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Abedini SS, Akhavantabasi S, Liang Y, Heng JIT, Alizadehsani R, Dehzangi I, Bauer DC, Alinejad-Rokny H. A critical review of the impact of candidate copy number variants on autism spectrum disorder. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 794:108509. [PMID: 38977176 DOI: 10.1016/j.mrrev.2024.108509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/14/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder (NDD) influenced by genetic, epigenetic, and environmental factors. Recent advancements in genomic analysis have shed light on numerous genes associated with ASD, highlighting the significant role of both common and rare genetic mutations, as well as copy number variations (CNVs), single nucleotide polymorphisms (SNPs) and unique de novo variants. These genetic variations disrupt neurodevelopmental pathways, contributing to the disorder's complexity. Notably, CNVs are present in 10 %-20 % of individuals with autism, with 3 %-7 % detectable through cytogenetic methods. While the role of submicroscopic CNVs in ASD has been recently studied, their association with genomic loci and genes has not been thoroughly explored. In this review, we focus on 47 CNV regions linked to ASD, encompassing 1632 genes, including protein-coding genes and long non-coding RNAs (lncRNAs), of which 659 show significant brain expression. Using a list of ASD-associated genes from SFARI, we detect 17 regions harboring at least one known ASD-related protein-coding gene. Of the remaining 30 regions, we identify 24 regions containing at least one protein-coding gene with brain-enriched expression and a nervous system phenotype in mouse mutants, and one lncRNA with both brain-enriched expression and upregulation in iPSC to neuron differentiation. This review not only expands our understanding of the genetic diversity associated with ASD but also underscores the potential of lncRNAs in contributing to its etiology. Additionally, the discovered CNVs will be a valuable resource for future diagnostic, therapeutic, and research endeavors aimed at prioritizing genetic variations in ASD.
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Affiliation(s)
- Seyedeh Sedigheh Abedini
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; School of Biotechnology & Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Shiva Akhavantabasi
- Department of Molecular Biology and Genetics, Yeni Yuzyil University, Istanbul, Turkey; Ghiaseddin Jamshid Kashani University, Andisheh University Town, Danesh Blvd, 3441356611, Abyek, Qazvin, Iran
| | - Yuheng Liang
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Julian Ik-Tsen Heng
- Curtin Health Innovation Research Institute, Curtin University, Bentley 6845, Australia
| | - Roohallah Alizadehsani
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria, Australia
| | - Iman Dehzangi
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Computer Science, Rutgers University, Camden, NJ 08102, USA
| | - Denis C Bauer
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia; Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, Australia
| | - Hamid Alinejad-Rokny
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; Tyree Institute of Health Engineering (IHealthE), UNSW Sydney, Sydney, NSW 2052, Australia.
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Drozd CJ, Chowdhury TA, Quinn CC. UNC-16 interacts with LRK-1 and WDFY-3 to regulate the termination of axon growth. Genetics 2024; 227:iyae053. [PMID: 38581414 PMCID: PMC11151918 DOI: 10.1093/genetics/iyae053] [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: 02/27/2024] [Revised: 02/27/2024] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
In humans, MAPK8IP3 (also known as JIP3) is a neurodevelopmental disorder-associated gene. In Caenorhabditis elegans, the UNC-16 ortholog of the MAPK8IP3 protein can regulate the termination of axon growth. However, its role in this process is not well understood. Here, we report that UNC-16 promotes axon termination through a process that includes the LRK-1 (LRRK-1/LRRK-2) kinase and the WDFY-3 (WDFY3/Alfy) selective autophagy protein. Genetic analysis suggests that UNC-16 promotes axon termination through an interaction between its RH1 domain and the dynein complex. Loss of unc-16 function causes accumulation of late endosomes specifically in the distal axon. Moreover, we observe synergistic interactions between loss of unc-16 function and disruptors of endolysosomal function, indicating that the endolysosomal system promotes axon termination. We also find that the axon termination defects caused by loss of UNC-16 function require the function of a genetic pathway that includes lrk-1 and wdfy-3, 2 genes that have been implicated in autophagy. These observations suggest a model where UNC-16 promotes axon termination by interacting with the endolysosomal system to regulate a pathway that includes LRK-1 and WDFY-3.
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Affiliation(s)
- Cody J Drozd
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | - Tamjid A Chowdhury
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | - Christopher C Quinn
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
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Colaço-Gaspar M, Hofer P, Oberer M, Zechner R. PNPLA-mediated lipid hydrolysis and transacylation - At the intersection of catabolism and anabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159410. [PMID: 37951382 DOI: 10.1016/j.bbalip.2023.159410] [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: 07/31/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
Patatin-like phospholipase domain containing proteins (PNPLAs) play diverse roles in lipid metabolism. In this review, we focus on the enzymatic properties and predicted 3D structures of PNPLA1-5. PNPLA2-4 exert both catabolic and anabolic functions. Whereas PNPLA1 is predominantly expressed in the epidermis and involved in sphingolipid biosynthesis, PNPLA2 and 4 are ubiquitously expressed and exhibit several enzymatic activities, including hydrolysis and transacylation of various (glycero-)lipid species. This review summarizes known biological roles for PNPLA-mediated hydrolysis and transacylation reactions and highlights open questions concerning their physiological function.
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Affiliation(s)
| | - Peter Hofer
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Monika Oberer
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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Drozd CJ, Chowdhury TA, Quinn CC. UNC-16 interacts with LRK-1 and WDFY-3 to regulate the termination of axon growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580526. [PMID: 38405875 PMCID: PMC10888800 DOI: 10.1101/2024.02.15.580526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
MAPK8IP3 (unc-16/JIP3) is a neurodevelopmental-disorder associated gene that can regulate the termination of axon growth. However, its role in this process is not well understood. Here, we report that UNC-16 promotes axon termination through a process that includes the LRK-1(LRRK-1/LRRK-2) kinase and the WDFY-3 (WDFY3/Alfy) selective autophagy protein. Genetic analysis suggests that UNC-16 promotes axon termination through an interaction between its RH1 domain and the dynein complex. Loss of unc-16 function causes accumulation of late endosomes specifically in the distal axon. Moreover, we observe synergistic interactions between loss of unc-16 function and disruptors of endolysosomal function, indicating that the endolysosomal system promotes axon termination. We also find that the axon termination defects caused by loss of UNC-16 function require the function of a genetic pathway that includes lrk-1 and wdfy-3, two genes that have been implicated in autophagy. These observations suggest a model where UNC-16 promotes axon termination by interacting with the endolysosomal system to regulate a pathway that includes LRK-1 and WDFY-3.
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Affiliation(s)
- Cody J. Drozd
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, WI, 53201, U.S.A
| | - Tamjid A. Chowdhury
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, WI, 53201, U.S.A
| | - Christopher C. Quinn
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, WI, 53201, U.S.A
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Park J, Cho YG, Kim JK, Kim HH. STS and PUDP Deletion Identified by Targeted Panel Sequencing with CNV Analysis in X-Linked Ichthyosis: A Case Report and Literature Review. Genes (Basel) 2023; 14:1925. [PMID: 37895274 PMCID: PMC10606178 DOI: 10.3390/genes14101925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
X-linked recessive ichthyosis (XLI) is clinically characterized by dark brown, widespread dryness with polygonal scales. We describe the identification of STS and PUDP deletions using targeted panel sequencing combined with copy-number variation (CNV) analysis in XLI. A 9-month-old infant was admitted for genetic counseling. Since the second day after birth, the infant's skin tended to be dry and polygonal scales had accumulated over the abdomen and upper extremities. The infant's maternal uncle and brother (who had also exhibited similar skin symptoms from birth) presented with polygonal scales on their trunks. CNV analysis revealed a hemizygous deletion spanning 719.3 Kb on chromosome Xp22 (chrX:7,108,996-7,828,312), which included a segment of the STS gene and exhibited a Z ratio of -2 in the proband. Multiplex ligation-dependent probe amplification (MLPA) confirmed this interstitial Xp22.31 deletion. Our report underscores the importance of implementing CNV screening techniques, including sequencing data analysis and gene dosage assays such as MLPA, to detect substantial deletions that encompass the STS gene region of Xq22 in individuals suspected of having XLI.
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Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea; (J.P.); (Y.G.C.)
| | - Yong Gon Cho
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea; (J.P.); (Y.G.C.)
| | - Jin Kyu Kim
- Department of Pediatrics, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
| | - Hyun Ho Kim
- Department of Pediatrics, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
- Research Institute of Clinical Medicine, Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
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Ben-Mahmoud A, Kishikawa S, Gupta V, Leach NT, Shen Y, Moldovan O, Goel H, Hopper B, Ranguin K, Gruchy N, Maas SM, Lacassie Y, Kim SH, Kim WY, Quade BJ, Morton CC, Kim CH, Layman LC, Kim HG. A cryptic microdeletion del(12)(p11.21p11.23) within an unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome. Sci Rep 2023; 13:12984. [PMID: 37563198 PMCID: PMC10415337 DOI: 10.1038/s41598-023-40037-4] [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: 02/10/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023] Open
Abstract
In a patient diagnosed with both Kallmann syndrome (KS) and intellectual disability (ID), who carried an apparently balanced translocation t(7;12)(q22;q24)dn, array comparative genomic hybridization (aCGH) disclosed a cryptic heterozygous 4.7 Mb deletion del(12)(p11.21p11.23), unrelated to the translocation breakpoint. This novel discovery prompted us to consider the possibility that the combination of KS and neurological disorder in this patient could be attributed to gene(s) within this specific deletion at 12p11.21-12p11.23, rather than disrupted or dysregulated genes at the translocation breakpoints. To further support this hypothesis, we expanded our study by screening five candidate genes at both breakpoints of the chromosomal translocation in a cohort of 48 KS patients. However, no mutations were found, thus reinforcing our supposition. In order to delve deeper into the characterization of the 12p11.21-12p11.23 region, we enlisted six additional patients with small copy number variations (CNVs) and analyzed eight individuals carrying small CNVs in this region from the DECIPHER database. Our investigation utilized a combination of complementary approaches. Firstly, we conducted a comprehensive phenotypic-genotypic comparison of reported CNV cases. Additionally, we reviewed knockout animal models that exhibit phenotypic similarities to human conditions. Moreover, we analyzed reported variants in candidate genes and explored their association with corresponding phenotypes. Lastly, we examined the interacting genes associated with these phenotypes to gain further insights. As a result, we identified a dozen candidate genes: TSPAN11 as a potential KS candidate gene, TM7SF3, STK38L, ARNTL2, ERGIC2, TMTC1, DENND5B, and ETFBKMT as candidate genes for the neurodevelopmental disorder, and INTS13, REP15, PPFIBP1, and FAR2 as candidate genes for KS with ID. Notably, the high-level expression pattern of these genes in relevant human tissues further supported their candidacy. Based on our findings, we propose that dosage alterations of these candidate genes may contribute to sexual and/or cognitive impairments observed in patients with KS and/or ID. However, the confirmation of their causal roles necessitates further identification of point mutations in these candidate genes through next-generation sequencing.
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Affiliation(s)
- Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Shotaro Kishikawa
- Gene Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Natalia T Leach
- Integrated Genetics, Laboratory Corporation of America Holdings, 3400 Computer Drive, Westborough, MA, 01581, USA
| | - Yiping Shen
- Division of Genetics and Genomics at Boston Children's Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Oana Moldovan
- Medical Genetics Service, Pediatric Department, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Himanshu Goel
- Hunter Genetics, Waratah, NSW, 2298, Australia
- University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Bruce Hopper
- Forster Genetics-Hunter New England Local Health District, Forster, NSW, 2428, Australia
| | - Kara Ranguin
- Department of Genetics, Reference Center for Rare Diseases of Developmental anomalies and polymalformative syndrome, CHU de Caen Normandie, Caen, France
| | - Nicolas Gruchy
- Department of Genetics, Reference Center for Rare Diseases of Developmental anomalies and polymalformative syndrome, CHU de Caen Normandie, Caen, France
| | - Saskia M Maas
- Department of Human Genetics, Amsterdam University Medical Center, Amsterdam, the Netherlands
- Reproduction and Development Research Institute, University of Amsterdam, Amsterdam, the Netherlands
| | - Yves Lacassie
- Division of Genetics, Department of Pediatrics, Louisiana State University, New Orleans, LA, 70118, USA
| | - Soo-Hyun Kim
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Woo-Yang Kim
- Department of Biological Sciences, Kent State University, Kent, OH, 44242, USA
| | - Bradley J Quade
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Cynthia C Morton
- Departments of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, UK
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, USA
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, USA
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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Cediel-Ulloa A, Lindner S, Rüegg J, Broberg K. Epigenetics of methylmercury. Neurotoxicology 2023; 97:34-46. [PMID: 37164037 DOI: 10.1016/j.neuro.2023.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023]
Abstract
PURPOSE OF REVIEW Methylmercury (MeHg) is neurotoxic at high levels and particularly affects the developing brain. One proposed mechanism of MeHg neurotoxicity is alteration of the epigenetic programming. In this review, we summarise the experimental and epidemiological literature on MeHg-associated epigenetic changes. RECENT FINDINGS Experimental and epidemiological studies have identified changes in DNA methylation following in utero exposure to MeHg, and some of the changes appear to be persistent. A few studies have evaluated associations between MeHg-related changes in DNA methylation and neurodevelopmental outcomes. Experimental studies reveal changes in histone modifications after MeHg exposure, but we lack epidemiological studies supporting such changes in humans. Experimental and epidemiological studies have identified microRNA-related changes associated with MeHg; however, more research is needed to conclude if these changes lead to persistent and toxic effects. SUMMARY MeHg appears to interfere with epigenetic processes, potentially leading to persistent changes. However, observed associations of mercury with epigenetic changes are as of yet of unknown relevance to neurodevelopmental outcomes.
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Affiliation(s)
- Andrea Cediel-Ulloa
- Department of Organism Biology, Uppsala University, Kåbovägen 4, 752 36 Uppsala, Sweden
| | - Sabrina Lindner
- Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Joëlle Rüegg
- Department of Organism Biology, Uppsala University, Kåbovägen 4, 752 36 Uppsala, Sweden
| | - Karin Broberg
- Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden; Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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Zhang X, Li J, Zhang L, Liu H, Yi H, Liang M, Luo J, Li J, Dong Y. Prenatally detected six duplications at Xp22.33-p11.22: a case report. BMC Pregnancy Childbirth 2023; 23:294. [PMID: 37106349 PMCID: PMC10134624 DOI: 10.1186/s12884-023-05627-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND The discrepancy between the results of cytogenetics and the results of chromosome microarray analysis (CMA) has often led to confusion over genetic counselling for prenatal diagnosis. CASE PRESENTATION The prenatal ultrasound results of a congenital heart defect (CHD) foetus displayed an apartial endocardial pad defect and permanently dilated coronary sinus and left superior vena cava at 21 weeks of gestation. Cytogenetic analysis, CMA, fluorescent in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA) with foetal cord blood samples were used to detect the genetic aetiology. Routine G-binding cytogenetic analysis showed normal karyotypes in both the foetus' and parents' blood samples. CMA results demonstrated that there were 53.973-Mb recurrent CNVs at Xp22.33-p11.22, as confirmed by MLPA assay. CONCLUSIONS Herein, we described the CNV of six duplications at Xp22.33-p11.22 and the 53.973 Mb duplication CNV that was not found in foetal cord blood samples by conventional cytogenetic methods, and it was confirmed by CMA and MLPA. Our novel findings will provide helpful information for prenatal diagnosis and genetic counselling for foetal CHDs.
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Affiliation(s)
- Xue Zhang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Yuzhong, Chongqing, 400016, People's Republic of China
- Chongqing Fetal Medical Centre, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Jian Li
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Yuzhong, Chongqing, 400016, People's Republic of China
- Chongqing Fetal Medical Centre, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Lan Zhang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Yuzhong, Chongqing, 400016, People's Republic of China
- Chongqing Fetal Medical Centre, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Hongli Liu
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Yuzhong, Chongqing, 400016, People's Republic of China
- Chongqing Fetal Medical Centre, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Hong Yi
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Yuzhong, Chongqing, 400016, People's Republic of China
- Chongqing Fetal Medical Centre, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Mingxing Liang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Yuzhong, Chongqing, 400016, People's Republic of China
- Chongqing Fetal Medical Centre, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Jianyu Luo
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Yuzhong, Chongqing, 400016, People's Republic of China
- Chongqing Fetal Medical Centre, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Junnan Li
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Yuzhong, Chongqing, 400016, People's Republic of China
- Chongqing Fetal Medical Centre, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Yanling Dong
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Yuzhong, Chongqing, 400016, People's Republic of China.
- Chongqing Fetal Medical Centre, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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Hu H, Huang Y, Hou R, Xu H, Liu Y, Liao X, Xu J, Jiang L, Wang D. Xp22.31 copy number variations in 87 fetuses: refined genotype-phenotype correlations by prenatal and postnatal follow-up. BMC Med Genomics 2023; 16:69. [PMID: 37013593 PMCID: PMC10069036 DOI: 10.1186/s12920-023-01493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Xp22.31 deletion and duplication have been described in various studies, but different laboratories interpret pathogenicity differently. OBJECTIVES Our study aimed to refine the genotype-phenotype associations between Xp22.31 copy number variants in fetuses, with the aim of providing data support to genetic counseling. METHODS We retrospectively analyzed karyotyping and single nucleotide polymorphism array results from 87 fetuses and their family members. Phenotypic data were obtained through follow-up visits. RESULTS The percentage of fetuses carrying the Xp22.31 deletions (9 females, 12 males) was 24.1% (n = 21), while duplications (38 females, 28 males) accounted for 75.9% (n = 66). Here, we noted that the typical region (from 6.4 to 8.1 Mb, hg19) was detected in the highest ratio, either in the fetuses with deletions (76.2%, 16 of 21) or duplications (69.7%, 46 of 66). In female deletion carriers, termination of pregnancy was chosen for two fetuses, and the remaining seven were born without distinct phenotypic abnormalities. In male deletion carriers, termination of pregnancy was chosen for four fetuses, and the remaining eight of them displayed ichthyosis without neurodevelopmental anomalies. In two of these cases, the chromosomal imbalance was inherited from the maternal grandfathers, who also only had ichthyosis phenotypes. Among the 66 duplication carriers, two cases were lost at follow-up, and pregnancy was terminated for eight cases. There were no other clinical findings in the rest of the 56 fetuses, including two with Xp22.31 tetrasomy, for either male or female carriers. CONCLUSION Our observations provide support for genetic counseling in male and female carriers of Xp22.31 copy number variants. Most of them are asymptomatic in male deletion carriers, except for skin findings. Our study is consistent with the view that the Xp22.31 duplication may be a benign variant in both sexes.
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Affiliation(s)
- Huamei Hu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yulin Huang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Renke Hou
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Huanhuan Xu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yalan Liu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xueqian Liao
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Juchun Xu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Lupin Jiang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
| | - Dan Wang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
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Ben-Mahmoud A, Kishikawa S, Gupta V, Leach NT, Shen Y, Moldovan O, Goel H, Hopper B, Ranguin K, Gruchy N, Maas SM, Lacassie Y, Kim SH, Kim WY, Quade BJ, Morton CC, Kim CH, Layman LC, Kim HG. A microdeletion del(12)(p11.21p11.23) with a cryptic unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome. RESEARCH SQUARE 2023:rs.3.rs-2572736. [PMID: 37034680 PMCID: PMC10081357 DOI: 10.21203/rs.3.rs-2572736/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
In an apparently balanced translocation t(7;12)(q22;q24)dn exhibiting both Kallmann syndrome (KS) and intellectual disability (ID), we detected a cryptic heterozygous 4.7 Mb del(12)(p11.21p11.23) unrelated to the translocation breakpoint. This new finding raised the possibility that KS combined with neurological disorder in this patient could be caused by gene(s) within this deletion at 12p11.21-12p11.23 instead of disrupted or dysregulated genes at the genomic breakpoints. Screening of five candidate genes at both breakpoints in 48 KS patients we recruited found no mutation, corroborating our supposition. To substantiate this hypothesis further, we recruited six additional subjects with small CNVs and analyzed eight individuals carrying small CNVs in this region from DECIPHER to dissect 12p11.21-12p11.23. We used multiple complementary approaches including a phenotypic-genotypic comparison of reported cases, a review of knockout animal models recapitulating the human phenotypes, and analyses of reported variants in the interacting genes with corresponding phenotypes. The results identified one potential KS candidate gene ( TSPAN11 ), seven candidate genes for the neurodevelopmental disorder ( TM7SF3 , STK38L , ARNTL2 , ERGIC2 , TMTC1 , DENND5B , and ETFBKMT ), and four candidate genes for KS with ID ( INTS13 , REP15 , PPFIBP1 , and FAR2 ). The high-level expression pattern in the relevant human tissues further suggested the candidacy of these genes. We propose that the dosage alterations of the candidate genes may contribute to sexual and/or cognitive impairment in patients with KS and/or ID. Further identification of point mutations through next generation sequencing will be necessary to confirm their causal roles.
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Affiliation(s)
| | | | | | | | | | - Oana Moldovan
- Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte
| | | | - Bruce Hopper
- Forster Genetics-Hunter New England Local Health District
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11
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Granata P, Cocciadiferro D, Zito A, Pessina C, Bassani A, Zambonin F, Novelli A, Fasano M, Casalone R. Whole Exome Sequencing in 16p13.11 Microdeletion Patients Reveals New Variants Through Deductive and Systems Medicine Approaches. Front Genet 2022; 13:798607. [PMID: 35368691 PMCID: PMC8965081 DOI: 10.3389/fgene.2022.798607] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/23/2022] [Indexed: 12/20/2022] Open
Abstract
The 16p13.11 microdeletion, whose prevalence in the general population is about 0.04%, is known in literature as a predisposition factor to neurodevelopmental disorders, being found in about 0.13% of patients with schizophrenia, in 0.5–0.6% of patient with epilepsy, cognitive impairment, autism spectrum disorder (ASD) and aggressiveness. The goal of this study was to identify a specific gene set pattern unique for the affected patients in comparison with other familial components. Due to the incomplete penetrance of this copy number variant (CNV), we studied by whole exome sequencing (WES), with particular regard of 850 SFARI genes, three families with an affected member carrier of inherited 16p13.11 and 16p13.11p12.3 microdeletion and one family with an affected member with a de novo 16p13.11 microdeletion. By combining a deductive approach together with personalized network models, we identified gene signatures potentially capable of explaining the clinical phenotype. Candidate variants in genes of interest were identified as possibly involved in determining the neurological phenotype of the four patients, such as compound heterozygosity in CECR2, variants in MTOR and RICTOR genes, compound heterozygous single nucleotide variants in the LRRK2 gene. Moreover, genes present in the microdeletion region were partially present as central nodes, with a focus on NDE1. No additional pathogenetic or uncertain CNVs were found in all four patients. No significant variants were detected in genes included in the microdeletion in patients 1, 2 and 3, excluding the finding of unmasked recessive variants. In conclusion, WES is a fundamental tool in the genetic investigation of patients having a predisposing variant, which is not sufficient to define the clinical phenotype. Moreover, the analysis of WES data using Systems medicine tools, such as personalized network models, led to the prioritization of genes on a high throughput scale and to discover variants in genes that were not prioritized at first.
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Affiliation(s)
- Paola Granata
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Alessandra Zito
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Chiara Pessina
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Alessandro Bassani
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
| | - Fabio Zambonin
- Child Neuropsychiatry Unit, Department of Maternal and Child Health, ASST dei Sette Laghi, Varese, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Mauro Fasano
- Department of Science and High Technology and Center of Bioinformatics, University of Insubria, Busto Arsizio, Italy
- *Correspondence: Mauro Fasano, ; Rosario Casalone,
| | - Rosario Casalone
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
- *Correspondence: Mauro Fasano, ; Rosario Casalone,
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12
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Grabner GF, Xie H, Schweiger M, Zechner R. Lipolysis: cellular mechanisms for lipid mobilization from fat stores. Nat Metab 2021; 3:1445-1465. [PMID: 34799702 DOI: 10.1038/s42255-021-00493-6] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
The perception that intracellular lipolysis is a straightforward process that releases fatty acids from fat stores in adipose tissue to generate energy has experienced major revisions over the last two decades. The discovery of new lipolytic enzymes and coregulators, the demonstration that lipophagy and lysosomal lipolysis contribute to the degradation of cellular lipid stores and the characterization of numerous factors and signalling pathways that regulate lipid hydrolysis on transcriptional and post-transcriptional levels have revolutionized our understanding of lipolysis. In this review, we focus on the mechanisms that facilitate intracellular fatty-acid mobilization, drawing on canonical and noncanonical enzymatic pathways. We summarize how intracellular lipolysis affects lipid-mediated signalling, metabolic regulation and energy homeostasis in multiple organs. Finally, we examine how these processes affect pathogenesis and how lipolysis may be targeted to potentially prevent or treat various diseases.
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Affiliation(s)
- Gernot F Grabner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Hao Xie
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Martina Schweiger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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13
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Park SJ, Park KH, Bae MH, Kim YM. Developmental Delay in Children with X-Linked Ichthyosis: A Case Series. ANNALS OF CHILD NEUROLOGY 2021. [DOI: 10.26815/acn.2021.00402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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14
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Masih S, Moirangthem A, Phadke SR. Homozygous Missense Variation in PNPLA8 Causes Prenatal-Onset Severe Neurodegeneration. Mol Syndromol 2021; 12:174-178. [PMID: 34177434 DOI: 10.1159/000513524] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
The patatin-like protein family plays an important role in various biological functions including lipid homeostasis, cellular growth, and signaling. Conserved across species, the patatin domain is shared by all 9 members of the PNPLA family without redundancy in the coding sequences. The defective function of PNPLA2, PNPLA6, and PNPLA9 are known to cause mitochondrial-related neurodegeneration. Recently, PNPLA8 has been associated with mitochondrial myopathy and poor weight gain with lactic acidosis in 3 unrelated families. Using whole-exome sequencing, we identified a homozygous novel missense variation c.1874A>G in the patatin domain of PNPLA8. The patient had prenatal-onset severe and progressive neurodegeneration with mortality in infancy.
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Affiliation(s)
- Suzena Masih
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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15
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Zito A, Lualdi M, Granata P, Cocciadiferro D, Novelli A, Alberio T, Casalone R, Fasano M. Gene Set Enrichment Analysis of Interaction Networks Weighted by Node Centrality. Front Genet 2021; 12:577623. [PMID: 33719329 PMCID: PMC7943873 DOI: 10.3389/fgene.2021.577623] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/04/2021] [Indexed: 01/24/2023] Open
Abstract
Gene set enrichment analysis (GSEA) is a powerful tool to associate a disease phenotype to a group of genes/proteins. GSEA attributes a specific weight to each gene/protein in the input list that depends on a metric of choice, which is usually represented by quantitative expression data. However, expression data are not always available. Here, GSEA based on betweenness centrality of a protein–protein interaction (PPI) network is described and applied to two cases, where an expression metric is missing. First, personalized PPI networks were generated from genes displaying alterations (assessed by array comparative genomic hybridization and whole exome sequencing) in four probands bearing a 16p13.11 microdeletion in common and several other point variants. Patients showed disease phenotypes linked to neurodevelopment. All networks were assembled around a cluster of first interactors of altered genes with high betweenness centrality. All four clusters included genes known to be involved in neurodevelopmental disorders with different centrality. Moreover, the GSEA results pointed out to the evidence of “cell cycle” among enriched pathways. Second, a large interaction network obtained by merging proteomics studies on three neurodegenerative disorders was analyzed from the topological point of view. We observed that most central proteins are often linked to Parkinson’s disease. The selection of these proteins improved the specificity of GSEA, with “Metabolism of amino acids and derivatives” and “Cellular response to stress or external stimuli” as top-ranked enriched pathways. In conclusion, betweenness centrality revealed to be a suitable metric for GSEA. Thus, centrality-based GSEA represents an opportunity for precision medicine and network medicine.
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Affiliation(s)
- Alessandra Zito
- Department of Science and High Technology, Center of Bioinformatics, University of Insubria, Busto Arsizio, Italy.,Unit of Cytogenetics and Medical Genetics, ASST dei Sette Laghi, Varese, Italy
| | - Marta Lualdi
- Department of Science and High Technology, Center of Bioinformatics, University of Insubria, Busto Arsizio, Italy
| | - Paola Granata
- Unit of Cytogenetics and Medical Genetics, ASST dei Sette Laghi, Varese, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Tiziana Alberio
- Department of Science and High Technology, Center of Bioinformatics, University of Insubria, Busto Arsizio, Italy
| | - Rosario Casalone
- Unit of Cytogenetics and Medical Genetics, ASST dei Sette Laghi, Varese, Italy
| | - Mauro Fasano
- Department of Science and High Technology, Center of Bioinformatics, University of Insubria, Busto Arsizio, Italy
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16
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Davies W. The contribution of Xp22.31 gene dosage to Turner and Klinefelter syndromes and sex-biased phenotypes. Eur J Med Genet 2021; 64:104169. [PMID: 33610733 DOI: 10.1016/j.ejmg.2021.104169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 02/16/2021] [Indexed: 11/27/2022]
Abstract
Turner syndrome (TS) is a rare developmental condition in females caused by complete, or partial, loss of the second sex chromosome; it is associated with a number of phenotypes including short stature, ovarian failure and infertility, as well as neurobehavioural and cognitive manifestations. In contrast, Klinefelter syndrome (KS) arises from an excess of X chromosome material in males (typical karyotype is 47,XXY); like TS, KS is associated with infertility and hormonal imbalance, and behavioural/neurocognitive differences from gonadal sex-matched counterparts. Lower dosage of genes that escape X-inactivation may partially explain TS phenotypes, whilst overdosage of these genes may contribute towards KS-related symptoms. Here, I discuss new findings from individuals with deletions or duplications limited to Xp22.31 (a region escaping X-inactivation), and consider the extent to which altered gene dosage within this small interval (and of the steroid sulfatase (STS) gene in particular) may influence the phenotypic profiles of TS and KS. The expression of X-escapees can be higher in female than male tissues; I conclude by considering how lower Xp22.31 gene dosage in males may increase their likelihood of exhibiting particular phenotypes relative to females. Understanding the genetic contribution to specific phenotypes in rare disorders such as TS and KS, and to more common sex-biased phenotypes, will be important for developing more effective, and more personalised, therapeutic approaches.
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Affiliation(s)
- William Davies
- School of Psychology, Cardiff University, Cardiff, UK; Division of Psychological Medicine and Clinical Neurosciences and Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK; Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK.
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