstrated that oxidative damage causes epigenetic silencing proteins to become part of a large complex that is localized to GC-rich regions of the genome, including promoter CpG islands that are epigenetically silenced in cancer. However, whether these proteins were recruited directly to damaged DNA or during the DNA repair process was unknown. Here we demonstrate that the mismatch repair protein heterodimer MSH2-MSH6 participates in the oxidative damage-induced recruitment of DNA methyltransferase 1 (DNMT1) to chromatin. Hydrogen peroxide treatment induces the interaction of MSH2-MSH6 with DNMT1, suggesting that the recruitment is through a protein-protein interaction. Importantly, the reduction in transcription for genes with CpG island-containing promoters caused by oxidative damage is abrogated by knockdown of MSH6 and/or DNMT1. Our findings provide evidence that the role of DNMT1 at sites of oxidative damage is to reduce transcription, potentially preventing transcription from interfering with the repair process. This study uniquely brings together several factors that are known to contribute to colon cancer, namely inflammation, mismatch repair proteins, and epigenetic changes.
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Affiliation(s)
- Ning Ding
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Emily M Bonham
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Brooke E Hannon
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Thomas R Amick
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Stephen B Baylin
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Heather M O'Hagan
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
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Grazielle-Silva V, Zeb TF, Bolderson J, Campos PC, Miranda JB, Alves CL, Machado CR, McCulloch R, Teixeira SMR. Distinct Phenotypes Caused by Mutation of MSH2 in Trypanosome Insect and Mammalian Life Cycle Forms Are Associated with Parasite Adaptation to Oxidative Stress. PLoS Negl Trop Dis 2015; 9:e0003870. [PMID: 26083967 PMCID: PMC4470938 DOI: 10.1371/journal.pntd.0003870] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 06/02/2015] [Indexed: 11/19/2022] Open
Abstract
Background DNA repair mechanisms are crucial for maintenance of the genome in all organisms, including parasites where successful infection is dependent both on genomic stability and sequence variation. MSH2 is an early acting, central component of the Mismatch Repair (MMR) pathway, which is responsible for the recognition and correction of base mismatches that occur during DNA replication and recombination. In addition, recent evidence suggests that MSH2 might also play an important, but poorly understood, role in responding to oxidative damage in both African and American trypanosomes. Methodology/Principal Findings To investigate the involvement of MMR in the oxidative stress response, null mutants of MSH2 were generated in Trypanosoma brucei procyclic forms and in Trypanosoma cruzi epimastigote forms. Unexpectedly, the MSH2 null mutants showed increased resistance to H2O2 exposure when compared with wild type cells, a phenotype distinct from the previously observed increased sensitivity of T. brucei bloodstream forms MSH2 mutants. Complementation studies indicated that the increased oxidative resistance of procyclic T. brucei was due to adaptation to MSH2 loss. In both parasites, loss of MSH2 was shown to result in increased tolerance to alkylation by MNNG and increased accumulation of 8-oxo-guanine in the nuclear and mitochondrial genomes, indicating impaired MMR. In T. cruzi, loss of MSH2 also increases the parasite capacity to survive within host macrophages. Conclusions/Significance Taken together, these results indicate MSH2 displays conserved, dual roles in MMR and in the response to oxidative stress. Loss of the latter function results in life cycle dependent differences in phenotypic outcomes in T. brucei MSH2 mutants, most likely because of the greater burden of oxidative stress in the insect stage of the parasite. Trypanosoma brucei and Trypanosoma cruzi are protozoa parasites that cause sleeping sickness and Chagas disease, respectively, two neglected tropical diseases endemic in sub-Saharan Africa and Latin America. The high genetic diversity found in the T. cruzi population and the highly diverse repertoire of surface glycoprotein genes found in T. brucei are crucial factors that ensure a successful infection in their hosts. Besides responding to host immune responses, these parasites must deal with various sources of oxidative stress that can cause DNA damage. Thus, by determining the right balance between genomic stability and genetic variation, DNA repair pathways have a big impact in the ability of these parasites to maintain infection. This study is focused on the role of a DNA mismatch repair (MMR) protein named MSH2 in protecting these parasites’ DNA against oxidative assault. Using knock-out mutants, we showed that, besides acting in the MMR pathway as a key protein that recognizes and repairs base mismatches, insertions or deletions that can occur after DNA replication, MSH2 has an additional role in the oxidative stress response. Importantly, this extra role of MSH2 seems to be independent of other MMR components and dependent on the parasite developmental stage.
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Affiliation(s)
- Viviane Grazielle-Silva
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- The Wellcome Trust Center for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Tehseen Fatima Zeb
- The Wellcome Trust Center for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Jason Bolderson
- The Wellcome Trust Center for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Priscila C. Campos
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Julia B. Miranda
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ceres L. Alves
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos R. Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Richard McCulloch
- The Wellcome Trust Center for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, United Kingdom
- * E-mail: (RM); (SMRT)
| | - Santuza M. R. Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail: (RM); (SMRT)
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Mitchell AL, Bøe Wolff A, MacArthur K, Weaver JU, Vaidya B, Erichsen MM, Darlay R, Husebye ES, Cordell HJ, Pearce SHS. Linkage Analysis in Autoimmune Addison's Disease: NFATC1 as a Potential Novel Susceptibility Locus. PLoS One 2015; 10:e0123550. [PMID: 26042420 PMCID: PMC4456164 DOI: 10.1371/journal.pone.0123550] [Citation(s) in RCA: 9] [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: 09/05/2014] [Accepted: 03/04/2015] [Indexed: 11/20/2022] Open
Abstract
Background Autoimmune Addison’s disease (AAD) is a rare, highly heritable autoimmune endocrinopathy. It is possible that there may be some highly penetrant variants which confer disease susceptibility that have yet to be discovered. Methods DNA samples from 23 multiplex AAD pedigrees from the UK and Norway (50 cases, 67 controls) were genotyped on the Affymetrix SNP 6.0 array. Linkage analysis was performed using Merlin. EMMAX was used to carry out a genome-wide association analysis comparing the familial AAD cases to 2706 UK WTCCC controls. To explore some of the linkage findings further, a replication study was performed by genotyping 64 SNPs in two of the four linked regions (chromosomes 7 and 18), on the Sequenom iPlex platform in three European AAD case-control cohorts (1097 cases, 1117 controls). The data were analysed using a meta-analysis approach. Results In a parametric analysis, applying a rare dominant model, loci on chromosomes 7, 9 and 18 had LOD scores >2.8. In a non-parametric analysis, a locus corresponding to the HLA region on chromosome 6, known to be associated with AAD, had a LOD score >3.0. In the genome-wide association analysis, a SNP cluster on chromosome 2 and a pair of SNPs on chromosome 6 were associated with AAD (P <5x10-7). A meta-analysis of the replication study data demonstrated that three chromosome 18 SNPs were associated with AAD, including a non-synonymous variant in the NFATC1 gene. Conclusion This linkage study has implicated a number of novel chromosomal regions in the pathogenesis of AAD in multiplex AAD families and adds further support to the role of HLA in AAD. The genome-wide association analysis has also identified a region of interest on chromosome 2. A replication study has demonstrated that the NFATC1 gene is worthy of future investigation, however each of the regions identified require further, systematic analysis.
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Affiliation(s)
- Anna L. Mitchell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
| | - Anette Bøe Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Katie MacArthur
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jolanta U. Weaver
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bijay Vaidya
- Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | | | | | - Rebecca Darlay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eystein S. Husebye
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Simon H. S. Pearce
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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84
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Sun L, Hartson SD, Matts RL. Identification of proteins associated with Aha1 in HeLa cells by quantitative proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:365-80. [PMID: 25614414 DOI: 10.1016/j.bbapap.2015.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/20/2014] [Accepted: 01/09/2015] [Indexed: 01/17/2023]
Abstract
The identification of the activator of heat shock protein 90 (Hsp90) ATPase's (Aha1) protein-protein interaction (PPI) network will provide critical insights into the relationship of Aha1 with multi-molecular complexes and shed light onto Aha1's interconnections with Hsp90-regulated biological functions. Flag-tagged Aha1 was over-expressed in HeLa cells and isolated by anti-Flag affinity pull downs, followed by trypsin digestion and identification co-adsorbing proteins by liquid chromatography-tandem mass spectroscopy (LC-MS/MS). A probability-based identification of Aha1 PPIs was generated from the LC-MS/MS analysis by using a relative quantification strategy, spectral counting (SC). By comparing the SC-based protein levels between Aha1 pull-down samples and negative controls, 164 Aha1-interacting proteins were identified that were quantitatively enriched in the pull-down samples over the controls. The identified Aha1-interacting proteins are involved in a wide number of intracellular bioprocesses, including DNA maintenance, chromatin structure, RNA processing, translation, nucleocytoplasmic and vesicle transport, among others. The interactions of 33 of the identified proteins with Aha1 were further confirmed by Western blotting, demonstrating the reliability of our affinity-purification-coupled quantitative SC-MS strategy. Our proteomic data suggests that Aha1 may participate in diverse biological pathways to facilitate Hsp90 chaperone functions in response to stress.
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Affiliation(s)
- Liang Sun
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Steven D Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert L Matts
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
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85
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Abstract
Three processes act in series to accurately replicate the eukaryotic nuclear genome. The major replicative DNA polymerases strongly prevent mismatch formation, occasional mismatches that do form are proofread during replication, and rare mismatches that escape proofreading are corrected by mismatch repair (MMR). This review focuses on MMR in light of increasing knowledge about nuclear DNA replication enzymology and the rate and specificity with which mismatches are generated during leading- and lagging-strand replication. We consider differences in MMR efficiency in relation to mismatch recognition, signaling to direct MMR to the nascent strand, mismatch removal, and the timing of MMR. These studies are refining our understanding of relationships between generating and repairing replication errors to achieve accurate replication of both DNA strands of the nuclear genome.
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Affiliation(s)
- Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina 27709;
| | - Dorothy A Erie
- Department of Chemistry and Curriculum in Applied Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599-3290;
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86
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Ahmad M, Tuteja R. Emerging importance of mismatch repair components including UvrD helicase and their cross-talk with the development of drug resistance in malaria parasite. Mutat Res 2014; 770:54-60. [PMID: 25771870 DOI: 10.1016/j.mrfmmm.2014.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/14/2014] [Accepted: 09/17/2014] [Indexed: 06/04/2023]
Abstract
Human malaria is an important parasitic infection responsible for a significant number of deaths worldwide, particularly in tropical and subtropical regions. The recent scenario has worsened mainly because of the emergence of drug-resistant malaria parasites having the potential to spread across the world. Drug-resistant parasites possess a defective mismatch repair (MMR); therefore, it is essential to explore its mechanism in detail to determine the underlying cause. Recently, artemisinin-resistant parasites have been reported to exhibit nonsynonymous single nucleotide polymorphisms in genes involved in MMR pathways such as MutL homolog (MLH) and UvrD. Plasmodium falciparum MLH is an endonuclease required to restore the defective MMR in drug-resistant W2 strain of P. falciparum. Although the role of helicases in eukaryotic MMR has been questioned, the identification and characterization of the UvrD helicase and their cross-talk with MLH in P. falciparum suggests the possible involvement of UvrD in MMR. A comparative genome-wide analysis revealed the presence of the UvrD helicase in Plasmodium species, while it is absent in human host. Therefore, PfUvrD may emerge as a suitable drug target to control malaria. This review study is focused on recent developments in MMR biochemistry, emerging importance of the UvrD helicase, possibility of its involvement in MMR and the emerging cross-talk between MMR components and drug resistance in malaria parasite.
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Affiliation(s)
- Moaz Ahmad
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Renu Tuteja
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi 110067, India.
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87
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Loconte DC, Patruno M, Lastella P, Di Gregorio C, Grossi V, Forte G, Ingravallo G, Varvara D, Bagnulo R, Simone C, Resta N, Stella A. A rare MSH2 mutation causes defective binding to hMSH6, normal hMSH2 staining, and loss of hMSH6 at advanced cancer stage. Hum Pathol 2014; 45:2162-7. [PMID: 25106712 DOI: 10.1016/j.humpath.2014.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 05/22/2014] [Accepted: 05/28/2014] [Indexed: 01/13/2023]
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88
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Bak ST, Sakellariou D, Pena-Diaz J. The dual nature of mismatch repair as antimutator and mutator: for better or for worse. Front Genet 2014; 5:287. [PMID: 25191341 PMCID: PMC4139959 DOI: 10.3389/fgene.2014.00287] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/04/2014] [Indexed: 01/19/2023] Open
Abstract
DNA is constantly under attack by a number of both exogenous and endogenous agents that challenge its integrity. Among the mechanisms that have evolved to counteract this deleterious action, mismatch repair (MMR) has specialized in removing DNA biosynthetic errors that occur when replicating the genome. Malfunction or inactivation of this system results in an increase in spontaneous mutability and a strong predisposition to tumor development. Besides this key corrective role, MMR proteins are involved in other pathways of DNA metabolism such as mitotic and meiotic recombination and processing of oxidative damage. Surprisingly, MMR is also required for certain mutagenic processes. The mutagenic MMR has beneficial consequences contributing to the generation of a vast repertoire of antibodies through class switch recombination and somatic hypermutation processes. However, this non-canonical mutagenic MMR also has detrimental effects; it promotes repeat expansions associated with neuromuscular and neurodegenerative diseases and may contribute to cancer/disease-related aberrant mutations and translocations. The reaction responsible for replication error correction has been the most thoroughly studied and it is the subject to numerous reviews. This review describes briefly the biochemistry of MMR and focuses primarily on the non-canonical MMR activities described in mammals as well as emerging research implicating interplay of MMR and chromatin.
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Affiliation(s)
- Sara Thornby Bak
- Department of Neuroscience and Pharmacology and Center for Healthy Aging, University of Copenhagen Copenhagen, Denmark
| | - Despoina Sakellariou
- Department of Neuroscience and Pharmacology and Center for Healthy Aging, University of Copenhagen Copenhagen, Denmark
| | - Javier Pena-Diaz
- Department of Neuroscience and Pharmacology and Center for Healthy Aging, University of Copenhagen Copenhagen, Denmark
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Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:206735. [PMID: 24701133 PMCID: PMC3950489 DOI: 10.1155/2014/206735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/27/2013] [Accepted: 11/29/2013] [Indexed: 12/28/2022]
Abstract
As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.
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Mismatch repair genes Mlh1 and Mlh3 modify CAG instability in Huntington's disease mice: genome-wide and candidate approaches. PLoS Genet 2013; 9:e1003930. [PMID: 24204323 PMCID: PMC3814320 DOI: 10.1371/journal.pgen.1003930] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 09/15/2013] [Indexed: 11/19/2022] Open
Abstract
The Huntington's disease gene (HTT) CAG repeat mutation undergoes somatic expansion that correlates with pathogenesis. Modifiers of somatic expansion may therefore provide routes for therapies targeting the underlying mutation, an approach that is likely applicable to other trinucleotide repeat diseases. Huntington's disease HdhQ111 mice exhibit higher levels of somatic HTT CAG expansion on a C57BL/6 genetic background (B6.HdhQ111) than on a 129 background (129.HdhQ111). Linkage mapping in (B6x129).HdhQ111 F2 intercross animals identified a single quantitative trait locus underlying the strain-specific difference in expansion in the striatum, implicating mismatch repair (MMR) gene Mlh1 as the most likely candidate modifier. Crossing B6.HdhQ111 mice onto an Mlh1 null background demonstrated that Mlh1 is essential for somatic CAG expansions and that it is an enhancer of nuclear huntingtin accumulation in striatal neurons. HdhQ111 somatic expansion was also abolished in mice deficient in the Mlh3 gene, implicating MutLγ (MLH1–MLH3) complex as a key driver of somatic expansion. Strikingly, Mlh1 and Mlh3 genes encoding MMR effector proteins were as critical to somatic expansion as Msh2 and Msh3 genes encoding DNA mismatch recognition complex MutSβ (MSH2–MSH3). The Mlh1 locus is highly polymorphic between B6 and 129 strains. While we were unable to detect any difference in base-base mismatch or short slipped-repeat repair activity between B6 and 129 MLH1 variants, repair efficiency was MLH1 dose-dependent. MLH1 mRNA and protein levels were significantly decreased in 129 mice compared to B6 mice, consistent with a dose-sensitive MLH1-dependent DNA repair mechanism underlying the somatic expansion difference between these strains. Together, these data identify Mlh1 and Mlh3 as novel critical genetic modifiers of HTT CAG instability, point to Mlh1 genetic variation as the likely source of the instability difference in B6 and 129 strains and suggest that MLH1 protein levels play an important role in driving of the efficiency of somatic expansions. The expansion of a CAG repeat underlies Huntington's disease (HD), with longer CAG tracts giving rise to earlier onset and more severe disease. In individuals harboring a CAG expansion the repeat undergoes further somatic expansion over time, particularly in brain cells most susceptible to disease pathogenesis. Preventing this repeat lengthening may delay disease onset and/or slow progression. We are using mouse models of HD to identify the factors that modify the somatic expansion of the HD CAG repeat, as these may provide novel targets for therapeutic intervention. To identify genetic modifiers of somatic expansion in HD mouse models we have used both an unbiased genetic mapping approach in inbred mouse strains that exhibit different levels of somatic expansion, as well as targeted gene knockout approaches. Our results demonstrate that: 1) Mlh1 and Mlh3 genes, encoding components of the DNA mismatch repair pathway, are critical for somatic CAG expansion; 2) in the absence of somatic expansion the pathogenic process in the mouse is slowed; 3) MLH1 protein levels are likely to be a driver of the efficiency of somatic expansion. Together, our data provide new insight into the factors underlying the process of somatic expansion of the HD CAG repeat.
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