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Liu H, Shi H, Sun Y. Identification of a novel lymphangiogenesis signature associated with immune cell infiltration in colorectal cancer based on bioinformatics analysis. BMC Med Genomics 2024; 17:2. [PMID: 38167072 PMCID: PMC10763205 DOI: 10.1186/s12920-023-01781-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Lymphangiogenesis plays an important role in tumor progression and is significantly associated with tumor immune infiltration. However, the role and mechanisms of lymphangiogenesis in colorectal cancer (CRC) are still unknown. Thus, the objective is to identify the lymphangiogenesis-related genes associated with immune infiltration and investigation of their prognosis value. METHODS mRNA expression profiles and corresponding clinical information of CRC samples were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The lymphangiogenesis-related genes (LymRGs) were collected from the Molecular Signatures database (MSigDB). Lymphangiogenesis score (LymScore) and immune cell infiltrating levels were quantified using ssGSEA. LymScore) and immune cell infiltrating levels-related hub genes were identified using weighted gene co-expression network analysis (WGCNA). Univariate Cox and LASSO regression analyses were performed to identify the prognostic gene signature and construct a risk model. Furthermore, a predictive nomogram was constructed based on the independent risk factor generated from a multivariate Cox model. RESULTS A total of 1076 LymScore and immune cell infiltrating levels-related hub genes from three key modules were identified by WGCNA. Lymscore is positively associated with natural killer cells as well as regulator T cells infiltrating. These modular genes were enriched in extracellular matrix and structure, collagen fibril organization, cell-substrate adhesion, etc. NUMBL, TSPAN11, PHF21A, PDGFRA, ZNF385A, and RIMKLB were eventually identified as the prognostic gene signature in CRC. And patients were divided into high-risk and low-risk groups based on the median risk score, the patients in the high-risk group indicated poor survival and were predisposed to metastasis and advanced stages. NUMBL and PHF21A were upregulated but PDGFRA was downregulated in tumor samples compared with normal samples in the Human Protein Atlas (HPA) database. CONCLUSION Our finding highlights the critical role of lymphangiogenesis in CRC progression and metastasis and provides a novel gene signature for CRC and novel therapeutic strategies for anti-lymphangiogenic therapies in CRC.
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Affiliation(s)
- Hong Liu
- Department of General Surgery, Wuxi Fifth People's Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu, China
| | - Huiwen Shi
- Department of General Surgery, No.971 Hospital of PLA Navy, Qingdao, China
| | - Yinggang Sun
- Department of General Surgery, The 960th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Jinan, China.
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2
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Mouti MA, Deng S, Pook M, Malzahn J, Rendek A, Militi S, Nibhani R, Soonawalla Z, Oppermann U, Hwang CI, Pauklin S. KMT2A associates with PHF5A-PHF14-HMG20A-RAI1 subcomplex in pancreatic cancer stem cells and epigenetically regulates their characteristics. Nat Commun 2023; 14:5685. [PMID: 37709746 PMCID: PMC10502114 DOI: 10.1038/s41467-023-41297-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Pancreatic cancer (PC), one of the most aggressive and life-threatening human malignancies, is known for its resistance to cytotoxic therapies. This is increasingly ascribed to the subpopulation of undifferentiated cells, known as pancreatic cancer stem cells (PCSCs), which display greater evolutionary fitness than other tumor cells to evade the cytotoxic effects of chemotherapy. PCSCs are crucial for tumor relapse as they possess 'stem cell-like' features that are characterized by self-renewal and differentiation. However, the molecular mechanisms that maintain the unique characteristics of PCSCs are poorly understood. Here, we identify the histone methyltransferase KMT2A as a physical binding partner of an RNA polymerase-associated PHF5A-PHF14-HMG20A-RAI1 protein subcomplex and an epigenetic regulator of PCSC properties and functions. Targeting the protein subcomplex in PCSCs with a KMT2A-WDR5 inhibitor attenuates their self-renewal capacity, cell viability, and in vivo tumorigenicity.
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Affiliation(s)
- Mai Abdel Mouti
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Siwei Deng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Martin Pook
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
- Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Jessica Malzahn
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Aniko Rendek
- Department of Histopathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stefania Militi
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Zahir Soonawalla
- Department of Hepatobiliary and Pancreatic Surgery, Oxford University Hospitals NHS, Oxford, UK
| | - Udo Oppermann
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Chang-Il Hwang
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, USA
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
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3
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Herchenröther A, Gossen S, Friedrich T, Reim A, Daus N, Diegmüller F, Leers J, Sani HM, Gerstner S, Schwarz L, Stellmacher I, Szymkowiak LV, Nist A, Stiewe T, Borggrefe T, Mann M, Mackay JP, Bartkuhn M, Borchers A, Lan J, Hake SB. The H2A.Z and NuRD associated protein HMG20A controls early head and heart developmental transcription programs. Nat Commun 2023; 14:472. [PMID: 36709316 PMCID: PMC9884267 DOI: 10.1038/s41467-023-36114-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 01/17/2023] [Indexed: 01/30/2023] Open
Abstract
Specialized chromatin-binding proteins are required for DNA-based processes during development. We recently established PWWP2A as a direct histone variant H2A.Z interactor involved in mitosis and craniofacial development. Here, we identify the H2A.Z/PWWP2A-associated protein HMG20A as part of several chromatin-modifying complexes, including NuRD, and show that it localizes to distinct genomic regulatory regions. Hmg20a depletion causes severe head and heart developmental defects in Xenopus laevis. Our data indicate that craniofacial malformations are caused by defects in neural crest cell (NCC) migration and cartilage formation. These developmental failures are phenocopied in Hmg20a-depleted mESCs, which show inefficient differentiation into NCCs and cardiomyocytes (CM). Consequently, loss of HMG20A, which marks open promoters and enhancers, results in chromatin accessibility changes and a striking deregulation of transcription programs involved in epithelial-mesenchymal transition (EMT) and differentiation processes. Collectively, our findings implicate HMG20A as part of the H2A.Z/PWWP2A/NuRD-axis and reveal it as a key modulator of intricate developmental transcription programs that guide the differentiation of NCCs and CMs.
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Affiliation(s)
| | - Stefanie Gossen
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany
| | - Tobias Friedrich
- Institute for Biochemistry, Justus-Liebig University Giessen, Giessen, Germany.,Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Institute for lung health, Justus-Liebig University Giessen, Giessen, Germany
| | - Alexander Reim
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Nadine Daus
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Felix Diegmüller
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Jörg Leers
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Hakimeh Moghaddas Sani
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Sarah Gerstner
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany
| | - Leah Schwarz
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany
| | - Inga Stellmacher
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Laura Victoria Szymkowiak
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany.,Institute for Physiological Chemistry, Technical University Dresden, Dresden, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Tilman Borggrefe
- Institute for Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Institute for lung health, Justus-Liebig University Giessen, Giessen, Germany.
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany.
| | - Jie Lan
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany.
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4
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Butera A, Nicotera AG, Di Rosa G, Musumeci SA, Vitello GA, Musumeci A, Vinci M, Gloria A, Federico C, Saccone S, Calì F. PHF21A Related Disorder: Description of a New Case. Int J Mol Sci 2022; 23:ijms232416130. [PMID: 36555772 PMCID: PMC9783151 DOI: 10.3390/ijms232416130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
PHF21A (PHD finger protein 21A) gene, located in the short arm of chromosome 11, encodes for BHC80, a component of the Lysine Specific Demethylase 1, Corepressor of REST (LSD1-CoREST) complex. BHC80 is mainly expressed in the human fetal brain and skeletal muscle and acts as a modulator of several neuronal genes during embryogenesis. Data from literature relates PHF21A variants with Potocki-Shaffer Syndrome (PSS), a contiguous gene deletion disorder caused by the haploinsufficiency of PHF21A, ALX4, and EXT2 genes. Clinical cardinal features of PSS syndrome are multiple exostoses (due to the EXT2 involvement), biparietal foramina (due to the ALX4 involvement), intellectual disability, and craniofacial anomalies (due to the PHF21A involvement). To date, to the best of our knowledge, a detailed description of PHF21A-related disorder clinical phenotype is not described in the literature; in fact, only 14 subjects with microdeletion frameshift or nonsense variants concerning only PHF21A gene have been reported. All reported cases did not present ALX4 or EXT2 variants, and their clinical features did not fit with PSS diagnosis. Herein, by using Exome sequencing, and Sanger sequencing of the region of interest, we describe a case of a child with a paternally inherited (mosaicism of 5%) truncating variant of the PHF21A gene (c.649_650del; p.Gln217ValfsTer6), and discuss the new evidence. In conclusion, these patients showed varied clinical expressions, mainly including the presence of intellectual disability, epilepsy, hypotonia, and dysmorphic features. Our study contributes to describing the genotype-phenotype spectrum of patients with PHF21A-related disorder; however, the limited data in the literature have been unable to provide a precise diagnostic protocol for patients with PHF21A-related disorder.
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Affiliation(s)
- Ambra Butera
- Department of Human Pathology of the Adult and Developmental Age, “Gaetano Barresi” University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
| | - Antonio Gennaro Nicotera
- Department of Human Pathology of the Adult and Developmental Age, “Gaetano Barresi” University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
| | - Gabriella Di Rosa
- Department of Human Pathology of the Adult and Developmental Age, “Gaetano Barresi” University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
| | | | | | - Antonino Musumeci
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy
| | - Mirella Vinci
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy
| | - Angelo Gloria
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy
| | - Concetta Federico
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Salvatore Saccone
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
- Correspondence: (S.S.); (F.C.)
| | - Francesco Calì
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy
- Correspondence: (S.S.); (F.C.)
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A unique Smith-Magenis patient with a de novo intragenic deletion on the maternally inherited overexpressed RAI1 allele. Eur J Hum Genet 2022; 30:1233-1238. [PMID: 35821519 PMCID: PMC9626456 DOI: 10.1038/s41431-022-01143-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/01/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
RAI1 is a dosage-sensitive gene whose decreased or increased expression by recurrent and non-recurrent 17p11.2 deletions or duplications causes Smith-Magenis (SMS) or Potocki-Lupski syndromes (PTLS), respectively. Here we report on a 21-year-old female patient showing SMS phenotype who was found to carry a 3.4 kb de novo intragenic RAI1 deletion. Interestingly, a significant increase in RAI1 transcript levels was identified in the patient's, brother's and mother's peripheral blood cells. Allele-specific dosage analysis revealed that the patient's maternally inherited overexpressed RAI1 allele harbors the intragenic deletion, confirming the SMS diagnosis due to the presence of a single wild-type RAI1 functional allele. The mother and brother do not present any PTLS neurologic/behavioral clinical features. Extensive sequencing of RAI1 promoter and predicted regulatory regions showed no potential causative variants accounting for gene overexpression. However, the mother and both children share a novel private missense variant in RAI1 exon 3, currently classified as a VUS (uncertain significance), though predicted by two bioinformatic tools to disrupt the binding site of one specific transcription factor. The reported familial case, the second showing RAI1 overexpression in the absence of RAI1 duplication, may help to understand the regulation of RAI1 dosage sensitivity although its phenotypic effect remains to be determined.
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6
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Srikanth K, von Pfeil DJF, Stanley BJ, Griffitts C, Huson HJ. Genome Wide Association Study with Imputed Whole Genome Sequence Data Identifies a 431 kb Risk Haplotype on CFA18 for Congenital Laryngeal Paralysis in Alaskan Sled Dogs. Genes (Basel) 2022; 13:genes13101808. [PMID: 36292693 PMCID: PMC9602090 DOI: 10.3390/genes13101808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Congenital laryngeal paralysis (CLP) is an inherited disorder that affects the ability of the dog to exercise and precludes it from functioning as a working sled dog. Though CLP is known to occur in Alaskan sled dogs (ASDs) since 1986, the genetic mutation underlying the disease has not been reported. Using a genome-wide association study (GWAS), we identified a 708 kb region on CFA 18 harboring 226 SNPs to be significantly associated with CLP. The significant SNPs explained 47.06% of the heritability of CLP. We narrowed the region to 431 kb through autozygosity mapping and found 18 of the 20 cases to be homozygous for the risk haplotype. Whole genome sequencing of two cases and a control ASD, and comparison with the genome of 657 dogs from various breeds, confirmed the homozygous status of the risk haplotype to be unique to the CLP cases. Most of the dogs that were homozygous for the risk allele had blue eyes. Gene annotation and a gene-based association study showed that the risk haplotype encompasses genes implicated in developmental and neurodegenerative disorders. Pathway analysis showed enrichment of glycoproteins and glycosaminoglycans biosynthesis, which play a key role in repairing damaged nerves. In conclusion, our results suggest an important role for the identified candidate region in CLP.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Department of Animal Science, College of Agriculture and Life Science, Cornell University, Ithaca, NY 14850, USA
| | | | - Bryden J. Stanley
- Department of Small Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | | | - Heather J. Huson
- Department of Animal Science, College of Agriculture and Life Science, Cornell University, Ithaca, NY 14850, USA
- Correspondence:
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7
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Schneider MF, Müller V, Müller SA, Lichtenthaler SF, Becker PB, Scheuermann JC. LncRNA RUS shapes the gene expression program towards neurogenesis. Life Sci Alliance 2022; 5:5/10/e202201504. [PMID: 35688487 PMCID: PMC9187872 DOI: 10.26508/lsa.202201504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022] Open
Abstract
The chromatin-associated lncRNA RUS binds in the vicinity to neural differentiation-associated genes and regulates them in a context-dependent manner to enable proper neuron development. The evolution of brain complexity correlates with an increased expression of long, noncoding (lnc) RNAs in neural tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during brain development. We present a first functional characterization of the lncRNA LINC01322, which we term RUS for “RNA upstream of Slitrk3.” The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation resulting in arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner.
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Affiliation(s)
- Marius F Schneider
- Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany.,Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center Munich (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Veronika Müller
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center Munich (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stephan A Müller
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE) Munich and Neuroproteomics Unit, Technical University, Munich, Germany
| | - Stefan F Lichtenthaler
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE) Munich and Neuroproteomics Unit, Technical University, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Peter B Becker
- Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Johanna C Scheuermann
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center Munich (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
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8
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Lee C, Yoon J, Park BG, Eun BL, Kwon JA. Novel Pathogenic Variant (c.1171A>T) in PHF21A in a Female with Intellectual Disability and Craniofacial Anomalies. Mol Syndromol 2022; 13:318-322. [PMID: 36158052 PMCID: PMC9421687 DOI: 10.1159/000520207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/13/2021] [Indexed: 01/03/2023] Open
Abstract
Background PHF21A, along with EXT2 and ALX4, is one of the causative genes of Potocki-Shaffer syndrome (PSS), a rare contiguous disorder involving chromosome region11p11.2. PHF21A has been associated with intellectual developmental disorders and craniofacial anomalies and suggested as a candidate for more extended phenotypes. However, variants in PHF21A and its associated phenotypes are yet to be fully explored, since reports on cases with variants affecting this gene are few worldwide. We present a novel heterogeneous variant in PHF21A in a 26-year-old Korean female. Methods The patient's clinical manifestations were recorded and physical examination, cognitive assessment, brain imaging, metabolic screening, and cytogenetic testing including whole exome sequencing were pursued. Results Whole exome sequencing identified a de novo nonsense variant c.1171A>T (p.Lys391Ter), affecting the AT-hook domain. The patient showed an extended phenotypic spectrum along with intellectual developmental disorders and craniofacial anomalies, such as attention-deficit hyperactivity disorder, epilepsy, overgrowth, and hypotonia. Variants affecting the AT-hook domain are few in PSS, however, the phenotypic spectrum of the patient was in line with previously reported cases. Conclusion This case further reinforced and adds to the extended data on the phenotypes associated with PHF21A haploinsufficiency.
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Affiliation(s)
- Cheonghwa Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jung Yoon
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Borae G. Park
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Baik-Lin Eun
- Department of Pediatrics, Korea University College of Medicine, Seoul, Republic of Korea,*Baik-Lin Eun,
| | - Jung Ah Kwon
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea,**Jung Ah Kwon,
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9
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Bonefas KM, Iwase S. Soma-to-germline transformation in chromatin-linked neurodevelopmental disorders? FEBS J 2022; 289:2301-2317. [PMID: 34514717 PMCID: PMC8918023 DOI: 10.1111/febs.16196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/16/2021] [Accepted: 09/10/2021] [Indexed: 01/22/2023]
Abstract
Mutations in numerous chromatin regulators cause neurodevelopmental disorders (NDDs) with unknown mechanisms. Understandably, most research has focused on how chromatin regulators control gene expression that is directly relevant to brain development and function, such as synaptic genes. However, some NDD models surprisingly show ectopic expression of germline genes in the brain. These germline genes are usually expressed only in the primordial germ cells, testis, and ovaries for germ cell development and sexual reproduction. Such ectopic germline gene expression has been reported in several NDDs, including immunodeficiency, centromeric instability, facial anomalies syndrome 1; Kleefstra syndrome 1; MeCP2 duplication syndrome; and mental retardation, X-linked syndromic, Claes-Jensen type. The responsible genes, DNMT3B, G9A/GLP, MECP2, and KDM5C, all encode chromatin regulators for gene silencing. These mutations may therefore lead to germline gene derepression and, in turn, a severe identity crisis of brain cells-potentially interfering with normal brain development. Thus, the ectopic expression of germline genes is a unique hallmark defining this NDD subset and further implicates the importance of germline gene silencing during brain development. The functional impact of germline gene expression on brain development, however, remains undetermined. This perspective article explores how this apparent soma-to-germline transformation arises and how it may interfere with neurodevelopment through genomic instability and impaired sensory cilium formation. Furthermore, we also discuss how to test these hypotheses experimentally to ultimately determine the contribution of ectopic germline transcripts to chromatin-linked NDDs.
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Affiliation(s)
- Katherine M. Bonefas
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109,The University of Michigan Neuroscience Graduate Program,Corresponding authors: Please address correspondence to: , and
| | - Shigeki Iwase
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109,The University of Michigan Neuroscience Graduate Program,Corresponding authors: Please address correspondence to: , and
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10
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Rinaldi B, Villa R, Sironi A, Garavelli L, Finelli P, Bedeschi MF. Smith-Magenis Syndrome—Clinical Review, Biological Background and Related Disorders. Genes (Basel) 2022; 13:genes13020335. [PMID: 35205380 PMCID: PMC8872351 DOI: 10.3390/genes13020335] [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] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 02/06/2023] Open
Abstract
Smith-Magenis syndrome (SMS) is a complex genetic disorder characterized by distinctive physical features, developmental delay, cognitive impairment, and a typical behavioral phenotype. SMS is caused by interstitial 17p11.2 deletions (90%), encompassing multiple genes and including the retinoic acid-induced 1 gene (RAI1), or by pathogenic variants in RAI1 itself (10%). RAI1 is a dosage-sensitive gene expressed in many tissues and acting as transcriptional regulator. The majority of individuals exhibit a mild-to-moderate range of intellectual disability. The behavioral phenotype includes significant sleep disturbance, stereotypes, maladaptive and self-injurious behaviors. In this review, we summarize current clinical knowledge and therapeutic approaches. We further discuss the common biological background shared with other conditions commonly retained in differential diagnosis.
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Affiliation(s)
- Berardo Rinaldi
- Clinical Genetics Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (B.R.); (R.V.)
| | - Roberta Villa
- Clinical Genetics Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (B.R.); (R.V.)
| | - Alessandra Sironi
- Experimental Research Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, 20145 Milan, Italy; (A.S.); (P.F.)
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090 Milan, Italy
| | - Livia Garavelli
- Clinical Genetics Unit, Azienda USL-IRCCS of Reggio Emilia, 42123 Reggio Emilia, Italy;
| | - Palma Finelli
- Experimental Research Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, 20145 Milan, Italy; (A.S.); (P.F.)
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090 Milan, Italy
| | - Maria Francesca Bedeschi
- Clinical Genetics Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (B.R.); (R.V.)
- Correspondence:
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Yin W, Arkilo D, Khudyakov P, Hazel J, Gupta S, Quinton MS, Lin J, Hartman DS, Bednar MM, Rosen L, Wendland JR. Safety, pharmacokinetics and pharmacodynamics of TAK-418, a novel inhibitor of the epigenetic modulator lysine-specific demethylase 1A. Br J Clin Pharmacol 2021; 87:4756-4768. [PMID: 33990969 PMCID: PMC9290503 DOI: 10.1111/bcp.14912] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 01/10/2023] Open
Abstract
Aims Dysregulation of histone methylation epigenetic marks may result in intellectual and developmental disability, as seen in Kabuki syndrome. Animal data suggest that increasing histone methylation by inhibiting lysine‐specific demethylase 1A (LSD1) may improve cognitive outcomes in a model of Kabuki syndrome. TAK‐418 is a novel LSD1 inhibitor, developed as a potential therapeutic agent for central nervous system disorders such as Kabuki syndrome. Here, we report safety, tolerability, pharmacokinetic and pharmacodynamic profiles of single and multiple doses of TAK‐418 (ClinicalTrials.gov: NCT03228433, NCT03501069). Methods Two randomized, double‐blind, placebo‐controlled, phase 1 studies of oral TAK‐418 were performed, a first‐in‐human single‐rising‐dose (SRD) study (5–60 mg) in healthy adult male and female volunteers (placebo, n = 10; TAK‐418, n = 30), and an SRD (120–160 mg) and multiple‐rising‐dose (MRD) study (20–160 mg once daily for 10 days) in healthy female volunteers (placebo, n = 2 [SRD] and n = 6 [MRD]; TAK‐418, n = 6 [SRD] and n = 18 [MRD]). Results TAK‐418 was well tolerated. No clinically significant changes in laboratory test results or vital signs were observed and no serious adverse events were reported. TAK‐418 had a nearly linear pharmacokinetic profile, with rapid absorption and short terminal half‐life across the evaluated dose range. No obvious accumulation was observed after daily administration for 10 days. Administration with food delayed peak plasma concentrations but overall exposure was unaffected. TAK‐418 rapidly crossed the blood–brain barrier and generally showed a dose‐dependent response in the peripheral pharmacodynamic biomarker formyl‐flavin adenine dinucleotide. Conclusion The brain‐penetrant LSD1 inhibitor TAK‐418 was well tolerated, with pharmacokinetic and pharmacodynamic effects that support further investigation.
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Affiliation(s)
- Wei Yin
- Takeda Pharmaceuticals USA, Ltd, Cambridge, MA, USA
| | | | | | - Jim Hazel
- Takeda Pharmaceuticals USA, Ltd, Cambridge, MA, USA
| | | | | | - Jie Lin
- Takeda Pharmaceuticals USA, Ltd, Cambridge, MA, USA
| | | | | | - Laura Rosen
- Takeda Pharmaceuticals USA, Ltd, Cambridge, MA, USA
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12
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Lorenzo PI, Martin Vazquez E, López-Noriega L, Fuente-Martín E, Mellado-Gil JM, Franco JM, Cobo-Vuilleumier N, Guerrero Martínez JA, Romero-Zerbo SY, Perez-Cabello JA, Rivero Canalejo S, Campos-Caro A, Lachaud CC, Crespo Barreda A, Aguilar-Diosdado M, García Fuentes E, Martin-Montalvo A, Álvarez Dolado M, Martin F, Rojo-Martinez G, Pozo D, Bérmudez-Silva FJ, Comaills V, Reyes JC, Gauthier BR. The metabesity factor HMG20A potentiates astrocyte survival and reactive astrogliosis preserving neuronal integrity. Theranostics 2021; 11:6983-7004. [PMID: 34093866 PMCID: PMC8171100 DOI: 10.7150/thno.57237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Rationale: We recently demonstrated that the 'Metabesity' factor HMG20A regulates islet beta-cell functional maturity and adaptation to physiological stress such as pregnancy and pre-diabetes. HMG20A also dictates central nervous system (CNS) development via inhibition of the LSD1-CoREST complex but its expression pattern and function in adult brain remains unknown. Herein we sought to determine whether HMG20A is expressed in the adult CNS, specifically in hypothalamic astrocytes that are key in glucose homeostasis and whether similar to islets, HMG20A potentiates astrocyte function in response to environmental cues. Methods: HMG20A expression profile was assessed by quantitative PCR (QT-PCR), Western blotting and/or immunofluorescence in: 1) the hypothalamus of mice exposed or not to either a high-fat diet or a high-fat high-sucrose regimen, 2) human blood leukocytes and adipose tissue obtained from healthy or diabetic individuals and 3) primary mouse hypothalamic astrocytes exposed to either high glucose or palmitate. RNA-seq and cell metabolic parameters were performed on astrocytes treated or not with a siHMG20A. Astrocyte-mediated neuronal survival was evaluated using conditioned media from siHMG20A-treated astrocytes. The impact of ORY1001, an inhibitor of the LSD1-CoREST complex, on HMG20A expression, reactive astrogliosis and glucose metabolism was evaluated in vitro and in vivo in high-fat high-sucrose fed mice. Results: We show that Hmg20a is predominantly expressed in hypothalamic astrocytes, the main nutrient-sensing cell type of the brain. HMG20A expression was upregulated in diet-induced obesity and glucose intolerant mice, correlating with increased transcript levels of Gfap and Il1b indicative of inflammation and reactive astrogliosis. Hmg20a transcript levels were also increased in adipose tissue of obese non-diabetic individuals as compared to obese diabetic patients. HMG20A silencing in astrocytes resulted in repression of inflammatory, cholesterol biogenesis and epithelial-to-mesenchymal transition pathways which are hallmarks of reactive astrogliosis. Accordingly, HMG20A depleted astrocytes exhibited reduced mitochondrial bioenergetics and increased susceptibility to apoptosis. Neuron viability was also hindered in HMG20A-depleted astrocyte-derived conditioned media. ORY1001 treatment rescued expression of reactive astrogliosis-linked genes in HMG20A ablated astrocytes while enhancing cell surface area, GFAP intensity and STAT3 expression in healthy astrocytes, mimicking the effect of HMG20A. Furthermore, ORY1001 treatment protected against obesity-associated glucose intolerance in mice correlating with a regression of hypothalamic HMG20A expression, indicative of reactive astrogliosis attenuation with improved health status. Conclusion: HMG20A coordinates the astrocyte polarization state. Under physiological pressure such as obesity and insulin resistance that induces low grade inflammation, HMG20A expression is increased to induce reactive astrogliosis in an attempt to preserve the neuronal network and re-establish glucose homeostasis. Nonetheless, a chronic metabesity state or functional mutations will result in lower levels of HMG20A, failure to promote reactive astrogliosis and increase susceptibility of neurons to stress-induced apoptosis. Such effects could be reversed by ORY1001 treatment both in vitro and in vivo, paving the way for a new therapeutic approach for Type 2 Diabetes Mellitus.
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Affiliation(s)
- Petra I. Lorenzo
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Eugenia Martin Vazquez
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Livia López-Noriega
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Esther Fuente-Martín
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - José M. Mellado-Gil
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Jaime M. Franco
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Nadia Cobo-Vuilleumier
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - José A. Guerrero Martínez
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Silvana Y. Romero-Zerbo
- Unidad de Gestión Clínica Intercentros de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga, Spain
| | - Jesús A. Perez-Cabello
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Sabrina Rivero Canalejo
- Department of Normal and Pathological Histology and Cytology, University of Seville School of Medicine, Seville, Spain
| | - Antonio Campos-Caro
- University Hospital “Puerta del Mar”, Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain
| | - Christian Claude Lachaud
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Alejandra Crespo Barreda
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Manuel Aguilar-Diosdado
- University Hospital “Puerta del Mar”, Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain
- Endocrinology and Metabolism Department, University Hospital “Puerta del Mar”, Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain
| | - Eduardo García Fuentes
- Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Spain
| | - Alejandro Martin-Montalvo
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Manuel Álvarez Dolado
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Franz Martin
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Gemma Rojo-Martinez
- Unidad de Gestión Clínica Intercentros de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - David Pozo
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Francisco J. Bérmudez-Silva
- Unidad de Gestión Clínica Intercentros de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Valentine Comaills
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - José C. Reyes
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Benoit R. Gauthier
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucía-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
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13
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Trajkova S, Di Gregorio E, Ferrero GB, Carli D, Pavinato L, Delplancq G, Kuentz P, Brusco A. New Insights into Potocki-Shaffer Syndrome: Report of Two Novel Cases and Literature Review. Brain Sci 2020; 10:brainsci10110788. [PMID: 33126574 PMCID: PMC7693731 DOI: 10.3390/brainsci10110788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/16/2020] [Accepted: 10/27/2020] [Indexed: 12/24/2022] Open
Abstract
Potocki-Shaffer syndrome (PSS) is a rare non-recurrent contiguous gene deletion syndrome involving chromosome 11p11.2. Current literature implies a minimal region with haploinsufficiency of three genes, ALX4 (parietal foramina), EXT2 (multiple exostoses), and PHF21A (craniofacial anomalies, and intellectual disability). The rest of the PSS phenotype is still not associated with a specific gene. We report a systematic review of the literature and included two novel cases. Because deletions are highly variable in size, we defined three groups of patients considering the PSS-genes involved. We found 23 full PSS cases (ALX4, EXT2, and PHF21A), 14 cases with EXT2-ALX4, and three with PHF21A only. Among the latter, we describe a novel male child showing developmental delay, café-au-lait spots, liner postnatal overgrowth and West-like epileptic encephalopathy. We suggest PSS cases may have epileptic spasms early in life, and PHF21A is likely to be the causative gene. Given their subtle presentation these may be overlooked and if left untreated could lead to a severe type or deterioration in the developmental plateau. If our hypothesis is correct, a timely therapy may ameliorate PSS phenotype and improve patients’ outcomes. Our analysis also shows PHF21A is a candidate for the overgrowth phenotype.
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Affiliation(s)
- Slavica Trajkova
- Department of Medical Sciences, University of Torino, 10126 Turin, Italy; (S.T.); (L.P.)
| | - Eleonora Di Gregorio
- Medical Genetics Unit, Città della Salute e della Scienza, University Hospital, 10126 Turin, Italy; (E.D.)
| | - Giovanni Battista Ferrero
- Department of Public Health and Paediatrics, University of Torino, 10126 Turin, Italy; (G.B.F.); (D.C.)
| | - Diana Carli
- Department of Public Health and Paediatrics, University of Torino, 10126 Turin, Italy; (G.B.F.); (D.C.)
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, 10126 Turin, Italy; (S.T.); (L.P.)
| | - Geoffroy Delplancq
- Centre de Génétique Humaine, Université de Franche-Comté, 25000 Besançon, France; (G.D.)
- Service de Pédiatrie, CHU, 25000 Besançon, France
| | - Paul Kuentz
- Oncobiologie Génétique Bioinformatique, PCBio, Centre Hospitalier Universitaire de Besançon, 25000 Besançon, France; (P.K.)
- UMR-Inserm 1231 GAD, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, 21000 Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), Centre Hospitalier Universitaire de Dijon et Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126 Turin, Italy; (S.T.); (L.P.)
- Medical Genetics Unit, Città della Salute e della Scienza, University Hospital, 10126 Turin, Italy; (E.D.)
- Correspondence: (A.B.)
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14
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Lamaa A, Humbert J, Aguirrebengoa M, Cheng X, Nicolas E, Côté J, Trouche D. Integrated analysis of H2A.Z isoforms function reveals a complex interplay in gene regulation. eLife 2020; 9:53375. [PMID: 32109204 PMCID: PMC7048395 DOI: 10.7554/elife.53375] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/12/2020] [Indexed: 12/13/2022] Open
Abstract
The H2A.Z histone variant plays major roles in the control of gene expression. In human, H2A.Z is encoded by two genes expressing two isoforms, H2A.Z.1 and H2A.Z.2 differing by three amino acids. Here, we undertook an integrated analysis of their functions in gene expression using endogenously-tagged proteins. RNA-Seq analysis in untransformed cells showed that they can regulate both distinct and overlapping sets of genes positively or negatively in a context-dependent manner. Furthermore, they have similar or antagonistic function depending on genes. H2A.Z.1 and H2A.Z.2 can replace each other at Transcription Start Sites, providing a molecular explanation for this interplay. Mass spectrometry analysis showed that H2A.Z.1 and H2A.Z.2 have specific interactors, which can mediate their functional antagonism. Our data indicate that the balance between H2A.Z.1 and H2A.Z.2 at promoters is critically important to regulate specific gene expression, providing an additional layer of complexity to the control of gene expression by histone variants.
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Affiliation(s)
- Assala Lamaa
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jonathan Humbert
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Marion Aguirrebengoa
- BigA Core Facility, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Estelle Nicolas
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Didier Trouche
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
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15
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Chaix R, Fagny M, Cosin-Tomás M, Alvarez-López M, Lemee L, Regnault B, Davidson RJ, Lutz A, Kaliman P. Differential DNA methylation in experienced meditators after an intensive day of mindfulness-based practice: Implications for immune-related pathways. Brain Behav Immun 2020; 84:36-44. [PMID: 31733290 PMCID: PMC7010561 DOI: 10.1016/j.bbi.2019.11.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
The human methylome is dynamically influenced by psychological stress. However, its responsiveness to stress management remains underexplored. Meditation practice has been shown to significantly reduce stress level, among other beneficial neurophysiological outcomes. Here, we evaluated the impact of a day of intensive meditation practice (t2-t1 = 8 h) on the methylome of peripheral blood mononuclear cells in experienced meditators (n = 17). In parallel, we assessed the influence of a day of leisure activities in the same environment on the methylome of matched control subjects with no meditation experience (n = 17). DNA methylation profiles were analyzed using the Illumina 450 K beadchip array. We fitted for each methylation site a linear model for multi-level experiments which adjusts the variation between t1 and t2 for baseline differences. No significant baseline differences in methylation profiles was detected between groups. In the meditation group, we identified 61 differentially methylated sites (DMS) after the intervention. These DMS were enriched in genes mostly associated with immune cell metabolism and ageing and in binding sites for several transcription factors involved in immune response and inflammation, among other functions. In the control group, no significant change in methylation level was observed after the day of leisure activities. These results suggest that a short meditation intervention in trained subjects may rapidly influence the epigenome at sites of potential relevance for immune function and provide a better understanding of the dynamics of the human methylome over short time windows.
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Affiliation(s)
- R Chaix
- Unité d'Eco-anthropologie (EA), Museum National d'Histoire Naturelle, CNRS, Université Paris Diderot, 75016 Paris, France.
| | - M Fagny
- Génétique Quantitative et Évolution, Evolution - Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, France
| | - M Cosin-Tomás
- Department of Human Genetics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - M Alvarez-López
- Unitat de Farmacologia, Facultat de Farmàcia, Institut de Biomedicina, Universitat de Barcelona (IBUB), Nucli Universitari de Pedralbes, Barcelone, Spain
| | - L Lemee
- Plate-forme de Génotypage des Eucaryotes, Pôle Biomics, Institut Pasteur, Paris, France; Plateforme Biomics, Institut Pasteur, Paris, France
| | - B Regnault
- Plate-forme de Génotypage des Eucaryotes, Pôle Biomics, Institut Pasteur, Paris, France; Biology of Infection Unit, Inserm U1117. Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
| | - R J Davidson
- Center for Healthy Minds, University of Wisconsin-Madison, USA
| | - A Lutz
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR5292, Lyon 1 University, Lyon, France
| | - P Kaliman
- Center for Healthy Minds, University of Wisconsin-Madison, USA; Faculty of Health Sciences, Universitat Oberta de Catalunya, Barcelona, Spain.
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16
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Friedenson B. A Genome Model to Explain Major Features of Neurodevelopmental Disorders in Newborns. BIOMEDICAL INFORMATICS INSIGHTS 2019; 11:1178222619863369. [PMID: 31391780 PMCID: PMC6669855 DOI: 10.1177/1178222619863369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 12/15/2022]
Abstract
The purpose of this study was to test the hypothesis that infections are linked to chromosomal anomalies that cause neurodevelopmental disorders. In children with disorders in the development of their nervous systems, chromosome anomalies known to cause these disorders were compared with foreign DNAs, including known teratogens. Genes essential for neurons, lymphatic drainage, immunity, circulation, angiogenesis, cell barriers, structure, epigenetic and chromatin modifications were all found close together in polyfunctional clusters that were deleted or rearranged in neurodevelopmental disorders. In some patients, epigenetic driver mutations also changed access to large chromosome segments. These changes account for immune, circulatory, and structural deficits that accompany neurologic deficits. Specific and repetitive human DNA encompassing large deletions matched infections and passed rigorous artifact tests. Deletions of up to millions of bases accompanied infection-matching sequences and caused massive changes in human homologies to foreign DNAs. In data from 3 independent studies of private, familial, and recurrent chromosomal rearrangements, massive changes in homologous microbiomes were found and may drive rearrangements and encourage pathogens. At least 1 chromosomal anomaly was found to consist of human DNA fragments with a gap that corresponded to a piece of integrated foreign DNA. Microbial DNAs that match repetitive or specific human DNA segments are thus proposed to interfere with the epigenome and highly active recombination during meiosis, driven by massive changes in human DNA-foreign DNA homologies. Abnormal recombination in gametes produces zygotes containing rare chromosome anomalies that cause neurologic disorders and nonneurologic signs. Neurodevelopmental disorders may be examples of assault on the human genome by foreign DNAs at a critical stage. Some infections may be more likely tolerated because they resemble human DNA segments. Even rare developmental disorders can be screened for homology to infections within altered epigenomes and chromatin structures. Considering effects of foreign DNAs can assist prenatal and genetic counseling, diagnosis, prevention, and early intervention.
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Affiliation(s)
- Bernard Friedenson
- Department of Biochemistry and Molecular Genetics, College of Medicine, The University of Illinois at Chicago, Chicago, IL, USA
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17
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Giaimo BD, Ferrante F, Herchenröther A, Hake SB, Borggrefe T. The histone variant H2A.Z in gene regulation. Epigenetics Chromatin 2019; 12:37. [PMID: 31200754 PMCID: PMC6570943 DOI: 10.1186/s13072-019-0274-9] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The histone variant H2A.Z is involved in several processes such as transcriptional control, DNA repair, regulation of centromeric heterochromatin and, not surprisingly, is implicated in diseases such as cancer. Here, we review the recent developments on H2A.Z focusing on its role in transcriptional activation and repression. H2A.Z, as a replication-independent histone, has been studied in several model organisms and inducible mammalian model systems. Its loading machinery and several modifying enzymes have been recently identified, and some of the long-standing discrepancies in transcriptional activation and/or repression are about to be resolved. The buffering functions of H2A.Z, as supported by genome-wide localization and analyzed in several dynamic systems, are an excellent example of transcriptional control. Posttranslational modifications such as acetylation and ubiquitination of H2A.Z, as well as its specific binding partners, are in our view central players in the control of gene expression. Understanding the key-mechanisms in either turnover or stabilization of H2A.Z-containing nucleosomes as well as defining the H2A.Z interactome will pave the way for therapeutic applications in the future.
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Affiliation(s)
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Andreas Herchenröther
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
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18
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Sakai A, Sugiyama S. Experience-dependent transcriptional regulation in juvenile brain development. Dev Growth Differ 2019; 60:473-482. [PMID: 30368782 DOI: 10.1111/dgd.12571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 12/26/2022]
Abstract
During brain development, once primary neural networks are formed, they are largely sculpted by environmental stimuli. The juvenile brain has a unique time window termed the critical period, in which neuronal circuits are remodeled by experience. Accumulating evidence indicates that abnormal rewiring of circuits in early life contributes to various neurodevelopmental disorders at later stages of life. Recent studies implicate two important aspects for activation of the critical period, both of which are experience-dependent: (a) proper excitatory/inhibitory (E/I) balance of neural circuit achieved during developmental trajectory of inhibitory interneurons, and (b) epigenetic regulation allowing flexible gene expression for neuronal plasticity. In this review, we discuss the molecular mechanisms of juvenile brain plasticity from the viewpoints of transcriptional and chromatin regulation, with a focus on Otx2 homeoprotein. Depending on experience, Otx2 is transported into cortical parvalbumin-positive interneurons (PV cells), where it induces PV cell maturation to activate the critical period. Understanding the unique behavior and function of Otx2 as a "messenger" of experience should therefore provide insights into mechanisms of juvenile brain development. Recently identified downstream targets of Otx2 suggest novel roles of Otx2 in homeostasis of PV cells, and, moreover, in regulation of chromatin state, which is important for neuronal plasticity. We further discuss epigenetic changes during postnatal brain development spanning the critical period. Different aspects of chromatin regulation may underlie experience-dependent neuronal development and plasticity.
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Affiliation(s)
- Akiko Sakai
- Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Sayaka Sugiyama
- Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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Chen YJ, Chang WA, Wu LY, Huang CF, Chen CH, Kuo PL. Identification of Novel Genes in Osteoarthritic Fibroblast-Like Synoviocytes Using Next-Generation Sequencing and Bioinformatics Approaches. Int J Med Sci 2019; 16:1057-1071. [PMID: 31523167 PMCID: PMC6743272 DOI: 10.7150/ijms.35611] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/05/2019] [Indexed: 01/15/2023] Open
Abstract
Synovitis in osteoarthritis (OA) the consequence of low grade inflammatory process caused by cartilage breakdown products that stimulated the production of pro-inflammatory mediators by fibroblast-like synoviocytes (FLS). FLS participate in joint homeostasis and low grade inflammation in the joint microenvironment triggers FLS transformation. In the current study, we aimed to identify differentially expressed genes and potential miRNA regulations in human OA FLS through deep sequencing and bioinformatics approaches. The 245 differentially expressed genes in OA FLS were identified, and pathway analysis using various bioinformatics databases indicated their enrichment in functions related to altered extracellular matrix organization, cell adhesion and cellular movement. Moreover, among the 14 dysregulated genes with potential miRNA regulations identified, src kinase associated phosphoprotein 2 (SKAP2), adaptor related protein complex 1 sigma 2 subunit (AP1S2), PHD finger protein 21A (PHF21A), lipoma preferred partner (LPP), and transcription factor AP-2 alpha (TFAP2A) showed similar expression patterns in OA FLS and OA synovial tissue datasets in Gene Expression Omnibus database. Ingenuity Pathway Analysis identified the dysregulated LPP participated in cell migration and cell spreading of OA FLS, which was potentially regulated by miR-141-3p. The current findings suggested new perspectives into understanding the novel molecular signatures of FLS involved in the pathogenesis of OA, which may be potential therapeutic targets.
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Affiliation(s)
- Yi-Jen Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Department of Physical Medicine and Rehabilitation, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Wei-An Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Ling-Yu Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ching-Fen Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Department of Physical Medicine and Rehabilitation, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Chia-Hsin Chen
- Department of Physical Medicine and Rehabilitation, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan.,Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Orthopaedic Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Po-Lin Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Center for Cancer Research, Kaohsiung Medical University
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Epigenetic mechanisms in amyotrophic lateral sclerosis: A short review. Mech Ageing Dev 2018; 174:103-110. [DOI: 10.1016/j.mad.2018.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 03/08/2018] [Accepted: 03/11/2018] [Indexed: 12/13/2022]
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21
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Larizza L, Finelli P. Developmental disorders with intellectual disability driven by chromatin dysregulation: Clinical overlaps and molecular mechanisms. Clin Genet 2018; 95:231-240. [DOI: 10.1111/cge.13365] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/28/2018] [Accepted: 04/14/2018] [Indexed: 12/30/2022]
Affiliation(s)
- L. Larizza
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
| | - P. Finelli
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
- Department of Medical Biotechnology and Translational Medicine; Università degli Studi di Milano; Milan Italy
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Epigenetic Etiology of Intellectual Disability. J Neurosci 2017; 37:10773-10782. [PMID: 29118205 DOI: 10.1523/jneurosci.1840-17.2017] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/26/2017] [Accepted: 09/26/2017] [Indexed: 12/31/2022] Open
Abstract
Intellectual disability (ID) is a prevailing neurodevelopmental condition associated with impaired cognitive and adaptive behaviors. Many chromatin-modifying enzymes and other epigenetic regulators have been genetically associated with ID disorders (IDDs). Here we review how alterations in the function of histone modifiers, chromatin remodelers, and methyl-DNA binding proteins contribute to neurodevelopmental defects and altered brain plasticity. We also discuss how progress in human genetics has led to the generation of mouse models that unveil the molecular etiology of ID, and outline the direction in which this field is moving to identify therapeutic strategies for IDDs. Importantly, because the chromatin regulators linked to IDDs often target common downstream genes and cellular processes, the impact of research in individual syndromes goes well beyond each syndrome and can also contribute to the understanding and therapy of other IDDs. Furthermore, the investigation of these disorders helps us to understand the role of chromatin regulators in brain development, plasticity, and gene expression, thereby answering fundamental questions in neurobiology.
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