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Odabasi Y, Yanasik S, Saglam-Metiner P, Kaymaz Y, Yesil-Celiktas O. Comprehensive Transcriptomic Investigation of Rett Syndrome Reveals Increasing Complexity Trends from Induced Pluripotent Stem Cells to Neurons with Implications for Enriched Pathways. ACS OMEGA 2023; 8:44148-44162. [PMID: 38027357 PMCID: PMC10666228 DOI: 10.1021/acsomega.3c06448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
Rett syndrome (RTT) is a rare genetic neurodevelopmental disorder that has no cure apart from symptomatic treatments. While intense research efforts are required to fulfill this unmet need, the fundamental challenge is to obtain sufficient patient data. In this study, we used human transcriptomic data of four different sample types from RTT patients including induced pluripotent stem cells, differentiated neural progenitor cells, differentiated neurons, and postmortem brain tissues with an increasing in vivo-like complexity to unveil specific trends in gene expressions across the samples. Based on DEG analysis, we identified F8A3, CNTN6, RPE65, and COL19A1 to have differential expression levels in three sample types and also observed previously reported genes such as MECP2, FOXG1, CACNA1G, SATB2, GABBR2, MEF2C, KCNJ10, and CUX2 in our study. Considering the significantly enriched pathways for each sample type, we observed a consistent increase in numbers from iPSCs to NEUs where MECP2 displayed profound effects. We also validated our GSEA results by using single-cell RNA-seq data. In WGCNA, we elicited a connection among MECP2, TNRC6A, and HOXA5. Our findings highlight the utility of transcriptomic analyses to determine genes that might lead to therapeutic strategies.
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Affiliation(s)
- Yusuf
Caglar Odabasi
- Department of Bioengineering,
Faculty of Engineering, Ege University, Izmir 35100, Turkey
| | - Sena Yanasik
- Department of Bioengineering,
Faculty of Engineering, Ege University, Izmir 35100, Turkey
| | - Pelin Saglam-Metiner
- Department of Bioengineering,
Faculty of Engineering, Ege University, Izmir 35100, Turkey
| | - Yasin Kaymaz
- Department of Bioengineering,
Faculty of Engineering, Ege University, Izmir 35100, Turkey
| | - Ozlem Yesil-Celiktas
- Department of Bioengineering,
Faculty of Engineering, Ege University, Izmir 35100, Turkey
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2
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Frankel E, Podder A, Sharifi M, Pillai R, Belnap N, Ramsey K, Dodson J, Venugopal P, Brzezinski M, Llaci L, Gerald B, Mills G, Sanchez-Castillo M, Balak CD, Szelinger S, Jepsen WM, Siniard AL, Richholt R, Naymik M, Schrauwen I, Craig DW, Piras IS, Huentelman MJ, Schork NJ, Narayanan V, Rangasamy S. Genetic and Protein Network Underlying the Convergence of Rett-Syndrome-like (RTT-L) Phenotype in Neurodevelopmental Disorders. Cells 2023; 12:1437. [PMID: 37408271 DOI: 10.3390/cells12101437] [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: 02/07/2023] [Revised: 04/20/2023] [Accepted: 04/29/2023] [Indexed: 07/07/2023] Open
Abstract
Mutations of the X-linked gene encoding methyl-CpG-binding protein 2 (MECP2) cause classical forms of Rett syndrome (RTT) in girls. A subset of patients who are recognized to have an overlapping neurological phenotype with RTT but are lacking a mutation in a gene that causes classical or atypical RTT can be described as having a 'Rett-syndrome-like phenotype (RTT-L). Here, we report eight patients from our cohort diagnosed as having RTT-L who carry mutations in genes unrelated to RTT. We annotated the list of genes associated with RTT-L from our patient cohort, considered them in the light of peer-reviewed articles on the genetics of RTT-L, and constructed an integrated protein-protein interaction network (PPIN) consisting of 2871 interactions connecting 2192 neighboring proteins among RTT- and RTT-L-associated genes. Functional enrichment analysis of RTT and RTT-L genes identified a number of intuitive biological processes. We also identified transcription factors (TFs) whose binding sites are common across the set of RTT and RTT-L genes and appear as important regulatory motifs for them. Investigation of the most significant over-represented pathway analysis suggests that HDAC1 and CHD4 likely play a central role in the interactome between RTT and RTT-L genes.
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Affiliation(s)
- Eric Frankel
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Avijit Podder
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Megan Sharifi
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Roshan Pillai
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Newell Belnap
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Julius Dodson
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Pooja Venugopal
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Molly Brzezinski
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Lorida Llaci
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Brittany Gerald
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Gabrielle Mills
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Meredith Sanchez-Castillo
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Chris D Balak
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Szabolcs Szelinger
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Wayne M Jepsen
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Ashley L Siniard
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Ryan Richholt
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Neurology, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY 10032, USA
| | - David W Craig
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90033, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Nicholas J Schork
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Vinodh Narayanan
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Sampathkumar Rangasamy
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
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Li W. Excitation and Inhibition Imbalance in Rett Syndrome. Front Neurosci 2022; 16:825063. [PMID: 35250460 PMCID: PMC8894599 DOI: 10.3389/fnins.2022.825063] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
A loss of the excitation/inhibition (E/I) balance in the neural circuit has emerged as a common neuropathological feature in many neurodevelopmental disorders. Rett syndrome (RTT), a prevalent neurodevelopmental disorder that affects 1:10,000-15,000 women globally, is caused by loss-of-function mutations in the Methyl-CpG-binding Protein-2 (Mecp2) gene. E/I imbalance is recognized as the leading cellular and synaptic hallmark that is fundamental to diverse RTT neurological symptoms, including stereotypic hand movements, impaired motor coordination, breathing irregularities, seizures, and learning/memory dysfunctions. E/I balance in RTT is not homogeneously altered but demonstrates brain region and cell type specificity instead. In this review, I elaborate on the current understanding of the loss of E/I balance in a range of brain areas at molecular and cellular levels. I further describe how the underlying cellular mechanisms contribute to the disturbance of the proper E/I ratio. Last, I discuss current pharmacologic innervations for RTT and their role in modifying the E/I balance.
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Affiliation(s)
- Wei Li
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
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Zhao H, Mao X, Zhu C, Zou X, Peng F, Yang W, Li B, Li G, Ge T, Cui R. GABAergic System Dysfunction in Autism Spectrum Disorders. Front Cell Dev Biol 2022; 9:781327. [PMID: 35198562 PMCID: PMC8858939 DOI: 10.3389/fcell.2021.781327] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/16/2021] [Indexed: 12/19/2022] Open
Abstract
Autism spectrum disorder (ASD) refers to a series of neurodevelopmental diseases characterized by two hallmark symptoms, social communication deficits and repetitive behaviors. Gamma-aminobutyric acid (GABA) is one of the most important inhibitory neurotransmitters in the central nervous system (CNS). GABAergic inhibitory neurotransmission is critical for the regulation of brain rhythm and spontaneous neuronal activities during neurodevelopment. Genetic evidence has identified some variations of genes associated with the GABA system, indicating an abnormal excitatory/inhibitory (E/I) neurotransmission ratio implicated in the pathogenesis of ASD. However, the specific molecular mechanism by which GABA and GABAergic synaptic transmission affect ASD remains unclear. Transgenic technology enables translating genetic variations into rodent models to further investigate the structural and functional synaptic dysregulation related to ASD. In this review, we summarized evidence from human neuroimaging, postmortem, and genetic and pharmacological studies, and put emphasis on the GABAergic synaptic dysregulation and consequent E/I imbalance. We attempt to illuminate the pathophysiological role of structural and functional synaptic dysregulation in ASD and provide insights for future investigation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ranji Cui
- *Correspondence: Tongtong Ge, ; Ranji Cui,
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Marballi K, MacDonald JL. Proteomic and transcriptional changes associated with MeCP2 dysfunction reveal nodes for therapeutic intervention in Rett syndrome. Neurochem Int 2021; 148:105076. [PMID: 34048843 PMCID: PMC8286335 DOI: 10.1016/j.neuint.2021.105076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 04/13/2021] [Accepted: 05/17/2021] [Indexed: 12/28/2022]
Abstract
Mutations in the methyl-CpG binding protein 2 (MECP2) gene cause Rett syndrome (RTT), an X-linked neurodevelopmental disorder predominantly impacting females. MECP2 is an epigenetic transcriptional regulator acting mainly to repress gene expression, though it plays multiple gene regulatory roles and has distinct molecular targets across different cell types and specific developmental stages. In this review, we summarize MECP2 loss-of-function associated transcriptome and proteome disruptions, delving deeper into the latter which have been comparatively severely understudied. These disruptions converge on multiple biochemical and cellular pathways, including those involved in synaptic function and neurodevelopment, NF-κB signaling and inflammation, and the vitamin D pathway. RTT is a complex neurological disorder characterized by myriad physiological disruptions, in both the central nervous system and peripheral systems. Thus, treating RTT will likely require a combinatorial approach, targeting multiple nodes within the interactomes of these cellular pathways. To this end, we discuss the use of dietary supplements and factors, namely, vitamin D and polyunsaturated fatty acids (PUFAs), as possible partial therapeutic agents given their demonstrated benefit in RTT and their ability to restore homeostasis to multiple disrupted cellular pathways simultaneously. Further unravelling the complex molecular alterations induced by MECP2 loss-of-function, and contextualizing them at the level of proteome homeostasis, will identify new therapeutic avenues for this complex disorder.
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Affiliation(s)
- Ketan Marballi
- Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, NY, USA
| | - Jessica L MacDonald
- Department of Biology, Program in Neuroscience, Syracuse University, Syracuse, NY, USA.
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Belaïdouni Y, Diabira D, Zhang J, Graziano JC, Bader F, Montheil A, Menuet C, Wayman GA, Gaiarsa JL. The Chloride Homeostasis of CA3 Hippocampal Neurons Is Not Altered in Fully Symptomatic Mepc2-null Mice. Front Cell Neurosci 2021; 15:724976. [PMID: 34602980 PMCID: PMC8484709 DOI: 10.3389/fncel.2021.724976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/27/2021] [Indexed: 02/05/2023] Open
Abstract
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused mainly by mutations in the MECP2 gene. Mouse models of RTT show reduced expression of the cation-chloride cotransporter KCC2 and altered chloride homeostasis at presymptomatic stages. However, whether these alterations persist to late symptomatic stages has not been studied. Here we assess KCC2 and NKCC1 expressions and chloride homeostasis in the hippocampus of early [postnatal (P) day 30-35] and late (P50-60) symptomatic male Mecp2-null (Mecp2 -/y) mice. We found (i) no difference in the relative amount, but an over-phosphorylation, of KCC2 and NKCC1 between wild-type (WT) and Mecp2 -/y hippocampi and (ii) no difference in the inhibitory strength, nor reversal potential, of GABA A -receptor-mediated responses in Mecp2 -/y CA3 pyramidal neurons compared to WT at any stages studied. Altogether, these data indicate the presence of a functional chloride extrusion mechanism in Mecp2 -/y CA3 pyramidal neurons at symptomatic stages.
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Affiliation(s)
- Yasmine Belaïdouni
- Aix-Marseille University UMR 1249, Institut de Neurobiologie de la Méditerranée, Institut National de la Santé et de la Recherche Médicale Unité 1249, Parc Scientifique de Luminy, Marseille, France
| | - Diabe Diabira
- Aix-Marseille University UMR 1249, Institut de Neurobiologie de la Méditerranée, Institut National de la Santé et de la Recherche Médicale Unité 1249, Parc Scientifique de Luminy, Marseille, France
| | - Jinwei Zhang
- Institute of Biomedical and Clinical Sciences, College of Medicine and Health, University of Exeter, Hatherly Laboratories, Exeter, United Kingdom
| | - Jean-Charles Graziano
- Aix-Marseille University 105, Institut Paoli Calmettes, U1068, Institut National de la Santé et de la Recherche Médicale U7258, Centre National de Recherche Scientifique, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Francesca Bader
- Aix-Marseille University UMR 1249, Institut de Neurobiologie de la Méditerranée, Institut National de la Santé et de la Recherche Médicale Unité 1249, Parc Scientifique de Luminy, Marseille, France
| | - Aurelie Montheil
- Aix-Marseille University UMR 1249, Institut de Neurobiologie de la Méditerranée, Institut National de la Santé et de la Recherche Médicale Unité 1249, Parc Scientifique de Luminy, Marseille, France
| | - Clément Menuet
- Aix-Marseille University UMR 1249, Institut de Neurobiologie de la Méditerranée, Institut National de la Santé et de la Recherche Médicale Unité 1249, Parc Scientifique de Luminy, Marseille, France
| | - Gary A. Wayman
- Program in Neuroscience, Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, United States
| | - Jean-Luc Gaiarsa
- Aix-Marseille University UMR 1249, Institut de Neurobiologie de la Méditerranée, Institut National de la Santé et de la Recherche Médicale Unité 1249, Parc Scientifique de Luminy, Marseille, France
- *Correspondence: Jean-Luc Gaiarsa,
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