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Zanobio M, Nardecchia F, Cappuccio G, Onore ME, Di Letto P, Rahman SI, Terrone G, Ugga L, De Giorgi A, Cas MD, Trinchera M, Leuzzi V, Piluso G, Nigro V, Brunetti-Pierri N, TUDP consortium, Torella A. Deletion Testing of the DEGS1 Gene Should Be Part of the Diagnostic Pipeline for Hypomyelinating Leukodystrophy (HLD18). Hum Mutat 2025; 2025:3531508. [PMID: 40371095 PMCID: PMC12077970 DOI: 10.1155/humu/3531508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Accepted: 03/21/2025] [Indexed: 05/16/2025]
Abstract
Hypomyelinating leukodystrophies are a heterogeneous group of disorders characterized by abnormal myelin formation in the central nervous system. Thanks to the increased use of NGS, a growing number of pathogenic single nucleotide variants in DEGS1 have recently been reported to be responsible for hypomyelinating leukodystrophy 18 (HLD18), a rare and severe autosomal recessive form. DEGS1 is a small gene (4 exons and 17 kb) encoding Δ4-dihydroceramide desaturase, which catalyzes the final step in ceramide biosynthesis. Here, we present two patients from unrelated families affected by severe and progressive white matter disease with developmental delay with or without regression and severe intellectual disability. Trio exome sequencing (ES) revealed in both probands two homozygous missense variants in the DEGS1 gene, p.Asp16His and p.Asn255Ser, both inherited from their heterozygous healthy mothers and with a noncarrier father. This curious finding of inconsistent segregation data raises the need for further testing. There is no MLPA test available for this gene, as no deletions have been reported. However, we tried a customized high-resolution 1 M CGH array, which was surprisingly positive in both cases: a 63-kb heterozygous deletion encompassing the entire gene in one proband and a 7-kb heterozygous deletion of Exons 2-3 in the second case. Previously reported cases of HLD18 have all been found to carry single nucleotide pathogenic variants in DEGS1, and the two patients described here are the first to carry whole or partial microdeletions involving DEGS1 that unmask pathogenic missense variants on the other allele. These two cases report the first examples of microdeletions of DEGS1 that unmask recessive allele pathogenic variants, underscoring the importance of considering whole or partial gene deletions in the diagnostic pipeline.
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Affiliation(s)
- Mariateresa Zanobio
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | | | - Gerarda Cappuccio
- Child Neurology, Department of Translational Medicine, Federico II University, Naples, Italy
| | - Maria Elena Onore
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Pasquale Di Letto
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Sarah Iffat Rahman
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Gaetano Terrone
- Child Neurology, Department of Translational Medicine, Federico II University, Naples, Italy
| | - Lorenzo Ugga
- Department of Translational Medicine, University of Naples “Federico II”, Naples, Italy
| | - Agnese De Giorgi
- Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Michele Dei Cas
- Department of Health Sciences, University of Milan, Milano, Italy
| | - Marco Trinchera
- Department of Medicine and Surgery (DMC), University of Insubria, Varese, Italy
| | - Vincenzo Leuzzi
- Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Giulio Piluso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, University of Naples “Federico II”, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | | | - Annalaura Torella
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
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Ma K, Yang X, Mao Y. Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies. Trends Genet 2025; 41:201-217. [PMID: 39627062 DOI: 10.1016/j.tig.2024.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 11/03/2024] [Accepted: 11/06/2024] [Indexed: 03/06/2025]
Abstract
Evolutionary medicine, which integrates evolutionary biology and medicine, significantly enhances our understanding of human traits and disease susceptibility. However, previous studies in this field have often focused on single-nucleotide variants due to technological limitations in characterizing complex genomic regions, hindering the comprehensive analyses of their evolutionary origins and clinical significance. In this review, we summarize recent advancements in complete telomere-to-telomere (T2T), primate genomes and other primate resources, and illustrate how these resources facilitate the research of complex regions. We focus on several biomedically relevant regions to examine the relationship between primate genome evolution and human diseases. We also highlight the potentials of high-throughput functional genomic technologies for assessing candidate loci. Finally, we discuss future directions for primate research within the context of evolutionary medicine.
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Affiliation(s)
- Kaiyue Ma
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China; Center for Genomic Research, International Institutes of Medicine, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang, China.
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Lau NKC, Tong TTY, Chong YK, Ching CK. Solving a diagnostic challenge with nanopore long-read sequencing: a novel Alu element exonic insertion with false positive MLPA finding in SLC25A13 for citrin deficiency. Pathology 2025; 57:116-120. [PMID: 39472270 DOI: 10.1016/j.pathol.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/03/2024] [Accepted: 07/17/2024] [Indexed: 01/11/2025]
Affiliation(s)
- Nike Kwai Cheung Lau
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China.
| | - Tammy Tsz Yan Tong
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Yeow Kuan Chong
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Chor Kwan Ching
- Kowloon West Cluster Laboratory Genetic Service, Chemical Pathology Laboratory, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
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Shah S, Yu S, Zhang C, Ali I, Wang X, Qian Y, Xiao T. Retrotransposon SINEs in age-related diseases: Mechanisms and therapeutic implications. Ageing Res Rev 2024; 101:102539. [PMID: 39395576 DOI: 10.1016/j.arr.2024.102539] [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: 06/27/2024] [Revised: 09/27/2024] [Accepted: 10/03/2024] [Indexed: 10/14/2024]
Abstract
Retrotransposons are self-replicating genomic elements that move from one genomic location to another using a "copy-and-paste" method involving RNA intermediaries. One family of retrotransposon that has garnered considerable attention for its association with age-related diseases and anti-aging interventions is the short interspersed nuclear elements (SINEs). This review summarizes current knowledge on the roles of SINEs in aging processes and therapies. To underscore the significant research on the involvement of SINEs in aging-related diseases, we commence by outlining compelling evidence on the classification and mechanism, highlighting implications in age-related phenomena. The intricate relationship between SINEs and diseases such as neurodegenerative disorders, heart failure, high blood pressure, atherosclerosis, type 2 diabetes mellitus, osteoporosis, visual system dysfunctions, and cancer is explored, emphasizing their roles in various age-related diseases. Recent investigations into the anti-aging potential of SINE-targeted treatments are examined, with particular attention to how SINE antisense RNA mitigate age-related alterations at the cellular and molecular levels, offering insights into potential therapeutic targets for age-related pathologies. This review aims to compile the most recent advances on the multifaceted roles of SINE retrotransposons in age-related diseases and anti-aging interventions, providing valuable insights into underlying mechanisms and therapeutic avenues for promoting healthy aging.
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Affiliation(s)
- Suleman Shah
- Thoracic Surgery Department of the First Affiliated Hospital, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Genetics, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical school, Shenzhen 518055, China
| | - Siyi Yu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Chen Zhang
- Department of Thoracic Surgery, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning 530021, China
| | - Ilyas Ali
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical school, Shenzhen 518055, China
| | - Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang 050017, China
| | - Youhui Qian
- Thoracic Surgery Department of the First Affiliated Hospital, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Genetics, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China.
| | - Tian Xiao
- Thoracic Surgery Department of the First Affiliated Hospital, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Genetics, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China.
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Wang N, Jiao K, He J, Zhu B, Cheng N, Sun J, Chen L, Chen W, Gong L, Qiao K, Xi J, Wu Q, Zhao C, Zhu W. Diagnosis of Challenging Spinal Muscular Atrophy Cases with Long-Read Sequencing. J Mol Diagn 2024; 26:364-373. [PMID: 38490302 DOI: 10.1016/j.jmoldx.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/17/2024] [Accepted: 02/07/2024] [Indexed: 03/17/2024] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder primarily caused by the deletion or mutation of the survival motor neuron 1 (SMN1) gene. This study assesses the diagnostic potential of long-read sequencing (LRS) in three patients with SMA. For Patient 1, who has a heterozygous SMN1 deletion, LRS unveiled a missense mutation in SMN1 exon 5. In Patient 2, an Alu/Alu-mediated rearrangement covering the SMN1 promoter and exon 1 was identified through a blend of multiplex ligation-dependent probe amplification, LRS, and PCR across the breakpoint. The third patient, born to a consanguineous family, bore four copies of hybrid SMN genes. LRS determined the genomic structures, indicating two distinct hybrids of SMN2 exon 7 and SMN1 exon 8. However, a discrepancy was found between the SMN1/SMN2 ratio interpretations by LRS (0:2) and multiplex ligation-dependent probe amplification (0:4), which suggested a limitation of LRS in SMA diagnosis. In conclusion, this newly adapted long PCR-based third-generation sequencing introduces an additional avenue for SMA diagnosis.
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Affiliation(s)
- Ningning Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kexin Jiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin He
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Bochen Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Nachuan Cheng
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian Sun
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lan Chen
- Department of Neurology, Nantong First People's Hospital, Nantong, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Lingyun Gong
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kai Qiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qihan Wu
- Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, National Health Commission Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
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Walker M, Mayr EM, Koppermann ML, Terron A, Wagner Y, Kling C, Pfarr N. [Molecular pathological analysis through the ages]. PATHOLOGIE (HEIDELBERG, GERMANY) 2024; 45:173-179. [PMID: 38619582 PMCID: PMC11045621 DOI: 10.1007/s00292-024-01326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Molecular pathological examinations of tumor samples encompass a wide range of diagnostic analyses. Especially in recent years, numerous new biomarkers have come to the forefront-the analysis of which is crucial for therapy decisions. OBJECTIVES Within the field of molecular pathology, the demands of next generation sequencing (NGS)-based requirements have experienced massive growth in recent years. To meet this demand, methods are constantly being adapted and further developed. The following sections aim to illuminate how this trend arises and which analyses are gaining importance. METHODS The article provides an overview of the essential nucleic acid-based analysis techniques in the field of massive parallel sequencing. Terms such as DNA- and RNA-based techniques, as well as the associated analysis methods, are described, particularly with regard to their use in routine molecular pathological diagnostics. RESULTS The breadth of genomic sequencing has been steadily growing in recent years, particularly due to the increasing relevance of personalized medicine, along with the rising approvals of targeted therapeutics. This necessitates, among other things, the analysis of new biomarkers. The diagnostics as part of interdisciplinary molecular tumor boards (MTB) are now based on large gene panels (> 1 megabase). Furthermore, through the "Modellvorhaben Genomsequenzierung" § 64e, whole exome or whole genome sequencing has been made available for oncological patients. Given these developments, it is evident that future analyses will require the integration of additional omics fields, such as whole transcriptome analysis, epigenomics, and proteomics. CONCLUSION The challenges of personalized medicine along with the necessity of simultaneously assessing numerous new biomarkers require the implementation and execution of new techniques in molecular pathology whose complexity is steadily increasing.
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Affiliation(s)
- Maria Walker
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Eva-Maria Mayr
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Mai-Lan Koppermann
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Ana Terron
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Yoko Wagner
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Charlotte Kling
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Deutschland
| | - Nicole Pfarr
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland.
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Misceo D, Strømme P, Bitarafan F, Chawla MS, Sheng Y, Bach de Courtade SM, Eide L, Frengen E. Biallelic NDUFA4 Deletion Causes Mitochondrial Complex IV Deficiency in a Patient with Leigh Syndrome. Genes (Basel) 2024; 15:500. [PMID: 38674434 PMCID: PMC11050323 DOI: 10.3390/genes15040500] [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: 03/27/2024] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Oxidative phosphorylation involves a complex multi-enzymatic mitochondrial machinery critical for proper functioning of the cell, and defects herein cause a wide range of diseases called "primary mitochondrial disorders" (PMDs). Mutations in about 400 nuclear and 37 mitochondrial genes have been documented to cause PMDs, which have an estimated birth prevalence of 1:5000. Here, we describe a 4-year-old female presenting from early childhood with psychomotor delay and white matter signal changes affecting several brain regions, including the brainstem, in addition to lactic and phytanic acidosis, compatible with Leigh syndrome, a genetically heterogeneous subgroup of PMDs. Whole genome sequencing of the family trio identified a homozygous 12.9 Kb deletion, entirely overlapping the NDUFA4 gene. Sanger sequencing of the breakpoints revealed that the genomic rearrangement was likely triggered by Alu elements flanking the gene. NDUFA4 encodes for a subunit of the respiratory chain Complex IV, whose activity was significantly reduced in the patient's fibroblasts. In one family, dysfunction of NDUFA4 was previously documented as causing mitochondrial Complex IV deficiency nuclear type 21 (MC4DN21, OMIM 619065), a relatively mild form of Leigh syndrome. Our finding confirms the loss of NDUFA4 function as an ultra-rare cause of Complex IV defect, clinically presenting as Leigh syndrome.
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Affiliation(s)
- Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (F.B.); (Y.S.); (E.F.)
| | - Petter Strømme
- Division of Pediatrics and Adolescent Medicine, Oslo University Hospital and Faculty of Medicine, University of Oslo, 0450 Oslo, Norway;
| | - Fatemeh Bitarafan
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (F.B.); (Y.S.); (E.F.)
| | | | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (F.B.); (Y.S.); (E.F.)
| | | | - Lars Eide
- Department of Biochemistry, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (S.M.B.d.C.); (L.E.)
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (F.B.); (Y.S.); (E.F.)
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Zamora-Cánovas A, de la Morena-Barrio B, Marín-Quilez A, Sierra-Aisa C, Male C, Fernández-Mosteirin N, Trapero-Marugán M, Padilla J, Garrido-Rodriguez P, Sánchez-Fuentes A, Rodríguez-Alen A, Gómez-González PL, Revilla N, de la Morena-Barrio ME, Bastida JM, Corral J, Rivera J, Lozano ML. Targeted long-read sequencing identifies and characterizes structural variants in cases of inherited platelet disorders. J Thromb Haemost 2024; 22:851-859. [PMID: 38007062 DOI: 10.1016/j.jtha.2023.11.007] [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: 06/23/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND Genetic diagnosis of inherited platelet disorders (IPDs) is mainly performed by high-throughput sequencing (HTS). These short-read-based sequencing methods sometimes fail to characterize the genetics of the disease. OBJECTIVES To evaluate nanopore long-read DNA sequencing for characterization of structural variants (SVs) in patients with IPDs. METHODS Four patients with a clinical and laboratory diagnosis of Glanzmann thrombasthenia (GT) (P1 and P2) and Hermansky-Pudlak syndrome (HPS) (P3 and P4) in whom HTS missed the underlying molecular cause were included. DNA was analyzed by both standard HTS and nanopore sequencing on a MinION device (Oxford Nanopore Technologies) after enrichment of DNA spanning regions covering GT and HPS genes. RESULTS In patients with GT, HTS identified only 1 heterozygous ITGB3 splice variant c.2301+1G>C in P2. In patients with HPS, a homozygous deletion in HPS5 was suspected in P3, and 2 heterozygous HPS3 variants, c.2464C>T (p.Arg822∗) and a deletion affecting 2 exons, were reported in P4. Nanopore sequencing revealed a complex SV affecting exons 2 to 6 in ITGB3 (deletion-inversion-duplication) in homozygosity in P1 and compound heterozygosity with the splice variant in P2. In the 2 patients with HPS, nanopore defined the length of the SVs, which were characterized at nucleotide resolution. This allowed the identification of repetitive Alu elements at the breakpoints and the design of specific polymerase chain reactions for family screening. CONCLUSION The nanopore technology overcomes the limitations of standard short-read sequencing techniques in SV characterization. Using nanopore, we characterized novel defects in ITGB3, HPS5, and HPS3, highlighting the utility of long-read sequencing as an additional diagnostic tool in IPDs.
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Affiliation(s)
- Ana Zamora-Cánovas
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Belén de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Ana Marín-Quilez
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Cristina Sierra-Aisa
- Servicio de Hematología, Hospital Universitario Cruces, Baracaldo, Bilbao, Spain
| | - Christoph Male
- Department of Paediatrics, Medical University of Vienna, Vienna, Austria
| | | | | | - José Padilla
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Pedro Garrido-Rodriguez
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Ana Sánchez-Fuentes
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Agustín Rodríguez-Alen
- Servicio de Hematología, Hospital Virgen de la Salud, Complejo Hospitalario de Toledo, Toledo, Spain
| | - Pedro Luis Gómez-González
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Nuria Revilla
- Department of Hematology, Hospital Universitario Fundación Jiménez Díaz, Instituto Investigación Sanitaria FJD, Madrid, Spain
| | - María Eugenia de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - José María Bastida
- Departmento de Hematología, Complejo Asistencial Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca, Universidad de Salamanca, Salamanca, Spain; On behalf of Grupo Español de Alteraciones Plaquetarias Congénitas (GEAPC), Spanish Society of Thrombosis and Haemostasis, Madrid, Spain
| | - Javier Corral
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - José Rivera
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain; On behalf of Grupo Español de Alteraciones Plaquetarias Congénitas (GEAPC), Spanish Society of Thrombosis and Haemostasis, Madrid, Spain.
| | - María L Lozano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
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9
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Wambach JA, Wegner DJ, Kitzmiller J, White FV, Heins HB, Yang P, Paul AJ, Granadillo JL, Eghtesady P, Kuklinski C, Turner T, Fairman K, Stone K, Wilson T, Breman A, Smith J, Schroeder MC, Neidich JA, Whitsett JA, Cole FS. Homozygous, Intragenic Tandem Duplication of SFTPB Causes Neonatal Respiratory Failure. Am J Respir Cell Mol Biol 2024; 70:78-80. [PMID: 38156804 PMCID: PMC10768837 DOI: 10.1165/rcmb.2023-0156le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Affiliation(s)
| | | | | | | | | | - Ping Yang
- Washington University School of MedicineSt. Louis, Missouri
| | | | | | | | | | - Tiffany Turner
- Indiana University School of MedicineIndianapolis, Indiana
| | - Korre Fairman
- Indiana University School of MedicineIndianapolis, Indiana
| | - Kristyne Stone
- Indiana University School of MedicineIndianapolis, Indiana
| | | | - Amy Breman
- Indiana University School of MedicineIndianapolis, Indiana
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Ghasemi A, Sadr Z, Babanejad M, Rohani M, Alavi A. Copy Number Variations in Hereditary Spastic Paraplegia-Related Genes: Evaluation of an Iranian Hereditary Spastic Paraplegia Cohort and Literature Review. Mol Syndromol 2023; 14:477-484. [PMID: 38058755 PMCID: PMC10697729 DOI: 10.1159/000531507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/07/2023] [Indexed: 12/08/2023] Open
Abstract
Introduction In human genetic disorders, copy number variations (CNVs) are considered a considerable underlying cause. CNVs are generally detected by array-based methods but can also be discovered by read-depth analysis of whole-exome sequencing (WES) data. We performed WES-based CNV identification in a cohort of 35 Iranian families with hereditary spastic paraplegia (HSP) patients. Methods Thirty-five patients whose routine single-nucleotide variants (SNVs) and insertion/deletion analyses from exome data were unrevealing underwent a pipeline of CNV analysis using the read-depth detection method. Subsequently, a comprehensive search about the existence of CNVs in all 84 known HSP-causing genes was carried out in all reported HSP cases, so far. Results and Discussion CNV analysis of exome data indicated that 1 patient harbored a heterozygous deletion in exon 17 of the SPAST gene. Multiplex ligation-dependent probe amplification analysis confirmed this deletion in the proband and his affected father. Literature review demonstrated that, to date, pathogenic CNVs have been identified in 30 out of 84 HSP-causing genes (∼36%). However, CNVs in only 17 of these genes were specifically associated with the HSP phenotype. Among them, CNVs were more common in L1CAM, PLP1, SPAST, SPG7, SPG11, and REEP1 genes. The identification of the CNV in 1 of our patients suggests that WES allows the detection of both SNVs and CNVs from a single method without additional costs and execution time. However, because of intrinsic issues of WES in the detection of large rearrangements, it may not yet be exploited to replace the CNV detection methods in standard clinical practice.
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Affiliation(s)
- Aida Ghasemi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zahra Sadr
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Rohani
- Department of Neurology, Iran University of Medical Sciences, Hazrat Rasool Hospital, Tehran, Iran
| | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Neuromuscular Research Center, Tehran University of Medical Sciences, Tehran, Iran
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11
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Khan M, Shah S, Lv B, Lv Z, Ji N, Song Z, Wu P, Wang X, Mehmood A. Molecular Mechanisms of Alu and LINE-1 Interspersed Repetitive Sequences Reveal Diseases of Visual System Dysfunction. Ocul Immunol Inflamm 2023; 31:1848-1858. [PMID: 36040959 DOI: 10.1080/09273948.2022.2112238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINE-1s) are the abundant and well-characterized repetitive elements in the human genome. METHODS For this review, all relevant original research studies were assessed by searching electronic databases, including PubMed, Google Scholar, and Web of Science, by using relevant keywords. Accumulating evidence indicates that the disorder of gene expression regulated by these repetitive sequences is one of the causes of the diseases of visual system dysfunction, including retinal degenerations, glaucoma, retinitis punctata albescens, retinitis pigmentosa, geographic atrophy, and age-related macular degeneration, suggesting that SINEs and LINE-1s may have great potential implications in ophthalmology. RESULTS Alu elements belonging to the SINEs are present in more than one million copies, comprising 10% of the human genome. CONCLUSION This study offers recent advances in Alu and LINE-1 mechanisms in the development of eye diseases. The current study could advance our knowledge of the roles of SINEs and LINE-1s in the developing process of eye diseases, suggesting new diagnostic biomarkers, therapeutic strategies, and significant points for future studies.
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Affiliation(s)
- Murad Khan
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Suleman Shah
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Baixue Lv
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, Hubei Province, China
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Ning Ji
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Zhixue Song
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Peiyuan Wu
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Arshad Mehmood
- Department of Neurology, the Second Hospital of Hebei Medical University, City Shijiazhuang, P.R. China
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12
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Di Lazzaro Filho R, Yamamoto GL, Silva TJ, Rocha LA, Linnenkamp BDW, Castro MAA, Bartholdi D, Schaller A, Leeb T, Kelmann S, Utagawa CY, Steiner CE, Steinmetz L, Honjo RS, Kim CA, Wang L, Abourjaili-Bilodeau R, Campeau PM, Warman M, Passos-Bueno MR, Hoch NC, Bertola DR. Biallelic variants in DNA2 cause poikiloderma with congenital cataracts and severe growth failure reminiscent of Rothmund-Thomson syndrome. J Med Genet 2023; 60:1127-1132. [PMID: 37055165 DOI: 10.1136/jmg-2022-109119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/27/2023] [Indexed: 04/15/2023]
Abstract
Rothmund-Thomson syndrome (RTS) is a rare, heterogeneous autosomal recessive genodermatosis, with poikiloderma as its hallmark. It is classified into two types: type I, with biallelic variants in ANAPC1 and juvenile cataracts, and type II, with biallelic variants in RECQL4, increased cancer risk and no cataracts. We report on six Brazilian probands and two siblings of Swiss/Portuguese ancestry presenting with severe short stature, widespread poikiloderma and congenital ocular anomalies. Genomic and functional analysis revealed compound heterozygosis for a deep intronic splicing variant in trans with loss of function variants in DNA2, with reduction of the protein levels and impaired DNA double-strand break repair. The intronic variant is shared by all patients, as well as the Portuguese father of the European siblings, indicating a probable founder effect. Biallelic variants in DNA2 were previously associated with microcephalic osteodysplastic primordial dwarfism. Although the individuals reported here present a similar growth pattern, the presence of poikiloderma and ocular anomalies is unique. Thus, we have broadened the phenotypical spectrum of DNA2 mutations, incorporating clinical characteristics of RTS. Although a clear genotype-phenotype correlation cannot be definitively established at this moment, we speculate that the residual activity of the splicing variant allele could be responsible for the distinct manifestations of DNA2-related syndromes.
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Affiliation(s)
- Ricardo Di Lazzaro Filho
- Departamento de Genética e Biologia Evolutiva do Instituto de Biociências, Universidade de São Paulo, Sao Paulo, Brazil
- Genômica/Genera, Diagnósticos da América SA, Barueri, Brazil
| | - Guilherme Lopes Yamamoto
- Genômica/Genera, Diagnósticos da América SA, Barueri, Brazil
- Departamento de Pediatria do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, Sao Paulo, Brazil
| | - Tiago J Silva
- Departamento de Bioquímica do Instituto de Química, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Leticia A Rocha
- Departamento de Genética e Biologia Evolutiva do Instituto de Biociências, Universidade de São Paulo, Sao Paulo, Brazil
| | - Bianca D W Linnenkamp
- Departamento de Pediatria do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, Sao Paulo, Brazil
| | - Matheus Augusto Araújo Castro
- Departamento de Pediatria do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, Sao Paulo, Brazil
| | | | - André Schaller
- Department of Human Genetics, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern, Switzerland
| | - Samantha Kelmann
- Departamento de Pediatria do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, Sao Paulo, Brazil
| | | | | | - Leandra Steinmetz
- Departamento de Pediatria do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, Sao Paulo, Brazil
| | - Rachel Sayuri Honjo
- Departamento de Pediatria do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, Sao Paulo, Brazil
| | - Chong Ae Kim
- Departamento de Pediatria do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, Sao Paulo, Brazil
| | - Lisa Wang
- 9Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Québec, Canada
| | - Matthew Warman
- Department of Orthopedics, Boston Children's Hospital, Boston, Massachusetts, USA
- Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Maria Rita Passos-Bueno
- Departamento de Genética e Biologia Evolutiva do Instituto de Biociências, Universidade de São Paulo, Sao Paulo, Brazil
| | - Nicolas C Hoch
- Departamento de Bioquímica do Instituto de Química, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Debora Romeo Bertola
- Departamento de Genética e Biologia Evolutiva do Instituto de Biociências, Universidade de São Paulo, Sao Paulo, Brazil
- Departamento de Pediatria do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, Sao Paulo, Brazil
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13
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Omichi N, Kishita Y, Nakama M, Sasai H, Terazawa A, Kobayashi E, Fushimi T, Sugiyama Y, Ichimoto K, Nitta KR, Yatsuka Y, Ohtake A, Murayama K, Okazaki Y. Novel ITPA variants identified by whole genome sequencing and RNA sequencing. J Hum Genet 2023; 68:649-652. [PMID: 37246162 DOI: 10.1038/s10038-023-01156-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/30/2023]
Abstract
Approximately 80% of rare diseases have a genetic cause, and an accurate genetic diagnosis is necessary for disease management, prognosis prediction, and genetic counseling. Whole-exome sequencing (WES) is a cost-effective approach for exploring the genetic cause, but several cases often remain undiagnosed. We combined whole genome sequencing (WGS) and RNA sequencing (RNA-seq) to identify the pathogenic variants in an unsolved case using WES. RNA-seq revealed aberrant exon 4 and exon 6 splicing of ITPA. WGS showed a previously unreported splicing donor variant, c.263+1G>A, and a novel heterozygous deletion, including exon 6. Detailed examination of the breakpoint indicated the deletion caused by recombination between Alu elements in different introns. The proband was found to have developmental and epileptic encephalopathies caused by variants in the ITPA gene. The combination of WGS and RNA-seq may be effective in diagnosing conditions in proband who could not be diagnosed using WES.
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Affiliation(s)
- Nanako Omichi
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Yoshihito Kishita
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Mina Nakama
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
- Clinical Genetics Center, Gifu University Hospital, Gifu, Japan
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Hideo Sasai
- Clinical Genetics Center, Gifu University Hospital, Gifu, Japan
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Atsushi Terazawa
- Department of Pediatric Cardiology, Gifu Prefectural General Medical Center, Gifu, Japan
| | - Emiko Kobayashi
- Department of Pediatrics, Gifu Prefectural General Medical Center, Gifu, Japan
| | - Takuya Fushimi
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Yohei Sugiyama
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Keiko Ichimoto
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Kazuhiro R Nitta
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yukiko Yatsuka
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Akira Ohtake
- Department of Pediatrics and Clinical Genomics, Saitama Medical University, Moroyama, Saitama, Japan
- Center for Intractable Diseases, Saitama Medical University Hospital, Moroyama, Saitama, Japan
| | - Kei Murayama
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
- Center for Medical Genetics, Chiba Children's Hospital, Chiba, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan.
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14
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Fröhlich A, Pfaff AL, Bubb VJ, Quinn JP, Koks S. Reference LINE-1 insertion polymorphisms correlate with Parkinson's disease progression and differential transcript expression in the PPMI cohort. Sci Rep 2023; 13:13857. [PMID: 37620405 PMCID: PMC10449770 DOI: 10.1038/s41598-023-41052-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023] Open
Abstract
Long interspersed nuclear element-1 (LINE-1/L1) retrotransposons make up 17% of the human genome. They represent one class of transposable elements with the capacity to both mobilize autonomously and in trans via the mobilization of other elements, primarily Alu and SVA elements. Reference LINE-1 elements are, by definition, found in the reference genome, however, due to the polymorphic nature of these elements, variation for presence or absence is present within the population. We used a combination of clinical and transcriptomic data from the Parkinson's Progression Markers Initiative (PPMI) and applied matrix expression quantitative trait loci analysis and linear mixed-effects models involving 114 clinical, biochemical and imaging data from the PPMI cohort to elucidate the role of reference LINE-1 insertion polymorphism on both gene expression genome-wide and progression of Parkinson's disease (PD). We demonstrate that most LINE-1 insertion polymorphisms are capable of regulating gene expression, preferentially in trans, including previously identified PD risk loci. In addition, we show that 70 LINE-1 elements were associated with longitudinal changes of at least one PD progression marker, including ipsilateral count density ratio and UPDRS scores which are indicators of degeneration and severity. In conclusion, this study highlights the effect of the polymorphic nature of LINE-1 retrotransposons on gene regulation and progression of PD which underlines the importance of analyzing transposable elements within complex diseases.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia.
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.
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15
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de Tribolet-Hardy J, Thorball CW, Forey R, Planet E, Duc J, Coudray A, Khubieh B, Offner S, Pulver C, Fellay J, Imbeault M, Turelli P, Trono D. Genetic features and genomic targets of human KRAB-zinc finger proteins. Genome Res 2023; 33:1409-1423. [PMID: 37730438 PMCID: PMC10547255 DOI: 10.1101/gr.277722.123] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/18/2023] [Indexed: 09/22/2023]
Abstract
Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on close to a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation.
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Affiliation(s)
- Jonas de Tribolet-Hardy
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Christian W Thorball
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Romain Forey
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Bara Khubieh
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Cyril Pulver
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, 1010 Lausanne, Switzerland
| | - Michael Imbeault
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
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16
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Soejima M, Koda Y. Detection of c.375A>G, c.385A>T, c.571C>T, and sedel2 of FUT2 via Real-Time PCR in a Single Tube. Diagnostics (Basel) 2023; 13:2022. [PMID: 37370917 DOI: 10.3390/diagnostics13122022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
α(1,2)fucosyltransferase (Se enzyme) encoded by FUT2 is involved in the secretor status of ABH(O) blood group antigens. The sedel2 allele is one of the non-functional FUT2 (se) alleles in which 9.3 kb, containing the entire coding region of FUT2, is deleted by Alu-mediated nonhomologous recombination. In addition to this allele, three SNPs of FUT2, c.375A>G, c.385A>T, and c.571C>T, appear to be prevalent in certain Oceanian populations such as Polynesians. Recently, we developed an endpoint genotyping assay to determine sedel2 zygosity, using a FAM-labeled probe for detection of the sedel2 allele and a VIC-labeled probe for the detection of FUT2. In this study, instead of the VIC probe, a HEX-labeled probe covering both c.375A>G and c.385A>T and a Cy5-labeled probe covering c.571C>T were added to the sedel2 allele assay mixture to allow for the simultaneous detection of these four variations via endpoint genotyping for sedel2 zygosity and fluorescence melting curve analysis for c.375A>G, c.385A>T, and c.571C>T genotyping. The results obtained from 24 Samoan subjects using this method were identical to those obtained using previous methods. Therefore, it appears that the present method can accurately determine these four variations simultaneously.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
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17
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Mao B, Lin N, Guo D, He D, Xue H, Chen L, He Q, Zhang M, Chen M, Huang H, Xu L. Molecular analysis and prenatal diagnosis of seven Chinese families with genetic epilepsy. Front Neurosci 2023; 17:1165601. [PMID: 37250406 PMCID: PMC10213446 DOI: 10.3389/fnins.2023.1165601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction Genetic epilepsy is a large group of clinically and genetically heterogeneous neurological disorders characterized by recurrent seizures, which have a clear association with genetic defects. In this study, we have recruited seven families from China with neurodevelopmental abnormalities in which epilepsy was a predominant manifestation, aiming to elucidate the underlying causes and make a precise diagnosis for the cases. Methods Whole-exome sequencing (WES) combined with Sanger sequencing was used to identify the causative variants associated with the diseases in addition to essential imaging and biomedical examination. Results A gross intragenic deletion detected in MFSD8 was investigated via gap-polymerase chain reaction (PCR), real-time quantitative PCR (qPCR), and mRNA sequence analysis. We identified 11 variants in seven genes (ALDH7A1, CDKL5, PCDH19, QARS1, POLG, GRIN2A, and MFSD8) responsible for genetic epilepsy in the seven families, respectively. A total of six variants (c.1408T>G in ALDH7A1, c.1994_1997del in CDKL5, c.794G>A in QARS1, c.2453C>T in GRIN2A, and c.217dup and c.863+995_998+1480del in MFSD8) have not yet been reported to be associated with diseases and were all evaluated to be pathogenic or likely pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Methods Based on the molecular findings, we have associated the intragenic deletion in MFSD8 with the mutagenesis mechanism of Alu-mediated genomic rearrangements for the first time and provided genetic counseling, medical suggestions, and prenatal diagnosis for the families. In conclusion, molecular diagnosis is crucial to obtain improved medical outcomes and recurrence risk evaluation for genetic epilepsy.
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Affiliation(s)
- Bin Mao
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Danhua Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Deqin He
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Qianqian He
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Min Zhang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
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18
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Groza C, Chen X, Pacis A, Simon MM, Pramatarova A, Aracena KA, Pastinen T, Barreiro LB, Bourque G. Genome graphs detect human polymorphisms in active epigenomic state during influenza infection. CELL GENOMICS 2023; 3:100294. [PMID: 37228750 PMCID: PMC10203048 DOI: 10.1016/j.xgen.2023.100294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/26/2022] [Accepted: 03/09/2023] [Indexed: 05/27/2023]
Abstract
Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that genome graphs, which encapsulate genetic diversity, could reveal missing epigenomic signals. To test this, we sequenced the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after influenza infection, allowing us to investigate the role of MEIs in immunity. We characterized genetic variants and MEIs using linked reads and built a genome graph. Mapping epigenetic data revealed 2.3%-3% novel peaks for H3K4me1, H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq), and ATAC-seq. Additionally, the use of a genome graph modified some quantitative trait loci estimates and revealed 375 polymorphic MEIs in an active epigenomic state. Among these is an AluYh3 polymorphism whose chromatin state changed after infection and was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.
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Affiliation(s)
- Cristian Groza
- Quantitative Life Sciences, McGill University, Montréal, QC, Canada
| | - Xun Chen
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Alain Pacis
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
| | - Marie-Michelle Simon
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada
| | - Albena Pramatarova
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada
| | | | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Hospital and Research Institute, Kansas City, MO, USA
| | - Luis B. Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Guillaume Bourque
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada
- Human Genetics, McGill University, Montréal, QC, Canada
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19
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Hu B, Ma JX, Duerfeldt AS. The cGAS-STING pathway in diabetic retinopathy and age-related macular degeneration. Future Med Chem 2023; 15:717-729. [PMID: 37166075 PMCID: PMC10194038 DOI: 10.4155/fmc-2022-0301] [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: 12/08/2022] [Accepted: 03/28/2023] [Indexed: 05/12/2023] Open
Abstract
Diabetic retinopathy and age-related macular degeneration are common retinal diseases with shared pathophysiology, including oxidative stress-induced inflammation. Cellular mechanisms responsible for converting oxidative stress into retinal damage are ill-defined but have begun to clarify. One common outcome of retinal oxidative stress is mitochondrial damage and subsequent release of mitochondrial DNA into the cytosol. This leads to activation of the cGAS-STING pathway, resulting in interferon release and disease-amplifying inflammation. This review summarizes the evolving link between aberrant cGAS-STING signaling and inflammation in common retinal diseases and provides prospective for targeting this system in diabetic retinopathy and age-related macular degeneration. Further defining the roles of this system in the retina is expected to reveal new disease pathology and novel therapeutic approaches.
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Affiliation(s)
- Bo Hu
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
| | - Jian-Xing Ma
- Department of Biochemistry, Wake Forest University School of Medicine, Winston Salem, NC 27101, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN 55414, USA
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20
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Bai J, Qu Y, OuYang S, Jiao H, Wang Y, Li J, Huang W, Zhao Y, Peng X, Wang D, Jin Y, Wang H, Song F. Novel Alu-mediated deletions of the SMN1 gene were identified by ultra-long read sequencing technology in patients with spinal muscular atrophy. Neuromuscul Disord 2023; 33:382-390. [PMID: 37023488 DOI: 10.1016/j.nmd.2023.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease caused by biallelic variants of the survival motor neuron 1 (SMN1) gene. In this study, our aim was to make a molecular diagnosis in two patients with SMA carrying only one SMN1 copy number. Using ultra-long read sequencing (Ultra-LRS), 1415 bp deletion and 3348 bp deletion of the SMN1 gene were identified in patient 1 and the father of patient 2, respectively. Ultra-LRS revealed two novel deletions, starting from the SMN1 promoter to intron 1. It also accurately provided the location of the deletion breakpoints in the SMN1 gene: chr5 g.70,924,798-70,926,212 for a 1415 bp deletion; chr5 g.70,922,695-70,926,042 for a 3348 bp deletion. By analyzing the breakpoint junctions, we identified that these genomic sequences were composed of Alu sequences, including AluJb, AluYm1, AluSq, and AluYm1, indicating that Alu-mediated rearrangements are a mechanism of SMN1 deletion events. In addition, full-length SMN1 transcripts and SMN protein in patient 1 were significantly decreased (p < 0.01), suggesting that a 1415 bp deletion that included the transcription and translation initiation sites of the SMN1 gene had severe consequences for SMN expression. Ultra-LRS can easily distinguish highly homozygous genes compared to other detection technologies, which is useful for detecting SMN1 intragenic mutations, to quickly discover structural rearrangements and to precisely present the breakpoint positions.
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21
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Magrinelli F, Rocca C, Simone R, Zenezini Chiozzi R, Jaunmuktane Z, Mencacci NE, Tinazzi M, Jayawant S, Nemeth AH, Demidov G, Houlden H, Bhatia KP. Detection and Characterization of a De Novo Alu Retrotransposition Event Causing NKX2-1-Related Disorder. Mov Disord 2023; 38:347-353. [PMID: 36420574 DOI: 10.1002/mds.29280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/17/2022] [Accepted: 11/06/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Heterozygous NKX2-1 loss-of-function variants cause combinations of hyperkinetic movement disorders (MDs, particularly childhood-onset chorea), pulmonary dysfunction, and hypothyroidism. Mobile element insertions (MEIs) are potential disease-causing structural variants whose detection in routine diagnostics remains challenging. OBJECTIVE To establish the molecular diagnosis of two first-degree relatives with clinically suspected NKX2-1-related disorder who had negative NKX2-1 Sanger (SS), whole-exome (WES), and whole-genome (WGS) sequencing. METHODS The proband's WES was analyzed for MEIs. A candidate MEI in NKX2-1 underwent optimized SS after plasmid cloning. Functional studies exploring NKX2-1 haploinsufficiency at RNA and protein levels were performed. RESULTS A 347-bp AluYa5 insertion with a 65-bp poly-A tail followed by a 16-bp duplication of the pre-insertion wild-type sequence in exon 3 of NKX2-1 (ENST00000354822.7:c.556_557insAlu541_556dup) segregated with the disease phenotype. CONCLUSIONS We identified a de novo exonic AluYa5 insertion causing NKX2-1-related disorder in SS/WES/WGS-negative cases, suggesting that MEI analysis of short-read sequencing data or targeted long-read sequencing could unmask the molecular diagnosis of unsolved MD cases. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
- William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Roberto Simone
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | | | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Niccolò E Mencacci
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Michele Tinazzi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Sandeep Jayawant
- Paediatric Neurology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Andrea H Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
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22
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Gasparotto E, Burattin FV, Di Gioia V, Panepuccia M, Ranzani V, Marasca F, Bodega B. Transposable Elements Co-Option in Genome Evolution and Gene Regulation. Int J Mol Sci 2023; 24:ijms24032610. [PMID: 36768929 PMCID: PMC9917352 DOI: 10.3390/ijms24032610] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
The genome is no longer deemed as a fixed and inert item but rather as a moldable matter that is continuously evolving and adapting. Within this frame, Transposable Elements (TEs), ubiquitous, mobile, repetitive elements, are considered an alive portion of the genomes to date, whose functions, although long considered "dark", are now coming to light. Here we will review that, besides the detrimental effects that TE mobilization can induce, TEs have shaped genomes in their current form, promoting genome sizing, genomic rearrangements and shuffling of DNA sequences. Although TEs are mostly represented in the genomes by evolutionarily old, short, degenerated, and sedentary fossils, they have been thoroughly co-opted by the hosts as a prolific and original source of regulatory instruments for the control of gene transcription and genome organization in the nuclear space. For these reasons, the deregulation of TE expression and/or activity is implicated in the onset and progression of several diseases. It is likely that we have just revealed the outermost layers of TE functions. Further studies on this portion of the genome are required to unlock novel regulatory functions that could also be exploited for diagnostic and therapeutic approaches.
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Affiliation(s)
- Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Filippo Vittorio Burattin
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Valeria Di Gioia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Michele Panepuccia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
- Correspondence:
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23
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Kołat D, Zhao LY, Kciuk M, Płuciennik E, Kałuzińska-Kołat Ż. AP-2δ Is the Most Relevant Target of AP-2 Family-Focused Cancer Therapy and Affects Genome Organization. Cells 2022; 11:4124. [PMID: 36552887 PMCID: PMC9776946 DOI: 10.3390/cells11244124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/26/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Formerly hailed as "undruggable" proteins, transcription factors (TFs) are now under investigation for targeted therapy. In cancer, this may alter, inter alia, immune evasion or replicative immortality, which are implicated in genome organization, a process that accompanies multi-step tumorigenesis and which frequently develops in a non-random manner. Still, targeting-related research on some TFs is scarce, e.g., among AP-2 proteins, which are known for their altered functionality in cancer and prognostic importance. Using public repositories, bioinformatics tools, and RNA-seq data, the present study examined the ligandability of all AP-2 members, selecting the best one, which was investigated in terms of mutations, targets, co-activators, correlated genes, and impact on genome organization. AP-2 proteins were found to have the conserved "TF_AP-2" domain, but manifested different binding characteristics and evolution. Among them, AP-2δ has not only the highest number of post-translational modifications and extended strands but also contains a specific histidine-rich region and cleft that can receive a ligand. Uterine, colon, lung, and stomach tumors are most susceptible to AP-2δ mutations, which also co-depend with cancer hallmark genes and drug targets. Considering AP-2δ targets, some of them were located proximally in the spatial genome or served as co-factors of the genes regulated by AP-2δ. Correlation and functional analyses suggested that AP-2δ affects various processes, including genome organization, via its targets; this has been eventually verified in lung adenocarcinoma using expression and immunohistochemistry data of chromosomal conformation-related genes. In conclusion, AP-2δ affects chromosomal conformation and is the most appropriate target for cancer therapy focused on the AP-2 family.
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Affiliation(s)
- Damian Kołat
- Department of Experimental Surgery, Medical University of Lodz, 90-136 Lodz, Poland
| | - Lin-Yong Zhao
- Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Centre for Biotherapy, Chengdu 610041, China
| | - Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, 90-237 Lodz, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, 90-237 Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, 90-752 Lodz, Poland
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24
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Erdman VV, Karimov DD, Tuktarova IA, Timasheva YR, Nasibullin TR, Korytina GF. Alu Deletions in LAMA2 and CDH4 Genes Are Key Components of Polygenic Predictors of Longevity. Int J Mol Sci 2022; 23:13492. [PMID: 36362280 PMCID: PMC9657309 DOI: 10.3390/ijms232113492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 10/18/2023] Open
Abstract
Longevity is a unique human phenomenon and a highly stable trait, characterized by polygenicity. The longevity phenotype occurs due to the ability to successfully withstand the age-related genomic instability triggered by Alu elements. The purpose of our cross-sectional study was to evaluate the combined contribution of ACE*Ya5ACE, CDH4*Yb8NBC516, COL13A1*Ya5ac1986, HECW1*Ya5NBC182, LAMA2*Ya5-MLS19, PLAT*TPA25, PKHD1L1*Yb8AC702, SEMA6A*Yb8NBC597, STK38L*Ya5ac2145 and TEAD1*Ya5ac2013 Alu elements to longevity. The study group included 2054 unrelated individuals aged from 18 to 113 years who are ethnic Tatars from Russia. We analyzed the dynamics of the allele and genotype frequencies of the studied Alu polymorphic loci in the age groups of young (18-44 years old), middle-aged (45-59 years old), elderly (60-74 years old), old seniors (75-89 years old) and long-livers (90-113 years old). Most significant changes in allele and genotype frequencies were observed between the long-livers and other groups. The search for polygenic predictors of longevity was performed using the APSampler program. Attaining longevity was associated with the combinations LAMA2*ID + CDH4*D (OR = 2.23, PBonf = 1.90 × 10-2) and CDH4*DD + LAMA2*ID + HECW1*D (OR = 4.58, PBonf = 9.00 × 10-3) among persons aged between 18 and 89 years, LAMA2*ID + CDH4*D + SEMA6A*I for individuals below 75 years of age (OR = 3.13, PBonf = 2.00 × 10-2), LAMA2*ID + HECW1*I for elderly people aged 60 and older (OR = 3.13, PBonf = 2.00 × 10-2) and CDH4*DD + LAMA2*D + HECW1*D (OR = 4.21, PBonf = 2.60 × 10-2) and CDH4*DD + LAMA2*D + ACE*I (OR = 3.68, PBonf = 1.90 × 10-2) among old seniors (75-89 years old). The key elements of combinations associated with longevity were the deletion alleles of CDH4 and LAMA2 genes. Our results point to the significance for human longevity of the Alu polymorphic loci in CDH4, LAMA2, HECW1, SEMA6A and ACE genes, involved in the integration systems.
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Affiliation(s)
- Vera V. Erdman
- Institute of Biochemistry and Genetics, Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
| | - Denis D. Karimov
- Ufa Research Institute of Labor Medicine and Human Ecology, 450106 Ufa, Russia
| | - Ilsia A. Tuktarova
- Institute of Biochemistry and Genetics, Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
| | - Yanina R. Timasheva
- Institute of Biochemistry and Genetics, Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
| | - Timur R. Nasibullin
- Institute of Biochemistry and Genetics, Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
| | - Gulnaz F. Korytina
- Institute of Biochemistry and Genetics, Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
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25
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Lee H, Min JW, Mun S, Han K. Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101583. [PMID: 36295018 PMCID: PMC9605557 DOI: 10.3390/life12101583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are classified into two classes according to their mobilization mechanism. Compared to DNA transposons that move by the "cut and paste" mechanism, retrotransposons mobilize via the "copy and paste" method. They have been an essential research topic because some of the active elements, such as Long interspersed element 1 (LINE-1), Alu, and SVA elements, have contributed to the genetic diversity of primates beyond humans. In addition, they can cause genetic disorders by altering gene expression and generating structural variations (SVs). The development and rapid technological advances in next-generation sequencing (NGS) have led to new perspectives on detecting retrotransposon-mediated SVs, especially insertions. Moreover, various computational methods have been developed based on NGS data to precisely detect the insertions and deletions in the human genome. Therefore, this review discusses details about the recently studied and utilized NGS technologies and the effective computational approaches for discovering retrotransposons through it. The final part covers a diverse range of computational methods for detecting retrotransposon insertions with human NGS data. This review will give researchers insights into understanding the TEs and how to investigate them and find connections with research interests.
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Affiliation(s)
- Haeun Lee
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea
| | - Jun Won Min
- Department of Surgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Seyoung Mun
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- Correspondence: (S.M.); (K.H.)
| | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- HuNbiome Co., Ltd., R&D Center, Seoul 08507, Korea
- Correspondence: (S.M.); (K.H.)
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26
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Pluta N, Hoffjan S, Zimmer F, Köhler C, Lücke T, Mohr J, Vorgerd M, Nguyen HHP, Atlan D, Wolf B, Zaum AK, Rost S. Homozygous Inversion on Chromosome 13 Involving SGCG Detected by Short Read Whole Genome Sequencing in a Patient Suffering from Limb-Girdle Muscular Dystrophy. Genes (Basel) 2022; 13:genes13101752. [PMID: 36292638 PMCID: PMC9601614 DOI: 10.3390/genes13101752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/15/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
New techniques in molecular genetic diagnostics now allow for accurate diagnosis in a large proportion of patients with muscular diseases. Nevertheless, many patients remain unsolved, although the clinical history and/or the muscle biopsy give a clear indication of the involved genes. In many cases, there is a strong suspicion that the cause must lie in unexplored gene areas, such as deep-intronic or other non-coding regions. In order to find these changes, next-generation sequencing (NGS) methods are constantly evolving, making it possible to sequence entire genomes to reveal these previously uninvestigated regions. Here, we present a young woman who was strongly suspected of having a so far genetically unsolved sarcoglycanopathy based on her clinical history and muscle biopsy. Using short read whole genome sequencing (WGS), a homozygous inversion on chromosome 13 involving SGCG and LINC00621 was detected. The breakpoint in intron 2 of SGCG led to the absence of γ-sarcoglycan, resulting in the manifestation of autosomal recessive limb-girdle muscular dystrophy 5 (LGMDR5) in the young woman.
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Affiliation(s)
- Natalie Pluta
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sabine Hoffjan
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany
- Correspondence:
| | - Frederic Zimmer
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Cornelia Köhler
- Department of Neuropaediatrics, University Children’s Hospital, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Thomas Lücke
- Department of Neuropaediatrics, University Children’s Hospital, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Jennifer Mohr
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44789 Bochum, Germany
| | - Matthias Vorgerd
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44789 Bochum, Germany
| | | | - David Atlan
- Phenosystems SA, 1440 Braine le Chateau, Belgium
| | - Beat Wolf
- iCoSys, University of Applied Sciences Western Switzerland, 1700 Fribourg, Switzerland
| | - Ann-Kathrin Zaum
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Simone Rost
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- Medical Genetics Center (MGZ), 80335 Munich, Germany
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27
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Lee J, Mohammad N, Lu Y, Kang K, Han K, Brantly M. Alu RNA induces NLRP3 expression through TLR7 activation in α-1-antitrypsin-deficient macrophages. JCI Insight 2022; 7:158791. [PMID: 35730566 DOI: 10.1172/jci.insight.158791] [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: 01/25/2022] [Accepted: 04/29/2022] [Indexed: 11/17/2022] Open
Abstract
α-1 antitrypsin (AAT) is a serine protease inhibitor that plays a pivotal role in maintaining lung homeostasis. The most common AAT allele associated with AAT deficiency (AATD) is PiZ. Z-AAT accumulates in cells due to misfolding, causing severe AATD. The major function of AAT is to neutralize neutrophil elastase in the lung. It is generally accepted that loss of antiprotease function is a major cause of COPD in individuals with AATD. However, it is now being recognized that the toxic gain-of-function effect of Z-AAT in macrophage likely contributes to lung disease. In the present study, we determined that TLR7 signaling is activated in Z-MDMs, and the expression level of NLRP3, one of the targets of TLR7 signaling, is significantly higher in Z- compared with M-MDMs. We also determined that the level of endosomal Alu RNA is significantly higher in Z-compared with M-MDMs. Alu RNA is a known endogenous ligand that activates TLR7 signaling. Z-AAT likely induces the expression of Alu elements in MDMs and accelerates monocyte death, leading to the higher level of endosomal Alu RNA in Z-MDMs. Taken together,this study identifies a mechanism responsible for the toxic gain of function of Z-AAT macrophages.
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Affiliation(s)
- Jungnam Lee
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| | - Naweed Mohammad
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| | - Yuanqing Lu
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| | - Keunsoo Kang
- Department of Microbiology, Dankook University College of Natural Science, Cheonan, Republic of Korea
| | - Kyudong Han
- Department of Microbiology, Dankook University College of Natural Science, Cheonan, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, Republic of Korea
| | - Mark Brantly
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, Florida, USA
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Pinto A, Cunha C, Chaves R, Butchbach MER, Adega F. Comprehensive In Silico Analysis of Retrotransposon Insertions within the Survival Motor Neuron Genes Involved in Spinal Muscular Atrophy. BIOLOGY 2022; 11:824. [PMID: 35741345 PMCID: PMC9219815 DOI: 10.3390/biology11060824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are interspersed repetitive and mobile DNA sequences within the genome. Better tools for evaluating TE-derived sequences have provided insights into the contribution of TEs to human development and disease. Spinal muscular atrophy (SMA) is an autosomal recessive motor neuron disease that is caused by deletions or mutations in the Survival Motor Neuron 1 (SMN1) gene but retention of its nearly perfect orthologue SMN2. Both genes are highly enriched in TEs. To establish a link between TEs and SMA, we conducted a comprehensive, in silico analysis of TE insertions within the SMN1/2 loci of SMA, carrier and healthy genomes. We found an Alu insertion in the promoter region and one L1 element in the 3'UTR that may play an important role in alternative promoter as well as in alternative transcriptional termination. Additionally, several intronic Alu repeats may influence alternative splicing via RNA circularization and causes the presence of new alternative exons. These Alu repeats present throughout the genes are also prone to recombination events that could lead to SMN1 exons deletions and, ultimately, SMA. TE characterization of the SMA genomic region could provide for a better understanding of the implications of TEs on human disease and genomic evolution.
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Affiliation(s)
- Albano Pinto
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Catarina Cunha
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Matthew E. R. Butchbach
- Division of Neurology, Nemours Children’s Hospital Delaware, Wilmington, DE 19803, USA;
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
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Prakrithi P, Singhal K, Sharma D, Jain A, Bhoyar RC, Imran M, Senthilvel V, Divakar MK, Mishra A, Scaria V, Sivasubbu S, Mukerji M. An Alu insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project. NAR Genom Bioinform 2022; 4:lqac009. [PMID: 35178516 PMCID: PMC8846365 DOI: 10.1093/nargab/lqac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Actively retrotransposing primate-specific Alu repeats display insertion-deletion (InDel) polymorphism through their insertion at new loci. In the global datasets, Indian populations remain under-represented and so do their Alu InDels. Here, we report the genomic landscape of Alu InDels from the recently released 1021 Indian Genomes (IndiGen) (available at https://clingen.igib.res.in/indigen). We identified 9239 polymorphic Alu insertions that include private (3831), rare (3974) and common (1434) insertions with an average of 770 insertions per individual. We achieved an 89% PCR validation of the predicted genotypes in 94 samples tested. About 60% of identified InDels are unique to IndiGen when compared to other global datasets; 23% of sites were shared with both SGDP and HGSVC; among these, 58% (1289 sites) were common polymorphisms in IndiGen. The insertions not only show a bias for genic regions, with a preference for introns but also for the associated genes showing enrichment for processes like cell morphogenesis and neurogenesis (P-value < 0.05). Approximately, 60% of InDels mapped to genes present in the OMIM database. Finally, we show that 558 InDels can serve as ancestry informative markers to segregate global populations. This study provides a valuable resource for baseline Alu InDels that would be useful in population genomics.
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Affiliation(s)
- P Prakrithi
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Khushboo Singhal
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Disha Sharma
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Vigneshwar Senthilvel
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Anushree Mishra
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mitali Mukerji
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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30
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Solakoglu Ö, Steinbach B, Götz W, Heydecke G, Schwarzenbach H. Characterization of circulating molecules and activities in plasma of patients after allogeneic and autologous intraoral bone grafting procedures: a prospective randomized controlled clinical trial in humans. BMC Oral Health 2022; 22:24. [PMID: 35094679 PMCID: PMC8802434 DOI: 10.1186/s12903-021-02036-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/08/2021] [Indexed: 11/23/2022] Open
Abstract
Background The objective was to assess whether intraoral bone augmentation procedures have an impact on the patient’s plasma levels of circulating nucleic acids, exosomes, miRNA levels and caspase activities. The null hypothesis was tested, that no significant differences between the two groups will be found. Methods In this prospective randomized controlled clinical trial 35 systemically healthy non-smoking participants were randomly allocated using sealed envelopes by a blinded clinician not involved in the clinical setting. Plasma samples were collected preoperatively and 3 times postoperatively (immediately, 5 weeks and 4 months postoperatively). The test group consisted of twenty-five patients who received allogeneic bone grafting material and the control group of ten patients who received autologous bone grafts. Levels of cell-free DNA (cfDNA) and microRNAs (miR-21, miR-27a, miR-218) were quantified by real-time PCR, caspase activities and exosome concentrations were determined by ELISA. Results Statistical evaluation reveled a significantly higher exosome level before surgery (p = 0.013) and the first postsurgical sample (p = 0.017) in the control group compared to the test group. The levels of miR-27a and miR-218 significantly differed between the plasma samples before surgery and after surgery in both groups. The levels of miR-21 only significantly differed between the pre- and postsurgical plasma samples in the test group, but not in the control group. All patients completed the study, no adverse events were recorded. Conclusions Our data show the diagnostic potential of the plasma levels of miR-27a, miR-218 and miR-21 in detecting changes in bone metabolism after alveolar bone augmentation. Our very promising results indicate that there might be a high diagnostic potential in evaluating the plasma levels of the before mentioned miRNAs in order to detect bone resorption activities before they become clinically relevant. Trial registration Ethical commission of the Ärztekammer Hamburg, Germany (PV5211) on 11/03/2016 as well as by the German Registry of Clinical Studies (DRKS 00,013,010) on 30/07/2018 (http://apps.who.int/trialsearch/). Supplementary Information The online version contains supplementary material available at 10.1186/s12903-021-02036-7.
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31
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Laine P, Rowell WJ, Paulin L, Kujawa S, Raterman D, Mayhew G, Wendt J, Burgess DL, Partonen T, Paunio T, Auvinen P, Ekholm JM. Alu element in the RNA binding motif protein, X-linked 2 (RBMX2) gene found to be linked to bipolar disorder. PLoS One 2021; 16:e0261170. [PMID: 34914762 PMCID: PMC8675739 DOI: 10.1371/journal.pone.0261170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022] Open
Abstract
Objective We have used long-read single molecule, real-time (SMRT) sequencing to fully characterize a ~12Mb genomic region on chromosome Xq24-q27, significantly linked to bipolar disorder (BD) in an extended family from a genetic sub-isolate. This family segregates BD in at least four generations with 24 affected individuals. Methods We selected 16 family members for targeted sequencing. The selected individuals either carried the disease haplotype, were non-carriers of the disease haplotype, or served as married-in controls. We designed hybrid capture probes enriching for 5-9Kb fragments spanning the entire 12Mb region that were then sequenced to screen for candidate structural variants (SVs) that could explain the increased risk for BD in this extended family. Results Altogether, 201 variants were detected in the critically linked region. Although most of these represented common variants, three variants emerged that showed near-perfect segregation among all BD type I affected individuals. Two of the SVs were identified in or near genes belonging to the RNA Binding Motif Protein, X-Linked (RBMX) gene family—a 330bp Alu (subfamily AluYa5) deletion in intron 3 of the RBMX2 gene and an intergenic 27bp tandem repeat deletion between the RBMX and G protein-coupled receptor 101 (GPR101) genes. The third SV was a 50bp tandem repeat insertion in intron 1 of the Coagulation Factor IX (F9) gene. Conclusions Among the three genetically linked SVs, additional evidence supported the Alu element deletion in RBMX2 as the leading candidate for contributing directly to the disease development of BD type I in this extended family.
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Affiliation(s)
- Pia Laine
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Steve Kujawa
- Pacific Biosciences, Menlo Park, CA, United States of America
| | - Denise Raterman
- Roche Sequencing Solutions, Madison, WI, United States of America
| | - George Mayhew
- Roche Sequencing Solutions, Madison, WI, United States of America
| | - Jennifer Wendt
- Roche Sequencing Solutions, Madison, WI, United States of America
| | | | - Timo Partonen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Tiina Paunio
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jenny M. Ekholm
- Pacific Biosciences, Menlo Park, CA, United States of America
- * E-mail:
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32
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Soejima M, Koda Y. Real-time PCR-based detection of the Alu-mediated deletion of FUT2 (se del2). Leg Med (Tokyo) 2021; 54:101986. [PMID: 34736142 DOI: 10.1016/j.legalmed.2021.101986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/16/2021] [Accepted: 10/25/2021] [Indexed: 10/19/2022]
Abstract
Secretor status of the ABH(O) histoblood group antigens is regulated by secretor type α(1,2)fucosyltransferase encoded by FUT2. The sedel2 allele is a complete deletion of the FUT2 coding region generated by Alu-mediated homologous recombination. This deletion seems to be exclusively encountered in certain Oceanian populations. From the perspective of forensic science, sedel2 is considered to be one of ancestry informative markers for these populations. Real-time PCR followed by melting curve analysis was employed to find primer set to specifically amplify sedel2. We designed primers which produced a 231-bp amplicon specific to sedel2. The specificity of these primers was also confirmed by gel electrophoresis and sequencing of the PCR product. Then, two real-time PCR methods based on melting curve analysis and a hydrolysis probe were designed to determine sedel2 zygosity by adding FUT2-specific primers. These two methods were validated by analyzing 24 Samoan subjects. The results obtained from 24 Samoan subjects by the two methods were fully in accordance with those obtained by a previous conventional PCR method that amplified a 2.7-kb fragment of sedel2. Therefore, these two methods seemed to accurately determine the zygosity of sedel2 and were useful for investigation of the distribution and origin of this deletion.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan.
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Kishita Y, Shimura M, Kohda M, Fushimi T, Nitta KR, Yatsuka Y, Hirose S, Ideguchi H, Ohtake A, Murayama K, Okazaki Y. Genome sequencing and RNA-seq analyses of mitochondrial complex I deficiency revealed Alu insertion-mediated deletion in NDUFV2. Hum Mutat 2021; 42:1422-1428. [PMID: 34405929 DOI: 10.1002/humu.24274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/25/2021] [Accepted: 07/15/2021] [Indexed: 11/08/2022]
Abstract
Isolated complex I deficiency is the most common cause of pediatric mitochondrial disease. Exome sequencing (ES) has revealed many complex I causative genes. However, there are limitations associated with identifying causative genes by ES analysis. In this study, we performed multiomics analysis to reveal the causal variants. We here report two cases with mitochondrial complex I deficiency. In both cases, ES identified a novel c.580G>A (p.Glu194Lys) variant in NDUFV2. One case additionally harbored c.427C>T (p.Arg143*), but no other variants were observed in the other case. RNA sequencing showed aberrant exon splicing of NDUFV2 in the unsolved case. Genome sequencing revealed a novel heterozygous deletion in NDUFV2, which included one exon and resulted in exon skipping. Detailed examination of the breakpoint revealed that an Alu insertion-mediated rearrangement caused the deletion. Our report reveals that combined use of transcriptome sequencing and GS was effective for diagnosing cases that were unresolved by ES.
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Affiliation(s)
- Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Masaru Shimura
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Masakazu Kohda
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Takuya Fushimi
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Kazuhiro R Nitta
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yukiko Yatsuka
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Shinichi Hirose
- General Medical Research Center, School of Medicine, Fukuoka University, Fukuoka, Japan
| | - Hiroshi Ideguchi
- Department of Pediatrics, Fukuoka Sanno Hospital, Fukuoka, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Saitama, Japan.,Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - Kei Murayama
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Metabolism, Chiba Children's Hospital, Chiba, Japan.,Center for Medical Genetics, Chiba Children's Hospital, Chiba, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Laboratory for Comprehensive Genomic Analysis, RIKEN Centre for Integrative Medical Sciences, Kanagawa, Japan
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Suzuki H, Matsuoka M. Proline-arginine poly-dipeptide encoded by the C9orf72 repeat expansion inhibits adenosine deaminase acting on RNA. J Neurochem 2021; 158:753-765. [PMID: 34081786 DOI: 10.1111/jnc.15445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022]
Abstract
A GGGGCC hexanucleotide repeat expansion in the C9orf72 gene is linked to the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (C9-ALS/FTD). Unconventional translation of the hexanucleotide repeat expansion generates five dipeptide repeat proteins (DPRs). The molecular mechanism underlying the DPR-linked neurotoxicity is under investigation. In this study, using cell-based models, we show that poly-proline-arginine DPR (poly-PR), the most neurotoxic DPR in vitro, binds to adenosine deaminase acting on RNA (ADAR)1p110 and ADAR2 and inhibits their RNA editing activity. We further show that poly-PR impairs cellular stress response that is mediated by ADAR1p110. These results together suggest that the poly-PR-mediated inhibition of the ADAR activity contributes to C9-ALS/FTD-linked neurotoxicity.
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Affiliation(s)
- Hiroaki Suzuki
- Department of Pharmacology, School of Medicine, Tokyo Medical University, Tokyo, Japan
| | - Masaaki Matsuoka
- Department of Pharmacology, School of Medicine, Tokyo Medical University, Tokyo, Japan
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Robust Benchmark Structural Variant Calls of An Asian Using the State-of-art Long Fragment Sequencing Technologies. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 20:192-204. [PMID: 33662625 PMCID: PMC9510867 DOI: 10.1016/j.gpb.2020.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/17/2020] [Accepted: 12/26/2020] [Indexed: 12/12/2022]
Abstract
The importance of structural variants (SVs) for human phenotypes and diseases is now recognized. Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed, few benchmarking procedures are available to confidently assess their performances in biological and clinical research. To facilitate the validation and application of these SV detection approaches, we established an Asian reference material by characterizing the genome of an Epstein-Barr virus (EBV)-immortalized B lymphocyte line along with identified benchmark regions and high-confidence SV calls. We established a high-confidence SV callset with 8938 SVs by integrating four alignment-based SV callers, including 109× Pacific Biosciences (PacBio) continuous long reads (CLRs), 22× PacBio circular consensus sequencing (CCS) reads, 104× Oxford Nanopore Technologies (ONT) long reads, and 114× Bionano optical mapping platform, and one de novo assembly-based SV caller using CCS reads. A total of 544 randomly selected SVs were validated by PCR amplification and Sanger sequencing, demonstrating the robustness of our SV calls. Combining trio-binning-based haplotype assemblies, we established an SV benchmark for identifying false negatives and false positives by constructing the continuous high-confidence regions (CHCRs), which covered 1.46 gigabase pairs (Gb) and 6882 SVs supported by at least one diploid haplotype assembly. Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology, disease, and clinical research.
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36
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Xu F, Li W, Yang X, Na L, Chen L, Liu G. The Roles of Epigenetics Regulation in Bone Metabolism and Osteoporosis. Front Cell Dev Biol 2021; 8:619301. [PMID: 33569383 PMCID: PMC7868402 DOI: 10.3389/fcell.2020.619301] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Osteoporosis is a metabolic disease characterized by decreased bone mineral density and the destruction of bone microstructure, which can lead to increased bone fragility and risk of fracture. In recent years, with the deepening of the research on the pathological mechanism of osteoporosis, the research on epigenetics has made significant progress. Epigenetics refers to changes in gene expression levels that are not caused by changes in gene sequences, mainly including DNA methylation, histone modification, and non-coding RNAs (lncRNA, microRNA, and circRNA). Epigenetics play mainly a post-transcriptional regulatory role and have important functions in the biological signal regulatory network. Studies have shown that epigenetic mechanisms are closely related to osteogenic differentiation, osteogenesis, bone remodeling and other bone metabolism-related processes. Abnormal epigenetic regulation can lead to a series of bone metabolism-related diseases, such as osteoporosis. Considering the important role of epigenetic mechanisms in the regulation of bone metabolism, we mainly review the research progress on epigenetic mechanisms (DNA methylation, histone modification, and non-coding RNAs) in the osteogenic differentiation and the pathogenesis of osteoporosis to provide a new direction for the treatment of bone metabolism-related diseases.
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Affiliation(s)
- Fei Xu
- College of Medical Technology, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Collaborative Innovation Center, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Wenhui Li
- Collaborative Innovation Center, Shanghai University of Medicine and Health Sciences, Shanghai, China
- College of Clinical Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Xiao Yang
- Traditional Chinese Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lixin Na
- Collaborative Innovation Center, Shanghai University of Medicine and Health Sciences, Shanghai, China
- College of Public Health, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Linjun Chen
- College of Medical Technology, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Guobin Liu
- Traditional Chinese Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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37
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Li L, Jia C, Tang Y, Kong Y, Xia Y, Ma L. Novel Gross Deletion Mutations in NTRK1 Gene Associated With Congenital Insensitivity to Pain With Anhidrosis. Front Pediatr 2021; 9:638190. [PMID: 33748046 PMCID: PMC7969531 DOI: 10.3389/fped.2021.638190] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 01/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Congenital insensitivity to pain with anhidrosis (CIPA) is a rare inherited autosomal recessive disorder characterized by insensitivity to noxious stimuli, anhidrosis, recurrent fever, and intellectual disability. CIPA is mainly caused by mutations in the neurotrophic tyrosine kinase receptor type 1 gene (NTRK1). This study aims to identify pathogenic mutations underlying CIPA in two unrelated Chinese families. Methods: DNA was extracted from blood samples of patients and their available family members and subjected to whole exome sequencing (WES). Real-time PCR (qPCR), Gap-PCR, and Sanger sequencing were applied to verify the identified variants. Result: We found novel compound gross deletion mutations [exon1-6 del (g.1-1258_10169del); exon5-7 del (g.6995_11999del)] of NTRK1 (MIM 191315) gene in family 1 and the compound heterozygous mutations [c.851-33T>A; exon5-7 del (g.6995_11999del)] in family 2. Interestingly, we discovered the intragenic novel gross deletion [exon5-7 del (g.6995_11999del)] mediated by recombination between Alu elements. Conclusions: The present study highlights two rare gross deletion mutations in the NTRK1 gene associated with CIPA in two unrelated Chinese families. The deletion of exon1-6 (g.1-1258_10169del) is thought to be the largest NTRK1 deletion reported to date. Our findings expand the mutation spectrum of NTRK1 mutations in the Chinese and could be useful for prenatal interventions and more precise pharmacological treatments to patients. WES conducted in our study is a convenient and useful tool for clinical diagnosis of CIPA and other associated disorders.
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Affiliation(s)
- Lulu Li
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Chao Jia
- Department of Neonatology, Hebei Provincial Children's Hospital, Shijiazhuang, China
| | - Yue Tang
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Yuanyuan Kong
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Yaofang Xia
- Department of Neonatology, Hebei Provincial Children's Hospital, Shijiazhuang, China
| | - Li Ma
- Department of Neonatology, Hebei Provincial Children's Hospital, Shijiazhuang, China
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38
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Neroev V, Malishevskaya T, Weinert D, Astakhov S, Kolomeichuk S, Cornelissen G, Kabitskaya Y, Boiko E, Nemtsova I, Gubin D. Disruption of 24-Hour Rhythm in Intraocular Pressure Correlates with Retinal Ganglion Cell Loss in Glaucoma. Int J Mol Sci 2020; 22:359. [PMID: 33396443 PMCID: PMC7795318 DOI: 10.3390/ijms22010359] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 02/08/2023] Open
Abstract
Parameters of 24-h rhythm in intraocular pressure (IOP) were assessed in patients with stable or advanced primary open-angle glaucoma (S-POAG/A-POAG) and referenced to the phase of "marker" circadian temperature rhythm of each patient. Body temperature and IOP were measured over a 72-h span in 115 participants (65 S-POAG and 50 A-POAG). Retinal Ganglion Cell (RGC) damage was assessed by high-definition optical coherence tomography. The 24-h IOP rhythm in A-POAG patients peaked during the night, opposite to the daytime phase position in S-POAG patients (p < 0.0001). The 24-h IOP phase correlated with RGC loss (p < 0.0001). The internal phase shift between IOP and body temperature gradually increased with POAG progression (p < 0.001). Angiotensin converting enzyme Alu-repeat deletion/insertion (ACE I/D) emerged as a candidate gene polymorphism, which may play a role in the alteration of the circadian IOP variability in advanced glaucoma. To conclude, a reliable estimation of the 24-h rhythm in IOP requires the degree of RGC damage to be assessed. In advanced POAG, the 24-h phase of IOP tended to occur during the night and correlated with RGC loss, being progressively delayed relative to the phase of temperature.
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Affiliation(s)
- Vladimir Neroev
- Helmholtz Research Institute of Eye Diseases, 105062 Moscow, Russia; (V.N.); (T.M.)
| | | | - Dietmar Weinert
- Institute of Biology/Zoology, Martin Luther University, 06108 Halle-Wittenberg, Germany;
| | - Sergei Astakhov
- Department of Ophthalmology, Pavlov First Saint Petersburg State Medical University, 197022 St. Petersburg, Russia;
| | - Sergey Kolomeichuk
- Laboratory of Genetics, Institute of Biology of the Karelian Science Center of the Russian Academy of Sciences, 185910 Petrozavodsk, Russia;
| | - Germaine Cornelissen
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Yana Kabitskaya
- Сenter for Genomic Technologies, Northern Trans-Ural State Agricultural University, 625003 Tyumen, Russia; (Y.K.); (E.B.)
| | - Elena Boiko
- Сenter for Genomic Technologies, Northern Trans-Ural State Agricultural University, 625003 Tyumen, Russia; (Y.K.); (E.B.)
| | - Irina Nemtsova
- State Autonomous Health Care Institution Tyumen Regional Ophthalmological Dispensary, 625048 Tyumen, Russia;
| | - Denis Gubin
- Department of Biology, Medical University, 625023 Tyumen, Russia
- Tyumen Cardiology Research Center, Tomsk National Research Medical Center, Russian Academy of Science, 634009 Tomsk, Russia
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Ahmadi A, De Toma I, Vilor-Tejedor N, Eftekhariyan Ghamsari MR, Sadeghi I. Transposable elements in brain health and disease. Ageing Res Rev 2020; 64:101153. [PMID: 32977057 DOI: 10.1016/j.arr.2020.101153] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/22/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022]
Abstract
Transposable elements (TEs) occupy a large fraction of the human genome but only a small proportion of these elements are still active today. Recent works have suggested that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in behavior and cognition, and contribute to vulnerability to disease. As active TEs could induce genetic diversity and mutagenesis, their influences on human brain development and diseases are of great interest. In this review, we will focus on the active TEs in the human genome and discuss in detail their impacts on human brain development. Furthermore, the association between TEs and brain-related diseases is discussed.
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Gisatulin M, Dobricic V, Zühlke C, Hellenbroich Y, Tadic V, Münchau A, Isenhardt K, Bürk K, Bahlo M, Lockhart PJ, Lohmann K, Helmchen C, Brüggemann N. Clinical spectrum of the pentanucleotide repeat expansion in the RFC1 gene in ataxia syndromes. Neurology 2020; 95:e2912-e2923. [PMID: 32873692 DOI: 10.1212/wnl.0000000000010744] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/25/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To determine the clinical significance of an intronic biallelic pentanucleotide repeat expansion in the gene encoding replication factor C subunit 1 (RFC1) in patients with late-onset cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS), in patients with other ataxias, and in healthy controls by comprehensive genetic analyses. METHODS In this case-control study, we included 457 individuals comprising 26 patients with complete or incomplete CANVAS, 70 patients with late-onset cerebellar ataxia, 208 healthy controls, and 153 individuals from 39 multigenerational families without ataxia to determine repeat stability. All 96 patients were screened for the repeat expansion by duplex PCR. To further characterize the repeat type and lengths, we used fragment length analysis, repeat-primed PCR, Sanger sequencing, and Southern blotting. Expression of RFC1 and the neighboring gene WDR19 were determined by quantitative PCR. RESULTS Massive biallelic pentanucleotide expansions were found in 15/17 patients with complete CANVAS (88%), in 2/9 patients with incomplete CANVAS (22%), in 4/70 patients with unspecified, late-onset cerebellar ataxia (6%), but not in controls. In patients, the expansion comprised 800-1,000 mostly AAGGG repeats. Nonmassively expanded repeat numbers were in the range of 7-137 repeats and relatively stable during transmission. Expression of RFC1 and WDR19 were unchanged and RFC1 intron retention was not found. CONCLUSIONS A biallelic pentanucleotide repeat expansion is a frequent cause of CANVAS and found in a considerable number of patients with an incomplete clinical presentation or other forms of cerebellar ataxia. The mechanism by which the repeat expansions are causing disease remains unclear and warrants further investigations.
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Affiliation(s)
- Maria Gisatulin
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Valerija Dobricic
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Christine Zühlke
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Yorck Hellenbroich
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Vera Tadic
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Alexander Münchau
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Klaus Isenhardt
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Katrin Bürk
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Melanie Bahlo
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Paul J Lockhart
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Katja Lohmann
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Christoph Helmchen
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Norbert Brüggemann
- From the Institute of Neurogenetics (M.G., V.D., V.T., K.L., N.B.), Institute of Human Genetics (C.Z., Y.H.), Institute of Systems Motor Science (A.M.), and Center of Brain, Behavior and Metabolism (N.B.), University of Lübeck; Department of Neurology (V.T., C.H., N.B.), University Medical Center Schleswig-Holstein, Campus Lübeck; Department of Neurology (K.I.), Klinikum Aschaffenburg; Department of Neurology (K.B.), Kliniken Schmieder, Stuttgart, Germany; Population Health and Immunity Division (M.B.), The Walter and Eliza Hall Institute of Medical Research; Department of Medical Biology (M.B.), University of Melbourne; Bruce Lefroy Centre (P.J.L.), Murdoch Children's Research Institute; and Department of Pediatrics (P.J.L.), University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.
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A comprehensive analysis of chimpanzee (Pan Troglodytes)-specific AluYb8 element. Genes Genomics 2020; 42:1207-1213. [PMID: 32860627 DOI: 10.1007/s13258-020-00989-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Alu elements are most abundant retrotransposons with > 1.2 million copies in the primate genome. AluYb8 subfamily was diverged from AluY lineage, and has accumulated eight diagnostic mutations and 7-bp duplication during primate evolution. A total of 1851 AluYb copies are present in the human genome, and most of them are human-specific. On the other hand, only a few AluYb8 copies were identified in the chimpanzee genome by previous studies on AluYb8. The significantly different number of species-specific AluYb8 elements between human and chimpanzee might result from the incompletion of chimpanzee reference genome sequences at the time of the previous study. OBJECTIVE AluYb8 elements could generate genomic structural variations in the chimpanzee genome. This study aimed to identify and characterize chimpanzee-specific AluYb elements using the most updated chimpanzee reference genome sequences (Jan. 2018, panTro6). METHODS To identify chimpanzee-specific AluYb8, we carried out genomic comparison with non-chimpanzee primate genome using the UCSC table browser. In addition, chimpanzee-specific AluYb8 candidates were manually inspected and experimentally verified using PCR and Sanger sequencing. RESULTS Among a total of 231 chimpanzee-specific AluYb8 candidates, 11 of the candidates are chimpanzee-specific AluYb8, and 29 elements are shared between the chimpanzee and non-chimpanzee primate genomes. Through the sequence analysis of AluYb8 and other Alu subfamilies, we were able to observe various diagnostic mutations and variable length duplications in 7-bp duplication region of AluYb8 element. In addition, we further validated two of the chimpanzee-specific AluYb8 elements (CS8 and CS20) that were not previously discovered by display PCR and Sanger sequencing. Interestingly, we identified a AluYb8 insertion-mediated deletion (CS8 locus) in the chimpanzee genome. CONCLUSION Our study found that AluYb8 elements are much more abundant in the human genome than chimpanzee genome, and that it could be due to the absence of hyperactive "master" AluYb8 elements in the chimpanzee genome.
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Kaarniranta K, Pawlowska E, Szczepanska J, Blasiak J. DICER1 in the Pathogenesis of Age-related Macular Degeneration (AMD) - Alu RNA Accumulation versus miRNA Dysregulation. Aging Dis 2020; 11:851-862. [PMID: 32765950 PMCID: PMC7390522 DOI: 10.14336/ad.2019.0809] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022] Open
Abstract
DICER1 deficiency in the retinal pigment epithelium (RPE) was associated with the accumulation of Alu transcripts and implicated in geographic atrophy (GA), a form of age-related macular degeneration (AMD), an eye disease leading to blindness in millions of people. Although the exact mechanism of this association is not fully known, the activation of the NLRP3 inflammasome, maturation of caspase-1 and disruption in mitochondrial homeostasis in RPE cells were shown as critical for it. DICER1 deficiency results in dysregulation of miRNAs and changes in the expression of many genes important for RPE homeostasis, which may also contribute to AMD. DICER1 deficiency can change the functions of the miR-183/96/182 cluster that regulates photoreceptors and their synaptic transmission. Aging, the main AMD risk factor, is associated with decreased expression of DICER1 and changes in its diurnal pattern that are not synchronized with circadian regulation in the retina. The initial insult inducing DICER1 deficiency in AMD may be oxidative stress, another major risk factor of AMD, but further studies on the role of deficient DICER1 in AMD pathogenesis and its therapeutic potential are needed.
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Affiliation(s)
- Kai Kaarniranta
- 1Department of Ophthalmology, University of Eastern Finland, Kuopio 70211, Finland and Department of Ophthalmology, Kuopio University Hospital, Kuopio 70029, Finland
| | - Elzbieta Pawlowska
- 2Department of Orthodontics, Medical University of Lodz, 92-216 Lodz, Poland
| | - Joanna Szczepanska
- 3Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland
| | - Janusz Blasiak
- 4Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
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Choe SH, Park SJ, Cho HM, Park HR, Lee JR, Kim YH, Huh JW. A single mutation in the ACTR8 gene associated with lineage-specific expression in primates. BMC Evol Biol 2020; 20:66. [PMID: 32503430 PMCID: PMC7275561 DOI: 10.1186/s12862-020-01620-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/29/2020] [Indexed: 12/17/2022] Open
Abstract
Background Alternative splicing (AS) generates various transcripts from a single gene and thus plays a significant role in transcriptomic diversity and proteomic complexity. Alu elements are primate-specific transposable elements (TEs) and can provide a donor or acceptor site for AS. In a study on TE-mediated AS, we recently identified a novel AluSz6-exonized ACTR8 transcript of the crab-eating monkey (Macaca fascicularis). In the present study, we sought to determine the molecular mechanism of AluSz6 exonization of the ACTR8 gene and investigate its evolutionary and functional consequences in the crab-eating monkey. Results We performed RT-PCR and genomic PCR to analyze AluSz6 exonization in the ACTR8 gene and the expression of the AluSz6-exonized transcript in nine primate samples, including prosimians, New world monkeys, Old world monkeys, and hominoids. AluSz6 integration was estimated to have occurred before the divergence of simians and prosimians. The Alu-exonized transcript obtained by AS was lineage-specific and expressed only in Old world monkeys and apes, and humans. This lineage-specific expression was caused by a single G duplication in AluSz6, which provides a new canonical 5′ splicing site. We further identified other alternative transcripts that were unaffected by the AluSz6 insertion. Finally, we observed that the alternative transcripts were transcribed into new isoforms with C-terminus deletion, and in silico analysis showed that these isoforms do not have a destructive function. Conclusions The single G duplication in the TE sequence is the source of TE exonization and AS, and this mutation may suffer a different fate of ACTR8 gene expression during primate evolution.
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Affiliation(s)
- Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea
| | - Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Hye-Ri Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Ja-Rang Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56216, Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.
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Kim S, Shin W, Lee YM, Mun S, Han K. Differential expressions of L1-chimeric transcripts in normal and matched-cancer tissues. Anal Biochem 2020; 600:113769. [PMID: 32430276 DOI: 10.1016/j.ab.2020.113769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/25/2020] [Accepted: 05/05/2020] [Indexed: 01/20/2023]
Abstract
L1s are a cis-regulatory elements and contain bidirectional internal promoters within the 5' untranslated region (UTR). L1s provide bidirectional promoters that generate alternative transcripts and affect differential expressions in the human genome. In particular, L1 antisense promoters (L1ASPs) could produce aberrant transcripts in cancer tissues compared to normal tissues. In this study, we identified the L1-chimeric transcripts derived from L1ASPs and analyzed relative expression of L1-chimeric transcripts between normal and matched-cancer tissues. First, we collected 425 L1-chimeric transcripts by referring to previous studies. Through the manual inspection, we identified 144 L1-chimeric transcripts derived from 44 L1 antisense promoters, suggesting that the antisense promoter acted as an alternative promoter. We analyzed relative gene expression levels of 16 L1-chimeric transcripts between matched cancer-normal tissue pair (lung, liver, gastric, kidney, thyroid, breast, ovary, uterus, and prostate) using real-time quantitative PCR (RT-qPCR) and investigated putative transcription factor binding motifs to determine activity of L1ASPs. Taken together, we propose that L1ASPs could contribute to the differential gene expression between normal and cancer tissues.
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Affiliation(s)
- Songmi Kim
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - Wonseok Shin
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea
| | - Yong-Moon Lee
- Department of Pathology, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea; Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea; NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea; Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
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Jedličková I, Přistoupilová A, Nosková L, Majer F, Stránecký V, Hartmannová H, Hodaňová K, Trešlová H, Hýblová M, Solár P, Minárik G, Giertlová M, Kmoch S. Spinal muscular atrophy caused by a novel Alu-mediated deletion of exons 2a-5 in SMN1 undetectable with routine genetic testing. Mol Genet Genomic Med 2020; 8:e1238. [PMID: 32337852 PMCID: PMC7336725 DOI: 10.1002/mgg3.1238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 12/26/2022] Open
Abstract
Background Spinal muscular atrophy (SMA) is an inherited neuromuscular disease affecting 1 in 8,000 newborns. The majority of patients carry bi‐allelic variants in the survival of motor neuron 1 gene (SMN1). SMN1 is located in a duplicated region on chromosome 5q13 that contains Alu elements and is predisposed to genomic rearrangements. Due to the genomic complexity of the SMN region and genetic heterogeneity, approximately 50% of SMA patients remain without genetic diagnosis that is a prerequisite for genetic treatments. In this work we describe the diagnostic odyssey of one SMA patient in whom routine diagnostics identified only a maternal heterozygous SMN1Δ(7–8) deletion. Methods We characterized SMN transcripts, assessed SMN protein content in peripheral blood mononuclear cells (PBMC), estimated SMN genes dosage, and mapped genomic rearrangement in the SMN region. Results We identified an Alu‐mediated deletion encompassing exons 2a‐5 of SMN1 on the paternal allele and a complete deletion of SMN1 on the maternal allele as the cause of SMA in this patient. Conclusion Alu‐mediated rearrangements in SMN1 can escape routine diagnostic testing. Parallel analysis of SMN gene dosage, SMN transcripts, and total SMN protein levels in PBMC can identify genomic rearrangements and should be considered in genetically undefined SMA cases.
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Affiliation(s)
- Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Filip Majer
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Peter Solár
- Department of Medical Biology, Faculty of Medicine, P.J. Safarik University, Kosice, Slovakia
| | - Gabriel Minárik
- Department of Clinical Genetics, Medirex A.S., Kosice, Slovakia
| | - Mária Giertlová
- Department of Clinical Genetics, Medirex A.S., Kosice, Slovakia
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
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46
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Lou C, Goodier JL, Qiang R. A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage. Reprod Biol Endocrinol 2020; 18:6. [PMID: 31964400 PMCID: PMC6971995 DOI: 10.1186/s12958-020-0564-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022] Open
Abstract
LINE1 retrotransposons are mobile DNA elements that copy and paste themselves into new sites in the genome. To ensure their evolutionary success, heritable new LINE-1 insertions accumulate in cells that can transmit genetic information to the next generation (i.e., germ cells and embryonic stem cells). It is our hypothesis that LINE1 retrotransposons, insertional mutagens that affect expression of genes, may be causal agents of early miscarriage in humans. The cell has evolved various defenses restricting retrotransposition-caused mutation, but these are occasionally relaxed in certain somatic cell types, including those of the early embryo. We predict that reduced suppression of L1s in germ cells or early-stage embryos may lead to excessive genome mutation by retrotransposon insertion, or to the induction of an inflammatory response or apoptosis due to increased expression of L1-derived nucleic acids and proteins, and so disrupt gene function important for embryogenesis. If correct, a novel threat to normal human development is revealed, and reverse transcriptase therapy could be one future strategy for controlling this cause of embryonic damage in patients with recurrent miscarriages.
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Affiliation(s)
- Chao Lou
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
| | - John L. Goodier
- 0000 0001 2171 9311grid.21107.35McKusick-Nathans Deartment of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Rong Qiang
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
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47
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Shi M, Chen X, Zeng L, Li Z, Liang D, Wu L. The rare Alus element-mediated chimerism of multiple de novo complex rearrangement sequences in GAN result in giant axonal neuropathy. Clin Chim Acta 2019; 502:91-98. [PMID: 31877298 DOI: 10.1016/j.cca.2019.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 02/02/2023]
Abstract
Giant axonal neuropathy (GAN) is a rare and grievous autosomal recessive neurodegenerative disease due to loss-of-function mutation in GAN. However, the chimerism of complex rearrangement sequences of GAN has not been reported so far, and the mechanism for its complex rearrangements remains to be determined. We identified a family with clinical symptoms of GAN and aimed to reveal a genetic cause underlying this disease. By whole-exome sequencing in the patient we identified a novel homozygous frameshift mutation with 1 bp deletion (c.27delC) in GAN. However, when analyzed the patient's genomic DNA (gDNA) by quantitative real-time PCR and breakpoint DNA sequencing, we found the chimerism of multiple complex rearrangement sequences encompassing exon 1 of GAN in the patient's genome. The microhomology and localization of the breakpoint indicated that they may be caused by Alu repeat elements. We also found that the mRNA expression level of GAN in patient's lymphocyte was decreased, confirming the pathogenicity of these mutations. Our study is the first reported on many complex rearrangement sequences mosaic in GAN mediated by Alu element. The patient here is not a simple homozygous frameshift mutation, but a compound heterozygous paternal c.27delC mutation and the chimerism of multiple de novo complex rearrangement sequences in GAN. Our results may also provide new insights into the formation and pathogenicity of complex rearrangement in GAN, and may be helpful to genetic counseling and genetic testing. It also enriches the Alu-mediated disease-associated database which are important for correct clinical interpretation.
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Affiliation(s)
- Meizhen Shi
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, PR China
| | - Xin Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, PR China
| | - Lanlan Zeng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, PR China
| | - Zhuo Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, PR China
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, PR China.
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, PR China.
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48
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Wang Y, Bernhardy AJ, Nacson J, Krais JJ, Tan YF, Nicolas E, Radke MR, Handorf E, Llop-Guevara A, Balmaña J, Swisher EM, Serra V, Peri S, Johnson N. BRCA1 intronic Alu elements drive gene rearrangements and PARP inhibitor resistance. Nat Commun 2019; 10:5661. [PMID: 31827092 PMCID: PMC6906494 DOI: 10.1038/s41467-019-13530-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/14/2019] [Indexed: 12/28/2022] Open
Abstract
BRCA1 mutant carcinomas are sensitive to PARP inhibitor (PARPi) therapy; however, resistance arises. BRCA1 BRCT domain mutant proteins do not fold correctly and are subject to proteasomal degradation, resulting in PARPi sensitivity. In this study, we show that cell lines and patient-derived tumors, with highly disruptive BRCT domain mutations, have readily detectable BRCA1 protein expression, and are able to proliferate in the presence of PARPi. Peptide analyses reveal that chemo-resistant cancers contain residues encoded by BRCA1 intron 15. Mechanistically, cancers with BRCT domain mutations harbor BRCA1 gene breakpoints within or adjacent to Alu elements in intron 15; producing partial gene duplications, inversions and translocations, and terminating transcription prior to the mutation-containing BRCT domain. BRCA1 BRCT domain-deficient protein isoforms avoid mutation-induced proteasomal degradation, support homology-dependent DNA repair, and promote PARPi resistance. Taken together, Alu-mediated BRCA1 gene rearrangements are responsible for generating hypomorphic proteins, and may represent a biomarker of PARPi resistance.
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Affiliation(s)
- Yifan Wang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Andrea J Bernhardy
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Joseph Nacson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19111, USA
| | - John J Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Yin-Fei Tan
- Genomics Facility, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Emmanuelle Nicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Genomics Facility, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Marc R Radke
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Elizabeth Handorf
- Bioinformatics and Statistics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Suraj Peri
- Bioinformatics and Statistics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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Zheng Y, Hlady RA, Joyce BT, Robertson KD, He C, Nannini DR, Kibbe WA, Achenbach CJ, Murphy RL, Roberts LR, Hou L. DNA methylation of individual repetitive elements in hepatitis C virus infection-induced hepatocellular carcinoma. Clin Epigenetics 2019; 11:145. [PMID: 31639042 PMCID: PMC6802191 DOI: 10.1186/s13148-019-0733-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023] Open
Abstract
Background The two most common repetitive elements (REs) in humans, long interspersed nuclear element-1 (LINE-1) and Alu element (Alu), have been linked to various cancers. Hepatitis C virus (HCV) may cause hepatocellular carcinoma (HCC) by suppressing host defenses, through DNA methylation that controls the mobilization of REs. We aimed to investigate the role of RE methylation in HCV-induced HCC (HCV-HCC). Results We studied methylation of over 30,000 locus-specific REs across the genome in HCC, cirrhotic, and healthy liver tissues obtained by surgical resection. Relative to normal liver tissue, we observed the largest number of differentially methylated REs in HCV-HCC followed by alcohol-induced HCC (EtOH-HCC). After excluding EtOH-HCC-associated RE methylation (FDR < 0.001) and those unable to be validated in The Cancer Genome Atlas (TCGA), we identified 13 hypomethylated REs (11 LINE-1 and 2 Alu) and 2 hypermethylated REs (1 LINE-1 and 1 Alu) in HCV-HCC (FDR < 0.001). A majority of these REs were located in non-coding regions, preferentially enriched with chromatin repressive marks H3K27me3, and positively associated with gene expression (median correlation r = 0.32 across REs). We further constructed an HCV-HCC RE methylation score that distinguished HCV-HCC (lowest score), HCV-cirrhosis, and normal liver (highest score) in a dose-responsive manner (p for trend < 0.001). HCV-cirrhosis had a lower score than EtOH-cirrhosis (p = 0.038) and HCV-HCC had a lower score than EtOH-HCC in TCGA (p = 0.024). Conclusions Our findings indicate that HCV infection is associated with loss of DNA methylation in specific REs, which could implicate molecular mechanisms in liver cancer development. If our findings are validated in larger sample sizes, methylation of these REs may be useful as an early detection biomarker for HCV-HCC and/or a target for prevention of HCC in HCV-positive individuals. Electronic supplementary material The online version of this article (10.1186/s13148-019-0733-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yinan Zheng
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA.
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Brian T Joyce
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Chunyan He
- University of Kentucky Markey Cancer Center, Lexington, KY, USA.,Department of Internal Medicine, Division of Medical Oncology, University of Kentucky, Lexington, KY, USA
| | - Drew R Nannini
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA
| | - Warren A Kibbe
- Duke Cancer Institute and Duke School of Medicine, Duke University, Durham, NC, USA
| | - Chad J Achenbach
- Center for Global Health, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Robert L Murphy
- Center for Global Health, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lifang Hou
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA
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50
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Kim S, Mun S, Kim T, Lee KH, Kang K, Cho JY, Han K. Transposable element-mediated structural variation analysis in dog breeds using whole-genome sequencing. Mamm Genome 2019; 30:289-300. [PMID: 31414176 DOI: 10.1007/s00335-019-09812-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/23/2019] [Indexed: 12/26/2022]
Abstract
Naturally occurring diseases in dogs provide an important animal model for studying human disease including cancer, heart disease, and autoimmune disorders. Transposable elements (TEs) make up ~ 31% of the dog (Canis lupus familiaris) genome and are one of main drivers to cause genomic variations and alter gene expression patterns of the host genes, which could result in genetic diseases. To detect structural variations (SVs), we conducted whole-genome sequencing of three different breeds, including Maltese, Poodle, and Yorkshire Terrier. Genomic SVs were detected and visualized using BreakDancer program. We identified a total of 2328 deletion SV events in the three breeds compared with the dog reference genome of Boxer. The majority of the genetic variants were found to be TE insertion polymorphism (1229) and the others were TE-mediated deletion (489), non-TE-mediated deletion (542), simple repeat-mediated deletion (32), and other indel (36). Among the TE insertion polymorphism, 286 elements were full-length LINE-1s (L1s). In addition, the 49 SV candidates located in the genic regions were experimentally verified and their polymorphic rates within each breed were examined using PCR assay. Polymorphism analysis of the genomic variants revealed that some of the variants exist polymorphic in the three dog breeds, suggesting that their SV events recently occurred in the dog genome. The findings suggest that TEs have contributed to the genomic variations among the three dog breeds of Maltese, Poodle, and Yorkshire Terrier. In addition, the polymorphic events between the dog breeds indicate that TEs were recently retrotransposed in the dog genome.
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Affiliation(s)
- Songmi Kim
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - Taemook Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Kang-Hoon Lee
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
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