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Mercer HM, Nair AM, Ridgel A, Piontkivska H. Alterations in RNA editing in skeletal muscle following exercise training in individuals with Parkinson's disease. PLoS One 2023; 18:e0287078. [PMID: 38134032 PMCID: PMC10745226 DOI: 10.1371/journal.pone.0287078] [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: 05/29/2023] [Accepted: 09/01/2023] [Indexed: 12/24/2023] Open
Abstract
Parkinson's Disease (PD) is the second most common neurodegenerative disease behind Alzheimer's Disease, currently affecting more than 10 million people worldwide and 1.5 times more males than females. The progression of PD results in the loss of function due to neurodegeneration and neuroinflammation. The etiology of PD is multifactorial, including both genetic and environmental origins. Here we explored changes in RNA editing, specifically editing through the actions of the Adenosine Deaminases Acting on RNA (ADARs), in the progression of PD. Analysis of ADAR editing of skeletal muscle transcriptomes from PD patients and controls, including those that engaged in a rehabilitative exercise training program revealed significant differences in ADAR editing patterns based on age, disease status, and following rehabilitative exercise. Further, deleterious editing events in protein coding regions were identified in multiple genes with known associations to PD pathogenesis. Our findings of differential ADAR editing complement findings of changes in transcriptional networks identified by a recent study and offer insights into dynamic ADAR editing changes associated with PD pathogenesis.
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Affiliation(s)
- Heather Milliken Mercer
- Department of Biological Sciences, Kent State University, Kent, OH, United States of America
- Department of Biological and Environmental Sciences, University of Mount Union, Alliance, OH, United States of America
- Healthy Communities Research Institute, Kent State University, Kent, OH, United States of America
| | - Aiswarya Mukundan Nair
- Department of Biological Sciences, Kent State University, Kent, OH, United States of America
| | - Angela Ridgel
- School of Health Sciences, Kent State University, Kent, OH, United States of America
- Brain Health Research Institute, Kent State University, Kent, OH, United States of America
- Healthy Communities Research Institute, Kent State University, Kent, OH, United States of America
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH, United States of America
- Brain Health Research Institute, Kent State University, Kent, OH, United States of America
- Healthy Communities Research Institute, Kent State University, Kent, OH, United States of America
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2
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Kilpatrick S, Irwin C, Singh KK. Human pluripotent stem cell (hPSC) and organoid models of autism: opportunities and limitations. Transl Psychiatry 2023; 13:217. [PMID: 37344450 DOI: 10.1038/s41398-023-02510-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/09/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder caused by genetic or environmental perturbations during early development. Diagnoses are dependent on the identification of behavioral abnormalities that likely emerge well after the disorder is established, leaving critical developmental windows uncharacterized. This is further complicated by the incredible clinical and genetic heterogeneity of the disorder that is not captured in most mammalian models. In recent years, advancements in stem cell technology have created the opportunity to model ASD in a human context through the use of pluripotent stem cells (hPSCs), which can be used to generate 2D cellular models as well as 3D unguided- and region-specific neural organoids. These models produce profoundly intricate systems, capable of modeling the developing brain spatiotemporally to reproduce key developmental milestones throughout early development. When complemented with multi-omics, genome editing, and electrophysiology analysis, they can be used as a powerful tool to profile the neurobiological mechanisms underlying this complex disorder. In this review, we will explore the recent advancements in hPSC-based modeling, discuss present and future applications of the model to ASD research, and finally consider the limitations and future directions within the field to make this system more robust and broadly applicable.
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Affiliation(s)
- Savannah Kilpatrick
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON, Canada
| | - Courtney Irwin
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Karun K Singh
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada.
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Zhang J, Ji G, Gao X, Guan J. Single-nucleus gene and gene set expression-based similarity network fusion identifies autism molecular subtypes. BMC Bioinformatics 2023; 24:142. [PMID: 37041460 PMCID: PMC10091652 DOI: 10.1186/s12859-023-05278-0] [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: 01/05/2023] [Accepted: 04/07/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that is highly phenotypically and genetically heterogeneous. With the accumulation of biological sequencing data, more and more studies shift to molecular subtype-first approach, from identifying molecular subtypes based on genetic and molecular data to linking molecular subtypes with clinical manifestation, which can reduce heterogeneity before phenotypic profiling. RESULTS In this study, we perform similarity network fusion to integrate gene and gene set expression data of multiple human brain cell types for ASD molecular subtype identification. Then we apply subtype-specific differential gene and gene set expression analyses to study expression patterns specific to molecular subtypes in each cell type. To demonstrate the biological and practical significance, we analyze the molecular subtypes, investigate their correlation with ASD clinical phenotype, and construct ASD molecular subtype prediction models. CONCLUSIONS The identified molecular subtype-specific gene and gene set expression may be used to differentiate ASD molecular subtypes, facilitating the diagnosis and treatment of ASD. Our method provides an analytical pipeline for the identification of molecular subtypes and even disease subtypes of complex disorders.
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Affiliation(s)
- Junjie Zhang
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, China
| | - Xilin Gao
- Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian, China.
| | - Jinting Guan
- Department of Automation, Xiamen University, Xiamen, Fujian, China.
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, China.
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Sharma M, Jha IP, Chawla S, Pandey N, Chandra O, Mishra S, Kumar V. Associating pathways with diseases using single-cell expression profiles and making inferences about potential drugs. Brief Bioinform 2022; 23:6623725. [PMID: 35772850 DOI: 10.1093/bib/bbac241] [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: 03/03/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 11/14/2022] Open
Abstract
Finding direct dependencies between genetic pathways and diseases has been the target of multiple studies as it has many applications. However, due to cellular heterogeneity and limitations of the number of samples for bulk expression profiles, such studies have faced hurdles in the past. Here, we propose a method to perform single-cell expression-based inference of association between pathway, disease and cell-type (sci-PDC), which can help to understand their cause and effect and guide precision therapy. Our approach highlighted reliable relationships between a few diseases and pathways. Using the example of diabetes, we have demonstrated how sci-PDC helps in tracking variation of association between pathways and diseases with changes in age and species. The variation in pathways-disease associations in mice and humans revealed critical facts about the suitability of the mouse model for a few pathways in the context of diabetes. The coherence between results from our method and previous reports, including information about the drug target pathways, highlights its reliability for multidimensional utility.
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Affiliation(s)
- Madhu Sharma
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Indra Prakash Jha
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Smriti Chawla
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Neetesh Pandey
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Omkar Chandra
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Shreya Mishra
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Vibhor Kumar
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
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Qu J, Liu Z, Li L, Zou Z, He Z, Zhou L, Luo Y, Zhang M, Ye J. Efficacy and Safety of Stem Cell Therapy in Children With Autism Spectrum Disorders: A Systematic Review and Meta-Analysis. Front Pediatr 2022; 10:897398. [PMID: 35601435 PMCID: PMC9114801 DOI: 10.3389/fped.2022.897398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/01/2022] [Indexed: 01/08/2023] Open
Abstract
AIM There is insufficient evidence regarding the efficacy and safety of stem cell therapy for autism spectrum disorders. We performed the first meta-analysis of stem cell therapy for autism spectrum disorders in children to provide evidence for clinical rehabilitation. METHODS The data source includes PubMed/Medline, Web of Science, EMBASE, Cochrane Library and China Academic Journal, from inception to 24th JULY 2021. After sifting through the literature, the Cochrane tool was applied to assess the risk of bias. Finally, we extracted data from these studies and calculated pooled efficacy and safety. RESULTS 5 studies that met the inclusion criteria were included in current analysis. Meta-analysis was performed using rehabilitation therapy as the reference standard. Data showed that the Childhood Autism Rating Scale score of stem cell group was striking lower than the control group (WMD: -5.96; 95%CI [-8.87, -3.06]; p < 0.0001). The Clinical Global Impression score consolidated effect size RR = 1.01, 95%CI [0.87, 1.18], Z = 0.14 (p = 0.89), the effective rate for The Clinical Global Impression was 62% and 60% in the stem cell group and the control group, respectively. The occurrence events of adverse reactions in each group (RR = 1.55; 95%CI = 0.60 to 3.98; p = 0.36), there was no significant difference in the incidence of adverse reactions between the stem cell group and the control group. CONCLUSIONS The results of this meta-analysis suggested that stem cell therapy for children with autism might be safe and effective. However, the evidence was compromised by the limitations in current study size, lacking standardized injection routes and doses of stem cells, as well as shortages in diagnostic tools and long period follow-up studies. Hence, it calls for more studies to systematically confirm the efficacy and safety of stem cell therapy for children with autism spectrum disorders.
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Affiliation(s)
- Jiayang Qu
- The First Clinical Medicine College of Gannan Medical University, Ganzhou, China.,Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.,School of Rehabilitation Medicine Gannan Medical University, GanZhou, China
| | - Zicai Liu
- School of Rehabilitation Medicine Gannan Medical University, GanZhou, China
| | - Lincai Li
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.,Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, GanZhou, China
| | - Zhengwei Zou
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.,Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, GanZhou, China
| | - Zhengyi He
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.,Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, GanZhou, China.,Clinical Medicine Research Center, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Lin Zhou
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.,Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, GanZhou, China
| | - Yaolin Luo
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.,Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, GanZhou, China.,Clinical Medicine Research Center, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Minhong Zhang
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.,Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, GanZhou, China.,Clinical Medicine Research Center, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Junsong Ye
- The First Clinical Medicine College of Gannan Medical University, Ganzhou, China.,Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, China.,Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, GanZhou, China.,Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, China.,Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, China
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Zuo Y, Wei D, Zhu C, Naveed O, Hong W, Yang X. Unveiling the Pathogenesis of Psychiatric Disorders Using Network Models. Genes (Basel) 2021; 12:1101. [PMID: 34356117 PMCID: PMC8304351 DOI: 10.3390/genes12071101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
Psychiatric disorders are complex brain disorders with a high degree of genetic heterogeneity, affecting millions of people worldwide. Despite advances in psychiatric genetics, the underlying pathogenic mechanisms of psychiatric disorders are still largely elusive, which impedes the development of novel rational therapies. There has been accumulating evidence suggesting that the genetics of complex disorders can be viewed through an omnigenic lens, which involves contextualizing genes in highly interconnected networks. Thus, applying network-based multi-omics integration methods could cast new light on the pathophysiology of psychiatric disorders. In this review, we first provide an overview of the recent advances in psychiatric genetics and highlight gaps in translating molecular associations into mechanistic insights. We then present an overview of network methodologies and review previous applications of network methods in the study of psychiatric disorders. Lastly, we describe the potential of such methodologies within a multi-tissue, multi-omics approach, and summarize the future directions in adopting diverse network approaches.
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Affiliation(s)
- Yanning Zuo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Don Wei
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Semel Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Carissa Zhu
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Ormina Naveed
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Weizhe Hong
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Brain Research Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
- Brain Research Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA 90095, USA
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Garbulowski M, Smolinska K, Diamanti K, Pan G, Maqbool K, Feuk L, Komorowski J. Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder. Front Genet 2021; 12:618277. [PMID: 33719335 PMCID: PMC7946989 DOI: 10.3389/fgene.2021.618277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/12/2021] [Indexed: 01/16/2023] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous neuropsychiatric disorder with a complex genetic background. Analysis of altered molecular processes in ASD patients requires linear and nonlinear methods that provide interpretable solutions. Interpretable machine learning provides legible models that allow explaining biological mechanisms and support analysis of clinical subgroups. In this work, we investigated several case-control studies of gene expression measurements of ASD individuals. We constructed a rule-based learning model from three independent datasets that we further visualized as a nonlinear gene-gene co-predictive network. To find dissimilarities between ASD subtypes, we scrutinized a topological structure of the network and estimated a centrality distance. Our analysis revealed that autism is the most severe subtype of ASD, while pervasive developmental disorder-not otherwise specified and Asperger syndrome are closely related and milder ASD subtypes. Furthermore, we analyzed the most important ASD-related features that were described in terms of gene co-predictors. Among others, we found a strong co-predictive mechanism between EMC4 and TMEM30A, which may suggest a co-regulation between these genes. The present study demonstrates the potential of applying interpretable machine learning in bioinformatics analyses. Although the proposed methodology was designed for transcriptomics data, it can be applied to other omics disciplines.
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Affiliation(s)
- Mateusz Garbulowski
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Karolina Smolinska
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Klev Diamanti
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Khurram Maqbool
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lars Feuk
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jan Komorowski
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Swedish Collegium for Advanced Study, Uppsala, Sweden.,Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Washington National Primate Research Center, Seattle, WA, United States
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