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Brancato D, Bruno F, Coniglio E, Sturiale V, Saccone S, Federico C. The Chromatin Organization Close to SNP rs12913832, Involved in Eye Color Variation, Is Evolutionary Conserved in Vertebrates. Int J Mol Sci 2024; 25:6602. [PMID: 38928306 PMCID: PMC11204186 DOI: 10.3390/ijms25126602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The most significant genetic influence on eye color pigmentation is attributed to the intronic SNP rs12913832 in the HERC2 gene, which interacts with the promoter region of the contiguous OCA2 gene. This interaction, through the formation of a chromatin loop, modulates the transcriptional activity of OCA2, directly affecting eye color pigmentation. Recent advancements in technology have elucidated the precise spatial organization of the genome within the cell nucleus, with chromatin architecture playing a pivotal role in regulating various genome functions. In this study, we investigated the organization of the chromatin close to the HERC2/OCA2 locus in human lymphocyte nuclei using fluorescence in situ hybridization (FISH) and high-throughput chromosome conformation capture (Hi-C) data. The 3 Mb of genomic DNA that belonged to the chromosomal region 15q12-q13.1 revealed the presence of three contiguous chromatin loops, which exhibited a different level of compaction depending on the presence of the A or G allele in the SNP rs12913832. Moreover, the analysis of the genomic organization of the genes has demonstrated that this chromosomal region is evolutionarily highly conserved, as evidenced by the analysis of syntenic regions in species from other Vertebrate classes. Thus, the role of rs12913832 variant is relevant not only in determining the transcriptional activation of the OCA2 gene but also in the chromatin compaction of a larger region, underscoring the critical role of chromatin organization in the proper regulation of the involved genes. It is crucial to consider the broader implications of this finding, especially regarding the potential regulatory role of similar polymorphisms located within intronic regions, which do not influence the same gene by modulating the splicing process, but they regulate the expression of adjacent genes. Therefore, caution should be exercised when utilizing whole-exome sequencing for diagnostic purposes, as intron sequences may provide valuable gene regulation information on the region where they reside. Thus, future research efforts should also be directed towards gaining a deeper understanding of the precise mechanisms underlying the role and mode of action of intronic SNPs in chromatin loop organization and transcriptional regulation.
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Affiliation(s)
| | | | | | | | - Salvatore Saccone
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (F.B.); (E.C.); (V.S.); (C.F.)
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Tritto V, Bettinaglio P, Mangano E, Cesaretti C, Marasca F, Castronovo C, Bordoni R, Battaglia C, Saletti V, Ranzani V, Bodega B, Eoli M, Natacci F, Riva P. Genetic/epigenetic effects in NF1 microdeletion syndrome: beyond the haploinsufficiency, looking at the contribution of not deleted genes. Hum Genet 2024; 143:775-795. [PMID: 38874808 PMCID: PMC11186880 DOI: 10.1007/s00439-024-02683-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
NF1 microdeletion syndrome, accounting for 5-11% of NF1 patients, is caused by a deletion in the NF1 region and it is generally characterized by a severe phenotype. Although 70% of NF1 microdeletion patients presents the same 1.4 Mb type-I deletion, some patients may show additional clinical features. Therefore, the contribution of several pathogenic mechanisms, besides haploinsufficiency of some genes within the deletion interval, is expected and needs to be defined. We investigated an altered expression of deletion flanking genes by qPCR in patients with type-1 NF1 deletion, compared to healthy donors, possibly contributing to the clinical traits of NF1 microdeletion syndrome. In addition, the 1.4-Mb deletion leads to changes in the 3D chromatin structure in the 17q11.2 region. Specifically, this deletion alters DNA-DNA interactions in the regions flanking the breakpoints, as demonstrated by our 4C-seq analysis. This alteration likely causes position effect on the expression of deletion flanking genes.Interestingly, 4C-seq analysis revealed that in microdeletion patients, an interaction was established between the RHOT1 promoter and the SLC6A4 gene, which showed increased expression. We performed NGS on putative modifier genes, and identified two "likely pathogenic" rare variants in RAS pathway, possibly contributing to incidental phenotypic features.This study provides new insights into understanding the pathogenesis of NF1 microdeletion syndrome and suggests a novel pathomechanism that contributes to the expression phenotype in addition to haploinsufficiency of genes located within the deletion.This is a pivotal approach that can be applied to unravel microdeletion syndromes, improving precision medicine, prognosis and patients' follow-up.
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Affiliation(s)
- Viviana Tritto
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy
| | - Paola Bettinaglio
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy
| | - Eleonora Mangano
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Claudia Cesaretti
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Federica Marasca
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Chiara Castronovo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Roberta Bordoni
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Cristina Battaglia
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Valeria Ranzani
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Beatrice Bodega
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
- Department of Biosciences (DBS), University of Milan, Milan, Italy
| | - Marica Eoli
- Molecular Neuroncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Federica Natacci
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy.
| | - Paola Riva
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy.
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3
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Schmitz D, Li Z, Lo Faro V, Rask-Andersen M, Ameur A, Rafati N, Johansson Å. Copy number variations and their effect on the plasma proteome. Genetics 2023; 225:iyad179. [PMID: 37793096 PMCID: PMC10697815 DOI: 10.1093/genetics/iyad179] [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: 08/25/2023] [Revised: 08/25/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
Structural variations, including copy number variations (CNVs), affect around 20 million bases in the human genome and are common causes of rare conditions. CNVs are rarely investigated in complex disease research because most CNVs are not targeted on the genotyping arrays or the reference panels for genetic imputation. In this study, we characterize CNVs in a Swedish cohort (N = 1,021) using short-read whole-genome sequencing (WGS) and use long-read WGS for validation in a subcohort (N = 15), and explore their effect on 438 plasma proteins. We detected 184,182 polymorphic CNVs and identified 15 CNVs to be associated with 16 proteins (P < 8.22×10-10). Of these, 5 CNVs could be perfectly validated using long-read sequencing, including a CNV which was associated with measurements of the osteoclast-associated immunoglobulin-like receptor (OSCAR) and located upstream of OSCAR, a gene important for bone health. Two other CNVs were identified to be clusters of many short repetitive elements and another represented a complex rearrangement including an inversion. Our findings provide insights into the structure of common CNVs and their effects on the plasma proteome, and highlights the importance of investigating common CNVs, also in relation to complex diseases.
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Affiliation(s)
- Daniel Schmitz
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Zhiwei Li
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Valeria Lo Faro
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Mathias Rask-Andersen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Nima Rafati
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
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Davis O. Abnormal Chromatin Folding in the Molecular Pathogenesis of Epilepsy and Autism Spectrum Disorder: a Meta-synthesis with Systematic Searching. Mol Neurobiol 2023; 60:768-779. [PMID: 36367658 PMCID: PMC9849311 DOI: 10.1007/s12035-022-03106-9] [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: 07/25/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022]
Abstract
How DNA is folded and packaged in nucleosomes is an essential regulator of gene expression. Abnormal patterns of chromatin folding are implicated in a wide range of diseases and disorders, including epilepsy and autism spectrum disorder (ASD). These disorders are thought to have a shared pathogenesis involving an imbalance in the number of excitatory-inhibitory neurons formed during neurodevelopment; however, the underlying pathological mechanism behind this imbalance is poorly understood. Studies are increasingly implicating abnormal chromatin folding in neural stem cells as one of the candidate pathological mechanisms, but no review has yet attempted to summarise the knowledge in this field. This meta-synthesis is a systematic search of all the articles on epilepsy, ASD, and chromatin folding. Its two main objectives were to determine to what extent abnormal chromatin folding is implicated in the pathogenesis of epilepsy and ASD, and secondly how abnormal chromatin folding leads to pathological disease processes. This search produced 22 relevant articles, which together strongly implicate abnormal chromatin folding in the pathogenesis of epilepsy and ASD. A range of mutations and chromosomal structural abnormalities lead to this effect, including single nucleotide polymorphisms, copy number variants, translocations and mutations in chromatin modifying. However, knowledge is much more limited into how abnormal chromatin organisation subsequently causes pathological disease processes, not yet showing, for example, whether it leads to abnormal excitation-inhibitory neuron imbalance in human brain organoids.
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Affiliation(s)
- Oliver Davis
- grid.5335.00000000121885934Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
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Chen CY, Seward CH, Song Y, Inamdar M, Leddy AM, Zhang H, Yoo J, Kao WC, Pawlowski H, Stubbs LJ. Galnt17 loss-of-function leads to developmental delay and abnormal coordination, activity, and social interactions with cerebellar vermis pathology. Dev Biol 2022; 490:155-171. [PMID: 36002036 PMCID: PMC10671221 DOI: 10.1016/j.ydbio.2022.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/30/2022]
Abstract
GALNT17 encodes a N-acetylgalactosaminyltransferase (GalNAc-T) protein specifically involved in mucin-type O-linked glycosylation of target proteins, a process important for cell adhesion, cell signaling, neurotransmitter activity, neurite outgrowth, and neurite sensing. GALNT17, also known as WBSCR17, is located at the edge of the Williams-Beuren Syndrome (WBS) critical region and adjacent to the AUTS2 locus, genomic regions associated with neurodevelopmental phenotypes that are thought to be co-regulated. Although previous data have implicated Galnt17 in neurodevelopment, the in vivo functions of this gene have not been investigated. In this study, we have analyzed behavioral, brain pathology, and molecular phenotypes exhibited by Galnt17 knockout (Galnt17-/-) mice. We show that Galnt17-/- mutants exhibit developmental neuropathology within the cerebellar vermis, along with abnormal activity, coordination, and social interaction deficits. Transcriptomic and protein analysis revealed reductions in both mucin type O-glycosylation and heparan sulfate synthesis in the developing mutant cerebellum along with disruption of pathways central to neuron differentiation, axon pathfinding, and synaptic signaling, consistent with the mutant neuropathology. These brain and behavioral phenotypes and molecular data confirm a specific role for Galnt17 in brain development and suggest new clues to factors that could contribute to phenotypes in certain WBS and AUTS2 syndrome patients.
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Affiliation(s)
- Chih-Ying Chen
- Pacific Northwest Research Institute, Seattle, WA, 98122, USA; Carl R. Woese Institute for Genomic Biology and School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.
| | - Christopher H Seward
- Pacific Northwest Research Institute, Seattle, WA, 98122, USA; Carl R. Woese Institute for Genomic Biology and School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Yunshu Song
- Pacific Northwest Research Institute, Seattle, WA, 98122, USA; Carl R. Woese Institute for Genomic Biology and School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Manasi Inamdar
- Pacific Northwest Research Institute, Seattle, WA, 98122, USA
| | - Analise M Leddy
- Pacific Northwest Research Institute, Seattle, WA, 98122, USA
| | - Huimin Zhang
- Carl R. Woese Institute for Genomic Biology and School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Jennifer Yoo
- Carl R. Woese Institute for Genomic Biology and School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Wei-Chun Kao
- Carl R. Woese Institute for Genomic Biology and School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Hanna Pawlowski
- Carl R. Woese Institute for Genomic Biology and School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Lisa J Stubbs
- Pacific Northwest Research Institute, Seattle, WA, 98122, USA; Carl R. Woese Institute for Genomic Biology and School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.
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Rajabi F, Jabalameli N, Rezaei N. The Concept of Immunogenetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:1-17. [DOI: 10.1007/978-3-030-92616-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Chromosomal Rearrangements and Altered Nuclear Organization: Recent Mechanistic Models in Cancer. Cancers (Basel) 2021; 13:cancers13225860. [PMID: 34831011 PMCID: PMC8616464 DOI: 10.3390/cancers13225860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/09/2021] [Accepted: 11/19/2021] [Indexed: 01/07/2023] Open
Abstract
Simple Summary New methodologies and technologies developed in the last few decades have highlighted the precise spatial organization of the genome into the cell nucleus, with chromatin architecture playing a central role in controlling several genome functions. Genes are expressed in a well-defined way and at a well-defined time during cell differentiation, and alterations in genome organization can lead to genetic diseases, such as cancers. Here we review how the genome is organized in the cell nucleus and the evidence of genome misorganization leading to cancer diseases. Abstract The last decade has seen significant progress in understanding how the genome is organized spatially within interphase nuclei. Recent analyses have confirmed earlier molecular cytogenetic studies on chromosome positioning within interphase nuclei and provided new information about the topologically associated domains (TADs). Examining the nuances of how genomes are organized within interphase nuclei will provide information fundamental to understanding gene regulation and expression in health and disease. Indeed, the radial spatial positioning of individual gene loci within nuclei has been associated with up- and down-regulation of specific genes, and disruption of normal genome organization within nuclei will result in compromised cellular health. In cancer cells, where reorganization of the nuclear architecture may occur in the presence of chromosomal rearrangements such as translocations, inversions, or deletions, gene repositioning can change their expression. To date, very few studies have focused on radial gene positioning and the correlation to gene expression in cancers. Further investigations would improve our understanding of the biological mechanisms at the basis of cancer and, in particular, in leukemia initiation and progression, especially in those cases where the molecular consequences of chromosomal rearrangements are still unclear. In this review, we summarize the main milestones in the field of genome organization in the nucleus and the alterations to this organization that can lead to cancer diseases.
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8
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Stockinger EJ. The Breeding of Winter-Hardy Malting Barley. PLANTS 2021; 10:plants10071415. [PMID: 34371618 PMCID: PMC8309344 DOI: 10.3390/plants10071415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/20/2022]
Abstract
In breeding winter malting barley, one recurring strategy is to cross a current preferred spring malting barley to a winter barley. This is because spring malting barleys have the greatest amalgamation of trait qualities desirable for malting and brewing. Spring barley breeding programs can also cycle their material through numerous generations each year-some managing even six-which greatly accelerates combining desirable alleles to generate new lines. In a winter barley breeding program, a single generation per year is the limit when the field environment is used and about two generations per year if vernalization and greenhouse facilities are used. However, crossing the current favored spring malting barley to a winter barley may have its downsides, as winter-hardiness too may be an amalgamation of desirable alleles assembled together that confers the capacity for prolonged cold temperature conditions. In this review I touch on some general criteria that give a variety the distinction of being a malting barley and some of the general trends made in the breeding of spring malting barleys. But the main objective of this review is to pull together different aspects of what we know about winter-hardiness from the seemingly most essential aspect, which is survival in the field, to molecular genetics and gene regulation, and then finish with ideas that might help further our insight for predictability purposes.
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Affiliation(s)
- Eric J Stockinger
- Ohio Agricultural Research and Development Center (OARDC), Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH 44691, USA
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9
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Dai L, Weiss RB, Dunn DM, Ramirez A, Paul S, Korenberg JR. Core transcriptional networks in Williams syndrome: IGF1-PI3K-AKT-mTOR, MAPK and actin signaling at the synapse echo autism. Hum Mol Genet 2021; 30:411-429. [PMID: 33564861 DOI: 10.1093/hmg/ddab041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Gene networks for disorders of social behavior provide the mechanisms critical for identifying therapeutic targets and biomarkers. Large behavioral phenotypic effects of small human deletions make the positive sociality of Williams syndrome (WS) ideal for determining transcriptional networks for social dysfunction currently based on DNA variations for disorders such as autistic spectrum disorder (ASD) and schizophrenia (SCHZ). Consensus on WS networks has been elusive due to the need for larger cohort size, sensitive genome-wide detection and analytic tools. We report a core set of WS network perturbations in a cohort of 58 individuals (34 with typical, 6 atypical deletions and 18 controls). Genome-wide exon-level expression arrays robustly detected changes in differentially expressed gene (DEG) transcripts from WS deleted genes that ranked in the top 11 of 12 122 transcripts, validated by quantitative reverse transcription PCR, RNASeq and western blots. WS DEG's were strictly dosed in the full but not the atypical deletions that revealed a breakpoint position effect on non-deleted CLIP2, a caveat for current phenotypic mapping based on copy number variants. Network analyses tested the top WS DEG's role in the dendritic spine, employing GeneMANIA to harmonize WS DEGs with comparable query gene-sets. The results indicate perturbed actin cytoskeletal signaling analogous to the excitatory dendritic spines. Independent protein-protein interaction analyses of top WS DEGs generated a 100-node graph annotated topologically revealing three interacting pathways, MAPK, IGF1-PI3K-AKT-mTOR/insulin and actin signaling at the synapse. The results indicate striking similarity of WS transcriptional networks to genome-wide association study-based ASD and SCHZ risk suggesting common network dysfunction for these disorders of divergent sociality.
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Affiliation(s)
- Li Dai
- Center for Integrated Neuroscience and Human Behavior, Brain Institute, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Diane M Dunn
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Anna Ramirez
- Center for Integrated Neuroscience and Human Behavior, Brain Institute, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - Sharan Paul
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Julie R Korenberg
- Center for Integrated Neuroscience and Human Behavior, Brain Institute, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA.,Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
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Pytte J, Flynn LL, Anderton RS, Mastaglia FL, Theunissen F, James I, Pfaff A, Koks S, Saunders AM, Bedlack R, Burns DK, Lutz MW, Siddique N, Siddique T, Roses AD, Akkari PA. Disease-modifying effects of an SCAF4 structural variant in a predominantly SOD1 ALS cohort. Neurol Genet 2020; 6:e470. [PMID: 32754644 PMCID: PMC7357414 DOI: 10.1212/nxg.0000000000000470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To test the hypothesis that rs573116164 will have disease-modifying effects in patients with superoxide dismutase 1 (SOD1) familial amyotrophic lateral sclerosis (fALS), we characterized rs573116164 within a cohort of 190 patients with fALS and 560 healthy age-matched controls to assess the variant for association with various measures of disease. METHODS Using a previously described bioinformatics evaluation algorithm, a polymorphic short structural variant associated with SOD1 was identified according to its theoretical effect on gene expression. An 12-18 poly-T repeat (rs573116164) within the 3' untranslated region of serine and arginine rich proteins-related carboxy terminal domain associated factor 4 (SCAF4), a gene that is adjacent to SOD1, was assessed for disease association and influence on survival and age at onset in an fALS cohort using PCR, Sanger sequencing, and capillary separation techniques for allele detection. RESULTS In a North American cohort of predominantly SOD1 fALS patients (n =190) and age-matched healthy controls (n = 560), we showed that carriage of an 18T SCAF4 allele was associated with disease within this cohort (odds ratio [OR] 6.6; 95% confidence interval [CI] 3.9-11.2; p = 4.0e-11), but also within non-SOD1 cases (n = 27; OR 5.3; 95% CI 1.9-14.5; p = 0.0014). This finding suggests genetically SOD1-independent effects of SCAF4 on fALS susceptibility. Furthermore, carriage of an 18T allele was associated with a 26-month reduction in survival time (95% CI 6.6-40.8; p = 0.014), but did not affect age at onset of disease. CONCLUSIONS The findings in this fALS cohort suggest that rs573116164 could have SOD1-independent and broader relevance in ALS, warranting further investigation in other fALS and sporadic ALS cohorts, as well as studies of functional effects of the 18T variant on gene expression.
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Affiliation(s)
- Julia Pytte
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Loren L Flynn
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Ryan S Anderton
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Frank L Mastaglia
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Frances Theunissen
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Ian James
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Abigail Pfaff
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Sulev Koks
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Ann M Saunders
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Richard Bedlack
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Daniel K Burns
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Michael W Lutz
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Nailah Siddique
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Teepu Siddique
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Allen D Roses
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - P Anthony Akkari
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
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11
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Abstract
Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies. Detection methods that use ensemble algorithms and emerging sequencing technologies have enabled the discovery of thousands of SVs, uncovering information about their ubiquity, relationship to disease and possible effects on biological mechanisms. Given the variability in SV type and size, along with unique detection biases of emerging genomic platforms, multiplatform discovery is necessary to resolve the full spectrum of variation. Here, we review modern approaches for investigating SVs and proffer that, moving forwards, studies integrating biological information with detection will be necessary to comprehensively understand the impact of SV in the human genome.
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Affiliation(s)
- Steve S Ho
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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12
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Ribosomal flavours: an acquired taste for specific mRNAs? Biochem Soc Trans 2018; 46:1529-1539. [PMID: 30420413 DOI: 10.1042/bst20180160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 12/20/2022]
Abstract
The regulation of translation is critical in almost every aspect of gene expression. Nonetheless, the ribosome is historically viewed as a passive player in this process. However, evidence is accumulating to suggest that variations in the ribosome can have an important influence on which mRNAs are translated. Scope for variation is provided via multiple avenues, including heterogeneity at the level of both ribosomal proteins and ribosomal RNAs and their covalent modifications. Together, these variations provide the potential for hundreds, if not thousands, of flavours of ribosome, each of which could have idiosyncratic preferences for the translation of certain messenger RNAs. Indeed, perturbations to this heterogeneity appear to affect specific subsets of transcripts and manifest as cell-type-specific diseases. This review provides a historical perspective of the ribosomal code hypothesis, before outlining the various sources of heterogeneity, their regulation and functional consequences for the cell.
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13
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Renault V, Tost J, Pichon F, Wang-Renault SF, Letouzé E, Imbeaud S, Zucman-Rossi J, Deleuze JF, How-Kit A. aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations. PLoS One 2017; 12:e0189334. [PMID: 29261730 PMCID: PMC5736239 DOI: 10.1371/journal.pone.0189334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/23/2017] [Indexed: 11/26/2022] Open
Abstract
Motivation Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. Results To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). Availability and implementation aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/. Contact aCNViewer@cephb.fr
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Affiliation(s)
- Victor Renault
- Laboratory for Bioinformatics, Fondation Jean Dausset–CEPH, Paris, France
- Laboratory of Excellence GenMed, Paris, France
- * E-mail: (VR); (AHK)
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Fabien Pichon
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Shu-Fang Wang-Renault
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Eric Letouzé
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Institut Universitaire d'Hématologie (IUH), Paris, France
| | - Sandrine Imbeaud
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Institut Universitaire d'Hématologie (IUH), Paris, France
| | - Jessica Zucman-Rossi
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Institut Universitaire d'Hématologie (IUH), Paris, France
| | - Jean-François Deleuze
- Laboratory for Bioinformatics, Fondation Jean Dausset–CEPH, Paris, France
- Laboratory of Excellence GenMed, Paris, France
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
- Laboratory for Genomics, Fondation Jean Dausset–CEPH, Paris, France
| | - Alexandre How-Kit
- Laboratory of Excellence GenMed, Paris, France
- Laboratory for Genomics, Fondation Jean Dausset–CEPH, Paris, France
- * E-mail: (VR); (AHK)
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14
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Schmidt HD. Cocaine Rearranges the Neuronal Epigenome. Biol Psychiatry 2017; 82:776-778. [PMID: 29110817 DOI: 10.1016/j.biopsych.2017.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Heath D Schmidt
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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15
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Engmann O, Labonte B, Mitchell A, Bashtrykov P, Calipari ES, Rosenbluh C, Loh YHE, Walker DM, Burek D, Hamilton PJ, Issler O, Neve RL, Turecki G, Hurd Y, Chess A, Shen L, Mansuy I, Jeltsch A, Akbarian S, Nestler EJ. Cocaine-Induced Chromatin Modifications Associate With Increased Expression and Three-Dimensional Looping of Auts2. Biol Psychiatry 2017; 82:794-805. [PMID: 28577753 PMCID: PMC5671915 DOI: 10.1016/j.biopsych.2017.04.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND Exposure to drugs of abuse alters the epigenetic landscape of the brain's reward regions, such as the nucleus accumbens. We investigated how combinations of chromatin modifications affect genes that regulate responses to cocaine. We focused on Auts2, a gene linked to human evolution and cognitive disorders, which displays strong clustering of cocaine-induced chromatin modifications in this brain region. METHODS We combined chromosome conformation capture, circularized chromosome conformation capture, and related approaches with behavioral paradigms relevant to cocaine phenotypes. Cell type-specific functions were assessed by fluorescence-activated cell sorting and viral-mediated overexpression in Cre-dependent mouse lines. RESULTS We observed that Auts2 gene expression is increased by repeated cocaine administration specifically in D2-type medium spiny neurons in the nucleus accumbens, an effect seen in male but not female mice. Auts2 messenger RNA expression was also upregulated postmortem in the nucleus accumbens of male human cocaine addicts. We obtained evidence that chromosomal looping, bypassing 1524 kb of linear genome, connects Auts2 to the Caln1 gene locus under baseline conditions. This looping was disrupted after repeated cocaine exposure, resulting in increased expression of both genes in D2-type medium spiny neurons. Cocaine exposure reduces binding of CCCTC-binding factor, a chromosomal scaffolding protein, and increases histone and DNA methylation at the Auts-Caln1 loop base in the nucleus accumbens. Cell type-specific overexpression of Auts2 or Caln1 in D2-type medium spiny neurons demonstrated that both genes promote cocaine reward. CONCLUSIONS These findings suggest that cocaine-induced alterations of neuronal three-dimensional genome organization destabilize higher order chromatin at specific loci that regulate responses to the drug.
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Affiliation(s)
- Olivia Engmann
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Benoit Labonte
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Amanda Mitchell
- Departments of Psychiatry and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pavel Bashtrykov
- Institute of Biochemistry, Stuttgart University, Stuttgart, Germany
| | - Erin S. Calipari
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Chaggai Rosenbluh
- Departments of Developmental and Regenerative Biology and of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yong-Hwee E. Loh
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Deena M. Walker
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Dominika Burek
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Peter J. Hamilton
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Orna Issler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Rachael L. Neve
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gustavo Turecki
- Douglas Mental Health University Institute, Montreal, Canada
| | - Yasmin Hurd
- Departments of Psychiatry and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Chess
- Departments of Developmental and Regenerative Biology and of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Shen
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Isabelle Mansuy
- University of Zurich / ETH Zurich, Brain Research Institute, Zurich, Switzerland
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Stuttgart, Germany
| | - Schahram Akbarian
- Departments of Psychiatry and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric J. Nestler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
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16
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Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. Mol Psychiatry 2017; 22:836-849. [PMID: 27240531 PMCID: PMC5508252 DOI: 10.1038/mp.2016.84] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/18/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
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17
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Loviglio MN, Beck CR, White JJ, Leleu M, Harel T, Guex N, Niknejad A, Bi W, Chen ES, Crespo I, Yan J, Charng WL, Gu S, Fang P, Coban-Akdemir Z, Shaw CA, Jhangiani SN, Muzny DM, Gibbs RA, Rougemont J, Xenarios I, Lupski JR, Reymond A. Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics. Genome Med 2016; 8:105. [PMID: 27799067 PMCID: PMC5088687 DOI: 10.1186/s13073-016-0359-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/16/2016] [Indexed: 02/13/2023] Open
Abstract
Background Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. Methods We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes. Results Potentially deleterious variants were identified in nine of these individuals using whole-exome sequencing. Eight of these changes affect KMT2D, ZEB2, MAP2K2, GLDC, CASK, MECP2, KDM5C, and POGZ, known to be associated with Kabuki syndrome 1, Mowat-Wilson syndrome, cardiofaciocutaneous syndrome, glycine encephalopathy, mental retardation and microcephaly with pontine and cerebellar hypoplasia, X-linked mental retardation 13, X-linked mental retardation Claes-Jensen type, and White-Sutton syndrome, respectively. The ninth individual carries a de novo variant in JAKMIP1, a regulator of neuronal translation that was recently found deleted in a patient with autism spectrum disorder. Analyses of co-expression and biomedical text mining suggest that these pathologies and SMS are part of the same disease network. Further support for this hypothesis was obtained from transcriptome profiling that showed that the expression levels of both Zeb2 and Map2k2 are perturbed in Rai1–/– mice. As an orthogonal approach to potentially contributory disease gene variants, we used chromatin conformation capture to reveal chromatin contacts between RAI1 and the loci flanking ZEB2 and GLDC, as well as between RAI1 and human orthologs of the genes that show perturbed expression in our Rai1–/– mouse model. Conclusions These holistic studies of RAI1 and its interactions allow insights into SMS and other disorders associated with intellectual disability and behavioral abnormalities. Our findings support a pan-genomic approach to the molecular diagnosis of a distinctive disorder. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0359-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Nicla Loviglio
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Marion Leleu
- School of Life Sciences, EPFL (Ecole Polytechnique Fédérale de Lausanne), 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicolas Guex
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Anne Niknejad
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Isaac Crespo
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Jiong Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Laboratory Medicine Program, UHN, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5G 2C4, Canada
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ping Fang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: WuXiNextCODE, 101Main Street, Cambridge, MA, 02142, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jacques Rougemont
- School of Life Sciences, EPFL (Ecole Polytechnique Fédérale de Lausanne), 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.
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18
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Beunders G, van de Kamp J, Vasudevan P, Morton J, Smets K, Kleefstra T, de Munnik SA, Schuurs-Hoeijmakers J, Ceulemans B, Zollino M, Hoffjan S, Wieczorek S, So J, Mercer L, Walker T, Velsher L, Parker MJ, Magee AC, Elffers B, Kooy RF, Yntema HG, Meijers-Heijboer EJ, Sistermans EA. A detailed clinical analysis of 13 patients with AUTS2 syndrome further delineates the phenotypic spectrum and underscores the behavioural phenotype. J Med Genet 2016; 53:523-32. [DOI: 10.1136/jmedgenet-2015-103601] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/09/2016] [Indexed: 12/31/2022]
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19
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Lupiáñez DG, Spielmann M, Mundlos S. Breaking TADs: How Alterations of Chromatin Domains Result in Disease. Trends Genet 2016; 32:225-237. [DOI: 10.1016/j.tig.2016.01.003] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/05/2016] [Accepted: 01/11/2016] [Indexed: 12/13/2022]
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20
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Carvalho CMB, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet 2016; 17:224-38. [PMID: 26924765 DOI: 10.1038/nrg.2015.25] [Citation(s) in RCA: 414] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, MG 30190-002, Brazil
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Texas Children's Hospital, Houston, Texas 77030, USA
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21
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Frye RE, Cox D, Slattery J, Tippett M, Kahler S, Granpeesheh D, Damle S, Legido A, Goldenthal MJ. Mitochondrial Dysfunction may explain symptom variation in Phelan-McDermid Syndrome. Sci Rep 2016; 6:19544. [PMID: 26822410 PMCID: PMC4731780 DOI: 10.1038/srep19544] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/09/2015] [Indexed: 12/02/2022] Open
Abstract
Phelan-McDermid Syndrome (PMS), which is defined by a deletion within 22q13, demonstrates significant phenotypic variation. Given that six mitochondrial genes are located within 22q13, including complex I and IV genes, we hypothesize that mitochondrial complex activity abnormalities may explain phenotypic variation in PMS symptoms. Complex I, II, II + III and IV activity was measured in 51 PMS participants. Caretakers completed questionnaires and provided genetic information through the PMS foundation registry. Complex activity was abnormal in 59% of PMS participants. Abnormalities were found in complex I and IV but not complex II + III and II activity, consistent with disruption of genes within the 22q13 region. However, complex activity abnormalities were not related to specific gene deletions suggesting a "neighboring effect" of regional deletions on adjacent gene expression. A specific combination of symptoms (autism spectrum disorder, developmental regression, failure-to-thrive, exercise intolerance/fatigue) was associated with complex activity abnormalities. 64% of 106 individuals in the PMS foundation registry who did not have complex activity measured also endorsed this pattern of symptoms. These data suggest that mitochondrial abnormalities, specifically abnormalities in complex I and IV activity, may explain some phenotypic variation in PMS individuals. These results point to novel pathophysiology mechanisms and treatment targets for PMS patients.
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Affiliation(s)
- Richard E. Frye
- University of Arkansas for Medical Sciences, Department of Pediatrics, Arkansas Children’s Hospital Research Institute, Little Rock, Arkansas, AR 72202, USA
| | - Devin Cox
- Kansas University Medical Center, Kansas City, Kansas, KS, USA
| | - John Slattery
- University of Arkansas for Medical Sciences, Department of Pediatrics, Arkansas Children’s Hospital Research Institute, Little Rock, Arkansas, AR 72202, USA
| | - Marie Tippett
- University of Arkansas for Medical Sciences, Department of Pediatrics, Arkansas Children’s Hospital Research Institute, Little Rock, Arkansas, AR 72202, USA
| | - Stephen Kahler
- University of Arkansas for Medical Sciences, Department of Pediatrics, Arkansas Children’s Hospital Research Institute, Little Rock, Arkansas, AR 72202, USA
| | - Doreen Granpeesheh
- Center for Autism and Related Disorders, Inc., Woodland Hills, California, CA, USA
| | - Shirish Damle
- Drexel University College of Medicine, Department of Pediatrics, Neurology Section, St. Christopher’s Hospital for Children, Philadelphia, PA 19134, USA
| | - Agustin Legido
- Drexel University College of Medicine, Department of Pediatrics, Neurology Section, St. Christopher’s Hospital for Children, Philadelphia, PA 19134, USA
| | - Michael J. Goldenthal
- Drexel University College of Medicine, Department of Pediatrics, Neurology Section, St. Christopher’s Hospital for Children, Philadelphia, PA 19134, USA
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22
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Zhang F, Lupski JR. Non-coding genetic variants in human disease. Hum Mol Genet 2015; 24:R102-10. [PMID: 26152199 DOI: 10.1093/hmg/ddv259] [Citation(s) in RCA: 383] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/03/2015] [Indexed: 01/16/2023] Open
Abstract
Genetic variants, including single-nucleotide variants (SNVs) and copy number variants (CNVs), in the non-coding regions of the human genome can play an important role in human traits and complex diseases. Most of the genome-wide association study (GWAS) signals map to non-coding regions and potentially point to non-coding variants, whereas their functional interpretation is challenging. In this review, we discuss the human non-coding variants and their contributions to human diseases in the following four parts. (i) Functional annotations of non-coding SNPs mapped by GWAS: we discuss recent progress revealing some of the molecular mechanisms for GWAS signals affecting gene function. (ii) Technical progress in interpretation of non-coding variants: we briefly describe some of the technologies for functional annotations of non-coding variants, including the methods for genome-wide mapping of chromatin interaction, computational tools for functional predictions and the new genome editing technologies useful for dissecting potential functional consequences of non-coding variants. (iii) Non-coding CNVs in human diseases: we review our emerging understanding the role of non-coding CNVs in human disease. (iv) Compound inheritance of large genomic deletions and non-coding variants: compound inheritance at a locus consisting of coding variants plus non-coding ones is described.
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Affiliation(s)
- Feng Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA and Texas Children's Hospital, Houston, TX 77030, USA
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23
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Abstract
Recent years have witnessed a flurry of important technological and methodological developments in the discovery and analysis of copy number variations (CNVs), which are increasingly enabling the systematic evaluation of their impact on a broad range of phenotypes from molecular-level (intermediate) traits to higher-order clinical phenotypes. Like single nucleotide variants in the human genome, CNVs have been linked to complex traits in humans, including disease and drug response. These recent developments underscore the importance of incorporating complex forms of genetic variation into disease mapping studies and promise to transform our understanding of genome function and the genetic basis of disease. Here we review some of the findings that have emerged from transcriptome studies of CNVs facilitated by the rapid advances in -omics technologies and corresponding methodologies.
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24
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Kloosterman WP, Hochstenbach R. Deciphering the pathogenic consequences of chromosomal aberrations in human genetic disease. Mol Cytogenet 2014; 7:100. [PMID: 25606056 PMCID: PMC4299681 DOI: 10.1186/s13039-014-0100-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/08/2014] [Indexed: 01/14/2023] Open
Abstract
Chromosomal aberrations include translocations, deletions, duplications, inversions, aneuploidies and complex rearrangements. They underlie genetic disease in roughly 15% of patients with multiple congenital abnormalities and/or mental retardation (MCA/MR). In genetic diagnostics, the pathogenicity of chromosomal aberrations in these patients is typically assessed based on criteria such as phenotypic similarity to other patients with the same or overlapping aberration, absence in healthy individuals, de novo occurrence, and protein coding gene content. However, a thorough understanding of the molecular mechanisms that lead to MCA/MR as a result of chromosome aberrations is often lacking. Chromosome aberrations can affect one or more genes in a complex manner, such as by changing the regulation of gene expression, by disrupting exons, and by creating fusion genes. The precise delineation of breakpoints by whole-genome sequencing enables the construction of local genomic architecture and facilitates the prediction of the molecular determinants of the patient's phenotype. Here, we review current methods for breakpoint identification and their impact on the interpretation of chromosome aberrations in patients with MCA/MR. In addition, we discuss opportunities to dissect disease mechanisms based on large-scale genomic technologies and studies in model organisms.
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Affiliation(s)
- Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, P.O. Box 85060, 3508 AB Utrecht, The Netherlands
| | - Ron Hochstenbach
- Department of Medical Genetics, Genome Diagnostics, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
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25
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Keane TM, Wong K, Adams DJ, Flint J, Reymond A, Yalcin B. Identification of structural variation in mouse genomes. Front Genet 2014; 5:192. [PMID: 25071822 PMCID: PMC4079067 DOI: 10.3389/fgene.2014.00192] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/12/2014] [Indexed: 01/25/2023] Open
Abstract
Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation.
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Affiliation(s)
| | - Kim Wong
- Wellcome Trust Sanger Institute Hinxton, Cambridge, UK
| | - David J Adams
- Wellcome Trust Sanger Institute Hinxton, Cambridge, UK
| | | | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne Lausanne, Switzerland
| | - Binnaz Yalcin
- Center for Integrative Genomics, University of Lausanne Lausanne, Switzerland ; Institute of Genetics and Molecular and Cellular Biology Illkirch, France
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26
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Ebert G, Steininger A, Weißmann R, Boldt V, Lind-Thomsen A, Grune J, Badelt S, Heßler M, Peiser M, Hitzler M, Jensen LR, Müller I, Hu H, Arndt PF, Kuss AW, Tebel K, Ullmann R. Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7. BMC Genomics 2014; 15:537. [PMID: 24973960 PMCID: PMC4092221 DOI: 10.1186/1471-2164-15-537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/17/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-Beuren syndrome. Despite these adverse effects, SDs have become fixed in the human genome. Focusing on chromosome 7, which is particularly rich in interstitial SDs, we have investigated the distribution of SDs in the context of evolution and the three dimensional organisation of the chromosome in order to gain insights into the mutual relationship of SDs and chromatin topology. RESULTS Intrachromosomal SDs preferentially accumulate in those segments of chromosome 7 that are homologous to marmoset chromosome 2. Although this formerly compact segment has been re-distributed to three different sites during primate evolution, we can show by means of public data on long distance chromatin interactions that these three intervals, and consequently the paralogous SDs mapping to them, have retained their spatial proximity in the nucleus. Focusing on SD clusters implicated in the aetiology of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation. CONCLUSIONS Our study suggests a link of nuclear architecture and the propagation of SDs across chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome.
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Affiliation(s)
- Grit Ebert
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Anne Steininger
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Robert Weißmann
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Vivien Boldt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Allan Lind-Thomsen
- />Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Jana Grune
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Stefan Badelt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Institute for Theoretical Chemistry, University of Vienna, Waehringer Straße 17, A-1090 Vienna, Austria
| | - Melanie Heßler
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Matthias Peiser
- />Unit Experimental Research, Department of Product Safety, Federal Institute for Bundeswehr Institute of Radiobiology affiliated, the University of Ulm, Neuherbergstraße 11, 80937 Munich, Germany
| | - Manuel Hitzler
- />Unit Experimental Research, Department of Product Safety, Federal Institute for Bundeswehr Institute of Radiobiology affiliated, the University of Ulm, Neuherbergstraße 11, 80937 Munich, Germany
| | - Lars R Jensen
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Ines Müller
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Hao Hu
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Peter F Arndt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Andreas W Kuss
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Katrin Tebel
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Reinhard Ullmann
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
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27
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Harewood L, Fraser P. The impact of chromosomal rearrangements on regulation of gene expression. Hum Mol Genet 2014; 23:R76-82. [PMID: 24907073 DOI: 10.1093/hmg/ddu278] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The effects that coding region single-nucleotide polymorphisms or mutations have on gene expression have been well documented, predominantly owing to their association with disease. The effects of structural chromosomal rearrangements are also receiving increasing attention with the development of new techniques that allow accurate, high-resolution data, whether genomic interaction or transcriptome data, to be generated right down to the single-cell level. Over the past 18 months, these advances in experimental techniques have been used to further confirm and delineate the substantial effects that chromosome rearrangements can have on the regulation of gene expression and provide evidence of direct links between the two.
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Affiliation(s)
- Louise Harewood
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
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