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Kanlayaprasit S, Saeliw T, Thongkorn S, Panjabud P, Kasitipradit K, Lertpeerapan P, Songsritaya K, Yuwattana W, Jantheang T, Jindatip D, Hu VW, Kikkawa T, Osumi N, Sarachana T. Sex-specific impacts of prenatal bisphenol A exposure on genes associated with cortical development, social behaviors, and autism in the offspring's prefrontal cortex. Biol Sex Differ 2024; 15:40. [PMID: 38750585 PMCID: PMC11094985 DOI: 10.1186/s13293-024-00614-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Recent studies have shown that prenatal BPA exposure altered the transcriptome profiles of autism-related genes in the offspring's hippocampus, disrupting hippocampal neuritogenesis and causing male-specific deficits in learning. However, the sex differences in the effects of prenatal BPA exposure on the developing prefrontal cortex, which is another brain region highly implicated in autism spectrum disorder (ASD), have not been investigated. METHODS We obtained transcriptome data from RNA sequencing analysis of the prefrontal cortex of male and female rat pups prenatally exposed to BPA or control and reanalyzed. BPA-responsive genes associated with cortical development and social behaviors were selected for confirmation by qRT-PCR analysis. Neuritogenesis of primary cells from the prefrontal cortex of pups prenatally exposed to BPA or control was examined. The social behaviors of the pups were assessed using the two-trial and three-chamber tests. The male-specific impact of the downregulation of a selected BPA-responsive gene (i.e., Sema5a) on cortical development in vivo was interrogated using siRNA-mediated knockdown by an in utero electroporation technique. RESULTS Genes disrupted by prenatal BPA exposure were associated with ASD and showed sex-specific dysregulation. Sema5a and Slc9a9, which were involved in neuritogenesis and social behaviors, were downregulated only in males, while Anxa2 and Junb, which were also linked to neuritogenesis and social behaviors, were suppressed only in females. Neuritogenesis was increased in males and showed a strong inverse correlation with Sema5a and Slc9a9 expression levels, whereas, in the females, neuritogenesis was decreased and correlated with Anxa2 and Junb levels. The siRNA-mediated knockdown of Sema5a in males also impaired cortical development in utero. Consistent with Anxa2 and Junb downregulations, deficits in social novelty were observed only in female offspring but not in males. CONCLUSION This is the first study to show that prenatal BPA exposure dysregulated the expression of ASD-related genes and functions, including cortical neuritogenesis and development and social behaviors, in a sex-dependent manner. Our findings suggest that, besides the hippocampus, BPA could also exert its adverse effects through sex-specific molecular mechanisms in the offspring's prefrontal cortex, which in turn would lead to sex differences in ASD-related neuropathology and clinical manifestations, which deserves further investigation.
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Grants
- NRU59-031-HR National Research University Project, Office of Higher Education Commission
- HEA663700091 Thailand Science Research and Innovation Fund Chulalongkorn University
- GRU 6300437001-1 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- GRU_64_033_37_004 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- GRU 6506537004-1 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand
- the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand
- the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand
- the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand
- PHD/0029/2561 a Royal Golden Jubilee Ph.D. Programme Scholarship, the Thailand Research Fund and National Research Council of Thailand
- N41A650065 a Royal Golden Jubilee Ph.D. Programme Scholarship, the Thailand Research Fund and National Research Council of Thailand
- NRCT5-RGJ63001-018 a Royal Golden Jubilee Ph.D. Programme Scholarship, the Thailand Research Fund and National Research Council of Thailand
- GCUGR1125632108D-108 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- GCUGR1125632109D-109 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- GCUGR1125651062D-062 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- GCUGR1125651060D-060 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship
- The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship
- The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship
- The National Research Council of Thailand (NRCT) fund for research and innovation activity The National Research Council of Thailand (NRCT) fund for research and innovation activity
- The National Research Council of Thailand (NRCT) fund for research and innovation activity The National Research Council of Thailand (NRCT) fund for research and innovation activity
- The National Research Council of Thailand (NRCT) fund for research and innovation activity The National Research Council of Thailand (NRCT) fund for research and innovation activity
- The National Research Council of Thailand (NRCT) fund for research and innovation activity The National Research Council of Thailand (NRCT) fund for research and innovation activity
- The National Research Council of Thailand (NRCT) fund for research and innovation activity The National Research Council of Thailand (NRCT) fund for research and innovation activity
- Scholarship from the Graduate School Chulalongkorn University to commemorate the 72nd anniversary of His Majesty King Bhumibala Aduladeja Scholarship from the Graduate School Chulalongkorn University to commemorate the 72nd anniversary of His Majesty King Bhumibala Aduladeja
- Chulalongkorn University Laboratory Animal Center (CULAC) Grant Chulalongkorn University Laboratory Animal Center (CULAC) Grant
- PMU-B; B36G660008 Program Management Unit for Human Resources and Institutional Development, Research and Innovation
- CE66_046_3700_003 Ratchadapisek Somphot Fund for Supporting Center of Excellence, Chulalongkorn University
- The National Research Council of Thailand (NRCT) fund for research and innovation activity
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Affiliation(s)
- Songphon Kanlayaprasit
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Bangkok, Wangmai, Pathumwan, 10330, Thailand
| | - Thanit Saeliw
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Bangkok, Wangmai, Pathumwan, 10330, Thailand
| | - Surangrat Thongkorn
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Bangkok, Wangmai, Pathumwan, 10330, Thailand
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pawinee Panjabud
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kasidit Kasitipradit
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Pattanachat Lertpeerapan
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kwanjira Songsritaya
- The M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Wasana Yuwattana
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Thanawin Jantheang
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Depicha Jindatip
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Bangkok, Wangmai, Pathumwan, 10330, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Takako Kikkawa
- Department of Developmental Neuroscience, Centers for Advanced Research and Translational Medicine (ART), Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, Centers for Advanced Research and Translational Medicine (ART), Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Tewarit Sarachana
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Bangkok, Wangmai, Pathumwan, 10330, Thailand.
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2
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Altered distribution and localization of organellar Na +/H + exchangers in postmortem schizophrenia dorsolateral prefrontal cortex. Transl Psychiatry 2023; 13:34. [PMID: 36732328 PMCID: PMC9895429 DOI: 10.1038/s41398-023-02336-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023] Open
Abstract
Schizophrenia is a complex and multifactorial disorder associated with altered neurotransmission as well as numerous signaling pathway and protein trafficking disruptions. The pH of intracellular organelles involved in protein trafficking is tightly regulated and impacts their functioning. The SLC9A family of Na+/H+ exchangers (NHEs) plays a fundamental role in cellular and intracellular pH homeostasis. Four organellar NHE isoforms (NHE6-NHE9) are targeted to intracellular organelles involved in protein trafficking. Increased interactions between organellar NHEs and receptor of activated protein C kinase 1 (RACK1) can lead to redistribution of NHEs to the plasma membrane and hyperacidification of target organelles. Given their role in organelle pH regulation, altered expression and/or localization of organellar NHEs could be an underlying cellular mechanism contributing to abnormal intracellular trafficking and disrupted neurotransmitter systems in schizophrenia. We thus characterized organellar NHE expression, co-immunoprecipitation with RACK1, and Triton X-114 (TX-114) phase partitioning in dorsolateral prefrontal cortex of 25 schizophrenia and 25 comparison subjects by Western blot analysis. In schizophrenia after controlling for subject age at time of death, postmortem interval, tissue pH, and sex, there was significantly decreased total expression of NHE8, decreased co-immunoprecipitation of NHE8 (64%) and NHE9 (56%) with RACK1, and increased TX-114 detergent phase partitioning of NHE6 (283%), NHE9 (75%), and RACK1 (367%). Importantly, none of these dependent measures was significantly impacted when comparing those in the schizophrenia group on antipsychotics to those off of antipsychotics for at least 6 weeks at their time of death and none of these same proteins were affected in rats chronically treated with haloperidol. In summary, we characterized organellar NHE expression and distribution in schizophrenia DLPFC and identified abnormalities that could represent a novel mechanism contributing to disruptions in protein trafficking and neurotransmission in schizophrenia.
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Zhang Z, Liu L, Zhang H, Li C, Chen Y, Zhang J, Pan C, Cheng S, Yang X, Meng P, Yao Y, Jia Y, Wen Y, Zhang F. The genetic structure of pain in depression patients: A genome-wide association study and proteome-wide association study. J Psychiatr Res 2022; 156:547-556. [PMID: 36368244 DOI: 10.1016/j.jpsychires.2022.10.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/18/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Comparing with the general population, the pain in depression patients has more complex biological mechanism. We aim to explore the etiological mechanism of pain in depression patients from the perspective of genetics. METHODS Utilizing the UK Biobank samples with self-reported depression status or PHQ score ≥10, we conducted genome-wide association studies (GWAS) of seven pain traits (N = 1,133-58,349). Additionally, we used FUSION pipeline to perform proteome-wide association study (PWAS) and transcriptome-wide association study (TWAS) by integrating GWAS summary data with two different proteome reference weights (ROS/MAP and Banner) and Rnaseq gene expression reference weights, respectively. RESULTS GWAS identified 3 significant genes associated with different pain traits in depression patients, including TRIOBP (PGWAS = 4.48 × 10-8) for stomach or abdominal pain, SLC9A9(PGWAS = 2.77 × 10-8) for multisite chronic pain (MCP) and ADGRF1 (PGWAS = 1.51 × 10-8) for neck or shoulder pain. In addition, PWAS and TWAS analysis also identified multiple candidate genes associated with different pain traits in depression patients, such as TPRG1L (PPWAS-Banner = 3.38 × 10-2) and SIRPA (PPWAS-Banner = 3.65 × 10-2) for MCP, etc. Notably, when comparing the results of PWAS and TWAS analysis, we found overlapping candidate genes in these pain traits, such as GSTM3 (PPWAS-Banner = 3.38 × 10-2, PTWAS = 6.92 × 10-3) in the stomach or abdominal pain phenotype, ATG7 (PPWAS-Rosmap = 3.15 × 10-2, PTWAS = 2.98 × 10-2) in the MCP, etc. CONCLUSIONS: We identified multiple novel candidate genes for pain traits in depression patients from different perspectives of genetics, which provided novel clues for understanding the genetic mechanisms underlying the pain in depression patients.
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Affiliation(s)
- Zhen Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Huijie Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chun'e Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yujing Chen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jingxi Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yao Yao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.
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The sodium proton exchanger NHE9 regulates phagosome maturation and bactericidal activity in macrophages. J Biol Chem 2022; 298:102150. [PMID: 35716776 PMCID: PMC9293770 DOI: 10.1016/j.jbc.2022.102150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
Acidification of phagosomes is essential for the bactericidal activity of macrophages. Targeting machinery that regulates pH within the phagosomes is a prominent strategy employed by various pathogens that have emerged as major threats to public health. Nascent phagosomes acquire the machinery for pH regulation through a graded maturation process involving fusion with endolysosomes. In addition, meticulous coordination between proton pumping and leakage mechanisms is crucial for maintaining optimal pH within the phagosome. However, relative to mechanisms involved in acidifying the phagosome lumen, little is known about proton leakage pathways in this organelle. Sodium proton transporter NHE9 is a known proton leakage pathway located on the endosomes. As phagosomes acquire proteins through fusions with endosomes during maturation, NHE9 seemed a promising candidate for regulating proton fluxes on the phagosome. Here, using genetic and biophysical approaches, we show NHE9 is an important proton leakage pathway associated with the maturing phagosome. NHE9 is highly expressed in immune cells, specifically macrophages; however, NHE9 expression is strongly downregulated upon bacterial infection. We show that compensatory ectopic NHE9 expression hinders the directed motion of phagosomes along microtubules and promotes early detachment from the microtubule tracks. As a result, these phagosomes have shorter run lengths and are not successful in reaching the lysosome. In accordance with this observation, we demonstrate that NHE9 expression levels negatively correlate with bacterial survival. Together, our findings show that NHE9 regulates lumenal pH to affect phagosome maturation, and consequently, microbicidal activity in macrophages.
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5
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Shen L, Zhang H, Lin J, Gao Y, Chen M, Khan NU, Tang X, Hong Q, Feng C, Zhao Y, Cao X. A Combined Proteomics and Metabolomics Profiling to Investigate the Genetic Heterogeneity of Autistic Children. Mol Neurobiol 2022; 59:3529-3545. [PMID: 35348996 DOI: 10.1007/s12035-022-02801-x] [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: 10/08/2021] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Abstract
Autism spectrum disorder (ASD) has become one of the most common neurological developmental disorders in children. However, the study of ASD diagnostic markers faces significant challenges due to the existence of heterogeneity. In this study, genetic testing was performed on children who were clinically diagnosed with ASD. Children with ASD susceptibility genes and healthy controls were studied. The proteomics of plasma and peripheral blood mononuclear cells (PBMCs) as well as plasma metabolomics were carried out. The results showed that although there was genetic heterogeneity in children with ASD, the differentially expressed proteins (DEPs) in plasma, peripheral blood mononuclear cells, and differential metabolites in plasma could still effectively distinguish autistic children from controls. The mechanism associated with them focuses on several common and previously reported mechanisms of ASD. The biomarkers for ASD diagnosis could be found by taking differentially expressed proteins and differential metabolites into consideration. Integrating omics data, glycerophospholipid metabolism and N-glycan biosynthesis might play a critical role in the pathogenesis of ASD.
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Affiliation(s)
- Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Huajie Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China.,Brain Disease and Big Data Research Institute, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Jing Lin
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China.,Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, People's Republic of China
| | - Yan Gao
- Maternal and Child Health Hospital of Baoan, Shenzhen, 518100, People's Republic of China
| | - Margy Chen
- Department of Psychology, Emory University, Atlanta, GA, 30322, USA
| | - Naseer Ullah Khan
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Xiaoxiao Tang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China
| | - Qi Hong
- Maternal and Child Health Hospital of Baoan, Shenzhen, 518100, People's Republic of China
| | - Chengyun Feng
- Maternal and Child Health Hospital of Baoan, Shenzhen, 518100, People's Republic of China
| | - Yuxi Zhao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China.
| | - Xueshan Cao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, People's Republic of China.
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Hearing Function: Identification of New Candidate Genes Further Explaining the Complexity of This Sensory Ability. Genes (Basel) 2021; 12:genes12081228. [PMID: 34440402 PMCID: PMC8394865 DOI: 10.3390/genes12081228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
To date, the knowledge of the genetic determinants behind the modulation of hearing ability is relatively limited. To investigate this trait, we performed Genome-Wide Association Study (GWAS) meta-analysis using genotype and audiometric data (hearing thresholds at 0.25, 0.5, 1, 2, 4, and 8 kHz, and pure-tone averages of thresholds at low, medium, and high frequencies) collected in nine cohorts from Europe, South-Eastern USA, Caucasus, and Central Asia, for an overall number of ~9000 subjects. Three hundred seventy-five genes across all nine analyses were tagged by single nucleotide polymorphisms (SNPs) reaching a suggestive p-value (p < 10−5). Amongst these, 15 were successfully replicated using a gene-based approach in the independent Italian Salus in the Apulia cohort (n = 1774) at the nominal significance threshold (p < 0.05). In addition, the expression level of the replicated genes was assessed in published human and mouse inner ear datasets. Considering expression patterns in humans and mice, eleven genes were considered particularly promising candidates for the hearing function: BNIP3L, ELP5, MAP3K20, MATN2, MTMR7, MYO1E, PCNT, R3HDM1, SLC9A9, TGFB2, and YTHDC2. These findings represent a further contribution to our understanding of the genetic basis of hearing function and its related diseases.
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7
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Halewa J, Marouillat S, Dixneuf M, Thépault RA, Ung DC, Chatron N, Gérard B, Ghoumid J, Lesca G, Till M, Smol T, Couque N, Ruaud L, Chune V, Grotto S, Verloes A, Vuillaume ML, Toutain A, Raynaud M, Laumonnier F. Novel missense mutations in PTCHD1 alter its plasma membrane subcellular localization and cause intellectual disability and autism spectrum disorder. Hum Mutat 2021; 42:848-861. [PMID: 33856728 PMCID: PMC8359977 DOI: 10.1002/humu.24208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/29/2021] [Accepted: 04/08/2021] [Indexed: 12/22/2022]
Abstract
The X-linked PTCHD1 gene, encoding a synaptic membrane protein, has been involved in neurodevelopmental disorders with the description of deleterious genomic microdeletions or truncating coding mutations. Missense variants were also identified, however, without any functional evidence supporting their pathogenicity level. We investigated 13 missense variants of PTCHD1, including eight previously described (c.152G>A,p.(Ser51Asn); c.217C>T,p.(Leu73Phe); c.517A>G,p.(Ile173Val); c.542A>C,p.(Lys181Thr); c.583G>A,p.(Val195Ile); c.1076A>G,p.(His359Arg); c.1409C>A,p.(Ala470Asp); c.1436A>G,p.(Glu479Gly)), and five novel ones (c.95C>T,p.(Pro32Leu); c.95C>G,p.(Pro32Arg); c.638A>G,p.(Tyr213Cys); c.898G>C,p.(Gly300Arg); c.928G>C,p.(Ala310Pro)) identified in male patients with intellectual disability (ID) and/or autism spectrum disorder (ASD). Interestingly, several of these variants involve amino acids localized in structural domains such as transmembrane segments. To evaluate their potentially deleterious impact on PTCHD1 protein function, we performed in vitro overexpression experiments of the wild-type and mutated forms of PTCHD1-GFP in HEK 293T and in Neuro-2a cell lines as well as in mouse hippocampal primary neuronal cultures. We found that six variants impaired the expression level of the PTCHD1 protein, and were retained in the endoplasmic reticulum suggesting abnormal protein folding. Our functional analyses thus provided evidence of the pathogenic impact of missense variants in PTCHD1, which reinforces the involvement of the PTCHD1 gene in ID and in ASD.
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Affiliation(s)
- Judith Halewa
- UMR1253, iBrain, INSERM, University of Tours, Tours, France
| | | | - Manon Dixneuf
- UMR1253, iBrain, INSERM, University of Tours, Tours, France
| | | | - Dévina C Ung
- UMR1253, iBrain, INSERM, University of Tours, Tours, France
| | - Nicolas Chatron
- Department of Genetics, Hospices Civils de Lyon, Lyon, France.,Institut NeuroMyoGène, CNRS UMR-5310, INSERM U-1217, Univ Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Bénédicte Gérard
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jamal Ghoumid
- EA7364 RADEME, Clinique de Génétique Guy Fontaine, Université de Lille, CHU de Lille, Lille, France
| | - Gaëtan Lesca
- Department of Genetics, Hospices Civils de Lyon, Lyon, France.,Institut NeuroMyoGène, CNRS UMR-5310, INSERM U-1217, Univ Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Marianne Till
- Department of Genetics, Hospices Civils de Lyon, Lyon, France
| | - Thomas Smol
- EA7364 RADEME, Institut de Génétique Médicale, Université de Lille, CHU de Lille, Lille, France
| | - Nathalie Couque
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France
| | - Lyse Ruaud
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France.,INSERM, UMR1141, Denis Diderot School of Medicine, Paris University, Paris, France
| | - Valérie Chune
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France
| | - Sarah Grotto
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France.,INSERM, UMR1141, Denis Diderot School of Medicine, Paris University, Paris, France
| | - Alain Verloes
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France.,INSERM, UMR1141, Denis Diderot School of Medicine, Paris University, Paris, France
| | - Marie-Laure Vuillaume
- UMR1253, iBrain, INSERM, University of Tours, Tours, France.,Service de Génétique, Centre hospitalier régional universitaire de Tours, Tours, France
| | - Annick Toutain
- UMR1253, iBrain, INSERM, University of Tours, Tours, France.,Service de Génétique, Centre hospitalier régional universitaire de Tours, Tours, France
| | - Martine Raynaud
- UMR1253, iBrain, INSERM, University of Tours, Tours, France.,Service de Génétique, Centre hospitalier régional universitaire de Tours, Tours, France
| | - Frédéric Laumonnier
- UMR1253, iBrain, INSERM, University of Tours, Tours, France.,Service de Génétique, Centre hospitalier régional universitaire de Tours, Tours, France
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8
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Winklemann I, Matsuoka R, Meier PF, Shutin D, Zhang C, Orellana L, Sexton R, Landreh M, Robinson CV, Beckstein O, Drew D. Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9. EMBO J 2020; 39:e105908. [PMID: 33118634 PMCID: PMC7737618 DOI: 10.15252/embj.2020105908] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/21/2022] Open
Abstract
Na+ /H+ exchangers (NHEs) are ancient membrane-bound nanomachines that work to regulate intracellular pH, sodium levels and cell volume. NHE activities contribute to the control of the cell cycle, cell proliferation, cell migration and vesicle trafficking. NHE dysfunction has been linked to many diseases, and they are targets of pharmaceutical drugs. Despite their fundamental importance to cell homeostasis and human physiology, structural information for the mammalian NHE was lacking. Here, we report the cryogenic electron microscopy structure of NHE isoform 9 (SLC9A9) from Equus caballus at 3.2 Å resolution, an endosomal isoform highly expressed in the brain and associated with autism spectrum (ASD) and attention deficit hyperactivity (ADHD) disorders. Despite low sequence identity, the NHE9 architecture and ion-binding site are remarkably similar to distantly related bacterial Na+ /H+ antiporters with 13 transmembrane segments. Collectively, we reveal the conserved architecture of the NHE ion-binding site, their elevator-like structural transitions, the functional implications of autism disease mutations and the role of phosphoinositide lipids to promote homodimerization that, together, have important physiological ramifications.
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Affiliation(s)
- Iven Winklemann
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Rei Matsuoka
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Pascal F Meier
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Denis Shutin
- Department of ChemistryUniversity of OxfordOxfordUK
| | - Chenou Zhang
- Department of PhysicsCenter for Biological PhysicsArizona State UniversityTempeAZUSA
| | - Laura Orellana
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Ricky Sexton
- Department of PhysicsCenter for Biological PhysicsArizona State UniversityTempeAZUSA
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstituteStockholmSweden
| | | | - Oliver Beckstein
- Department of PhysicsCenter for Biological PhysicsArizona State UniversityTempeAZUSA
| | - David Drew
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
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9
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Patak J, Faraone SV, Zhang-James Y. Sodium hydrogen exchanger 9 NHE9 (SLC9A9) and its emerging roles in neuropsychiatric comorbidity. Am J Med Genet B Neuropsychiatr Genet 2020; 183:289-305. [PMID: 32400953 DOI: 10.1002/ajmg.b.32787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 12/09/2019] [Accepted: 02/22/2020] [Indexed: 12/16/2022]
Abstract
Variations in SLC9A9 gene expression and protein function are associated with multiple human diseases, which range from Attention-deficit/hyperactivity disorder (ADHD) to glioblastoma multiforme. In an effort to determine the full spectrum of human disease associations with SLC9A9, we performed a systematic review of the literature. We also review SLC9A9's biochemistry, protein structure, and function, as well as its interacting partners with the goal of identifying mechanisms of disease and druggable targets. We report gaps in the literature regarding the genes function along with consistent trends in disease associations that can be used to further research into treating the respective diseases. We report that SLC9A9 has strong associations with neuropsychiatric diseases and various cancers. Interestingly, we find strong overlap in SLC9A9 disease associations and propose a novel role for SLC9A9 in neuropsychiatric comorbidity. In conclusion, SLC9A9 is a multifunctional protein that, through both its endosome regulatory function and its protein-protein interaction network, has the ability to modulate signaling axes, such as the PI3K pathway, among others.
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Affiliation(s)
- Jameson Patak
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York, USA.,College of Medicine, MD Program, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Stephen V Faraone
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York, USA.,Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Yanli Zhang-James
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York, USA
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10
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Murtaza N, Uy J, Singh KK. Emerging proteomic approaches to identify the underlying pathophysiology of neurodevelopmental and neurodegenerative disorders. Mol Autism 2020; 11:27. [PMID: 32317014 PMCID: PMC7171839 DOI: 10.1186/s13229-020-00334-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/06/2020] [Indexed: 12/18/2022] Open
Abstract
Proteomics is the large-scale study of the total protein content and their overall function within a cell through multiple facets of research. Advancements in proteomic methods have moved past the simple quantification of proteins to the identification of post-translational modifications (PTMs) and the ability to probe interactions between these proteins, spatially and temporally. Increased sensitivity and resolution of mass spectrometers and sample preparation protocols have drastically reduced the large amount of cells required and the experimental variability that had previously hindered its use in studying human neurological disorders. Proteomics offers a new perspective to study the altered molecular pathways and networks that are associated with autism spectrum disorders (ASD). The differences between the transcriptome and proteome, combined with the various types of post-translation modifications that regulate protein function and localization, highlight a novel level of research that has not been appropriately investigated. In this review, we will discuss strategies using proteomics to study ASD and other neurological disorders, with a focus on how these approaches can be combined with induced pluripotent stem cell (iPSC) studies. Proteomic analysis of iPSC-derived neurons have already been used to measure changes in the proteome caused by patient mutations, analyze changes in PTMs that resulted in altered biological pathways, and identify potential biomarkers. Further advancements in both proteomic techniques and human iPSC differentiation protocols will continue to push the field towards better understanding ASD disease pathophysiology. Proteomics using iPSC-derived neurons from individuals with ASD offers a window for observing the altered proteome, which is necessary in the future development of therapeutics against specific targets.
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Affiliation(s)
- Nadeem Murtaza
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Jarryll Uy
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada
| | - Karun K Singh
- Stem Cell and Cancer Research Institute, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 3Z5, Canada.
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11
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Franke B, Banaschewski T, Rohde LA, Gerlach M. Special edition on the occasion of Jan K. Buitelaar’s 65th anniversary. ACTA ACUST UNITED AC 2019; 11:1-3. [DOI: 10.1007/s12402-019-00290-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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