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Lazarev D, Chau G, Bloemendal A, Churchhouse C, Neale BM. GUIDE deconstructs genetic architectures using association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592285. [PMID: 38766146 PMCID: PMC11100597 DOI: 10.1101/2024.05.03.592285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genome-wide association studies have revealed that the genetic architecture of most complex traits is characterized by a large number of distinct effects scattered across the genome. Functional enrichment analyses of these results suggest that the associations for any given complex trait are not purely random. Thus, we set out to leverage the genetic association results from many traits with a view to identifying the set of modules, or latent factors, that mediate these associations. The identification of such modules may aid in disease classification as well as the elucidation of complex disease mechanisms. We propose a method, Genetic Unmixing by Independent Decomposition (GUIDE), to estimate a set of statistically independent latent factors that best express the patterns of association across many traits. The resulting latent factors not only have desirable mathematical properties, such as sparsity and a higher variance explained (for both traits and variants), but are also able to single out and prioritize key biological features or pathophysiological mechanisms underlying a given trait or disease. Moreover, we show that these latent factors can index biological pathways as well as epidemiological and environmental influences that compose the genetic architecture of complex traits.
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Alowaysi M, Al-Shehri M, Badkok A, Attas H, Aboalola D, Baadhaim M, Alzahrani H, Daghestani M, Zia A, Al-Ghamdi K, Al-Ghamdi A, Zakri S, Aouabdi S, Tegner J, Alsayegh K. Generation of iPSC lines (KAIMRCi003A, KAIMRCi003B) from a Saudi patient with Dravet syndrome carrying homozygous mutation in the CPLX1 gene and heterozygous mutation in SCN9A. Hum Cell 2024; 37:502-510. [PMID: 38110787 PMCID: PMC10890977 DOI: 10.1007/s13577-023-01016-z] [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: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 12/20/2023]
Abstract
The most prevalent form of epileptic encephalopathy is Dravet syndrome (DRVT), which is triggered by the pathogenic variant SCN1A in 80% of cases. iPSCs with different SCN1A mutations have been constructed by several groups to model DRVT syndrome. However, no studies involving DRVT-iPSCs with rare genetic variants have been conducted. Here, we established two DRVT-iPSC lines harboring a homozygous mutation in the CPLX1 gene and heterozygous mutation in SCN9A gene. Therefore, the derivation of these iPSC lines provides a unique cellular platform to dissect the molecular mechanisms underlying the cellular dysfunctions consequent to CPLX1 and SCN9A mutations.
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Affiliation(s)
- Maryam Alowaysi
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Mohammad Al-Shehri
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Amani Badkok
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Hanouf Attas
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Doaa Aboalola
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Moayad Baadhaim
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Hajar Alzahrani
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Mustafa Daghestani
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- Department of Pathology and Laboratory Medicine, Ministry of the National Guard-Health Affairs, Jeddah, Saudi Arabia
| | - Asima Zia
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Khalid Al-Ghamdi
- Forensic Laboratories, Criminal Evidence Department, Jeddah, Saudi Arabia
| | - Asayil Al-Ghamdi
- Forensic Laboratories, Criminal Evidence Department, Jeddah, Saudi Arabia
| | - Samer Zakri
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Sihem Aouabdi
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Jesper Tegner
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Khaled Alsayegh
- King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.
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Modzelewski AJ, Shao W, Chen J, Lee A, Qi X, Noon M, Tjokro K, Sales G, Biton A, Anand A, Speed TP, Xuan Z, Wang T, Risso D, He L. A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. Cell 2021; 184:5541-5558.e22. [PMID: 34644528 PMCID: PMC8787082 DOI: 10.1016/j.cell.2021.09.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022]
Abstract
Retrotransposons mediate gene regulation in important developmental and pathological processes. Here, we characterized the transient retrotransposon induction during preimplantation development of eight mammals. Induced retrotransposons exhibit similar preimplantation profiles across species, conferring gene regulatory activities, particularly through long terminal repeat (LTR) retrotransposon promoters. A mouse-specific MT2B2 retrotransposon promoter generates an N-terminally truncated Cdk2ap1ΔN that peaks in preimplantation embryos and promotes proliferation. In contrast, the canonical Cdk2ap1 peaks in mid-gestation and represses cell proliferation. This MT2B2 promoter, whose deletion abolishes Cdk2ap1ΔN production, reduces cell proliferation and impairs embryo implantation, is developmentally essential. Intriguingly, Cdk2ap1ΔN is evolutionarily conserved in sequence and function yet is driven by different promoters across mammals. The distinct preimplantation Cdk2ap1ΔN expression in each mammalian species correlates with the duration of its preimplantation development. Hence, species-specific transposon promoters can yield evolutionarily conserved, alternative protein isoforms, bestowing them with new functions and species-specific expression to govern essential biological divergence.
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Affiliation(s)
- Andrew J Modzelewski
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wanqing Shao
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jingqi Chen
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Angus Lee
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xin Qi
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mackenzie Noon
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kristy Tjokro
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gabriele Sales
- Department of Biology, University of Padova, Padova 35122, Italy
| | - Anne Biton
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA; Bioinformatics and Biostatistics, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris 75015, France
| | - Aparna Anand
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Terence P Speed
- Bioinformatics Division, WEHI, Parkville, VIC 3052, Australia
| | - Zhenyu Xuan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Ting Wang
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova 35122, Italy.
| | - Lin He
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA.
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Al-Shehri M, Baadhaim M, Jamalalddin S, Aboalola D, Daghestani M, AlZahrani H, Malibari D, Mubaraki M, Aldubayan K, AlBalwi M, Alsayegh K. Generation of induced pluripotent stem cell Line KAIMRCi001-A by reprogramming erythroid progenitors from peripheral blood of a healthy Saudi donor. Stem Cell Res 2021; 56:102548. [PMID: 34592601 DOI: 10.1016/j.scr.2021.102548] [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] [Received: 08/10/2021] [Revised: 09/08/2021] [Accepted: 09/19/2021] [Indexed: 11/25/2022] Open
Abstract
In this study we isolated and enriched erythroid progenitor cells (EPCs) from a 10 ml peripheral blood sample from a 37-year old healthy Saudi donor. After expansion, these EPCs were reprogrammed using episomal plasmids to generate an induced pluripotent stem (iPS) cell line, KAIMRCi001-A. The pluripotency of this line was confirmed by measuring the expression of typical pluripotency markers and assessing differentiation potential in vitro.
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Affiliation(s)
- Mohammad Al-Shehri
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard - Health Affairs, Jeddah, Saudi Arabia
| | - Moayad Baadhaim
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard - Health Affairs, Jeddah, Saudi Arabia
| | - Shereen Jamalalddin
- College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Doaa Aboalola
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard - Health Affairs, Jeddah, Saudi Arabia
| | - Mustafa Daghestani
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard - Health Affairs, Jeddah, Saudi Arabia; Department of Pathology and Laboratory Medicine, Ministry of the National Guard-Health Affairs, Jeddah Saudi Arabia
| | - Hajar AlZahrani
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard - Health Affairs, Jeddah, Saudi Arabia
| | - Dalal Malibari
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard - Health Affairs, Jeddah, Saudi Arabia
| | - Mohammad Mubaraki
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), MNGHA, Riyadh 11426, Saudi Arabia; King Abdullah International Medical Research Center, Department of Medical Genomic Research, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Kholoud Aldubayan
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), MNGHA, Riyadh 11426, Saudi Arabia; King Abdullah International Medical Research Center, Department of Medical Genomic Research, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Mohammed AlBalwi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), MNGHA, Riyadh 11426, Saudi Arabia; King Abdullah International Medical Research Center, Department of Medical Genomic Research, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia; College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Khaled Alsayegh
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard - Health Affairs, Jeddah, Saudi Arabia.
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Dehghan Z, Mohammadi-Yeganeh S, Rezaee D, Salehi M. MicroRNA-21 is involved in oocyte maturation, blastocyst formation, and pre-implantation embryo development. Dev Biol 2021; 480:69-77. [PMID: 34411594 DOI: 10.1016/j.ydbio.2021.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 07/25/2021] [Accepted: 08/15/2021] [Indexed: 10/20/2022]
Abstract
Follicular fluid is one source of microRNAs (miRNAs). These miRNAs originate from oocytes and their neighboring cells. The changes in the miRNAs profile in the follicular fluid could alter folliculogenesis and oocyte maturation, and lead to infertility. Polycystic ovary syndrome (PCOS) patients have increased miR-21 levels in their sera, granulosa cells, and follicular fluid, and this mi-RNA plays a role in the pathophysiology and follicular dysfunction of PCOS patients. In the current study, we intend to examine whether expression levels of miR-21 influence oocyte maturation and embryo development. We examined miR-21 over-expression and down-regulation of miR-21 by miR-off 21 during in vitro maturation (IVM) to assess its influence on oocyte maturation and embryo development in mice. Over-expression of miR-21 in cumulus cells decreased expansion, meiotic progression, Glutathione-S-transferase GSH levels, and decreased expressions of Bmpr2 and Ptx3 genes. Subsequently, we noted that in vitro fertilization, and the cleavage rate and blastocyst formation significantly increased in cumulus oocyte complexes (COCs) that over-expressed miR-21. Inhibition of miR-21 by miR-off 21 led to increased cumulus expansion and GSH levels, along with decreased cleavage rate and blastocyst formation by alterations in Cdk2ap1 and Oct4 gene expressions. However, oocyte progression from the germinal vesicle (GV) to the metaphase II (MII) stage was not significant. miR-21 altered the gene expression levels in cumulus cells and influenced cytoplasmic oocyte maturation, cumulus expansion, and subsequent embryonic development in mice.
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Affiliation(s)
- Zeinab Dehghan
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular & Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Mohammadi-Yeganeh
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular & Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Delsuz Rezaee
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular & Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Salehi
- Cellular & Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Medical Biotechnology, School of Advanced Technologies in Medicine Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Xiang B, Wang Q, Lei W, Li M, Li Y, Zhao L, Ma X, Wang Y, Yu H, Li X, Meng Y, Guo W, Deng W, Ren H, Li T. Genes in immune pathways associated with abnormal white matter integrity in first-episode and treatment-naïve patients with schizophrenia. Br J Psychiatry 2019; 214:281-287. [PMID: 30722794 DOI: 10.1192/bjp.2018.297] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Previous studies have inferred a strong genetic component in schizophrenia. However, the genetic variants involved in the susceptibility to schizophrenia remain unclear.AimsTo detect potential gene pathways and networks associated with schizophrenia, and to explore the relationship between common and rare variants in these pathways and abnormal white matter integrity in schizophrenia. METHOD The analysis included 100 first-episode treatment-naïve patients with schizophrenia and 140 healthy controls. A network-based analysis was carried out on the data collected from the Psychiatric Genomics Consortium Phase I (PGC-I). Based on our genome-wide association study and whole-exome sequencing data-sets, we performed a gene-set analysis to detect associations between the combining effects of common and rare genetic variants and abnormal white matter integrity in schizophrenia. RESULTS Patients had significantly reduced functional anisotropy in the left and right anterior cingulate cortex, left and right precuneus and extra-nuclear (t = 4.61-5.10, PFDR < 0.01), compared with controls. Generated from co-expression network analysis of the PGC-1 summary statistics of schizophrenia, a subnetwork of 207 genes associated with schizophrenia was identified (P < 0.01), and 176 genes were co-expressed in four gene modules. Functional enrichment analysis for genes in each module revealed that the yellow module was enriched with highly co-expressed, innate immune response genes. Furthermore, rare variants of enriched genes in the yellow module were associated with reduced functional anisotropy in the left anterior cingulate cortex (P = 0.006; Padjusted = 0.024) in patients only. CONCLUSIONS The pathogenesis of schizophrenia may be substantially influenced by genes involved in the immune system, via both pathway and network.Declaration of interestsNone.
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Affiliation(s)
- Bo Xiang
- Assistant Professor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University; andDepartment of Psychiatry,Affiliated Hospital of Southwest Medical University,China
| | - Qiang Wang
- Professor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Wei Lei
- Assistant Professor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University; andDepartment of Psychiatry,Affiliated Hospital of Southwest Medical University,China
| | - Mingli Li
- Associate Professor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Yinfei Li
- Attending Doctor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Liansheng Zhao
- Assistant Professor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Xiaohong Ma
- Professor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Yingcheng Wang
- Assistant Professor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Hua Yu
- Attending Doctor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Xiaojing Li
- Attending Doctor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Yajing Meng
- Attending Doctor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Wanjun Guo
- Associate Professor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Wei Deng
- Associate Professor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Hongyan Ren
- Attending Doctor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
| | - Tao Li
- Professor,Mental Health Center and Psychiatric Laboratory,State Key Laboratory of Biotherapy,West China Brain Research Center,West China Hospital of Sichuan University,China
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