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João S, Quental R, Pinto J, Almeida C, Santos H, Dória S. Impact of copy number variants in epilepsy plus neurodevelopment disorders. Seizure 2024; 117:6-12. [PMID: 38277927 DOI: 10.1016/j.seizure.2024.01.009] [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: 12/13/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
INTRODUCTION Epilepsy, a neurological disorder characterized by recurring unprovoked seizures due to excessive neuronal excitability, is primarily attributed to genetic factors, accounting for an estimated 70 % of cases. Array-comparative genomic hybridization (aCGH) is a crucial genetic test for detecting copy number variants (CNVs) associated with epilepsy. This study aimed to analyze a cohort of epilepsy patients with CNVs detected through aCGH to enhance our understanding of the genetic underpinnings of epilepsy. METHODS A retrospective cross-sectional study was conducted using the aCGH database from the Genetics Department of the Faculty of Medicine of the University of Porto, encompassing 146 patients diagnosed with epilepsy, epileptic encephalopathy, or seizures. Clinical data were collected, and aCGH was performed following established guidelines. CNVs were classified based on ACMG standards, and patients were categorized into four groups according to their clinical phenotype. RESULTS Among the 146 included patients, 94 (64 %) had at least one CNV, with 22 (15.1 %) classified as pathogenic or likely pathogenic. Chromosomes 1, 2, 16, and X were frequently implicated, with Xp22.33 being the most reported region (8 CNVs). The phenotype "Epilepsy and global developmental delay/intellectual disability" showed the highest prevalence of clinically relevant CNVs. Various CNVs were identified across different groups, suggesting potential roles in epilepsy. CONCLUSIONS This study highlights the significance of aCGH in unraveling the genetic basis of epilepsy and tailoring treatment strategies. It contributes valuable insights to the expanding knowledge in the field, emphasizing the need for research to elucidate the diverse genetic causes of epilepsy.
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Affiliation(s)
- Sofia João
- Department of Pathology - Genetics, Faculty of Medicine, University of Porto, Portugal.
| | - Rita Quental
- Medical Genetics Service, Centro Hospitalar Universitário de São João - CHUSJ, Porto, Portugal.
| | - Joel Pinto
- Department of Pathology - Genetics, Faculty of Medicine, University of Porto, Portugal; I3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
| | - Carolina Almeida
- Department of Pathology - Genetics, Faculty of Medicine, University of Porto, Portugal; I3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
| | - Helena Santos
- Child and Adolescent Neuroscience Unit, Centro Hospitalar Vila Nova de Gaia/Espinho - CHNVG, Vila Nova de Gaia, Portugal.
| | - Sofia Dória
- Department of Pathology - Genetics, Faculty of Medicine, University of Porto, Portugal; I3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
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Zhou C, Wei X, Xiao Y, Liu S, Wang J. Novel compound heterozygous variants in lectin mannose-binding 2-like gene identified in a Chinese autosomal recessive mental retardation-52 (MRT52) patient with phenotype expansion. Chin Med J (Engl) 2023; 136:2107-2109. [PMID: 37667433 PMCID: PMC10476734 DOI: 10.1097/cm9.0000000000002285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Indexed: 09/06/2023] Open
Affiliation(s)
- Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xing Wei
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuanyuan Xiao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shanling Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan 610041, China
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Levchenko A, Plotnikova M. Genomic regulatory sequences in the pathogenesis of bipolar disorder. Front Psychiatry 2023; 14:1115924. [PMID: 36824672 PMCID: PMC9941178 DOI: 10.3389/fpsyt.2023.1115924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
The lifetime prevalence of bipolar disorder is estimated to be about 2%. Epigenetics defines regulatory mechanisms that determine relatively stable patterns of gene expression by controlling all key steps, from DNA to messenger RNA to protein. This Mini Review highlights recent discoveries of modified epigenetic control resulting from genetic variants associated with bipolar disorder in genome-wide association studies. The revealed epigenetic abnormalities implicate gene transcription and post-transcriptional regulation. In the light of these discoveries, the Mini Review focuses on the genes PACS1, MCHR1, DCLK3, HAPLN4, LMAN2L, TMEM258, GNL3, LRRC57, CACNA1C, CACNA1D, and NOVA2 and their potential biological role in the pathogenesis of bipolar disorder. Molecular mechanisms under control of these genes do not translate into a unified picture and substantially more research is needed to fill the gaps in knowledge and to solve current limitations in prognosis and treatment of bipolar disorder. In conclusion, the genetic and functional studies confirm the complex nature of bipolar disorder and indicate future research directions to explore possible targeted treatment options, eventually working toward a personalized approach.
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Affiliation(s)
- Anastasia Levchenko
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Maria Plotnikova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
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Li W, Lan Y, Wang L, He L, Tang R, Price M, Yue B, Fan Z. Comparative transcriptomes of nine tissues for the Heilongjiang brown frog (Rana amurensis). Sci Rep 2022; 12:20759. [PMID: 36456629 PMCID: PMC9715712 DOI: 10.1038/s41598-022-24631-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
The Heilongjiang brown frog (Rana amurensis) is widely used in traditional Chinese medicine. In particular, the oviduct and skin have been developed into various health products. However, limited numbers of complete genomes of amphibian species have been reported, excluding the Heilongjiang brown frog. Here, the transcriptomes of 45 samples from the liver, spleen, heart, ovaries, thigh muscles, skin, oviduct, stomach and intestine of five Heilongjiang brown frog were reassembled and analyzed. A total of 1,085,532 unigenes with an average length of 676.6 bp and N50 of 722 bp were obtained. Comparative transcriptomics of different tissues detected tissue-specific expression. There were 3248 differentially expressed genes (DEGs) in the ovary, and the number of unique DEGs between the ovary and spleen was the largest. The results of DEGs enrichment showed there were many pathways and items related to protein synthesis and metabolism in the oviduct. The DEGs of the skin were enriched with many bacterial defense items, indicating that there were a large number of antimicrobial peptides in the skin. Thus, these were suitable as biological sources for the development and extraction of antimicrobial peptides. Through the assembly of transcriptome sequencing data and functional annotation of the Heilongjiang brown frog genome, this study provides reference materials for further exploring and utilizing functional gene resources of frogs and lays a foundation for medical research and the development of new products.
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Affiliation(s)
- Wanyu Li
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Yue Lan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Lei Wang
- grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,Sichuan Engineering Research Center for Medicinal Animals, Xichang, 615000 Sichuan China
| | - Lewei He
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Ruixiang Tang
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Megan Price
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
| | - Bisong Yue
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,Sichuan Engineering Research Center for Medicinal Animals, Xichang, 615000 Sichuan China
| | - Zhenxin Fan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan China
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Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
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Geng Y, Wu Y, Xu C, Li T, Zhang L. Long Non-Coding RNA LINC00662 Regulated Proliferation and Migration by Targeting miR-34a-5p/LMAN2L Axis in Glioma. Onco Targets Ther 2020; 13:10161-10172. [PMID: 33116598 PMCID: PMC7553658 DOI: 10.2147/ott.s272616] [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] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Background Numerous studies suggest that long non-coding RNAs (lncRNAs) participate in the biological process of diverse malignancies, including glioma. Although many differentially expressed lncRNAs have been identified in glioma, to our best knowledge, the role of LINC00662 and its potential underlying mechanism in glioma progression remains unclear. This study aimed to explore the function and regulatory network of LINC00662 in glioma. Methods Expressions of LINC00662, miR-34a-5p and lectin mannose-binding 2-like (LMAN2L) in glioma tissues were analyzed using The Cancer Genome Atlas Program (TCGA) and the Chinese Glioma Genome Atlas (CGGA) databases. Colony formation, Celltiter-Glo and BrdU (5-bromo-2'-deoxyuridine) incorporation assays were used to detect cell proliferation in vitro. Xenograft mouse models were established to determine cell proliferation in vivo. Transwell and wound healing assay was used to detect cell migration. In addition, epithelial-mesenchymal transition (EMT) markers were detected by Western blot. Annexin V and 7-AAD were used to stain apoptotic cells. Interactions between miR-34a-5p and LINC00662 or the 3'-UTR of LMAN2L were predicted and determined by bioinformatics analysis, luciferase reporter assay and RNA immunoprecipitation (RIP) assays. Results High LINC00662 level predicted poor overall survival of glioma patients. Functional studies revealed that suppression of LINC00662 remarkably inhibited cell proliferation, clonogenicity and EMT pathway. Mechanistically, LINC00662 sponged miR-34a-5p to regulate LMAN2L expression. Furthermore, miR-34a-5p inhibitor reversed the anti-proliferation and anti-migration effect of LINC00662 knockdown, which could be rescued by downregulation of LMAN2L in glioma cells. Conclusion Our study was the first to report that LINC00662 acted as a competing endogenous RNA (ceRNA) to regulate glioma progression by targeting miR-34a-5p/LMAN2L axis, providing a new therapeutic target for glioma.
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Affiliation(s)
- Yibo Geng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yuliang Wu
- Department of Neurosurgery, Qilu Children's Hospital, Shandong University, Jinan, Shandong, People's Republic of China
| | - Cheng Xu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Tian Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China.,China National Clinical Research Center for Neurological Disease, Beijing, People's Republic of China
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