1
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Morgan RK, Wang K, Svoboda LK, Rygiel CA, Lalancette C, Cavalcante R, Bartolomei MS, Prasasya R, Neier K, Perera BP, Jones TR, Colacino JA, Sartor MA, Dolinoy DC. Effects of Developmental Lead and Phthalate Exposures on DNA Methylation in Adult Mouse Blood, Brain, and Liver: A Focus on Genomic Imprinting by Tissue and Sex. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:67003. [PMID: 38833407 PMCID: PMC11166413 DOI: 10.1289/ehp14074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Maternal exposure to environmental chemicals can cause adverse health effects in offspring. Mounting evidence supports that these effects are influenced, at least in part, by epigenetic modifications. It is unknown whether epigenetic changes in surrogate tissues such as the blood are reflective of similar changes in target tissues such as cortex or liver. OBJECTIVE We examined tissue- and sex-specific changes in DNA methylation (DNAm) associated with human-relevant lead (Pb) and di(2-ethylhexyl) phthalate (DEHP) exposure during perinatal development in cerebral cortex, blood, and liver. METHODS Female mice were exposed to human relevant doses of either Pb (32 ppm ) via drinking water or DEHP (5 mg / kg-day ) via chow for 2 weeks prior to mating through offspring weaning. Whole genome bisulfite sequencing (WGBS) was utilized to examine DNAm changes in offspring cortex, blood, and liver at 5 months of age. Metilene and methylSig were used to identify differentially methylated regions (DMRs). Annotatr and ChIP-enrich were used for genomic annotations and gene set enrichment tests of DMRs, respectively. RESULTS The cortex contained the majority of DMRs associated with Pb (66%) and DEHP (57%) exposure. The cortex also contained the greatest degree of overlap in DMR signatures between sexes (n = 13 and 8 DMRs with Pb and DEHP exposure, respectively) and exposure types (n = 55 and 39 DMRs in males and females, respectively). In all tissues, detected DMRs were preferentially found at genomic regions associated with gene expression regulation (e.g., CpG islands and shores, 5' UTRs, promoters, and exons). An analysis of GO terms associated with DMR-containing genes identified imprinted genes to be impacted by both Pb and DEHP exposure. Of these, Gnas and Grb10 contained DMRs across tissues, sexes, and exposures, with some signatures replicated between target and surrogate tissues. DMRs were enriched in the imprinting control regions (ICRs) of Gnas and Grb10, and we again observed a replication of DMR signatures between blood and target tissues. Specifically, we observed hypermethylation of the Grb10 ICR in both blood and liver of Pb-exposed male animals. CONCLUSIONS These data provide preliminary evidence that imprinted genes may be viable candidates in the search for epigenetic biomarkers of toxicant exposure in target tissues. Additional research is needed on allele- and developmental stage-specific effects, as well as whether other imprinted genes provide additional examples of this relationship. https://doi.org/10.1289/EHP14074.
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Affiliation(s)
- Rachel K. Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Claudia Lalancette
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Raymond Cavalcante
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rexxi Prasasya
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Bambarendage P.U. Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Tamara R. Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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Moorwood K, Smith FM, Garfield AS, Ward A. Imprinted Grb10, encoding growth factor receptor bound protein 10, regulates fetal growth independently of the insulin-like growth factor type 1 receptor (Igf1r) and insulin receptor (Insr) genes. BMC Biol 2024; 22:127. [PMID: 38816743 PMCID: PMC11140863 DOI: 10.1186/s12915-024-01926-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Optimal size at birth dictates perinatal survival and long-term risk of developing common disorders such as obesity, type 2 diabetes and cardiovascular disease. The imprinted Grb10 gene encodes a signalling adaptor protein capable of inhibiting receptor tyrosine kinases, including the insulin receptor (Insr) and insulin-like growth factor type 1 receptor (Igf1r). Grb10 restricts fetal growth such that Grb10 knockout (KO) mice are at birth some 25-35% larger than wild type. Using a mouse genetic approach, we test the widely held assumption that Grb10 influences growth through interaction with Igf1r, which has a highly conserved growth promoting role. RESULTS Should Grb10 interact with Igf1r to regulate growth Grb10:Igf1r double mutant mice should be indistinguishable from Igf1r KO single mutants, which are around half normal size at birth. Instead, Grb10:Igf1r double mutants were intermediate in size between Grb10 KO and Igf1r KO single mutants, indicating additive effects of the two signalling proteins having opposite actions in separate pathways. Some organs examined followed a similar pattern, though Grb10 KO neonates exhibited sparing of the brain and kidneys, whereas the influence of Igf1r extended to all organs. An interaction between Grb10 and Insr was similarly investigated. While there was no general evidence for a major interaction for fetal growth regulation, the liver was an exception. The liver in Grb10 KO mutants was disproportionately overgrown with evidence of excess lipid storage in hepatocytes, whereas Grb10:Insr double mutants were indistinguishable from Insr single mutants or wild types. CONCLUSIONS Grb10 acts largely independently of Igf1r or Insr to control fetal growth and has a more variable influence on individual organs. Only the disproportionate overgrowth and excess lipid storage seen in the Grb10 KO neonatal liver can be explained through an interaction between Grb10 and the Insr. Our findings are important for understanding how positive and negative influences on fetal growth dictate size and tissue proportions at birth.
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Affiliation(s)
- Kim Moorwood
- Department of Life Sciences, University of Bath, Building 4 South, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Florentia M Smith
- Department of Life Sciences, University of Bath, Building 4 South, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Alastair S Garfield
- Department of Life Sciences, University of Bath, Building 4 South, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Andrew Ward
- Department of Life Sciences, University of Bath, Building 4 South, Claverton Down, Bath, BA2 7AY, United Kingdom.
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Morgan RK, Wang K, Svoboda LK, Rygiel CA, Lalancette C, Cavalcante R, Bartolomei MS, Prasasya R, Neier K, Perera BP, Jones TR, Colacino JA, Sartor MA, Dolinoy DC. Effects of Developmental Lead and Phthalate Exposures on DNA Methylation in Adult Mouse Blood, Brain, and Liver Identifies Tissue- and Sex-Specific Changes with Implications for Genomic Imprinting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560131. [PMID: 37873115 PMCID: PMC10592650 DOI: 10.1101/2023.09.29.560131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Maternal exposure to environmental chemicals can cause adverse health effects in offspring. Mounting evidence supports that these effects are influenced, at least in part, by epigenetic modifications. Objective We examined tissue- and sex-specific changes in DNA methylation (DNAm) associated with human-relevant lead (Pb) and di(2-ethylhexyl) phthalate (DEHP) exposure during perinatal development in cerebral cortex, blood, and liver. Methods Female mice were exposed to human relevant doses of either Pb (32ppm) via drinking water or DEHP (5 mg/kg-day) via chow for two weeks prior to mating through offspring weaning. Whole genome bisulfite sequencing (WGBS) was utilized to examine DNAm changes in offspring cortex, blood, and liver at 5 months of age. Metilene and methylSig were used to identify differentially methylated regions (DMRs). Annotatr and Chipenrich were used for genomic annotations and geneset enrichment tests of DMRs, respectively. Results The cortex contained the majority of DMRs associated with Pb (69%) and DEHP (58%) exposure. The cortex also contained the greatest degree of overlap in DMR signatures between sexes (n = 17 and 14 DMRs with Pb and DEHP exposure, respectively) and exposure types (n = 79 and 47 DMRs in males and females, respectively). In all tissues, detected DMRs were preferentially found at genomic regions associated with gene expression regulation (e.g., CpG islands and shores, 5' UTRs, promoters, and exons). An analysis of GO terms associated with DMR-containing genes identified imprinted genes to be impacted by both Pb and DEHP exposure. Of these, Gnas and Grb10 contained DMRs across tissues, sexes, and exposures. DMRs were enriched in the imprinting control regions (ICRs) of Gnas and Grb10, with 15 and 17 ICR-located DMRs across cortex, blood, and liver in each gene, respectively. The ICRs were also the location of DMRs replicated across target and surrogate tissues, suggesting epigenetic changes these regions may be potentially viable biomarkers. Conclusions We observed Pb- and DEHP-specific DNAm changes in cortex, blood, and liver, and the greatest degree of overlap in DMR signatures was seen between exposures followed by sex and tissue type. DNAm at imprinted control regions was altered by both Pb and DEHP, highlighting the susceptibility of genomic imprinting to these exposures during the perinatal window of development.
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Affiliation(s)
- Rachel K. Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Claudia Lalancette
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond Cavalcante
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi Prasasya
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bambarendage P.U. Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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Wei Z, Xia K, Zheng D, Gong C, Guo W. RILP inhibits tumor progression in osteosarcoma via Grb10-mediated inhibition of the PI3K/AKT/mTOR pathway. Mol Med 2023; 29:133. [PMID: 37789274 PMCID: PMC10548720 DOI: 10.1186/s10020-023-00722-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/31/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND Rab-interacting lysosomal protein (RILP) contains an alpha-helical coil with an unexplored biological function in osteosarcoma. This study investigated the expression of RILP in osteosarcoma cells and tissues to determine the effect of RILP on the biological behaviors of osteosarcoma cells and the underlying mechanism. METHODS Tumor Immune Estimation Resource (TIMER) database, The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database were used for bioinformatic analysis. Co-immunoprecipitation experiment was used to determine whether the two proteins were interacting. In functional tests, cell counting kit-8 (CCK-8) assay, colony formation assay, wound healing assay, transwell invasion assay, Immunofluorescence (IF) assay and immunohistochemical (IHC) assay were performed. RESULTS Overexpression of RILP significantly inhibited proliferation and impaired metastasis ability of osteosarcoma cells, while silencing of RILP showed the opposite trend. RNA-seq data analysis was applied in 143B cells and pathway enrichment analysis revealed that differentially expressed genes were mainly enriched in the PI3K/AKT pathway. We further verified that overexpression of RILP restrained the PI3K/AKT/mTOR signaling pathway and induced autophagy in osteosarcoma cells, while the opposite trend was observed when PI3K pathway activator 740Y-P was used. 3-Methyladenine (3-MA), a selective autophagy inhibitor, partially attenuated the inhibitory effect of RILP on the migration and invasion ability of osteosarcoma cells, suggesting the involvement of autophagy in epithelial-mesenchymal transition regulation in osteosarcoma cells. Growth factor receptor binding protein-10 (Grb10), an adaptor protein, was confirmed as a potential target of RILP to restrain the PI3K/AKT signaling pathway. We subcutaneously injected stably overexpressing 143B osteosarcoma cells into nude mice and observed that overexpression of RILP inhibited tumor growth by inhibiting the PI3K/AKT/mTOR pathway. CONCLUSION Our study revealed that the expression of RILP was associated with favorable prognosis of osteosarcoma and RILP inhibits proliferation, migration, and invasion and promotes autophagy in osteosarcoma cells via Grb10-mediated inhibition of the PI3K/AKT/mTOR signaling pathway. In the future, targeting RILP may be a potential strategy for osteosarcoma treatment.
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Affiliation(s)
- Zhun Wei
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei, China
| | - Kezhou Xia
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei, China
| | - Di Zheng
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei, China
| | - Changtian Gong
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei, China
| | - Weichun Guo
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei, China.
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Restoring Age-Related Cognitive Decline through Environmental Enrichment: A Transcriptomic Approach. Cells 2022; 11:cells11233864. [PMID: 36497123 PMCID: PMC9736066 DOI: 10.3390/cells11233864] [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: 08/30/2022] [Revised: 11/15/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Cognitive decline is one of the greatest health threats of old age and the maintenance of optimal brain function across a lifespan remains a big challenge. The hippocampus is considered particularly vulnerable but there is cross-species consensus that its functional integrity benefits from the early and continuous exercise of demanding physical, social and mental activities, also referred to as environmental enrichment (EE). Here, we investigated the extent to which late-onset EE can improve the already-impaired cognitive abilities of lifelong deprived C57BL/6 mice and how it affects gene expression in the hippocampus. To this end, 5- and 24-month-old mice housed in standard cages (5mSC and 24mSC) and 24-month-old mice exposed to EE in the last 2 months of their life (24mEE) were subjected to a Barnes maze task followed by next-generation RNA sequencing of the hippocampal tissue. Our analyses showed that late-onset EE was able to restore deficits in spatial learning and short-term memory in 24-month-old mice. These positive cognitive effects were reflected by specific changes in the hippocampal transcriptome, where late-onset EE affected transcription much more than age (24mSC vs. 24mEE: 1311 DEGs, 24mSC vs. 5mSC: 860 DEGs). Remarkably, a small intersection of 72 age-related DEGs was counter-regulated by late-onset EE. Of these, Bcl3, Cttnbp2, Diexf, Esr2, Grb10, Il4ra, Inhba, Rras2, Rps6ka1 and Socs3 appear to be particularly relevant as key regulators involved in dendritic spine plasticity and in age-relevant molecular signaling cascades mediating senescence, insulin resistance, apoptosis and tissue regeneration. In summary, our observations suggest that the brains of aged mice in standard cage housing preserve a considerable degree of plasticity. Switching them to EE proved to be a promising and non-pharmacological intervention against cognitive decline.
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Kim IB, Lee T, Lee J, Kim J, Lee S, Koh IG, Kim JH, An JY, Lee H, Kim WK, Ju YS, Cho Y, Yu SJ, Kim SA, Oh M, Han DW, Kim E, Choi JK, Yoo HJ, Lee JH. Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder. Mol Psychiatry 2022; 27:4680-4694. [PMID: 35840799 DOI: 10.1038/s41380-022-01697-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 12/14/2022]
Abstract
Three-dimensional chromatin interactions regulate gene expressions. The significance of de novo mutations (DNMs) in chromatin interactions remains poorly understood for autism spectrum disorder (ASD). We generated 813 whole-genome sequences from 242 Korean simplex families to detect DNMs, and identified target genes which were putatively affected by non-coding DNMs in chromatin interactions. Non-coding DNMs in chromatin interactions were significantly involved in transcriptional dysregulations related to ASD risk. Correspondingly, target genes showed spatiotemporal expressions relevant to ASD in developing brains and enrichment in biological pathways implicated in ASD, such as histone modification. Regarding clinical features of ASD, non-coding DNMs in chromatin interactions particularly contributed to low intelligence quotient levels in ASD probands. We further validated our findings using two replication cohorts, Simons Simplex Collection (SSC) and MSSNG, and showed the consistent enrichment of non-coding DNM-disrupted chromatin interactions in ASD probands. Generating human induced pluripotent stem cells in two ASD families, we were able to demonstrate that non-coding DNMs in chromatin interactions alter the expression of target genes at the stage of early neural development. Taken together, our findings indicate that non-coding DNMs in ASD probands lead to early neurodevelopmental disruption implicated in ASD risk via chromatin interactions.
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Affiliation(s)
- Il Bin Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, Hanyang University Guri Hospital, Guri, 11923, Republic of Korea
| | - Taeyeop Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Suho Lee
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea
| | - In Gyeong Koh
- Industry-University Cooperation Foundation, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Hyunseong Lee
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, 05030, Republic of Korea
| | - Woo Kyeong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yongseong Cho
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Seok Jong Yu
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Soon Ae Kim
- Department of Pharmacology, Eulji University, Daejeon, 13135, Republic of Korea
| | - Miae Oh
- Department of Psychiatry, Kyung Hee University Hospital, Seoul, 02447, Republic of Korea
| | - Dong Wook Han
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.,Organoid sciences, Ltd., Bundang-gu, Seongnam, 13488, Republic of Korea
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea. .,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea. .,Department of Psychiatry, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea. .,Sovargen Co. Ltd., Daejeon, 34051, Republic of Korea.
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Simper MS, Coletta LD, Gaddis S, Lin K, Mikulec CD, Takata T, Tomida MW, Zhang D, Tang DG, Estecio MR, Shen J, Lu Y. Commercial ChIP-Seq Library Preparation Kits Performed Differently for Different Classes of Protein Targets. J Biomol Tech 2022; 33:3fc1f5fe.7910785e. [PMID: 36910579 PMCID: PMC10001930 DOI: 10.7171/3fc1f5fe.7910785e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) is a powerful method commonly used to study global protein-DNA interactions including both transcription factors and histone modifications. We have found that the choice of ChIP-Seq library preparation protocol plays an important role in overall ChIP-Seq data quality. However, very few studies have compared ChIP-Seq libraries prepared by different protocols using multiple targets and a broad range of input DNA levels. Results In this study, we evaluated the performance of 4 ChIP-Seq library preparation protocols (New England Biolabs [NEB] NEBNext Ultra II, Roche KAPA HyperPrep, Diagenode MicroPlex, and Bioo [now PerkinElmer] NEXTflex) on 3 target proteins, chosen to represent the 3 typical signal enrichment patterns in ChIP-Seq experiments: sharp peaks (H3K4me3), broad domains (H3K27me3), and punctate peaks with a protein binding motif (CTCF). We also tested a broad range of different input DNA levels from 0.10 to 10 ng for H3K4me3 and H3K27me3 experiments. Conclusions Our results suggest that the NEB protocol may be better for preparing H3K4me3 (and potentially other histone modifications with sharp peak enrichment) libraries; the Bioo protocol may be better for preparing H3K27me3 (and potentially other histone modifications with broad domain enrichment) libraries, and the Diagenode protocol may be better for preparing CTCF (and potentially other transcription factors with well-defined binding motifs) libraries. For ChIP-Seq experiments using novel targets without a known signal enrichment pattern, the NEB protocol might be the best choice, as it performed well for each of the 3 targets we tested across a wide array of input DNA levels.
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Affiliation(s)
- M S Simper
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - L Della Coletta
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - S Gaddis
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - K Lin
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - C D Mikulec
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - True Takata
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - M W Tomida
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - D Zhang
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Present Address: College of Biology Hunan University Changsha410082 China
| | - D G Tang
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Present Address: Department of Pharmacology and Therapeutics Roswell Park Cancer Institute BuffaloNew York14263 USA
| | - M R Estecio
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - J Shen
- Department of Epigenetics and Molecular Carcinogenesis.,Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Program in Genetics and Epigenetics MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences The University of Texas MD Anderson Cancer Center SmithvilleTexas78957 USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
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8
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Juan AM, Foong YH, Thorvaldsen JL, Lan Y, Leu NA, Rurik JG, Li L, Krapp C, Rosier CL, Epstein JA, Bartolomei MS. Tissue-specific Grb10/Ddc insulator drives allelic architecture for cardiac development. Mol Cell 2022; 82:3613-3631.e7. [PMID: 36108632 PMCID: PMC9547965 DOI: 10.1016/j.molcel.2022.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 07/12/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022]
Abstract
Allele-specific expression of imprinted gene clusters is governed by gametic DNA methylation at master regulators called imprinting control regions (ICRs). Non-gametic or secondary differentially methylated regions (DMRs) at promoters and exonic regions reinforce monoallelic expression but do not control an entire cluster. Here, we unveil an unconventional secondary DMR that is indispensable for tissue-specific imprinting of two previously unlinked genes, Grb10 and Ddc. Using polymorphic mice, we mapped an intronic secondary DMR at Grb10 with paternal-specific CTCF binding (CBR2.3) that forms contacts with Ddc. Deletion of paternal CBR2.3 removed a critical insulator, resulting in substantial shifting of chromatin looping and ectopic enhancer-promoter contacts. Destabilized gene architecture precipitated abnormal Grb10-Ddc expression with developmental consequences in the heart and muscle. Thus, we redefine the Grb10-Ddc imprinting domain by uncovering an unconventional intronic secondary DMR that functions as an insulator to instruct the tissue-specific, monoallelic expression of multiple genes-a feature previously ICR exclusive.
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Affiliation(s)
- Aimee M Juan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yee Hoon Foong
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joanne L Thorvaldsen
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicolae A Leu
- Department of Biomedical Sciences, Center for Animal Transgenesis and Germ Cell Research, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Joel G Rurik
- Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Li Li
- Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher Krapp
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Casey L Rosier
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan A Epstein
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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9
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Schrott R, Greeson KW, King D, Crow KMS, Easley CA, Murphy SK. Cannabis alters DNA methylation at maternally imprinted and autism candidate genes in spermatogenic cells. Syst Biol Reprod Med 2022; 68:357-369. [PMID: 35687495 PMCID: PMC10032331 DOI: 10.1080/19396368.2022.2073292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 04/18/2022] [Accepted: 04/23/2022] [Indexed: 10/18/2022]
Abstract
Cannabis use in the United States is increasing, with highest consumption among men at their peak reproductive years. We previously demonstrated widespread changes in sperm DNA methylation with cannabis exposure in humans and rats, including genes important in neurodevelopment. Here, we use an in vitro human spermatogenesis model to recapitulate chronic cannabis use and assess DNA methylation at imprinted and autism spectrum disorder (ASD) candidate genes in spermatogonial stem cell (SSC)- and spermatid-like cells. Methylation at maternally imprinted genes SGCE and GRB10 was significantly altered in SSC- and spermatid-like cells, respectively, while PEG3 was significantly differentially methylated in spermatid-like cells. Two of ten randomly selected ASD candidate genes, HCN1 and NR4A2, had significantly altered methylation with cannabis exposure in SSC-like cells. These results support our findings in human cohorts and provide a new tool with which to gain mechanistic insights into the association between paternal cannabis use and risk of ASD in offspring.
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Affiliation(s)
- Rose Schrott
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
- Integrated Toxicology and Environmental Health Program, Nicholas School of the Environment, Duke University, Durham, NC, 27701, USA
| | - Katherine W. Greeson
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA
| | - Dillon King
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
- Integrated Toxicology and Environmental Health Program, Nicholas School of the Environment, Duke University, Durham, NC, 27701, USA
| | - Krista M. Symosko Crow
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA
| | - Charles A. Easley
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA
| | - Susan K. Murphy
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
- Integrated Toxicology and Environmental Health Program, Nicholas School of the Environment, Duke University, Durham, NC, 27701, USA
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10
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St Pierre CL, Macias-Velasco JF, Wayhart JP, Yin L, Semenkovich CF, Lawson HA. Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression. Genome Res 2022; 32:1042-1057. [PMID: 35501130 PMCID: PMC9248887 DOI: 10.1101/gr.276193.121] [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: 09/10/2021] [Accepted: 04/14/2022] [Indexed: 12/03/2022]
Abstract
Allele-specific expression (ASE) is a phenomenon in which one allele is preferentially expressed over the other. Genetic and epigenetic factors cause ASE by altering the final composition of a gene's product, leading to expression imbalances that can have functional consequences on phenotypes. Environmental signals also impact allele-specific expression, but how they contribute to this cross talk remains understudied. Here, we explored how genotype, parent-of-origin, tissue, sex, and dietary fat simultaneously influence ASE biases. Male and female mice from a F1 reciprocal cross of the LG/J and SM/J strains were fed a high or low fat diet. We harnessed strain-specific variants to distinguish between two ASE classes: parent-of-origin-dependent (unequal expression based on parental origin) and sequence-dependent (unequal expression based on nucleotide identity). We present a comprehensive map of ASE patterns in 2853 genes across three tissues and nine environmental contexts. We found that both ASE classes are highly dependent on tissue and environmental context. They vary across metabolically relevant tissues, between males and females, and in response to dietary fat. We also found 45 genes with inconsistent ASE biases that switched direction across tissues and/or environments. Finally, we integrated ASE and QTL data from published intercrosses of the LG/J and SM/J strains. Our ASE genes are often enriched in QTLs for metabolic and musculoskeletal traits, highlighting how this orthogonal approach can prioritize candidate genes. Together, our results provide novel insights into how genetic, epigenetic, and environmental mechanisms govern allele-specific expression, which is an essential step toward deciphering the genotype-to-phenotype map.
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Affiliation(s)
| | | | | | - Li Yin
- Washington University in Saint Louis
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11
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Abstract
PURPOSE OF REVIEW HRI is the heme-regulated elF2α kinase that phosphorylates the α-subunit of elF2. Although the role of HRI in inhibiting globin synthesis in erythroid cells is well established, broader roles of HRI in translation have been uncovered recently. This review is to summarize the new discoveries of HRI in stress erythropoiesis and in fetal γ-globin expression. RECENT FINDINGS HRI and activating transcription factor 4 (ATF4) mRNAs are highly expressed in early erythroblasts. Inhibition of protein synthesis by HRI-phosphorylated elF2α (elF2αP) is necessary to maintain protein homeostasis in both the cytoplasm and mitochondria. In addition, HRI-elF2αP specifically enhances translation of ATF4 mRNA leading to the repression of mechanistic target of rapamycin complex 1 (mTORC1) signaling. ATF4-target genes are most highly activated during iron deficiency to maintain mitochondrial function, redox homeostasis, and to enable erythroid differentiation. HRI is therefore a master translation regulator of erythropoiesis sensing intracellular heme concentrations and oxidative stress for effective erythropoiesis. Intriguingly, HRI-elF2αP-ATF4 signaling also inhibits fetal hemoglobin production in human erythroid cells. SUMMARY The primary function of HRI is to maintain protein homeostasis accompanied by the induction of ATF4 to mitigate stress. Role of HRI-ATF4 in γ-globin expression raises the potential of HRI as a therapeutic target for hemoglobinopathy.
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Affiliation(s)
- Jane-Jane Chen
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shuping Zhang
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
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12
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Dollet L, Kuefner M, Caria E, Rizo-Roca D, Pendergrast L, Abdelmoez AM, Karlsson HK, Björnholm M, Dalbram E, Treebak JT, Harada J, Näslund E, Rydén M, Zierath JR, Pillon NJ, Krook A. Glutamine Regulates Skeletal Muscle Immunometabolism in Type 2 Diabetes. Diabetes 2022; 71:624-636. [PMID: 35040927 PMCID: PMC8965677 DOI: 10.2337/db20-0814] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/23/2021] [Indexed: 11/23/2022]
Abstract
Dysregulation of skeletal muscle metabolism influences whole-body insulin sensitivity and glucose homeostasis. We hypothesized that type 2 diabetes-associated alterations in the plasma metabolome directly contribute to skeletal muscle immunometabolism and the subsequent development of insulin resistance. To this end, we analyzed the plasma and skeletal muscle metabolite profile and identified glutamine as a key amino acid that correlates inversely with BMI and insulin resistance index (HOMA-IR) in men with normal glucose tolerance or type 2 diabetes. Using an in vitro model of human myotubes and an in vivo model of diet-induced obesity and insulin resistance in male mice, we provide evidence that glutamine levels directly influence the inflammatory response of skeletal muscle and regulate the expression of the adaptor protein GRB10, an inhibitor of insulin signaling. Moreover, we demonstrate that a systemic increase in glutamine levels in a mouse model of obesity improves insulin sensitivity and restores glucose homeostasis. We conclude that glutamine supplementation may represent a potential therapeutic strategy to prevent or delay the onset of insulin resistance in obesity by reducing inflammatory markers and promoting skeletal muscle insulin sensitivity.
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Affiliation(s)
- Lucile Dollet
- Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Michael Kuefner
- Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Elena Caria
- Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - David Rizo-Roca
- Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Logan Pendergrast
- Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ahmed M. Abdelmoez
- Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Håkan K.R. Karlsson
- Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Marie Björnholm
- Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Emilie Dalbram
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas T. Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jun Harada
- Cardiovascular-Metabolics Research Laboratories, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Erik Näslund
- Division of Surgery, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Rydén
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R. Zierath
- Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Nicolas J. Pillon
- Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Krook
- Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Corresponding author: Anna Krook,
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13
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Jurgens SJ, Choi SH, Morrill VN, Chaffin M, Pirruccello JP, Halford JL, Weng LC, Nauffal V, Roselli C, Hall AW, Oetjens MT, Lagerman B, vanMaanen DP, Aragam KG, Lunetta KL, Haggerty CM, Lubitz SA, Ellinor PT. Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank. Nat Genet 2022; 54:240-250. [PMID: 35177841 PMCID: PMC8930703 DOI: 10.1038/s41588-021-01011-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 12/22/2021] [Indexed: 12/30/2022]
Abstract
Cardiometabolic diseases are the leading cause of death worldwide. Despite a known genetic component, our understanding of these diseases remains incomplete. Here, we analyzed the contribution of rare variants to 57 diseases and 26 cardiometabolic traits, using data from 200,337 UK Biobank participants with whole-exome sequencing. We identified 57 gene-based associations, with broad replication of novel signals in Geisinger MyCode. There was a striking risk associated with mutations in known Mendelian disease genes, including MYBPC3, LDLR, GCK, PKD1 and TTN. Many genes showed independent convergence of rare and common variant evidence, including an association between GIGYF1 and type 2 diabetes. We identified several large effect associations for height and 18 unique genes associated with blood lipid or glucose levels. Finally, we found that between 1.0% and 2.4% of participants carried rare potentially pathogenic variants for cardiometabolic disorders. These findings may facilitate studies aimed at therapeutics and screening of these common disorders.
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Affiliation(s)
- Sean J. Jurgens
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Valerie N. Morrill
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Chaffin
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James P. Pirruccello
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jennifer L. Halford
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lu-Chen Weng
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Victor Nauffal
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Carolina Roselli
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amelia W. Hall
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Braxton Lagerman
- Department of Translational Data Science and Informatics, Geisinger, Danville, PA, USA
| | - David P. vanMaanen
- Department of Translational Data Science and Informatics, Geisinger, Danville, PA, USA
| | | | - Krishna G. Aragam
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn L. Lunetta
- NHLBI and Boston University’s Framingham Heart Study, Framingham, MA, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Christopher M. Haggerty
- Department of Translational Data Science and Informatics, Geisinger, Danville, PA, USA.,Heart Institute, Geisinger, Danville, PA, USA
| | - Steven A. Lubitz
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.,Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.,Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA.,
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14
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Xu Z, Shi J, Zhang Y, Liu Y, Zhao J, Chen Q, Song C, Geng S, Xie W, Wu F, Bai Y, Yang Y, Li X. Zfp57 Exerts Maternal and Sexually Dimorphic Effects on Genomic Imprinting. Front Cell Dev Biol 2022; 10:784128. [PMID: 35252168 PMCID: PMC8895500 DOI: 10.3389/fcell.2022.784128] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/04/2022] [Indexed: 12/05/2022] Open
Abstract
Zfp57 has both maternal and zygotic functions in mouse. It maintains genomic imprinting at most known imprinted regions and controls allelic expression of the target imprinted genes in mouse embryos. The DNA methylation imprint at many imprinting control regions (ICRs) is lost when both maternal and zygotic Zfp57 are absent in Zfp57 maternal–zygotic mutant mouse embryos. Interestingly, we found that DNA methylation at a few ICRs was partially lost without maternal Zfp57 in Zfp57 heterozygous mouse embryos derived from Zfp57 homozygous female mice. This suggests that maternal Zfp57 is essential for the maintenance of DNA methylation at a small subset of imprinted regions in mouse embryos. This maternal effect of Zfp57 was applied to allelic expression switch as well as expression levels of the corresponding imprinted genes. It is rather surprising that DNA methylation imprint was affected differently at Rasgrf1 and AK008011 imprinted regions in the female or male Zfp57 maternal–zygotic mutant embryos, with more significant loss of DNA methylation observed in the male mutant embryos. Loss of ZFP57 resulted in gender-specific differences in allelic expression switch and expression level changes of some imprinted genes in female or male mutant embryos. These results indicate maternal and sexually dimorphic effects of ZFP57 on genomic imprinting in mouse.
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Affiliation(s)
- Zhen Xu
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Jiajia Shi
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuhan Liu
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Junzheng Zhao
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Qian Chen
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Chenglin Song
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Shuhui Geng
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Feizhen Wu
- Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yun Bai
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Yang Yang
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Xiajun Li
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
- *Correspondence: Xiajun Li,
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15
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Wang Z, Meng Z, Chen C. Screening of potential biomarkers in peripheral blood of patients with depression based on weighted gene co-expression network analysis and machine learning algorithms. Front Psychiatry 2022; 13:1009911. [PMID: 36325528 PMCID: PMC9621316 DOI: 10.3389/fpsyt.2022.1009911] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/23/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The prevalence of depression has been increasing worldwide in recent years, posing a heavy burden on patients and society. However, the diagnostic and therapeutic tools available for this disease are inadequate. Therefore, this research focused on the identification of potential biomarkers in the peripheral blood of patients with depression. METHODS The expression dataset GSE98793 of depression was provided by the Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/gds). Initially, differentially expressed genes (DEGs) were detected in GSE98793. Subsequently, the most relevant modules for depression were screened according to weighted gene co-expression network analysis (WGCNA). Finally, the identified DEGs were mapped to the WGCNA module genes to obtain the intersection genes. In addition, Gene Ontology (GO), Disease Ontology (DO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses were conducted on these genes. Moreover, biomarker screening was carried out by protein-protein interaction (PPI) network construction of intersection genes on the basis of various machine learning algorithms. Furthermore, the gene set enrichment analysis (GSEA), immune function analysis, transcription factor (TF) analysis, and the prediction of the regulatory mechanism were collectively performed on the identified biomarkers. In addition, we also estimated the clinical diagnostic ability of the obtained biomarkers, and performed Mfuzz expression pattern clustering and functional enrichment of the most potential biomarkers to explore their regulatory mechanisms. Finally, we also perform biomarker-related drug prediction. RESULTS Differential analysis was used for obtaining a total of 550 DEGs and WGCNA for obtaining 1,194 significant genes. Intersection analysis of the two yielded 140 intersection genes. Biological functional analysis indicated that these genes had a major role in inflammation-related bacterial infection pathways and cardiovascular diseases such as atherosclerosis. Subsequently, the genes S100A12, SERPINB2, TIGIT, GRB10, and LHFPL2 in peripheral serum were identified as depression biomarkers by using machine learning algorithms. Among them, S100A12 is the most valuable biomarker for clinical diagnosis. Finally, antidepressants, including disodium selenite and eplerenone, were predicted. CONCLUSION The genes S100A12, TIGIT, SERPINB2, GRB10, and LHFPL2 in peripheral serum are viable diagnostic biomarkers for depression. and contribute to the diagnosis and prevention of depression in clinical practice.
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Affiliation(s)
- Zhe Wang
- School of Chinese Medicine, Ningxia Medical University, Yinchuan, China
| | - Zhe Meng
- School of Chinese Medicine, Ningxia Medical University, Yinchuan, China
| | - Che Chen
- School of Chinese Medicine, Ningxia Medical University, Yinchuan, China
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16
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McArthur E, Rinker DC, Capra JA. Quantifying the contribution of Neanderthal introgression to the heritability of complex traits. Nat Commun 2021; 12:4481. [PMID: 34294692 PMCID: PMC8298587 DOI: 10.1038/s41467-021-24582-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 06/24/2021] [Indexed: 11/15/2022] Open
Abstract
Eurasians have ~2% Neanderthal ancestry, but we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits. Here, we quantify the contribution of introgressed alleles to the heritability of more than 400 diverse traits. We show that genomic regions in which detectable Neanderthal ancestry remains are depleted of heritability for all traits considered, except those related to skin and hair. Introgressed variants themselves are also depleted for contributions to the heritability of most traits. However, introgressed variants shared across multiple Neanderthal populations are enriched for heritability and have consistent directions of effect on several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. Integrating our results, we propose a model in which selection against introgressed functional variation was the dominant trend (especially for cognitive traits); however, for a few traits, introgressed variants provided beneficial variation via uni-directional (e.g., lightening skin color) or bi-directional (e.g., modulating immune response) effects. We lack a comprehensive understanding of how Neanderthal ancestry influences human traits. This study finds that regions with Neanderthal ancestry are broadly depleted of trait-associated variation; yet, introgressed variants likely contributed to human adaptation in a few traits, like skin color and immune response modulation.
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Affiliation(s)
- Evonne McArthur
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - David C Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37235, USA. .,Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA. .,Bakar Computational Health Sciences Institute and Department of Epidemiology and Statistics, University of California San Francisco, San Francisco, CA, 94107, USA.
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17
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Prickett AR, Montibus B, Barkas N, Amante SM, Franco MM, Cowley M, Puszyk W, Shannon MF, Irving MD, Madon-Simon M, Ward A, Schulz R, Baldwin HS, Oakey RJ. Imprinted Gene Expression and Function of the Dopa Decarboxylase Gene in the Developing Heart. Front Cell Dev Biol 2021; 9:676543. [PMID: 34239874 PMCID: PMC8258389 DOI: 10.3389/fcell.2021.676543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
Dopa decarboxylase (DDC) synthesizes serotonin in the developing mouse heart where it is encoded by Ddc_exon1a, a tissue-specific paternally expressed imprinted gene. Ddc_exon1a shares an imprinting control region (ICR) with the imprinted, maternally expressed (outside of the central nervous system) Grb10 gene on mouse chromosome 11, but little else is known about the tissue-specific imprinted expression of Ddc_exon1a. Fluorescent immunostaining localizes DDC to the developing myocardium in the pre-natal mouse heart, in a region susceptible to abnormal development and implicated in congenital heart defects in human. Ddc_exon1a and Grb10 are not co-expressed in heart nor in brain where Grb10 is also paternally expressed, despite sharing an ICR, indicating they are mechanistically linked by their shared ICR but not by Grb10 gene expression. Evidence from a Ddc_exon1a gene knockout mouse model suggests that it mediates the growth of the developing myocardium and a thinning of the myocardium is observed in a small number of mutant mice examined, with changes in gene expression detected by microarray analysis. Comparative studies in the human developing heart reveal a paternal expression bias with polymorphic imprinting patterns between individual human hearts at DDC_EXON1a, a finding consistent with other imprinted genes in human.
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Affiliation(s)
- Adam R. Prickett
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Bertille Montibus
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Nikolaos Barkas
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Samuele M. Amante
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Maurício M. Franco
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Michael Cowley
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - William Puszyk
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Matthew F. Shannon
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Melita D. Irving
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
- Department of Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Marta Madon-Simon
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - Andrew Ward
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - Reiner Schulz
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - H. Scott Baldwin
- Department of Pediatrics (Cardiology), Vanderbilt University Medical Center, Nashville, TN, United States
| | - Rebecca J. Oakey
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
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Abstract
PURPOSE OF REVIEW To review susceptibility genes and how they could integrate in systemic sclerosis (SSc) pathophysiology providing insight and perspectives for innovative therapies. RECENT FINDINGS SSc is a rare disease characterized by vasculopathy, dysregulated immunity and fibrosis. Genome-Wide association studies and ImmunoChip studies performed in recent years revealed associated genetic variants mainly localized in noncoding regions and mostly affecting the immune system of SSc patients. Gene variants were described in innate immunity (IRF5, IRF7 and TLR2), T and B cells activation (CD247, TNFAIP3, STAT4 and BLK) and NF-κB pathway (TNFAIP3 and TNIP1) confirming previous biological data. In addition to impacting immune response, CSK, DDX6, DNASE1L3 and GSDMA/B could also act in the vascular and fibrotic components of SSc. SUMMARY Although genetic studies highlighted the dysregulated immune response in SSc, future research must focus on a deeper characterization of these variants with determination of their functional effects. Moreover, the role of these genes or others on specific vasculopathy and fibrosis would provide insight. Establishment of polygenic score or integrated genome approaches could identify new targets specific of SSc clinical features. This will allow physicians to propose new therapies to SSc patients.
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Gross N, Taylor T, Crenshaw T, Khatib H. The Intergenerational Impacts of Paternal Diet on DNA Methylation and Offspring Phenotypes in Sheep. Front Genet 2020; 11:597943. [PMID: 33250925 PMCID: PMC7674940 DOI: 10.3389/fgene.2020.597943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/14/2020] [Indexed: 11/13/2022] Open
Abstract
Knowledge of non-genomic inheritance of traits is currently limited. Although it is well established that maternal diet influences offspring inheritance of traits through DNA methylation, studies on the impact of prepubertal paternal diet on DNA methylation are rare. This study aimed to evaluate the impact of prepubertal diet in Polypay rams on complex traits, DNA methylation, and transmission of traits to offspring. A total of 10 littermate pairs of F0 rams were divided so that one ram was fed a control diet, and the other was fed the control diet with supplemental methionine. Diet was associated with earlier age at puberty in treatment vs. control F0 rams. F0 treatment rams tended to show decreased pubertal weight compared to control rams; however, no differences were detected in overall growth. A total of ten F0 rams were bred, and the entire F1 generation was fed a control diet. Diet of F0 rams had a significant association with scrotal circumference (SC) and weight at puberty of F1 offspring. The paternal diet was not significantly associated with F1 ram growth or age at puberty. The DNA methylation of F0 ram sperm was assessed, and genes related to both sexual development (e.g., DAZAP1, CHD7, TAB1, MTMR2, CELSR1, MGAT1) and body weight (e.g., DUOX2, DUOXA2) were prevalent in the data. These results provide novel information about the mechanisms through which the prepubertal paternal diet may alter body weight at puberty and sexual development.
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Affiliation(s)
- Nicole Gross
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Todd Taylor
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas Crenshaw
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
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20
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Bier A, Hong X, Cazacu S, Goldstein H, Rand D, Xiang C, Jiang W, Ben-Asher HW, Attia M, Brodie A, She R, Poisson LM, Brodie C. miR-504 modulates the stemness and mesenchymal transition of glioma stem cells and their interaction with microglia via delivery by extracellular vesicles. Cell Death Dis 2020; 11:899. [PMID: 33093452 PMCID: PMC7581800 DOI: 10.1038/s41419-020-03088-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 08/13/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022]
Abstract
Glioblastoma (GBM) is a highly aggressive tumor with poor prognosis. A small subpopulation of glioma stem cells (GSCs) has been implicated in radiation resistance and tumor recurrence. In this study we analyzed the expression of miRNAs associated with the functions of GSCs using miRNA microarray analysis of these cells compared with human neural stem cells. These analyses identified gene clusters associated with glioma cell invasiveness, axonal guidance, and TGF-β signaling. miR-504 was significantly downregulated in GSCs compared with NSCs, its expression was lower in GBM compared with normal brain specimens and further decreased in the mesenchymal glioma subtype. Overexpression of miR-504 in GSCs inhibited their self-renewal, migration and the expression of mesenchymal markers. The inhibitory effect of miR-504 was mediated by targeting Grb10 expression which acts as an oncogene in GSCs and GBM. Overexpression of exogenous miR-504 resulted also in its delivery to cocultured microglia by GSC-secreted extracellular vesicles (EVs) and in the abrogation of the GSC-induced polarization of microglia to M2 subtype. Finally, miR-504 overexpression prolonged the survival of mice harboring GSC-derived xenografts and decreased tumor growth. In summary, we identified miRNAs and potential target networks that play a role in the stemness and mesenchymal transition of GSCs and the miR-504/Grb10 pathway as an important regulator of this process. Overexpression of miR-504 exerted antitumor effects in GSCs as well as bystander effects on the polarization of microglia via delivery by EVs.
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Affiliation(s)
- Ariel Bier
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Xin Hong
- Davidson Laboratory of Cell Signaling and Tumorigenesis, Hermelin Brain Tumor Center, Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
| | - Simona Cazacu
- Davidson Laboratory of Cell Signaling and Tumorigenesis, Hermelin Brain Tumor Center, Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
| | - Hodaya Goldstein
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Daniel Rand
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Cunli Xiang
- Davidson Laboratory of Cell Signaling and Tumorigenesis, Hermelin Brain Tumor Center, Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
| | - Wei Jiang
- Davidson Laboratory of Cell Signaling and Tumorigenesis, Hermelin Brain Tumor Center, Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
| | - Hiba Waldman Ben-Asher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Moshe Attia
- Department of Neurosurgery, Sheba Medical Center, Henry Ford Hospital, Detroit, MI, USA
| | - Aharon Brodie
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Ruicong She
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Laila M Poisson
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Chaya Brodie
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
- Davidson Laboratory of Cell Signaling and Tumorigenesis, Hermelin Brain Tumor Center, Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA.
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21
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Laukoter S, Pauler FM, Beattie R, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex. Neuron 2020; 107:1160-1179.e9. [PMID: 32707083 PMCID: PMC7523403 DOI: 10.1016/j.neuron.2020.06.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 05/20/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.
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Affiliation(s)
- Susanne Laukoter
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Florian M Pauler
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Robert Beattie
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Nicole Amberg
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Andi H Hansen
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Carmen Streicher
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
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22
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Varrault A, Dubois E, Le Digarcher A, Bouschet T. Quantifying Genomic Imprinting at Tissue and Cell Resolution in the Brain. EPIGENOMES 2020; 4:21. [PMID: 34968292 PMCID: PMC8594728 DOI: 10.3390/epigenomes4030021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Imprinted genes are a group of ~150 genes that are preferentially expressed from one parental allele owing to epigenetic marks asymmetrically distributed on inherited maternal and paternal chromosomes. Altered imprinted gene expression causes human brain disorders such as Prader-Willi and Angelman syndromes and additional rare brain diseases. Research data principally obtained from the mouse model revealed how imprinted genes act in the normal and pathological brain. However, a better understanding of imprinted gene functions calls for building detailed maps of their parent-of-origin-dependent expression and of associated epigenetic signatures. Here we review current methods for quantifying genomic imprinting at tissue and cell resolutions, with a special emphasis on methods to detect parent-of-origin dependent expression and their applications to the brain. We first focus on bulk RNA-sequencing, the main method to detect parent-of-origin-dependent expression transcriptome-wide. We discuss the benefits and caveats of bulk RNA-sequencing and provide a guideline to use it on F1 hybrid mice. We then review methods for detecting parent-of-origin-dependent expression at cell resolution, including single-cell RNA-seq, genetic reporters, and molecular probes. Finally, we provide an overview of single-cell epigenomics technologies that profile additional features of genomic imprinting, including DNA methylation, histone modifications and chromatin conformation and their combination into sc-multimodal omics approaches, which are expected to yield important insights into genomic imprinting in individual brain cells.
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Affiliation(s)
- Annie Varrault
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| | - Emeric Dubois
- Montpellier GenomiX (MGX), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France;
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
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23
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Heme-regulated eIF2α kinase in erythropoiesis and hemoglobinopathies. Blood 2020; 134:1697-1707. [PMID: 31554636 DOI: 10.1182/blood.2019001915] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/11/2019] [Indexed: 12/12/2022] Open
Abstract
As essential components of hemoglobin, iron and heme play central roles in terminal erythropoiesis. The impairment of this process in iron/heme deficiency results in microcytic hypochromic anemia, the most prevalent anemia globally. Heme-regulated eIF2α kinase, also known as heme-regulated inhibitor (HRI), is a key heme-binding protein that senses intracellular heme concentrations to balance globin protein synthesis with the amount of heme available for hemoglobin production. HRI is activated during heme deficiency to phosphorylate eIF2α (eIF2αP), which simultaneously inhibits the translation of globin messenger RNAs (mRNAs) and selectively enhances the translation of activating transcription factor 4 (ATF4) mRNA to induce stress response genes. This coordinated translational regulation is a universal hallmark across the eIF2α kinase family under various stress conditions and is termed the integrated stress response (ISR). Inhibition of general protein synthesis by HRI-eIF2αP in erythroblasts is necessary to prevent proteotoxicity and maintain protein homeostasis in the cytoplasm and mitochondria. Additionally, the HRI-eIF2αP-ATF4 pathway represses mechanistic target of rapamycin complex 1 (mTORC1) signaling, specifically in the erythroid lineage as a feedback mechanism of erythropoietin-stimulated erythropoiesis during iron/heme deficiency. Furthermore, ATF4 target genes are most highly activated during iron deficiency to maintain mitochondrial function and redox homeostasis, as well as to enable erythroid differentiation. Thus, heme and translation regulate erythropoiesis through 2 key signaling pathways, ISR and mTORC1, which are coordinated by HRI to circumvent ineffective erythropoiesis (IE). HRI-ISR is also activated to reduce the severity of β-thalassemia intermedia in the Hbbth1/th1 murine model. Recently, HRI has been implicated in the regulation of human fetal hemoglobin production. Therefore, HRI-ISR has emerged as a potential therapeutic target for hemoglobinopathies.
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24
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25
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Thamban T, Agarwaal V, Khosla S. Role of genomic imprinting in mammalian development. J Biosci 2020; 45:20. [PMID: 31965998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-mendelian inheritance refers to the group of phenomena and observations related to the inheritance of genetic information that cannot be merely explained by Mendel's laws of inheritance. Phenomenon including Genomic imprinting, X-chromosome Inactivation, Paramutations are some of the best studied examples of non-mendelian inheritance. Genomic imprinting is a process that reversibly marks one of the two homologous loci, chromosome or chromosomal sets during development, resulting in functional non-equivalence of gene expression. Genomic imprinting is known to occur in a few insect species, plants, and placental mammals. Over the years, studies on imprinted genes have contributed immensely to highlighting the role of epigenetic modifications and the epigenetic circuitry during gene expression and development. In this review, we discuss the phenomenon of genomic imprinting in mammals and the role it plays especially during fetoplacental growth and early development.
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Affiliation(s)
- Thushara Thamban
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
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26
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Matsumoto H, Hayashi T, Ozaki H, Tsuyuzaki K, Umeda M, Iida T, Nakamura M, Okano H, Nikaido I. An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data. NAR Genom Bioinform 2019; 2:lqz020. [PMID: 34632380 PMCID: PMC8499053 DOI: 10.1093/nargab/lqz020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 11/05/2019] [Accepted: 11/29/2019] [Indexed: 12/31/2022] Open
Abstract
Single-cell RNA sequencing has enabled researchers to quantify the transcriptomes of individual cells, infer cell types and investigate differential expression among cell types, which will lead to a better understanding of the regulatory mechanisms of cell states. Transcript diversity caused by phenomena such as aberrant splicing events have been revealed, and differential expression of previously unannotated transcripts might be overlooked by annotation-based analyses. Accordingly, we have developed an approach to discover overlooked differentially expressed (DE) gene regions that complements annotation-based methods. Our algorithm decomposes mapped count data matrix for a gene region using non-negative matrix factorization, quantifies the differential expression level based on the decomposed matrix, and compares the differential expression level based on annotation-based approach to discover previously unannotated DE transcripts. We performed single-cell RNA sequencing for human neural stem cells and applied our algorithm to the dataset. We also applied our algorithm to two public single-cell RNA sequencing datasets correspond to mouse ES and primitive endoderm cells, and human preimplantation embryos. As a result, we discovered several intriguing DE transcripts, including a transcript related to the modulation of neural stem/progenitor cell differentiation.
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Affiliation(s)
- Hirotaka Matsumoto
- Medical Image Analysis Team, RIKEN Center for Advanced Intelligence Project, Nihonbashi 1-chome Mitsui Building 15F, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan.,Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tetsutaro Hayashi
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Haruka Ozaki
- Center for Artificial Intelligence Research, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.,Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Koki Tsuyuzaki
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mana Umeda
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tsuyoshi Iida
- Department of Orthopaedic Surgery, Keio University School of Medicine, 35 Sinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masaya Nakamura
- Department of Orthopaedic Surgery, Keio University School of Medicine, 35 Sinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Sinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Bioinformatics Course, Master's/Doctoral Program in Life Science Innovation (T-LSI), School of Integrative and Global Majors (SIGMA), University of Tsukuba, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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27
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28
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Yang M, Perisse I, Fan Z, Regouski M, Meyer-Ficca M, Polejaeva IA. Increased pregnancy losses following serial somatic cell nuclear transfer in goats. Reprod Fertil Dev 2019; 30:1443-1453. [PMID: 29769162 DOI: 10.1071/rd17323] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 04/09/2018] [Indexed: 12/26/2022] Open
Abstract
Serial cloning by somatic cell nuclear transfer (SCNT) is a critical tool for the expansion of precious transgenic lines or resetting the lifespan of primary transgenic cells for multiple genetic modifications. We successfully produced second-generation cloned goats using donor neonatal fibroblasts from first-generation clones. However, our attempts to produce any third-generation clones failed. SCNT efficiency decreased progressively with the clonal generations. The rate of pregnancy loss was significantly greater in recloning groups (P<0.05). While no pregnancy loss was observed during the first round of SCNT, 14 out of 21 pregnancies aborted in the second round of SCNT and all pregnancies aborted in the third round of SCNT. In this retrospective study, we also investigated the expression of 21 developmentally important genes in muscle tissue of cloned (G1) and recloned (G2) offspring. The expression of most of these genes in live clones was found to be largely comparable to naturally reproduced control goats, but fibroblast growth factor 10 (FGF10), methyl CpG binding protein 2 (MECP2) and growth factor receptor bound protein 10 (GRB10) were differentially expressed (P<0.05) in G2 goats compared with G1 and controls. To study the effects of serial cloning on DNA methylation, the methylation pattern of differentially methylated regions in imprinted genes H19 and insulin like growth factor 2 receptor (IGF2R) were also analysed. Aberrant H19 DNA methylation patterns were detected in G1 and G2 clones.
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Affiliation(s)
- Min Yang
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-4815, USA
| | - Iuri Perisse
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-4815, USA
| | - Zhiqiang Fan
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-4815, USA
| | - Misha Regouski
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-4815, USA
| | - Mirella Meyer-Ficca
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-4815, USA
| | - Irina A Polejaeva
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-4815, USA
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29
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Kochmanski J, VanOeveren SE, Patterson JR, Bernstein AI. Developmental Dieldrin Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development and Parkinson's Disease in Mouse Midbrain. Toxicol Sci 2019; 169:593-607. [PMID: 30859219 PMCID: PMC6542339 DOI: 10.1093/toxsci/kfz069] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human and animal studies have shown that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson's disease (PD). Despite previous work showing a link between developmental dieldrin exposure and increased neuronal susceptibility to MPTP toxicity in male C57BL/6 mice, the mechanism mediating this effect has not been identified. Here, we tested the hypothesis that developmental exposure to dieldrin increases neuronal susceptibility via genome-wide changes in DNA methylation. Starting at 8 weeks of age and prior to mating, female C57BL/6 mice were exposed to 0.3 mg/kg dieldrin by feeding (every 3 days) throughout breeding, gestation, and lactation. At 12 weeks of age, pups were sacrificed and ventral mesencephalon, containing primarily substantia nigra, was microdissected. DNA was isolated and dieldrin-related changes in DNA methylation were assessed via reduced representation bisulfite sequencing. We identified significant, sex-specific differentially methylated CpGs (DMCs) and regions (DMRs) by developmental dieldrin exposure (false discovery rate < 0.05), including DMCs at the Nr4a2 and Lmx1b genes, which are involved in dopaminergic neuron development and maintenance. Developmental dieldrin exposure had distinct effects on the male and female epigenome. Together, our data suggest that developmental dieldrin exposure establishes sex-specific poised epigenetic states early in life. These poised epigenomes may mediate sensitivity to subsequent toxic stimuli and contribute to the development of late-life neurodegenerative disease, including PD.
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Affiliation(s)
- Joseph Kochmanski
- Department of Translational Science & Molecular Medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503
| | - Sarah E VanOeveren
- Department of Translational Science & Molecular Medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503
| | - Joseph R Patterson
- Department of Translational Science & Molecular Medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503
| | - Alison I Bernstein
- Department of Translational Science & Molecular Medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503
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30
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Zhang S, Macias-Garcia A, Ulirsch JC, Velazquez J, Butty VL, Levine SS, Sankaran VG, Chen JJ. HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis. eLife 2019; 8:46976. [PMID: 31033440 PMCID: PMC6533081 DOI: 10.7554/elife.46976] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/26/2019] [Indexed: 12/05/2022] Open
Abstract
Iron and heme play central roles in the production of red blood cells, but the underlying mechanisms remain incompletely understood. Heme-regulated eIF2α kinase (HRI) controls translation by phosphorylating eIF2α. Here, we investigate the global impact of iron, heme, and HRI on protein translation in vivo in murine primary erythroblasts using ribosome profiling. We validate the known role of HRI-mediated translational stimulation of integratedstressresponse mRNAs during iron deficiency in vivo. Moreover, we find that the translation of mRNAs encoding cytosolic and mitochondrial ribosomal proteins is substantially repressed by HRI during iron deficiency, causing a decrease in cytosolic and mitochondrial protein synthesis. The absence of HRI during iron deficiency elicits a prominent cytoplasmic unfolded protein response and impairs mitochondrial respiration. Importantly, ATF4 target genes are activated during iron deficiency to maintain mitochondrial function and to enable erythroid differentiation. We further identify GRB10 as a previously unappreciated regulator of terminal erythropoiesis. Red blood cells use a molecule called hemoglobin to transport oxygen around the body. To make hemoglobin, cells require iron to build a component called heme. If an individual does not get enough iron in their diet, the body cannot produce enough red blood cells, or the cells lack hemoglobin. This condition is known as iron deficiency anemia, and it affects around one-third of the world’s population. Researchers did not know exactly how iron levels control red blood cell production, though several proteins had been identified to play important roles. Heme forms in the cell's mitochondria: the compartments in the cell that supply it with energy. When heme levels in a developing red blood cell are low, a protein called HRI reduces the production of many proteins, most importantly the proteins that make up hemoglobin. HRI also boosts the production of a protein called ATF4, which switches on a set of genes that help both the cell and its mitochondria to adapt to the lack of heme. In turn, HRI and ATF4 reduce the activity of a signaling pathway called mTORC1, which controls the production of proteins that help cells to grow and divide. To understand in more detail how iron and heme regulate the production of new red blood cells, Zhang et al. looked at immature red blood cells from the livers of developing mice. Some of the mice lacked the gene that produces HRI, and some experienced iron deficiency. Comparing gene activity in the different mice revealed that in the developing blood cells of iron-deficient mice, HRI largely reduces the rate of protein production in both the mitochondria and the wider cell. At the same time, the increased activity of ATF4 allows the mitochondria to carry on releasing energy and the cells to continue developing. Zhang et al. also found that a protein that inhibits the mTORC1 signaling pathway needs to be active for the new red blood cells to mature. Overall, the results suggest that drugs that activate HRI or block the activity of the mTORC1 pathway could help to treat anemia. The next step is to test the effects that such drugs have in anemic mice and cells from anemic people.
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Affiliation(s)
- Shuping Zhang
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Alejandra Macias-Garcia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, United States.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, United States
| | - Jason Velazquez
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Vincent L Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Stuart S Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, United States
| | - Jane-Jane Chen
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
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31
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Zhou T, Ma Y, Tang J, Guo F, Dong M, Wei Q. Modulation of IGF1R Signaling Pathway by GIGYF1 in High Glucose-Induced SHSY-5Y Cells. DNA Cell Biol 2018; 37:1044-1054. [PMID: 30376373 DOI: 10.1089/dna.2018.4336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Ting Zhou
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuefei Ma
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Tang
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fengqi Guo
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mingxia Dong
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qianping Wei
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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32
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La HM, Chan AL, Legrand JMD, Rossello FJ, Gangemi CG, Papa A, Cheng Q, Morand EF, Hobbs RM. GILZ-dependent modulation of mTORC1 regulates spermatogonial maintenance. Development 2018; 145:dev.165324. [PMID: 30126904 DOI: 10.1242/dev.165324] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/06/2018] [Indexed: 12/15/2022]
Abstract
Male fertility is dependent on spermatogonial stem cells (SSCs) that self-renew and produce differentiating germ cells. Growth factors produced within the testis are essential for SSC maintenance but intrinsic factors that dictate the SSC response to these stimuli are poorly characterised. Here, we have studied the role of GILZ, a TSC22D family protein and spermatogenesis regulator, in spermatogonial function and signalling. Although broadly expressed in the germline, GILZ was prominent in undifferentiated spermatogonia and Gilz deletion in adults resulted in exhaustion of the GFRα1+ SSC-containing population and germline degeneration. GILZ loss was associated with mTORC1 activation, suggesting enhanced growth factor signalling. Expression of deubiquitylase USP9X, an mTORC1 modulator required for spermatogenesis, was disrupted in Gilz mutants. Treatment with an mTOR inhibitor rescued GFRα1+ spermatogonial failure, indicating that GILZ-dependent mTORC1 inhibition is crucial for SSC maintenance. Analysis of cultured undifferentiated spermatogonia lacking GILZ confirmed aberrant activation of ERK MAPK upstream mTORC1 plus USP9X downregulation and interaction of GILZ with TSC22D proteins. Our data indicate an essential role for GILZ-TSC22D complexes in ensuring the appropriate response of undifferentiated spermatogonia to growth factors via distinct inputs to mTORC1.
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Affiliation(s)
- Hue M La
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Ai-Leen Chan
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Julien M D Legrand
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Fernando J Rossello
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Christina G Gangemi
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Antonella Papa
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Qiang Cheng
- Centre for Inflammatory Diseases, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria 3800, Australia
| | - Eric F Morand
- Centre for Inflammatory Diseases, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria 3800, Australia
| | - Robin M Hobbs
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria 3800, Australia .,Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria 3800, Australia
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33
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Kochmanski JJ, Marchlewicz EH, Cavalcante RG, Perera BPU, Sartor MA, Dolinoy DC. Longitudinal Effects of Developmental Bisphenol A Exposure on Epigenome-Wide DNA Hydroxymethylation at Imprinted Loci in Mouse Blood. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:077006. [PMID: 30044229 PMCID: PMC6108846 DOI: 10.1289/ehp3441] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/04/2018] [Accepted: 06/15/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Epigenetic machinery plays an important role in genomic imprinting, a developmental process that establishes parent-of-origin-specific monoallelic gene expression. Although a number of studies have investigated the role of 5-methylcytosine in imprinting control, the contribution of 5-hydroxymethylcytosine (5-hmC) to this epigenetic phenomenon remains unclear. OBJECTIVES Using matched mouse blood samples (from mice at 2, 4, and 10 months of age), our objective was to examine the effects of perinatal bisphenol A (BPA) exposure (50 μg/kg diet) on longitudinal 5-hmC patterns at imprinted regions. We also aimed to test the hypothesis that 5-hmC would show defined patterns at imprinted genes that persist across the life course. METHODS Genome-wide 5-hmC levels were measured using hydroxymethylated DNA immunoprecipitation sequencing (HMeDIP-seq). Modeling of differential hydroxymethylation by BPA exposure was performed using a pipeline of bioinformatics tools, including the csaw R package. RESULTS Based on BPA exposure, we identified 5,950 differentially hydroxymethylated regions (DHMRs), including 12 DHMRs that were annotated to murine imprinted genes—Gnas, Grb10, Plagl1, Klf14, Pde10a, Snrpn, Airn, Cmah, Ppp1r9a, Kcnq1, Phactr2, and Pde4d. When visualized, these imprinted gene DHMRs showed clear, consistent patterns of differential 5-hmC by developmental BPA exposure that persisted throughout adulthood. CONCLUSIONS These data show long-term establishment of 5-hmC marks at imprinted loci during development. Further, the effect of perinatal BPA exposure on 5-hmC at specific imprinted loci indicates that developmental exposure to environmental toxicants may alter long-term imprinted gene regulation via an epigenetic mechanism. https://doi.org/10.1289/EHP3441.
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Affiliation(s)
- Joseph J Kochmanski
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Elizabeth H Marchlewicz
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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34
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Li H, Gao S, Huang H, Liu W, Huang H, Liu X, Gao Y, Le R, Kou X, Zhao Y, Kou Z, Li J, Wang H, Zhang Y, Wang H, Cai T, Sun Q, Gao S, Han Z. High throughput sequencing identifies an imprinted gene, Grb10, associated with the pluripotency state in nuclear transfer embryonic stem cells. Oncotarget 2018; 8:47344-47355. [PMID: 28476045 PMCID: PMC5564569 DOI: 10.18632/oncotarget.17185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/24/2017] [Indexed: 02/05/2023] Open
Abstract
Somatic cell nuclear transfer and transcription factor mediated reprogramming are two widely used techniques for somatic cell reprogramming. Both fully reprogrammed nuclear transfer embryonic stem cells and induced pluripotent stem cells hold potential for regenerative medicine, and evaluation of the stem cell pluripotency state is crucial for these applications. Previous reports have shown that the Dlk1-Dio3 region is associated with pluripotency in induced pluripotent stem cells and the incomplete somatic cell reprogramming causes abnormally elevated levels of genomic 5-methylcytosine in induced pluripotent stem cells compared to nuclear transfer embryonic stem cells and embryonic stem cells. In this study, we compared pluripotency associated genes Rian and Gtl2 in the Dlk1-Dio3 region in exactly syngeneic nuclear transfer embryonic stem cells and induced pluripotent stem cells with same genomic insertion. We also assessed 5-methylcytosine and 5-hydroxymethylcytosine levels and performed high-throughput sequencing in these cells. Our results showed that Rian and Gtl2 in the Dlk1-Dio3 region related to pluripotency in induced pluripotent stem cells did not correlate with the genes in nuclear transfer embryonic stem cells, and no significant difference in 5-methylcytosine and 5-hydroxymethylcytosine levels were observed between fully and partially reprogrammed nuclear transfer embryonic stem cells and induced pluripotent stem cells. Through syngeneic comparison, our study identifies for the first time that Grb10 is associated with the pluripotency state in nuclear transfer embryonic stem cells.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China.,University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, People's Republic of China.,National Institute of Biological Sciences, NIBS, Beijing, People's Republic of China
| | - Shuai Gao
- National Institute of Biological Sciences, NIBS, Beijing, People's Republic of China
| | - Hua Huang
- State Key Laboratory of Environment Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing, People's Republic of China
| | - Wenqiang Liu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Huanwei Huang
- National Institute of Biological Sciences, NIBS, Beijing, People's Republic of China
| | - Xiaoyu Liu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Yawei Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Yanhong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Zhaohui Kou
- National Institute of Biological Sciences, NIBS, Beijing, People's Republic of China
| | - Jia Li
- National Institute of Biological Sciences, NIBS, Beijing, People's Republic of China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Yu Zhang
- National Institute of Biological Sciences, NIBS, Beijing, People's Republic of China
| | - Hailin Wang
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, People's Republic of China.,State Key Laboratory of Environment Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing, People's Republic of China
| | - Tao Cai
- National Institute of Biological Sciences, NIBS, Beijing, People's Republic of China
| | - Qingyuan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China.,University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, People's Republic of China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Zhiming Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
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35
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Cowley M, Skaar DA, Jima DD, Maguire RL, Hudson KM, Park SS, Sorrow P, Hoyo C. Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:037003. [PMID: 29529597 PMCID: PMC6071808 DOI: 10.1289/ehp2085] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Imprinted genes are defined by their preferential expression from one of the two parental alleles. This unique mode of gene expression is dependent on allele-specific DNA methylation profiles established at regulatory sequences called imprinting control regions (ICRs). These loci have been used as biosensors to study how environmental exposures affect methylation and transcription. However, a critical unanswered question is whether they are more, less, or equally sensitive to environmental stressors as the rest of the genome. OBJECTIVES Using cadmium exposure in humans as a model, we aimed to determine the relative sensitivity of ICRs to perturbation of methylation compared to similar, nonimprinted loci in the genome. METHODS We assayed DNA methylation genome-wide using bisulfite sequencing of 19 newborn cord blood and 20 maternal blood samples selected on the basis of maternal blood cadmium levels. Differentially methylated regions (DMRs) associated with cadmium exposure were identified. RESULTS In newborn cord blood and maternal blood, 641 and 1,945 cadmium-associated DMRs were identified, respectively. DMRs were more common at the 15 maternally methylated ICRs than at similar nonimprinted loci in newborn cord blood (p=5.64×10-8) and maternal blood (p=6.22×10-14), suggesting a higher sensitivity for ICRs to cadmium. Genome-wide, Enrichr analysis indicated that the top three functional categories for genes that overlapped DMRs in maternal blood were body mass index (BMI) (p=2.0×10-5), blood pressure (p=3.8×10-5), and body weight (p=0.0014). In newborn cord blood, the top three functional categories were BMI, atrial fibrillation, and hypertension, although associations were not significant after correction for multiple testing (p=0.098). These findings suggest that epigenetic changes may contribute to the etiology of cadmium-associated diseases. CONCLUSIONS We analyzed cord blood and maternal blood DNA methylation profiles genome-wide at nucleotide resolution in individuals selected for high and low blood cadmium levels in the first trimester. Our findings suggest that ICRs may be hot spots for perturbation by cadmium, motivating further study of these loci to investigate potential mechanisms of cadmium action. https://doi.org/10.1289/EHP2085.
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Affiliation(s)
- Michael Cowley
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
- W.M. Keck Center for Behavioral Biology , North Carolina State University , Raleigh, North Carolina, USA
| | - David A Skaar
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Dereje D Jima
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University , Raleigh, North Carolina, USA
| | - Rachel L Maguire
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Kathleen M Hudson
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Sarah S Park
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Patricia Sorrow
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
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36
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Yan X, Himburg HA, Pohl K, Quarmyne M, Tran E, Zhang Y, Fang T, Kan J, Chao NJ, Zhao L, Doan PL, Chute JP. Deletion of the Imprinted Gene Grb10 Promotes Hematopoietic Stem Cell Self-Renewal and Regeneration. Cell Rep 2017; 17:1584-1594. [PMID: 27806297 DOI: 10.1016/j.celrep.2016.10.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 09/06/2016] [Accepted: 10/07/2016] [Indexed: 01/30/2023] Open
Abstract
Imprinted genes are differentially expressed by adult stem cells, but their functions in regulating adult stem cell fate are incompletely understood. Here we show that growth factor receptor-bound protein 10 (Grb10), an imprinted gene, regulates hematopoietic stem cell (HSC) self-renewal and regeneration. Deletion of the maternal allele of Grb10 in mice (Grb10m/+ mice) substantially increased HSC long-term repopulating capacity, as compared to that of Grb10+/+ mice. After total body irradiation (TBI), Grb10m/+ mice demonstrated accelerated HSC regeneration and hematopoietic reconstitution, as compared to Grb10+/+ mice. Grb10-deficient HSCs displayed increased proliferation after competitive transplantation or TBI, commensurate with upregulation of CDK4 and Cyclin E. Furthermore, the enhanced HSC regeneration observed in Grb10-deficient mice was dependent on activation of the Akt/mTORC1 pathway. This study reveals a function for the imprinted gene Grb10 in regulating HSC self-renewal and regeneration and suggests that the inhibition of Grb10 can promote hematopoietic regeneration in vivo.
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Affiliation(s)
- Xiao Yan
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Heather A Himburg
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Katherine Pohl
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Mamle Quarmyne
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Evelyn Tran
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Yurun Zhang
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Tiancheng Fang
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Jenny Kan
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Nelson J Chao
- Division of Hematologic Malignancies and Cellular Therapy, Duke University, Durham, NC 27710, USA
| | - Liman Zhao
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Phuong L Doan
- Division of Hematologic Malignancies and Cellular Therapy, Duke University, Durham, NC 27710, USA
| | - John P Chute
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA.
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37
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Lee CC, Peng SH, Shen L, Lee CF, Du TH, Kang ML, Xu GL, Upadhyay AK, Cheng X, Yan YT, Zhang Y, Juan LJ. The Role of N-α-acetyltransferase 10 Protein in DNA Methylation and Genomic Imprinting. Mol Cell 2017; 68:89-103.e7. [PMID: 28943313 DOI: 10.1016/j.molcel.2017.08.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/13/2017] [Accepted: 08/24/2017] [Indexed: 01/21/2023]
Abstract
Genomic imprinting is an allelic gene expression phenomenon primarily controlled by allele-specific DNA methylation at the imprinting control region (ICR), but the underlying mechanism remains largely unclear. N-α-acetyltransferase 10 protein (Naa10p) catalyzes N-α-acetylation of nascent proteins, and mutation of human Naa10p is linked to severe developmental delays. Here we report that Naa10-null mice display partial embryonic lethality, growth retardation, brain disorders, and maternal effect lethality, phenotypes commonly observed in defective genomic imprinting. Genome-wide analyses further revealed global DNA hypomethylation and enriched dysregulation of imprinted genes in Naa10p-knockout embryos and embryonic stem cells. Mechanistically, Naa10p facilitates binding of DNA methyltransferase 1 (Dnmt1) to DNA substrates, including the ICRs of the imprinted allele during S phase. Moreover, the lethal Ogden syndrome-associated mutation of human Naa10p disrupts its binding to the ICR of H19 and Dnmt1 recruitment. Our study thus links Naa10p mutation-associated Ogden syndrome to defective DNA methylation and genomic imprinting.
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Affiliation(s)
- Chen-Cheng Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Shih-Huan Peng
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan, ROC
| | - Li Shen
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Chung-Fan Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Ting-Huei Du
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Ming-Lun Kang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Guo-Liang Xu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Anup K Upadhyay
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yu-Ting Yan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Yi Zhang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Li-Jung Juan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC.
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38
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Maternal GRB10 microdeletion is a novel cause of cystic placenta: Spectrum of genomic changes in the etiology of enlarged cystic placenta. Placenta 2017; 57:33-41. [DOI: 10.1016/j.placenta.2017.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 01/30/2023]
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39
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Bouschet T, Dubois E, Reynès C, Kota SK, Rialle S, Maupetit-Méhouas S, Pezet M, Le Digarcher A, Nidelet S, Demolombe V, Cavelier P, Meusnier C, Maurizy C, Sabatier R, Feil R, Arnaud P, Journot L, Varrault A. In Vitro Corticogenesis from Embryonic Stem Cells Recapitulates the In Vivo Epigenetic Control of Imprinted Gene Expression. Cereb Cortex 2017; 27:2418-2433. [PMID: 27095822 DOI: 10.1093/cercor/bhw102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In vitro corticogenesis from embryonic stem cells (ESCs) is an attractive model of cortical development and a promising tool for cortical therapy. It is unknown to which extent epigenetic mechanisms crucial for cortex development and function, such as parental genomic imprinting, are recapitulated by in vitro corticogenesis. Here, using genome-wide transcriptomic and methylation analyses on hybrid mouse tissues and cells, we find a high concordance of imprinting status between in vivo and ESC-derived cortices. Notably, in vitro corticogenesis strictly reproduced the in vivo parent-of-origin-dependent expression of 41 imprinted genes (IGs), including Mest and Cdkn1c known to control corticogenesis. Parent-of-origin-dependent DNA methylation was also conserved at 14 of 18 imprinted differentially methylated regions. The least concordant imprinted locus was Gpr1-Zdbf2, where the aberrant bi-allelic expression of Zdbf2 and Adam23 was concomitant with a gain of methylation on the maternal allele in vitro. Combined, our data argue for a broad conservation of the epigenetic mechanisms at imprinted loci in cortical cells derived from ESCs. We propose that in vitro corticogenesis helps to define the still poorly understood mechanisms that regulate imprinting in the brain and the roles of IGs in cortical development.
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Affiliation(s)
- Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Emeric Dubois
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Christelle Reynès
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Satya K Kota
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Stéphanie Rialle
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Stéphanie Maupetit-Méhouas
- GReD (Genetics, Reproduction and Development), CNRS UMR6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mikael Pezet
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Sabine Nidelet
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Vincent Demolombe
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Patricia Cavelier
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Céline Meusnier
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Chloé Maurizy
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France.,Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Robert Sabatier
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Philippe Arnaud
- GReD (Genetics, Reproduction and Development), CNRS UMR6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France.,Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Annie Varrault
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
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40
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Histone Acetylome-wide Association Study of Autism Spectrum Disorder. Cell 2017; 167:1385-1397.e11. [PMID: 27863250 DOI: 10.1016/j.cell.2016.10.031] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 07/14/2016] [Accepted: 10/18/2016] [Indexed: 02/06/2023]
Abstract
The association of histone modification changes with autism spectrum disorder (ASD) has not been systematically examined. We conducted a histone acetylome-wide association study (HAWAS) by performing H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) on 257 postmortem samples from ASD and matched control brains. Despite etiological heterogeneity, ≥68% of syndromic and idiopathic ASD cases shared a common acetylome signature at >5,000 cis-regulatory elements in prefrontal and temporal cortex. Similarly, multiple genes associated with rare genetic mutations in ASD showed common "epimutations." Acetylome aberrations in ASD were not attributable to genetic differentiation at cis-SNPs and highlighted genes involved in synaptic transmission, ion transport, epilepsy, behavioral abnormality, chemokinesis, histone deacetylation, and immunity. By correlating histone acetylation with genotype, we discovered >2,000 histone acetylation quantitative trait loci (haQTLs) in human brain regions, including four candidate causal variants for psychiatric diseases. Due to the relative stability of histone modifications postmortem, we anticipate that the HAWAS approach will be applicable to multiple diseases.
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Song ZJ, Reitman ZJ, Ma ZY, Chen JH, Zhang QL, Shou XF, Huang CX, Wang YF, Li SQ, Mao Y, Zhou LF, Lian BF, Yan H, Shi YY, Zhao Y. The genome-wide mutational landscape of pituitary adenomas. Cell Res 2016; 26:1255-1259. [PMID: 27670697 PMCID: PMC5099864 DOI: 10.1038/cr.2016.114] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Zhi-Jian Song
- Bio-X Institutes, Ministry of Education Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zachary J Reitman
- Harvard Radiation Oncology Program, Harvard Medical School, Boston, MA02115, USA
| | - Zeng-Yi Ma
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China.,Shanghai Pituitary Tumor Center, Shanghai 200040, China
| | - Jian-Hua Chen
- Bio-X Institutes, Ministry of Education Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Qi-Lin Zhang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China.,Shanghai Pituitary Tumor Center, Shanghai 200040, China
| | - Xue-Fei Shou
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China.,Shanghai Pituitary Tumor Center, Shanghai 200040, China
| | - Chuan-Xin Huang
- Shanghai Institute of Immunology & Department of Immunobiology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yong-Fei Wang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China.,Shanghai Pituitary Tumor Center, Shanghai 200040, China
| | - Shi-Qi Li
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China.,Shanghai Pituitary Tumor Center, Shanghai 200040, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China.,State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai 200040, China.,Institute of Neurosurgery, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Liang-Fu Zhou
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China.,Shanghai Pituitary Tumor Center, Shanghai 200040, China
| | - Bao-Feng Lian
- Shanghai Center for Bioinformation Technology (SCBIT), Shanghai Academy of Science and Technology, Shanghai 201203, China
| | - Hai Yan
- Department of Pathology, The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Yong-Yong Shi
- Bio-X Institutes, Ministry of Education Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yao Zhao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China.,Shanghai Pituitary Tumor Center, Shanghai 200040, China.,State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai 200040, China.,Institute of Neurosurgery, Shanghai Medical College, Fudan University, Shanghai 200040, China
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42
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Epigenetic changes in the developing brain: Effects on behavior. Proc Natl Acad Sci U S A 2015; 112:6789-95. [PMID: 26034282 DOI: 10.1073/pnas.1501482112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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43
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Abstract
Variation in body composition is a popular obsession. The culturally 'ideal' body type is light on fat and heavy on muscle but the human population is collectively laying on fat. A new study finds antagonistic effects of two imprinted genes, Grb10 and Dlk1, on body composition in mice. These findings pose the question whether there is an evolutionary conflict between genes of maternal and paternal origin over the optimal proportions of body fat and lean muscle mass.
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Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge 02138, MA, USA.
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