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Najafi P, Reimer C, Gilthorpe JD, Jacobsen KR, Ramløse M, Paul NF, Simianer H, Tetens J, Falker-Gieske C. Genomic evidence for the suitability of Göttingen Minipigs with a rare seizure phenotype as a model for human epilepsy. Neurogenetics 2024; 25:103-117. [PMID: 38383918 PMCID: PMC11076379 DOI: 10.1007/s10048-024-00750-2] [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: 11/29/2023] [Accepted: 02/02/2024] [Indexed: 02/23/2024]
Abstract
Epilepsy is a complex genetic disorder that affects about 2% of the global population. Although the frequency and severity of epileptic seizures can be reduced by a range of pharmacological interventions, there are no disease-modifying treatments for epilepsy. The development of new and more effective drugs is hindered by a lack of suitable animal models. Available rodent models may not recapitulate all key aspects of the disease. Spontaneous epileptic convulsions were observed in few Göttingen Minipigs (GMPs), which may provide a valuable alternative animal model for the characterisation of epilepsy-type diseases and for testing new treatments. We have characterised affected GMPs at the genome level and have taken advantage of primary fibroblast cultures to validate the functional impact of fixed genetic variants on the transcriptome level. We found numerous genes connected to calcium metabolism that have not been associated with epilepsy before, such as ADORA2B, CAMK1D, ITPKB, MCOLN2, MYLK, NFATC3, PDGFD, and PHKB. Our results have identified two transcription factor genes, EGR3 and HOXB6, as potential key regulators of CACNA1H, which was previously linked to epilepsy-type disorders in humans. Our findings provide the first set of conclusive results to support the use of affected subsets of GMPs as an alternative and more reliable model system to study human epilepsy. Further neurological and pharmacological validation of the suitability of GMPs as an epilepsy model is therefore warranted.
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Affiliation(s)
- Pardis Najafi
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Christian Reimer
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
- Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Höltystr. 10, 31535, Neustadt, Germany
| | - Jonathan D Gilthorpe
- Department of Integrative Medical Biology, Umeå University, 901 87, Umeå, Sweden
| | - Kirsten R Jacobsen
- Ellegaard Göttingen Minipigs A/S, Sorø Landevej 302, 4261, Dalmose, Denmark
| | - Maja Ramløse
- Ellegaard Göttingen Minipigs A/S, Sorø Landevej 302, 4261, Dalmose, Denmark
| | - Nora-Fabienne Paul
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany
| | - Henner Simianer
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Clemens Falker-Gieske
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.
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Prajapat M, Kaur G, Choudhary G, Pahwa P, Bansal S, Joshi R, Batra G, Mishra A, Singla R, Kaur H, Prabha PK, Patel AP, Medhi B. A systematic review for the development of Alzheimer's disease in in vitro models: a focus on different inducing agents. Front Aging Neurosci 2023; 15:1296919. [PMID: 38173557 PMCID: PMC10761490 DOI: 10.3389/fnagi.2023.1296919] [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: 09/19/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Alzheimer's disease (AD) is the most common progressive neurodegenerative disease and is associated with dementia. Presently, various chemical and environmental agents are used to induce in-vitro models of Alzheimer disease to investigate the efficacy of different therapeutic drugs. We screened literature from databases such as PubMed, ScienceDirect, and Google scholar, emphasizing the diverse targeting mechanisms of neuro degeneration explored in in-vitro models. The results revealed studies in which different types of chemicals and environmental agents were used for in-vitro development of Alzheimer-targeting mechanisms of neurodegeneration. Studies using chemically induced in-vitro AD models included in this systematic review will contribute to a deeper understanding of AD. However, none of these models can reproduce all the characteristics of disease progression seen in the majority of Alzheimer's disease subtypes. Additional modifications would be required to replicate the complex conditions of human AD in an exact manner. In-vitro models of Alzheimer's disease developed using chemicals and environmental agents are instrumental in providing insights into the disease's pathophysiology; therefore, chemical-induced in-vitro AD models will continue to play vital role in future AD research. This systematic screening revealed the pivotal role of chemical-induced in-vitro AD models in advancing our understanding of AD pathophysiology and is therefore important to understand the potential of these chemicals in AD pathogenesis.
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Affiliation(s)
| | - Gurjeet Kaur
- Department of Pharmacology, PGIMER, Chandigarh, India
| | | | - Paras Pahwa
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Seema Bansal
- MM College of Pharmacy, Maharishi Markandeshwar (DU) University, Mullana, Ambala, India
| | - Rupa Joshi
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Gitika Batra
- Department of Neurology, PGIMER, Chandigarh, India
| | - Abhishek Mishra
- Department of Biomedical Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Rubal Singla
- Department of Pharmacology, PGIMER, Chandigarh, India
| | | | | | | | - Bikash Medhi
- Department of Pharmacology, PGIMER, Chandigarh, India
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Chitra U, Arnold BJ, Sarkar H, Ma C, Lopez-Darwin S, Sanno K, Raphael BJ. Mapping the topography of spatial gene expression with interpretable deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561757. [PMID: 37873258 PMCID: PMC10592770 DOI: 10.1101/2023.10.10.561757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of this data complicates the analysis of spatial gene expression patterns such as gene expression gradients. We address these issues by deriving a topographic map of a tissue slice-analogous to a map of elevation in a landscape-using a novel quantity called the isodepth. Contours of constant isodepth enclose spatial domains with distinct cell type composition, while gradients of the isodepth indicate spatial directions of maximum change in gene expression. We develop GASTON, an unsupervised and interpretable deep learning algorithm that simultaneously learns the isodepth, spatial gene expression gradients, and piecewise linear functions of the isodepth that model both continuous gradients and discontinuous spatial variation in the expression of individual genes. We validate GASTON by showing that it accurately identifies spatial domains and marker genes across several biological systems. In SRT data from the brain, GASTON reveals gradients of neuronal differentiation and firing, and in SRT data from a tumor sample, GASTON infers gradients of metabolic activity and epithelial-mesenchymal transition (EMT)-related gene expression in the tumor microenvironment.
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Affiliation(s)
- Uthsav Chitra
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Brian J. Arnold
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Hirak Sarkar
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Ludwig Cancer Institute, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Cong Ma
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | | | - Kohei Sanno
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
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Hu C, Du R, Xiao Q, Geng M. Differences between cultured cortical neurons by trypsin and papain digestion. IBRAIN 2022; 8:93-99. [PMID: 37786412 PMCID: PMC10529170 DOI: 10.1002/ibra.12028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 02/05/2023]
Abstract
The objective of this study was to compare the efficiency of trypsin and papain in neuronal digestion and determine which enzyme is more efficient. Cortical tissues were obtained from Sprague-Dawley (SD) rats. According to the different digestive enzymes, the samples were divided into the trypsin group and the papain group. After being digested by each of the two enzymes, cortical neurons were collected from the samples. Then, the morphology of the cortical neurons was determined. Moreover, the cortical neurons were transfected with the negative control (NC) lentivirus. The transfection efficiency and morphology were determined and compared. Compared with the papain group, cortical neurons in the trypsin group were more in number, had larger cell size, had longer axonal length, and had fewer impurities. The transfection efficiency of the trypsin group (57.77%) was higher than that of the papain group (53.83%). The morphology of neurons that was displayed showed that the cell body of most neurons shrank and became smaller, and the axis mutation became shorter and less in the papain group 6 days after transfection with the NC lentivirus. Trypsin is more efficient in digesting neurons because the neurons digested by this enzyme are more in number, have a larger cell body, longer axons, and greater transfection efficiency.
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Affiliation(s)
- Chang‐Yan Hu
- Animal Zoology DepartmentKunming Medical UniversityKunmingYunnanChina
| | - Ruo‐Lan Du
- Institute of Neurological Disease, West China HospitalSichuan UniversityChengduSichuanChina
| | - Qiu‐Xia Xiao
- Animal Zoology DepartmentKunming Medical UniversityKunmingYunnanChina
| | - Min‐Jian Geng
- Department of AnesthesiologyNanchong Central HospitalNanchongSichuanChina
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