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Nicolle R, Boutaud L, Loeuillet L, Talhi N, Grotto S, Bourgon N, Feresin A, Coussement A, Barrois M, Beaujard MP, Rambaud T, Razavi F, Attié-Bitach T. Expanding the phenotypic spectrum of LIG4 pathogenic variations: neuro-histopathological description of 4 fetuses with stenosis of the aqueduct. Eur J Hum Genet 2024; 32:545-549. [PMID: 38351293 PMCID: PMC11061308 DOI: 10.1038/s41431-024-01558-2] [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: 09/03/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 05/02/2024] Open
Abstract
Severe ventriculomegaly is a rare congenital brain defect, usually detected in utero, of poor neurodevelopmental prognosis. This ventricular enlargement can be the consequence of different mechanisms: either by a disruption of the cerebrospinal fluid circulation or abnormalities of its production/absorption. The aqueduct stenosis is one of the most frequent causes of obstructive ventriculomegaly, however, fewer than 10 genes have been linked to this condition and molecular bases remain often unknown. We report here 4 fetuses from 2 unrelated families presenting with ventriculomegaly at prenatal ultra-sonography as well as an aqueduct stenosis and skeletal abnormalities as revealed by fetal autopsy. Genome sequencing identified biallelic pathogenic variations in LIG4, a DNA-repair gene responsible for the LIG4 syndrome which associates a wide range of clinical manifestations including developmental delay, microcephaly, short stature, radiation hypersensitivity and immunodeficiency. Thus, not only this report expands the phenotype spectrum of LIG4-related disorders, adding ventriculomegaly due to aqueduct stenosis, but we also provide the first neuropathological description of fetuses carrying LIG4 pathogenic biallelic variations.
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Affiliation(s)
- Romain Nicolle
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
| | - Lucile Boutaud
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Genetics and development of the cerebral cortex, F-75015, Paris, France
| | - Laurence Loeuillet
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
| | - Naima Talhi
- Centre Hospitalier Intercommunal de Créteil, Service d'anatomie pathologique, Université Paris-Est Créteil, 94000, Créteil, France
| | - Sarah Grotto
- AP-HP, Hôpital Trousseau, UF de génétique clinique, Centre de Référence anomalies du développement et syndromes malformatifs, Paris, France
| | - Nicolas Bourgon
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Genetics and development of the cerebral cortex, F-75015, Paris, France
- AP-HP, Hôpital Necker-Enfants Malades, Department of Obstetrics and Fetal Medicine, Paris, France
| | - Agnese Feresin
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
- University of Trieste, Department of medicine, Surgery and Health Sciences, Trieste, Italy
| | - Aurélie Coussement
- AP-HP, Hôpital Cochin, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies de Système et d'Organes, Paris, France
| | - Mathilde Barrois
- AP-HP, Hôpital Cochin, Service de Maternité Port-Royal, Paris, France
| | - Marie-Paule Beaujard
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
| | - Thomas Rambaud
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr), Paris, France
| | - Férechté Razavi
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Genetics and development of the cerebral cortex, F-75015, Paris, France
| | - Tania Attié-Bitach
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France.
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Genetics and development of the cerebral cortex, F-75015, Paris, France.
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr), Paris, France.
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Gemmell P, Sackton TB, Edwards SV, Liu JS. A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution. PLoS Comput Biol 2024; 20:e1011995. [PMID: 38656999 PMCID: PMC11078400 DOI: 10.1371/journal.pcbi.1011995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/08/2024] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
Genomes contain conserved non-coding sequences that perform important biological functions, such as gene regulation. We present a phylogenetic method, PhyloAcc-C, that associates nucleotide substitution rates with changes in a continuous trait of interest. The method takes as input a multiple sequence alignment of conserved elements, continuous trait data observed in extant species, and a background phylogeny and substitution process. Gibbs sampling is used to assign rate categories (background, conserved, accelerated) to lineages and explore whether the assigned rate categories are associated with increases or decreases in the rate of trait evolution. We test our method using simulations and then illustrate its application using mammalian body size and lifespan data previously analyzed with respect to protein coding genes. Like other studies, we find processes such as tumor suppression, telomere maintenance, and p53 regulation to be related to changes in longevity and body size. In addition, we also find that skeletal genes, and developmental processes, such as sprouting angiogenesis, are relevant.
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Affiliation(s)
- Patrick Gemmell
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Timothy B. Sackton
- FAS Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jun S. Liu
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
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3
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Pearce B, Jacobs C, Benjeddou M. Genetic preservation of SLC22A3 in the Admixed and Xhosa populations living in the Western Cape. Mol Biol Rep 2023; 50:10199-10206. [PMID: 37924453 PMCID: PMC10676312 DOI: 10.1007/s11033-023-08884-6] [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: 09/01/2023] [Accepted: 10/03/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Amphiphilic solute facilitator organic cation transporters mediate the movement of various endogenous and exogenous organic cations, including crucial drugs like metformin, oxaliplatin, and lamivudine. These transporters are now seen as a potential explanation for inter-individual differences in drug effectiveness, contributing to 15-30% of such variability due to genetic factors.The aim of this study was to determine the baseline minor allele frequency distribution of 18 known coding SNPs in the SLC22A3 gene of 278 Cape Admixed (130) and Xhosa (148) individuals residing in Cape Town, South Africa. METHODS A convenience sampling method was used for sample collection. DNA extraction and subsequent amplification of target sites was carried out according to standard established methodologies. All genotyping was performed using the SNaPshot™ mini-seuqencing platform. RESULTS This study found no genetic polymorphisms in the coding region of the SLC22A3 gene of both the Xhosa and Cape Admixed individuals investigated. CONCLUSION This study has shown that SLC22A3 coding SNPs observed in other populations are absent in the sample of both Cape Admixed and Xhosa individuals studied. The lack of protein sequence variation was consistent with other studies and may reflect the significant physiological role of human organic cation transporter 3 in maintaining cellular and organismal homeostasis.
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Affiliation(s)
- Brendon Pearce
- Genetics Department, Faculty of Agriscience, Stellenbosch University, Van Der Bijl Street, Stellenbosch, 7600, South Africa.
| | - Clifford Jacobs
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa
| | - Mongi Benjeddou
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa
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4
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Nix JL, Schettini GP, Speckhart SL, Ealy AD, Biase FH. Ablation of OCT4 function in cattle embryos by double electroporation of CRISPR-Cas for DNA and RNA targeting (CRISPR-DART). PNAS NEXUS 2023; 2:pgad343. [PMID: 37954164 PMCID: PMC10637268 DOI: 10.1093/pnasnexus/pgad343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
CRISPR-Cas ribonucleoproteins (RNPs) are important tools for gene editing in preimplantation embryos. However, the inefficient production of biallelic deletions in cattle zygotes has hindered mechanistic studies of gene function. In addition, the presence of maternal RNAs that support embryo development until embryonic genome activation may cause confounding phenotypes. Here, we aimed to improve the efficiency of biallelic deletions and deplete specific maternal RNAs in cattle zygotes using CRISPR-Cas editing technology. Two electroporation sessions with Cas9D10A RNPs targeting exon 1 and the promoter of OCT4 produced biallelic deletions in 91% of the embryos tested. In most cases, the deletions were longer than 1,000 nucleotides long. Electroporation of Cas13a RNPs prevents the production of the corresponding proteins. We electroporated Cas9D10A RNPs targeting exon 1, including the promoter region, of OCT4 in two sessions with inclusion of Cas13a RNPs targeting OCT4 mRNAs in the second session to ablate OCT4 function in cattle embryos. A lack of OCT4 resulted in embryos arresting development prior to blastocyst formation at a greater proportion (13%) than controls (31.6%, P < 0.001). The few embryos that developed past the morula stage did not form a normal inner cell mass. Transcriptome analysis of single blastocysts, confirmed to lack exon 1 and promoter region of OCT4, revealed a significant (False Discovery Rate, FDR < 0.1) reduction in transcript abundance of many genes functionally connected to stemness, including markers of pluripotency (CADHD1, DPPA4, GNL3, RRM2). The results confirm that OCT4 is a key regulator of genes that modulate pluripotency and is required to form a functional blastocyst in cattle.
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Affiliation(s)
- Jada L Nix
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 W Campus dr, Blacksburg, VA 24061, USA
| | - Gustavo P Schettini
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 W Campus dr, Blacksburg, VA 24061, USA
| | - Savannah L Speckhart
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 W Campus dr, Blacksburg, VA 24061, USA
| | - Alan D Ealy
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 W Campus dr, Blacksburg, VA 24061, USA
| | - Fernando H Biase
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 W Campus dr, Blacksburg, VA 24061, USA
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Liu X, Matsunami M, Horikoshi M, Ito S, Ishikawa Y, Suzuki K, Momozawa Y, Niida S, Kimura R, Ozaki K, Maeda S, Imamura M, Terao C. Natural Selection Signatures in the Hondo and Ryukyu Japanese Subpopulations. Mol Biol Evol 2023; 40:msad231. [PMID: 37903429 PMCID: PMC10615566 DOI: 10.1093/molbev/msad231] [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: 03/27/2023] [Revised: 09/20/2023] [Accepted: 10/06/2023] [Indexed: 11/01/2023] Open
Abstract
Natural selection signatures across Japanese subpopulations are under-explored. Here we conducted genome-wide selection scans with 622,926 single nucleotide polymorphisms for 20,366 Japanese individuals, who were recruited from the main-islands of Japanese Archipelago (Hondo) and the Ryukyu Archipelago (Ryukyu), representing two major Japanese subpopulations. The integrated haplotype score (iHS) analysis identified several signals in one or both subpopulations. We found a novel candidate locus at IKZF2, especially in Ryukyu. Significant signals were observed in the major histocompatibility complex region in both subpopulations. The lead variants differed and demonstrated substantial allele frequency differences between Hondo and Ryukyu. The lead variant in Hondo tags HLA-A*33:03-C*14:03-B*44:03-DRB1*13:02-DQB1*06:04-DPB1*04:01, a haplotype specific to Japanese and Korean. While in Ryukyu, the lead variant tags DRB1*15:01-DQB1*06:02, which had been recognized as a genetic risk factor for narcolepsy. In contrast, it is reported to confer protective effects against type 1 diabetes and human T lymphotropic virus type 1-associated myelopathy/tropical spastic paraparesis. The FastSMC analysis identified 8 loci potentially affected by selection within the past 20-150 generations, including 2 novel candidate loci. The analysis also showed differences in selection patterns of ALDH2 between Hondo and Ryukyu, a gene recognized to be specifically targeted by selection in East Asian. In summary, our study provided insights into the selection signatures within the Japanese and nominated potential sources of selection pressure.
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Affiliation(s)
- Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
| | - Masatoshi Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shuji Ito
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuki Ishikawa
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kunihiko Suzuki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shumpei Niida
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Shiro Maeda
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Minako Imamura
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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6
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Stenberg K, Novotny GW, Lutz TA, Mandrup-Poulsen T, Bjørnvad CR. Obesity-induced changes in gene expression in feline adipose and skeletal muscle tissue. J Anim Physiol Anim Nutr (Berl) 2023; 107:1262-1278. [PMID: 36591865 DOI: 10.1111/jpn.13802] [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: 03/21/2022] [Revised: 11/14/2022] [Accepted: 12/05/2022] [Indexed: 01/03/2023]
Abstract
Indoor-confined cats are prone to developing obesity due to a sedentary life and an energy intake exceeding energy requirements. As in humans, feline obesity decreases insulin sensitivity and increases the risk of developing feline diabetes mellitus, but the pathophysiological mechanisms are currently poorly understood. Human obesity-related metabolic alterations seem to relate to changes in the expression of genes involved in glucose metabolism, insulin action and inflammation. The objective of the current study was to investigate changes in the expression of genes relating to obesity, glucose metabolism and inflammation in cats with non-experimentally induced obesity. Biopsies from the sartorius muscle and subcutaneous adipose tissue were obtained from 73 healthy, neutered, indoor-confined domestic shorthaired cats ranging from lean to obese. Quantification of obesity-related gene expression levels relative to glyceraldehyde-3-phosphate dehydrogenase was performed by quantitative real-time polymerase chain reaction. A negative association between obesity and adiponectin expression was observed in the adipose tissue (mean ± SD; normal weight, 27.30 × 10-3 ± 77.14 × 10-3 ; overweight, 2.89 × 10-3 ± 0.38 × 10-3 and obese, 2.93 × 10-3 ± 4.20 × 10-3 , p < 0.05). In muscle, the expression of peroxisome proliferative activated receptor-γ2 and plasminogen activator inhibitor-1 was increased in the obese compared to the normal-weight cats, and resistin was increased in the normal-weight compared to the overweight cats. There were no detectable obesity-related changes in the messenger RNA levels of inflammatory cytokines. In conclusion, a possible obesity-related low-grade inflammation caused by increased expression of key proinflammatory regulators was not observed. This could imply that the development of feline obesity and ensuing insulin resistance may not be based on tissue-derived inflammation, but caused by several determining factors, many of which still need further investigation.
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Affiliation(s)
- Kathrine Stenberg
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Guy W Novotny
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Departments of Hematology/Pathology, Herlev Hospital, Herlev, Denmark
| | - Thomas A Lutz
- Institute of Veterinary Physiology, Vetsuisse-Faculty University of Zurich, Zurich, Switzerland
| | | | - Charlotte Reinhard Bjørnvad
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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Duan Y, Xiong J, Lai Z, Zhong Y, Tian C, Du Z, Luo Z, Yu J, Li W, Xu W, Wang Y, Ding T, Zhong X, Pan M, Qiu Y, Lan X, Chen T, Li P, Liu K, Gao M, Hu Y, Liu Z. Analysis of the genetic contribution to thoracic aortic aneurysm or dissection in a prospective cohort of patients with familial and sporadic cases in East China. Orphanet J Rare Dis 2023; 18:251. [PMID: 37644562 PMCID: PMC10466872 DOI: 10.1186/s13023-023-02855-7] [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: 04/15/2022] [Accepted: 07/26/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Thoracic aortic aneurysm or dissections (TAADs) represent a group of life-threatening diseases. Genetic aetiology can affect the age of onset, clinical phenotype, and timing of intervention. We conducted a prospective trial to determine the prevalence of pathogenic variants in TAAD patients and to elucidate the traits related to harbouring the pathogenic variants. One hundred and one unrelated TAAD patients underwent genetic sequencing and analysis for 23 TAAD-associated genes using a targeted PCR and next-generation sequencing-based panel. RESULTS A total of 47 variants were identified in 52 TAAD patients (51.5%), including 5 pathogenic, 1 likely pathogenic and 41 variants of uncertain significance. The pathogenic or likely pathogenic (P/LP) variants in 4 disease-causing genes were carried by 1 patient with familial and 5 patients with sporadic TAAD (5.9%). In addition to harbouring one variant causing familial TAAD, the FBN1 gene harboured half of the P/LP variants causing sporadic TAAD. Individuals with an age of onset less than 50 years or normotension had a significantly increased genetic risk. CONCLUSIONS TAAD patients with a younger age at diagnosis or normotension were more likely to carry a P/LP variant; thus, routine genetic testing will be beneficial to a better prognosis through genetically personalized care prior to acute rupture or dissection.
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Affiliation(s)
- Yanyu Duan
- Engineering Research Center of Intelligent Acoustic Signals of Jiangxi Province, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Cardiovascular Rare Disease Diagnosis and Treatment Technology Innovation Center, Gannan Medical University, Ganzhou, China
| | - Jianxian Xiong
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Zhenghong Lai
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yiming Zhong
- Engineering Research Center of Intelligent Acoustic Signals of Jiangxi Province, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Cardiovascular Rare Disease Diagnosis and Treatment Technology Innovation Center, Gannan Medical University, Ganzhou, China
| | - Chengnan Tian
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Zhiming Du
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Zhifang Luo
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Junjian Yu
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Wentong Li
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Weichang Xu
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yabing Wang
- Engineering Research Center of Intelligent Acoustic Signals of Jiangxi Province, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China
| | - Ting Ding
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xuehong Zhong
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Mengmeng Pan
- Engineering Research Center of Intelligent Acoustic Signals of Jiangxi Province, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China
| | - Yu Qiu
- Engineering Research Center of Intelligent Acoustic Signals of Jiangxi Province, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Cardiovascular Rare Disease Diagnosis and Treatment Technology Innovation Center, Gannan Medical University, Ganzhou, China
| | - Xuemei Lan
- Engineering Research Center of Intelligent Acoustic Signals of Jiangxi Province, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Cardiovascular Rare Disease Diagnosis and Treatment Technology Innovation Center, Gannan Medical University, Ganzhou, China
| | - Taihua Chen
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Peijun Li
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Kang Liu
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Meng Gao
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yanqiu Hu
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Ziyou Liu
- Engineering Research Center of Intelligent Acoustic Signals of Jiangxi Province, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China.
- Heart Medical Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.
- Ganzhou Cardiovascular Rare Disease Diagnosis and Treatment Technology Innovation Center, Gannan Medical University, Ganzhou, China.
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8
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Amiri Ghanatsaman Z, Ayatolahi Mehrgardi A, Asadollahpour Nanaei H, Esmailizadeh A. Comparative genomic analysis uncovers candidate genes related with milk production and adaptive traits in goat breeds. Sci Rep 2023; 13:8722. [PMID: 37253766 DOI: 10.1038/s41598-023-35973-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/26/2023] [Indexed: 06/01/2023] Open
Abstract
During the process of animal domestication, both natural and artificial selection cause variation in allele frequencies among populations. Identifying genomic areas of selection in domestic animals may aid in the detection of genomic areas linked to ecological and economic traits. We studied genomic variation in 140 worldwide goat individuals, including 75 Asian, 30 African and 35 European goats. We further carried out comparative population genomics to detect genomic regions under selection for adaptability to harsh conditions in local Asian ecotypes and also milk production traits in European commercial breeds. In addition, we estimated the genetic distances among 140 goat individuals. The results showed that among all studied goat groups, local breeds from West and South Asia emerged as an independent group. Our search for selection signatures in local goats from West and South Asia revealed candidate genes related to adaptation to hot climate (HSPB6, HSF4, VPS13A and NBEA genes) and immune response (IL7, IL5, IL23A and LRFN5) traits. Furthermore, selection signatures in European commercial goats involved several milk production related genes, such as VPS13C, NCAM2, TMPRSS15, CSN3 and ABCG2. The identified candidate genes could be the fundamental genetic resource for enhancement of goat production and environmental-adaptive traits, and as such they should be used in goat breeding programs to select more efficient breeds.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Ahmad Ayatolahi Mehrgardi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran.
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, PB, Iran.
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9
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Nix JL, Schettini GP, Biase FH. Sexing of cattle embryos using RNA-sequencing data or polymerase chain reaction based on a complete sequence of cattle chromosome Y. Front Genet 2023; 14:1038291. [PMID: 37077537 PMCID: PMC10106624 DOI: 10.3389/fgene.2023.1038291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
When necessary, RNA-sequencing data or polymerase chain reaction (PCR) assays can be used to determine the presence of the chromosome Y (ChrY) in samples. This information allows for biological variation due to sexual dimorphism to be studied. A prime example is when researchers conduct RNA-sequencing of single embryos, or conceptuses, prior to the development of gonads. A recent publication of a complete sequence of the ChrY has removed limitations for the development of these procedures in cattle, otherwise imposed by the absence of a ChrY in the reference genome. Using the sequence of the cattle ChrY and transcriptome data, we conducted a systematic search for genes in the ChrY that are exclusively expressed in male tissues. The genes ENSBIXG00000029763, ENSBIXG00000029774, ENSBIXG00000029788, and ENSBIXG00000029892 were consistently expressed across male tissues and lowly expressed or absent in female samples. We observed that the cumulative values of counts per million were 2688-fold greater in males than the equivalent values in female samples. Thus, we deemed these genes suitable for the sexing of samples using RNA-sequencing data. We successfully used this set of genes to infer the sex of 22 cattle blastocysts (8 females and 14 males). Additionally, the completed sequence of the cattle ChrY has segments in the male-specific region that are not repeated. We designed a pair of oligonucleotides that targets one of these non-repeated regions in the male-specific sequence of the ChrY. Using this pair of oligonucleotides, in a multiplexed PCR assay with oligonucleotides that anneal to an autosome chromosome, we accurately identified the sex of cattle blastocysts. We developed efficient procedures for the sexing of samples in cattle using either transcriptome data or their DNA. The procedures using RNA-sequencing will greatly benefit researchers who work with samples limited in cell numbers which are only sufficient to produce transcriptome data. The oligonucleotides used for the accurate sexing of samples using PCR are transferable to other cattle tissue samples.
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10
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Ma C, Li C, Ma H, Yu D, Zhang Y, Zhang D, Su T, Wu J, Wang X, Zhang L, Chen CL, Zhang YE. Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum. Genome Biol 2022; 23:251. [PMID: 36474250 PMCID: PMC9724437 DOI: 10.1186/s13059-022-02821-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite having been extensively studied, it remains largely unclear why humans bear a particularly high risk of cancer. The antagonistic pleiotropy hypothesis predicts that primate-specific genes (PSGs) tend to promote tumorigenesis, while the molecular atavism hypothesis predicts that PSGs involved in tumors may represent recently derived duplicates of unicellular genes. However, these predictions have not been tested. RESULTS By taking advantage of pan-cancer genomic data, we find the upregulation of PSGs across 13 cancer types, which is facilitated by copy-number gain and promoter hypomethylation. Meta-analyses indicate that upregulated PSGs (uPSGs) tend to promote tumorigenesis and to play cell cycle-related roles. The cell cycle-related uPSGs predominantly represent derived duplicates of unicellular genes. We prioritize 15 uPSGs and perform an in-depth analysis of one unicellular gene-derived duplicate involved in the cell cycle, DDX11. Genome-wide screening data and knockdown experiments demonstrate that DDX11 is broadly essential across cancer cell lines. Importantly, non-neutral amino acid substitution patterns and increased expression indicate that DDX11 has been under positive selection. Finally, we find that cell cycle-related uPSGs are also preferentially upregulated in the highly proliferative embryonic cerebrum. CONCLUSIONS Consistent with the predictions of the atavism and antagonistic pleiotropy hypotheses, primate-specific genes, especially those PSGs derived from cell cycle-related genes that emerged in unicellular ancestors, contribute to the early proliferation of the human cerebrum at the cost of hitchhiking by similarly highly proliferative cancer cells.
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Affiliation(s)
- Chenyu Ma
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chunyan Li
- grid.64939.310000 0000 9999 1211School of Engineering Medicine, Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), and Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191 China
| | - Huijing Ma
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Daqi Yu
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yufei Zhang
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.41156.370000 0001 2314 964XSchool of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Dan Zhang
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tianhan Su
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jianmin Wu
- grid.412474.00000 0001 0027 0586Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing, 100142 China
| | - Xiaoyue Wang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Li Zhang
- grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, 102206 China
| | - Chun-Long Chen
- grid.462584.90000 0004 0367 1475Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France
| | - Yong E. Zhang
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, 102206 China ,grid.9227.e0000000119573309CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
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11
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Panahi-Moghadam S, Hassani S, Farivar S, Vakhshiteh F. Emerging Role of Enhancer RNAs as Potential Diagnostic and Prognostic Biomarkers in Cancer. Noncoding RNA 2022; 8:ncrna8050066. [PMID: 36287118 PMCID: PMC9607539 DOI: 10.3390/ncrna8050066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Enhancers are distal cis-acting elements that are commonly recognized to regulate gene expression via cooperation with promoters. Along with regulating gene expression, enhancers can be transcribed and generate a class of non-coding RNAs called enhancer RNAs (eRNAs). The current discovery of abundant tissue-specific transcription of enhancers in various diseases such as cancers raises questions about the potential role of eRNAs in disease diagnosis and therapy. This review aimed to demonstrate the current understanding of eRNAs in cancer research with a focus on the potential roles of eRNAs as prognostic and diagnostic biomarkers in cancers.
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Affiliation(s)
- Somayeh Panahi-Moghadam
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Shokoufeh Hassani
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences (TUMS), Tehran 1417614411, Iran
| | - Shirin Farivar
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Faezeh Vakhshiteh
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran 1449614535, Iran
- Correspondence:
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12
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Appetite regulating genes in zebrafish gut; a gene expression study. PLoS One 2022; 17:e0255201. [PMID: 35853004 PMCID: PMC9295983 DOI: 10.1371/journal.pone.0255201] [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: 07/09/2021] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
The underlying molecular pathophysiology of feeding disorders, particularly in peripheral organs, is still largely unknown. A range of molecular factors encoded by appetite-regulating genes are already described to control feeding behaviour in the brain. However, the important role of the gastrointestinal tract in the regulation of appetite and feeding in connection to the brain has gained more attention in the recent years. An example of such inter-organ connection can be the signals mediated by leptin, a key regulator of body weight, food intake and metabolism, with conserved anorexigenic effects in vertebrates. Leptin signals functions through its receptor (lepr) in multiple organs, including the brain and the gastrointestinal tract. So far, the regulatory connections between leptin signal and other appetite-regulating genes remain unclear, particularly in the gastrointestinal system. In this study, we used a zebrafish mutant with impaired function of leptin receptor to explore gut expression patterns of appetite-regulating genes, under different feeding conditions (normal feeding, 7-day fasting, 2 and 6-hours refeeding). We provide evidence that most appetite-regulating genes are expressed in the zebrafish gut. On one hand, we did not observed significant differences in the expression of orexigenic genes (except for hcrt) after changes in the feeding condition. On the other hand, we found 8 anorexigenic genes in wild-types (cart2, cart3, dbi, oxt, nmu, nucb2a, pacap and pomc), as well as 4 genes in lepr mutants (cart3, kiss1, kiss1r and nucb2a), to be differentially expressed in the zebrafish gut after changes in feeding conditions. Most of these genes also showed significant differences in their expression between wild-type and lepr mutant. Finally, we observed that impaired leptin signalling influences potential regulatory connections between anorexigenic genes in zebrafish gut. Altogether, these transcriptional changes propose a potential role of leptin signal in the regulation of feeding through changes in expression of certain anorexigenic genes in the gastrointestinal tract of zebrafish.
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13
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Thioredoxin Domain Containing 5 Suppression Elicits Serum Amyloid A-Containing High-Density Lipoproteins. Biomedicines 2022; 10:biomedicines10030709. [PMID: 35327511 PMCID: PMC8945230 DOI: 10.3390/biomedicines10030709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022] Open
Abstract
Thioredoxin domain containing 5 (TXNDC5) is a protein disulfide isomerase involved in several diseases related to oxidative stress, energy metabolism and cellular inflammation. In a previous manuscript, a negative association between fatty liver development and hepatic Txndc5 expression was observed. To study the role of TXNDC5 in the liver, we generated Txndc5-deficient mice. The absence of the protein caused an increased metabolic need to gain weight along with a bigger and fatter liver. RNAseq was performed to elucidate the putative mechanisms, showing a substantial liver overexpression of serum amyloid genes (Saa1, Saa2) with no changes in hepatic protein, but discrete plasma augmentation by the gene inactivation. Higher levels of malonyldialdehyde, apolipoprotein A1 and platelet activating factor-aryl esterase activity were also found in serum from Txndc5-deficient mice. However, no difference in the distribution of high-density lipoproteins (HDL)-mayor components and SAA was found between groups, and even the reactive oxygen species decreased in HDL coming from Txndc5-deficient mice. These results confirm the relation of this gene with hepatic steatosis and with a fasting metabolic derive remedying an acute phase response. Likewise, they pose a new role in modulating the nature of HDL particles, and SAA-containing HDL particles are not particularly oxidized.
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14
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Genome-Wide Investigation and Functional Verification of the ZIP Family Transporters in Wild Emmer Wheat. Int J Mol Sci 2022; 23:ijms23052866. [PMID: 35270007 PMCID: PMC8911026 DOI: 10.3390/ijms23052866] [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: 01/16/2022] [Revised: 02/18/2022] [Accepted: 02/19/2022] [Indexed: 12/02/2022] Open
Abstract
The zinc/iron-regulated transporter-like protein (ZIP) family has a crucial role in Zn homeostasis of plants. Although the ZIP genes have been systematically studied in many plant species, the significance of this family in wild emmer wheat (Triticum turgidum ssp. dicoccoides) is not yet well understood. In this study, a genome-wide investigation of ZIPs genes based on the wild emmer reference genome was conducted, and 33 TdZIP genes were identified. Protein structure analysis revealed that TdZIP proteins had 1 to 13 transmembrane (TM) domains and most of them were predicted to be located on the plasma membrane. These TdZIPs can be classified into three clades in a phylogenetic tree. They were annotated as being involved in inorganic ion transport and metabolism. Cis-acting analysis showed that several elements were involved in hormone, stresses, grain-filling, and plant development. Expression pattern analysis indicated that TdZIP genes were highly expressed in different tissues. TdZIP genes showed different expression patterns in response to Zn deficiency and that 11 genes were significantly induced in either roots or both roots and shoots of Zn-deficient plants. Yeast complementation analysis showed that TdZIP1A-3, TdZIP6B-1, TdZIP6B-2, TdZIP7A-3, and TdZIP7B-2 have the capacity to transport Zn. Overexpression of TdZIP6B-1 in rice showed increased Zn concentration in roots compared with wild-type plants. The expression levels of TdZIP6B-1 in transgenic rice were upregulated in normal Zn concentration compared to that of no Zn. This work provides a comprehensive understanding of the ZIP gene family in wild emmer wheat and paves the way for future functional analysis and genetic improvement of Zn deficiency tolerance in wheat.
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15
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Ghosh B, Sarkar A, Mondal S, Bhattacharya N, Khatua S, Ghosh Z. piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species. RNA Biol 2021; 19:12-25. [PMID: 34965192 PMCID: PMC8786328 DOI: 10.1080/15476286.2021.2010960] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
PIWI interacting RNAs (piRNAs) have emerged as important gene regulators in recent times. Since the release of our first version of piRNAQuest in 2014, lots of novel piRNAs have been annotated in different species other than human, mouse and rat. Such new developments in piRNA research have led us to develop an updated database piRNAQuest V.2. It consists of 92,77,689 piRNA entries for 25 new species of different phylum along with human, mouse and rat. Besides providing primary piRNA features which include their genomic location, with further information on piRNAs overlapping with repeat elements, pseudogenes and syntenic regions, etc., the novel features of this version includes (i) density based cluster prediction, (ii) piRNA expression profile across various healthy and disease systems and (iii) piRNA target prediction. The concept of density-based piRNA cluster identification is robust as it does not consider parametric distribution in its model. The piRNA expression profile for 21 disease systems including cancer have been hosted in addition to 32 tissue specific piRNA expression profile for various species. Further, the piRNA target prediction section includes both predicted and curated piRNA targets within eight disease systems and developmental stages of mouse testis. Further, users can visualize the piRNA-target duplex structure and the ping-pong signature pattern for all the ping-pong piRNA partners in different species. Overall, piRNAQuest V.2 is an updated user-friendly database which will serve as a useful resource to survey, search and retrieve information on piRNAs for multiple species. This freely accessible database is available at http://dibresources.jcbose.ac.in/zhumur/pirnaquest2.
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Affiliation(s)
- Byapti Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Arijita Sarkar
- Division of Bioinformatics, Bose Institute, Kolkata, India.,Present Affiliation: Department of Orthopaedic Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sudip Mondal
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Namrata Bhattacharya
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Delhi, India
| | - Sunirmal Khatua
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
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16
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Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants. Am J Hum Genet 2021; 108:2301-2318. [PMID: 34762822 DOI: 10.1016/j.ajhg.2021.10.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying whether a given genetic mutation results in a gene product with increased (gain-of-function; GOF) or diminished (loss-of-function; LOF) activity is an important step toward understanding disease mechanisms because they may result in markedly different clinical phenotypes. Here, we generated an extensive database of documented germline GOF and LOF pathogenic variants by employing natural language processing (NLP) on the available abstracts in the Human Gene Mutation Database. We then investigated various gene- and protein-level features of GOF and LOF variants and applied machine learning and statistical analyses to identify discriminative features. We found that GOF variants were enriched in essential genes, for autosomal-dominant inheritance, and in protein binding and interaction domains, whereas LOF variants were enriched in singleton genes, for protein-truncating variants, and in protein core regions. We developed a user-friendly web-based interface that enables the extraction of selected subsets from the GOF/LOF database by a broad set of annotated features and downloading of up-to-date versions. These results improve our understanding of how variants affect gene/protein function and may ultimately guide future treatment options.
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17
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Gao T, Zheng Z, Pan Y, Zhu C, Wei F, Yuan J, Sun R, Fang S, Wang N, Zhou Y, Qian J. scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species. Nucleic Acids Res 2021; 50:D371-D379. [PMID: 34761274 PMCID: PMC8728125 DOI: 10.1093/nar/gkab1032] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/04/2021] [Accepted: 10/19/2021] [Indexed: 12/14/2022] Open
Abstract
Previous studies on enhancers and their target genes were largely based on bulk samples that represent ‘average’ regulatory activities from a large population of millions of cells, masking the heterogeneity and important effects from the sub-populations. In recent years, single-cell sequencing technology has enabled the profiling of open chromatin accessibility at the single-cell level (scATAC-seq), which can be used to annotate the enhancers and promoters in specific cell types. A comprehensive resource is highly desirable for exploring how the enhancers regulate the target genes at the single-cell level. Hence, we designed a single-cell database scEnhancer (http://enhanceratlas.net/scenhancer/), covering 14 527 776 enhancers and 63 658 600 enhancer-gene interactions from 1 196 906 single cells across 775 tissue/cell types in three species. An unsupervised learning method was employed to sort and combine tens or hundreds of single cells in each tissue/cell type to obtain the consensus enhancers. In addition, we utilized a cis-regulatory network algorithm to identify the enhancer-gene connections. Finally, we provided a user-friendly platform with seven useful modules to search, visualize, and browse the enhancers/genes. This database will facilitate the research community towards a functional analysis of enhancers at the single-cell level.
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Affiliation(s)
- Tianshun Gao
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.,Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Zilong Zheng
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Yihang Pan
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.,Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Chengming Zhu
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Fuxin Wei
- Department of Orthopaedics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Jinqiu Yuan
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.,Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Rui Sun
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.,Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Shuo Fang
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.,Department of Oncology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Nan Wang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Yang Zhou
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China
| | - Jiang Qian
- The Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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18
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Saverimuttu SCC, Kramarz B, Rodríguez-López M, Garmiri P, Attrill H, Thurlow KE, Makris M, de Miranda Pinheiro S, Orchard S, Lovering RC. Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases. Database (Oxford) 2021; 2021:baab067. [PMID: 34697638 PMCID: PMC8546235 DOI: 10.1093/database/baab067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/07/2021] [Accepted: 10/06/2021] [Indexed: 01/08/2023]
Abstract
The role of the blood-brain barrier (BBB) in Alzheimer's and other neurodegenerative diseases is still the subject of many studies. However, those studies using high-throughput methods have been compromised by the lack of Gene Ontology (GO) annotations describing the role of proteins in the normal function of the BBB. The GO Consortium provides a gold-standard bioinformatics resource used for analysis and interpretation of large biomedical data sets. However, the GO is also used by other research communities and, therefore, must meet a variety of demands on the breadth and depth of information that is provided. To meet the needs of the Alzheimer's research community we have focused on the GO annotation of the BBB, with over 100 transport or junctional proteins prioritized for annotation. This project has led to a substantial increase in the number of human proteins associated with BBB-relevant GO terms as well as more comprehensive annotation of these proteins in many other processes. Furthermore, data describing the microRNAs that regulate the expression of these priority proteins have also been curated. Thus, this project has increased both the breadth and depth of annotation for these prioritized BBB proteins. Database URLhttps://www.ebi.ac.uk/QuickGO/.
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Affiliation(s)
- Shirin C C Saverimuttu
- Functional Gene Annotation, Pre-clinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), Rayne Building, 5 University Street, London WC1E 6JF, UK
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1ST, UK
| | - Barbara Kramarz
- Functional Gene Annotation, Pre-clinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), Rayne Building, 5 University Street, London WC1E 6JF, UK
| | - Milagros Rodríguez-López
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1ST, UK
| | - Penelope Garmiri
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1ST, UK
| | - Helen Attrill
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Katherine E Thurlow
- Functional Gene Annotation, Pre-clinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), Rayne Building, 5 University Street, London WC1E 6JF, UK
| | - Marios Makris
- Functional Gene Annotation, Pre-clinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), Rayne Building, 5 University Street, London WC1E 6JF, UK
| | - Sandra de Miranda Pinheiro
- Functional Gene Annotation, Pre-clinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), Rayne Building, 5 University Street, London WC1E 6JF, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1ST, UK
| | - Ruth C Lovering
- Functional Gene Annotation, Pre-clinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), Rayne Building, 5 University Street, London WC1E 6JF, UK
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19
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Zhang Y, Zhang Y, Aman Y, Ng CT, Chau WH, Zhang Z, Yue M, Bohm C, Jia Y, Li S, Yuan Q, Griffin J, Chiu K, Wong DSM, Wang B, Jin D, Rogaeva E, Fraser PE, Fang EF, St George-Hyslop P, Song YQ. Amyloid-β toxicity modulates tau phosphorylation through the PAX6 signalling pathway. Brain 2021; 144:2759-2770. [PMID: 34428276 DOI: 10.1093/brain/awab134] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/08/2021] [Accepted: 03/14/2021] [Indexed: 11/13/2022] Open
Abstract
The molecular link between amyloid-β plaques and neurofibrillary tangles, the two pathological hallmarks of Alzheimer's disease, is still unclear. Increasing evidence suggests that amyloid-β peptide activates multiple regulators of cell cycle pathways, including transcription factors CDKs and E2F1, leading to hyperphosphorylation of tau protein. However, the exact pathways downstream of amyloid-β-induced cell cycle imbalance are unknown. Here, we show that PAX6, a transcription factor essential for eye and brain development which is quiescent in adults, is increased in the brains of patients with Alzheimer's disease and in APP transgenic mice, and plays a key role between amyloid-β and tau hyperphosphorylation. Downregulation of PAX6 protects against amyloid-β peptide-induced neuronal death, suggesting that PAX6 is a key executor of the amyloid-β toxicity pathway. Mechanistically, amyloid-β upregulates E2F1, followed by the induction of PAX6 and c-Myb, while Pax6 is a direct target for both E2F1 and its downstream target c-Myb. Furthermore, PAX6 directly regulates transcription of GSK-3β, a kinase involved in tau hyperphosphorylation and neurofibrillary tangles formation, and its phosphorylation of tau at Ser356, Ser396 and Ser404. In conclusion, we show that signalling pathways that include CDK/pRB/E2F1 modulate neuronal death signals by activating downstream transcription factors c-Myb and PAX6, leading to GSK-3β activation and tau pathology, providing novel potential targets for pharmaceutical intervention.
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Affiliation(s)
- Yalun Zhang
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China.,HKU-Shenzhen Institute of Research and Innovation, University of Hong Kong, Hong Kong, China.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, M5T 0S8, Canada.,Department of Medical Biophysics, and Medicine (Neurology), University of Toronto, Krembil Discovery Tower, Toronto, ON, M5T 2S8, Canada
| | - Yi Zhang
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Yahyah Aman
- Department of Clinical Molecular Biology, University of Oslo and the Akershus University Hospital, 1478 Lørenskog, Norway
| | - Cheung Toa Ng
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China.,HKU-Shenzhen Institute of Research and Innovation, University of Hong Kong, Hong Kong, China
| | - Wing-Hin Chau
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Zhigang Zhang
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Ming Yue
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Christopher Bohm
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, M5T 0S8, Canada.,Department of Medical Biophysics, and Medicine (Neurology), University of Toronto, Krembil Discovery Tower, Toronto, ON, M5T 2S8, Canada
| | - Yizhen Jia
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Siwen Li
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Qiuju Yuan
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jennifer Griffin
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, M5T 0S8, Canada.,Department of Medical Biophysics, and Medicine (Neurology), University of Toronto, Krembil Discovery Tower, Toronto, ON, M5T 2S8, Canada
| | - Kin Chiu
- Department of Ophthalmology, University of Hong Kong, Hong Kong, China
| | - Dana S M Wong
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Binbin Wang
- Department of Genetics, National Research Institute for Family Planning, Beijing, China
| | - Dongyan Jin
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, M5T 0S8, Canada.,Department of Medical Biophysics, and Medicine (Neurology), University of Toronto, Krembil Discovery Tower, Toronto, ON, M5T 2S8, Canada
| | - Paul E Fraser
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, M5T 0S8, Canada.,Department of Medical Biophysics, and Medicine (Neurology), University of Toronto, Krembil Discovery Tower, Toronto, ON, M5T 2S8, Canada
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and the Akershus University Hospital, 1478 Lørenskog, Norway
| | - Peter St George-Hyslop
- Department of Medical Biophysics, and Medicine (Neurology), University of Toronto, Krembil Discovery Tower, Toronto, ON, M5T 2S8, Canada.,Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0XY, UK
| | - You-Qiang Song
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China.,HKU-Shenzhen Institute of Research and Innovation, University of Hong Kong, Hong Kong, China.,The State Key Laboratory of Brain and Cognitive Sciences, University of Hong Kong, Hong Kong, China
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20
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Spitz MA, Lenaers G, Charif M, Wirth T, Chelly J, Abi-Warde MT, Meyer P, Leboucq N, Schaefer E, Anheim M, Roubertie A. Paroxysmal Dyskinesias Revealing 3-Hydroxy-Isobutyryl-CoA Hydrolase (HIBCH) Deficiency. Neuropediatrics 2021; 52:410-414. [PMID: 33506479 DOI: 10.1055/s-0040-1722678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Paroxysmal dyskinesias (PD) are rare movement disorders characterized by recurrent attacks of dystonia, chorea, athetosis, or their combination, with large phenotypic and genetic heterogeneity. 3-Hydroxy-isobutyryl-CoA hydrolase (HIBCH) deficiency is a neurodegenerative disease characterized in most patients by a continuous decline in psychomotor abilities or a secondary regression triggered by febrile infections and metabolic crises.We describe two PD patients from two pedigrees, both carrying a homozygous c.913A > G, p.Thr305Ala mutation in the HIBCH gene, associated with an unusual clinical presentation. The first patient presented in the second year of life with right paroxysmal hemidystonia lasting for 30 minutes, without any loss of consciousness and without any triggering factor. The second patient has presented since the age of 3 recurrent exercise-induced PD episodes which have been described as abnormal equinovarus, contractures of the lower limbs, lasting for 1 to 4 hours, associated with choreic movements of the hands. Their neurological examination and metabolic screening were normal, while brain magnetic resonance imaging showed abnormal signal of the pallidi.We suggest that HIBCH deficiency, through the accumulation of metabolic intermediates of the valine catabolic pathway, leads to a secondary defect in respiratory chain activity and pyruvate dehydrogenase (PDH) activity and to a broad phenotypic spectrum ranging from Leigh syndrome to milder phenotypes. The two patients presented herein expand the spectrum of the disease to include unusual paroxysmal phenotypes and HIBCH deficiency should be considered in the diagnostic strategy of PD to enable adequate preventive treatment.
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Affiliation(s)
| | - Guy Lenaers
- Équipe Mitolab, Institut MITOVASC, INSERM U1083, CNRS 6015, Université d'Angers, Angers, France
| | - Majida Charif
- Équipe Mitolab, Institut MITOVASC, INSERM U1083, CNRS 6015, Université d'Angers, Angers, France
| | - Thomas Wirth
- Service de Neurologie, CHRU Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS/Unistra, INSERM U1258, Illkirch, France.,Unit of Functional Neurosurgery, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Jameleddine Chelly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS/Unistra, INSERM U1258, Illkirch, France
| | | | - Pierre Meyer
- Département de Neuropédiatrie, CHU Gui de Chauliac, Montpellier, France
| | - Nicolas Leboucq
- Service de Neuroradiologie, Hôpital Gui de Chauliac, CHRU Montpellier, Montpellier, France
| | - Elise Schaefer
- Service de Génétique Médicale, CHRU Strasbourg, Strasbourg, France
| | - Mathieu Anheim
- Service de Neurologie, CHRU Strasbourg, Strasbourg, France
| | - Agathe Roubertie
- Département de Neuropédiatrie, CHU Gui de Chauliac, Montpellier, France.,INSERM U 1051, Institut des Neurosciences de Montpellier, Montpellier, France
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21
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Ahi EP, Tsakoumis E, Brunel M, Schmitz M. Transcriptional study reveals a potential leptin-dependent gene regulatory network in zebrafish brain. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:1283-1298. [PMID: 34236575 PMCID: PMC8302498 DOI: 10.1007/s10695-021-00967-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/12/2021] [Indexed: 06/01/2023]
Abstract
The signal mediated by leptin hormone and its receptor is a major regulator of body weight, food intake and metabolism. In mammals and many teleost fish species, leptin has an anorexigenic role and inhibits food intake by influencing the appetite centres in the hypothalamus. However, the regulatory connections between leptin and downstream genes mediating its appetite-regulating effects are still not fully explored in teleost fish. In this study, we used a loss of function leptin receptor zebrafish mutant and real-time quantitative PCR to assess brain expression patterns of several previously identified anorexigenic genes downstream of leptin signal under different feeding conditions (normal feeding, 7-day fasting, 2 and 6-h refeeding). These downstream factors include members of cart genes, crhb and gnrh2, as well as selected genes co-expressed with them based on a zebrafish co-expression database. Here, we found a potential gene expression network (GRN) comprising the abovementioned genes by a stepwise approach of identifying co-expression modules and predicting their upstream regulators. Among the transcription factors (TFs) predicted as potential upstream regulators of this GRN, we found expression pattern of sp3a to be correlated with transcriptional changes of the downstream gene network. Interestingly, the expression and transcriptional activity of Sp3 orthologous gene in mammals have already been implicated to be under the influence of leptin signal. These findings suggest a potentially conserved regulatory connection between leptin and sp3a, which is predicted to act as a transcriptional driver of a downstream gene network in the zebrafish brain.
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Affiliation(s)
- Ehsan Pashay Ahi
- Department of Organismal Biology, Comparative Physiology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, SE-752 36 Uppsala, Sweden
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Emmanouil Tsakoumis
- Department of Organismal Biology, Comparative Physiology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, SE-752 36 Uppsala, Sweden
| | - Mathilde Brunel
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Allmas Allé 5, SE-750 07 Uppsala, Sweden
| | - Monika Schmitz
- Department of Organismal Biology, Comparative Physiology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, SE-752 36 Uppsala, Sweden
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22
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Claes KBM, Rosseel T, De Leeneer K. Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era. Methods Mol Biol 2021; 2324:363-381. [PMID: 34165726 DOI: 10.1007/978-1-0716-1503-4_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Presence of pseudogenes is a dreadful issue in next generation sequencing (NGS), because their contamination can interfere with the detection of variants in the genuine gene and generate false positive and false negative variants.In this chapter we focus on issues related to the application of NGS strategies for analysis of genes with pseudogenes in a clinical setting. The degree to which a pseudogene impacts the ability to accurately detect and map variants in its parent gene depends on the degree of similarity (homology) with the parent gene itself. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences. For target enrichment, we describe advantages and disadvantages of PCR- and capture-based strategies. For mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some examples of genes associated with Mendelian disorders, for which interesting NGS approaches are described to avoid interference with pseudogene sequences.
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Affiliation(s)
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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23
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Rare functional genetic variants in COL7A1, COL6A5, COL1A2 and COL5A2 frequently occur in Chiari Malformation Type 1. PLoS One 2021; 16:e0251289. [PMID: 33974636 PMCID: PMC8112708 DOI: 10.1371/journal.pone.0251289] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/24/2021] [Indexed: 11/19/2022] Open
Abstract
Chiari Malformation Type 1 (CM-1) is characterized by herniation of the cerebellar tonsils below the foramen magnum and the presence of headaches and other neurologic symptoms. Cranial bone constriction is suspected to be the most common biologic mechanism leading to CM-1. However, other mechanisms may also contribute, particularly in the presence of connective tissue disorders (CTDs), such as Ehlers Danlos Syndrome (EDS). Accumulating data suggest CM-1 with connective tissue disorders (CTD+) may have a different patho-mechanism and different genetic risk factors than CM-1 without CTDs (CTD-). To identify CM-1 genetic risk variants, we performed whole exome sequencing on a single large, multiplex family from Spain and targeted sequencing on a cohort of 186 unrelated adult, Caucasian females with CM-1. Targeted sequencing captured the coding regions of 21 CM-1 and EDS candidate genes, including two genes identified in the Spanish family. Using gene burden analysis, we compared the frequency of rare, functional variants detected in CM-1 cases versus publically available ethnically-matched controls from gnomAD. A secondary analysis compared the presence of rare variants in these genes between CTD+ and CTD- CM-1 cases. In the Spanish family, rare variants co-segregated with CM-1 in COL6A5, ADGRB3 and DST. A variant in COL7A1 was present in affected and unaffected family members. In the targeted sequencing analysis, rare variants in six genes (COL7A1, COL5A2, COL6A5, COL1A2, VEGFB, FLT1) were significantly more frequent in CM-1 cases compared to public controls. In total, 47% of CM-1 cases presented with rare variants in at least one of the four significant collagen genes and 10% of cases harbored variants in multiple significant collagen genes. Moreover, 26% of CM-1 cases presented with rare variants in the COL6A5 gene. We also identified two genes (COL7A1, COL3A1) for which the burden of rare variants differed significantly between CTD+ and CTD- CM-1 cases. A higher percentage of CTD+ patients had variants in COL7A1 compared to CTD+ patients, while CTD+ patients had fewer rare variants in COL3A1 than did CTD- patients. In summary, rare variants in several collagen genes are particularly frequent in CM-1 cases and those in COL6A5 co-segregated with CM-1 in a Spanish multiplex family. COL6A5 has been previously associated with musculoskeletal phenotypes, but this is the first association with CM-1. Our findings underscore the contribution of rare genetic variants in collagen genes to CM-1, and suggest that CM-1 in the presence and absence of CTD symptoms is driven by different genes.
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24
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Li P, Su T, Zhao X, Wang W, Zhang D, Yu Y, Bayer PE, Edwards D, Yu S, Zhang F. Assembly of the non-heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:966-976. [PMID: 33283404 PMCID: PMC8131043 DOI: 10.1111/pbi.13522] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/11/2020] [Accepted: 12/01/2020] [Indexed: 05/10/2023]
Abstract
Brassica rapa displays a wide range of morphological diversity which is exploited for a variety of food crops. Here we present a high-quality genome assembly for pak choi (Brassica rapa L. subsp. chinensis), an important non-heading leafy vegetable, and comparison with the genomes of heading type Chinese cabbage and the oilseed form, yellow sarson. Gene presence-absence variation (PAV) and genomic structural variations (SV) were identified, together with single nucleotide polymorphisms (SNPs). The structure and expression of genes for leaf morphology and flowering were compared between the three morphotypes revealing candidate genes for these traits in B. rapa. The pak choi genome assembly and its comparison with other B. rapa genome assemblies provides a valuable resource for the genetic improvement of this important vegetable crop and as a model to understand the diversity of morphological variation across Brassica species.
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Affiliation(s)
- Peirong Li
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
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25
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Nikolaou N, Hodson L, Tomlinson JW. The role of 5-reduction in physiology and metabolic disease: evidence from cellular, pre-clinical and human studies. J Steroid Biochem Mol Biol 2021; 207:105808. [PMID: 33418075 DOI: 10.1016/j.jsbmb.2021.105808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 01/01/2023]
Abstract
The 5-reductases (5α-reductase types 1, 2 and 3 [5αR1-3], 5β-reductase [5βR]) are steroid hormone metabolising enzymes that hold fundamental roles in human physiology and pathology. They possess broad substrate specificity converting many steroid hormones to their 5α- and 5β-reduced metabolites, as well as catalysing crucial steps in bile acid synthesis. 5αRs are fundamentally important in urogenital development by converting testosterone to the more potent androgen 5α-dihydrotestosterone (5αDHT); inactivating mutations in 5αR2 lead to disorders of sexual development. Due to the ability of the 5αRs to generate 5αDHT, they are an established drug target, and 5αR inhibitors are widely used for the treatment of androgen-dependent benign or malignant prostatic diseases. There is an emerging body of evidence to suggest that the 5-reductases can impact upon aspects of health and disease (other than urogenital development); alterations in their expression and activity have been associated with metabolic disease, polycystic ovarian syndrome, inflammation and bone metabolism. This review will outline the evidence base for the extra-urogenital role of 5-reductases from in vitro cell systems, pre-clinical models and human studies, and highlight the potential adverse effects of 5αR inhibition in human health and disease.
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Affiliation(s)
- Nikolaos Nikolaou
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK
| | - Leanne Hodson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK
| | - Jeremy W Tomlinson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK.
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26
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Ma Y, Liu S, Gao J, Chen C, Zhang X, Yuan H, Chen Z, Yin X, Sun C, Mao Y, Zhou F, Shao Y, Liu Q, Xu J, Cheng L, Yu D, Li P, Yi P, He J, Geng G, Guo Q, Si Y, Zhao H, Li H, Banes GL, Liu H, Nakamura Y, Kurita R, Huang Y, Wang X, Wang F, Fang G, Engel JD, Shi L, Zhang YE, Yu J. Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia. Dev Cell 2021; 56:478-493.e11. [PMID: 33476555 DOI: 10.1016/j.devcel.2020.12.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/16/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023]
Abstract
The human genome harbors 14,000 duplicated or retroposed pseudogenes. Given their functionality as regulatory RNAs and low conservation, we hypothesized that pseudogenes could shape human-specific phenotypes. To test this, we performed co-expression analyses and found that pseudogene exhibited tissue-specific expression, especially in the bone marrow. By incorporating genetic data, we identified a bone-marrow-specific duplicated pseudogene, HBBP1 (η-globin), which has been implicated in β-thalassemia. Extensive functional assays demonstrated that HBBP1 is essential for erythropoiesis by binding the RNA-binding protein (RBP), HNRNPA1, to upregulate TAL1, a key regulator of erythropoiesis. The HBBP1/TAL1 interaction contributes to a milder symptom in β-thalassemia patients. Comparative studies further indicated that the HBBP1/TAL1 interaction is human-specific. Genome-wide analyses showed that duplicated pseudogenes are often bound by RBPs and less commonly bound by microRNAs compared with retropseudogenes. Taken together, we not only demonstrate that pseudogenes can drive human evolution but also provide insights on their functional landscapes.
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Affiliation(s)
- Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China.
| | - Siqi Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Chunyan Chen
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Zhang
- Laboratory of Molecular Cardiology & Medical Molecular Imaging, First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Hao Yuan
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongyang Chen
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Xiaolin Yin
- 923rd Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army, Guangxi 530021, China
| | - Chenguang Sun
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yanan Mao
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanqi Zhou
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yi Shao
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Liu
- Shantou University Medical College, Shantou 515041, China
| | - Jiayue Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Li Cheng
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China
| | - Daqi Yu
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pingping Li
- 923rd Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army, Guangxi 530021, China
| | - Ping Yi
- Department of Obstetrics and Gynecology, the Third Affiliated Hospital of Chongqing Medical University (General Hospital), Chongqing 401120, China
| | - Jiahuan He
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Guangfeng Geng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Qing Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yanmin Si
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Hualu Zhao
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Haipeng Li
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Graham L Banes
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China; Wisconsin National Primate Research Center, University of Wisconsin Madison, 1220 Capitol Court, Madison, WI 53715, USA
| | - He Liu
- Beijing Key Laboratory of Captive Wildlife Technology, Beijing Zoo, Beijing 100044, China
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo 105-8521, Japan
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China
| | - Xiaoshuang Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Fang Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Gang Fang
- NYU Shanghai, 1555 Century Avenue, Shanghai 20012, China; Department of Biology, 1009 Silver Center, New York University, New York, NY 10003, USA; School of Computer Science and Software Engineering, East China Normal University, Shanghai 200062, China
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Chinese Institute for Brain Research, Beijing 102206, China.
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China; State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
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Das T, Deb A, Parida S, Mondal S, Khatua S, Ghosh Z. LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients. RNA Biol 2020; 18:1136-1151. [PMID: 33112702 DOI: 10.1080/15476286.2020.1833529] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and C.elegans. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at http://dibresources.jcbose.ac.in/zhumur/lncrbase2/.
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Affiliation(s)
- Troyee Das
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Aritra Deb
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sibun Parida
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sudip Mondal
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Sunirmal Khatua
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
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Kalfakakou D, Konstantopoulou I, Yannoukakos D, Fostira F. Pitfalls in variant annotation for hereditary cancer diagnostics: The example of Illumina® VariantStudio®. Genomics 2020; 113:748-754. [PMID: 33053411 DOI: 10.1016/j.ygeno.2020.10.005] [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: 03/23/2020] [Revised: 08/04/2020] [Accepted: 10/08/2020] [Indexed: 11/27/2022]
Abstract
Next Generation Sequencing (NGS), and specifically targeted panel sequencing is the state-of-the-art in clinical genetic diagnosis of Mendelian diseases. However, the bioinformatics analysis and interpretation of the generated data can be challenging. A spotlight on the default transcript selection of a user-friendly, commercially available software that is widely used by genetics professionals, i.e. Illumina® VariantStudio®, is presented. For the sake of comparison, we employed Ensembl VEP, an open-source command-line tool, as it provides flexibility regarding transcript selection. The analysis of NGS data deriving from sequencing of 857 germline DNA samples of cancer patients indicated a concordance of 82.82% between the two software programs. Significantly, using the default transcript configuration of VariantStudio®, we failed to annotate correctly 11.45% of the identified loss-of-function variants. Our results underline the importance of cautious software and transcript selection and the need for reliable, white-box data analysis, along with bioinformatics expertise in clinical diagnostics.
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Affiliation(s)
- Despoina Kalfakakou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Greece
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Greece.
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Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples. Cancers (Basel) 2020; 12:cancers12102844. [PMID: 33019720 PMCID: PMC7650602 DOI: 10.3390/cancers12102844] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/20/2020] [Accepted: 09/23/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Alterations in long noncoding RNAs and their mutations have been increasingly recognized in tumorogenesis and cancer progression awakening especial interest as potential novel cancer biomarkers and therapeutic targets. The use of adjuvant chemotherapy in stage II colorectal cancer patients is challenging, and new biomarkers are required to identify patients with high probability of relapse. We focused on translational potential of non-coding RNAs in colorectal cancer. In this study, we aim to validate a new tool which couples target enrichment and RNAseq for transcriptomics studies of lncRNAs in formalin-fixed paraffin embedded (FFPE) tissue samples. Our results show that this new approach efficiently detects lncRNAs and differences in their expression between healthy and tumor FFPE tissues, as well as somatic mutations in expressed lncRNAs, identifying novel lncRNAs as potential candidates for colorectal cancer. This new approach could represent a promising avenue that would reduce costs and enable more efficient translational research. Abstract Long non-coding RNAs (lncRNAs) play important roles in cancer and are potential new biomarkers or targets for therapy. However, given the low and tissue-specific expression of lncRNAs, linking these molecules to particular cancer types and processes through transcriptional profiling is challenging. Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant resources for research but are prone to nucleic acid degradation, thereby complicating the study of lncRNAs. Here, we designed and validated a probe-based enrichment strategy to efficiently profile lncRNA expression in FFPE samples, and we applied it for the detection of lncRNAs associated with colorectal cancer (CRC). Our approach efficiently enriched targeted lncRNAs from FFPE samples, while preserving their relative abundance, and enabled the detection of tumor-specific mutations. We identified 379 lncRNAs differentially expressed between CRC tumors and matched healthy tissues and found tumor-specific lncRNA variants. Our results show that numerous lncRNAs are differentially expressed and/or accumulate variants in CRC tumors, thereby suggesting a role in CRC progression. More generally, our approach unlocks the study of lncRNAs in FFPE samples, thus enabling the retrospective use of abundant, well documented material available in hospital biobanks.
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Amiri Ghanatsaman Z, Wang GD, Asadi Fozi M, Zhang YP, Esmailizadeh A. Genome resequencing data for Iranian local dogs and wolves. BMC Res Notes 2020; 13:436. [PMID: 32938490 PMCID: PMC7493879 DOI: 10.1186/s13104-020-05271-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/04/2020] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The data provided herein represent the whole-genome resequencing data related to three wolves and three Iranian local dogs. The understanding of genome evolution during animal domestication is an interesting subject in genome biology. Dog is an excellent model for understanding of domestication due to its considerable variety of behavioral and physical traits. The Zagros area of current day Iran has been identified as one of the initial centers of animal domestication. The availability of the complete genome sequences of Iranian local canids can be a valuable resource for researchers to address questions and testing hypotheses on the dog domestication process. DATA DESCRIPTION We collected blood samples from six Iranian local canids including two hunting dogs (Saluki breed), a mastiff dog (Qahderijani ecotype) and three wolves. We extracted genomic DNA from blood samples. Sequence data were produced using the Illumina HiSeq 2500 system. All sequence data are available in the National Genomics Data Center (NGDC), Genome Sequence Archive (GSA) database under the accession of CRA001324 and the National Center for Biotechnology Information (NCBI) under the accession of PRJNA639312. The short-read sequences with the mean depth of 16X were aligned to the dog reference genome (CanFam3.1) and achieved 99% coverage of the reference assembly. The obtained information from this experiment will be useful in evolutionary biology.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Young Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
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Pajkos M, Zeke A, Dosztányi Z. Ancient Evolutionary Origin of Intrinsically Disordered Cancer Risk Regions. Biomolecules 2020; 10:biom10081115. [PMID: 32731489 PMCID: PMC7465906 DOI: 10.3390/biom10081115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer is a heterogeneous genetic disease that alters the proper functioning of proteins involved in key regulatory processes such as cell cycle, DNA repair, survival, or apoptosis. Mutations often accumulate in hot-spots regions, highlighting critical functional modules within these proteins that need to be altered, amplified, or abolished for tumor formation. Recent evidence suggests that these mutational hotspots can correspond not only to globular domains, but also to intrinsically disordered regions (IDRs), which play a significant role in a subset of cancer types. IDRs have distinct functional properties that originate from their inherent flexibility. Generally, they correspond to more recent evolutionary inventions and show larger sequence variations across species. In this work, we analyzed the evolutionary origin of disordered regions that are specifically targeted in cancer. Surprisingly, the majority of these disordered cancer risk regions showed remarkable conservation with ancient evolutionary origin, stemming from the earliest multicellular animals or even beyond. Nevertheless, we encountered several examples where the mutated region emerged at a later stage compared with the origin of the gene family. We also showed the cancer risk regions become quickly fixated after their emergence, but evolution continues to tinker with their genes with novel regulatory elements introduced even at the level of humans. Our concise analysis provides a much clearer picture of the emergence of key regulatory elements in proteins and highlights the importance of taking into account the modular organisation of proteins for the analyses of evolutionary origin.
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Affiliation(s)
- Mátyás Pajkos
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter stny 1/c, H-1117 Budapest, Hungary;
| | - András Zeke
- Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary;
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter stny 1/c, H-1117 Budapest, Hungary;
- Correspondence:
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Adaptive evolution of peptidoglycan recognition protein family regulates the innate signaling against microbial pathogens in vertebrates. Microb Pathog 2020; 147:104361. [PMID: 32622926 DOI: 10.1016/j.micpath.2020.104361] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/28/2020] [Accepted: 06/22/2020] [Indexed: 12/16/2022]
Abstract
The innate immune system is the first line of defense in vertebrates against microbial pathogens. This defense system depends on the peptidoglycan pathogen recognition of receptors (PGRPs) existing in both invertebrates and vertebrates. Although some studies revealed the structural and functional differences between them, however, the evolutionary history and the selection pressures on these genes during adaptive evolution are poorly understood. In this study, we examined four (PGLYRP1, PGLYRP2, PGLYRP3, and PGLYRP4) genes of 127 vertebrates' species, conserved across vertebrates to evaluate positive selection pressure drives by adaptive evolution. The codons under positive selection were recognized through likelihood tests by comparing different models based on ω ratios in these genes across the vertebrate species. The positive selection test used two sets of models M1a vs. M2a and M7 vs. M8. The results showed that the test of these genes in M1a vs. M2a was not significant with the likelihood value 2ΔlnL = 0, while the likelihood ratios (2ΔlnL) were 2ΔlnL = 12.386, 2ΔlnL = 4.9283, 2ΔlnL = 24.031, and 2ΔlnL = 103.39 for PGLYRP1, PGLYRP2, PGLYRP3, and PGLYRP4 in M7 vs. M8, respectively. Our study identified the evidence of robust positive selection for these four genes across the vertebrates. These protuberant changes in PGRPs evolution of vertebrates reveal their role in innate immunity. Our study provides an insight based on PGRP genes to understand the evolution of host and pathogens interaction that leads to the progress of the novel conducts for immune diseases that include proteins linked to the recognition of pathogens.
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Piard J, Béreau M, XiangWei W, Wirth T, Amsallem D, Buisson L, Richard P, Liu N, Xu Y, Myers SJ, Traynelis SF, Chelly J, Anheim M, Raynaud M, Van Maldergem L, Yuan H. The GRIA3 c.2477G > A Variant Causes an Exaggerated Startle Reflex, Chorea, and Multifocal Myoclonus. Mov Disord 2020; 35:1224-1232. [PMID: 32369665 PMCID: PMC9190290 DOI: 10.1002/mds.28058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/24/2020] [Accepted: 03/03/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Hemizygous mutations in GRIA3 encoding the GluA3 subunit of the amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor are known to be associated with neurodevelopmental disorders, including intellectual disability, hypotonia, an autism spectrum disorder, sleep disturbances, and epilepsy in males. OBJECTIVE To describe a new and consistent phenotype in 4 affected male patients associated with an undescribed deleterious variant in GRIA3. METHODS We evaluated a large French family in which segregate a singular phenotype according to an apparent X-linked mode of inheritance. Molecular analyses using next generation sequencing and in vitro functional studies using 2-electrode voltage clamp recordings on Xenopus laevis oocytes and a β-lactamase reporter assay in transfected human embryonic kidney (HEK293) cells were performed. RESULTS In addition to mild intellectual disability and dysarthria, affected patients presented a tightly consistent early-onset movement disorder combining an exaggerated startle reflex with generalized chorea and multifocal myoclonus. The unreported GRIA3 missense variant c.2477G > A; p.(Gly826Asp) affecting the fourth transmembrane domain of the protein was identified in index patients and their unaffected mothers. Functional studies revealed that variant receptors show decreased current response evoked by agonist (ie, kainic acid and glutamate) and reduced expression on the cell surface in favor of pathogenicity by a loss-of-function mechanism. CONCLUSIONS Taken together, our results suggest that apart from known GRIA3-related disorders, an undescribed mutation-specific singular movement disorder does exist. We thus advocate considering GRIA3 mutations in the differential diagnosis of hyperekplexia and generalized chorea with myoclonus. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Juliette Piard
- Centre de Génétique Humaine, Université de Franche-Comté, CHU, Besançon, France
- Unité de recherche en neurosciences intégratives et cognitives EA481, Université de Franche-Comté, Besançon, France
| | - Matthieu Béreau
- Unité de recherche en neurosciences intégratives et cognitives EA481, Université de Franche-Comté, Besançon, France
- Service de Neurologie, CHU, Besançon, France
| | - Wenshu XiangWei
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Thomas Wirth
- Département de Neurologie, Häpital de Hautepierre, Häpitaux Universitaires de Strasbourg, Strasbourg, France
| | | | | | | | - Nana Liu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yuchen Xu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Scott J. Myers
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Functional Evaluation of Rare Variants, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Stephen F. Traynelis
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Functional Evaluation of Rare Variants, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jameleddine Chelly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Mathieu Anheim
- Département de Neurologie, Häpital de Hautepierre, Häpitaux Universitaires de Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, Strasbourg, France
| | - Martine Raynaud
- CHRU de Tours, Service de Génétique, Tours, France
- UMR1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Lionel Van Maldergem
- Centre de Génétique Humaine, Université de Franche-Comté, CHU, Besançon, France
- Unité de recherche en neurosciences intégratives et cognitives EA481, Université de Franche-Comté, Besançon, France
- Clinical Investigation Center 1431, National Institute of Health and Medical Research, Besançon, France
| | - Hongjie Yuan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Functional Evaluation of Rare Variants, Emory University School of Medicine, Atlanta, Georgia, USA
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Characterization of the primate TRIM gene family reveals the recent evolution in primates. Mol Genet Genomics 2020; 295:1281-1294. [PMID: 32564135 DOI: 10.1007/s00438-020-01698-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
Abstract
The tripartite motif (TRIM) gene family encodes diverse distinct proteins that play important roles in many biological processes. However, the molecular evolution and phylogenetic relationships of TRIM genes in primates are still elusive. We performed a genomic approach to identify and characterize TRIM genes in human and other six primate genomes. In total, 537 putative functional TRIM genes were identified and TRIM members varied among primates. A neighbor joining (NJ) tree based on the protein sequences of 82 human TRIM genes indicates seven TRIM groups, which is consistent with the results based on the architectural motifs. Many TRIM gene duplication events were identified, indicating a recent expansion of TRIM family in primate lineages. Interestingly, the chimpanzee genome shows the greatest TRIM gene expansion among the primates; however, its congeneric species, bonobo, has the least number of TRIM genes and no duplication event. Moreover, we identified a ~ 200 kb deletion on chromosome 11 of bonobos that results in a loss of cluster3 TRIM genes. The loss of TRIM genes might have occurred within the last 2 mys. Analysis of positive selection recovered 9 previously reported and 21 newly identified positively selected TRIM genes. In particular, most positive selected sites are located in the B30.2 domains. Our results have provided new insight into the evolution of primate TRIM genes and will broaden our understanding on the functions of the TRIM family.
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Evaluation of CNV detection tools for NGS panel data in genetic diagnostics. Eur J Hum Genet 2020; 28:1645-1655. [PMID: 32561899 PMCID: PMC7784926 DOI: 10.1038/s41431-020-0675-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/21/2020] [Accepted: 04/28/2020] [Indexed: 01/01/2023] Open
Abstract
Although germline copy-number variants (CNVs) are the genetic cause of multiple hereditary diseases, detecting them from targeted next-generation sequencing data (NGS) remains a challenge. Existing tools perform well for large CNVs but struggle with single and multi-exon alterations. The aim of this work is to evaluate CNV calling tools working on gene panel NGS data and their suitability as a screening step before orthogonal confirmation in genetic diagnostics strategies. Five tools (DECoN, CoNVaDING, panelcn.MOPS, ExomeDepth, and CODEX2) were tested against four genetic diagnostics datasets (two in-house and two external) for a total of 495 samples with 231 single and multi-exon validated CNVs. The evaluation was performed using the default and sensitivity-optimized parameters. Results showed that most tools were highly sensitive and specific, but the performance was dataset dependant. When evaluating them in our diagnostics scenario, DECoN and panelcn.MOPS detected all CNVs with the exception of one mosaic CNV missed by DECoN. However, DECoN outperformed panelcn.MOPS specificity achieving values greater than 0.90 when using the optimized parameters. In our in-house datasets, DECoN and panelcn.MOPS showed the highest performance for CNV screening before orthogonal confirmation. Benchmarking and optimization code is freely available at https://github.com/TranslationalBioinformaticsIGTP/CNVbenchmarkeR .
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Gao T, Qian J. EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species. Nucleic Acids Res 2020; 48:D58-D64. [PMID: 31740966 PMCID: PMC7145677 DOI: 10.1093/nar/gkz980] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/02/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023] Open
Abstract
Enhancers are distal cis-regulatory elements that activate the transcription of their target genes. They regulate a wide range of important biological functions and processes, including embryogenesis, development, and homeostasis. As more and more large-scale technologies were developed for enhancer identification, a comprehensive database is highly desirable for enhancer annotation based on various genome-wide profiling datasets across different species. Here, we present an updated database EnhancerAtlas 2.0 (http://www.enhanceratlas.org/indexv2.php), covering 586 tissue/cell types that include a large number of normal tissues, cancer cell lines, and cells at different development stages across nine species. Overall, the database contains 13 494 603 enhancers, which were obtained from 16 055 datasets using 12 high-throughput experiment methods (e.g. H3K4me1/H3K27ac, DNase-seq/ATAC-seq, P300, POLR2A, CAGE, ChIA-PET, GRO-seq, STARR-seq and MPRA). The updated version is a huge expansion of the first version, which only contains the enhancers in human cells. In addition, we predicted enhancer–target gene relationships in human, mouse and fly. Finally, the users can search enhancers and enhancer–target gene relationships through five user-friendly, interactive modules. We believe the new annotation of enhancers in EnhancerAtlas 2.0 will facilitate users to perform useful functional analysis of enhancers in various genomes.
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Affiliation(s)
- Tianshun Gao
- The Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
| | - Jiang Qian
- The Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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Meyer X, Dib L, Salamin N. CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates. Nucleic Acids Res 2020; 47:D50-D54. [PMID: 30357342 PMCID: PMC6324051 DOI: 10.1093/nar/gky986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/10/2018] [Indexed: 01/15/2023] Open
Abstract
The study of molecular coevolution, due to its potential to identify gene regions under functional or structural constraints, has recently been subject to numerous scientific inquiries. Particular efforts have been conducted to develop methods predicting the presence of coevolution in molecular sequences. Among these methods, a few aim to model the underlying evolutionary process of coevolution, which enable to differentiate the shared history of genes to coevolution and thus improve their accuracy. However, the usage of such methods remains sparse due to their expensive computational cost and the lack of resources alleviating this issue. Here we present CoevDB (http://phylodb.unil.ch/CoevDB), a database containing the result of a large-scale analysis of intramolecular coevolution of 8201 protein-coding genes of bony vertebrates. The web interface of CoevDB gives access to the results to 800 millions of statistical tests corresponding to all the pairs of sites analyzed. Several type of queries enable users to explore the database by either targeting specific genes or by discovering genes having promising estimations of coevolution.
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Affiliation(s)
- Xavier Meyer
- Department of Computational Biology, University of Lausanne, Biophore, 1015 Lausanne, Switzerland.,Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg, Berkeley, CA 94720-3140, USA
| | - Linda Dib
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Biophore, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
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38
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Chang SY, Carpena NT, Mun S, Jung JY, Chung PS, Shim H, Han K, Ahn JC, Lee MY. Enhanced Inner-Ear Organoid Formation from Mouse Embryonic Stem Cells by Photobiomodulation. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:556-567. [PMID: 32258218 PMCID: PMC7118273 DOI: 10.1016/j.omtm.2020.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/09/2020] [Accepted: 03/10/2020] [Indexed: 12/18/2022]
Abstract
Photobiomodulation (PBM) stimulates different types of stem cells to migrate, proliferate, and differentiate in vitro and in vivo. However, little is known about the effects of PBM on the differentiation of embryonic stem cells (ESCs) toward the otic lineage. Only a few reports have documented the in vitro differentiation of ESCs into inner-ear hair cells (HCs) due to the complexity of HCs compared with other target cell types. In this study, we determined the optimal condition to differentiate the ESCs into the otic organoid using different culture techniques and PBM parameters. The efficiency of organoid formation within the embryoid body (EB) was dependent on the cell density of the hanging drop. PBM, using 630 nm wavelength light-emitting diodes (LEDs), further improved the differentiation of inner-ear hair cell-like cells coupled with reactive oxygen species (ROS) overexpression. Transcriptome analysis showed the factors that are responsible for the effect of PBM in the formation of otic organoids, notably, the downregulation of neural development-associated genes and the hairy and enhancer of split 5 (Hes5) gene, which inhibits the differentiation of prosensory cells to hair cells. These data enrich the current differentiation protocols for generating inner-ear hair cells.
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Affiliation(s)
- So-Young Chang
- Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Nathaniel T Carpena
- Department of Otolaryngology-Head & Neck Surgery, College of Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,DKU-Theragen Institute for NGS Analysis (DTiNa), 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Jae Yun Jung
- Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,Department of Otolaryngology-Head & Neck Surgery, College of Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Phil-Sang Chung
- Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,Department of Otolaryngology-Head & Neck Surgery, College of Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Hosup Shim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,DKU-Theragen Institute for NGS Analysis (DTiNa), 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Jin-Chul Ahn
- Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,Department of Biomedical Science, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Min Young Lee
- Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,Department of Otolaryngology-Head & Neck Surgery, College of Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
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Amiri Ghanatsaman Z, Wang GD, Asadollahpour Nanaei H, Asadi Fozi M, Peng MS, Esmailizadeh A, Zhang YP. Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication. BMC Genomics 2020; 21:207. [PMID: 32131720 PMCID: PMC7057629 DOI: 10.1186/s12864-020-6619-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/25/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported. RESULTS Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3'-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work. CONCLUSIONS Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
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Clinical Profiles of DFNA11 at Diverse Stages of Development and Aging in a Large Family Identified by Linkage Analysis. Otol Neurotol 2020; 41:e663-e673. [DOI: 10.1097/mao.0000000000002604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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41
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Wang J, Koganti PP, Yao J. Systematic identification of long intergenic non-coding RNAs expressed in bovine oocytes. Reprod Biol Endocrinol 2020; 18:13. [PMID: 32085734 PMCID: PMC7035783 DOI: 10.1186/s12958-020-00573-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/11/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are key regulators of diverse cellular processes. Although a number of studies have reported the identification of bovine lncRNAs across many tissues, very little is known about the identity and characteristics of lncRNAs in bovine oocytes. METHODS A bovine oocyte cDNA library was constructed and sequenced using the Illumina HiSeq 2000 sequencing system. The oocyte transcriptome was constructed using the ab initio assembly software Scripture and Cufflinks. The assembled transcripts were categorized to identify the novel intergenic transcripts, and the coding potential of these novel transcripts was assessed using CPAT and PhyloCSF. The resulting candidate long intergenic non-coding RNAs (lincRNAs) transcripts were further evaluated to determine if any of them contain any known protein coding domains in the Pfam database. RT-PCR was used to analyze the expression of oocyte-expressed lincRNAs in various bovine tissues. RESULTS A total of 85 million raw reads were generated from sequencing of the bovine oocyte library. Transcriptome reconstruction resulted in the assembly of a total of 42,396 transcripts from 37,678 genomic loci. Analysis of the assembled transcripts using the step-wide pipeline resulted in the identification of 1535 oocyte lincRNAs corresponding to 1183 putative non-coding genes. A comparison of the oocyte lincRNAs with the lncRNAs reported in other bovine tissues indicated that 970 of the 1535 oocyte lincRNAs appear to be unique to bovine oocytes. RT-PCR analysis of 5 selected lincRNAs showed either specific or predominant expression of 4 lincRNAs in the fetal ovary. Functional prediction of the oocyte-expressed lincRNAs suggested their involvement in oogenesis through regulating their neighboring protein-coding genes. CONCLUSIONS This study provides a starting point for future research aimed at understanding the roles of lncRNAs in controlling oocyte development and early embryogenesis in cattle.
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Affiliation(s)
- Jian Wang
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Prasanthi P Koganti
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Jianbo Yao
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA.
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42
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Ahmad HI, Zhou J, Ahmad MJ, Afzal G, Jiang H, Zhang X, Elokil AA, Khan MA, Li L, Li H, Ping L, Chen J. Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates. Aging (Albany NY) 2020; 12:3516-3557. [PMID: 32045365 PMCID: PMC7066927 DOI: 10.18632/aging.102827] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Programmed cell death-1 (PD-1) and its ligands, particularly PD-L1 and PD-L2, are the most important proteins responsible for signaling T-cell inhibition and arbitrating immune homeostasis and tolerance mechanisms. However, the adaptive evolution of these genes is poorly understood. In this study, we aligned protein-coding genes from vertebrate species to evaluate positive selection constraints and evolution in the PD1, PD-L1 and PD-L2 genes conserved across up to 166 vertebrate species, with an average of 55 species per gene. We determined that although the positive selection was obvious, an average of 5.3% of codons underwent positive selection in the three genes across vertebrate lineages, and increased positive selection pressure was detected in both the Ig-like domains and transmembrane domains of the proteins. Moreover, the PD1, PD-L1 and PD-L2 genes were highly expressed in almost all tissues of the selected species indicating a distinct expression pattern in different tissues among most species. Our study reveals that adaptive selection plays a key role in the evolution of PD1 and its ligands in the majority of vertebrate species, which is in agreement with the contribution of these residues to the mechanisms of pathogen identification and coevolution in the complexity and novelties of vertebrate immune systems.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jiabin Zhou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Muhammad Jamil Ahmad
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gulnaz Afzal
- Department of Zoology, The Islamia University, Bahawalpur, Pakistan
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Abdelmotaleb A. Elokil
- Department of Zoology, The Islamia University, Bahawalpur, Pakistan
- Animal Production Department, Faculty of Agriculture, Benha University, Moshtohor, Egypt
| | - Musarrat Abbas Khan
- Department of Animal Breeding and Genetics, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Huiming Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Liu Ping
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
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43
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Ahi EP, Brunel M, Tsakoumis E, Schmitz M. Transcriptional study of appetite regulating genes in the brain of zebrafish (Danio rerio) with impaired leptin signalling. Sci Rep 2019; 9:20166. [PMID: 31882937 PMCID: PMC6934527 DOI: 10.1038/s41598-019-56779-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/10/2019] [Indexed: 12/26/2022] Open
Abstract
The hormone leptin is a key regulator of body weight, food intake and metabolism. In mammals, leptin acts as an anorexigen and inhibits food intake centrally by affecting the appetite centres in the hypothalamus. In teleost fish, the regulatory connections between leptin and other appetite-regulating genes are largely unknown. In the present study, we used a zebrafish mutant with a loss of function leptin receptor to investigate brain expression patterns of 12 orexigenic and 24 anorexigenic genes under different feeding conditions (normal feeding, 7-day fasting, 2 and 6-hours refeeding). Expression patterns were compared to wild-type zebrafish, in order to identify leptin-dependent differentially expressed genes under different feeding conditions. We provide evidence that the transcription of certain orexigenic and anorexigenic genes is influenced by leptin signalling in the zebrafish brain. We found that the expression of orexigenic genes was not affected by impaired leptin signalling under normal feeding conditions; however, several orexigenic genes showed increased transcription during fasting and refeeding, including agrp, apln, galr1a and cnr1. This suggests an inhibitory effect of leptin signal on the transcription of these orexigenic genes during short-term fasting and refeeding in functional zebrafish. Most pronounced effects were observed in the group of anorexigenic genes, where the impairment of leptin signalling resulted in reduced gene expression in several genes, including cart family, crhb, gnrh2, mc4r, pomc and spx, in the control group. This suggests a stimulatory effect of leptin signal on the transcription of these anorexigenic genes under normal feeding condition. In addition, we found multiple gain and loss in expression correlations between the appetite-regulating genes, in zebrafish with impaired leptin signal, suggesting the presence of gene regulatory networks downstream of leptin signal in zebrafish brain. The results provide the first evidence for the effects of leptin signal on the transcription of various appetite-regulating genes in zebrafish brain, under different feeding conditions. Altogether, these transcriptional changes suggest an anorexigenic role for leptin signal, which is likely to be mediated through distinct set of appetite-regulating genes under different feeding conditions.
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Affiliation(s)
- Ehsan Pashay Ahi
- Department of Organismal Biology, Comparative Physiology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, SE-752 36, Uppsala, Sweden
| | - Mathilde Brunel
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, BioCentrum, Allmas Allé 5, SE-750 07 Uppsala, Sweden
| | - Emmanouil Tsakoumis
- Department of Organismal Biology, Comparative Physiology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, SE-752 36, Uppsala, Sweden
| | - Monika Schmitz
- Department of Organismal Biology, Comparative Physiology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, SE-752 36, Uppsala, Sweden.
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Domínguez-Ruiz M, García-Martínez A, Corral-Juan M, Pérez-Álvarez ÁI, Plasencia AM, Villamar M, Moreno-Pelayo MA, Matilla-Dueñas A, Menéndez-González M, Del Castillo I. Perrault syndrome with neurological features in a compound heterozygote for two TWNK mutations: overlap of TWNK-related recessive disorders. J Transl Med 2019; 17:290. [PMID: 31455392 PMCID: PMC6712801 DOI: 10.1186/s12967-019-2041-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/18/2019] [Indexed: 01/22/2023] Open
Abstract
Background Perrault syndrome is a rare autosomal recessive disorder that is characterized by the association of sensorineural hearing impairment and ovarian dysgenesis in females, whereas males have only hearing impairment. In some cases, patients present with a diversity of neurological signs. To date, mutations in six genes are known to cause Perrault syndrome, but they do not explain all clinically-diagnosed cases. In addition, the number of reported cases and the spectra of mutations are still small to establish conclusive genotype–phenotype correlations. Methods Affected siblings from family SH19, who presented with features that were suggestive of Perrault syndrome, were subjected to audiological, neurological and gynecological examination. The genetic study included genotyping and haplotype analysis for microsatellite markers close to the genes involved in Perrault syndrome, whole-exome sequencing, and Sanger sequencing of the coding region of the TWNK gene. Results Three siblings from family SH19 shared similar clinical features: childhood-onset bilateral sensorineural hearing impairment, which progressed to profound deafness in the second decade of life; neurological signs (spinocerebellar ataxia, polyneuropathy), with onset in the fourth decade of life in the two females and at age 20 years in the male; gonadal dysfunction with early cessation of menses in the two females. The genetic study revealed two compound heterozygous pathogenic mutations in the TWNK gene in the three affected subjects: c.85C>T (p.Arg29*), previously reported in a case of hepatocerebral syndrome; and a novel missense mutation, c.1886C>T (p.Ser629Phe). Mutations segregated in the family according to an autosomal recessive inheritance pattern. Conclusions Our results further illustrate the utility of genetic testing as a tool to confirm a tentative clinical diagnosis of Perrault syndrome. Studies on genotype–phenotype correlation from the hitherto reported cases indicate that patients with Perrault syndrome caused by TWNK mutations will manifest neurological signs in adulthood. Molecular and clinical characterization of novel cases of recessive disorders caused by TWNK mutations is strongly needed to get further insight into the genotype–phenotype correlations of a phenotypic continuum encompassing Perrault syndrome, infantile-onset spinocerebellar ataxia, and hepatocerebral syndrome.
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Affiliation(s)
- María Domínguez-Ruiz
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Alberto García-Martínez
- Department of Neurology, Servicio de Neurología, Hospital Universitario Central de Asturias, Avenida Roma sn, 33011, Oviedo, Spain
| | - Marc Corral-Juan
- Functional and Translational Neurogenetics Unit, Department of Neuroscience, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Universitat Autónoma de Barcelona, Can Ruti Campus, Badalona, Barcelona, Spain
| | - Ángel I Pérez-Álvarez
- Department of Neurology, Servicio de Neurología, Hospital Universitario Central de Asturias, Avenida Roma sn, 33011, Oviedo, Spain
| | - Ana M Plasencia
- Servicio de Pediatría, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Manuela Villamar
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Miguel A Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Antoni Matilla-Dueñas
- Functional and Translational Neurogenetics Unit, Department of Neuroscience, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Universitat Autónoma de Barcelona, Can Ruti Campus, Badalona, Barcelona, Spain
| | - Manuel Menéndez-González
- Department of Neurology, Servicio de Neurología, Hospital Universitario Central de Asturias, Avenida Roma sn, 33011, Oviedo, Spain.
| | - Ignacio Del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.
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Karagkouni D, Paraskevopoulou MD, Chatzopoulos S, Vlachos IS, Tastsoglou S, Kanellos I, Papadimitriou D, Kavakiotis I, Maniou S, Skoufos G, Vergoulis T, Dalamagas T, Hatzigeorgiou AG. DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. Nucleic Acids Res 2019; 46:D239-D245. [PMID: 29156006 PMCID: PMC5753203 DOI: 10.1093/nar/gkx1141] [Citation(s) in RCA: 690] [Impact Index Per Article: 138.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/10/2017] [Indexed: 12/21/2022] Open
Abstract
DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database devoted to the indexing of experimentally supported microRNA (miRNA) targets. Its eighth version is the first database indexing >1 million entries, corresponding to ∼670 000 unique miRNA-target pairs. The interactions are supported by >33 experimental methodologies, applied to ∼600 cell types/tissues under ∼451 experimental conditions. It integrates information on cell-type specific miRNA–gene regulation, while hundreds of thousands of miRNA-binding locations are reported. TarBase is coming of age, with more than a decade of continuous support in the non-coding RNA field. A new module has been implemented that enables the browsing of interactions through different filtering combinations. It permits easy retrieval of positive and negative miRNA targets per species, methodology, cell type and tissue. An incorporated ranking system is utilized for the display of interactions based on the robustness of their supporting methodologies. Statistics, pie-charts and interactive bar-plots depicting the database content are available through a dedicated result page. An intuitive interface is introduced, providing a user-friendly application with flexible options to different queries.
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Affiliation(s)
- Dimitra Karagkouni
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece.,DIANA-Lab, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
| | - Maria D Paraskevopoulou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece
| | - Serafeim Chatzopoulos
- 'Athena' Research and Innovation Center, 11524 Athens, Greece.,University of Peloponnese, Department of Informatics and Telecommunications, 22100 Tripoli, Greece
| | - Ioannis S Vlachos
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece.,Department of Neurology, Brigham & Women's Hospital, Harvard Medical School, Boston, 02115 MA, USA
| | - Spyros Tastsoglou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece.,DIANA-Lab, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
| | - Ilias Kanellos
- 'Athena' Research and Innovation Center, 11524 Athens, Greece.,School of Electrical and Computer Engineering, National Technical University of Athens, 15773 Zografou, Greece
| | - Dimitris Papadimitriou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece.,DIANA-Lab, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
| | - Ioannis Kavakiotis
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece.,DIANA-Lab, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
| | - Sofia Maniou
- Department of Informatics and Telecommunications, Postgraduate Program: 'Information Technologies in Medicine and Biology', University of Athens, 15784 Athens, Greece
| | - Giorgos Skoufos
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece.,DIANA-Lab, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
| | | | | | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece.,DIANA-Lab, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece
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Abstract
The computer software used for genomic analysis has become a crucial component of the infrastructure for life sciences. However, genomic software is still typically developed in an ad hoc manner, with inadequate funding, and by academic researchers not trained in software development, at substantial costs to the research community. I examine the roots of the incongruity between the importance of and the degree of investment in genomic software, and I suggest several potential remedies for current problems. As genomics continues to grow, new strategies for funding and developing the software that powers the field will become increasingly essential.
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Affiliation(s)
- Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
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47
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Przanowski P, Mondal SS, Cabaj A, Dębski KJ, Wojtas B, Gielniewski B, Kaza B, Kaminska B, Dabrowski M. Open chromatin landscape of rat microglia upon proinvasive or inflammatory polarization. Glia 2019; 67:2312-2328. [PMID: 31339627 DOI: 10.1002/glia.23686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 01/02/2023]
Abstract
Microglia are brain-resident, myeloid cells that play important roles in health and brain pathologies. Herein, we report a comprehensive, replicated, false discovery rate-controlled dataset of DNase-hypersensitive (DHS) open chromatin regions for rat microglia. We compared the open chromatin landscapes in untreated primary microglial cultures and cultures stimulated for 6 hr with either glioma-conditioned medium (GCM) or lipopolysaccharide (LPS). Glioma-secreted factors induce proinvasive and immunosuppressive activation of microglia, and these cells then promote tumor growth. The open chromatin landscape of the rat microglia consisted of 126,640 reproducible DHS regions, among which 2,303 and 12,357 showed a significant change in openness following stimulation with GCM or LPS, respectively. Active genes exhibited constitutively open promoters, but there was no direct dependence between the aggregated openness of DHS regions near a gene and its expression. Individual regions mapped to the same gene often presented different patterns of openness changes. GCM-regulated DHS regions were more frequent in areas away from gene bodies, while LPS-regulated regions were more frequent in introns. GCM and LPS differentially affected the openness of regions mapped to immune checkpoint genes. The two treatments differentially affected the aggregated openness of regions mapped to genes in the Toll-like receptor signaling and axon guidance pathways, suggesting that the molecular machinery used by migrating microglia is similar to that of growing axons and that modulation of these pathways is instrumental in the induction of proinvasive polarization of microglia by glioma. Our dataset of open chromatin regions paves the way for studies of gene regulation in rat microglia.
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Affiliation(s)
- Piotr Przanowski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Shamba S Mondal
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Cabaj
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Konrad J Dębski
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Bartłomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Beata Kaza
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Michal Dabrowski
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
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48
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Gemmell P, Hein J, Katzourakis A. The Exaptation of HERV-H: Evolutionary Analyses Reveal the Genomic Features of Highly Transcribed Elements. Front Immunol 2019; 10:1339. [PMID: 31338090 PMCID: PMC6629862 DOI: 10.3389/fimmu.2019.01339] [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] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 05/28/2019] [Indexed: 12/25/2022] Open
Abstract
HERV-H endogenous retroviruses are thought to be essential to stem cell identity in humans. We embrace several decades of HERV-H research in order to relate the transcription of HERV-H loci to their genomic structure. We find that highly transcribed HERV-H loci are younger, more fragmented, and less likely to be present in other primate genomes. We also show that repeats in HERV-H LTRs are correlated to where loci are transcribed: type-I LTRs associate with stem cells while type-II repeats associate with embryonic cells. Our findings are generally in line with what is known about endogenous retrovirus biology but we find that the presence of the zinc finger motif containing region of gag is positively correlated with transcription. This leads us to suggest a possible explanation for why an unusually large proportion of HERV-H loci have been preserved in non-solo-LTR form.
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Affiliation(s)
- Patrick Gemmell
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jotun Hein
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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49
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Distinct Profiles of Cell-Free MicroRNAs in Plasma of Veterans with Post-Traumatic Stress Disorder. J Clin Med 2019; 8:jcm8070963. [PMID: 31277223 PMCID: PMC6678393 DOI: 10.3390/jcm8070963] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/02/2019] [Indexed: 12/29/2022] Open
Abstract
Dysregulation of circulating microRNAs (miRNAs) in body fluids has been reported in psychiatric disorders such as schizophrenia, bipolar disorder, major depressive disorder, and post-traumatic stress disorder (PTSD). Recent studies of various diseases showed that extracellular vesicles (EV) in body fluids can provide different spectra of circulating miRNAs and disease-associated signatures from whole fluid or EV-depleted fraction. However, the association of miRNAs in EVs to PTSD has not been studied. In this study, we performed a comprehensive profiling of miRNAs in whole plasma, extracellular vesicles (EV) and EV-depleted plasma (EVD) samples collected from combat veterans with PTSD and matched controls by utilizing a next-generation sequencing (NGS) platform. In total, 520 circulating miRNAs were quantified from 24 male Iraq and Afghanistan combat veterans with (n = 12) and without (n = 12) PTSD. The overall miRNA profiles in whole plasma, EV and EVD fractions were different and miRNAs affected by PTSD were also distinct in each sample type. The concentration changes of miR-203a-3p in EV and miR-339-5p in EVD were confirmed in an independent validation cohort that consisted of 20 veterans (10 with and 10 without PTSD) using qPCR. The target genes of these two miRNAs were involved in signaling pathways and comorbid conditions associated with PTSD (e.g., neurotransmitter systems such as dopaminergic and serotonergic signaling, inflammatory response, and cardiovascular diseases). Our findings suggest that PTSD may have different impacts on miRNAs encapsulated in vesicles and outside of vesicles. Further studies using larger samples are needed to evaluate the utility of these miRNAs as diagnostic biomarkers for PTSD.
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50
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Rollins JA, Shaffer D, Snow SS, Kapahi P, Rogers AN. Dietary restriction induces posttranscriptional regulation of longevity genes. Life Sci Alliance 2019; 2:2/4/e201800281. [PMID: 31253655 PMCID: PMC6600014 DOI: 10.26508/lsa.201800281] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/12/2022] Open
Abstract
Dietary restriction (DR) increases life span through adaptive changes in gene expression. To understand more about these changes, we analyzed the transcriptome and translatome of Caenorhabditis elegans subjected to DR. Transcription of muscle regulatory and structural genes increased, whereas increased expression of amino acid metabolism and neuropeptide signaling genes was controlled at the level of translation. Evaluation of posttranscriptional regulation identified putative roles for RNA-binding proteins, RNA editing, miRNA, alternative splicing, and nonsense-mediated decay in response to nutrient limitation. Using RNA interference, we discovered several differentially expressed genes that regulate life span. We also found a compensatory role for translational regulation, which offsets dampened expression of a large subset of transcriptionally down-regulated genes. Furthermore, 3' UTR editing and intron retention increase under DR and correlate with diminished translation, whereas trans-spliced genes are refractory to reduced translation efficiency compared with messages with the native 5' UTR. Finally, we find that smg-6 and smg-7, which are genes governing selection and turnover of nonsense-mediated decay targets, are required for increased life span under DR.
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Affiliation(s)
- Jarod A Rollins
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Dan Shaffer
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Santina S Snow
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Aric N Rogers
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
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