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Morani F, Doccini S, Galatolo D, Pezzini F, Soliymani R, Simonati A, Lalowski MM, Gemignani F, Santorelli FM. Integrative Organelle-Based Functional Proteomics: In Silico Prediction of Impaired Functional Annotations in SACS KO Cell Model. Biomolecules 2022; 12:biom12081024. [PMID: 35892334 PMCID: PMC9331974 DOI: 10.3390/biom12081024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 02/07/2023] Open
Abstract
Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is an inherited neurodegenerative disease characterized by early-onset spasticity in the lower limbs, axonal-demyelinating sensorimotor peripheral neuropathy, and cerebellar ataxia. Our understanding of ARSACS (genetic basis, protein function, and disease mechanisms) remains partial. The integrative use of organelle-based quantitative proteomics and whole-genome analysis proposed in the present study allowed identifying the affected disease-specific pathways, upstream regulators, and biological functions related to ARSACS, which exemplify a rationale for the development of improved early diagnostic strategies and alternative treatment options in this rare condition that currently lacks a cure. Our integrated results strengthen the evidence for disease-specific defects related to bioenergetics and protein quality control systems and reinforce the role of dysregulated cytoskeletal organization in the pathogenesis of ARSACS.
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Affiliation(s)
- Federica Morani
- Department of Biology, University of Pisa, 56126 Pisa, Italy; (F.M.); (F.G.)
| | - Stefano Doccini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit—IRCCS Stella Maris, 56128 Pisa, Italy; (S.D.); (D.G.)
| | - Daniele Galatolo
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit—IRCCS Stella Maris, 56128 Pisa, Italy; (S.D.); (D.G.)
| | - Francesco Pezzini
- Department of Surgery, Dentistry, Paediatrics and Gynaecology, University of Verona, 37129 Verona, Italy; (F.P.); (A.S.)
| | - Rabah Soliymani
- HiLIFE, Meilahti Clinical Proteomics Core Facility, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland; (R.S.); (M.M.L.)
| | - Alessandro Simonati
- Department of Surgery, Dentistry, Paediatrics and Gynaecology, University of Verona, 37129 Verona, Italy; (F.P.); (A.S.)
| | - Maciej M. Lalowski
- HiLIFE, Meilahti Clinical Proteomics Core Facility, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland; (R.S.); (M.M.L.)
- Institute of Bioorganic Chemistry, PAS, Department of Biomedical Proteomics, 61-704 Poznań, Poland
| | - Federica Gemignani
- Department of Biology, University of Pisa, 56126 Pisa, Italy; (F.M.); (F.G.)
| | - Filippo M. Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit—IRCCS Stella Maris, 56128 Pisa, Italy; (S.D.); (D.G.)
- Correspondence: ; Tel.: +39-050-886311
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Zheng L, Liu J, Niu L, Kamran M, Yang AWH, Jolma A, Dai Q, Hughes TR, Patel DJ, Zhang L, Prasanth SG, Yu Y, Ren A, Lai EC. Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. Genes Dev 2022; 36:225-240. [PMID: 35144965 PMCID: PMC8887127 DOI: 10.1101/gad.348993.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/05/2022] [Indexed: 11/24/2022]
Abstract
The BEN domain is a recently recognized DNA binding module that is present in diverse metazoans and certain viruses. Several BEN domain factors are known as transcriptional repressors, but, overall, relatively little is known of how BEN factors identify their targets in humans. In particular, X-ray structures of BEN domain:DNA complexes are only known for Drosophila factors bearing a single BEN domain, which lack direct vertebrate orthologs. Here, we characterize several mammalian BEN domain (BD) factors, including from two NACC family BTB-BEN proteins and from BEND3, which has four BDs. In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. We conducted detailed functional, genomic, and structural studies of BEND3. We show that BD4 is a major determinant for in vivo association and repression of endogenous BEND3 targets. We obtained a high-resolution structure of BEND3-BD4 bound to its preferred binding site, which reveals how BEND3 identifies cognate DNA targets and shows differences with one of its non-DNA-binding BEN domains (BD1). Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins. Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins.
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Affiliation(s)
- Luqian Zheng
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong 518033, China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jingjing Liu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Lijie Niu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Mohammad Kamran
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ally W H Yang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Arttu Jolma
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Qi Dai
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Dinshaw J Patel
- Structural Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Long Zhang
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong 518033, China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yang Yu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
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3
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Kotian V, Sarmah D, Kaur H, Kesharwani R, Verma G, Mounica L, Veeresh P, Kalia K, Borah A, Wang X, Dave KR, Yavagal DR, Bhattacharya P. Evolving Evidence of Calreticulin as a Pharmacological Target in Neurological Disorders. ACS Chem Neurosci 2019; 10:2629-2646. [PMID: 31017385 DOI: 10.1021/acschemneuro.9b00158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Calreticulin (CALR), a lectin-like ER chaperone, was initially known only for its housekeeping function, but today it is recognized for many versatile roles in different compartments of a cell. Apart from canonical roles in protein folding and calcium homeostasis, it performs a variety of noncanonical roles, mostly in CNS development. In the past, studies have linked Calreticulin with various other biological components which are detrimental in deciding the fate of neurons. Many neurological disorders that differ in their etiology are commonly associated with aberrant levels of Calreticulin, that lead to modulation of apoptosis and phagocytosis, and impact on transcriptional pathways, impairment in proteostatis, and calcium imbalances. Such multifaceted properties of Calreticulin are the reason why it has been implicated in vital roles of the nervous system in recent years. Hence, understanding its role in the physiology of neurons would help to unearth its involvement in the spectrum of neurological disorders. This Review aims toward exploring the interplay of Calreticulin in neurological disorders which would aid in targeting Calreticulin for developing novel neurotherapeutics.
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Affiliation(s)
- Vignesh Kotian
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Deepaneeta Sarmah
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Harpreet Kaur
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Radhika Kesharwani
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Geetesh Verma
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Leela Mounica
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Pabbala Veeresh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Kiran Kalia
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Anupom Borah
- Cellular and Molecular Neurobiology Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, Assam 788011, India
| | - Xin Wang
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Kunjan R. Dave
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
| | - Dileep R. Yavagal
- Department of Neurology and Neurosurgery, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
| | - Pallab Bhattacharya
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
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4
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Emamalizadeh B, Movafagh A, Darvish H, Kazeminasab S, Andarva M, Namdar-Aligoodarzi P, Ohadi M. The human RIT2 core promoter short tandem repeat predominant allele is species-specific in length: a selective advantage for human evolution? Mol Genet Genomics 2017; 292:611-617. [DOI: 10.1007/s00438-017-1294-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022]
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5
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Alelú-Paz R, Carmona FJ, Sanchez-Mut JV, Cariaga-Martínez A, González-Corpas A, Ashour N, Orea MJ, Escanilla A, Monje A, Guerrero Márquez C, Saiz-Ruiz J, Esteller M, Ropero S. Epigenetics in Schizophrenia: A Pilot Study of Global DNA Methylation in Different Brain Regions Associated with Higher Cognitive Functions. Front Psychol 2016; 7:1496. [PMID: 27746755 PMCID: PMC5044511 DOI: 10.3389/fpsyg.2016.01496] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/20/2016] [Indexed: 12/29/2022] Open
Abstract
Attempts to discover genes that are involved in the pathogenesis of major psychiatric disorders have been frustrating and often fruitless. Concern is building about the need to understand the complex ways in which nature and nurture interact to produce mental illness. We analyze the epigenome in several brain regions from schizophrenic patients with severe cognitive impairment using high-resolution (450K) DNA methylation array. We identified 139 differentially methylated CpG sites included in known and novel candidate genes sequences as well as in and intergenic sequences which functions remain unknown. We found that altered DNA methylation is not restricted to a particular region, but includes others such as CpG shelves and gene bodies, indicating the presence of different DNA methylation signatures depending on the brain area analyzed. Our findings suggest that epimutations are not relatables between different tissues or even between tissues' regions, highlighting the need to adequately study brain samples to obtain reliable data concerning the epigenetics of schizophrenia.
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Affiliation(s)
- Raúl Alelú-Paz
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of AlcaláMadrid, Spain; Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, University of AlcaláMadrid, Spain; Department of Psychiatry, CIBERSAM, IRYCIS, Hospital Ramón y CajalMadrid, Spain
| | - Francisco J Carmona
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat Barcelona, Spain
| | - José V Sanchez-Mut
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat Barcelona, Spain
| | - Ariel Cariaga-Martínez
- Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, University of Alcalá Madrid, Spain
| | - Ana González-Corpas
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
| | - Nadia Ashour
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
| | - Maria J Orea
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
| | - Ana Escanilla
- Neurological Brain Bank, Parc Sanitari Sant Joan de Déu Barcelona, Spain
| | - Alfonso Monje
- Neurological Brain Bank, Parc Sanitari Sant Joan de Déu Barcelona, Spain
| | | | - Jerónimo Saiz-Ruiz
- Department of Psychiatry, CIBERSAM, IRYCIS, Hospital Ramón y Cajal Madrid, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de LlobregatBarcelona, Spain; Institució Catalana de Recerca i Estudis AvançatsBarcelona, Spain; Department of Physiological Sciences II, School of Medicine, University of BarcelonaBarcelona, Spain
| | - Santiago Ropero
- Biochemistry and Molecular Biology Unit, Department of Systems Biology, School of Medicine, University of Alcalá Madrid, Spain
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6
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Farashi S, Ohadi M, Hosseinkhani S, Darvish H, Mirabzadeh A. Decreased gene expression activity as a result of a mutation in the calreticulin gene promoter in a family case of schizoaffective disorder. Cogn Neurodyn 2016; 10:269-74. [PMID: 27275382 DOI: 10.1007/s11571-015-9366-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 10/28/2015] [Accepted: 11/05/2015] [Indexed: 12/22/2022] Open
Abstract
Accumulating evidence of population association studies support the hypothesis that the high heritability of major psychiatric disorders is a combination of relatively common alleles of modest effect, and rare alleles some with relatively larger effects. We have previously reported low frequency mutations in the proximal promoter of the human calreticulin (CALR) gene that co-occur with the spectrum of major psychiatric disorders. One of those mutations at -205C>T (rs556992558) was detected in an isolate case of schizoaffective disorder. In the current study, the functional implication of mutation -205T is studied in the human neuronal cell lines LAN-5, BE(2)-C and HEK-293. In contrast with other mutations in the promoter region which increase gene expression activity, the -205T mutation significantly decreased gene expression in those cell lines in comparison with the wild-type -205C nucleotide (p < 0.000001, p < 0.0005, and p < 0.017, respectively). Treatment of the cell lines with the mood-stabilizing drug, valproic acid (VPA) resulted in differential gene expression activity in the mutant -205T versus the wild-type -205C construct. VPA increased gene expression activity in both constructs, while a significantly higher expression activity was observed in the mutant construct (p < 0.01), indicative of the creation of a positive effector binding site for VPA as a result of the -205T mutation. We conclude that deviation from normalcy in the level of CALR in either direction is associated with major psychiatric disorders.
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Affiliation(s)
- S Farashi
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands ; Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran ; Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - S Hosseinkhani
- Department of Biophysics & Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - H Darvish
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences and Health Services, Tehran, Iran
| | - A Mirabzadeh
- Department of Psychiatry, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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7
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Bushehri A, Barez MRM, Mansouri SK, Biglarian A, Ohadi M. Genome-wide identification of human- and primate-specific core promoter short tandem repeats. Gene 2016; 587:83-90. [PMID: 27108803 DOI: 10.1016/j.gene.2016.04.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/23/2016] [Accepted: 04/19/2016] [Indexed: 12/12/2022]
Abstract
Recent reports of a link between human- and primate-specific genetic factors and human/primate-specific characteristics and diseases necessitate genome-wide identification of those factors. We have previously reported core promoter short tandem repeats (STRs) of extreme length (≥6-repeats) that have expanded exceptionally in primates vs. non-primates, and may have a function in adaptive evolution. In the study reported here, we extended our study to the human STRs of ≥3-repeats in the category of penta and hexaucleotide STRs, across the entire human protein coding gene core promoters, and analyzed their status in several superorders and orders of vertebrates, using the Ensembl database. The ConSite software was used to identify the transcription factor (TF) sets binding to those STRs. STR specificity was observed at different levels of human and non-human primate (NHP) evolution. 73% of the pentanucleotide STRs and 68% of the hexanucleotide STRs were found to be specific to human and NHPs. AP-2alpha, Sp1, and MZF were the predominantly selected TFs (90%) binding to the human-specific STRs. Furthermore, the number of TF sets binding to a given STR was found to be a selection factor for that STR. Our findings indicate that selected STRs, the cognate binding TFs, and the number of TF set binding to those STRs function as switch codes at different levels of human and NHP evolution and speciation.
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Affiliation(s)
- A Bushehri
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M R Mashhoudi Barez
- Cell and Molecular Biology Research Center, Department of Anatomy and Biology, Faculty of Medicine, Shahid Beheshti University, Velenjak, Tehran, Iran
| | - S K Mansouri
- Clinical Psychology Department, Faculty of Science and Research, Qazvin Azad University, Qazvin, Iran
| | - A Biglarian
- Department of Biostatistics, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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8
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Aghajanirefah A, Nguyen LN, Ohadi M. BEND3 is involved in the human-specific repression of calreticulin: Implication for the evolution of higher brain functions in human. Gene 2015; 576:577-80. [PMID: 26481236 DOI: 10.1016/j.gene.2015.10.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/01/2015] [Accepted: 10/15/2015] [Indexed: 01/27/2023]
Abstract
Recent emerging evidence indicates that changes in gene expression levels are linked to human evolution. We have previously reported a human-specific nucleotide in the promoter sequence of the calreticulin (CALR) gene at position -220C, which is the site of action of valproic acid. Reversion of this nucleotide to the ancestral A-allele has been detected in patients with degrees of deficit in higher brain cognitive functions. This mutation has since been reported in the 1000 genomes database at an approximate frequency of <0.0004 in humans (rs138452745). In the study reported here, we present update on the status of rs138452745 across evolution, based on the Ensembl and NCBI databases. The DNA pulldown assay was also used to identify the proteins binding to the C- and A-alleles, using two cell lines, SK-N-BE and HeLa. Consistent with our previous findings, the C-allele is human-specific, and the A-allele is the rule across all other species (N=38). This nucleotide resides in a block of 12-nucleotides that is strictly conserved across evolution. The DNA pulldown experiments revealed that in both SK-N-BE and HeLa cells, the transcription repressor BEN domain containing 3 (BEND3) binds to the human-specific C-allele, whereas the nuclear factor I (NFI) family members, NF1A, B, C, and X, specifically bind to the ancestral A-allele. This binding pattern is consistent with a previously reported decreased promoter activity of the C-allele vs. the A-allele. We propose that there is a link between binding of BEND3 to the CALR rs138452745 C-allele and removal of NFI binding site from this nucleotide, and the evolution of human-specific higher brain functions. To our knowledge, CALR rs138452745 is the first instance of enormous nucleotide conservation across evolution, except in the human species.
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Affiliation(s)
- A Aghajanirefah
- Department of Molecular Biology, Faculty of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - L N Nguyen
- Department of Molecular Biology, Faculty of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - M Ohadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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9
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Nikkhah M, Rezazadeh M, Khorram Khorshid HR, Biglarian A, Ohadi M. An exceptionally long CA-repeat in the core promoter of SCGB2B2 links with the evolution of apes and Old World monkeys. Gene 2015; 576:109-14. [PMID: 26437309 DOI: 10.1016/j.gene.2015.09.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 12/31/2022]
Abstract
We have recently reported a genome-scale catalog of human protein-coding genes that contain "exceptionally long" STRs (≥6-repeats) in their core promoter, which may be of selective advantage in this species. At the top of that list, SCGB2B2 (also known as SCGBL), contains one of the longest CA-repeat STRs identified in a human gene core promoter, at 25-repeats. In the study reported here, we analyzed the conservation status of this CA-STR across evolution. The functional implication of this STR to alter gene expression activity was also analyzed in the HEK-293 cell line. We report that the SCGB2B2 core promoter CA-repeat reaches exceptional lengths, ranging from 9- to 25-repeats, across Apes (Hominoids) and the Old World monkeys (CA>2-repeats were not detected in any other species). The longest CA-repeats and highest identity in the SCGB2B2 protein sequence were observed between human and bonobo. A trend for increased gene expression activity was observed from the shorter to the longer CA-repeats (p<0.009), and the CA-repeat increased gene expression activity, per se (p<0.02). We propose that the SCGB2B2 gene core promoter CA-repeat functions as an expression code for the evolution of Apes and the Old World monkeys.
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Affiliation(s)
- M Nikkhah
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Rezazadeh
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Biglarian
- Department of Biostatistics, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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10
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Rezazadeh M, Gharesouran J, Movafagh A, Taheri M, Darvish H, Emamalizadeh B, Shahmohammadibeni N, Khorram Khorshid HR, Behmanesh M, Sahraian MA, Ohadi M. Dominant and Protective Role of the CYTH4 Primate-Specific GTTT-Repeat Longer Alleles Against Neurodegeneration. J Mol Neurosci 2015; 56:593-6. [PMID: 25823437 DOI: 10.1007/s12031-015-0542-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 03/06/2015] [Indexed: 12/25/2022]
Abstract
Primate-specific genes and regulatory mechanisms could provide insight into human brain functioning and disease. In a genome-scale analysis of the entire protein-coding genes listed in the GeneCards database, we have recently reported human genes that contain "exceptionally long" short tandem repeats (STRs) in their core promoter, which may be of adaptive/selective evolutionary advantage in this species. The longest tetra-nucleotide repeat identified in a human gene core promoter belongs to the CYTH4 gene. This GTTT-repeat is specific to Hominidae and Old World monkeys, and the shortest allele of this repeat, (GTTT)6, is linked with neural dysfunction and type I bipolar disorder in human. In the present study, we sought a possibly broader role for the CYTH4 gene core promoter GTTT-repeat in neural functioning and investigated its allelic distribution in a total of 949 human subjects, consisting of two neurodegenerative disorders, multiple sclerosis (MS) (n = 272) and Alzheimer's disease (AD) (n = 257), and controls (n = 420). The range of the alleles of this GTTT-repeat in the human sample studied was between 6- and 9-repeats. The shortest allele, (GTTT)6, was significantly in excess in the MS and AD patients in comparison with the controls (p < 0.004). The 6/6, 6/7, and 7/7 genotypes were in excess in the MS and AD patients, whereas the overall frequency of all other genotypes (consisting of at least one longer allele, i.e., 8- or 9-repeat) was higher in the controls (p < 0.005), indicating a dominant and protective effect for the longer alleles against neurodegeneration. This is the first indication of the involvement of a primate-specific STR in neurodegeneration in humans. We propose an adaptive evolutionary role for the expansion of the CYTH4 gene core promoter GTTT-repeat in the human brain, which is supported by a link between the shortest allele of this repeat with neuropsychiatric disorders.
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Rezazadeh M, Gharesouran J, Mirabzadeh A, Khorram Khorshid HR, Biglarian A, Ohadi M. A primate-specific functional GTTT-repeat in the core promoter of CYTH4 is linked to bipolar disorder in human. Prog Neuropsychopharmacol Biol Psychiatry 2015; 56:161-7. [PMID: 25240857 DOI: 10.1016/j.pnpbp.2014.09.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/10/2014] [Indexed: 12/20/2022]
Abstract
Evidence of primate-specific genes and gene regulatory mechanisms linked to bipolar disorder (BD) lend support to evolutionary/adaptive processes in the pathogenesis of this disorder. Following a genome-scale analysis of the entire protein coding genes annotated in the GeneCards database, we have recently reported that cytohesin-4 (CYTH4) contains the longest tetra-nucleotide short tandem repeat (STR) identified in a human protein-coding gene core promoter, which may be of adaptive advantage to this species. In the current study, we analyzed the evolutionary trend of this STR across evolution. We also analyzed the functional implication and distribution of this STR in a group of patients with type 1 BD (n=233) and controls (n=262). We found that this STR is exceptionally expanded in primates (Fisher exact p<0.00003). Association was observed between type I BD and the 6-repeat allele of this STR, (GTTT)₆ (Yates corrected Χ(2)=12.68, p<0.0001, OR: 1.68). This allele is the shortest length of the GTTT-repeat identified in the human subjects studied. Consistent with that finding, excess homozygosity was observed for the shorter alleles, (GTTT)₆ and (GTTT)₇, vs. the longer alleles, (GTTT)₈ and (GTTT)₉ in the BD group (Yates corrected Χ(2)=5.18, p<0.01, 1 df, OR: 1.96). Using Dual Glo luciferase system in HEK-293 cells, a trend for gene expression repression was observed from the 6- to the 9-repeat allele (p<0.003), and the GTTT-repeat significantly down-regulated gene expression, per se (p<0.0006). This is the first evidence of a link between a primate-specific STR and a major psychiatric disorder in human. It may be speculated that the CYTH4 GTTT-repeat in primates may have conferred selective advantage to this order, reflected in neural function and neurophenotypes. The role of the CYTH4 gene in the pathogenesis of type I BD remains to be clarified in the future studies.
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Abstract
Psychiatric disorders are a diverse set of diseases that affect all aspects of mental function including social interaction, thinking, feeling, and mood. Although psychiatric disorders place a large economic burden on society, the drugs available to treat them are often palliative with variable efficacy and intolerable side-effects. The development of novel drugs has been hindered by a lack of knowledge about the etiology of these diseases. It is thus necessary to further investigate psychiatric disorders using a combination of human molecular genetics, gene-by-environment studies, in vitro pharmacological and biochemistry experiments, animal models, and investigation of the non-biological basis of these diseases, such as environmental effects. Many psychiatric disorders, including autism spectrum disorder, attention-deficit/hyperactivity disorder, mental retardation, and schizophrenia can be triggered by alterations to neural development. The zebrafish is a popular model for developmental biology that is increasingly used to study human disease. Recent work has extended this approach to examine psychiatric disorders as well. However, since psychiatric disorders affect complex mental functions that might be human specific, it is not possible to fully model them in fish. In this review, I will propose that the suitability of zebrafish for developmental studies, and the genetic tools available to manipulate them, provide a powerful model to study the roles of genes that are linked to psychiatric disorders during neural development. The relative speed and ease of conducting experiments in zebrafish can be used to address two areas of future research: the contribution of environmental factors to disease onset, and screening for novel therapeutic compounds.
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Affiliation(s)
- William H J Norton
- Department of Biology, College of Medicine, Biological Sciences and Psychiatry, University of Leicester Leicester, UK
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Kazeminasab S, Esmaeilzadeh-Gharehdaghi E, Oladnabi M, Ohadi M, Mirabzadeh A, Hosseinkhani S. Aberrant expression of Activating Transcription Factor 6 (ATF6) in major psychiatric disorders. Psychiatry Res 2012; 200:1086-7. [PMID: 22572160 DOI: 10.1016/j.psychres.2012.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 04/04/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
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Ohadi M, Mirabzadeh A, Esmaeilzadeh-Gharehdaghi E, Rezazadeh M, Hosseinkhanni S, Oladnabi M, Firouzabadi SG, Darvish H. Novel evidence of the involvement of calreticulin in major psychiatric disorders. Prog Neuropsychopharmacol Biol Psychiatry 2012; 37:276-81. [PMID: 22507216 DOI: 10.1016/j.pnpbp.2012.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/12/2012] [Accepted: 02/14/2012] [Indexed: 12/20/2022]
Abstract
Calreticulin (CALR) is a multi-functional protein that is strictly conserved across species. Two mRNA transcripts have been recognized for the CALR gene in humans, which use a common promoter sequence. We have recently reported mutations in the CALR promoter that co-occur with psychosis. One of those mutations at -220A increases gene expression in human BE(2)-C and HEK-293 cell lines. This mutation is the first instance of a functional cognition-deficit mutation reversing a human gene promoter to the primitive type. In the current study, we analyzed the effect of the most widely-used mood-stabilizing drug, valproic acid (VPA), on nucleotide -220 in two neuronal cell lines, LAN-5 and N2A. Remarkably, VPA increased gene expression in the cells with the wild-type -220C construct, whereas a dramatic decrease in gene expression was observed in the cell lines with the mutant construct (p<0.000004 and p<0.016, respectively). We also sequenced the 600-bp CALR promoter, and the highly conserved intron 1 sequence in an independent sample of patients afflicted with major psychiatric disorders and controls. A new case of major depressive disorder with psychotic features with the -220A mutation was identified. A novel 1-bp insertion was also detected in intron 1 at IVSI-310, in a case of amphetamine-induced psychosis. As for the psychosis-linked CALR promoter mutations identified to-date, the IVSI mutation was not detected in the control pool. This mutation creates a RREB-1 transcription factor binding site within the first intron. Our present findings identify the site of action of VPA in the CALR promoter, and introduce a novel mutation in a case of substance-induced psychosis in the first intron of CALR.
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Affiliation(s)
- M Ohadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Esmaeilzadeh-Gharehdaghi E, Banan M, Farashi S, Mirabzadeh A, Farokhashtiani T, Hosseinkhani S, Heidari A, Najmabadi H, Ohadi M. Support for down-tuning of the calreticulin gene in the process of human evolution. Prog Neuropsychopharmacol Biol Psychiatry 2011; 35:1770-3. [PMID: 21723904 DOI: 10.1016/j.pnpbp.2011.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/07/2011] [Accepted: 06/16/2011] [Indexed: 11/21/2022]
Abstract
Tissue-specific expression of the CALR gene in the brain gray matter in late-adolescence and early adulthood coincides with the expression of the psychoses phenotypes. Indeed, increased expression of the chaperone genes in the prefrontal cortex has been reported in patients affected by schizophrenia. We have previously reported cases of psychosis-associated mutations in the CALR gene promoter. One of those mutations at -48 was found to increase the expression of the gene in comparison with the wild type sequence. A recently identified mutation at -220 reverts the conserved block harboring nucleotide -220 to the ancestral type, and has an approximate prevalence of 0.7% in psychoses. In this study, we analyzed the functional implication of this mutation in the human neuroblastoma cell line BE(2)-C, and non-neural Human Embryonic Kidney 293 (HEK-293), and show that the -220A mutation results in a constitutive increase in the expression of the CALR gene (p<0.0003). We checked homology of the first 1000-bp CALR promoter sequence across species, and found that nucleotide -220C is the only human-unique nucleotide in that stretch. The -220A mutation, on the other hand, co-occurs with severe cognition deficit in humans, and is the rule across the species except humans. To our knowledge, the -220A mutation is the first reported instance of a cognition-deficit-associated mutation which reverses a human gene promoter to the primitive type. It may be speculated that, at least the basal transcription of the CALR gene, relating to the proximal promoter region, has been decreased during the process of evolution to humans.
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