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Baduel P, Sammarco I, Barrett R, Coronado‐Zamora M, Crespel A, Díez‐Rodríguez B, Fox J, Galanti D, González J, Jueterbock A, Wootton E, Harney E. The evolutionary consequences of interactions between the epigenome, the genome and the environment. Evol Appl 2024; 17:e13730. [PMID: 39050763 PMCID: PMC11266121 DOI: 10.1111/eva.13730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/30/2024] [Accepted: 05/22/2024] [Indexed: 07/27/2024] Open
Abstract
The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'Ecole Normale SupérieurePSL University, CNRSParisFrance
| | - Iris Sammarco
- Institute of Botany of the Czech Academy of SciencesPrůhoniceCzechia
| | - Rowan Barrett
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | | | | | | | - Janay Fox
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | - Dario Galanti
- Institute of Evolution and Ecology (EvE)University of TuebingenTübingenGermany
| | | | - Alexander Jueterbock
- Algal and Microbial Biotechnology Division, Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Eric Wootton
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | - Ewan Harney
- Institute of Evolutionary BiologyCSIC, UPFBarcelonaSpain
- School of BiosciencesUniversity of SheffieldSheffieldUK
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Shilkin ES, Petrova DV, Novikova AA, Boldinova EO, Zharkov DO, Makarova AV. Methylation and hydroxymethylation of cytosine alter activity and fidelity of translesion DNA polymerases. DNA Repair (Amst) 2024; 141:103712. [PMID: 38959714 DOI: 10.1016/j.dnarep.2024.103712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
Epigenetic cytosine methylation covers most of genomic CpG dinucleotides in human cells. In addition to common deamination-mediated mutagenesis at CpG sites, an alternative deamination-independent pathway associated with DNA polymerase activity was previously described. This mutagenesis is characterized by the TCG→TTG mutational signature and is believed to arise from dAMP misincorporation opposite 5-methylcytosine (mC) or its oxidized derivative 5-hydroxymethylcytosine (hmC) by B-family replicative DNA polymerases with disrupted proofreading 3→5'-exonuclease activity. In addition to being less stable and pro-mutagenic themselves, cytosine modifications also increase the risk of adjacent nucleotides damage, including the formation of 8-oxo-2'-deoxyguanosine (8-oxoG), a well-known mutagenic lesion. The effect of cytosine methylation on error-prone DNA polymerases lacking proofreading activity and involved in repair and DNA translesion synthesis remains unexplored. Here we analyze the efficiency and fidelity of translesion Y-family polymerases (Pol κ, Pol η, Pol ι and REV1) and primase-polymerase PrimPol opposite mC and hmC as well as opposite 8-oxoG adjacent to mC in the TCG context. We demonstrate that epigenetic cytosine modifications suppress Pol ι and REV1 activities and lead to increasing dAMP misincorporation by PrimPol, Pol κ and Pol ι in vitro. Cytosine methylation also increases misincorporation of dAMP opposite the adjacent 8-oxoG by PrimPol, decreases the TLS activity of Pol η opposite the lesion but increases dCMP incorporation opposite 8-oxoG by REV1. Altogether, these data suggest that methylation and hydroxymethylation of cytosine alter activity and fidelity of translesion DNA polymerases.
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Affiliation(s)
- Evgeniy S Shilkin
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia; Institute of Gene Biology of Russian Academy of Sciences, Moscow 119334, Russia
| | - Daria V Petrova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 63009, Russia
| | - Anna A Novikova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia; Institute of Gene Biology of Russian Academy of Sciences, Moscow 119334, Russia
| | - Elizaveta O Boldinova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia; Institute of Gene Biology of Russian Academy of Sciences, Moscow 119334, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 63009, Russia.
| | - Alena V Makarova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia; Institute of Gene Biology of Russian Academy of Sciences, Moscow 119334, Russia.
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Sugiyama T. Biochemical reconstitution of a major age-related cancer mutational signature by heat-induced spontaneous deamination of 5-methylcytosine residues, repair of uracil residues, and DNA replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595323. [PMID: 38826364 PMCID: PMC11142167 DOI: 10.1101/2024.05.22.595323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Non-enzymatic spontaneous deamination of 5-methylcytosine, producing thymine, is the proposed etiology of cancer mutational signature 1, which is the most predominant signature in all cancers. Here, the proposed mutational process was reconstituted using synthetic DNA and purified proteins. First, single-stranded DNA containing 5-methylcytosine at CpG context was incubated at an elevated temperature to accelerate spontaneous DNA damage. Then, the DNA was treated with uracil DNA glycosylase to remove uracil residues that were formed by deamination of cytosine. The resulting DNA was then used as a template for DNA synthesis by yeast DNA polymerase δ. The DNA products were analyzed by next-generation DNA sequencing, and mutation frequencies were quantified. The observed mutations after this process were exclusively C>T mutations at CpG context, which was very similar to signature 1. When 5-methylcytosine modification and uracil DNA glycosylase were both omitted, C>T mutations were produced on C residues in all sequence contexts, but these mutations were diminished by uracil DNA glycosylase-treatment. These results indicate that the CpG>TpG mutations were produced by the deamination of 5-methylcytosine. Additional mutations, mainly C>G, were introduced by yeast DNA polymerase ζ on the heat-damaged DNA, indicating that G residues of the templates were also damaged. However, the damage on G residues was not converted to mutations with DNA polymerase δ or ε. These results provide biochemical evidence to support that the majority of mutations in cancers are produced by ordinary DNA replication on spontaneously damaged DNA.
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Bomsztyk K, Mar D, Denisenko O, Powell S, Vishnoi M, Delegard J, Patel A, Ellenbogen RG, Ramakrishna R, Rostomily R. Analysis of gliomas DNA methylation: Assessment of pre-analytical variables. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586350. [PMID: 38586048 PMCID: PMC10996653 DOI: 10.1101/2024.03.26.586350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Precision oncology is driven by molecular biomarkers. For glioblastoma multiforme (GBM), the most common malignant adult primary brain tumor, O6-methylguanine-DNA methyltransferase ( MGMT ) gene DNA promoter methylation is an important prognostic and treatment clinical biomarker. Time consuming pre-analytical steps such as biospecimen storage before fixing, sampling, and processing are major sources of errors and batch effects, that are further confounded by intra-tumor heterogeneity of MGMT promoter methylation. To assess the effect of pre-analytical variables on GBM DNA methylation, tissue storage/sampling (CryoGrid), sample preparation multi-sonicator (PIXUL) and 5-methylcytosine (5mC) DNA immunoprecipitation (Matrix MeDIP-qPCR/seq) platforms were used. MGMT promoter CpG methylation was examined in 173 surgical samples from 90 individuals, 50 of these were used for intra-tumor heterogeneity studies. MGMT promoter methylation levels in paired frozen and formalin fixed paraffin embedded (FFPE) samples were very close, confirming suitability of FFPE for MGMT promoter methylation analysis in clinical settings. Matrix MeDIP-qPCR yielded similar results to methylation specific PCR (MS-PCR). Warm ex-vivo ischemia (37°C up to 4hrs) and 3 cycles of repeated sample thawing and freezing did not alter 5mC levels at MGMT promoter, exon and upstream enhancer regions, demonstrating the resistance of DNA methylation to the most common variations in sample processing conditions that might be encountered in research and clinical settings. 20-30% of specimens exhibited intratumor heterogeneity in the MGMT DNA promoter methylation. Collectively these data demonstrate that variations in sample fixation, ischemia duration and temperature, and DNA methylation assay technique do not have significant impact on assessment of MGMT promoter methylation status. However, intratumor methylation heterogeneity underscores the need for histologic verification and value of multiple biopsies at different GBM geographic tumor sites in assessment of MGMT promoter methylation. Matrix-MeDIP-seq analysis revealed that MGMT promoter methylation status clustered with other differentially methylated genomic loci (e.g. HOXA and lncRNAs), that are likewise resilient to variation in above post-resection pre-analytical conditions. These MGMT -associated global DNA methylation patterns offer new opportunities to validate more granular data-based epigenetic GBM clinical biomarkers where the CryoGrid-PIXUL-Matrix toolbox could prove to be useful.
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Richau CS, Scherer NDM, Matta BP, de Armas EM, de Barros Moreira FC, Bergmann A, Pereira Chaves CB, Boroni M, dos Santos ACE, Moreira MAM. BRCA1, BRCA2, and TP53 germline and somatic variants and clinicopathological characteristics of Brazilian patients with epithelial ovarian cancer. Cancer Med 2024; 13:e6729. [PMID: 38308422 PMCID: PMC10905552 DOI: 10.1002/cam4.6729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/20/2023] [Accepted: 11/07/2023] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Approximately 3/4 of ovarian cancers are diagnosed in advanced stages, with the high-grade epithelial ovarian carcinoma (EOC) accounting for 90% of the cases. EOC present high genomic instability and somatic loss-of-function variants in genes associated with homologous recombination mutational repair pathway (HR), such as BRCA1 and BRCA2, and in TP53. The identification of germline variants in HR genes in EOC is relevant for treatment of platinum resistant tumors and relapsed tumors with therapies based in synthetic lethality such as PARP inhibitors. Patients with somatic variants in HR genes may also benefit from these therapies. In this work was analyzed the frequency of somatic variants in BRCA1, BRCA2, and TP53 in an EOC cohort of Brazilian patients, estimating the proportion of variants in tumoral tissue and their association with progression-free survival and overall survival. METHODS The study was conducted with paired blood/tumor samples from 56 patients. Germline and tumoral sequences of BRCA1, BRCA2, and TP53 were obtained by massive parallel sequencing. The HaplotypeCaller method was used for calling germline variants, and somatic variants were called with Mutect2. RESULTS A total of 26 germline variants were found, and seven patients presented germline pathogenic or likely pathogenic variants in BRCA1 or BRCA2. The analysis of tumoral tissue identified 52 somatic variants in 41 patients, being 43 somatic variants affecting or likely affecting protein functionality. Survival analyses showed that tumor staging was associated with overall survival (OS), while the presence of somatic mutation in TP53 was not associated with OS or progression-free survival. CONCLUSION Frequency of pathogenic or likely pathogenic germline variants in BRCA1 and BRCA2 (12.5%) was lower in comparison with other studies. TP53 was the most altered gene in tumors, with 62.5% presenting likely non-functional or non-functional somatic variants, while eight 14.2% presented likely non-functional or non-functional somatic variants in BRCA1 or BRCA2.
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Affiliation(s)
| | | | - Bruna Palma Matta
- Tumoral Genetics and Virology ProgramInstituto Nacional de CâncerRio de JaneiroBrazil
- Present address:
Hospital BP ‐ A Beneficência Portuguesa de São PauloSão PauloBrazil
| | | | | | - Anke Bergmann
- Clinical EpidemiologyInstituto Nacional de CâncerRio de JaneiroBrazil
| | | | - Mariana Boroni
- Bioinformatics and Computational Biology LaboratoryInstituto Nacional de CâncerRio de JaneiroBrazil
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Liu C, Li K, Sui Y, Liu H, Zhang Y, Lu Y, Lu W, Chen Y, Wang G, Xu S, Xiang T, Cai Y, Huang K. Different gene alterations in patients with non-small-cell lung cancer between the eastern and southern China. Heliyon 2023; 9:e20171. [PMID: 37767514 PMCID: PMC10520317 DOI: 10.1016/j.heliyon.2023.e20171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Geographical differences are conspicuous in lung cancer, and the distinct molecular features of lung tumor between Western patients and Asian patients have been demonstrated. However, the etiology of non-small-cell lung cancer (NSCLC) and the distribution of associated molecular aberrations in China have not been fully elucidated. The mutational profiles of 12 lung cancer-related genes were investigated in 85 patients from eastern China and 88 patients from southern China who had been histologically confirmed NSCLC. Overall, 93.6% (162/173) of tumor samples harbored at least one somatic alteration. The most frequently mutated genes were TP53 (56.1%), EGFR (50.3%), and KRAS (14.5%). We found that EGFR mutated much more frequently (60.0% vs 40.9%, P = 0.012) and TP53 mutations had significantly lower incidence (47.1% vs 64.8%, P = 0.019) in eastern cohort than that in southern cohort. Mutational signature analysis revealed a region-related mutagenesis mechanism characterized by a high prevalence of C to T transitions mainly occurring at CpG dinucleotides in southern patients. This study reveals the difference in the mutational features between NSCLC patients in eastern and southern China. The distinct patterns of gene mutation could provide clues for the mechanism of carcinogenesis of lung cancer, offering opportunities to stratify patients into optimal treatment plans based on genomic profiles.
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Affiliation(s)
- Chengdong Liu
- Department of thoracic surgery, Naval Medical Center of PLA, 338 Huaihai Road, Changning District, Shanghai 200052, China
| | - Kangbao Li
- Department of Geriatrics, Gastroenterology Ward, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Yi Sui
- Singlera Genomics Inc., Shanghai 201318, China
| | - Hongmei Liu
- Singlera Genomics Inc., Shanghai 201318, China
| | | | - Yuan Lu
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Wei Lu
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Yongfeng Chen
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Gehui Wang
- Singlera Genomics Inc., Shanghai 201318, China
| | - Suqian Xu
- Singlera Genomics Inc., Shanghai 201318, China
| | | | - Yongguang Cai
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Kenan Huang
- Department of Thoracic Surgery, Shanghai Changzheng Hospital, Navy Military Medical University, 415 Fengyang Road, Huangpu District, Shanghai 200003, China
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
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7
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Baker BH, Zhang S, Simon JM, McLarnan SM, Chung WK, Pearson BL. Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders. Front Neurosci 2023; 17:1106573. [PMID: 37599994 PMCID: PMC10435087 DOI: 10.3389/fnins.2023.1106573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction De novo mutations contribute to a large proportion of sporadic psychiatric and developmental disorders, yet the potential role of environmental carcinogens as drivers of causal de novo mutations in neurodevelopmental disorders is poorly studied. Methods To explore environmental mutation vulnerability of disease-associated gene sets, we analyzed publicly available whole genome sequencing datasets of mutations in human induced pluripotent stem cell clonal lines exposed to 12 classes of environmental carcinogens, and human lung cancers from individuals living in highly polluted regions. We compared observed rates of exposure-induced mutations in disease-related gene sets with the expected rates of mutations based on control genes randomly sampled from the genome using exact binomial tests. To explore the role of sequence characteristics in mutation vulnerability, we modeled the effects of sequence length, gene expression, and percent GC content on mutation rates of entire genes and gene coding sequences using multivariate Quasi-Poisson regressions. Results We demonstrate that several mutagens, including radiation and polycyclic aromatic hydrocarbons, disproportionately mutate genes related to neurodevelopmental disorders including autism spectrum disorders, schizophrenia, and attention deficit hyperactivity disorder. Other disease genes including amyotrophic lateral sclerosis, Alzheimer's disease, congenital heart disease, orofacial clefts, and coronary artery disease were generally not mutated more than expected. Longer sequence length was more strongly associated with elevated mutations in entire genes compared with mutations in coding sequences. Increased expression was associated with decreased coding sequence mutation rate, but not with the mutability of entire genes. Increased GC content was associated with increased coding sequence mutation rates but decreased mutation rates in entire genes. Discussion Our findings support the possibility that neurodevelopmental disorder genetic etiology is partially driven by a contribution of environment-induced germ line and somatic mutations.
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Affiliation(s)
- Brennan H. Baker
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shaoyi Zhang
- Master of Public Health Program, Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Jeremy M. Simon
- Department of Genetics and Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah M. McLarnan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Wendy K. Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Brandon L. Pearson
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
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The Mutagenic Consequences of DNA Methylation within and across Generations. EPIGENOMES 2022; 6:epigenomes6040033. [PMID: 36278679 PMCID: PMC9624357 DOI: 10.3390/epigenomes6040033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is an epigenetic modification with wide-ranging consequences across the life of an organism. This modification can be stable, persisting through development despite changing environmental conditions. However, in other contexts, DNA methylation can also be flexible, underlying organismal phenotypic plasticity. One underappreciated aspect of DNA methylation is that it is a potent mutagen; methylated cytosines mutate at a much faster rate than other genetic motifs. This mutagenic property of DNA methylation has been largely ignored in eco-evolutionary literature, despite its prevalence. Here, we explore how DNA methylation induced by environmental and other factors could promote mutation and lead to evolutionary change at a more rapid rate and in a more directed manner than through stochastic genetic mutations alone. We argue for future research on the evolutionary implications of DNA methylation driven mutations both within the lifetime of organisms, as well as across timescales.
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9
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Wang YP, Yang LN, Feng YY, Liu S, Zhan J. Single Amino Acid Substitution the DNA Repairing Gene Radiation-Sensitive 4 Contributes to Ultraviolet Tolerance of a Plant Pathogen. Front Microbiol 2022; 13:927139. [PMID: 35910660 PMCID: PMC9330021 DOI: 10.3389/fmicb.2022.927139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
To successfully survive and reproduce, all species constantly modify the structure and expression of their genomes to cope with changing environmental conditions including ultraviolet (UV) radiation. Thus, knowledge of species adaptation to environmental changes is a central theme of evolutionary studies which could have important implication for disease management and social-ecological sustainability in the future but is generally insufficient. Here, we investigated the evolution of UV adaptation in organisms by population genetic analysis of sequence structure, physiochemistry, transcription, and fitness variation in the radiation-sensitive 4 (RAD4) gene of the Irish potato famine pathogen Phytophthora infestans sampled from various altitudes. We found that RAD4 is a key gene determining the resistance of the pathogen to UV stress as indicated by strong phenotype-genotype-geography associations and upregulated transcription after UV exposure. We also found conserved evolution in the RAD4 gene. Only five nucleotide haplotypes corresponding to three protein isoforms generated by point mutations were detected in the 140 sequences analyzed and the mutations were constrained to the N-terminal domain of the protein. Physiochemical changes associated with non-synonymous mutations generate severe fitness penalty to mutants, which are purged out by natural selection, leading to the conserved evolution observed in the gene.
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Affiliation(s)
- Yan-Ping Wang
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, China
| | - Li-Na Yang
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Yuan-Yuan Feng
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, China
| | - Songqing Liu
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, China
- *Correspondence: Songqing Liu,
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Jiasui Zhan,
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Peng C, Jian X, Xie Y, Li L, Ouyang J, Tang L, Zhang X, Su J, Zhao S, Liu H, Yin M, Wu D, Wan M, Xie L, Chen X. Genomic alterations of dermatofibrosarcoma protuberans revealed by whole-genome sequencing. Br J Dermatol 2022; 186:997-1009. [PMID: 35441365 PMCID: PMC9325047 DOI: 10.1111/bjd.20976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 12/18/2021] [Accepted: 12/30/2021] [Indexed: 11/29/2022]
Abstract
Background Dermatofibrosarcoma protuberans (DFSP) is a rare and marginal cutaneous sarcoma of intermediate‐grade malignancy, for which the genomic landscape remains unclear. Understanding the landscape of DFSP will help to further classify the genomic pathway of malignant development in soft tissue. Objectives To identify the comprehensive molecular pathogenesis of DFSP. Methods In this study, the comprehensive genomic features, with 53 tumour‐normal pairs of DFSP, were revealed by whole‐genome sequencing. Results The mutational signature 1 (C > T mutation at CpG dinucleotides) is featured in DFSP, resulting in higher mutations in DNA replication. Interestingly, the recurrence of DFSP is correlated with low tumour mutation burden. Novel mutation genes in DFSP were identified, including MUC4/6, KMT2C and BRCA1, and subsequently, three molecular subtypes of DFSP were classified on the basis of MUC4 and MUC6 mutations. Various structural aberrations including genomic rearrangements were identified in DSFPs, particularly in 17q and 22q, which cause oncogene amplification (AKT1, SPHK1, COL1A1, PDGFβ) or tumour suppressor deletion (CDKN2A/B). In addition to gene fusion of COL1A1‐PDGFβ [t(17;22)], we identified gene fusion of SLC2A5‐BTBD7 [t(1;14)] in DFSP through whole‐genome sequencing, and verified it experimentally. Enrichment analysis of altered molecules revealed that DNA repair, cell cycle, phosphoinositide 3‐kinase and Janus kinase pathways were primarily involved in DFSP. Conclusions This is the first large‐scale whole‐genome sequencing for DFSP, and our findings describe the comprehensive genomic landscape, highlighting the molecular complexity and genomic aberrations of DFSP. Our findings also provide novel potential diagnostic and therapeutic targets for this disease. What is already known about this topic?Chromosomal translocation between chromosome 17 and chromosome 22 is the main feature in the pathogenesis of dermatofibrosarcoma protuberans (DFSP).
What does this study add?We describe the comprehensive genomic landscape of DFSP, highlighting the molecular complexity and genomic aberrations. Our findings provide novel potential diagnostic and therapeutic targets for this disease.
What is the translational message?Our study revealed novel molecular subtypes of DFSP based on genetic mutations, which benefits precision diagnosis. We also found oncogene amplification, including AKT1 and SPHK1, which provides novel potential target molecules for further DFSP treatment. In addition to gene fusion of COL1A1‐PDGFβ, we identified a novel gene fusion of SLC2A5‐BTBD7 in DFSP, which is a novel potential diagnostic and therapeutic target for this disease.
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Affiliation(s)
- Cong Peng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Xingxing Jian
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Yang Xie
- Department of Dermatology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lingfeng Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Jian Ouyang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Ling Tang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Xu Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Shuang Zhao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Hong Liu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Mingzhu Yin
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Dan Wu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Miaojian Wan
- Department of Dermatology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lu Xie
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
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11
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Prell A, Sen MO, Potabattula R, Bernhardt L, Dittrich M, Hahn T, Schorsch M, Zacchini F, Ptak GE, Niemann H, Haaf T. Species-Specific Paternal Age Effects and Sperm Methylation Levels of Developmentally Important Genes. Cells 2022; 11:cells11040731. [PMID: 35203380 PMCID: PMC8870257 DOI: 10.3390/cells11040731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/11/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
A growing number of sperm methylome analyses have identified genomic loci that are susceptible to paternal age effects in a variety of mammalian species, including human, bovine, and mouse. However, there is little overlap between different data sets. Here, we studied whether or not paternal age effects on the sperm epigenome have been conserved in mammalian evolution and compared methylation patterns of orthologous regulatory regions (mainly gene promoters) containing both conserved and non-conserved CpG sites in 94 human, 36 bovine, and 94 mouse sperm samples, using bisulfite pyrosequencing. We discovered three (NFKB2, RASGEF1C, and RPL6) age-related differentially methylated regions (ageDMRs) in humans, four (CHD7, HDAC11, PAK1, and PTK2B) in bovines, and three (Def6, Nrxn2, and Tbx19) in mice. Remarkably, the identified sperm ageDMRs were all species-specific. Most ageDMRs were in genomic regions with medium methylation levels and large methylation variation. Orthologous regions in species not showing this age effect were either hypermethylated (>80%) or hypomethylated (<20%). In humans and mice, ageDMRs lost methylation, whereas bovine ageDMRs gained methylation with age. Our results are in line with the hypothesis that sperm ageDMRs are in regions under epigenomic evolution and may be part of an epigenetic mechanism(s) for lineage-specific environmental adaptations and provide a solid basis for studies on downstream effects in the genes analyzed here.
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Affiliation(s)
- Andreas Prell
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
| | - Mustafa Orkun Sen
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
| | - Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
| | - Laura Bernhardt
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
- Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Thomas Hahn
- Fertility Center, 65189 Wiesbaden, Germany; (T.H.); (M.S.)
| | | | - Federica Zacchini
- PERCUROS BV, 2333 CL Leiden, The Netherlands;
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland;
- Wolfson Centre for Age-Related Diseases, King’s College London, London SE1 1UL, UK
| | - Grazyna Ewa Ptak
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland;
| | - Heiner Niemann
- Clinic for Gastroenterology, Hepatology and Endocrinology, Medical University Hannover, 30625 Hannover, Germany;
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (A.P.); (M.O.S.); (R.P.); (L.B.); (M.D.)
- Correspondence: ; Tel.: +49-931-3188738
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12
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Liu Y, Gusev A, Heng YJ, Alexandrov LB, Kraft P. Somatic mutational profiles and germline polygenic risk scores in human cancer. Genome Med 2022; 14:14. [PMID: 35144655 PMCID: PMC8832866 DOI: 10.1186/s13073-022-01016-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 01/24/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The mutational profile of cancer reflects the activity of the mutagenic processes which have been operative throughout the lineage of the cancer cell. These processes leave characteristic profiles of somatic mutations called mutational signatures. Mutational signatures, including single-base substitution (SBS) signatures, may reflect the effects of exogenous or endogenous exposures. METHODS We used polygenic risk scores (PRS) to summarize common germline variation associated with cancer risk and other cancer-related traits and examined the association between somatic mutational profiles and germline PRS in 12 cancer types from The Cancer Genome Atlas. Somatic mutational profiles were constructed from whole-exome sequencing data of primary tumors. PRS were calculated for the 12 selected cancer types and 9 non-cancer traits, including cancer risk determinants, hormonal factors, and immune-mediated inflammatory diseases, using germline genetic data and published summary statistics from genome-wide association studies. RESULTS We found 17 statistically significant associations between somatic mutational profiles and germline PRS after Bonferroni correction (p < 3.15 × 10-5), including positive associations between germline inflammatory bowel disease PRS and number of somatic mutations attributed to signature SBS1 in prostate cancer and APOBEC-related signatures in breast cancer. Positive associations were also found between age at menarche PRS and mutation counts of SBS1 in overall and estrogen receptor-positive breast cancer. Consistent with prior studies that found an inverse association between the pubertal development PRS and risk of prostate cancer, likely reflecting hormone-related mechanisms, we found an inverse association between age at menarche PRS and mutation counts of SBS1 in prostate cancer. Inverse associations were also found between several cancer PRS and tumor mutation counts. CONCLUSIONS Our analysis suggests that there are robust associations between tumor somatic mutational profiles and germline PRS. These may reflect the mechanisms through hormone regulation and immune responses that contribute to cancer etiology and drive cancer progression.
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Affiliation(s)
- Yuxi Liu
- grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115 USA
| | - Alexander Gusev
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215 USA
| | - Yujing J. Heng
- grid.38142.3c000000041936754XDepartment of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Ludmil B. Alexandrov
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Peter Kraft
- grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
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13
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Kuzmina NS. Radiation-Induced DNA Methylation Disorders: In Vitro and In Vivo Studies. BIOL BULL+ 2022. [DOI: 10.1134/s1062359021110066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Kucher OV, Vydyborets SV. LONG/TERM GENETIC AND EPIGENETIC DISORDERS IN PERSONS EXPOSED TO IONIZING RADIATION AND THEIR DESCENDANTS (review). PROBLEMY RADIATSIINOI MEDYTSYNY TA RADIOBIOLOHII 2021; 26:36-56. [PMID: 34965542 DOI: 10.33145/2304-8336-2021-26-36-56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 06/14/2023]
Abstract
The review is devoted to long-term genetic and epigenetic disorders in exposed individuals and their descendants,namely to cytogenetic effects in the Chornobyl NPP accident clean-up workers and their children, DNA methylation as an epigenetic modification of human genome. Data presented in review expand the understanding of risk of the prolonged exposure for the present and future generations, which is one of key problems posed by fundamental radiation genetics and human radiobiology.
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Affiliation(s)
- O V Kucher
- Shupyk National Healthcare University of Ukraine, 9 Dorohozhytska Str., Kyiv, 04112, Ukraine
| | - S V Vydyborets
- Shupyk National Healthcare University of Ukraine, 9 Dorohozhytska Str., Kyiv, 04112, Ukraine
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15
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Sirovy KA, Johnson KM, Casas SM, La Peyre JF, Kelly MW. Lack of genotype-by-environment interaction suggests limited potential for evolutionary changes in plasticity in the eastern oyster, Crassostrea virginica. Mol Ecol 2021; 30:5721-5734. [PMID: 34462983 DOI: 10.1111/mec.16156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/13/2022]
Abstract
Eastern oysters in the northern Gulf of Mexico are facing rapid environmental changes and can respond to this change via plasticity or evolution. Plasticity can act as an immediate buffer against environmental change, but this buffering could impact the organism's ability to evolve in subsequent generations. While plasticity and evolution are not mutually exclusive, the relative contribution and interaction between them remains unclear. In this study, we investigate the roles of plastic and evolved responses to environmental variation and Perkinsus marinus infection in Crassostrea virginica by using a common garden experiment with 80 oysters from six families outplanted at two field sites naturally differing in salinity. We use growth data, P. marinus infection intensities, 3' RNA sequencing (TagSeq) and low-coverage whole-genome sequencing to identify the effect of genotype, environment and genotype-by-environment interaction on the oyster's response to site. As one of first studies to characterize the joint effects of genotype and environment on transcriptomic and morphological profiles in a natural setting, we demonstrate that C. virginica has a highly plastic response to environment and that this response is parallel among genotypes. We also find that genes responding to genotype have distinct and opposing profiles compared to genes responding to environment with regard to expression levels, Ka/Ks ratios and nucleotide diversity. Our findings suggest that C. virginica may be able to buffer the immediate impacts of future environmental changes by altering gene expression and physiology, but the lack of genetic variation in plasticity suggests limited capacity for evolved responses.
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Affiliation(s)
- Kyle A Sirovy
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Kevin M Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Sandra M Casas
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Jerome F La Peyre
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Morgan W Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
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16
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Aoki Y, Ohno M, Matsumoto M, Matsumoto M, Masumura K, Nohmi T, Tsuzuki T. Characteristic mutations induced in the small intestine of Msh2-knockout gpt delta mice. Genes Environ 2021; 43:27. [PMID: 34225823 PMCID: PMC8256579 DOI: 10.1186/s41021-021-00196-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/28/2021] [Indexed: 11/17/2022] Open
Abstract
Background Base pair mismatches in genomic DNA can result in mutagenesis, and consequently in tumorigenesis. To investigate how mismatch repair deficiency increases mutagenicity under oxidative stress, we examined the type and frequency of mutations arising in the mucosa of the small intestine of mice carrying a reporter gene encoding guanine phosphoribosyltransferase (gpt) and in which the Msh2 gene, which encodes a component of the mismatch repair system, was either intact (Msh2+/+::gpt/0; Msh2-bearing) or homozygously knockout (KO) (Msh2−/−::gpt/0; Msh2-KO). Results Gpt mutant frequency in the small intestine of Msh2-KO mice was about 10 times that in Msh2-bearing mice. Mutant frequency in the Msh2-KO mice was not further enhanced by administration of potassium bromate, an oxidative stress inducer, in the drinking water at a dose of 1.5 g/L for 28 days. Mutation analysis showed that the characteristic mutation in the small intestine of the Msh2-KO mice was G-to-A transition, irrespective of whether potassium bromate was administered. Furthermore, administration of potassium bromate induced mutations at specific sites in gpt in the Msh2-KO mice: G-to-A transition was frequently induced at two known sites of spontaneous mutation (nucleotides 110 and 115, CpG sites) and at nucleotides 92 and 113 (3′-side of 5′-GpG-3′), and these sites were confirmed to be mutation hotspots in potassium bromate-administered Msh2-KO mice. Administration of potassium bromate also induced characteristic mutations, mainly single-base deletion and insertion of an adenine residue, in sequences of three to five adenine nucleotides (A-runs) in Msh2-KO mice, and elevated the overall proportion of single-base deletions plus insertions in Msh2-KO mice. Conclusions Our previous study revealed that administration of potassium bromate enhanced tumorigenesis in the small intestine of Msh2-KO mice and induced G-to-A transition in the Ctnnb1 gene. Based on our present and previous observations, we propose that oxidative stress under conditions of mismatch repair deficiency accelerates the induction of single-adenine deletions at specific sites in oncogenes, which enhances tumorigenesis in a synergistic manner with G-to-A transition in other oncogenes (e.g., Ctnnb1). Supplementary Information The online version contains supplementary material available at 10.1186/s41021-021-00196-0.
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Affiliation(s)
- Yasunobu Aoki
- Health and Environmental Risk Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.
| | - Mizuki Ohno
- Kyushu University, Faculty of Medical Sciences, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Michiyo Matsumoto
- Health and Environmental Risk Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Michi Matsumoto
- Health and Environmental Risk Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Kenichi Masumura
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takehiko Nohmi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Teruhisa Tsuzuki
- Kyushu University, Faculty of Medical Sciences, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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17
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Larose H, Prokoph N, Matthews JD, Schlederer M, Högler S, Alsulami AF, Ducray SP, Nuglozeh E, Fazaludeen MF, Elmouna A, Ceccon M, Mologni L, Gambacorti-Passerini C, Hoefler G, Lobello C, Pospisilova S, Janikova A, Woessmann W, Welk CD, Zimmermann MT, Fedorova A, Malone A, Smith O, Wasik M, Inghirami G, Lamant L, Blundell TL, Klapper W, Merkel O, Burke GAA, Mian S, Ashankyty I, Kenner L, Turner SD. Whole Exome Sequencing reveals NOTCH1 mutations in anaplastic large cell lymphoma and points to Notch both as a key pathway and a potential therapeutic target. Haematologica 2021; 106:1693-1704. [PMID: 32327503 PMCID: PMC8168516 DOI: 10.3324/haematol.2019.238766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
Patients diagnosed with Anaplastic Large Cell Lymphoma (ALCL) are still treated with toxic multi-agent chemotherapy and as many as 25-50% of patients relapse. To understand disease pathology and to uncover novel targets for therapy, Whole-Exome Sequencing (WES) of Anaplastic Lymphoma Kinase (ALK)+ ALCL was performed as well as Gene-Set Enrichment Analysis. This revealed that the T-cell receptor (TCR) and Notch pathways were the most enriched in mutations. In particular, variant T349P of NOTCH1, which confers a growth advantage to cells in which it is expressed, was detected in 12% of ALK+ and ALK- ALCL patient samples. Furthermore, we demonstrate that NPM-ALK promotes NOTCH1 expression through binding of STAT3 upstream of NOTCH1. Moreover, inhibition of NOTCH1 with γ-secretase inhibitors (GSIs) or silencing by shRNA leads to apoptosis; co-treatment in vitro with the ALK inhibitor Crizotinib led to additive/synergistic anti-tumour activity suggesting this may be an appropriate combination therapy for future use in the circumvention of ALK inhibitor resistance. Indeed, Crizotinib-resistant and sensitive ALCL were equally sensitive to GSIs. In conclusion, we show a variant in the extracellular domain of NOTCH1 that provides a growth advantage to cells and confirm the suitability of the Notch pathway as a second-line druggable target in ALK+ ALCL.
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Affiliation(s)
- Hugo Larose
- Department of Pathology, University of Cambridge, Cambridge, UK
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
| | - Nina Prokoph
- Department of Pathology, University of Cambridge, Cambridge, UK
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
| | | | | | - Sandra Högler
- Unit of Laborator y Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ali F. Alsulami
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Stephen P. Ducray
- Department of Pathology, University of Cambridge, Cambridge, UK
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
| | - Edem Nuglozeh
- Molecular Diagnostics and Personalised Therapeutics Unit, Colleges of Medicine and Applied Medical Sciences, University of Ha’il, Ha’il, Saudi Arabia
| | - Mohammad Feroze Fazaludeen
- Neuroinflammation Research Group, Depar tment of Neurobiology, A.I Virtanen Institute for Molecular Sciences, University of Eastern Finland, Finland
| | - Ahmed Elmouna
- Molecular Diagnostics and Personalised Therapeutics Unit, Colleges of Medicine and Applied Medical Sciences, University of Ha’il, Ha’il, Saudi Arabia
| | - Monica Ceccon
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- University of Milano-Bicocca, Monza, Italy
| | - Luca Mologni
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- University of Milano-Bicocca, Monza, Italy
| | - Carlo Gambacorti-Passerini
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- University of Milano-Bicocca, Monza, Italy
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Cosimo Lobello
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Center of Molecular Medicine, CEITEC, Masar yk University, Brno, Czech Republic
| | - Sarka Pospisilova
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Center of Molecular Medicine, CEITEC, Masar yk University, Brno, Czech Republic
- Department of Internal Medicine – Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Andrea Janikova
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Department of Internal Medicine – Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Wilhelm Woessmann
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- University Hospital Hamburg-Eppendor f, Pediatric Hematology and Oncology, Hamburg, Germany
| | - Christine Damm- Welk
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- University Hospital Hamburg-Eppendor f, Pediatric Hematology and Oncology, Hamburg, Germany
| | - Mar tin Zimmermann
- Department of Pediatric Hematology/Oncology and Blood Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Alina Fedorova
- Belarusian Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | | | - Owen Smith
- Our Lady’s Children’s Hospital, Crumlin, Ireland
| | - Mariusz Wasik
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Perelman School of Medicine, Philadelphia, PA, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Cornell University, New York, NY USA
| | - Laurence Lamant
- Institut Universitaire du Cancer Toulouse, Oncopole et Universite Paul-Sabatier, Toulouse, France
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Wolfram Klapper
- Department of Pathology, Hematopathology Section, UKSH Campus Kiel, Kiel, Germany
| | - Olaf Merkel
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - G. A. Amos Burke
- Department of Paediatric Oncology, Addenbrooke’s Hospital, Cambridge, UK
| | - Shahid Mian
- Molecular Diagnostics and Personalised Therapeutics Unit, Colleges of Medicine and Applied Medical Sciences, University of Ha’il, Ha’il, Saudi Arabia
| | - Ibraheem Ashankyty
- Department of Medical Technology Laboratory, College of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Lukas Kenner
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Department of Pathology, Medical University of Vienna, Vienna, Austria
- Ludwig-Boltzmann Institute for Cancer Research, Vienna, Austria
| | - Suzanne D. Turner
- Department of Pathology, University of Cambridge, Cambridge, UK
- European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net)
- Center of Molecular Medicine, CEITEC, Masar yk University, Brno, Czech Republic
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18
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Wang YP, Waheed A, Liu ST, Li WY, Nkurikiyimfura O, Lurwanu Y, Wang Z, Grenville-Briggs LJ, Yang L, Zheng L, Zhan J. Altitudinal Heterogeneity of UV Adaptation in Phytophthorainfestans Is Associated with the Spatial Distribution of a DNA Repair Gene. J Fungi (Basel) 2021; 7:245. [PMID: 33805198 PMCID: PMC8064308 DOI: 10.3390/jof7040245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 11/16/2022] Open
Abstract
Climate change is considered a major threat to society and nature. UV irradiation is the most important environmental genotoxic agent. Thus, how elevated UV irradiation may influence human health and ecosystems has generated wide concern in the scientific community, as well as with policy makers and the public in general. In this study, we investigated patterns and mechanisms of UV adaptation in natural ecosystems by studying a gene-specific variation in the potato late blight pathogen, Phytophthora infestans. We compared the sequence characteristics of radiation sensitive 23 (RAD23), a gene involved in the nucleotide excision repair (NER) pathway and UV tolerance, in P. infestans isolates sampled from various altitudes. We found that lower genetic variation in the RAD23 gene was caused by natural selection. The hypothesis that UV irradiation drives this selection was supported by strong correlations between the genomic characteristics and altitudinal origin (historic UV irradiation) of the RAD23 sequences with UV tolerance of the P. infestans isolates. These results indicate that the RAD23 gene plays an important role in the adaptation of P. infestans to UV stress. We also found that different climatic factors could work synergistically to determine the evolutionary adaptation of species, making the influence of climate change on ecological functions and resilience more difficult to predict. Future attention should aim at understanding the collective impact generated by simultaneous change in several climate factors on species adaptation and ecological sustainability, using state of the art technologies such as experimental evolution, genome-wide scanning, and proteomics.
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Affiliation(s)
- Yan-Ping Wang
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; (Y.-P.W.); (A.W.); (S.-T.L.); (W.-Y.L.); (O.N.)
| | - Abdul Waheed
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; (Y.-P.W.); (A.W.); (S.-T.L.); (W.-Y.L.); (O.N.)
| | - Shi-Ting Liu
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; (Y.-P.W.); (A.W.); (S.-T.L.); (W.-Y.L.); (O.N.)
| | - Wen-Yang Li
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; (Y.-P.W.); (A.W.); (S.-T.L.); (W.-Y.L.); (O.N.)
| | - Oswald Nkurikiyimfura
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; (Y.-P.W.); (A.W.); (S.-T.L.); (W.-Y.L.); (O.N.)
| | - Yahuza Lurwanu
- Department of Crop Protection, Bayero University Kano, Kano 70001, Nigeria;
| | - Zonghua Wang
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China;
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian 350108, China
| | - Laura J. Grenville-Briggs
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, 23053 Alnarp, Sweden;
| | - Lina Yang
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; (Y.-P.W.); (A.W.); (S.-T.L.); (W.-Y.L.); (O.N.)
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian 350108, China
| | - Luping Zheng
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; (Y.-P.W.); (A.W.); (S.-T.L.); (W.-Y.L.); (O.N.)
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden;
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19
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The emergence of the brain non-CpG methylation system in vertebrates. Nat Ecol Evol 2021; 5:369-378. [PMID: 33462491 PMCID: PMC7116863 DOI: 10.1038/s41559-020-01371-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023]
Abstract
Mammalian brains feature exceptionally high levels of non-CpG DNA methylation alongside the canonical form of CpG methylation. Non-CpG methylation plays a critical regulatory role in cognitive function, which is mediated by the binding of MeCP2, the transcriptional regulator that when mutated causes Rett syndrome. However, it is unclear whether the non-CpG neural methylation system is restricted to mammalian species with complex cognitive abilities or has deeper evolutionary origins. To test this, we investigated brain DNA methylation across 12 distantly related animal lineages, revealing that non-CpG methylation is restricted to vertebrates. We discovered that in vertebrates, non-CpG methylation is enriched within a highly conserved set of developmental genes transcriptionally repressed in adult brains, indicating that it demarcates a deeply conserved regulatory program. We also found that the writer of non-CpG methylation, DNMT3A, and the reader, MeCP2, originated at the onset of vertebrates as a result of the ancestral vertebrate whole-genome duplication. Together, we demonstrate how this novel layer of epigenetic information assembled at the root of vertebrates and gained new regulatory roles independent of the ancestral form of the canonical CpG methylation. This suggests that the emergence of non-CpG methylation may have fostered the evolution of sophisticated cognitive abilities found in the vertebrate lineage.
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20
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Afsari B, Kuo A, Zhang Y, Li L, Lahouel K, Danilova L, Favorov A, Rosenquist TA, Grollman AP, Kinzler KW, Cope L, Vogelstein B, Tomasetti C. Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer. eLife 2021; 10:61082. [PMID: 33491650 PMCID: PMC7872524 DOI: 10.7554/elife.61082] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/24/2021] [Indexed: 12/21/2022] Open
Abstract
Determining the etiologic basis of the mutations that are responsible for cancer is one of the fundamental challenges in modern cancer research. Different mutational processes induce different types of DNA mutations, providing 'mutational signatures' that have led to key insights into cancer etiology. The most widely used signatures for assessing genomic data are based on unsupervised patterns that are then retrospectively correlated with certain features of cancer. We show here that supervised machine-learning techniques can identify signatures, called SuperSigs, that are more predictive than those currently available. Surprisingly, we found that aging yields different SuperSigs in different tissues, and the same is true for environmental exposures. We were able to discover SuperSigs associated with obesity, the most important lifestyle factor contributing to cancer in Western populations.
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Affiliation(s)
- Bahman Afsari
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Albert Kuo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - YiFan Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Lu Li
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Kamel Lahouel
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ludmila Danilova
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russian Federation
| | - Alexander Favorov
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russian Federation
| | | | - Arthur P Grollman
- State University of New York at Stony Brook, Stony Brook, United States
| | - Ken W Kinzler
- Ludwig Center & Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, United States
| | - Leslie Cope
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Bert Vogelstein
- Ludwig Center & Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, United States
| | - Cristian Tomasetti
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
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21
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Seto MTY, Bertoli-Avella AM, Cheung KW, Chan KYK, Yeung KS, Fung JLF, Beetz C, Bauer P, Luk HM, Lo IFM, Lee CP, Chung BHY, Kan ASY. Prenatal and postnatal diagnosis of Schuurs-Hoeijmakers syndrome: Case series and review of the literature. Am J Med Genet A 2020; 185:384-389. [PMID: 33166031 DOI: 10.1002/ajmg.a.61964] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/17/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022]
Abstract
Schuurs-Hoeijmakers syndrome (SHS) is a rare syndrome involving a de novo variant in the PACS1 gene on chromosome 11q13. There are 36 individuals published in the literature so far, mostly diagnosed postnatally (34/36) after recognizing the typical facial features co-occurring with developmental delay, intellectual disability, and multiple malformations. Herein, we present one prenatal and 15 postnatal cases with the recurrent heterozygous pathogenic variant NM_018026.3:c.607C>T p.(Arg203Trp) in the PACS1 gene detected by exome sequencing. These 16 cases were identified by mining Centogene and the Hong Kong clinical genetic service databases. Collectively, the 49 postnatally diagnosed individuals present with typical facial features and developmental delay, while the three prenatally diagnosed individuals present with multiple congenital anomalies. In the current study, the use of exome sequencing as an unbiased diagnostic tool aided the diagnosis of SHS (pre- and postnatally). The identification of additional cases with SHS add to the current understanding of the clinical phenotype associated with pathogenic PACS1 variants. Databases combining clinical and genetic information are helpful for the study of rare diseases.
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Affiliation(s)
- Mimi Tin-Yan Seto
- Department of Obstetrics and Gynecology, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | | | - Ka Wang Cheung
- Department of Obstetrics and Gynecology, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kelvin Yuen-Kwong Chan
- Department of Obstetrics and Gynecology, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Sai Ying Pun, Hong Kong
| | - Kit San Yeung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Jasmine Lee-Fong Fung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | | | | | - Ho Ming Luk
- Department of Health, Clinical Genetic Service, Kowloon Bay, Hong Kong
| | - Ivan Fai-Man Lo
- Department of Health, Clinical Genetic Service, Kowloon Bay, Hong Kong
| | - Chin Peng Lee
- Department of Obstetrics and Gynecology, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Brian Hon-Yin Chung
- Department of Obstetrics and Gynecology, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Anita Sik-Yau Kan
- Department of Obstetrics and Gynecology, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Sai Ying Pun, Hong Kong
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22
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McLaren TL, De Roach JN, Thompson JA, Chen FK, Mackey DA, Hoffmann L, Urwin IR, Lamey TM. Expanding the genetic spectrum of choroideremia in an Australian cohort: report of five novel CHM variants. Hum Genome Var 2020; 7:35. [PMID: 33110609 PMCID: PMC7584600 DOI: 10.1038/s41439-020-00122-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/04/2020] [Accepted: 09/11/2020] [Indexed: 12/23/2022] Open
Abstract
Choroideremia is an X-linked chorioretinal dystrophy caused by mutations in the CHM gene. Several CHM gene replacement clinical trials are in advanced stages. In this study, we report the molecular confirmation of choroideremia in 14 Australian families sourced from the Australian Inherited Retinal Disease Registry and DNA Bank. Sixteen males (14 symptomatic) and 18 females (4 symptomatic; 14 obligate carriers) were identified for analysis. Participants' DNA was analyzed for disease-causing CHM variants by Sanger sequencing, TaqMan qPCR and targeted NGS. We report phenotypic and genotypic data for the 14 symptomatic males and four females manifesting disease symptoms. A pathogenic or likely pathogenic CHM variant was detected in all families. Eight variants were previously reported, and five were novel. Two de novo variants were identified. We previously reported the molecular confirmation of choroideremia in 11 Australian families. This study expands the CHM genetically confirmed Australian cohort to 32 males and four affected carrier females.
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Affiliation(s)
- Terri L. McLaren
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia Australia
| | - John N. De Roach
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia Australia
| | - Jennifer A. Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia Australia
| | - Fred K. Chen
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia Australia
- Lions Eye Institute, 2 Verdun Street, Nedlands, Western Australia Australia
- Department of Ophthalmology, Royal Perth Hospital, Victoria Square, Perth, Western Australia Australia
- Department of Ophthalmology, Perth Children’s Hospital, Hospital Avenue, Nedlands, Western Australia Australia
| | - David A. Mackey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia Australia
- Lions Eye Institute, 2 Verdun Street, Nedlands, Western Australia Australia
| | - Ling Hoffmann
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia Australia
| | - Isabella R. Urwin
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia Australia
| | - Tina M. Lamey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, Western Australia Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, Western Australia Australia
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23
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[Mutation signatures in head and neck squamous cell carcinoma : Pathogenesis and therapeutic potential]. HNO 2020; 68:922-926. [PMID: 33044581 DOI: 10.1007/s00106-020-00954-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND The pathogenesis of head and neck squamous cell carcinoma (HNSCC) is a complex and multistage process which results from the interaction of exogenous and endogenous cellular processes. Each of these processes leaves a characteristic pattern of mutations on the tumor genome, a so-called mutational signature. STATE OF THE ART The subject of current studies is to decipher specific signatures of mutational processes operating during HNSCC pathogenesis and to address their prognostic value. Computational analysis of genomic sequencing data by The Cancer Genome Atlas (TCGA) revealed mutational signatures 1, 2, 4, 5, 7, and 13 as the main players in HNSCC pathogenesis. Signature 16 was first discovered in human papillomavirus (HPV)-negative oral and oropharyngeal tumors. In many studies, an association of signature 16 with alcohol and tobacco consumption as well as with an unfavorable prognosis was described.
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24
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Kuzmina NS, Luong TM, Rubanovich AV. Changes in DNA Methylation Induced by Dioxins and Dioxin-Like Compounds as Potential Predictor of Disease Risk. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420100063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Meyerson W, Leisman J, Navarro FCP, Gerstein M. Origins and characterization of variants shared between databases of somatic and germline human mutations. BMC Bioinformatics 2020; 21:227. [PMID: 32498674 PMCID: PMC7273669 DOI: 10.1186/s12859-020-3508-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/20/2020] [Indexed: 01/26/2023] Open
Abstract
Background Mutations arise in the human genome in two major settings: the germline and the soma. These settings involve different inheritance patterns, time scales, chromatin structures, and environmental exposures, all of which impact the resulting distribution of substitutions. Nonetheless, many of the same single nucleotide variants (SNVs) are shared between germline and somatic mutation databases, such as between the gnomAD database of 120,000 germline exomes and the TCGA database of 10,000 somatic exomes. Here, we sought to explain this overlap. Results After strict filtering to exclude common germline polymorphisms and sites with poor coverage or mappability, we found 336,987 variants shared between the somatic and germline databases. A uniform statistical model explains 34% of these shared variants; a model that incorporates the varying mutation rates of the basic mutation types explains another 50% of shared variants; and a model that includes extended nucleotide contexts (e.g. surrounding 3 bases on either side) explains an additional 4% of shared variants. Analysis of read depth finds mixed evidence that up to 4% of the shared variants may represent germline variants leaked into somatic call sets. 9% of the shared variants are not explained by any model. Sequencing errors and convergent evolution did not account for these. We surveyed other factors as well: Cancers driven by endogenous mutational processes share a greater fraction of variants with the germline, and recently derived germline variants were more likely to be somatically shared than were ancient germline ones. Conclusions Overall, we find that shared variants largely represent bona fide biological occurrences of the same variant in the germline and somatic setting and arise primarily because DNA has some of the same basic chemical vulnerabilities in either setting. Moreover, we find mixed evidence that somatic call-sets leak appreciable numbers of germline variants, which is relevant to genomic privacy regulations. In future studies, the similar chemical vulnerability of DNA between the somatic and germline settings might be used to help identify disease-related genes by guiding the development of background-mutation models that are informed by both somatic and germline patterns of variation.
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Affiliation(s)
- William Meyerson
- Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA. .,Yale School of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - John Leisman
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06510, USA
| | - Fabio C P Navarro
- Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA.,Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06511, USA
| | - Mark Gerstein
- Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA. .,Yale School of Medicine, Yale University, New Haven, CT, 06510, USA. .,Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06511, USA. .,Department of Computer Science, Yale University, New Haven, CT, 06511, USA.
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26
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Petljak M, Alexandrov LB, Brammeld JS, Price S, Wedge DC, Grossmann S, Dawson KJ, Ju YS, Iorio F, Tubio JMC, Koh CC, Georgakopoulos-Soares I, Rodríguez-Martín B, Otlu B, O'Meara S, Butler AP, Menzies A, Bhosle SG, Raine K, Jones DR, Teague JW, Beal K, Latimer C, O'Neill L, Zamora J, Anderson E, Patel N, Maddison M, Ng BL, Graham J, Garnett MJ, McDermott U, Nik-Zainal S, Campbell PJ, Stratton MR. Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis. Cell 2020; 176:1282-1294.e20. [PMID: 30849372 PMCID: PMC6424819 DOI: 10.1016/j.cell.2019.02.012] [Citation(s) in RCA: 256] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 09/19/2018] [Accepted: 01/27/2019] [Indexed: 12/20/2022]
Abstract
Multiple signatures of somatic mutations have been identified in cancer genomes. Exome sequences of 1,001 human cancer cell lines and 577 xenografts revealed most common mutational signatures, indicating past activity of the underlying processes, usually in appropriate cancer types. To investigate ongoing patterns of mutational-signature generation, cell lines were cultured for extended periods and subsequently DNA sequenced. Signatures of discontinued exposures, including tobacco smoke and ultraviolet light, were not generated in vitro. Signatures of normal and defective DNA repair and replication continued to be generated at roughly stable mutation rates. Signatures of APOBEC cytidine deaminase DNA-editing exhibited substantial fluctuations in mutation rate over time with episodic bursts of mutations. The initiating factors for the bursts are unclear, although retrotransposon mobilization may contribute. The examined cell lines constitute a resource of live experimental models of mutational processes, which potentially retain patterns of activity and regulation operative in primary human cancers. Annotation of mutational signatures across 1,001 cancer cell lines and 577 PDXs Activities of mutational processes determined over time in cancer cell lines APOBEC-associated mutagenesis is often ongoing and can be episodic Detection of mutational signatures by single-cell sequencing
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Affiliation(s)
- Mia Petljak
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ludmil B Alexandrov
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan S Brammeld
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Stacey Price
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David C Wedge
- Oxford Big Data Institute, Old Road Campus, Oxford OX3 7LF, UK; Oxford NIHR Biomedical Research Centre, Oxford, OX4 2PG, UK
| | - Sebastian Grossmann
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Kevin J Dawson
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Francesco Iorio
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jose M C Tubio
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; Mobile Genomes and Disease, Molecular Medicine and Chronic Diseases Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo 36310, Spain
| | - Ching Chiek Koh
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | - Bernardo Rodríguez-Martín
- Mobile Genomes and Disease, Molecular Medicine and Chronic Diseases Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo 36310, Spain
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sarah O'Meara
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Adam P Butler
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andrew Menzies
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Shriram G Bhosle
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Keiran Raine
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David R Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jon W Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Kathryn Beal
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Laura O'Neill
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jorge Zamora
- Mobile Genomes and Disease, Molecular Medicine and Chronic Diseases Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo 36310, Spain
| | - Elizabeth Anderson
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Nikita Patel
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mark Maddison
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Bee Ling Ng
- Cytometry Core Facility, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jennifer Graham
- Cytometry Core Facility, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mathew J Garnett
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ultan McDermott
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Serena Nik-Zainal
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
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Molecular Profiles and Metastasis Markers in Chinese Patients with Gastric Carcinoma. Sci Rep 2019; 9:13995. [PMID: 31570735 PMCID: PMC6769015 DOI: 10.1038/s41598-019-50171-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 09/06/2019] [Indexed: 02/08/2023] Open
Abstract
The goal of this work was to investigate the molecular profiles and metastasis markers in Chinese patients with gastric carcinoma (GC). In total, we performed whole exome sequencing (WES) on 74 GC patients with tumor and adjacent normal formalin-fixed, paraffin-embedded (FFPE) tissue samples. The mutation spectrum of these samples showed a high concordance with TCGA and other studies on GC. PTPRT is significantly associated with metastasis of GC, suggesting its predictive role in metastasis of GC. Patients carrying BRCA2 mutations tend not to metastasize, which may be related to their sensitivity to chemotherapy. Mutations in MACF1, CDC27, HMCN1, CDH1 and PDZD2 were moderately enriched in peritoneal metastasis (PM) samples. Furthermore, we found two genomic regions (1p36.21 and Xq26.3) were associated with PM of GC, and patients with amplification of 1p36.21 and Xq26.3 have a worse prognosis (P = 0.002, 0.01, respectively). Our analysis provides GC patients with potential markers for single and combination therapies.
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28
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Seymour DK, Gaut BS. Phylogenetic Shifts in Gene Body Methylation Correlate with Gene Expression and Reflect Trait Conservation. Mol Biol Evol 2019; 37:31-43. [DOI: 10.1093/molbev/msz195] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
A subset of genes in plant genomes are labeled with DNA methylation specifically at CG residues. These genes, known as gene-body methylated (gbM), have a number of associated characteristics. They tend to have longer sequences, to be enriched for intermediate expression levels, and to be associated with slower rates of molecular evolution. Most importantly, gbM genes tend to maintain their level of DNA methylation between species, suggesting that this trait is under evolutionary constraint. Given the degree of conservation in gbM, we still know surprisingly little about its function in plant genomes or whether gbM is itself a target of selection. To address these questions, we surveyed DNA methylation across eight grass (Poaceae) species that span a gradient of genome sizes. We first established that genome size correlates with genome-wide DNA methylation levels, but less so for genic levels. We then leveraged genomic data to identify a set of 2,982 putative orthologs among the eight species and examined shifts of methylation status for each ortholog in a phylogenetic context. A total of 55% of orthologs exhibited a shift in gbM, but these shifts occurred predominantly on terminal branches, indicating that shifts in gbM are rarely conveyed over time. Finally, we found that the degree of conservation of gbM across species is associated with increased gene length, reduced rates of molecular evolution, and increased gene expression level, but reduced gene expression variation across species. Overall, these observations suggest a basis for evolutionary pressure to maintain gbM status over evolutionary time.
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Affiliation(s)
- Danelle K Seymour
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA
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29
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Pfeifer GP, Szabó PE, Song J. Protein Interactions at Oxidized 5-Methylcytosine Bases. J Mol Biol 2019:S0022-2836(19)30501-7. [PMID: 31401118 DOI: 10.1016/j.jmb.2019.07.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/19/2022]
Abstract
5-Methylcytosine (5mC), the major modified DNA base in mammalian cells, can be oxidized enzymatically to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) by the Ten-Eleven-Translocation (TET) family of proteins. Whereas 5fC and 5caC are recognized and removed by base excision repair proteins, the 5hmC base accumulates to substantial levels in certain cell types such as brain-derived neurons and is viewed as a relatively stable DNA base. As such, the existence of "reader" proteins that recognize 5hmC would be a logical assumption, and various searches have been undertaken to identify proteins that specifically bind to 5hmC and the other oxidized 5mC bases. However, the existence of definitive 5hmC "readers" has remained unclear and proteins interacting specifically with 5fC or 5caC are also very few. On the other hand, 5hmC is incapable of interacting with a number of proteins that recognize 5mC at CpG sequences, suggesting that 5hmC is an anti-reader modification that may serve to displace 5mC readers from DNA. In this review article, we discuss candidate proteins that may interact with oxidized 5mC bases.
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Affiliation(s)
- Gerd P Pfeifer
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
| | - Piroska E Szabó
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jikui Song
- Department of Biochemistry, University of California Riverside, Riverside, CA 92521, USA
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30
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Wojtowicz D, Sason I, Huang X, Kim YA, Leiserson MDM, Przytycka TM, Sharan R. Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer. Genome Med 2019; 11:49. [PMID: 31349863 PMCID: PMC6660659 DOI: 10.1186/s13073-019-0659-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/12/2019] [Indexed: 12/19/2022] Open
Abstract
Knowing the activity of the mutational processes shaping a cancer genome may provide insight into tumorigenesis and personalized therapy. It is thus important to characterize the signatures of active mutational processes in patients from their patterns of single base substitutions. However, mutational processes do not act uniformly on the genome, leading to statistical dependencies among neighboring mutations. To account for such dependencies, we develop the first sequence-dependent model, SigMa, for mutation signatures. We apply SigMa to characterize genomic and other factors that influence the activity of mutation signatures in breast cancer. We show that SigMa outperforms previous approaches, revealing novel insights on signature etiology. The source code for SigMa is publicly available at https://github.com/lrgr/sigma.
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Affiliation(s)
- Damian Wojtowicz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, 20894, USA
| | - Itay Sason
- School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Xiaoqing Huang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, 20894, USA
| | - Yoo-Ah Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, 20894, USA
| | - Mark D M Leiserson
- Center for Bioinformatics and Computational Biology, University of Maryland, 8125 Paint Branch Dr, College Park, 20740, USA.
| | - Teresa M Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, 20894, USA.
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel.
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31
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Gardner HL, Sivaprakasam K, Briones N, Zismann V, Perdigones N, Drenner K, Facista S, Richholt R, Liang W, Aldrich J, Trent JM, Shields PG, Robinson N, Johnson J, Lana S, Houghton P, Fenger J, Lorch G, Janeway KA, London CA, Hendricks WPD. Canine osteosarcoma genome sequencing identifies recurrent mutations in DMD and the histone methyltransferase gene SETD2. Commun Biol 2019; 2:266. [PMID: 31341965 PMCID: PMC6642146 DOI: 10.1038/s42003-019-0487-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/29/2019] [Indexed: 02/08/2023] Open
Abstract
Osteosarcoma (OS) is a rare, metastatic, human adolescent cancer that also occurs in pet dogs. To define the genomic underpinnings of canine OS, we performed multi-platform analysis of OS tumors from 59 dogs, including whole genome sequencing (n = 24) and whole exome sequencing (WES; n = 13) of primary tumors and matched normal tissue, WES (n = 10) of matched primary/metastatic/normal samples and RNA sequencing (n = 54) of primary tumors. We found that canine OS recapitulates features of human OS including low point mutation burden (median 1.98 per Mb) with a trend towards higher burden in metastases, high structural complexity, frequent TP53 (71%), PI3K pathway (37%), and MAPK pathway mutations (17%), and low expression of immune-associated genes. We also identified novel features of canine OS including putatively inactivating somatic SETD2 (42%) and DMD (50%) aberrations. These findings set the stage for understanding OS development in dogs and humans, and establish genomic contexts for future comparative analyses.
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Affiliation(s)
- Heather L. Gardner
- Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111 USA
| | | | - Natalia Briones
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Victoria Zismann
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | | | - Kevin Drenner
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | | | - Ryan Richholt
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Winnie Liang
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Jessica Aldrich
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Jeffrey M. Trent
- Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Peter G. Shields
- College of Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Nicholas Robinson
- Cummings School of Veterinary Medicine, Tufts University, Grafton, MA 01536 USA
| | | | - Susan Lana
- Colorado State University, Fort Collins, CO 80525 USA
| | - Peter Houghton
- University of Texas Health Science Center, San Antonio, TX 78229 USA
| | - Joelle Fenger
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - Gwendolen Lorch
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, OH 43210 USA
| | | | - Cheryl A. London
- Cummings School of Veterinary Medicine, Tufts University, Grafton, MA 01536 USA
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32
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Ren Y, Huang S, Dai C, Xie D, Zheng L, Xie H, Zheng H, She Y, Zhou F, Wang Y, Li P, Fei K, Jiang G, Zhang Y, Su B, Sweet-Cordero EA, Tran NL, Yang Y, Patel JN, Rolfo C, Rocco G, Cardona AF, Tuzi A, Suter MB, Yang P, Xu W, Chen C. Germline Predisposition and Copy Number Alteration in Pre-stage Lung Adenocarcinomas Presenting as Ground-Glass Nodules. Front Oncol 2019; 9:288. [PMID: 31058088 PMCID: PMC6482264 DOI: 10.3389/fonc.2019.00288] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/29/2019] [Indexed: 12/11/2022] Open
Abstract
Objective: Synchronous multiple ground-glass nodules (SM-GGNs) are a distinct entity of lung cancer which has been emerging increasingly in recent years in China. The oncogenesis molecular mechanisms of SM-GGNs remain elusive. Methods: We investigated single nucleotide variations (SNV), insertions and deletions (INDEL), somatic copy number variations (CNV), and germline mutations of 69 SM-GGN samples collected from 31 patients, using target sequencing (TRS) and whole exome sequencing (WES). Results: In the entire cohort, many known driver mutations were found, including EGFR (21.7%), BRAF (14.5%), and KRAS (6%). However, only one out of the 31 patients had the same somatic missense or truncated events within SM-GGNs, indicating the independent origins for almost all of these SM-GGNs. Many germline mutations with a low frequency in the Chinese population, and genes harboring both germline and somatic variations, were discovered in these pre-stage GGNs. These GGNs also bore large segments of copy number gains and/or losses. The CNV segment number tended to be positively correlated with the germline mutations (r = 0.57). The CNV sizes were correlated with the somatic mutations (r = 0.55). A moderate correlation (r = 0.54) was also shown between the somatic and germline mutations. Conclusion: Our data suggests that the precancerous unstable CNVs with potentially predisposing genetic backgrounds may foster the onset of driver mutations and the development of independent SM-GGNs during the local stimulation of mutagens.
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Affiliation(s)
- Yijiu Ren
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shujun Huang
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Chenyang Dai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dong Xie
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Larry Zheng
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Huikang Xie
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hui Zheng
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yunlang She
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fangyu Zhou
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yue Wang
- Novogene Bioinformatics Technology Institute, Beijing, China
| | - Pengpeng Li
- Novogene Bioinformatics Technology Institute, Beijing, China
| | - Ke Fei
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yang Zhang
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Bo Su
- Laboratory center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - E Alejandro Sweet-Cordero
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Nhan Le Tran
- Departments of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Yanan Yang
- Thoracic Disease Research Unit, Division of Pulmonary and Critical Care Medicine, Developmental Therapeutics and Cell Biology Programs, Department of Biochemistry and Molecular Biology, Mayo Clinic Cancer Center, Mayo Clinic, Rochester, MN, United States
| | - Jai N Patel
- Division of Hematology/Oncology, Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, United States
| | - Christian Rolfo
- Thoracic Medical Oncology, Experimental Therapeutics Research Program, Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, United States
| | - Gaetano Rocco
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York City, NY, United States
| | - Andrés Felipe Cardona
- Thoracic Oncology Unit, Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia
| | | | | | - Ping Yang
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Wayne Xu
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada.,College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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33
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Liu S, Aageaard A, Bechsgaard J, Bilde T. DNA Methylation Patterns in the Social Spider, Stegodyphus dumicola. Genes (Basel) 2019; 10:E137. [PMID: 30759892 PMCID: PMC6409797 DOI: 10.3390/genes10020137] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
Variation in DNA methylation patterns among genes, individuals, and populations appears to be highly variable among taxa, but our understanding of the functional significance of this variation is still incomplete. We here present the first whole genome bisulfite sequencing of a chelicerate species, the social spider Stegodyphus dumicola. We show that DNA methylation occurs mainly in CpG context and is concentrated in genes. This is a pattern also documented in other invertebrates. We present RNA sequence data to investigate the role of DNA methylation in gene regulation and show that, within individuals, methylated genes are more expressed than genes that are not methylated and that methylated genes are more stably expressed across individuals than unmethylated genes. Although no causal association is shown, this lends support for the implication of DNA CpG methylation in regulating gene expression in invertebrates. Differential DNA methylation between populations showed a small but significant correlation with differential gene expression. This is consistent with a possible role of DNA methylation in local adaptation. Based on indirect inference of the presence and pattern of DNA methylation in chelicerate species whose genomes have been sequenced, we performed a comparative phylogenetic analysis. We found strong evidence for exon DNA methylation in the horseshoe crab Limulus polyphemus and in all spider and scorpion species, while most Parasitiformes and Acariformes species seem to have lost DNA methylation.
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Affiliation(s)
- Shenglin Liu
- Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.
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34
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Sa JK, Choi SW, Zhao J, Lee Y, Zhang J, Kong DS, Choi JW, Seol HJ, Lee JI, Iavarone A, Rabadan R, Nam DH. Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations. Int J Cancer 2019; 144:3023-3030. [PMID: 30536544 PMCID: PMC6590456 DOI: 10.1002/ijc.32054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/06/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022]
Abstract
Hypermutagenesis refers to marked increase in the number of mutations due to continuous mutagenic process. Hypermutated tumors, have being found in several tumor types, are associated with inherited or acquired alterations in the DNA repair pathways. Hypermutation has been observed in a subset of adult glioma patients as a direct result of temozolomide(TMZ)-induced mutagenesis. In our study, we have identified a rare subset of treatment-naïve adult gliomas with de novo hypermutator phenotype and explored the evolution of spontaneous and treatment-induced hypermutagenesis. We conducted Whole-Exome Sequencing (WES), Whole-Transcriptome Sequencing (WTS), and Single-Cell Sequencing (SCS) of TMZ-naïve and post-TMZ-treated hypermutated tumors to identify distinct clinical or genomic manifestations that contribute to the development of hypermutation in untreated adult gliomas. TMZ-naïve hypermutated tumors were marked by absence of IDH1 somatic mutation and MGMT promoter (pMGMT) methylation, two genomic traits that were significantly associated with the TMZ-induced hypermutagenic event in glioblastoma, and harbored inherited alterations in the mismatch repair (MMR) machinery. The immediate family members of the TMZ-naive hypermutated glioma patients were also previous diagnosed with cancer development history, suggesting that germline dysfunction of the MMR pathway could potentially pose hereditary risk to genetic predisposition of carcinogenesis in gliomas. Lastly, both TMZ-naïve and post-TMZ-treated hypermutated tumors exhibited a significant accumulation of neoantigen loads, suggesting immunotherapeutic alternatives. Our results present new and unique understanding of hypermutagenic process in adult gliomas and an important step towards clinical implication of immunotherapy in glioma treatment.
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Affiliation(s)
- Jason K Sa
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea.,Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Seung Won Choi
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea.,Deparment of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Junfei Zhao
- Department of Systems Biology, Columbia University, New York, New York, USA.,Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Yeri Lee
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea.,Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Jing Zhang
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Doo-Sik Kong
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jung Won Choi
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ho Jun Seol
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jung-Il Lee
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, New York, New York, USA.,Department of Pathology, Columbia University, New York, New York, USA.,Department of Neurology, Columbia University, New York, New York, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, New York, USA.,Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea.,Deparment of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea.,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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35
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Keogh MJ, Wei W, Aryaman J, Walker L, van den Ameele J, Coxhead J, Wilson I, Bashton M, Beck J, West J, Chen R, Haudenschild C, Bartha G, Luo S, Morris CM, Jones NS, Attems J, Chinnery PF. High prevalence of focal and multi-focal somatic genetic variants in the human brain. Nat Commun 2018; 9:4257. [PMID: 30323172 PMCID: PMC6189186 DOI: 10.1038/s41467-018-06331-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/30/2018] [Indexed: 12/16/2022] Open
Abstract
Somatic mutations during stem cell division are responsible for several cancers. In principle, a similar process could occur during the intense cell proliferation accompanying human brain development, leading to the accumulation of regionally distributed foci of mutations. Using dual platform >5000-fold depth sequencing of 102 genes in 173 adult human brain samples, we detect and validate somatic mutations in 27 of 54 brains. Using a mathematical model of neurodevelopment and approximate Bayesian inference, we predict that macroscopic islands of pathologically mutated neurons are likely to be common in the general population. The detected mutation spectrum also includes DNMT3A and TET2 which are likely to have originated from blood cell lineages. Together, these findings establish developmental mutagenesis as a potential mechanism for neurodegenerative disorders, and provide a novel mechanism for the regional onset and focal pathology in sporadic cases.
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Affiliation(s)
- Michael J Keogh
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Wei Wei
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Juvid Aryaman
- Department of Mathematics, Imperial College London, London, SW7 2AZ, UK
| | - Lauren Walker
- Institute of Neuroscience, Newcastle University, Campus for Aging and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Jelle van den Ameele
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Jon Coxhead
- Institute of Genetic Medicine, Central Parkway, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, UK
| | - Ian Wilson
- Institute of Genetic Medicine, Central Parkway, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, UK
| | - Matthew Bashton
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Jon Beck
- Personalis Inc, 1330O'Brien Dr, Menlo Park, CA, 94025, USA
| | - John West
- Personalis Inc, 1330O'Brien Dr, Menlo Park, CA, 94025, USA
| | - Richard Chen
- Personalis Inc, 1330O'Brien Dr, Menlo Park, CA, 94025, USA
| | | | - Gabor Bartha
- Personalis Inc, 1330O'Brien Dr, Menlo Park, CA, 94025, USA
| | - Shujun Luo
- Personalis Inc, 1330O'Brien Dr, Menlo Park, CA, 94025, USA
| | - Chris M Morris
- Institute of Neuroscience, Newcastle University, Campus for Aging and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Nick S Jones
- Department of Mathematics, Imperial College London, London, SW7 2AZ, UK
- EPSRC Centre for Mathematics of Precision Healthcare, Imperial College London, London, SW7 2AZ, UK
| | - Johannes Attems
- Institute of Neuroscience, Newcastle University, Campus for Aging and Vitality, Newcastle upon Tyne, NE4 5PL, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK.
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36
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Le Thi Thanh H, Do Thi Diem T, Duy CV, Thanh HLT, Phuong HBT, Thanh LN. Spectrum of MECP2 mutations in Vietnamese patients with RETT syndrome. BMC MEDICAL GENETICS 2018; 19:137. [PMID: 30081849 PMCID: PMC6090653 DOI: 10.1186/s12881-018-0658-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/30/2018] [Indexed: 11/29/2022]
Abstract
Background Rett syndrome (RTT) is a severe neurodevelopmental disorder in children characterized by a normal neurodevelopmental process in the first 6–18 months followed by a period of motor and vocal deterioration with stereotypic hand movements. Incidence of RTT is mostly due to de novo mutation in the MECP2 gene (methyl-CpG-binding protein 2). Methods The study assessed 27 female patients presented with classical RTT phenotype age range from 18 months to 48 months. Specialist carried out the clinical evaluation and diagnosis according to RTT diagnosis criteria. Blood samples from patients were then collected for genomic DNA extraction. We next performed MECP2 gene amplification and sequencing of the whole coding region to screen for mutations. Result MECP2 mutation was found in 20 patients (74%) including: 2 missense, 4 nonsense, 6 frameshift and 2 deletion mutation. The study identified 14 pathogenic mutations which we found 4 mutation, to our knowledge and extensive search, not priory reported in any mutation database or publication: c.1384-1385DelGT, c.1205insT, c.717delC and c.1132_1207del77. High percentage of C > T (70%) in CpG sites mutation was found. Conclusion Our result reveals a high percentage of C > T mutation in CpG hot spot, which is more prone to modification and more likely to be detected in RTT as a disorder is strictly due to de novo mutations. The study is the first to identify the mutation spectrum of MECP2 gene in Vietnamese patients and also an important step toward better diagnosis and care for RTT patients in Vietnam.
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Affiliation(s)
- Huong Le Thi Thanh
- Department of Gene Technology - Vinmec Research Institute of Stem cell and Gene Technology, 458 Minh Khai Street, Hanoi, Hai Ba Trung district, Vietnam.
| | - Trinh Do Thi Diem
- Department of Gene Technology - Vinmec Research Institute of Stem cell and Gene Technology, 458 Minh Khai Street, Hanoi, Hai Ba Trung district, Vietnam
| | - Chinh Vu Duy
- Vinmec International Hospital, 458 Minh Khai Street, Hai Ba Trung District, Hanoi, Vietnam
| | - Ha Ly Thi Thanh
- Department of Gene Technology - Vinmec Research Institute of Stem cell and Gene Technology, 458 Minh Khai Street, Hanoi, Hai Ba Trung district, Vietnam
| | - Hoa Bui Thi Phuong
- Department of Gene Technology - Vinmec Research Institute of Stem cell and Gene Technology, 458 Minh Khai Street, Hanoi, Hai Ba Trung district, Vietnam
| | - Liem Nguyen Thanh
- Department of Gene Technology - Vinmec Research Institute of Stem cell and Gene Technology, 458 Minh Khai Street, Hanoi, Hai Ba Trung district, Vietnam
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37
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Alexeeva M, Guragain P, Tesfahun AN, Tomkuvienė M, Arshad A, Gerasimaitė R, Rukšėnaitė A, Urbanavičiūtė G, Bjørås M, Laerdahl JK, Klungland A, Klimašauskas S, Bjelland S. Excision of the doubly methylated base N4,5-dimethylcytosine from DNA by Escherichia coli Nei and Fpg proteins. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170337. [PMID: 29685966 PMCID: PMC5915725 DOI: 10.1098/rstb.2017.0337] [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] [Accepted: 01/30/2018] [Indexed: 12/21/2022] Open
Abstract
Cytosine (C) in DNA is often modified to 5-methylcytosine (m5C) to execute important cellular functions. Despite the significance of m5C for epigenetic regulation in mammals, damage to m5C has received little attention. For instance, almost no studies exist on erroneous methylation of m5C by alkylating agents to doubly or triply methylated bases. Owing to chemical evidence, and because many prokaryotes express methyltransferases able to convert m5C into N4,5-dimethylcytosine (m N4,5C) in DNA, m N4,5C is probably present in vivo We screened a series of glycosylases from prokaryotic to human and found significant DNA incision activity of the Escherichia coli Nei and Fpg proteins at m N4,5C residues in vitro The activity of Nei was highest opposite cognate guanine followed by adenine, thymine (T) and C. Fpg-complemented Nei by exhibiting the highest activity opposite C followed by lower activity opposite T. To our knowledge, this is the first description of a repair enzyme activity at a further methylated m5C in DNA, as well as the first alkylated base allocated as a Nei or Fpg substrate. Based on our observed high sensitivity to nuclease S1 digestion, we suggest that m N4,5C occurs as a disturbing lesion in DNA and that Nei may serve as a major DNA glycosylase in E. coli to initiate its repair.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Marina Alexeeva
- Department of Chemistry, Bioscience and Environmental Technology-Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, PO Box 8600 Forus, 4021 Stavanger, Norway
| | - Prashanna Guragain
- Department of Chemistry, Bioscience and Environmental Technology-Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, PO Box 8600 Forus, 4021 Stavanger, Norway
| | - Almaz N Tesfahun
- Department of Chemistry, Bioscience and Environmental Technology-Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, PO Box 8600 Forus, 4021 Stavanger, Norway
| | - Miglė Tomkuvienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Aysha Arshad
- Department of Chemistry, Bioscience and Environmental Technology-Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, PO Box 8600 Forus, 4021 Stavanger, Norway
| | - Rūta Gerasimaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Audronė Rukšėnaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Giedrė Urbanavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Magnar Bjørås
- Institute for Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Jon K Laerdahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Svein Bjelland
- Department of Chemistry, Bioscience and Environmental Technology-Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, PO Box 8600 Forus, 4021 Stavanger, Norway
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38
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Pfeifer GP. Defining Driver DNA Methylation Changes in Human Cancer. Int J Mol Sci 2018; 19:ijms19041166. [PMID: 29649096 PMCID: PMC5979276 DOI: 10.3390/ijms19041166] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 12/11/2022] Open
Abstract
Human malignant tumors are characterized by pervasive changes in the patterns of DNA methylation. These changes include a globally hypomethylated tumor cell genome and the focal hypermethylation of numerous 5′-cytosine-phosphate-guanine-3′ (CpG) islands, many of them associated with gene promoters. It has been challenging to link specific DNA methylation changes with tumorigenesis in a cause-and-effect relationship. Some evidence suggests that cancer-associated DNA hypomethylation may increase genomic instability. Promoter hypermethylation events can lead to silencing of genes functioning in pathways reflecting hallmarks of cancer, including DNA repair, cell cycle regulation, promotion of apoptosis or control of key tumor-relevant signaling networks. A convincing argument for a tumor-driving role of DNA methylation can be made when the same genes are also frequently mutated in cancer. Many of the most commonly hypermethylated genes encode developmental transcription factors, the methylation of which may lead to permanent gene silencing. Inactivation of such genes will deprive the cells in which the tumor may initiate from the option of undergoing or maintaining lineage differentiation and will lock them into a perpetuated stem cell-like state thus providing an additional window for cell transformation.
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Affiliation(s)
- Gerd P Pfeifer
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA.
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39
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Huang Y, Gu L, Li GM. H3K36me3-mediated mismatch repair preferentially protects actively transcribed genes from mutation. J Biol Chem 2018; 293:7811-7823. [PMID: 29610279 DOI: 10.1074/jbc.ra118.002839] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 03/26/2018] [Indexed: 01/01/2023] Open
Abstract
Histone H3 trimethylation at lysine 36 (H3K36me3) is an important histone mark involved in both transcription elongation and DNA mismatch repair (MMR). It is known that H3K36me3 recruits the mismatch-recognition protein MutSα to replicating chromatin via its physical interaction with MutSα's PWWP domain, but the exact role of H3K36me3 in transcription is undefined. Using ChIP combined with whole-genome DNA sequencing analysis, we demonstrate here that H3K36me3, together with MutSα, is involved in protecting against mutation, preferentially in actively transcribed genomic regions. We found that H3K36me3 and MutSα are much more co-enriched in exons and actively transcribed regions than in introns and nontranscribed regions. The H3K36me3-MutSα co-enrichment correlated with a much lower mutation frequency in exons and actively transcribed regions than in introns and nontranscribed regions. Correspondingly, depleting H3K36me3 or disrupting the H3K36me3-MutSα interaction elevated the spontaneous mutation frequency in actively transcribed genes, but it had little influence on the mutation frequency in nontranscribed or transcriptionally inactive regions. Similarly, H2O2-induced mutations, which mainly cause base oxidations, preferentially occurred in actively transcribed genes in MMR-deficient cells. The data presented here suggest that H3K36me3-mediated MMR preferentially safeguards actively transcribed genes not only during replication by efficiently correcting mispairs in early replicating chromatin but also during transcription by directly or indirectly removing DNA lesions associated with a persistently open chromatin structure.
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Affiliation(s)
- Yaping Huang
- From the Department of Basic Medical Sciences, Tsinghua University School of Medicine, 100084 Beijing, China and
| | - Liya Gu
- the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Guo-Min Li
- From the Department of Basic Medical Sciences, Tsinghua University School of Medicine, 100084 Beijing, China and .,the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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40
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Lavi E, Carmel L. Alu exaptation enriches the human transcriptome by introducing new gene ends. RNA Biol 2018; 15:715-725. [PMID: 29493382 DOI: 10.1080/15476286.2018.1429880] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In mammals, transposable elements are largely silenced, but under fortuitous circumstances may be co-opted to play a functional role. Here, we show that when Alu elements are inserted within or nearby genes in sense orientation, they may contribute to the transcriptome diversity by forming new cleavage and polyadenylation sites. We mapped these new gene ends in human onto the Alu sequence and identified three hotspots of cleavage and polyadenylation site formation. Interestingly, the native Alu sequence does not contain any canonical polyadenylation signal. We therefore studied what evolutionary processes might explain the formation of these specific hotspots of novel gene ends. We show that two of the three hotspots might have emerged from mutational processes that turned sequences that resemble polyadenylation signals into full-blown canonical signals, whereas one hotspot is tightly linked to the process of Alu insertion into the genome. Overall, Alu elements may lie behind the formation of 302 new gene end variants, affecting a total of 243 genes. Intergenic Alu elements may elongate genes by creating a downstream cleavage site, intronic Alu elements may lead to gene variants which code for truncated proteins, and 3'UTR Alu elements may result in gene variants with alternative 3'UTR.
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Affiliation(s)
- Eitan Lavi
- a Department of Genetics , The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem , Jerusalem , Israel
| | - Liran Carmel
- a Department of Genetics , The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem , Jerusalem , Israel
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41
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Sa JK, Lee IH, Hong SD, Kong DS, Nam DH. Genomic and transcriptomic characterization of skull base chordoma. Oncotarget 2018; 8:1321-1328. [PMID: 27901492 PMCID: PMC5352057 DOI: 10.18632/oncotarget.13616] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/08/2016] [Indexed: 11/25/2022] Open
Abstract
Skull base chordoma is a primary rare malignant bone-origin tumor showing relatively slow growth pattern and locally destructive lesions, which can only be characterized by histologic components. There is no available prognostic or therapeutic biomarker to predict clinical outcome or treatment response and the molecular mechanisms underlying chordoma development still remain unexplored. Therefore, we sought out to identify novel somatic variations that are associated with chordoma progression and potentially employed as therapeutic targets. Thirteen skull base chordomas were subjected for whole-exome and/or whole-transcriptome sequencing. In process, we have identified chromosomal aberration in 1p, 7, 10, 13 and 17q, high frequency of functional germline SNP of the T gene, rs2305089 (P = 0.0038) and several recurrent alterations including MUC4, NBPF1, NPIPB15 mutations and novel gene fusion of SAMD5-SASH1 for the first time in skull base chordoma.
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Affiliation(s)
- Jason K Sa
- Graduate School of Health Science & Technology, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul, Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
| | - In-Hee Lee
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
| | - Sang Duk Hong
- Department of Otorhinolaryngology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Doo-Sik Kong
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea.,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Do-Hyun Nam
- Graduate School of Health Science & Technology, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul, Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea.,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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42
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Mutational signatures and chromosome alteration profiles of squamous cell carcinomas of the vulva. Exp Mol Med 2018; 50:e442. [PMID: 29422544 PMCID: PMC5903820 DOI: 10.1038/emm.2017.265] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/30/2017] [Accepted: 09/04/2017] [Indexed: 12/30/2022] Open
Abstract
Vulvar squamous cell carcinoma (SCC) consists of two different etiologic categories: human papilloma virus (HPV)-associated (HPV (+)) and HPV-non-associated (HPV (−)). There have been no genome-wide studies on the genetic alterations of vulvar SCCs or on the differences between HPV (+) and HPV (−) vulvar SCCs. In this study, we performed whole-exome sequencing and copy number profiling of 6 HPV (+) and 9 HPV (−) vulvar SCCs and found known mutations (TP53, CDKN2A and HRAS) and copy number alterations (CNAs) (7p and 8q gains and 2q loss) in HPV (−) SCCs. In HPV (+), we found novel mutations in PIK3CA, BRCA2 and FBXW7 that had not been reported in vulvar SCCs. HPV (−) SCCs exhibited more mutational loads (numbers of nonsilent mutations and driver mutations) than HPV (+) SCCs, but the CNA loads and mutation signatures between HPV (+) and HPV (−) SCCs did not differ. Of note, 40% and 40% of the 15 vulvar SCCs harbored PIK3CA and FAT1 alterations, respectively. In addition, we found that the SCCs harbored kataegis (a localized hypermutation) in 2 HPV (+) SCCs and copy-neutral losses of heterozygosity in 4 (one HPV (+) and 3 HPV (−)) SCCs. Our data indicate that HPV (+) and HPV (−) vulvar SCCs may have different mutation and CNA profiles but that there are genomic features common to SCCs. Our data provide useful information for both HPV (+) and HPV (−) vulvar SCCs and may aid in the development of clinical treatment strategies.
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43
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Ling L, Chen L, Zhang C, Gui S, Zhao H, Li Z. High glucose induces podocyte epithelial‑to‑mesenchymal transition by demethylation‑mediated enhancement of MMP9 expression. Mol Med Rep 2018; 17:5642-5651. [PMID: 29436620 PMCID: PMC5866005 DOI: 10.3892/mmr.2018.8554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 10/30/2017] [Indexed: 01/13/2023] Open
Abstract
Abnormal expression of matrix metalloproteinase 9 (MMP9) is correlated with podocyte epithelial-to-mesenchymal transition (EMT) in diabetic nephropathy (DN). However, the mechanisms underlying this process are not well defined. Site-specific demethylation may sustain high expression levels of target genes. In the present study, in order to investigate the association between DNA demethylation of MMP9 promoter and podocyte EMT in DN, human podocytes were cultured in high-glucose (HG) medium and a rat model of DN was established by intraperitoneal injection of streptozotocin (STZ) to determine whether site-specific demethylation of the MMP9 promoter was involved in regulating podocyte EMT in DN. The MTT assay was used to assess the effects of HG culture on the growth of podocytes, and the demethylation status of the MMP9 promoter was assessed by bisulfite sequencing polymerase chain reaction. mRNA and protein expression levels of MMP9, α-smooth muscle actin (α-SMA), podocalyxin and fibronectin-1 in podocytes were assessed by reverse transcription-quantitative PCR (RT-qPCR) and western blot analyses. The results demonstrated that HG treatment up regulated the expression of MMP9, α-SMA and fibronectin-1, but down regulated the expression of podocalyxin in podocytes. The MMP9 promoter region was revealed to contain a variety of demethylated CpG sites, and HG treatment reduced the rate of MMP9 promotermethylation, which, in turn, enhanced its promoter activity. In summary, these data suggested that demethylation of the MMP9 promoter may serve an important role in podocyte EMT in DN. The demethylation status of the MMP9 promoter maybe used as an important prognostic marker of DN in clinic.
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Affiliation(s)
- Li Ling
- Department of Endocrinology, Guangdong Medical College Affiliated Shenzhen Nanshan Hospital, Shenzhen, Guangdong 518052, P.R. China
| | - Libo Chen
- Department of Endocrinology, Guangdong Medical College Affiliated Shenzhen Nanshan Hospital, Shenzhen, Guangdong 518052, P.R. China
| | - Changning Zhang
- Department of Endocrinology, Guangdong Medical College Affiliated Shenzhen Nanshan Hospital, Shenzhen, Guangdong 518052, P.R. China
| | - Shuyan Gui
- Department of Endocrinology, Guangdong Medical College Affiliated Shenzhen Nanshan Hospital, Shenzhen, Guangdong 518052, P.R. China
| | - Haiyan Zhao
- Department of Endocrinology, Guangdong Medical College Affiliated Shenzhen Nanshan Hospital, Shenzhen, Guangdong 518052, P.R. China
| | - Zhengzhang Li
- Department of Endocrinology, Guangdong Medical College Affiliated Shenzhen Nanshan Hospital, Shenzhen, Guangdong 518052, P.R. China
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44
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Dao P, Kim YA, Wojtowicz D, Madan S, Sharan R, Przytycka TM. BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions. PLoS Comput Biol 2017; 13:e1005695. [PMID: 29023534 PMCID: PMC5638227 DOI: 10.1371/journal.pcbi.1005695] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 07/25/2017] [Indexed: 12/12/2022] Open
Abstract
The analysis of the mutational landscape of cancer, including mutual exclusivity and co-occurrence of mutations, has been instrumental in studying the disease. We hypothesized that exploring the interplay between co-occurrence, mutual exclusivity, and functional interactions between genes will further improve our understanding of the disease and help to uncover new relations between cancer driving genes and pathways. To this end, we designed a general framework, BeWith, for identifying modules with different combinations of mutation and interaction patterns. We focused on three different settings of the BeWith schema: (i) BeME-WithFun, in which the relations between modules are enriched with mutual exclusivity, while genes within each module are functionally related; (ii) BeME-WithCo, which combines mutual exclusivity between modules with co-occurrence within modules; and (iii) BeCo-WithMEFun, which ensures co-occurrence between modules, while the within module relations combine mutual exclusivity and functional interactions. We formulated the BeWith framework using Integer Linear Programming (ILP), enabling us to find optimally scoring sets of modules. Our results demonstrate the utility of BeWith in providing novel information about mutational patterns, driver genes, and pathways. In particular, BeME-WithFun helped identify functionally coherent modules that might be relevant for cancer progression. In addition to finding previously well-known drivers, the identified modules pointed to other novel findings such as the interaction between NCOR2 and NCOA3 in breast cancer. Additionally, an application of the BeME-WithCo setting revealed that gene groups differ with respect to their vulnerability to different mutagenic processes, and helped us to uncover pairs of genes with potentially synergistic effects, including a potential synergy between mutations in TP53 and the metastasis related DCC gene. Overall, BeWith not only helped us uncover relations between potential driver genes and pathways, but also provided additional insights on patterns of the mutational landscape, going beyond cancer driving mutations. Implementation is available at https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/software/bewith.html The genomic landscape of cancer obtained from large scale studies revealed mutational patterns such as mutual exclusivity and co-occurrences. Despite significant efforts, the understanding of the patterns harbored by specific genes and their interplay with functional interactions are still limited. Both mutual exclusivity and co-occurrence can arise due to several reasons. For example, two functionally interacting genes may dysregulate the same cancer related pathway when either of them is mutated, leading to mutually exclusive mutations. Alternatively, mutual exclusivity might reflect mutations specific to two different cancer types. Methods for joint analysis of co-occurrence, mutual exclusivity, and functional interaction relationships can lead to a better understanding of the causes and impacts of mutations in cancer. We report a new computational approach, BeWith, which identifies groups of genes (or gene modules) with coherent patterns within modules, but distinct properties among genes in different modules. The general formulation of our method allows us to investigate various aspects of the cancer mutational landscape, leading to uncovering relationships between mutated gene modules, cancer subtypes, and mutational signatures.
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Affiliation(s)
- Phuong Dao
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, United States of America
| | - Yoo-Ah Kim
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, United States of America
| | - Damian Wojtowicz
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, United States of America
| | - Sanna Madan
- Department of Computer Science, University of Maryland, College Park, MD, United States of America
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (RS); (TMP)
| | - Teresa M. Przytycka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, United States of America
- * E-mail: (RS); (TMP)
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45
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Poulos RC, Olivier J, Wong JWH. The interaction between cytosine methylation and processes of DNA replication and repair shape the mutational landscape of cancer genomes. Nucleic Acids Res 2017; 45:7786-7795. [PMID: 28531315 PMCID: PMC5737810 DOI: 10.1093/nar/gkx463] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/15/2017] [Indexed: 12/31/2022] Open
Abstract
Methylated cytosines (5mCs) are frequently mutated in the genome. However, no studies have yet comprehensively analysed mutation–methylation associations across cancer types. Here we analyse 916 cancer genomes, together with tissue type-specific methylation and replication timing data. We describe a strong mutation–methylation association across colorectal cancer subtypes, most interestingly in samples with microsatellite instability (MSI) or Polymerase epsilon (POLE) exonuclease domain mutations. By analysing genomic regions with differential mismatch repair (MMR) efficiency, we suggest a possible role for MMR in the correction of 5mC deamination events, potentially accounting for the high rate of 5mC mutation accumulation in MSI tumours. Additionally, we propose that mutant POLE asserts a mutator phenotype specifically at 5mCs, and we find coding mutation hotspots in POLE-mutant cancers at highly-methylated CpGs in the tumour-suppressor genes APC and TP53. Finally, using multivariable regression models, we demonstrate that different cancers exhibit distinct mutation–methylation associations, with DNA repair influencing such associations in certain cancer genomes. Taken together, we find differential associations with methylation that are vital for accurately predicting expected mutation loads across cancer types. Our findings reveal links between methylation and common mutation and repair processes, with these mechanisms defining a key part of the mutational landscape of cancer genomes.
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Affiliation(s)
- Rebecca C Poulos
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, NSW 2052, Australia
| | - Jake Olivier
- School of Mathematics and Statistics, The Red Centre, UNSW Sydney, NSW 2052, Australia
| | - Jason W H Wong
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, NSW 2052, Australia
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46
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Kohmoto T, Masuda K, Naruto T, Tange S, Shoda K, Hamada J, Saito M, Ichikawa D, Tajima A, Otsuji E, Imoto I. Construction of a combinatorial pipeline using two somatic variant calling methods for whole exome sequence data of gastric cancer. THE JOURNAL OF MEDICAL INVESTIGATION 2017; 64:233-240. [PMID: 28954988 DOI: 10.2152/jmi.64.233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
High-throughput next-generation sequencing is a powerful tool to identify the genotypic landscapes of somatic variants and therapeutic targets in various cancers including gastric cancer, forming the basis for personalized medicine in the clinical setting. Although the advent of many computational algorithms leads to higher accuracy in somatic variant calling, no standard method exists due to the limitations of each method. Here, we constructed a new pipeline. We combined two different somatic variant callers with different algorithms, Strelka and VarScan 2, and evaluated performance using whole exome sequencing data obtained from 19 Japanese cases with gastric cancer (GC); then, we characterized these tumors based on identified driver molecular alterations. More single nucleotide variants (SNVs) and small insertions/deletions were detected by Strelka and VarScan 2, respectively. SNVs detected by both tools showed higher accuracy for estimating somatic variants compared with those detected by only one of the two tools and accurately showed the mutation signature and mutations of driver genes reported for GC. Our combinatorial pipeline may have an advantage in detection of somatic mutations in GC and may be useful for further genomic characterization of Japanese patients with GC to improve the efficacy of GC treatments. J. Med. Invest. 64: 233-240, August, 2017.
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Affiliation(s)
- Tomohiro Kohmoto
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University
| | - Kiyoshi Masuda
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University
| | - Takuya Naruto
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University
| | - Shoichiro Tange
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University
| | - Katsutoshi Shoda
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University.,Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine
| | - Junichi Hamada
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University.,Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine
| | - Masako Saito
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University
| | - Daisuke Ichikawa
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine
| | - Atsushi Tajima
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University.,Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University
| | - Eigo Otsuji
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine
| | - Issei Imoto
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University
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47
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Sollis E, Deriziotis P, Saitsu H, Miyake N, Matsumoto N, Hoffer MJV, Ruivenkamp CAL, Alders M, Okamoto N, Bijlsma EK, Plomp AS, Fisher SE. Equivalent missense variant in the FOXP2 and FOXP1 transcription factors causes distinct neurodevelopmental disorders. Hum Mutat 2017; 38:1542-1554. [PMID: 28741757 DOI: 10.1002/humu.23303] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 07/11/2017] [Accepted: 07/22/2017] [Indexed: 12/28/2022]
Abstract
The closely related paralogues FOXP2 and FOXP1 encode transcription factors with shared functions in the development of many tissues, including the brain. However, while mutations in FOXP2 lead to a speech/language disorder characterized by childhood apraxia of speech (CAS), the clinical profile of FOXP1 variants includes a broader neurodevelopmental phenotype with global developmental delay, intellectual disability, and speech/language impairment. Using clinical whole-exome sequencing, we report an identical de novo missense FOXP1 variant identified in three unrelated patients. The variant, p.R514H, is located in the forkhead-box DNA-binding domain and is equivalent to the well-studied p.R553H FOXP2 variant that cosegregates with CAS in a large UK family. We present here for the first time a direct comparison of the molecular and clinical consequences of the same mutation affecting the equivalent residue in FOXP1 and FOXP2. Detailed functional characterization of the two variants in cell model systems revealed very similar molecular consequences, including aberrant subcellular localization, disruption of transcription factor activity, and deleterious effects on protein interactions. Nonetheless, clinical manifestations were broader and more severe in the three cases carrying the p.R514H FOXP1 variant than in individuals with the p.R553H variant related to CAS, highlighting divergent roles of FOXP2 and FOXP1 in neurodevelopment.
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Affiliation(s)
- Elliot Sollis
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Pelagia Deriziotis
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mariëlle Alders
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Astrid S Plomp
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
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48
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Dou Y, Yang X, Li Z, Wang S, Zhang Z, Ye AY, Yan L, Yang C, Wu Q, Li J, Zhao B, Huang AY, Wei L. Postzygotic single-nucleotide mosaicisms contribute to the etiology of autism spectrum disorder and autistic traits and the origin of mutations. Hum Mutat 2017; 38:1002-1013. [PMID: 28503910 PMCID: PMC5518181 DOI: 10.1002/humu.23255] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/01/2023]
Abstract
The roles and characteristics of postzygotic single‐nucleotide mosaicisms (pSNMs) in autism spectrum disorders (ASDs) remain unclear. In this study of the whole exomes of 2,361 families in the Simons Simplex Collection, we identified 1,248 putative pSNMs in children and 285 de novo SNPs in children with detectable parental mosaicism. Ultra‐deep amplicon resequencing suggested a validation rate of 51%. Analyses of validated pSNMs revealed that missense/loss‐of‐function (LoF) pSNMs with a high mutant allele fraction (MAF≥ 0.2) contributed to ASD diagnoses (P = 0.022, odds ratio [OR] = 5.25), whereas missense/LoF pSNMs with a low MAF (MAF<0.2) contributed to autistic traits in male non‐ASD siblings (P = 0.033). LoF pSNMs in parents were less likely to be transmitted to offspring than neutral pSNMs (P = 0.037), and missense/LoF pSNMs in parents with a low MAF were transmitted more to probands than to siblings (P = 0.016, OR = 1.45). We estimated that pSNMs in probands or de novo mutations inherited from parental pSNMs increased the risk of ASD by approximately 6%. Adding pSNMs into the transmission and de novo association test model revealed 13 new ASD risk genes. These results expand the existing repertoire of genes involved in ASD and shed new light on the contribution of genomic mosaicisms to ASD diagnoses and autistic traits.
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Affiliation(s)
- Yanmei Dou
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Xiaoxu Yang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Ziyi Li
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Sheng Wang
- National Institute of Biological Sciences, Beijing, China.,College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zheng Zhang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Adam Yongxin Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Linlin Yan
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Changhong Yang
- National Institute of Biological Sciences, Beijing, China.,College of Life Sciences Beijing Normal University, Beijing, China
| | - Qixi Wu
- Peking-Tsinghua Center for Life Sciences, Beijing, China.,Human Genetic Resources Core Facility, School of Life Sciences, Peking University, Beijing, China
| | - Jiarui Li
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Boxun Zhao
- National Institute of Biological Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - August Yue Huang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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49
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Abstract
Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation.
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Affiliation(s)
- Daniel Zilberman
- John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK.
- University of California, 211 Koshland Hall, Berkeley, CA, 94720, USA.
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50
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Weaver ICG, Korgan AC, Lee K, Wheeler RV, Hundert AS, Goguen D. Stress and the Emerging Roles of Chromatin Remodeling in Signal Integration and Stable Transmission of Reversible Phenotypes. Front Behav Neurosci 2017; 11:41. [PMID: 28360846 PMCID: PMC5350110 DOI: 10.3389/fnbeh.2017.00041] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/24/2017] [Indexed: 01/02/2023] Open
Abstract
The influence of early life experience and degree of parental-infant attachment on emotional development in children and adolescents has been comprehensively studied. Structural and mechanistic insight into the biological foundation and maintenance of mammalian defensive systems (metabolic, immune, nervous and behavioral) is slowly advancing through the emerging field of developmental molecular (epi)genetics. Initial evidence revealed that differential nurture early in life generates stable differences in offspring hypothalamic-pituitary-adrenal (HPA) regulation, in part, through chromatin remodeling and changes in DNA methylation of specific genes expressed in the brain, revealing physical, biochemical and molecular paths for the epidemiological concept of gene-environment interactions. Herein, a primary molecular mechanism underpinning the early developmental programming and lifelong maintenance of defensive (emotional) responses in the offspring is the alteration of chromatin domains of specific genomic regions from a condensed state (heterochromatin) to a transcriptionally accessible state (euchromatin). Conversely, DNA methylation promotes the formation of heterochromatin, which is essential for gene silencing, genomic integrity and chromosome segregation. Therefore, inter-individual differences in chromatin modifications and DNA methylation marks hold great potential for assessing the impact of both early life experience and effectiveness of intervention programs—from guided psychosocial strategies focused on changing behavior to pharmacological treatments that target chromatin remodeling and DNA methylation enzymes to dietary approaches that alter cellular pools of metabolic intermediates and methyl donors to affect nutrient bioavailability and metabolism. In this review article, we discuss the potential molecular mechanism(s) of gene regulation associated with chromatin modeling and programming of endocrine (e.g., HPA and metabolic or cardiovascular) and behavioral (e.g., fearfulness, vigilance) responses to stress, including alterations in DNA methylation and the role of DNA repair machinery. From parental history (e.g., drugs, housing, illness, nutrition, socialization) to maternal-offspring exchanges of nutrition, microbiota, antibodies and stimulation, the nature of nurture provides not only mechanistic insight into how experiences propagate from external to internal variables, but also identifies a composite therapeutic target, chromatin modeling, for gestational/prenatal stress, adolescent anxiety/depression and adult-onset neuropsychiatric disease.
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Affiliation(s)
- Ian C G Weaver
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Austin C Korgan
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Kristen Lee
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Ryan V Wheeler
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Amos S Hundert
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Donna Goguen
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
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