1
|
Veeraraghavan P, Engmann AK, Hatch JJ, Itoh Y, Nguyen D, Addison T, Macklis JD. Dynamic subtype- and context-specific subcellular RNA regulation in growth cones of developing neurons of the cerebral cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.24.559186. [PMID: 38328182 PMCID: PMC10849483 DOI: 10.1101/2023.09.24.559186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Molecular mechanisms that cells employ to compartmentalize function via localization of function-specific RNA and translation are only partially elucidated. We investigate long-range projection neurons of the cerebral cortex as highly polarized exemplars to elucidate dynamic regulation of RNA localization, stability, and translation within growth cones (GCs), leading tips of growing axons. Comparison of GC-localized transcriptomes between two distinct subtypes of projection neurons- interhemispheric-callosal and corticothalamic- across developmental stages identifies both distinct and shared subcellular machinery, and intriguingly highlights enrichment of genes associated with neurodevelopmental and neuropsychiatric disorders. Developmental context-specific components of GC-localized transcriptomes identify known and novel potential regulators of distinct phases of circuit formation: long-distance growth, target area innervation, and synapse formation. Further, we investigate mechanisms by which transcripts are enriched and dynamically regulated in GCs, and identify GC-enriched motifs in 3' untranslated regions. As one example, we identify cytoplasmic adenylation element binding protein 4 (CPEB4), an RNA binding protein regulating localization and translation of mRNAs encoding molecular machinery important for axonal branching and complexity. We also identify RNA binding motif single stranded interacting protein 1 (RBMS1) as a dynamically expressed regulator of RNA stabilization that enables successful callosal circuit formation. Subtly aberrant associative and integrative cortical circuitry can profoundly affect cortical function, often causing neurodevelopmental and neuropsychiatric disorders. Elucidation of context-specific subcellular RNA regulation for GC- and soma-localized molecular controls over precise circuit development, maintenance, and function offers generalizable insights for other polarized cells, and might contribute substantially to understanding neurodevelopmental and behavioral-cognitive disorders and toward targeted therapeutics.
Collapse
Affiliation(s)
- Priya Veeraraghavan
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Anne K. Engmann
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - John J. Hatch
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Yasuhiro Itoh
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Duane Nguyen
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Thomas Addison
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jeffrey D. Macklis
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| |
Collapse
|
2
|
Reyes-Pérez P, García-Marín LM, Aman AM, Antar T, Flores-Ocampo V, Mitchell BL, Medina-Rivera A, Rentería ME. Investigating the Shared Genetic Etiology Between Parkinson's Disease and Depression. JOURNAL OF PARKINSON'S DISEASE 2024; 14:483-493. [PMID: 38457145 DOI: 10.3233/jpd-230176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Background Depression is a common symptom in Parkinson's disease (PD), resulting from underlying neuropathological processes and psychological factors. However, the extent to which shared genetic risk factors contribute to the relationship between depression and PD is poorly understood. Objective To examine the effects of common genetic variants influencing the etiology of PD and depression risk at the genome-wide and local genomic regional level. Methods We comprehensively investigated the genetic relationship between PD and depression using genome-wide association studies data. First, we estimated the genetic correlation at the genome-wide level using linkage-disequilibrium score regression, followed by local genetic correlation analysis using the GWAS-pairwise method and functional annotation to identify genes that may jointly influence the risk for both traits. Also, we performed Latent Causal Variable, Latent Heritable Confounder Mendelian Randomization, and traditional Mendelian Randomization analyses to investigate the potential causal relationship. Results Although the genetic correlation between PD and depression was not statistically significant at the genome-wide level, GWAS-pairwise analyses identified 16 genomic segments associated with PD and depression, implicating nine genes. Further analyses revealed distinct patterns within individual genes, suggesting an intricate pattern. These genes involve various biological processes, including neurotransmitter regulation, senescence, and nucleo-cytoplasmic transport mechanisms. We did not observe genetic evidence of causality between PD and depression. Conclusions Our findings did not support a genome-wide genetic correlation or a causal association between both conditions. However, we identified genomic segments but identified genomic segments linked to distinct biological pathways influencing their etiology.Further research is needed to understand their functional consequences.
Collapse
Affiliation(s)
- Paula Reyes-Pérez
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Luis M García-Marín
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Asma M Aman
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Tarek Antar
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Victor Flores-Ocampo
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
- Licenciatura en Ciencias Genómicas, Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, Querétaro, México
| | - Brittany L Mitchell
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Miguel E Rentería
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD,Australia
| |
Collapse
|
3
|
Lin L, Liang Y, Cao T, Huang Y, Li W, Li J, Wang J, Peng X, Ge Y, Li Y, Li L. Transcriptome profiling and ceRNA network of small extracellular vesicles from resting and degranulated mast cells. Epigenomics 2023; 15:845-862. [PMID: 37846550 DOI: 10.2217/epi-2023-0175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Abstract
Aim: This study aimed to investigate the transcriptomic characteristics and interactions between competitive endogenous RNAs (ceRNAs) within small extracellular vesicles (sEVs) derived from mast cells (MCs). Methods: Transcriptome sequencing analyzed lncRNA, circRNA and mRNA expression in resting and degranulated MC-derived sEVs. Constructed ceRNA regulatory network through correlation analysis and target gene prediction. Results: Differentially expressed 1673 mRNAs, 173 lncRNAs and 531 circRNAs were observed between resting and degranulated MCs-derived sEVs. Enrichment analysis revealed involvement of neurodegeneration, infection and tumor pathways. CeRNA networks included interactions between lncRNA-miRNA, circRNA-miRNA and miRNA-mRNA, targeting genes in the hippo and wnt signaling pathways linked to tumor immune regulation. Conclusion: This study provides valuable insights into MC-sEV molecular mechanisms, offering significant data resources for further investigations.
Collapse
Affiliation(s)
- Lihui Lin
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, P.R. China
| | - Yuting Liang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University Suzhou, Jiangsu, 215006, P.R. China
| | - Tianyu Cao
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, P.R. China
| | - Yuji Huang
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, P.R. China
| | - Weize Li
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, P.R. China
| | - Jia Li
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, P.R. China
| | - Juan Wang
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, P.R. China
| | - Xia Peng
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, P.R. China
| | - Yiqin Ge
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P.R. China
| | - Yanning Li
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, P.R. China
| | - Li Li
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, P.R. China
| |
Collapse
|
4
|
Santos HP, Enggasser AE, Clark J, Roell K, Zhabotynsky V, Gower WA, Yanni D, Yang NG, Washburn L, Gogcu S, Marsit CJ, Kuban K, O'Shea TM, Fry RC. Sexually dimorphic methylation patterns characterize the placenta and blood from extremely preterm newborns. BMC Biol 2023; 21:173. [PMID: 37608375 PMCID: PMC10464100 DOI: 10.1186/s12915-023-01662-7] [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: 08/23/2022] [Accepted: 07/12/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Health outcomes among children born prematurely are known to be sexually dimorphic, with male infants often more affected, yet the mechanism behind this observation is not clear. CpG methylation levels in the placenta and blood also differ by sex and are associated with adverse health outcomes. We contrasted CpG methylation levels in the placenta and neonatal blood (n = 358) from the Extremely Low Gestational Age Newborn (ELGAN) cohort based on the EPIC array, which assays over 850,000 CpG sites across the epigenome. Sex-specific epigenome-wide association analyses were conducted for the placenta and neonatal blood samples independently, and the results were compared to determine tissue-specific differences between the methylation patterns in males and females. All models were adjusted for cell type heterogeneity. Enrichment pathway analysis was performed to identify the biological functions of genes related to the sexually dimorphic CpG sites. RESULTS Approximately 11,500 CpG sites were differentially methylated in relation to sex. Of these, 5949 were placenta-specific and 5361 were blood-specific, with only 233 CpG sites overlapping in both tissues. For placenta-specific CpG sites, 90% were hypermethylated in males. For blood-specific CpG sites, 95% were hypermethylated in females. In the placenta, keratinocyte differentiation biological pathways were enriched among the differentially methylated genes. No enrichment pathways were observed for blood. CONCLUSIONS Distinct methylation patterns were observed between male and female children born extremely premature, and keratinocyte differentiation pathways were enriched in the placenta. These findings provide new insights into the epigenetic mechanisms underlying sexually dimorphic health outcomes among extremely premature infants.
Collapse
Affiliation(s)
- Hudson P Santos
- School of Nursing and Health Studies, University of Miami, Coral Gables, FL, USA.
| | - Adam E Enggasser
- Gillings School of Global Public Health, Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeliyah Clark
- Gillings School of Global Public Health, Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kyle Roell
- Gillings School of Global Public Health, Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vasyl Zhabotynsky
- Gillings School of Global Public Health, Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William Adam Gower
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Diana Yanni
- Department of Neonatology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Nou Gao Yang
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Lisa Washburn
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Semsa Gogcu
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karl Kuban
- Division of Pediatric Neurology, Department of Pediatrics, School of Medicine, Boston. University, Boston, MA, USA
| | - T Michael O'Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C Fry
- Gillings School of Global Public Health, Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|