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Zhou H, Arapoglou T, Li X, Li Z, Zheng X, Moore J, Asok A, Kumar S, Blue E, Buyske S, Cox N, Felsenfeld A, Gerstein M, Kenny E, Li B, Matise T, Philippakis A, Rehm HL, Sofia HJ, Snyder G, Weng Z, Neale B, Sunyaev S, Lin X. FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Res 2023; 51:D1300-D1311. [PMID: 36350676 PMCID: PMC9825437 DOI: 10.1093/nar/gkac966] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/25/2022] [Accepted: 10/14/2022] [Indexed: 11/11/2022] Open
Abstract
Large biobank-scale whole genome sequencing (WGS) studies are rapidly identifying a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis of human diseases. Variant functional annotations play a critical role in WGS analysis, result interpretation, and prioritization of disease- or trait-associated causal variants. Existing functional annotation databases have limited scope to perform online queries and functionally annotate the genotype data of large biobank-scale WGS studies. We develop the Functional Annotation of Variants Online Resources (FAVOR) to meet these pressing needs. FAVOR provides a comprehensive multi-faceted variant functional annotation online portal that summarizes and visualizes findings of all possible nine billion single nucleotide variants (SNVs) across the genome. It allows for rapid variant-, gene- and region-level queries of variant functional annotations. FAVOR integrates variant functional information from multiple sources to describe the functional characteristics of variants and facilitates prioritizing plausible causal variants influencing human phenotypes. Furthermore, we provide a scalable annotation tool, FAVORannotator, to functionally annotate large-scale WGS studies and efficiently store the genotype and their variant functional annotation data in a single file using the annotated Genomic Data Structure (aGDS) format, making downstream analysis more convenient. FAVOR and FAVORannotator are available at https://favor.genohub.org.
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Affiliation(s)
- Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Theodore Arapoglou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jill Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Sushant Kumar
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Elizabeth E Blue
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Steven Buyske
- Department of Statistics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Nancy Cox
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Eimear Kenny
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tara Matise
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Anthony Philippakis
- Data Science Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Heidi J Sofia
- National Human Genome Research Institute, Bethesda, DC, USA
| | - Grace Snyder
- National Human Genome Research Institute, Bethesda, DC, USA
| | | | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Benjamin Neale
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Shamil R Sunyaev
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
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2
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Blanco E, Ballaré C, Di Croce L, Aranda S. Quantitative Comparison of Multiple Chromatin Immunoprecipitation-Sequencing (ChIP-seq) Experiments with spikChIP. Methods Mol Biol 2023; 2624:55-72. [PMID: 36723809 DOI: 10.1007/978-1-0716-2962-8_5] [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] [Indexed: 06/18/2023]
Abstract
The chromatin immunoprecipitation coupled with the next-generation sequencing (ChIP-seq) is a powerful technique that enables to characterize the genomic distribution of chromatin-associated proteins, histone posttranslational modifications, and histone variants. However, in the absence of a reference control for monitoring experimental and biological variations, the standard ChIP-seq scheme is unable to accurately assess changes in the abundance of chromatin targets across different experimental samples. To overcome this limitation, the combination of external spike-in material with the experimental chromatin is offered as an effective solution for quantitative comparison of ChIP-seq data across different conditions. Here, we detail (i) the experimental protocol for preparing quality control spike-in chromatin from Drosophila melanogaster cells and (ii) the computational protocol to compare ChIP-seq samples with spike-in based on the use of the spikChIP software.
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Affiliation(s)
- Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
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3
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Blanco E, Di Croce L, Aranda S. SpikChIP: a novel computational methodology to compare multiple ChIP-seq using spike-in chromatin. NAR Genom Bioinform 2021; 3:lqab064. [PMID: 34327329 PMCID: PMC8315120 DOI: 10.1093/nargab/lqab064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/06/2021] [Accepted: 07/01/2021] [Indexed: 01/17/2023] Open
Abstract
In order to evaluate cell- and disease-specific changes in the interacting strength of chromatin targets, ChIP-seq signal across multiple conditions must undergo robust normalization. However, this is not possible using the standard ChIP-seq scheme, which lacks a reference for the control of biological and experimental variabilities. While several studies have recently proposed different solutions to circumvent this problem, substantial analytical differences among methodologies could hamper the experimental reproducibility and quantitative accuracy. Here, we propose a computational method to accurately compare ChIP-seq experiments, with exogenous spike-in chromatin, across samples in a genome-wide manner by using a local regression strategy (spikChIP). In contrast to the previous methodologies, spikChIP reduces the influence of sequencing noise of spike-in material during ChIP-seq normalization, while minimizes the overcorrection of non-occupied genomic regions in the experimental ChIP-seq. We demonstrate the utility of spikChIP with both histone and non-histone chromatin protein, allowing us to monitor for experimental reproducibility and the accurate ChIP-seq comparison of distinct experimental schemes. spikChIP software is available on GitHub (https://github.com/eblancoga/spikChIP).
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Affiliation(s)
- Enrique Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
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4
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Abstract
Sarcopenia – the accelerated age-related loss of muscle mass and function – is an under-diagnosed condition, and is central to deteriorating mobility, disability and frailty in older age. There is a lack of treatment options for older adults at risk of sarcopenia. Although sarcopenia's pathogenesis is multifactorial, its major phenotypes – muscle mass and muscle strength – are highly heritable. Several genome-wide association studies of muscle-related traits were published recently, providing dozens of candidate genes, many with unknown function. Therefore, animal models are required not only to identify causal mechanisms, but also to clarify the underlying biology and translate this knowledge into new interventions. Over the past several decades, small teleost fishes had emerged as powerful systems for modeling the genetics of human diseases. Owing to their amenability to rapid genetic intervention and the large number of conserved genetic and physiological features, small teleosts – such as zebrafish, medaka and killifish – have become indispensable for skeletal muscle genomic studies. The goal of this Review is to summarize evidence supporting the utility of small fish models for accelerating our understanding of human skeletal muscle in health and disease. We do this by providing a basic foundation of the (zebra)fish skeletal muscle morphology and physiology, and evidence of muscle-related gene homology. We also outline challenges in interpreting zebrafish mutant phenotypes and in translating them to human disease. Finally, we conclude with recommendations on future directions to leverage the large body of tools developed in small fish for the needs of genomic exploration in sarcopenia. Summary: Zebrafish and other small fish have become powerful disease models. Here, we summarize the evidence for the utility of small teleost models for genetic research in sarcopenia – the age-related loss of muscle mass and function.
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Affiliation(s)
- Alon Daya
- The Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel
| | - Rajashekar Donaka
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 130010, Israel
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 130010, Israel .,Hebrew SeniorLife, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA 02131, USA
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Anglès F, Hutt DM, Balch WE. HDAC inhibitors rescue multiple disease-causing CFTR variants. Hum Mol Genet 2020; 28:1982-2000. [PMID: 30753450 DOI: 10.1093/hmg/ddz026] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/21/2018] [Accepted: 01/16/2019] [Indexed: 12/14/2022] Open
Abstract
Understanding the role of the epigenome in protein-misfolding diseases remains a challenge in light of genetic diversity found in the world-wide population revealed by human genome sequencing efforts and the highly variable response of the disease population to therapeutics. An ever-growing body of evidence has shown that histone deacetylase (HDAC) inhibitors (HDACi) can have significant benefit in correcting protein-misfolding diseases that occur in response to both familial and somatic mutation. Cystic fibrosis (CF) is a familial autosomal recessive disease, caused by genetic diversity in the CF transmembrane conductance regulator (CFTR) gene, a cyclic Adenosine MonoPhosphate (cAMP)-dependent chloride channel expressed at the apical plasma membrane of epithelial cells in multiple tissues. The potential utility of HDACi in correcting the phenylalanine 508 deletion (F508del) CFTR variant as well as the over 2000 CF-associated variants remains controversial. To address this concern, we examined the impact of US Food and Drug Administration-approved HDACi on the trafficking and function of a panel of CFTR variants. Our data reveal that panobinostat (LBH-589) and romidepsin (FK-228) provide functional correction of Class II and III CFTR variants, restoring cell surface chloride channel activity in primary human bronchial epithelial cells. We further demonstrate a synergistic effect of these HDACi with Vx809, which can significantly restore channel activity for multiple CFTR variants. These data suggest that HDACi can serve to level the cellular playing field for correcting CF-causing mutations, a leveling effect that might also extend to other protein-misfolding diseases.
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Affiliation(s)
- Frédéric Anglès
- Department of Molecular Medicine, Scripps Research, North Torrey Pines Rd, La Jolla, CA, USA
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, North Torrey Pines Rd, La Jolla, CA, USA
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, North Torrey Pines Rd, La Jolla, CA, USA.,Skaggs Institute of Chemical Biology, North Torrey Pines Rd, La Jolla, CA, USA
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6
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Fernández-Sanlés A, Sayols-Baixeras S, Castro DE Moura M, Esteller M, Subirana I, Torres-Cuevas S, Pérez-Fernández S, Aslibekyan S, Marrugat J, Elosua R. Physical Activity and Genome-wide DNA Methylation: The REgistre GIroní del COR Study. Med Sci Sports Exerc 2019; 52:589-597. [PMID: 31652233 DOI: 10.1249/mss.0000000000002174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION DNA methylation may be one of the biological mechanisms underlying the health benefits of physical activity (PA). Our objective was to determine the association between PA and genome-wide DNA methylation at CpG level. METHODS We designed a two-stage epigenome wide association study. In the discovery stage, we used 619 individuals from the REgistre GIroní del COR cohort. Next, we validated the CpG suggestively associated with PA (P < 10) in two independent populations (n = 1735 and 190, respectively). Physical activity was assessed with validated questionnaires and classified as light PA (LPA), moderate PA, vigorous PA, moderate-vigorous PA (MVPA) and total PA. We examined linear and nonlinear associations and meta-analyzed the results in the three populations. The linear associations were meta-analyzed with a fixed-effects model and the P values of the nonlinear associations with the Stouffer and Fisher methods. We established a P value threshold that fulfilled Bonferroni criteria over the number of CpG analyzed (0.05/421,940 = 1.185 × 10). RESULTS In the meta-analyses, two CpG sites had a statistically significant nonlinear association with MVPA. cg24155427 (P = 1.19 × 10), located in an intergenic region in chromosome 1, has been previously associated with smoking, lupus, and aging. cg09565397 (P = 1.59 × 10), located within DGAT1 in chromosome 8, which encodes an enzyme involved in triacylglycerol synthesis. CONCLUSIONS This population-based study identified two new, differentially methylated CpG sites with a nonlinear dose-response relationship to MVPA. These associations must be additionally validated and may be considered for further research on the biological mechanisms underlying health benefits of PA.
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Affiliation(s)
| | | | - Manuel Castro DE Moura
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, SPAIN
| | | | | | | | | | - Stella Aslibekyan
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
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Corley MJ, Vargas-Maya N, Pang APS, Lum-Jones A, Li D, Khadka V, Sultana R, Blanchard DC, Maunakea AK. Epigenetic Delay in the Neurodevelopmental Trajectory of DNA Methylation States in Autism Spectrum Disorders. Front Genet 2019; 10:907. [PMID: 31681403 PMCID: PMC6797928 DOI: 10.3389/fgene.2019.00907] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 08/28/2019] [Indexed: 12/16/2022] Open
Abstract
Autism spectrum disorders (ASD) are hypothesized to originate in utero from perturbations in neural stem cell niche regions of the developing brain. Dynamic epigenetic processes including DNA methylation are integral to coordinating typical brain development. However, the extent and consequences of alterations to DNA methylation states in neural stem cell compartments in ASD are unknown. Here, we report significant DNA methylation defects in the subventricular zone of the lateral ventricles from postmortem brain of 17 autism diagnosed compared to 17 age- and gender-matched typically developing individuals. Both array- and sequencing-based genome-wide methylome analyses independently revealed that these alterations were preferentially targeted to intragenic and bivalently modified chromatin domains of genes predominately involved in neurodevelopment, which associated with aberrant precursor messenger RNA splicing events of ASD-relevant genes. Integrative analysis of our ASD and typically developing postmortem brain methylome datasets with that from fetal brain at different neurodevelopmental stages revealed that the methylation states of differentially methylated loci associated with ASD remarkably resemble the methylation states at earlier time points in fetal brain development. This observation was confirmed using additional methylome datasets from three other brain regions. Altogether, these findings implicate an epigenetic delay in the trajectory of normal DNA methylation states during the course of brain development that may consequently lead to deleterious transcriptomic events in ASD and support the hypothesis of an early developmental origin of ASD.
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Affiliation(s)
- Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Nauru Vargas-Maya
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Alina P S Pang
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Annette Lum-Jones
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Dongmei Li
- Department of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, United States
| | - Vedbar Khadka
- Office of Biostatistics & Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Razvan Sultana
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - D Caroline Blanchard
- Bekesy Neurobiology Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Alika K Maunakea
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
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8
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Cielo D, Galatola M, Fernandez-Jimenez N, De Leo L, Garcia-Etxebarria K, Loganes C, Tommasini A, Not T, Auricchio R, Greco L, Bilbao JR. Combined Analysis of Methylation and Gene Expression Profiles in Separate Compartments of Small Bowel Mucosa Identified Celiac Disease Patients' Signatures. Sci Rep 2019; 9:10020. [PMID: 31292504 PMCID: PMC6620355 DOI: 10.1038/s41598-019-46468-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/14/2019] [Indexed: 02/07/2023] Open
Abstract
By GWAS studies on celiac disease, gene expression was studied at the level of the whole intestinal mucosa, composed by two different compartments: epithelium and lamina propria. Our aim is to analyse the gene-expression and DNA methylation of candidate genes in each of these compartments. Epithelium was separated from lamina propria in biopsies of CeD patients and CTRs using magnetic beads. Gene-expression was analysed by RT-PC; methylation analysis required bisulfite conversion and NGS. Reverse modulation of gene-expression and methylation in the same cellular compartment was observed for the IL21 and SH2B3 genes in CeD patients relative to CTRs. Bioinformatics analysis highlighted the regulatory elements in the genomic region of SH2B3 that altered methylation levels. The cREL and TNFAIP3 genes showed methylation patterns that were significantly different between CeD patients and CTRs. In CeD, the genes linked to inflammatory processes are up-regulated, whereas the genes involved in the cell adhesion/integrity of the intestinal barrier are down-regulated. These findings suggest a correlation between gene-expression and methylation profile for the IL21 and SH2B3 genes. We identified a “gene-expression phenotype” of CeD and showed that the abnormal response to dietary antigens in CeD might be related not to abnormalities of gene structure but to the regulation of molecular pathways.
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Affiliation(s)
- D Cielo
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy
| | - M Galatola
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy. .,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy.
| | - N Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
| | - L De Leo
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - K Garcia-Etxebarria
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
| | - C Loganes
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - A Tommasini
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - T Not
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain.,Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - R Auricchio
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy
| | - L Greco
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy
| | - J R Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
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9
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Aranda S, Alcaine-Colet A, Blanco E, Borràs E, Caillot C, Sabidó E, Di Croce L. Chromatin capture links the metabolic enzyme AHCY to stem cell proliferation. SCIENCE ADVANCES 2019; 5:eaav2448. [PMID: 30854431 PMCID: PMC6402848 DOI: 10.1126/sciadv.aav2448] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/28/2019] [Indexed: 05/19/2023]
Abstract
Profiling the chromatin-bound proteome (chromatome) in a simple, direct, and reliable manner might be key to uncovering the role of yet uncharacterized chromatin factors in physiology and disease. Here, we have designed an experimental strategy to survey the chromatome of proliferating cells by using the DNA-mediated chromatin pull-down (Dm-ChP) technology. Our approach provides a global view of cellular chromatome under normal physiological conditions and enables the identification of chromatin-bound proteins de novo. Integrating Dm-ChP with genomic and functional data, we have discovered an unexpected chromatin function for adenosylhomocysteinase, a major one-carbon pathway metabolic enzyme, in gene activation. Our study reveals a new regulatory axis between the metabolic state of pluripotent cells, ribosomal protein production, and cell division during the early phase of embryo development, in which the metabolic flux of methylation reactions is favored in a local milieu.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Corresponding author. (S.A.); (L.D.C.)
| | - Anna Alcaine-Colet
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Claire Caillot
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author. (S.A.); (L.D.C.)
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Evolutionary Loss of Genomic Proximity to Conserved Noncoding Elements Impacted the Gene Expression Dynamics During Mammalian Brain Development. Genetics 2019; 211:1239-1254. [PMID: 30796012 DOI: 10.1534/genetics.119.301973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/14/2019] [Indexed: 01/05/2023] Open
Abstract
Conserved noncoding elements (CNEs) have a significant regulatory influence on their neighboring genes. Loss of proximity to CNEs through genomic rearrangements can, therefore, impact the transcriptional states of the cognate genes. Yet, the evolutionary implications of such chromosomal alterations have not been studied. Through genome-wide analysis of CNEs and the cognate genes of representative species from five different mammalian orders, we observed a significant loss of genes' linear proximity to CNEs in the rat lineage. The CNEs and the genes losing proximity had a significant association with fetal, but not postnatal, brain development as assessed through ontology terms, developmental gene expression, chromatin marks, and genetic mutations. The loss of proximity to CNEs correlated with the independent evolutionary loss of fetus-specific upregulation of nearby genes in the rat brain. DNA breakpoints implicated in brain abnormalities of germline origin had significant representation between a CNE and the gene that exhibited loss of proximity, signifying the underlying developmental tolerance of genomic rearrangements that allowed the evolutionary splits of CNEs and the cognate genes in the rodent lineage. Our observations highlighted a nontrivial impact of chromosomal rearrangements in shaping the evolutionary dynamics of mammalian brain development and might explain the loss of brain traits, like cerebral folding of the cortex, in the rodent lineage.
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11
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Olazagoitia-Garmendia A, Santin I, Castellanos-Rubio A. Functional implication of celiac disease associated lncRNAs in disease pathogenesis. Comput Biol Med 2018; 102:369-375. [DOI: 10.1016/j.compbiomed.2018.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022]
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12
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Personalised Medicine: The Odyssey from Hope to Practice. J Pers Med 2018; 8:jpm8040031. [PMID: 30248964 PMCID: PMC6313378 DOI: 10.3390/jpm8040031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 01/08/2023] Open
Abstract
In this endeavour, inspired by the Odyssey, we aim to embark with the reader on a journey on a ship from Troy to Ithaca, coursing through the history of the momentous events and achievements that paved the way for personalised medicine. We will set sail amidst important genetic discoveries, beginning with the discovery of the first human genome, and voyage through the projects that contributed to the progress of pharmacogenomic studies. Concurrently, we will propose methods to overcome the obstacles that are slowing the potential full implementation of accumulated knowledge into everyday practice. This journey aims to reflect on the frontiers of current genetic knowledge and the practical use of this knowledge in preventive, diagnostic and pharmacogenomic approaches to directly impact the socio-economic aspects of public health.
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Uimari O, Rahmioglu N, Nyholt DR, Vincent K, Missmer SA, Becker C, Morris AP, Montgomery GW, Zondervan KT. Genome-wide genetic analyses highlight mitogen-activated protein kinase (MAPK) signaling in the pathogenesis of endometriosis. Hum Reprod 2017; 32:780-793. [PMID: 28333195 PMCID: PMC5400041 DOI: 10.1093/humrep/dex024] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/24/2017] [Indexed: 12/12/2022] Open
Abstract
STUDY QUESTION Do genome-wide association study (GWAS) data for endometriosis provide insight into novel biological pathways associated with its pathogenesis? SUMMARY ANSWER GWAS analysis uncovered multiple pathways that are statistically enriched for genetic association signals, analysis of Stage A disease highlighted a novel variant in MAP3K4, while top pathways significantly associated with all endometriosis and Stage A disease included several mitogen-activated protein kinase (MAPK)-related pathways. WHAT IS KNOWN ALREADY Endometriosis is a complex disease with an estimated heritability of 50%. To date, GWAS revealed 10 genomic regions associated with endometriosis, explaining <4% of heritability, while half of the heritability is estimated to be due to common risk variants. Pathway analyses combine the evidence of single variants into gene-based measures, leveraging the aggregate effect of variants in genes and uncovering biological pathways involved in disease pathogenesis. STUDY DESIGN, SIZE, DURATION Pathway analysis was conducted utilizing the International Endogene Consortium GWAS data, comprising 3194 surgically confirmed endometriosis cases and 7060 controls of European ancestry with genotype data imputed up to 1000 Genomes Phase three reference panel. GWAS was performed for all endometriosis cases and for Stage A (revised American Fertility Society (rAFS) I/II, n = 1686) and B (rAFS III/IV, n = 1364) cases separately. The identified significant pathways were compared with pathways previously investigated in the literature through candidate association studies. PARTICIPANTS/MATERIALS, SETTING, METHODS The most comprehensive biological pathway databases, MSigDB (including BioCarta, KEGG, PID, SA, SIG, ST and GO) and PANTHER were utilized to test for enrichment of genetic variants associated with endometriosis. Statistical enrichment analysis was performed using the MAGENTA (Meta-Analysis Gene-set Enrichment of variaNT Associations) software. MAIN RESULTS AND THE ROLE OF CHANCE The first genome-wide association analysis for Stage A endometriosis revealed a novel locus, rs144240142 (P = 6.45 × 10−8, OR = 1.71, 95% CI = 1.23–2.37), an intronic single-nucleotide polymorphism (SNP) within MAP3K4. This SNP was not associated with Stage B disease (P = 0.086). MAP3K4 was also shown to be differentially expressed in eutopic endometrium between Stage A endometriosis cases and controls (P = 3.8 × 10−4), but not with Stage B disease (P = 0.26). A total of 14 pathways enriched with genetic endometriosis associations were identified (false discovery rate (FDR)-P < 0.05). The pathways associated with any endometriosis were Grb2-Sos provides linkage to MAPK signaling for integrins pathway (P = 2.8 × 10−5, FDR-P = 3.0 × 10−3), Wnt signaling (P = 0.026, FDR-P = 0.026) and p130Cas linkage to MAPK signaling for integrins pathway (P = 6.0 × 10−4, FDR-P = 0.029); with Stage A endometriosis: extracellular signal-regulated kinase (ERK)1 ERK2 MAPK (P = 5.0 × 10−4, FDR-P = 5.0 × 10−4) and with Stage B endometriosis: two overlapping pathways that related to extracellular matrix biology—Core matrisome (P = 1.4 × 10−3, FDR-P = 0.013) and ECM glycoproteins (P = 1.8 × 10−3, FDR-P = 7.1 × 10−3). Genes arising from endometriosis candidate gene studies performed to date were enriched for Interleukin signaling pathway (P = 2.3 × 10−12), Apoptosis signaling pathway (P = 9.7 × 10−9) and Gonadotropin releasing hormone receptor pathway (P = 1.2 × 10−6); however, these pathways did not feature in the results based on GWAS data. LARGE SCALE DATA Not applicable. LIMITATIONS, REASONS FOR CAUTION The analysis is restricted to (i) variants in/near genes that can be assigned to pathways, excluding intergenic variants; (ii) the gene-based pathway definition as registered in the databases; (iii) women of European ancestry. WIDER IMPLICATIONS OF THE FINDINGS The top ranked pathways associated with overall and Stage A endometriosis in particular involve integrin-mediated MAPK activation and intracellular ERK/MAPK acting downstream in the MAPK cascade, both acting in the control of cell division, gene expression, cell movement and survival. Other top enriched pathways in Stage B disease include ECM glycoprotein pathways important for extracellular structure and biochemical support. The results highlight the need for increased efforts to understand the functional role of these pathways in endometriosis pathogenesis, including the investigation of the biological effects of the genetic variants on downstream molecular processes in tissue relevant to endometriosis. Additionally, our results offer further support for the hypothesis of at least partially distinct causal pathophysiology for minimal/mild (rAFS I/II) vs. moderate/severe (rAFS III/IV) endometriosis. STUDY FUNDING/COMPETING INTEREST(S) The genome-wide association data and Wellcome Trust Case Control Consortium (WTCCC) were generated through funding from the Wellcome Trust (WT084766/Z/08/Z, 076113 and 085475) and the National Health and Medical Research Council (NHMRC) of Australia (241944, 339462, 389927, 389875, 389891, 389892, 389938, 443036, 442915, 442981, 496610, 496739, 552485 and 552498). N.R. was funded by a grant from the Medical Research Council UK (MR/K011480/1). A.P.M. is a Wellcome Trust Senior Fellow in Basic Biomedical Science (grant WT098017). All authors declare there are no conflicts of interest.
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Affiliation(s)
- Outi Uimari
- Endometriosis CaRe Centre, Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford, UK.,Wellcome Trust Center for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Nilufer Rahmioglu
- Endometriosis CaRe Centre, Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford, UK.,Wellcome Trust Center for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Dale R Nyholt
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, Australia
| | - Katy Vincent
- Endometriosis CaRe Centre, Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford, UK
| | - Stacey A Missmer
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, Francis Street, Boston, MA, USA
| | - Christian Becker
- Endometriosis CaRe Centre, Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford, UK
| | - Andrew P Morris
- Wellcome Trust Center for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.,Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Krina T Zondervan
- Endometriosis CaRe Centre, Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford, UK.,Wellcome Trust Center for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
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14
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Association analyses based on false discovery rate implicate new loci for coronary artery disease. Nat Genet 2017; 49:1385-1391. [PMID: 28714975 DOI: 10.1038/ng.3913] [Citation(s) in RCA: 433] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/15/2017] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies (GWAS) in coronary artery disease (CAD) had identified 66 loci at 'genome-wide significance' (P < 5 × 10-8) at the time of this analysis, but a much larger number of putative loci at a false discovery rate (FDR) of 5% (refs. 1,2,3,4). Here we leverage an interim release of UK Biobank (UKBB) data to evaluate the validity of the FDR approach. We tested a CAD phenotype inclusive of angina (SOFT; ncases = 10,801) as well as a stricter definition without angina (HARD; ncases = 6,482) and selected cases with the former phenotype to conduct a meta-analysis using the two most recent CAD GWAS. This approach identified 13 new loci at genome-wide significance, 12 of which were on our previous list of loci meeting the 5% FDR threshold, thus providing strong support that the remaining loci identified by FDR represent genuine signals. The 304 independent variants associated at 5% FDR in this study explain 21.2% of CAD heritability and identify 243 loci that implicate pathways in blood vessel morphogenesis as well as lipid metabolism, nitric oxide signaling and inflammation.
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15
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Castellanos-Rubio A, Kratchmarov R, Sebastian M, Garcia-Etxebarria K, Garcia L, Irastorza I, Ghosh S. Cytoplasmic Form of Carlr lncRNA Facilitates Inflammatory Gene Expression upon NF-κB Activation. THE JOURNAL OF IMMUNOLOGY 2017. [PMID: 28626066 DOI: 10.4049/jimmunol.1700023] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as critical regulators of inflammation. To further understand the interaction between inflammatory signaling pathways and lncRNAs, we characterized the function of cardiac and apoptosis-related lncRNA (Carlr), an lncRNA expressed in both mouse and human cells of diverse tissues. Carlr expression is increased following NF-κB signaling in macrophages, with concomitant translocation to, and enrichment of, the transcript in the cytoplasm. Knockdown of Carlr results in impaired expression of NF-κB pathway genes and influences the interaction between macrophages and intestinal cells in an inflammatory environment. In human celiac disease patient samples, increased levels of the Carlr transcript were detected in the cytoplasm, alongside elevated expression of NF-κB pathway genes. These findings suggest that increased Carlr expression and/or cytoplasmic localization is required for efficient NF-κB signaling and is associated with the inflamed tissue state observed in human celiac disease.
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Affiliation(s)
- Ainara Castellanos-Rubio
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032; .,Immunogenetics Research Laboratory, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain.,BioCruces Health Research Institute, 48903 Barakaldo, Spain; and
| | - Radomir Kratchmarov
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Maialen Sebastian
- Immunogenetics Research Laboratory, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain.,BioCruces Health Research Institute, 48903 Barakaldo, Spain; and
| | - Koldo Garcia-Etxebarria
- Immunogenetics Research Laboratory, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain.,BioCruces Health Research Institute, 48903 Barakaldo, Spain; and
| | - Liher Garcia
- Immunogenetics Research Laboratory, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain.,BioCruces Health Research Institute, 48903 Barakaldo, Spain; and
| | - Iñaki Irastorza
- Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country, UPV/EHU, 48903 Barakaldo 48903, Spain
| | - Sankar Ghosh
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032;
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16
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Holland N. Future of environmental research in the age of epigenomics and exposomics. REVIEWS ON ENVIRONMENTAL HEALTH 2017; 32:45-54. [PMID: 27768585 PMCID: PMC5346048 DOI: 10.1515/reveh-2016-0032] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/15/2016] [Indexed: 05/14/2023]
Abstract
Environmental research and public health in the 21st century face serious challenges such as increased air pollution and global warming, widespread use of potentially harmful chemicals including pesticides, plasticizers, and other endocrine disruptors, and radical changes in nutrition and lifestyle typical of modern societies. In particular, exposure to environmental and occupational toxicants may contribute to the occurrence of adverse birth outcomes, neurodevelopmental deficits, and increased risk of cancer and other multifactorial diseases such as diabetes and asthma. Rapidly evolving methodologies of exposure assessment and the conceptual framework of the Exposome, first introduced in 2005, are new frontiers of environmental research. Metabolomics and adductomics provide remarkable opportunities for a better understanding of exposure and prediction of potential adverse health outcomes. Metabolomics, the study of metabolism at whole-body level, involves assessment of the total repertoire of small molecules present in a biological sample, shedding light on interactions between gene expression, protein expression, and the environment. Advances in genomics, transcriptomics, and epigenomics are generating multidimensional structures of biomarkers of effect and susceptibility, increasingly important for the understanding of molecular mechanisms and the emergence of personalized medicine. Epigenetic mechanisms, particularly DNA methylation and miRNA expression, attract increasing attention as potential links between the genetic and environmental determinants of health and disease. Unlike genetics, epigenetic mechanisms could be reversible and an understanding of their role may lead to better protection of susceptible populations and improved public health.
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17
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Castellanos-Rubio A, Fernandez-Jimenez N, Kratchmarov R, Luo X, Bhagat G, Green PHR, Schneider R, Kiledjian M, Bilbao JR, Ghosh S. A long noncoding RNA associated with susceptibility to celiac disease. Science 2016; 352:91-5. [PMID: 27034373 DOI: 10.1126/science.aad0467] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/18/2016] [Indexed: 12/15/2022]
Abstract
Recent studies have implicated long noncoding RNAs (lncRNAs) as regulators of many important biological processes. Here we report on the identification and characterization of a lncRNA, lnc13, that harbors a celiac disease-associated haplotype block and represses expression of certain inflammatory genes under homeostatic conditions. Lnc13 regulates gene expression by binding to hnRNPD, a member of a family of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). Upon stimulation, lnc13 levels are reduced, thereby allowing increased expression of the repressed genes. Lnc13 levels are significantly decreased in small intestinal biopsy samples from patients with celiac disease, which suggests that down-regulation of lnc13 may contribute to the inflammation seen in this disease. Furthermore, the lnc13 disease-associated variant binds hnRNPD less efficiently than its wild-type counterpart, thus helping to explain how these single-nucleotide polymorphisms contribute to celiac disease.
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Affiliation(s)
- Ainara Castellanos-Rubio
- Department of Microbiology and Immunology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Research Institute, Leioa 48940, Basque Country, Spain
| | - Radomir Kratchmarov
- Department of Microbiology and Immunology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
| | - Xiaobing Luo
- Department of Pathology and Cell Biology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
| | - Govind Bhagat
- Center for Celiac Disease, Department of Medicine, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA. Alexandria Center for Life Sciences, New York University School of Medicine, New York, NY 10016, USA
| | - Peter H R Green
- Alexandria Center for Life Sciences, New York University School of Medicine, New York, NY 10016, USA
| | - Robert Schneider
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Megerditch Kiledjian
- Department of Pathology and Cell Biology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Research Institute, Leioa 48940, Basque Country, Spain
| | - Sankar Ghosh
- Department of Microbiology and Immunology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA.
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18
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Cacace R, Sleegers K, Van Broeckhoven C. Molecular genetics of early-onset Alzheimer's disease revisited. Alzheimers Dement 2016; 12:733-48. [DOI: 10.1016/j.jalz.2016.01.012] [Citation(s) in RCA: 304] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/20/2016] [Accepted: 01/28/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Rita Cacace
- Neurodegenerative Brain Diseases group; Department of Molecular Genetics; VIB; Antwerp Belgium
- Laboratory of Neurogenetics; Institute Born-Bunge, University of Antwerp; Antwerp Belgium
| | - Kristel Sleegers
- Neurodegenerative Brain Diseases group; Department of Molecular Genetics; VIB; Antwerp Belgium
- Laboratory of Neurogenetics; Institute Born-Bunge, University of Antwerp; Antwerp Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases group; Department of Molecular Genetics; VIB; Antwerp Belgium
- Laboratory of Neurogenetics; Institute Born-Bunge, University of Antwerp; Antwerp Belgium
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19
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Abstract
Recent advances in the understanding of gene regulation have shown there to be much more regulation of the genome than first thought, through epigenetic mechanisms. These epigenetic mechanisms are systems that have evolved to either switch off gene activity altogether, or fine-tune any existing genetic activation. Such systems are present in all genes and include chromatin modifications and remodelling, DNA methylation (such as CpG island methylation rates) and histone covalent modifications (e.g. acetylation, methylation), RNA interference by short interfering RNAs (siRNAs) and long non-coding RNAs (ncRNAs). These systems regulate genomic activity 'beyond' simple transcriptional factor inducer or repressor function of genes to generate mRNA. Epigenetic regulation of gene activity has been shown to be important in maintaining normal phenotypic activity of cells, as well as having a role in development and diseases such as cancer and neurodegenerative disorders such as Alzheimer's. Newer classes of drugs regulate epigenetic mechanisms to counteract disease states in humans. The reports in this issue describe some advances in epigenetic understanding that relate to human disease, and our ability to control these mechanisms by pharmacological means. Increasingly the importance of epigenetics is being uncovered - it is pharmacology that will have to keep pace.
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Affiliation(s)
- Barbara Stefanska
- Department of Nutrition Science, Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - David J MacEwan
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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20
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Lin CY, Erkek S, Tong Y, Yin L, Federation AJ, Zapatka M, Haldipur P, Kawauchi D, Risch T, Warnatz HJ, Worst BC, Ju B, Orr BA, Zeid R, Polaski DR, Segura-Wang M, Waszak SM, Jones DTW, Kool M, Hovestadt V, Buchhalter I, Sieber L, Johann P, Chavez L, Gröschel S, Ryzhova M, Korshunov A, Chen W, Chizhikov VV, Millen KJ, Amstislavskiy V, Lehrach H, Yaspo ML, Eils R, Lichter P, Korbel JO, Pfister SM, Bradner JE, Northcott PA. Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Nature 2016; 530:57-62. [PMID: 26814967 DOI: 10.1038/nature16546] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 12/14/2015] [Indexed: 12/23/2022]
Abstract
Medulloblastoma is a highly malignant paediatric brain tumour, often inflicting devastating consequences on the developing child. Genomic studies have revealed four distinct molecular subgroups with divergent biology and clinical behaviour. An understanding of the regulatory circuitry governing the transcriptional landscapes of medulloblastoma subgroups, and how this relates to their respective developmental origins, is lacking. Here, using H3K27ac and BRD4 chromatin immunoprecipitation followed by sequencing (ChIP-seq) coupled with tissue-matched DNA methylation and transcriptome data, we describe the active cis-regulatory landscape across 28 primary medulloblastoma specimens. Analysis of differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity and revealed novel, clinically relevant insights into medulloblastoma biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors, validated by ChIP-seq, that is responsible for subgroup divergence, and implicates candidate cells of origin for Group 4. Our integrated analysis of enhancer elements in a large series of primary tumour samples reveals insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins.
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Affiliation(s)
- Charles Y Lin
- Medical Oncology, Dana Farber Cancer Institute (DFCI), Boston, Massachusetts 02215, USA
| | - Serap Erkek
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Yiai Tong
- Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Linlin Yin
- Department of Molecular Physiology &Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, USA
| | | | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98105, USA
| | - Daisuke Kawauchi
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Risch
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Hans-Jörg Warnatz
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Barbara C Worst
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Bensheng Ju
- Department of Bone Marrow Transplantation &Cellular Therapy, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Brent A Orr
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Rhamy Zeid
- Medical Oncology, Dana Farber Cancer Institute (DFCI), Boston, Massachusetts 02215, USA
| | - Donald R Polaski
- Medical Oncology, Dana Farber Cancer Institute (DFCI), Boston, Massachusetts 02215, USA
| | - Maia Segura-Wang
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Sebastian M Waszak
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ivo Buchhalter
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Laura Sieber
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Pascal Johann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefan Gröschel
- Department of Translational Oncology, NCT Heidelberg, 69120 Heidelberg, Germany
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, 125047 Moscow, Russia
| | - Andrey Korshunov
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), and Department of Neuropathology University Hospital, 69120 Heidelberg, Germany
| | - Wenbiao Chen
- Department of Molecular Physiology &Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, USA
| | - Victor V Chizhikov
- Department of Anatomy and Neurobiology, University of Tennessee Health Sciences Center, Memphis, Tennessee 38163, USA
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98105, USA.,Department of Pediatrics, Genetics Division, University of Washington, Seattle, Washington 98195, USA
| | - Vyacheslav Amstislavskiy
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology and BioQuant, University of Heidelberg, 69117 Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatrics, University of Heidelberg, 69117 Heidelberg, Germany
| | - James E Bradner
- Medical Oncology, Dana Farber Cancer Institute (DFCI), Boston, Massachusetts 02215, USA
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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21
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Low TY, Heck AJ. Reconciling proteomics with next generation sequencing. Curr Opin Chem Biol 2015; 30:14-20. [PMID: 26590485 DOI: 10.1016/j.cbpa.2015.10.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
Abstract
Both genomics and proteomics technologies have matured in the last decade to a level where they are able to deliver system-wide data on the qualitative and quantitative abundance of their respective molecular entities, that is DNA/RNA and proteins. A next logical step is the collective use of these technologies, ideally gathering data on matching samples. The first large scale so-called proteogenomics studies are emerging, and display the benefits each of these layers of analysis has on the other layers to together generate more meaningful insight into the connection between the phenotype/physiology and genotype of the system under study. Here we review a selected number of these studies, highlighting what they can uniquely deliver. We also discuss the future potential and remaining challenges, from a somewhat proteome biased perspective.
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Affiliation(s)
- Teck Yew Low
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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22
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Amaral MD, Balch WE. Hallmarks of therapeutic management of the cystic fibrosis functional landscape. J Cyst Fibros 2015; 14:687-99. [PMID: 26526359 PMCID: PMC4644672 DOI: 10.1016/j.jcf.2015.09.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/16/2015] [Accepted: 09/16/2015] [Indexed: 01/29/2023]
Abstract
The cystic fibrosis (CF) transmembrane conductance regulator (CFTR) protein does not operate in isolation, rather in a dynamic network of interacting components that impact its synthesis, folding, stability, intracellular location and function, referred to herein as the 'CFTR Functional Landscape (CFFL)'. For the prominent F508del mutation, many of these interactors are deeply connected to a protein fold management system, the proteostasis network (PN). However, CF encompasses an additional 2000 CFTR variants distributed along its entire coding sequence (referred to as CFTR2), and each variant contributes a differential liability to PN management of CFTR and to a protein 'social network' (SN) that directs the probability of the (patho)physiologic events that impact ion transport in each cell, tissue and patient in health and disease. Recognition of the importance of the PN and SN in driving the unique patient CFFL leading to disease highlights the importance of precision medicine in therapeutic management of disease progression. We take the view herein that it is not CFTR, rather the PN/SN, and their impact on the CFFL, that are the key physiologic forces driving onset and clinical progression of CF. We posit that a deep understanding of each patients PN/SN gained by merging genomic, proteomic (mass spectrometry (MS)), and high-content microscopy (HCM) technologies in the context of novel network learning algorithms will lead to a paradigm shift in CF clinical management. This should allow for generation of new classes of patient specific PN/SN directed therapeutics for personalized management of the CFFL in the clinic.
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Affiliation(s)
- Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal.
| | - William E Balch
- Department of Chemical Physiology, Department of Cell and Molecular Biology, The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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