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Diaw SH, Delcambre S, Much C, Ott F, Kostic VS, Gajos A, Münchau A, Zittel S, Busch H, Grünewald A, Klein C, Lohmann K. DYT-THAP1: exploring gene expression in fibroblasts for potential biomarker discovery. Neurogenetics 2024; 25:141-147. [PMID: 38498291 DOI: 10.1007/s10048-024-00752-0] [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: 12/22/2023] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
Dystonia due to pathogenic variants in the THAP1 gene (DYT-THAP1) shows variable expressivity and reduced penetrance of ~ 50%. Since THAP1 encodes a transcription factor, modifiers influencing this variability likely operate at the gene expression level. This study aimed to assess the transferability of differentially expressed genes (DEGs) in neuronal cells related to pathogenic variants in the THAP1 gene, which were previously identified by transcriptome analyses. For this, we performed quantitative (qPCR) and Digital PCR (dPCR) in cultured fibroblasts. RNA was extracted from THAP1 manifesting (MMCs) and non-manifesting mutation carriers (NMCs) as well as from healthy controls. The expression profiles of ten of 14 known neuronal DEGs demonstrated differences in fibroblasts between these three groups. This included transcription factors and targets (ATF4, CLN3, EIF2A, RRM1, YY1), genes involved in G protein-coupled receptor signaling (BDKRB2, LPAR1), and a gene linked to apoptosis and DNA replication/repair (CRADD), which all showed higher expression levels in MMCs and NMCs than in controls. Moreover, the analysis of genes linked to neurological disorders (STXBP1, TOR1A) unveiled differences in expression patterns between MMCs and controls. Notably, the genes CUEDC2, DRD4, ECH1, and SIX2 were not statistically significantly differentially expressed in fibroblast cultures. With > 70% of the tested genes being DEGs also in fibroblasts, fibroblasts seem to be a suitable model for DYT-THAP1 research despite some restrictions. Furthermore, at least some of these DEGs may potentially also serve as biomarkers of DYT-THAP1 and influence its penetrance and expressivity.
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Affiliation(s)
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, L-4362, Luxembourg
| | - Christoph Much
- Institute of Neurogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Fabian Ott
- Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Vladimir S Kostic
- Institute of Neurology, School of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Agata Gajos
- Department of Extrapyramidal Diseases, Medical University of Lodz, Lodz, 90-647, Poland
| | - Alexander Münchau
- Institute of Systems Motor Science, University of Lübeck, 23562, Lübeck, Germany
| | - Simone Zittel
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hauke Busch
- Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, L-4362, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, 23562, Lübeck, Germany.
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Sadhukhan D, Biswas A, Mishra S, Chatterjee K, Maji D, Mitra P, Mukherjee P, Podder G, Ray BK, Biswas A, Banerjee TK, Hui SP, Deb I. Genetic Variations and Altered Blood mRNA Level of Circadian Genes and BDNF as Risk Factors of Post-Stroke Cognitive Impairment Among Eastern Indians. Neuromolecular Med 2023; 25:586-595. [PMID: 37814155 DOI: 10.1007/s12017-023-08761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023]
Abstract
Post-stroke cognitive impairment (PSCI) is a clinical outcome in around 30% of post-stroke survivors. BDNF is a major gene in this regard. It is regulated by circadian rhythm. The circadian genes are correlated with stroke timings at molecular level. However, studies suggesting the role of these on susceptibility to PSCI are limited. We aim here to determine: (a) genetic risk variants in circadian clock genes, BDNF and (b) dysregulation in expression level of CLOCK, BMAL1, and BDNF that may be associated with PSCI. BDNF (rs6265G/A, rs56164415C/T), CLOCK (rs1801260T/C, rs4580704G/C), and CRY2 (rs2292912C/G) genes variants were genotyped among 119 post-stroke survivors and 292 controls from Eastern part of India. In addition, we analyzed their gene expression in Peripheral blood Mononuclear cells (PBMC) from 15 PSCI cases and 12 controls. The mRNA data for BDNF was further validated by its plasma level through ELISA (n = 38). Among the studied variants, only rs4580704/CLOCK showed an overall association with PSCI (P = 0.001) and lower Bengali Mini-Mental State Examination (BMSE) score. Its 'C' allele showed a correlation with attention deficiency. The language and memory impairments showed association with rs6265/BDNF, while the 'CC' genotype of rs2292912/CRY2 negatively influenced language and executive function. A significant decrease in gene expression for CLOCK and BDNF in PBMC (influenced by specific genotypes) of PSCI patients was observed than controls. Unlike Pro-BDNF, plasma-level mBDNF was also lower in them. Our results suggest the genetic variants in CLOCK, CRY2, and BDNF as risk factors for PSCI among eastern Indians. At the same time, a lowering expression of CLOCK and BDNF genes in PSCI patients than controls describes their transcriptional dysregulation as underlying mechanism for post-stroke cognitive decline.
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Affiliation(s)
- Dipanwita Sadhukhan
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India.
| | - Arindam Biswas
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India
| | - Smriti Mishra
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India
| | - Koustav Chatterjee
- Department of Neurology, Institute of Neurosciences Kolkata, Kolkata, India
| | - Daytee Maji
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Parama Mitra
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India
| | - Priyanka Mukherjee
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India
| | - Gargi Podder
- Institute of Post Graduate of Medical Education & Research and Bangur Institute of Neurosciences, Kolkata, India
| | - Biman Kanti Ray
- Institute of Post Graduate of Medical Education & Research and Bangur Institute of Neurosciences, Kolkata, India
| | - Atanu Biswas
- Institute of Post Graduate of Medical Education & Research and Bangur Institute of Neurosciences, Kolkata, India
| | - Tapas Kumar Banerjee
- Molecular Biology & Clinical Neuroscience Division, National Neurosciences Centre Calcutta, Kolkata, India
| | - Subhra Prakash Hui
- S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata, India
| | - Ishani Deb
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
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Lebedeva O, Poberezhniy D, Novosadova E, Gerasimova T, Novosadova L, Arsenyeva E, Stepanenko E, Shimchenko D, Volovikov E, Anufrieva K, Illarioshkin S, Lagarkova M, Grivennikov I, Tarantul V, Nenasheva V. Overexpression of Parkin in the Neuronal Progenitor Cells from a Patient with Parkinson's Disease Shifts the Transcriptome Towards the Normal State. Mol Neurobiol 2023; 60:3522-3533. [PMID: 36884134 DOI: 10.1007/s12035-023-03293-z] [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: 07/15/2022] [Accepted: 02/05/2023] [Indexed: 03/09/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative pathology caused by the progressive loss of dopaminergic neurons in the substantia nigra. Juvenile PD is known to be strongly associated with mutations in the PARK2 gene encoding E3 ubiquitin ligase Parkin. Despite numerous studies, molecular mechanisms that trigger PD remain largely unknown. Here, we compared the transcriptome of the neural progenitor (NP) cell line, derived from a PD patient with PARK2 mutation resulting in Parkin loss, with the transcriptome of the same NPs but expressing transgenic Parkin. We found that Parkin overexpression led to the substantial recovery of the transcriptome of NPs to a normal state indicating that alterations of transcription in PD-derived NPs were mainly caused by PARK2 mutations. Among genes significantly dysregulated in PD-derived NPs, 106 genes unambiguously restored their expression after reestablishing of the Parkin level. Based on the selected gene sets, we revealed the enriched Gene Ontology (GO) pathways including signaling, neurotransmitter transport and metabolism, response to stimulus, and apoptosis. Strikingly, dopamine receptor D4 that was previously associated with PD appears to be involved in the maximal number of GO-enriched pathways and therefore may be considered as a potential trigger of PD progression. Our findings may help in the screening for promising targets for PD treatment.
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Affiliation(s)
- Olga Lebedeva
- Lopukhin Federal Research and Clinical Center of Physical Chemical Medicine of the Federal Medical and Biological Agency of the Russian Federation, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daniil Poberezhniy
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia.,Faculty of Biotechnology and Industrial Ecology, D.I. Mendeleyev University of Chemical Technology of Russia, Moscow, Russia
| | - Ekaterina Novosadova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Tatiana Gerasimova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia.
| | - Lyudmila Novosadova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Elena Arsenyeva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ekaterina Stepanenko
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Darya Shimchenko
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Egor Volovikov
- Lopukhin Federal Research and Clinical Center of Physical Chemical Medicine of the Federal Medical and Biological Agency of the Russian Federation, Moscow, Russia
| | - Ksenia Anufrieva
- Lopukhin Federal Research and Clinical Center of Physical Chemical Medicine of the Federal Medical and Biological Agency of the Russian Federation, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | - Maria Lagarkova
- Lopukhin Federal Research and Clinical Center of Physical Chemical Medicine of the Federal Medical and Biological Agency of the Russian Federation, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Igor Grivennikov
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Vyacheslav Tarantul
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Valentina Nenasheva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia.
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