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López-Royo T, Moreno-Martínez L, Zaragoza P, García-Redondo A, Manzano R, Osta R. Differentially expressed lncRNAs in SOD1 G93A mice skeletal muscle: H19, Myhas and Neat1 as potential biomarkers in amyotrophic lateral sclerosis. Open Biol 2024; 14:240015. [PMID: 39406341 PMCID: PMC11479763 DOI: 10.1098/rsob.240015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/24/2024] [Accepted: 08/08/2024] [Indexed: 10/20/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neuromuscular disease characterized by progressive motor function and muscle mass loss. Despite extensive research in the field, the underlying causes of ALS remain incompletely understood, contributing to the absence of specific diagnostic and prognostic biomarkers and effective therapies. This study investigates the expression of long-non-coding RNAs (lncRNAs) in skeletal muscle as a potential source of biomarkers and therapeutic targets for the disease. The expression profiles of 12 lncRNAs, selected from the literature, were evaluated across different disease stages in tissue and muscle biopsies from the SOD1G93A transgenic mouse model of ALS. Nine out of the 12 lncRNAs were differentially expressed, with Pvt1, H19 and Neat1 showing notable increases in the symptomatic stages of the disease, and suggesting their potential as candidate biomarkers to support diagnosis and key players in muscle pathophysiology in ALS. Furthermore, the progression of Myhas and H19 RNA levels across disease stages correlated with longevity in the SOD1G93A animal model, effectively discriminating between long- and short-term survival individuals, thereby highlighting their potential as prognostic indicators. These findings underscore the involvement of lncRNAs, especially H19 and Myhas, in ALS pathophysiology, offering novel insights for diagnostic, prognostic and therapeutic targets.
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Affiliation(s)
- Tresa López-Royo
- LAGENBIO, Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Agroalimentary Institute of Aragon (IA2), Institute of Health Research of Aragon (IIS), University of Zaragoza, Calle Miguel Servet 177, 50013 Zaragoza, Spain
| | - Laura Moreno-Martínez
- LAGENBIO, Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Agroalimentary Institute of Aragon (IA2), Institute of Health Research of Aragon (IIS), University of Zaragoza, Calle Miguel Servet 177, 50013 Zaragoza, Spain
| | - Pilar Zaragoza
- LAGENBIO, Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Agroalimentary Institute of Aragon (IA2), Institute of Health Research of Aragon (IIS), University of Zaragoza, Calle Miguel Servet 177, 50013 Zaragoza, Spain
| | - Alberto García-Redondo
- Neurology Department, ALS Unit, Hospital 12 de Octubre Health Research Institute (i+12), CIBERER U-723 (Instituto de Salud Carlos III), Avenida Córdoba, s/n, 28041 Madrid, Spain
| | - Raquel Manzano
- LAGENBIO, Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Agroalimentary Institute of Aragon (IA2), Institute of Health Research of Aragon (IIS), University of Zaragoza, Calle Miguel Servet 177, 50013 Zaragoza, Spain
| | - Rosario Osta
- LAGENBIO, Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Agroalimentary Institute of Aragon (IA2), Institute of Health Research of Aragon (IIS), University of Zaragoza, Calle Miguel Servet 177, 50013 Zaragoza, Spain
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Pang D, Yu Y, Zhao B, Huang J, Cui Y, Li T, Li C, Shang H. The Long Non-Coding RNA NR3C2-8:1 Promotes p53-Mediated Apoptosis through the miR-129-5p/USP10 Axis in Amyotrophic Lateral Sclerosis. Mol Neurobiol 2024; 61:7466-7480. [PMID: 38388775 DOI: 10.1007/s12035-024-04059-x] [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: 11/20/2023] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Motor neuron degeneration in amyotrophic lateral sclerosis (ALS) is a form of apoptosis, but the mechanisms underlying this neuronal cell death remain unclear. Numerous studies demonstrate abnormally elevated and active p53 in the central nervous system of ALS patients. Activation of p53-regulated pro-apoptotic signaling pathways may trigger motor neuron death. We previously reported decreased expression of the long non-coding RNA NR3C2-8:1 (Lnc-NR3C) in leukocytes of ALS patients. Here, we show lnc-NR3C promotes p53-mediated cell death in ALS by upregulating USP10 and promoting lnc-NR3C-triggered p53 activation, resulting in cell death. Conversely, lnc-NR3C knockdown inhibited USP10-triggered p53 activation, thereby protecting cells against oxidative stress. As a competitive endogenous RNA, lnc-NR3C competitively binds miR-129-5p, regulating the usp10/p53 axis. Elucidating the link between Lnc-NR3C and the USP10/p53 axis in an ALS cell model reveals a role for long non-coding RNAs in activating apoptosis. This provides new therapeutic opportunities in ALS.
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Affiliation(s)
- Dejiang Pang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Yujiao Yu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Bi Zhao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Jingxuan Huang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Yiyuan Cui
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Tengfei Li
- Department of Neurosurgery, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China.
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China.
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Lin C, Wu J, Wang Z, Xiang Y. Long non-coding RNA LNC-POTEM-4 promotes HCC progression via the LNC-POTEM-4/miR-149-5p/Wnt4 signaling axis. Cell Signal 2024; 124:111412. [PMID: 39278454 DOI: 10.1016/j.cellsig.2024.111412] [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: 06/29/2024] [Revised: 08/27/2024] [Accepted: 09/10/2024] [Indexed: 09/18/2024]
Abstract
Information on the potential role of the long non-coding RNA LNC-POTEM-4 in cancer progression is limited. Our preliminary study found that LNC-POTEM-4 was overexpressed in hepatocellular carcinoma (HCC) tissues, which led us to further investigate the biological function and molecular mechanism of LNC-POTEM-4 in HCC development. LNC-POTEM-4 expression in HCC tissues was examined using transcriptome sequencing and quantitative reverse transcription PCR. The relationships between LNC-POTEM-4 and the stage and prognosis of HCC in patient data from the TCGA database were analyzed. The effects of LNC-POTEM-4 on proliferation, invasion/migration, and epithelial-mesenchymal transition marker expression in HCC cells were evaluated in vitro using gain- and loss-of-function assays, while its effects on tumor growth and metastasis were explored through animal experiments. A LNC-POTEM-4/microRNA (miR)-149-5p/Wnt4 regulatory signaling axis was identified using bioinformatics analysis, and dual luciferase reporter, RNA immunoprecipitation, and RNA pull-down assays. Co-transfection of LNC-POTEM-4 and Wnt4 expression plasmids was employed to confirm the new signaling pathway. We found that LNC-POTEM-4 was overexpressed in HCC tissues and was linked to poor staging and prognosis. LNC-POTEM-4 promoted proliferation, invasion, migration, and the epithelial-mesenchymal transition of HCC cells in vitro. Silencing of LNC-POTEM-4 inhibited HCC growth and distant metastasis in vivo. Mechanically, LNC-POTEM-4 was found to function as a competitive endogenous RNA, upregulating Wnt4 by sponging miR-149-5p to promote HCC progression. Wnt4 overexpression may have counteracted the tumor-inhibition effect of LNC-POTEM-4 silencing. In conclusion, LNC-POTEM-4 upregulated Wnt4 to activate the Wnt signaling pathway and stimulate the malignancy tendency of HCC by sponging miR-149-5p, providing a prospective target for the detection and therapy of HCC. However, the effects of LNC-POTEM-4 on the miR-149-5p/Wnt4 signaling axis should be further studied in animal experiments.
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Affiliation(s)
- Chao Lin
- Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun 130000, China
| | - Jiacheng Wu
- Hepatobiliary and Pancreatic Surgery, the Second Hospital of Jilin University, Changchun 130000, China
| | - Zhixuan Wang
- Intensive Care Medicine, China-Japan Union Hospital of Jilin University, Changchun 130000, China
| | - Yien Xiang
- Hepatobiliary and Pancreatic Surgery, the Second Hospital of Jilin University, Changchun 130000, China.
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Yu Y, Pang D, Huang J, Li C, Cui Y, Shang H. Downregulation of Lnc-ABCA12-3 modulates UBQLN1 expression and protein homeostasis pathways in amyotrophic lateral sclerosis. Sci Rep 2024; 14:21383. [PMID: 39271939 PMCID: PMC11399266 DOI: 10.1038/s41598-024-72666-8] [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: 02/01/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by motor neuron degeneration. Dysregulation of long non-coding RNAs (lncRNAs) has been implicated in ALS pathogenesis but their roles remain unclear. Previous studies found lnc-ABCA12-3 was downregulated in ALS patients. We aim to characterize the expression and function of lnc-ABCA12-3 in ALS and explore its mechanisms of action. Lnc-ABCA12-3 expression was analyzed in PBMCs from ALS patients and correlated with clinical outcomes. Effect of modulating lnc-ABCA12-3 expression was assessed in cell models using assays of apoptosis, protein homeostasis and pathway analysis. RNA pull-down and interaction studies were performed to identify lnc-ABCA12-3 binding partners. Lnc-ABCA12-3 was downregulated in ALS patients, correlating with faster progression and shorter survival. Overexpression of lnc-ABAC12-3 conferred protection against oxidative stress-induced apoptosis, while knockdown lnc-ABCA12-3 enhanced cell death. Lnc-ABCA12-3 maintained protein quality control pathways, including ubiquitination, autophagy and stress granule formation, by regulating the ubiquitin shuttle protein UBQLN1. This study identified lnc-ABCA12-3 as a novel regulatory lncRNA implicated in ALS pathogenesis by modulating cellular survival and stress responses through interactions with UBQLN1, influencing disease progression. Lnc-ABCA12-3 may influence ALS through regulating protein homeostasis pathways.
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Affiliation(s)
- Yujiao Yu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China
| | - Dejiang Pang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China
| | - Jingxuan Huang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China
| | - Yiyuan Cui
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China.
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Noches V, Campos-Melo D, Droppelmann CA, Strong MJ. Epigenetics in the formation of pathological aggregates in amyotrophic lateral sclerosis. Front Mol Neurosci 2024; 17:1417961. [PMID: 39290830 PMCID: PMC11405384 DOI: 10.3389/fnmol.2024.1417961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/23/2024] [Indexed: 09/19/2024] Open
Abstract
The progressive degeneration of motor neurons in amyotrophic lateral sclerosis (ALS) is accompanied by the formation of a broad array of cytoplasmic and nuclear neuronal inclusions (protein aggregates) largely containing RNA-binding proteins such as TAR DNA-binding protein 43 (TDP-43) or fused in sarcoma/translocated in liposarcoma (FUS/TLS). This process is driven by a liquid-to-solid phase separation generally from proteins in membrane-less organelles giving rise to pathological biomolecular condensates. The formation of these protein aggregates suggests a fundamental alteration in the mRNA expression or the levels of the proteins involved. Considering the role of the epigenome in gene expression, alterations in DNA methylation, histone modifications, chromatin remodeling, non-coding RNAs, and RNA modifications become highly relevant to understanding how this pathological process takes effect. In this review, we explore the evidence that links epigenetic mechanisms with the formation of protein aggregates in ALS. We propose that a greater understanding of the role of the epigenome and how this inter-relates with the formation of pathological LLPS in ALS will provide an attractive therapeutic target.
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Affiliation(s)
- Veronica Noches
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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Rajabi D, Khanmohammadi S, Rezaei N. The role of long noncoding RNAs in amyotrophic lateral sclerosis. Rev Neurosci 2024; 35:533-547. [PMID: 38452377 DOI: 10.1515/revneuro-2023-0155] [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: 12/14/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease with a poor prognosis leading to death. The diagnosis and treatment of ALS are inherently challenging due to its complex pathomechanism. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides involved in different cellular processes, incisively gene expression. In recent years, more studies have been conducted on lncRNA classes and interference in different disease pathologies, showing their promising contribution to diagnosing and treating neurodegenerative diseases. In this review, we discussed the role of lncRNAs like NEAT1 and C9orf72-as in ALS pathogenesis mechanisms caused by mutations in different genes, including TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), superoxide dismutase type 1 (SOD1). NEAT1 is a well-established lncRNA in ALS pathogenesis; hence, we elaborate on its involvement in forming paraspeckles, stress response, inflammatory response, and apoptosis. Furthermore, antisense lncRNAs (as-lncRNAs), a key group of transcripts from the opposite strand of genes, including ZEB1-AS1 and ATXN2-AS, are discussed as newly identified components in the pathology of ALS. Ultimately, we review the current standing of using lncRNAs as biomarkers and therapeutic agents and the future vision of further studies on lncRNA applications.
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Affiliation(s)
- Darya Rajabi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
| | - Shaghayegh Khanmohammadi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
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Huang J, Yu Y, Pang D, Li C, Wei Q, Cheng Y, Cui Y, Ou R, Shang H. Lnc-HIBADH-4 Regulates Autophagy-Lysosome Pathway in Amyotrophic Lateral Sclerosis by Targeting Cathepsin D. Mol Neurobiol 2024; 61:4768-4782. [PMID: 38135852 PMCID: PMC11236912 DOI: 10.1007/s12035-023-03835-5] [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: 08/24/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is the most prevalent and lethal class of severe motor neuron diseases (MND) with no efficacious treatment. The pathogenic mechanisms underlying ALS remain unclear. Nearly 90% of patients exhibit sporadic onset (sALS). Therefore, elucidating the pathophysiology of ALS is imperative. Long non-coding RNA (lncRNA) is a large class of non-coding RNAs that regulate transcription, translation, and post-translational processes. LncRNAs contribute to the pathogenesis of diverse neurodegenerative disorders and hold promise as targets for interference in the realm of neurodegeneration. However, the mechanisms of which lncRNAs are involved in ALS have not been thoroughly investigated. We identified and validated a downregulated lncRNA, lnc-HIBADH-4, in ALS which correlated with disease severity and overall survival. Lnc-HIBADH-4 acted as a "molecular sponge" regulating lysosomal function through the lnc-HIBADH-4/miR-326/CTSD pathway, thereby impacting autophagy-lysosome dynamics and the levels of cell proliferation and apoptosis. Therefore, this study discovered and revealed the role of lnc-HIBADH-4 in the pathogenesis of ALS. With further research, lnc-HIBADH-4 is expected to provide a new biomarker in the diagnosis and treatment of ALS.
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Affiliation(s)
- Jingxuan Huang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yujiao Yu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Dejiang Pang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Qianqian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yangfan Cheng
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yiyuan Cui
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Ruwei Ou
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, Sichuan, China.
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Ge T, Brickner JH. Inheritance of epigenetic transcriptional memory. Curr Opin Genet Dev 2024; 85:102174. [PMID: 38430840 PMCID: PMC10947848 DOI: 10.1016/j.gde.2024.102174] [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: 11/09/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Epigenetic memory allows organisms to stably alter their transcriptional program in response to developmental or environmental stimuli. Such transcriptional programs are mediated by heritable regulation of the function of enhancers and promoters. Memory involves read-write systems that enable self-propagation and mitotic inheritance of cis-acting epigenetic marks to induce stable changes in transcription. Also, in response to environmental cues, cells can induce epigenetic transcriptional memory to poise inducible genes for faster induction in the future. Here, we discuss modes of epigenetic inheritance and the molecular basis of epigenetic transcriptional memory.
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Affiliation(s)
- Tiffany Ge
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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Teixeira LCR, Mamede I, Luizon MR, Gomes KB. Role of long non-coding RNAs in the pathophysiology of Alzheimer's disease and other dementias. Mol Biol Rep 2024; 51:270. [PMID: 38302810 DOI: 10.1007/s11033-023-09178-7] [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: 11/04/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024]
Abstract
Dementia is the term used to describe a group of cognitive disorders characterized by a decline in memory, thinking, and reasoning abilities that interfere with daily life activities. Examples of dementia include Alzheimer's Disease (AD), Frontotemporal dementia (FTD), Amyotrophic lateral sclerosis (ALS), Vascular dementia (VaD) and Progressive supranuclear palsy (PSP). AD is the most common form of dementia. The hallmark pathology of AD includes formation of β-amyloid (Aβ) oligomers and tau hyperphosphorylation in the brain, which induces neuroinflammation, oxidative stress, synaptic dysfunction, and neuronal apoptosis. Emerging studies have associated long non-coding RNAs (lncRNAs) with the pathogenesis and progression of the neurodegenerative diseases. LncRNAs are defined as RNAs longer than 200 nucleotides that lack the ability to encode functional proteins. LncRNAs play crucial roles in numerous biological functions for their ability to interact with different molecules, such as proteins and microRNAs, and subsequently regulate the expression of their target genes at transcriptional and post-transcriptional levels. In this narrative review, we report the function and mechanisms of action of lncRNAs found to be deregulated in different types of dementia, with the focus on AD. Finally, we discuss the emerging role of lncRNAs as biomarkers of dementias.
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Affiliation(s)
- Lívia Cristina Ribeiro Teixeira
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Izabela Mamede
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcelo Rizzatti Luizon
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Karina Braga Gomes
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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Geraci J, Bhargava R, Qorri B, Leonchyk P, Cook D, Cook M, Sie F, Pani L. Machine learning hypothesis-generation for patient stratification and target discovery in rare disease: our experience with Open Science in ALS. Front Comput Neurosci 2024; 17:1199736. [PMID: 38260713 PMCID: PMC10801647 DOI: 10.3389/fncom.2023.1199736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/20/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Advances in machine learning (ML) methodologies, combined with multidisciplinary collaborations across biological and physical sciences, has the potential to propel drug discovery and development. Open Science fosters this collaboration by releasing datasets and methods into the public space; however, further education and widespread acceptance and adoption of Open Science approaches are necessary to tackle the plethora of known disease states. Motivation In addition to providing much needed insights into potential therapeutic protein targets, we also aim to demonstrate that small patient datasets have the potential to provide insights that usually require many samples (>5,000). There are many such datasets available and novel advancements in ML can provide valuable insights from these patient datasets. Problem statement Using a public dataset made available by patient advocacy group AnswerALS and a multidisciplinary Open Science approach with a systems biology augmented ML technology, we aim to validate previously reported drug targets in ALS and provide novel insights about ALS subpopulations and potential drug targets using a unique combination of ML methods and graph theory. Methodology We use NetraAI to generate hypotheses about specific patient subpopulations, which were then refined and validated through a combination of ML techniques, systems biology methods, and expert input. Results We extracted 8 target classes, each comprising of several genes that shed light into ALS pathophysiology and represent new avenues for treatment. These target classes are broadly categorized as inflammation, epigenetic, heat shock, neuromuscular junction, autophagy, apoptosis, axonal transport, and excitotoxicity. These findings are not mutually exclusive, and instead represent a systematic view of ALS pathophysiology. Based on these findings, we suggest that simultaneous targeting of ALS has the potential to mitigate ALS progression, with the plausibility of maintaining and sustaining an improved quality of life (QoL) for ALS patients. Even further, we identified subpopulations based on disease onset. Conclusion In the spirit of Open Science, this work aims to bridge the knowledge gap in ALS pathophysiology to aid in diagnostic, prognostic, and therapeutic strategies and pave the way for the development of personalized treatments tailored to the individual's needs.
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Affiliation(s)
- Joseph Geraci
- NetraMark Corp, Toronto, ON, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
- Centre for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
- Arthur C. Clarke Center for Human Imagination, School of Physical Sciences, University of California San Diego, San Diego, CA, United States
| | - Ravi Bhargava
- Department of Biomedical and Molecular Science, Queens University, Kingston, ON, Canada
- Science and Research, Roche Integrated Informatics, F. Hoffmann La-Roche, Toronto, ON, Canada
| | | | | | - Douglas Cook
- NetraMark Corp, Toronto, ON, Canada
- Department of Surgery, Queen's University, Kingston, ON, Canada
| | - Moses Cook
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Fanny Sie
- Science and Research, Roche Integrated Informatics, F. Hoffmann La-Roche, Toronto, ON, Canada
| | - Luca Pani
- NetraMark Corp, Toronto, ON, Canada
- Department of Psychiatry and Behavioral Sciences, Leonard M. Miller School of Medicine, University of Miami, Coral Gables, FL, United States
- Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
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Morello G, La Cognata V, Guarnaccia M, La Bella V, Conforti FL, Cavallaro S. A Diagnostic Gene-Expression Signature in Fibroblasts of Amyotrophic Lateral Sclerosis. Cells 2023; 12:1884. [PMID: 37508548 PMCID: PMC10378077 DOI: 10.3390/cells12141884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, progressive neurodegenerative disease with limited treatment options. Diagnosis can be difficult due to the heterogeneity and non-specific nature of the initial symptoms, resulting in delays that compromise prompt access to effective therapeutic strategies. Transcriptome profiling of patient-derived peripheral cells represents a valuable benchmark in overcoming such challenges, providing the opportunity to identify molecular diagnostic signatures. In this study, we characterized transcriptome changes in skin fibroblasts of sporadic ALS patients (sALS) and controls and evaluated their utility as a molecular classifier for ALS diagnosis. Our analysis identified 277 differentially expressed transcripts predominantly involved in transcriptional regulation, synaptic transmission, and the inflammatory response. A support vector machine classifier based on this 277-gene signature was developed to discriminate patients with sALS from controls, showing significant predictive power in both the discovery dataset and in six independent publicly available gene expression datasets obtained from different sALS tissue/cell samples. Taken together, our findings support the utility of transcriptional signatures in peripheral cells as valuable biomarkers for the diagnosis of ALS.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Vincenzo La Bella
- ALS Clinical Research Center and Neurochemistry Laboratory, BiND, University of Palermo, 90133 Palermo, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
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12
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Srinivas T, Mathias C, Oliveira-Mateos C, Guil S. Roles of lncRNAs in brain development and pathogenesis: Emerging therapeutic opportunities. Mol Ther 2023; 31:1550-1561. [PMID: 36793211 PMCID: PMC10277896 DOI: 10.1016/j.ymthe.2023.02.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The human genome is pervasively transcribed, producing a majority of short and long noncoding RNAs (lncRNAs) that can influence cellular programs through a variety of transcriptional and post-transcriptional regulatory mechanisms. The brain houses the richest repertoire of long noncoding transcripts, which function at every stage during central nervous system development and homeostasis. An example of functionally relevant lncRNAs is species involved in spatiotemporal organization of gene expression in different brain regions, which play roles at the nuclear level and in transport, translation, and decay of other transcripts in specific neuronal sites. Research in the field has enabled identification of the contributions of specific lncRNAs to certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders, resulting in notions of potential therapeutic strategies that target these RNAs to recover the normal phenotype. Here, we summarize the latest mechanistic findings associated with lncRNAs in the brain, focusing on their dysregulation in neurodevelopmental or neurodegenerative disorders, their use as biomarkers for central nervous system (CNS) diseases in vitro and in vivo, and their potential utility for therapeutic strategies.
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Affiliation(s)
- Tara Srinivas
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Catalonia, Spain
| | - Carolina Mathias
- Department of Genetics, Federal University of Parana, Post-graduation Program in Genetics, Curitiba, PR, Brazil; Laboratory of Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, PR, Brazil
| | | | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Catalonia, Spain; Germans Trias i Pujol Health Science Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain.
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13
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Ma J, Luo Y, Liu Y, Chen C, Chen A, Liang L, Wang W, Song Y. Exosome-mediated lnc-ABCA12-3 promotes proliferation and glycolysis but inhibits apoptosis by regulating the toll-like receptor 4/nuclear factor kappa-B signaling pathway in esophageal squamous cell carcinoma. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2023; 27:61-73. [PMID: 36575934 PMCID: PMC9806635 DOI: 10.4196/kjpp.2023.27.1.61] [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: 08/16/2022] [Revised: 10/23/2022] [Accepted: 11/03/2022] [Indexed: 12/29/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a kind of malignant tumor with high incidence and mortality in the digestive system. The aim of this study is to explore the function of lnc-ABCA12-3 in the development of ESCC and its unique mechanisms. RT-PCR was applied to detect gene transcription levels in tissues or cell lines like TE-1, EC9706, and HEEC cells. Western blot was conducted to identify protein expression levels of mitochondrial apoptosis and toll-like receptor 4 (TLR4)/nuclear factor kappa-B (NF-κB) signaling pathway. CCK-8 and EdU assays were carried out to measure cell proliferation, and cell apoptosis was examined by flow cytometry. ELISA was used for checking the changes in glycolysis-related indicators. Lnc-ABCA12-3 was highly expressed in ESCC tissues and cells, which preferred it to be a candidate target. The TE-1 and EC9706 cells proliferation and glycolysis were obviously inhibited with the downregulation of lnc-ABCA12-3, while apoptosis was promoted. TLR4 activator could largely reverse the apoptosis acceleration and relieved the proliferation and glycolysis suppression caused by lnc-ABCA12-3 downregulation. Moreover, the effect of lnc-ABCA12-3 on ESCC cells was actualized by activating the TLR4/NF-κB signaling pathway under the mediation of exosome. Taken together, the lnc-ABCA12-3 could promote the proliferation and glycolysis of ESCC, while repressing its apoptosis probably by regulating the TLR4/NF-κB signaling pathway under the mediation of exosome.
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Affiliation(s)
- Junliang Ma
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, China,Correspondence Junliang Ma, E-mail:
| | - Yijun Luo
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, China
| | - Yingjie Liu
- Department of Cardiovascular Surgery, Affiliated Hospital of Zuinyi Medical University, Zunyi, Guizhou 563003, China
| | - Cheng Chen
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, China
| | - Anping Chen
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, China
| | - Lubiao Liang
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, China
| | - Wenxiang Wang
- The Second Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410031, China
| | - Yongxiang Song
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, China
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14
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Ruffo P, De Amicis F, Giardina E, Conforti FL. Long-noncoding RNAs as epigenetic regulators in neurodegenerative diseases. Neural Regen Res 2022; 18:1243-1248. [PMID: 36453400 PMCID: PMC9838156 DOI: 10.4103/1673-5374.358615] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The growing and rapid development of high-throughput sequencing technologies have allowed a greater understanding of the mechanisms underlying gene expression regulation. Editing the epigenome and epitranscriptome directs the fate of the transcript influencing the functional outcome of each mRNA. In this context, non-coding RNAs play a decisive role in addressing the expression regulation at the gene and chromosomal levels. Long-noncoding RNAs, consisting of more than 200 nucleotides, have been shown to act as epigenetic regulators in several key molecular processes involving neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington's disease. Long-noncoding RNAs are abundantly expressed in the central nervous system, suggesting that their deregulation could trigger neuronal degeneration through RNA modifications. The evaluation of their diagnostic significance and therapeutic potential could lead to new treatments for these diseases for which there is no cure.
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Affiliation(s)
- Paola Ruffo
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Francesca De Amicis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Rome, Italy,Department of Biomedicine & Prevention, Tor Vergata University of Rome, Rome, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy,Correspondence to: Francesca Luisa Conforti, .
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15
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Glavač D, Mladinić M, Ban J, Mazzone GL, Sámano C, Tomljanović I, Jezernik G, Ravnik-Glavač M. The Potential Connection between Molecular Changes and Biomarkers Related to ALS and the Development and Regeneration of CNS. Int J Mol Sci 2022; 23:ijms231911360. [PMID: 36232667 PMCID: PMC9570269 DOI: 10.3390/ijms231911360] [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: 07/26/2022] [Revised: 09/10/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Neurodegenerative diseases are one of the greatest medical burdens of the modern age, being mostly incurable and with limited prognostic and diagnostic tools. Amyotrophic lateral sclerosis (ALS) is a fatal, progressive neurodegenerative disease characterized by the loss of motoneurons, with a complex etiology, combining genetic, epigenetic, and environmental causes. The neuroprotective therapeutic approaches are very limited, while the diagnostics rely on clinical examination and the exclusion of other diseases. The recent advancement in the discovery of molecular pathways and gene mutations involved in ALS has deepened the understanding of the disease pathology and opened the possibility for new treatments and diagnostic procedures. Recently, 15 risk loci with distinct genetic architectures and neuron-specific biology were identified as linked to ALS through common and rare variant association analyses. Interestingly, the quantity of related proteins to these genes has been found to change during early postnatal development in mammalian spinal cord tissue (opossum Monodelphis domestica) at the particular time when neuroregeneration stops being possible. Here, we discuss the possibility that the ALS-related genes/proteins could be connected to neuroregeneration and development. Moreover, since the regulation of gene expression in developmental checkpoints is frequently regulated by non-coding RNAs, we propose that studying the changes in the composition and quantity of non-coding RNA molecules, both in ALS patients and in the developing central nervous (CNS) system of the opossum at the time when neuroregeneration ceases, could reveal potential biomarkers useful in ALS prognosis and diagnosis.
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Affiliation(s)
- Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljublana, Slovenia
- Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Miranda Mladinić
- Laboratory for Molecular Neurobiology, Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Jelena Ban
- Laboratory for Molecular Neurobiology, Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Graciela L. Mazzone
- Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral, Buenos Aires B1629AHJ, Argentina
| | - Cynthia Sámano
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Mexico City 05348, Mexico
| | - Ivana Tomljanović
- Laboratory for Molecular Neurobiology, Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Gregor Jezernik
- Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Metka Ravnik-Glavač
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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