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https://www.readbyqxmd.com/read/29925043/molecular-characterization-and-putative-pathogenic-pathways-of-tuberous-sclerosis-complex-associated-renal-cell-carcinoma
#1
Jeong Hwan Park, Cheol Lee, Mee Soo Chang, Kwangsoo Kim, Seongmin Choi, Hyunjung Lee, Hyun-Seob Lee, Kyung Chul Moon
Tuberous sclerosis complex-associated renal cell carcinoma (TSC-RCC) has distinct clinical and histopathologic features and is considered a specific subtype of RCC. The genetic alterations of TSC1 or TSC2 are responsible for the development of TSC. In this study, we assessed the mTOR pathway activation and aimed to evaluate molecular characteristics and pathogenic pathways of TSC-RCC. Two cases of TSC-RCC, one from a 31-year-old female and the other from an 8-year-old male, were assessed. The mTOR pathway activation was determined by immunohistochemistry...
June 17, 2018: Translational Oncology
https://www.readbyqxmd.com/read/29920279/dual-requirement-of-chd8-for-chromatin-landscape-establishment-and-histone-methyltransferase-recruitment-to-promote-cns-myelination-and-repair
#2
Chuntao Zhao, Chen Dong, Magali Frah, Yaqi Deng, Corentine Marie, Feng Zhang, Lingli Xu, Zhixing Ma, Xinran Dong, Yifeng Lin, Scott Koenig, Brahim Nait-Oumesmar, Donna M Martin, Laiman N Wu, Mei Xin, Wenhao Zhou, Carlos Parras, Q Richard Lu
Disruptive mutations in chromatin remodeler CHD8 cause autism spectrum disorders, exhibiting widespread white matter abnormalities; however, the underlying mechanisms remain elusive. We show that cell-type specific Chd8 deletion in oligodendrocyte progenitors, but not in neurons, results in myelination defects, revealing a cell-intrinsic dependence on CHD8 for oligodendrocyte lineage development, myelination and post-injury remyelination. CHD8 activates expression of BRG1-associated SWI/SNF complexes that in turn activate CHD7, thus initiating a successive chromatin remodeling cascade that orchestrates oligodendrocyte lineage progression...
June 18, 2018: Developmental Cell
https://www.readbyqxmd.com/read/29768199/the-autism-related-protein-chd8-cooperates-with-c-ebp%C3%AE-to-regulate-adipogenesis
#3
Yasuyuki Kita, Yuta Katayama, Taichi Shiraishi, Takeru Oka, Tetsuya Sato, Mikita Suyama, Yasuyuki Ohkawa, Keishi Miyata, Yuichi Oike, Michiko Shirane, Masaaki Nishiyama, Keiichi I Nakayama
The gene encoding the chromatin remodeler CHD8 is the most frequently mutated gene in individuals with autism spectrum disorder (ASD). Heterozygous mutations in CHD8 give rise to ASD that is often accompanied by macrocephaly, gastrointestinal complaints, and slender habitus. Whereas most phenotypes of CHD8 haploinsufficiency likely result from delayed neurodevelopment, the mechanism underlying slender habitus has remained unknown. Here, we show that CHD8 interacts with CCAAT/enhancer-binding protein β (C/EBPβ) and promotes its transactivation activity during adipocyte differentiation...
May 15, 2018: Cell Reports
https://www.readbyqxmd.com/read/29668850/altered-neocortical-gene-expression-brain-overgrowth-and-functional-over-connectivity-in-chd8-haploinsufficient-mice
#4
Philipp Suetterlin, Shaun Hurley, Conor Mohan, Kimberley L H Riegman, Marco Pagani, Angela Caruso, Jacob Ellegood, Alberto Galbusera, Ivan Crespo-Enriquez, Caterina Michetti, Yohan Yee, Robert Ellingford, Olivier Brock, Alessio Delogu, Philippa Francis-West, Jason P Lerch, Maria Luisa Scattoni, Alessandro Gozzi, Cathy Fernandes, M Albert Basson
Truncating CHD8 mutations are amongst the highest confidence risk factors for autism spectrum disorder (ASD) identified to date. Here, we report that Chd8 heterozygous mice display increased brain size, motor delay, hypertelorism, pronounced hypoactivity, and anomalous responses to social stimuli. Whereas gene expression in the neocortex is only mildly affected at midgestation, over 600 genes are differentially expressed in the early postnatal neocortex. Genes involved in cell adhesion and axon guidance are particularly prominent amongst the downregulated transcripts...
June 1, 2018: Cerebral Cortex
https://www.readbyqxmd.com/read/29545257/advanced-whole-genome-sequencing-and-analysis-of-fetal-genomes-from-amniotic-fluid
#5
Qing Mao, Robert Chin, Weiwei Xie, Yuqing Deng, Wenwei Zhang, Huixin Xu, Rebecca Yu Zhang, Quan Shi, Erin E Peters, Natali Gulbahce, Zhenyu Li, Fang Chen, Radoje Drmanac, Brock A Peters
BACKGROUND: Amniocentesis is a common procedure, the primary purpose of which is to collect cells from the fetus to allow testing for abnormal chromosomes, altered chromosomal copy number, or a small number of genes that have small single- to multibase defects. Here we demonstrate the feasibility of generating an accurate whole-genome sequence of a fetus from either the cellular or cell-free DNA (cfDNA) of an amniotic sample. METHODS: cfDNA and DNA isolated from the cell pellet of 31 amniocenteses were sequenced to approximately 50× genome coverage by use of the Complete Genomics nanoarray platform...
April 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29486199/loss-of-chromatin-remodeling-proteins-and-or-cdkn2a-associates-with-metastasis-of-pancreatic-neuroendocrine-tumors-and-reduced-patient-survival-times
#6
Somak Roy, William A LaFramboise, Ta-Chiang Liu, Dengfeng Cao, Alyssa Luvison, Caitlyn Miller, Maureen A Lyons, Roderick J O'Sullivan, Amer H Zureikat, Melissa E Hogg, Allan Tsung, Kenneth K Lee, Nathan Bahary, Randall E Brand, Jennifer S Chennat, Kenneth E Fasanella, Kevin McGrath, Marina N Nikiforova, Georgios I Papachristou, Adam Slivka, Herbert J Zeh, Aatur D Singhi
Despite prognostic grading and staging systems, it is a challenge to predict outcomes for patients with pancreatic neuroendocrine tumors (PanNETs). Sequencing studies of PanNETs have identified alterations in death domain-associated protein (DAXX) and alpha-thalassemia/mental retardation X-linked chromatin remodeler (ATRX). In tumors, mutations in DAXX or ATRX and corresponding loss of protein expression correlate with shorter times of disease-free survival and disease-specific survival of patients. However, DAXX or ATRX proteins were lost in only 50% of distant metastases analyzed...
March 2, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29438503/lineage-specific-transcription-factors-and-epigenetic-regulators-mediate-tgf%C3%AE-dependent-enhancer-activation
#7
Raquel Fueyo, Simona Iacobucci, Stella Pappa, Conchi Estarás, Sergio Lois, Marta Vicioso-Mantis, Claudia Navarro, Sara Cruz-Molina, José Carlos Reyes, Álvaro Rada-Iglesias, Xavier de la Cruz, Marian A Martínez-Balbás
During neurogenesis, dynamic developmental cues, transcription factors and histone modifying enzymes regulate the gene expression programs by modulating the activity of neural-specific enhancers. How transient developmental signals coordinate transcription factor recruitment to enhancers and to which extent chromatin modifiers contribute to enhancer activity is starting to be uncovered. Here, we take advantage of neural stem cells as a model to unravel the mechanisms underlying neural enhancer activation in response to the TGFβ signaling...
February 9, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29317598/enriched-expression-of-genes-associated-with-autism-spectrum-disorders-in-human-inhibitory-neurons
#8
Ping Wang, Dejian Zhao, Herbert M Lachman, Deyou Zheng
Autism spectrum disorder (ASD) is highly heritable but genetically heterogeneous. The affected neural circuits and cell types remain unclear and may vary at different developmental stages. By analyzing multiple sets of human single cell transcriptome profiles, we found that ASD candidates showed relatively enriched gene expression in neurons, especially in inhibitory neurons. ASD candidates were also more likely to be the hubs of the co-expression gene module that is highly expressed in inhibitory neurons, a feature not detected for excitatory neurons...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29158550/exome-pool-seq-in-neurodevelopmental-disorders
#9
Bernt Popp, Arif B Ekici, Christian T Thiel, Juliane Hoyer, Antje Wiesener, Cornelia Kraus, André Reis, Christiane Zweier
High throughput sequencing has greatly advanced disease gene identification, especially in heterogeneous entities. Despite falling costs this is still an expensive and laborious technique, particularly when studying large cohorts. To address this problem we applied Exome Pool-Seq as an economic and fast screening technology in neurodevelopmental disorders (NDDs). Sequencing of 96 individuals can be performed in eight pools of 12 samples on less than one Illumina sequencer lane. In a pilot study with 96 cases we identified 27 variants, likely or possibly affecting function...
December 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29098713/large-scale-automated-function-prediction-of-protein-sequences-and-an-experimental-case-study-validation-on-pten-transcript-variants
#10
Ahmet Sureyya Rifaioglu, Tunca Doğan, Ömer Sinan Saraç, Tulin Ersahin, Rabie Saidi, Mehmet Volkan Atalay, Maria Jesus Martin, Rengul Cetin-Atalay
Recent advances in computing power and machine learning empower functional annotation of protein sequences and their transcript variations. Here, we present an automated prediction system UniGOPred, for GO annotations and a database of GO term predictions for proteomes of several organisms in UniProt Knowledgebase (UniProtKB). UniGOPred provides function predictions for 514 molecular function (MF), 2909 biological process (BP), and 438 cellular component (CC) GO terms for each protein sequence. UniGOPred covers nearly the whole functionality spectrum in Gene Ontology system and it can predict both generic and specific GO terms...
February 2018: Proteins
https://www.readbyqxmd.com/read/29079706/genome-wide-association-study-identified-copy-number-variants-associated-with-sporadic-colorectal-cancer-risk
#11
Lai Fun Thean, Yee Syuen Low, Michelle Lo, Yik-Ying Teo, Woon-Puay Koh, Jian-Min Yuan, Min Hoe Chew, Choong Leong Tang, Peh Yean Cheah
BACKGROUND: Multiple single nucleotide polymorphisms (SNPs) have been associated with colorectal cancer (CRC) risk. The role of structural or copy number variants (CNV) in CRC, however, remained unclear. We investigated the role of CNVs in patients with sporadic CRC. METHODS: A genome-wide association study (GWAS) was performed on 1000 Singapore Chinese patients aged 50 years or more with no family history of CRC and 1000 ethnicity-matched, age-matched and gender-matched healthy controls using the Affymetrix SNP 6 platform...
March 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29079199/chd8short-a-naturally-occurring-truncated-form-of-a-chromatin-remodeler-lacking-the-helicase-domain-is-a-potent-transcriptional-coregulator
#12
Gary R Kunkel, Jessica A Tracy, Frank L Jalufka, Arne C Lekven
Chromodomain-Helicase-DNA binding protein 8 (CHD8) is a member of a large family of eukaryotic ATP-dependent chromatin remodeling complexes. Loss of function alleles of human chd8 are correlated with autism spectrum disorder. The CHD subfamily members contain a tandem pair of chromodomains that are adjacent to a centrally located Snf2-like helicase domain. An alternatively spliced variant mRNA of CHD8 was identified years ago in mammals that encode a truncated form of the protein, called Duplin, that lacks the helicase domain and everything else in the carboxyl direction...
January 30, 2018: Gene
https://www.readbyqxmd.com/read/29034068/clinical-phenotype-of-asd-associated-dyrk1a-haploinsufficiency
#13
Rachel K Earl, Tychele N Turner, Heather C Mefford, Caitlin M Hudac, Jennifer Gerdts, Evan E Eichler, Raphael A Bernier
BACKGROUND: DYRK1A is a gene recurrently disrupted in 0.1-0.5% of the ASD population. A growing number of case reports with DYRK1A haploinsufficiency exhibit common phenotypic features including microcephaly, intellectual disability, speech delay, and facial dysmorphisms. METHODS: Phenotypic information from previously published DYRK1A cases ( n  = 51) and participants in an ongoing study at the University of Washington (UW, n  = 10) were compiled. Frequencies of recurrent phenotypic features in this population were compared to features observed in a large sample with idiopathic ASD from the Simons Simplex Collection ( n  = 1981)...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28867767/arid1b-haploinsufficiency-causes-abnormal-brain-gene-expression-and-autism-related-behaviors-in-mice
#14
Mihiro Shibutani, Takuro Horii, Hirotaka Shoji, Sumiyo Morita, Mika Kimura, Naomi Terawaki, Tsuyoshi Miyakawa, Izuho Hatada
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with core symptoms that include poor social communication, restricted interests, and repetitive behaviors. Several ASD mouse models exhibit impaired social interaction, anxiety-like behavior, and elevated perseveration. Large-scale whole exome sequencing studies identified many genes putatively associated with ASD. Like chromodomain helicase DNA binding protein 8 (CHD8), the most frequently mutated gene in individuals with ASD, the candidate gene AT-rich interaction domain 1B (ARID1B) encodes a chromatin remodeling factor...
August 30, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28840378/panel-sequencing-of-264-candidate-susceptibility-genes-and-segregation-analysis-in-a-cohort-of-non-brca1-non-brca2-breast-cancer-families
#15
Jun Li, Hongyan Li, Igor Makunin, Bryony A Thompson, Kayoko Tao, Erin L Young, Jacqueline Lopez, Nicola J Camp, Sean V Tavtigian, Esther M John, Irene L Andrulis, Kum Kum Khanna, David Goldgar, Georgia Chenevix-Trench
PURPOSE: The main aim of this study was to screen epigenetic modifier genes and known breast cancer driver genes for germline mutations in non-BRCA1/2 (BRCAx) breast cancer families in order to identify novel susceptibility genes of moderate-high penetrance. METHODS: We screened 264 candidate susceptibility genes in 656 index cases from non-BRCA1/2 families. Potentially pathogenic candidate mutations were then genotyped in all available family members for the assessment of co-segregation of the variant with disease in the family in order to estimate the breast cancer risks associated with these mutations...
December 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28831199/targeted-sequencing-and-functional-analysis-reveal-brain-size-related-genes-and-their-networks-in-autism-spectrum-disorders
#16
Jinchen Li, Lin Wang, Hui Guo, Leisheng Shi, Kun Zhang, Meina Tang, Shanshan Hu, Shanshan Dong, Yanling Liu, Tianyun Wang, Ping Yu, Xin He, Zhengmao Hu, Jinping Zhao, Chunyu Liu, Zhong Sheng Sun, Kun Xia
Autism spectrum disorder (ASD) represents a set of complex neurodevelopmental disorders with large degrees of heritability and heterogeneity. We sequenced 136 microcephaly or macrocephaly (Mic-Mac)-related genes and 158 possible ASD-risk genes in 536 Chinese ASD probands and detected 22 damaging de novo mutations (DNMs) in 20 genes, including CHD8 and SCN2A, with recurrent events. Nine of the 20 genes were previously reported to harbor DNMs in ASD patients from other populations, while 11 of them were first identified in present study...
September 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28781807/amplification-of-the-nsd3-brd4-chd8-pathway-in-pelvic-high-grade-serous-carcinomas-of-tubo-ovarian-and-endometrial-origin
#17
Derek H Jones, Douglas I Lin
Identification of novel therapeutics in pelvic high-grade serous carcinoma (HGSC) has been hampered by a paucity of actionable point mutations in target genes. The aim of the present study was to investigate the extent of amplification of the therapeutically targetable NSD3-CHD8-BRD4 pathway in pelvic HGSC, and to determine whether amplification is associated with worse prognosis. The Cancer Genome Atlas (TCGA) ovarian and endometrial cancer cohorts were retrospectively analyzed via online data-mining tools to test the association of NSD3, CHD8 and BRD4 genomic alterations with survival of pelvic HGSC patients...
August 2017: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/28671691/germline-chd8-haploinsufficiency-alters-brain-development-in-mouse
#18
Andrea L Gompers, Linda Su-Feher, Jacob Ellegood, Nycole A Copping, M Asrafuzzaman Riyadh, Tyler W Stradleigh, Michael C Pride, Melanie D Schaffler, A Ayanna Wade, Rinaldo Catta-Preta, Iva Zdilar, Shreya Louis, Gaurav Kaushik, Brandon J Mannion, Ingrid Plajzer-Frick, Veena Afzal, Axel Visel, Len A Pennacchio, Diane E Dickel, Jason P Lerch, Jacqueline N Crawley, Konstantinos S Zarbalis, Jill L Silverman, Alex S Nord
The chromatin remodeling gene CHD8 represents a central node in neurodevelopmental gene networks implicated in autism. We examined the impact of germline heterozygous frameshift Chd8 mutation on neurodevelopment in mice. Chd8+/del5 mice displayed normal social interactions with no repetitive behaviors but exhibited cognitive impairment correlated with increased regional brain volume, validating that phenotypes of Chd8+/del5 mice overlap pathology reported in humans with CHD8 mutations. We applied network analysis to characterize neurodevelopmental gene expression, revealing widespread transcriptional changes in Chd8+/del5 mice across pathways disrupted in neurodevelopmental disorders, including neurogenesis, synaptic processes and neuroimmune signaling...
August 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28584888/autism-spectrum-disorder-neuropathology-and-animal-models
#19
REVIEW
Merina Varghese, Neha Keshav, Sarah Jacot-Descombes, Tahia Warda, Bridget Wicinski, Dara L Dickstein, Hala Harony-Nicolas, Silvia De Rubeis, Elodie Drapeau, Joseph D Buxbaum, Patrick R Hof
Autism spectrum disorder (ASD) has a major impact on the development and social integration of affected individuals and is the most heritable of psychiatric disorders. An increase in the incidence of ASD cases has prompted a surge in research efforts on the underlying neuropathologic processes. We present an overview of current findings in neuropathology studies of ASD using two investigational approaches, postmortem human brains and ASD animal models, and discuss the overlap, limitations, and significance of each...
October 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28533432/the-atp-dependent-chromatin-remodeling-enzymes-chd6-chd7-and-chd8-exhibit-distinct-nucleosome-binding-and-remodeling-activities
#20
COMPARATIVE STUDY
Benjamin J Manning, Timur Yusufzai
Proper chromatin regulation is central to genome function and maintenance. The group III chromodomain-helicase-DNA-binding (CHD) family of ATP-dependent chromatin remodeling enzymes, comprising CHD6, CHD7, CHD8, and CHD9, has well-documented roles in transcription regulation, impacting both organism development and disease etiology. These four enzymes are similar in their constituent domains, but they fill surprisingly non-redundant roles in the cell, with deficiencies in individual enzymes leading to dissimilar disease states such as CHARGE syndrome or autism spectrum disorders...
July 14, 2017: Journal of Biological Chemistry
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