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Zhang Q, Ma S, Liu Z, Zhu B, Zhou Z, Li G, Meana JJ, González-Maeso J, Lu C. Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes. Nat Commun 2023; 14:4672. [PMID: 37537185 PMCID: PMC10400590 DOI: 10.1038/s41467-023-40411-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
The genome-wide DNA methylation profile, or DNA methylome, is a critical component of the overall epigenomic landscape that modulates gene activities and cell fate. Single-cell DNA methylomic studies offer unprecedented resolution for detecting and profiling cell subsets based on methylomic features. However, existing single-cell methylomic technologies are based on use of tubes or well plates and these platforms are not easily scalable for handling a large number of single cells. Here we demonstrate a droplet-based microfluidic technology, Drop-BS, to construct single-cell bisulfite sequencing libraries for DNA methylome profiling. Drop-BS takes advantage of the ultrahigh throughput offered by droplet microfluidics to prepare bisulfite sequencing libraries of up to 10,000 single cells within 2 days. We apply the technology to profile mixed cell lines, mouse and human brain tissues to reveal cell type heterogeneity. Drop-BS offers a promising solution for single-cell methylomic studies requiring examination of a large cell population.
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Affiliation(s)
- Qiang Zhang
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, 24061, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Gaoshan Li
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - J Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, CIBERSAM, Biocruces Health Research Institute, E-48940, Leioa, Bizkaia, Spain
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
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2
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Zhang Q, Ma S, Liu Z, Zhu B, Zhou Z, Li G, Meana JJ, González-Maeso J, Lu C. Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542421. [PMID: 37293095 PMCID: PMC10245959 DOI: 10.1101/2023.05.26.542421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Genome-wide DNA methylation profile, or DNA methylome, is a critical component of the overall epigenomic landscape that modulates gene activities and cell fate. Single-cell DNA methylomic studies offer unprecedented resolution for detecting and profiling cell subsets based on methylomic features. However, existing single-cell methylomic technologies are all based on use of tubes or well plates and these platforms are not easily scalable for handling a large number of single cells. Here we demonstrate a droplet-based microfluidic technology, Drop-BS, to construct single-cell bisulfite sequencing libraries for DNA methylome profiling. Drop-BS takes advantage of the ultrahigh throughput offered by droplet microfluidics to prepare bisulfite sequencing libraries of up to 10,000 single cells within 2 d. We applied the technology to profile mixed cell lines, mouse and human brain tissues to reveal cell type heterogeneity. Drop-BS will pave the way for single-cell methylomic studies requiring examination of a large cell population.
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Affiliation(s)
- Qiang Zhang
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
- Present address: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Gaoshan Li
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - J. Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, CIBERSAM, Biocruces Health Research Institute, E-48940 Leioa, Bizkaia, Spain
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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3
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Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform. BMC Bioinformatics 2023; 24:33. [PMID: 36721080 PMCID: PMC9890740 DOI: 10.1186/s12859-023-05163-w] [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: 10/25/2022] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Whole genome bisulfite sequencing (WGBS), possesses the aptitude to dissect methylation status at the nucleotide-level resolution of 5-methylcytosine (5-mC) on a genome-wide scale. It is a powerful technique for epigenome in various cell types, and tissues. As a recently established next-generation sequencing (NGS) platform, GenoLab M is a promising alternative platform. However, its comprehensive evaluation for WGBS has not been reported. We sequenced two bisulfite-converted mammal DNA in this research using our GenoLab M and NovaSeq 6000, respectively. Then, we systematically compared those data via four widely used WGBS tools (BSMAP, Bismark, BatMeth2, BS-Seeker2) and a new bisulfite-seq tool (BSBolt). We interrogated their computational time, genome depth and coverage, and evaluated their percentage of methylated Cs. RESULT Here, benchmarking a combination of pre- and post-processing methods, we found that trimming improved the performance of mapping efficiency in eight datasets. The data from two platforms uncovered ~ 80% of CpG sites genome-wide in the human cell line. Those data sequenced by GenoLab M achieved a far lower proportion of duplicates (~ 5.5%). Among pipelines, BSMAP provided an intriguing representation of 5-mC distribution at CpG sites with 5-mC levels > ~ 78% in datasets from human cell lines, especially in the GenoLab M. BSMAP performed more advantages in running time, uniquely mapped reads percentages, genomic coverage, and quantitative accuracy. Finally, compared with the previous methylation pattern of human cell line and mouse tissue, we confirmed that the data from GenoLab M performed similar consistency and accuracy in methylation levels of CpG sites with that from NovaSeq 6000. CONCLUSION Together we confirmed that GenoLab M was a qualified NGS platform for WGBS with high performance. Our results showed that BSMAP was the suitable pipeline that allowed for WGBS studies on the GenoLab M platform.
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Hernandez-Corchado A, Najafabadi HS. Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding. Genome Biol 2022; 23:151. [PMID: 35799193 PMCID: PMC9264634 DOI: 10.1186/s13059-022-02713-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 06/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background While methylation of CpG dinucleotides is traditionally considered antagonistic to the DNA-binding activity of most transcription factors (TFs), recent in vitro studies have revealed a more complex picture, suggesting that over a third of TFs may preferentially bind to methylated sequences. Expanding these in vitro observations to in vivo TF binding preferences is challenging since the effect of methylation of individual CpG sites cannot be easily isolated from the confounding effects of DNA accessibility and regional DNA methylation. Thus, in vivo methylation preferences of most TFs remain uncharacterized. Results We introduce joint accessibility-methylation-sequence (JAMS) models, which connect the strength of the binding signal observed in ChIP-seq to the DNA accessibility of the binding site, regional methylation level, DNA sequence, and base-resolution cytosine methylation. We show that JAMS models quantitatively explain TF occupancy, recapitulate cell type-specific TF binding, and have high positive predictive value for identification of TFs affected by intra-motif methylation. Analysis of 2209 ChIP-seq experiments results in high-confidence JAMS models for 260 TFs, revealing a negative association between in vivo TF occupancy and intra-motif methylation for 45% of studied TFs, as well as 16 TFs that are predicted to bind to methylated sites, including 11 novel methyl-binding TFs mostly from the multi-zinc finger family. Conclusions Our study substantially expands the repertoire of in vivo methyl-binding TFs, but also suggests that most TFs that prefer methylated CpGs in vitro present themselves as methylation agnostic in vivo, potentially due to the balancing effect of competition with other methyl-binding proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02713-y.
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Affiliation(s)
- Aldo Hernandez-Corchado
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada.,McGill Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada. .,McGill Genome Centre, Montreal, QC, H3A 0G1, Canada.
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5
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Abstract
Single-cell technologies measure unique cellular signatures but are typically limited to a single modality. Computational approaches allow the fusion of diverse single-cell data types, but their efficacy is difficult to validate in the absence of authentic multi-omic measurements. To comprehensively assess the molecular phenotypes of single cells, we devised single-nucleus methylcytosine, chromatin accessibility, and transcriptome sequencing (snmCAT-seq) and applied it to postmortem human frontal cortex tissue. We developed a cross-validation approach using multi-modal information to validate fine-grained cell types and assessed the effectiveness of computational data fusion methods. Correlation analysis in individual cells revealed distinct relations between methylation and gene expression. Our integrative approach enabled joint analyses of the methylome, transcriptome, chromatin accessibility, and conformation for 63 human cortical cell types. We reconstructed regulatory lineages for cortical cell populations and found specific enrichment of genetic risk for neuropsychiatric traits, enabling the prediction of cell types that are associated with diseases.
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Yang QY, Hu YH, Guo HL, Xia Y, Zhang Y, Fang WR, Li YM, Xu J, Chen F, Wang YR, Wang TF. Vincristine-Induced Peripheral Neuropathy in Childhood Acute Lymphoblastic Leukemia: Genetic Variation as a Potential Risk Factor. Front Pharmacol 2021; 12:771487. [PMID: 34955843 PMCID: PMC8696478 DOI: 10.3389/fphar.2021.771487] [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: 09/07/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022] Open
Abstract
Vincristine (VCR) is the first-line chemotherapeutic medication often co-administered with other drugs to treat childhood acute lymphoblastic leukemia. Dose-dependent neurotoxicity is the main factor restricting VCR’s clinical application. VCR-induced peripheral neuropathy (VIPN) sometimes results in dose reduction or omission, leading to clinical complications or affecting the patient’s quality of life. With regard to the genetic basis of drug responses, preemptive pharmacogenomic testing and simultaneous blood level monitoring could be helpful for the transformation of various findings into individualized therapies. In this review, we discussed the potential associations between genetic variants in genes contributing to the pharmacokinetics/pharmacodynamics of VCR and VIPN incidence and severity in patients with acute lymphoblastic leukemia. Of note, genetic variants in the CEP72 gene have great potential to be translated into clinical practice. Such a genetic biomarker may help clinicians diagnose VIPN earlier. Besides, genetic variants in other genes, such as CYP3A5, ABCB1, ABCC1, ABCC2, TTPA, ACTG1, CAPG, SYNE2, SLC5A7, COCH, and MRPL47, have been reported to be associated with the VIPN, but more evidence is needed to validate the findings in the future. In fact, a variety of complex factors jointly determine the VIPN. In implementing precision medicine, the combination of genetic, environmental, and personal variables, along with therapeutic drug monitoring, will allow for a better understanding of the mechanisms of VIPN, improving the effectiveness of VCR treatment, reducing adverse reactions, and improving patients’ quality of life.
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Affiliation(s)
- Qing-Yan Yang
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China.,School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Ya-Hui Hu
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Li Guo
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Ying Xia
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yong Zhang
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei-Rong Fang
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yun-Man Li
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jing Xu
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Chen
- Pharmaceutical Sciences Research Center, Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yong-Ren Wang
- Department of Hematology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Teng-Fei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, United States
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7
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Sánchez OF, Lin LF, Xie J, Freeman JL, Yuan C. Lead exposure induces dysregulation of constitutive heterochromatin hallmarks in live cells. Curr Res Toxicol 2021; 3:100061. [PMID: 35005634 PMCID: PMC8717252 DOI: 10.1016/j.crtox.2021.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/28/2022] Open
Abstract
Lead (Pb) is a heavy metal contaminant commonly found in air, soil, and drinking water due to legacy uses. Excretion of ingested Pb can result in extensive kidney damages due to elevated oxidative stress. Epigenetic alterations induced by exposure to Pb have also been implied but remain poorly understood. In this work, we assessed changes in repressive epigenetic marks, namely DNA methylation (meCpG) and histone 3 lysine 9 tri-methylation (H3K9me3) after exposure to Pb. Live cell epigenetic probes coupled to bimolecular fluorescence complementation (BiFC) were used to monitor changes in the selected epigenetic marks. Exposure to Pb significantly lowered meCpG and H3K9me3 levels in HEK293T cells suggesting global changes in constitutive heterochromatin. A heterodimeric pair of probes that tags chromatin regions enriched in both meCpG and H3K9me3 further confirmed our findings. The observed epigenetic changes can be partially attributed to aberrant transcriptional changes induced by Pb, such as overexpression of TET1 after Pb exposure. Lastly, we monitored changes in selected heterochromatin marks after removal of Pb and found that changes in these markers do not immediately recover to their original level suggesting potential long-term damages to chromatin structure.
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Affiliation(s)
- Oscar F. Sánchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Li F. Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Jennifer L. Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center of Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center of Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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8
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Goossens R, Tihaya MS, van den Heuvel A, Tabot-Ndip K, Willemsen IM, Tapscott SJ, González-Prieto R, Chang JG, Vertegaal ACO, Balog J, van der Maarel SM. A proteomics study identifying interactors of the FSHD2 gene product SMCHD1 reveals RUVBL1-dependent DUX4 repression. Sci Rep 2021; 11:23642. [PMID: 34880314 PMCID: PMC8654949 DOI: 10.1038/s41598-021-03030-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/23/2021] [Indexed: 11/25/2022] Open
Abstract
Structural Maintenance of Chromosomes Hinge Domain Containing 1 (SMCHD1) is a chromatin repressor, which is mutated in > 95% of Facioscapulohumeral dystrophy (FSHD) type 2 cases. In FSHD2, SMCHD1 mutations ultimately result in the presence of the cleavage stage transcription factor DUX4 in muscle cells due to a failure in epigenetic repression of the D4Z4 macrosatellite repeat on chromosome 4q, which contains the DUX4 locus. While binding of SMCHD1 to D4Z4 and its necessity to maintain a repressive D4Z4 chromatin structure in somatic cells are well documented, it is unclear how SMCHD1 is recruited to D4Z4, and how it exerts its repressive properties on chromatin. Here, we employ a quantitative proteomics approach to identify and characterize novel SMCHD1 interacting proteins, and assess their functionality in D4Z4 repression. We identify 28 robust SMCHD1 nuclear interactors, of which 12 are present in D4Z4 chromatin of myocytes. We demonstrate that loss of one of these SMCHD1 interacting proteins, RuvB-like 1 (RUVBL1), further derepresses DUX4 in FSHD myocytes. We also confirm the interaction of SMCHD1 with EZH inhibitory protein (EZHIP), a protein which prevents global H3K27me3 deposition by the Polycomb repressive complex PRC2, providing novel insights into the potential function of SMCHD1 in the repression of DUX4 in the early stages of embryogenesis. The SMCHD1 interactome outlined herein can thus provide further direction into research on the potential function of SMCHD1 at genomic loci where SMCHD1 is known to act, such as D4Z4 repeats, the inactive X chromosome, autosomal gene clusters, imprinted loci and telomeres.
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Affiliation(s)
- Remko Goossens
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mara S Tihaya
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anita van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Klorane Tabot-Ndip
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Iris M Willemsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jer-Gung Chang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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9
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Fan H, Guo Y, Tsai YH, Storey AJ, Kim A, Gong W, Edmondson RD, Mackintosh SG, Li H, Byrum SD, Tackett AJ, Cai L, Wang GG. A conserved BAH module within mammalian BAHD1 connects H3K27me3 to Polycomb gene silencing. Nucleic Acids Res 2021; 49:4441-4455. [PMID: 33823544 PMCID: PMC8096256 DOI: 10.1093/nar/gkab210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/28/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
Trimethylation of histone H3 lysine 27 (H3K27me3) is important for gene silencing and imprinting, (epi)genome organization and organismal development. In a prevalent model, the functional readout of H3K27me3 in mammalian cells is achieved through the H3K27me3-recognizing chromodomain harbored within the chromobox (CBX) component of canonical Polycomb repressive complex 1 (cPRC1), which induces chromatin compaction and gene repression. Here, we report that binding of H3K27me3 by a Bromo Adjacent Homology (BAH) domain harbored within BAH domain-containing protein 1 (BAHD1) is required for overall BAHD1 targeting to chromatin and for optimal repression of the H3K27me3-demarcated genes in mammalian cells. Disruption of direct interaction between BAHD1BAH and H3K27me3 by point mutagenesis leads to chromatin remodeling, notably, increased histone acetylation, at its Polycomb gene targets. Mice carrying an H3K27me3-interaction-defective mutation of Bahd1BAH causes marked embryonic lethality, showing a requirement of this pathway for normal development. Altogether, this work demonstrates an H3K27me3-initiated signaling cascade that operates through a conserved BAH ‘reader’ module within BAHD1 in mammals.
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Affiliation(s)
- Huitao Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Arum Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Haitao Li
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, and Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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10
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Bierne H, Hamon M. Targeting host epigenetic machinery: The Listeria paradigm. Cell Microbiol 2021; 22:e13169. [PMID: 32185898 DOI: 10.1111/cmi.13169] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 12/11/2022]
Abstract
By modifying the host cell transcription programme, pathogenic bacteria disrupt a wide range of cellular processes and take control of the host's immune system. Conversely, by mobilising a network of defence genes, the host cells trigger various responses that allow them to tolerate or eliminate invaders. The study of the molecular basis of this crosstalk is crucial to the understanding of infectious diseases. Although research has long focused on the targeting of eukaryotic DNA-binding transcription factors, more recently, another powerful way by which bacteria modify the expression of host genes has emerged: chromatin modifications in the cell nucleus. One of the most prolific bacterial models in this area has been Listeria monocytogenes, a facultative intracellular bacterium responsible for serious food-borne infections. Here, we aim to highlight the contribution of this model to the field of bacteria-mediated chromatin modifications. We will first recall the general principles of epigenetic regulation and then illustrate five mechanisms that mobilise the epigenetic machinery in response to Listeria factors, either through bacterial molecular patterns, a toxin, an invasion protein, or nucleomodulins. Strategies used by Listeria to control the expression of host genes at the chromatin level, by activation of cytosolic signalling pathways or direct targeting of epifactors in the nucleus, have contributed to the emergence of a new discipline combining cellular microbiology and epigenetics: "patho-epigenetics."
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Affiliation(s)
- Hélène Bierne
- Université Paris Saclay, INRAE, AgroParisTech, Micalis Institute, Epigenetics and Cellular Microbiology Team, Jouy-en-Josas, France
| | - Mélanie Hamon
- G5 Chromatin and Infection, Institut Pasteur, Paris, France
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11
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A ubiquitin ligase toggles red cell differentiation. Blood 2021; 137:143-144. [PMID: 33443559 DOI: 10.1182/blood.2020009697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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12
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Wells D, Bitoun E, Moralli D, Zhang G, Hinch A, Jankowska J, Donnelly P, Green C, Myers SR. ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair. eLife 2020; 9:53392. [PMID: 32744506 PMCID: PMC7494361 DOI: 10.7554/elife.53392] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
During meiosis, homologous chromosomes pair and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, double-strand breaks (DSBs) initiate recombination within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have been identified. We identified Zcwpw1, containing H3K4me3 and H3K36me3 recognition domains, as having highly correlated expression with Prdm9. Here, we show that ZCWPW1 has co-evolved with PRDM9 and, in human cells, is strongly and specifically recruited to PRDM9 binding sites, with higher affinity than sites possessing H3K4me3 alone. Surprisingly, ZCWPW1 also recognises CpG dinucleotides. Male Zcwpw1 knockout mice show completely normal DSB positioning, but persistent DMC1 foci, severe DSB repair and synapsis defects, and downstream sterility. Our findings suggest ZCWPW1 recognition of PRDM9-bound sites at DSB hotspots is critical for synapsis, and hence fertility. Sexual reproduction – that is, the combination of sex cells from two different individuals to produce an embryo – is one of the many mechanisms that have evolved to maintain genetic diversity. Most human cells contain 23 pairs of chromosomes, with each chromosome in a pair carrying either a paternal or maternal copy of the same gene. To form an embryo with the right number of chromosomes, each sex cell (the egg or sperm cell) must only contain one chromosome from each pair. Sex cells are produced from parent cells containing two sets of paternal and maternal chromosomes: these cells then divide twice to form four sex cells which contain only one chromosome from each pair. Before the parent cell divides, a process known as ‘recombination’ takes place, which allows chromosomes in a pair to exchange bits of genetic information. This reshuffling ensures that each chromosome in a sex cell is unique. A protein called PRDM9 helps control which sections of genetic information are recombined by modifying proteins attached to the chromosomes, marking them as locations for exchange. The DNA at each of these sites is then broken and repaired using the genetic sequence of the chromosome it is paired with as a template, thus causing the two chromosomes to swap genes. In 2019, a group of researchers found a set of genes in the testis of mice that are expressed at the same time as the gene for PRDM9. This suggested that another protein called ZCWPW1 is likely involved in recombination, but the precise role of this protein was unclear. To answer this question, Wells, Bitoun et al. – including many of the researchers involved in the 2019 study – examined human cells grown in the laboratory to determine where ZCWPW1 binds to in the chromosome. This revealed that ZCWPW1 can be found at the same sites as PRDM9, which is responsible for bringing it there. Furthermore, cells from male mice lacking the gene for ZCWPW1 cannot complete the exchange of genetic information between chromosomes, meaning that the mice are infertile. As such, ZCWPW1 seems to connect location selection by PRDM9 to the DNA repair mechanisms needed for gene exchange between chromosomes. Infertility is a significant issue for humans affecting as many as one in every six couples. Fertility is complex and many of the biological mechanisms involved are not fully understood. This work suggests that both PRDM9 and ZCWPW1 are key to the production of sex cells and may be worth investigating as factors that affect fertility in humans.
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Affiliation(s)
- Daniel Wells
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Emmanuelle Bitoun
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Daniela Moralli
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Gang Zhang
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Anjali Hinch
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Julia Jankowska
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Peter Donnelly
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Catherine Green
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Simon R Myers
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
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13
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Pourpre R, Naudon L, Meziane H, Lakisic G, Jouneau L, Varet H, Legendre R, Wendling O, Selloum M, Proux C, Coppée JY, Herault Y, Bierne H. BAHD1 haploinsufficiency results in anxiety-like phenotypes in male mice. PLoS One 2020; 15:e0232789. [PMID: 32407325 PMCID: PMC7224496 DOI: 10.1371/journal.pone.0232789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
BAHD1 is a heterochomatinization factor recently described as a component of a multiprotein complex associated with histone deacetylases HDAC1/2. The physiological and patho-physiological functions of BAHD1 are not yet well characterized. Here, we examined the consequences of BAHD1 deficiency in the brains of male mice. While Bahd1 knockout mice had no detectable defects in brain anatomy, RNA sequencing profiling revealed about 2500 deregulated genes in Bahd1-/- brains compared to Bahd1+/+ brains. A majority of these genes were involved in nervous system development and function, behavior, metabolism and immunity. Exploration of the Allen Brain Atlas and Dropviz databases, assessing gene expression in the brain, revealed that expression of the Bahd1 gene was limited to a few territories and cell subtypes, particularly in the hippocampal formation, the isocortex and the olfactory regions. The effect of partial BAHD1 deficiency on behavior was then evaluated on Bahd1 heterozygous male mice, which have no lethal or metabolic phenotypes. Bahd1+/- mice showed anxiety-like behavior and reduced prepulse inhibition (PPI) of the startle response. Altogether, these results suggest that BAHD1 plays a role in chromatin-dependent gene regulation in a subset of brain cells and support recent evidence linking genetic alteration of BAHD1 to psychiatric disorders in a human patient.
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Affiliation(s)
- Renaud Pourpre
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Laurent Naudon
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Micalis Institute, Université Paris-Saclay, CNRS, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Hamid Meziane
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
| | - Goran Lakisic
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Hugo Varet
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Olivia Wendling
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
| | - Mohammed Selloum
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
| | - Caroline Proux
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Yann Herault
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC), UMR7104, U1268, Illkirch, France
| | - Hélène Bierne
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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14
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Gavery MR, Nichols KM, Berejikian BA, Tatara CP, Goetz GW, Dickey JT, Van Doornik DM, Swanson P. Temporal Dynamics of DNA Methylation Patterns in Response to Rearing Juvenile Steelhead ( Oncorhynchus mykiss) in a Hatchery versus Simulated Stream Environment. Genes (Basel) 2019; 10:E356. [PMID: 31075961 PMCID: PMC6563097 DOI: 10.3390/genes10050356] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
Genetic selection is often implicated as the underlying cause of heritable phenotypic differences between hatchery and wild populations of steelhead trout (Oncorhynchus mykiss) that also differ in lifetime fitness. Developmental plasticity, which can also affect fitness, may be mediated by epigenetic mechanisms such as DNA methylation. Our previous study identified significant differences in DNA methylation between adult hatchery- and natural-origin steelhead from the same population that could not be distinguished by DNA sequence variation. In the current study, we tested whether hatchery-rearing conditions can influence patterns of DNA methylation in steelhead with known genetic backgrounds, and assessed the stability of these changes over time. Eyed-embryos from 22 families of Methow River steelhead were split across traditional hatchery tanks or a simulated stream-rearing environment for 8 months, followed by a second year in a common hatchery tank environment. Family assignments were made using a genetic parentage analysis to account for relatedness among individuals. DNA methylation patterns were examined in the liver, a relatively homogeneous organ that regulates metabolic processes and somatic growth, of juveniles at two time points: after eight months of rearing in either a tank or stream environment and after a subsequent year of rearing in a common tank environment. Further, we analyzed DNA methylation in the sperm of mature 2-year-old males from the earlier described treatments to assess the potential of environmentally-induced changes to be passed to offspring. Hepatic DNA methylation changes in response to hatchery versus stream-rearing in yearling fish were substantial, but few persisted after a second year in the tank environment. However, the early rearing environment appeared to affect how fish responded to developmental and environmental signals during the second year since novel DNA methylation differences were identified in the livers of hatchery versus stream-reared fish after a year of common tank rearing. Furthermore, we found profound differences in DNA methylation due to age, irrespective of rearing treatment. This could be due to smoltification associated changes in liver physiology after the second year of rearing. Although few rearing-treatment effects were observed in the sperm methylome, strong family effects were observed. These data suggest limited potential for intergenerational changes, but highlight the importance of understanding the effects of kinship among studied individuals in order to properly analyze and interpret DNA methylation data in natural populations. Our work is the first to study family effects and temporal dynamics of DNA methylation patterns in response to hatchery-rearing.
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Affiliation(s)
- Mackenzie R Gavery
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98105, USA.
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 2725 Montlake Blvd. E., Seattle, WA 98112, USA.
| | - Barry A Berejikian
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 7305 Beach Dr. East, Port Orchard, WA 98366, USA.
| | - Christopher P Tatara
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 7305 Beach Dr. East, Port Orchard, WA 98366, USA.
| | - Giles W Goetz
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98105, USA.
| | - Jon T Dickey
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98105, USA.
| | - Donald M Van Doornik
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 7305 Beach Dr. East, Port Orchard, WA 98366, USA.
| | - Penny Swanson
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 2725 Montlake Blvd. E., Seattle, WA 98112, USA.
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15
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Characterization of Genetic and Epigenetic Variation in Sperm and Red Blood Cells from Adult Hatchery and Natural-Origin Steelhead, Oncorhynchus mykiss. G3-GENES GENOMES GENETICS 2018; 8:3723-3736. [PMID: 30275172 PMCID: PMC6222570 DOI: 10.1534/g3.118.200458] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
While the goal of most conservation hatchery programs is to produce fish that are genetically and phenotypically indistinguishable from the wild stocks they aim to restore, there is considerable evidence that salmon and steelhead reared in hatcheries differ from wild fish in phenotypic traits related to fitness. Some evidence suggests that these phenotypic differences have a genetic basis (e.g., domestication selection) but another likely mechanism that remains largely unexplored is that differences between hatchery and wild populations arise as a result of environmentally-induced heritable epigenetic change. As a first step toward understanding the potential contribution of these two possible mechanisms, we describe genetic and epigenetic variation in hatchery and natural-origin adult steelhead, Oncorhynchus mykiss, from the Methow River, WA. Our main objectives were to determine if hatchery and natural-origin fish could be distinguished genetically and whether differences in epigenetic programming (DNA methylation) in somatic and germ cells could be detected between the two groups. Genetic analysis of 72 fish using 936 SNPs generated by Restriction Site Associated DNA Sequencing (RAD-Seq) did not reveal differentiation between hatchery and natural-origin fish at a population level. We performed Reduced Representation Bisulfite Sequencing (RRBS) on a subset of 10 hatchery and 10 natural-origin fish and report the first genome-wide characterization of somatic (red blood cells (RBCs)) and germ line (sperm) derived DNA methylomes in a salmonid, from which we identified considerable tissue-specific methylation. We identified 85 differentially methylated regions (DMRs) in RBCs and 108 DMRs in sperm of steelhead reared for their first year in a hatchery environment compared to those reared in the wild. This work provides support that epigenetic mechanisms may serve as a link between hatchery rearing and adult phenotype in steelhead; furthermore, DMRs identified in germ cells (sperm) highlight the potential for these changes to be passed on to future generations.
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16
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Abaji R, Ceppi F, Patel S, Gagné V, Xu CJ, Spinella JF, Colombini A, Parasole R, Buldini B, Basso G, Conter V, Cazzaniga G, Leclerc JM, Laverdière C, Sinnett D, Krajinovic M. Genetic risk factors for VIPN in childhood acute lymphoblastic leukemia patients identified using whole-exome sequencing. Pharmacogenomics 2018; 19:1181-1193. [PMID: 30191766 DOI: 10.2217/pgs-2018-0093] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AIM To identify genetic markers associated with vincristine-induced peripheral neuropathy (VIPN) in childhood acute lymphoblastic leukemia. PATIENTS & METHODS Whole-exome sequencing data were combined with exome-wide association study to identify predicted-functional germline variants associated with high-grade VIPN. Genotyping was then performed for top-ranked signals (n = 237), followed by validation in independent replication group (n = 405). RESULTS Minor alleles of rs2781377/SYNE2 (p = 0.01) and rs10513762/MRPL47 (p = 0.01) showed increased risk, whereas that of rs3803357/BAHD1 had a protective effect (p = 0.007). Using a genetic model based on weighted genetic risk scores, an additive effect of combining these loci was observed (p = 0.003). The addition of rs1135989/ACTG1 further enhanced model performance (p = 0.0001). CONCLUSION Variants in SYNE2, MRPL47 and BAHD1 genes are putative new risk factors for VIPN in childhood acute lymphoblastic leukemia.
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Affiliation(s)
- Rachid Abaji
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pharmacology & Physiology, Faculty of Medicine, University of Montreal, Montreal, QC, H3C 3J7, Canada
| | - Francesco Ceppi
- Pediatric Hematology-Oncology Unit & Pediatric Hematology-Oncology Research Laboratory, Division of Pediatrics, Department of Woman-Mother-Child, University Hospital of Lausanne, 1004 Lausanne, Switzerland
| | - Swati Patel
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Vincent Gagné
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Chang J Xu
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Jean-François Spinella
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Antonella Colombini
- Department of Pediatrics, University of Milano-Bicocca, Ospedale S Gerardo, 20835 Monza, Italy
| | - Rosanna Parasole
- Department of Pediatric Hemato-Oncology, Santobono-Pausilipon Hospital, 80129 Naples, Italy
| | - Barbara Buldini
- Department of Woman & Child Health, Laboratory of Haematology-Oncology, University of Padova, 35128 Padova, Italy
| | - Giuseppe Basso
- Department of Woman & Child Health, Laboratory of Haematology-Oncology, University of Padova, 35128 Padova, Italy
| | - Valentino Conter
- Department of Pediatrics, University of Milano-Bicocca, Ospedale S Gerardo, 20835 Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Department of Pediatrics, University Milano Bicocca, 20835 Monza, Italy
| | - Jean-Marie Leclerc
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, H4A 3J1, Canada
| | - Caroline Laverdière
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, H4A 3J1, Canada
| | - Daniel Sinnett
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, H4A 3J1, Canada
| | - Maja Krajinovic
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pharmacology & Physiology, Faculty of Medicine, University of Montreal, Montreal, QC, H3C 3J7, Canada.,Centro Ricerca Tettamanti, Department of Pediatrics, University Milano Bicocca, 20835 Monza, Italy
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17
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A pan-cancer analysis of MYC-PVT1 reveals CNV-unmediated deregulation and poor prognosis in renal carcinoma. Oncotarget 2018; 7:47033-47041. [PMID: 27366943 PMCID: PMC5216921 DOI: 10.18632/oncotarget.9487] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/28/2016] [Indexed: 12/14/2022] Open
Abstract
The PVT1 lncRNA has recently been involved in tumorigenesis by affecting the protein stability of the MYC proto-oncogene. Both MYC and PVT1 reside in a well-known cancer-risk locus and enhanced levels of their products have been reported in different human cancers. Nonetheless, the extension and relevance of the MYC-PVT1 deregulation in tumorigenesis has not yet been systematically addressed. Here we performed a pan-cancer analysis of matched copy number, transcriptomic, methylation, proteomic and clinicopathological profiles for almost 7000 patients from 17 different cancers represented in the TCGA cohorts. Among all cancers types, kidney renal clear cell carcinoma (KIRC) showed the strongest upregulation of PVT1 and increased levels of both MYC and PVT1 correlated with the clinical outcome. PVT1 misregulation in KIRC is mostly associated to promoter hypomethylation rather than locus amplification. Furthermore, we found an association between MYC levels and PVT1 expression, which impacted on MYC-target genes. Collectively, our study discloses the role of PVT1 as a novel prognostic factor and as a molecular target for novel therapeutic interventions in renal carcinoma.
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19
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Lakisic G, Lebreton A, Pourpre R, Wendling O, Libertini E, Radford EJ, Le Guillou M, Champy MF, Wattenhofer-Donzé M, Soubigou G, Ait-Si-Ali S, Feunteun J, Sorg T, Coppée JY, Ferguson-Smith AC, Cossart P, Bierne H. Role of the BAHD1 Chromatin-Repressive Complex in Placental Development and Regulation of Steroid Metabolism. PLoS Genet 2016; 12:e1005898. [PMID: 26938916 PMCID: PMC4777444 DOI: 10.1371/journal.pgen.1005898] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 02/04/2016] [Indexed: 11/18/2022] Open
Abstract
BAHD1 is a vertebrate protein that promotes heterochromatin formation and gene repression in association with several epigenetic regulators. However, its physiological roles remain unknown. Here, we demonstrate that ablation of the Bahd1 gene results in hypocholesterolemia, hypoglycemia and decreased body fat in mice. It also causes placental growth restriction with a drop of trophoblast glycogen cells, a reduction of fetal weight and a high neonatal mortality rate. By intersecting transcriptome data from murine Bahd1 knockout (KO) placentas at stages E16.5 and E18.5 of gestation, Bahd1-KO embryonic fibroblasts, and human cells stably expressing BAHD1, we also show that changes in BAHD1 levels alter expression of steroid/lipid metabolism genes. Biochemical analysis of the BAHD1-associated multiprotein complex identifies MIER proteins as novel partners of BAHD1 and suggests that BAHD1-MIER interaction forms a hub for histone deacetylases and methyltransferases, chromatin readers and transcription factors. We further show that overexpression of BAHD1 leads to an increase of MIER1 enrichment on the inactive X chromosome (Xi). In addition, BAHD1 and MIER1/3 repress expression of the steroid hormone receptor genes ESR1 and PGR, both playing important roles in placental development and energy metabolism. Moreover, modulation of BAHD1 expression in HEK293 cells triggers epigenetic changes at the ESR1 locus. Together, these results identify BAHD1 as a core component of a chromatin-repressive complex regulating placental morphogenesis and body fat storage and suggest that its dysfunction may contribute to several human diseases.
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Affiliation(s)
- Goran Lakisic
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Équipe Microbiologie Cellulaire et Epigénétique, Jouy-en-Josas, France
| | - Alice Lebreton
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France
- INSERM U604, Paris, France
- INRA USC2020, Paris, France
| | - Renaud Pourpre
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Équipe Microbiologie Cellulaire et Epigénétique, Jouy-en-Josas, France
| | - Olivia Wendling
- Institut Clinique de la Souris-ICS-MCI, PHENOMIN, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, France
| | - Emanuele Libertini
- Plateforme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur, Paris, France
| | - Elizabeth J. Radford
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Cambridge University Hospitals, NHS Foundation Trust, Cambridge, United Kingdom
| | - Morwenna Le Guillou
- CNRS UMR8200 Stabilité génétique et oncogenèse, Université Paris-Saclay, Villejuif, France
| | - Marie-France Champy
- Institut Clinique de la Souris-ICS-MCI, PHENOMIN, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, France
| | - Marie Wattenhofer-Donzé
- Institut Clinique de la Souris-ICS-MCI, PHENOMIN, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, France
| | - Guillaume Soubigou
- Plateforme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur, Paris, France
| | | | - Jean Feunteun
- CNRS UMR8200 Stabilité génétique et oncogenèse, Université Paris-Saclay, Villejuif, France
| | - Tania Sorg
- Institut Clinique de la Souris-ICS-MCI, PHENOMIN, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, France
| | - Jean-Yves Coppée
- Plateforme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur, Paris, France
| | | | - Pascale Cossart
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France
- INSERM U604, Paris, France
- INRA USC2020, Paris, France
| | - Hélène Bierne
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Équipe Microbiologie Cellulaire et Epigénétique, Jouy-en-Josas, France
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