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Lee MM, Stoodley CJ. Neural bases of reading fluency: A systematic review and meta-analysis. Neuropsychologia 2024; 202:108947. [PMID: 38964441 DOI: 10.1016/j.neuropsychologia.2024.108947] [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: 06/29/2023] [Revised: 06/26/2024] [Accepted: 06/29/2024] [Indexed: 07/06/2024]
Abstract
Reading fluency, the ability to read quickly and accurately, is a critical marker of successful reading and is notoriously difficult to improve in reading disabled populations. Despite its importance to functional literacy, fluency is a relatively under-studied aspect of reading, and the neural correlates of reading fluency are not well understood. Here, we review the literature of the neural correlates of reading fluency as well as rapid automatized naming (RAN), a task that is robustly related to reading fluency. In a qualitative review of the neuroimaging literature, we evaluated structural and functional MRI studies of reading fluency in readers from a range of skill levels. This was followed by a quantitative activation likelihood estimate (ALE) meta-analysis of fMRI studies of reading speed and RAN measures. We anticipated that reading speed, relative to untimed reading and reading-related tasks, would harness ventral reading pathways that are thought to enable the fast, visual recognition of words. The qualitative review showed that speeded reading taps the entire canonical reading network. The meta-analysis indicated a stronger role of the ventral reading pathway in rapid reading and rapid naming. Both reviews identified regions outside the canonical reading network that contribute to reading fluency, such as the bilateral insula and superior parietal lobule. We suggest that fluent reading engages both domain-specific reading pathways as well as domain-general regions that support overall task performance and discuss future avenues of research to expand our understanding of the neural bases of fluent reading.
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Affiliation(s)
- Marissa M Lee
- Department of Neuroscience, American University, USA; Center for Applied Brain and Cognitive Sciences, Tufts University, USA
| | - Catherine J Stoodley
- Department of Neuroscience, American University, USA; Developing Brain Institute, Children's National Hospital, USA; Departments of Neurology and Pediatrics, The George Washington University School of Medicine and Health Sciences, USA.
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2
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Pasquini L, Pereira FL, Seddighi S, Zeng Y, Wei Y, Illán-Gala I, Vatsavayai SC, Friedberg A, Lee AJ, Brown JA, Spina S, Grinberg LT, Sirkis DW, Bonham LW, Yokoyama JS, Boxer AL, Kramer JH, Rosen HJ, Humphrey J, Gitler AD, Miller BL, Pollard KS, Ward ME, Seeley WW. FTLD targets brain regions expressing recently evolved genes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.27.23297687. [PMID: 37961381 PMCID: PMC10635220 DOI: 10.1101/2023.10.27.23297687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In frontotemporal lobar degeneration (FTLD), pathological protein aggregation is associated with a decline in human-specialized social-emotional and language functions. Most disease protein aggregates contain either TDP-43 (FTLD-TDP) or tau (FTLD-tau). Here, we explored whether FTLD targets brain regions that express genes containing human accelerated regions (HARs), conserved sequences that have undergone positive selection during recent human evolution. To this end, we used structural neuroimaging from patients with FTLD and normative human regional transcriptomic data to identify genes expressed in FTLD-targeted brain regions. We then integrated primate comparative genomic data to test our hypothesis that FTLD targets brain regions expressing recently evolved genes. In addition, we asked whether genes expressed in FTLD-targeted brain regions are enriched for genes that undergo cryptic splicing when TDP-43 function is impaired. We found that FTLD-TDP and FTLD-tau subtypes target brain regions that express overlapping and distinct genes, including many linked to neuromodulatory functions. Genes whose normative brain regional expression pattern correlated with FTLD cortical atrophy were strongly associated with HARs. Atrophy-correlated genes in FTLD-TDP showed greater overlap with TDP-43 cryptic splicing genes compared with atrophy-correlated genes in FTLD-tau. Cryptic splicing genes were enriched for HAR genes, and vice versa, but this effect was due to the confounding influence of gene length. Analyses performed at the individual-patient level revealed that the expression of HAR genes and cryptically spliced genes within putative regions of disease onset differed across FTLD-TDP subtypes. Overall, our findings suggest that FTLD targets brain regions that have undergone recent evolutionary specialization and provide intriguing potential leads regarding the transcriptomic basis for selective vulnerability in distinct FTLD molecular-anatomical subtypes.
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Affiliation(s)
- Lorenzo Pasquini
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
- Department of Neurology, Neuroscape, University of California, San Francisco, CA, USA
| | - Felipe L Pereira
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Yi Zeng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yongbin Wei
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Ignacio Illán-Gala
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
- Global Brain Health Institute, University of California, San Francisco, San Francisco, CA, USA and Trinity College Dublin, Dublin, Ireland
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute, Universitat Autònoma de Barcelona, Barcelona, Catalunya, Spain
| | - Sarat C Vatsavayai
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Adit Friedberg
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
- Global Brain Health Institute, University of California, San Francisco, San Francisco, CA, USA and Trinity College Dublin, Dublin, Ireland
| | - Alex J Lee
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Jesse A Brown
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Salvatore Spina
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Lea T Grinberg
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Daniel W Sirkis
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Luke W Bonham
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
- Department of Radiology, University of California, San Francisco, CA, USA
| | - Jennifer S Yokoyama
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
- Department of Radiology, University of California, San Francisco, CA, USA
| | - Adam L Boxer
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Joel H Kramer
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Howard J Rosen
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Bruce L Miller
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics and Bakar Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - William W Seeley
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
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Alemany-Navarro M, Tubío-Fungueiriño M, Diz-de Almeida S, Cruz R, Lombroso A, Real E, Soria V, Bertolín S, Fernández-Prieto M, Alonso P, Menchón JM, Carracedo A, Segalàs C. The genomics of visuospatial neurocognition in obsessive-compulsive disorder: A preliminary GWAS. J Affect Disord 2023; 333:365-376. [PMID: 37094658 DOI: 10.1016/j.jad.2023.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/04/2023] [Accepted: 04/14/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND The study of Obsessive-Compulsive Disorder (OCD) genomics has primarily been tackled by Genome-wide association studies (GWAS), which have encountered troubles in identifying replicable single nucleotide polymorphisms (SNPs). Endophenotypes have emerged as a promising avenue of study in trying to elucidate the genomic bases of complex traits such as OCD. METHODS We analyzed the association of SNPs across the whole genome with the construction of visuospatial information and executive performance through four neurocognitive variables assessed by the Rey-Osterrieth Complex Figure Test (ROCFT) in a sample of 133 OCD probands. Analyses were performed at SNP- and gene-level. RESULTS No SNP reached genome-wide significance, although there was one SNP almost reaching significant association with copy organization (rs60360940; P = 9.98E-08). Suggestive signals were found for the four variables at both SNP- (P < 1E-05) and gene-levels (P < 1E-04). Most of the suggestive signals pointed to genes and genomic regions previously associated with neurological function and neuropsychological traits. LIMITATIONS Our main limitations were the sample size, which was limited to identify associated signals at a genome-wide level, and the composition of the sample, more representative of rather severe OCD cases than a population-based OCD sample with a broad severity spectrum. CONCLUSIONS Our results suggest that studying neurocognitive variables in GWAS would be more informative on the genetic basis of OCD than the classical case/control GWAS, facilitating the genetic characterization of OCD and its different clinical profiles, the development of individualized treatment approaches, and the improvement of prognosis and treatment response.
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Affiliation(s)
- M Alemany-Navarro
- Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; IBIS (Universidad de Sevilla, HUVR, Junta de Andalucia, CSIC) Sevilla, Spain; CIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Spain.
| | - M Tubío-Fungueiriño
- Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Santiago de Compostela, Spain; Genetics Group, GC05, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, U-711, Centro de Investigación en Red de Enfermedades Raras (CIBERER), Universidade de Santiago de Compostela, (USC), Spain
| | - S Diz-de Almeida
- Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - R Cruz
- Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, U-711, Centro de Investigación en Red de Enfermedades Raras (CIBERER), Universidade de Santiago de Compostela, (USC), Spain
| | - A Lombroso
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - E Real
- Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Department of Clinical Sciences, University of Barcelona, Bellvitge Campus, Barcelona, Spain; CIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Spain
| | - V Soria
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain; Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Department of Clinical Sciences, University of Barcelona, Bellvitge Campus, Barcelona, Spain; CIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Spain
| | - S Bertolín
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain; Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M Fernández-Prieto
- Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Santiago de Compostela, Spain; Genetics Group, GC05, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, U-711, Centro de Investigación en Red de Enfermedades Raras (CIBERER), Universidade de Santiago de Compostela, (USC), Spain
| | - P Alonso
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain; Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Department of Clinical Sciences, University of Barcelona, Bellvitge Campus, Barcelona, Spain; CIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Spain
| | - J M Menchón
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain; Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Department of Clinical Sciences, University of Barcelona, Bellvitge Campus, Barcelona, Spain; CIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Spain
| | - A Carracedo
- Grupo de Medicina Xenómica, U-711, Centro de Investigación en Red de Enfermedades Raras (CIBERER), Universidade de Santiago de Compostela, (USC), Spain; Genetics Group, GC05, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Servicio Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - C Segalàs
- OCD Clinical and Research Unit, Psychiatry Department, Hospital Universitari de Bellvitge, Barcelona, Spain; Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Department of Clinical Sciences, University of Barcelona, Bellvitge Campus, Barcelona, Spain; CIBERSAM (Centro de Investigación en Red de Salud Mental), Instituto de Salud Carlos III, Spain
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Das D, Podder S. Deregulation of ceRNA Networks in Frontal Cortex and Choroid Plexus of Brain during SARS-CoV-2 Infection Aggravates Neurological Manifestations: An Insight from Bulk and Single-Cell Transcriptomic Analyses. Adv Biol (Weinh) 2022; 6:e2101310. [PMID: 35661455 PMCID: PMC9348399 DOI: 10.1002/adbi.202101310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/20/2022] [Indexed: 01/28/2023]
Abstract
Although transcriptomic studies of SARS-CoV-2-infected brains have depicted variability in gene expression, the landscape of deregulated cell-specific regulatory circuits has not been elucidated yet. Hence, bulk and single-cell RNA-seq data are analyzed to gain detailed insights. Initially, two ceRNA networks with 19 and 3 differentially expressed (DE) hub lncRNAs are reconstructed in SARS-CoV-2 infected Frontal Cortex (FC) and Choroid Plexus (CP), respectively. Functional and pathway enrichment analyses of downstream mRNAs of deregulated ceRNA axes demonstrate impairment of neurological processes. Mapping of hub lncRNA-mRNA pairs from bulk RNA-seq with snRNA-seq data has indicated that NORAD, NEAT1, and STXBP5-AS1 are downregulated across 4, 4, and 2 FC cell types, respectively. At the same time, MIRLET7BHG and MALAT1 are upregulated in excitatory neurons of FC and neurons of CP, respectively. Here, it is hypothesized that downregulation of NORAD, NEAT1, and STXBP5-AS1, and upregulation of MIRLET7BHG and MALAT1 might deregulate respectively 51, 6, and 37, and 31 and 19 mRNAs in cell types of FC and CP. Afterward, 13 therapeutic miRNAs are traced that might safeguard against deregulated lncRNA-mRNA pairs of NORAD, NEAT1, and MIRLET7BHG in FC. This study helps to explain the plausible mechanism of post-COVID neurological manifestation and also to devise therapeutics against it.
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Affiliation(s)
- Deepyaman Das
- Department of MicrobiologyRaiganj UniversityRaiganjUttar DinajpurWest Bengal733134India
| | - Soumita Podder
- Department of MicrobiologyRaiganj UniversityRaiganjUttar DinajpurWest Bengal733134India
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5
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Gong M, Shi R, Liu Y, Ke J, Liu X, Du HZ, Liu CM. Abnormal microglial polarization induced by Arid1a deletion leads to neuronal differentiation deficits. Cell Prolif 2022; 55:e13314. [PMID: 35854653 DOI: 10.1111/cpr.13314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/03/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE Microglia, the prototypical innate immune cells of the central nervous system (CNS), are highly plastic and assume their phenotypes dependent on intrinsically genetic, epigenetic regulation or extrinsically microenvironmental cues. Microglia has been recognized as key regulators of neural stem/progenitor cells (NSPCs) and brain functions. Chromatin accessibility is implicated in immune cell development and functional regulation. However, it is still unknown whether and how chromatin remodelling regulates the phenotypic plasticity of microglia and exerts what kind of effects on NSPCs. METHODS We investigated the role of chromatin accessibility in microglia by deleting chromatin remodelling gene Arid1a using microglia-specific Cx3cr1-cre and Cx3cr1-CreERT2 mice. RNA-seq and ATAC-seq were performed to dissect the molecular mechanisms. In addition, we examined postnatal M1/M2 microglia polarization and analysed neuronal differentiation of NSPCs. Finally, we tested the effects of microglial Arid1a deletion on mouse behaviours. RESULTS Increased chromatin accessibility upon Arid1a ablation resulted in enhanced M1 microglial polarization and weakened M2 polarization, which led to abnormal neurogenesis and anxiety-like behaviours. Switching the polarization state under IL4 stimulation could rescue abnormal neurogenesis, supporting an essential role for chromatin remodeler ARID1A in balancing microglial polarization and brain functions. CONCLUSIONS Our study identifies ARID1A as a central regulator of microglia polarization, establishing a mechanistic link between chromatin remodelling, neurogenesis and mouse behaviours, and highlights the potential development of innovative therapeutics exploiting the innate regenerative capacity of the nervous system.
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Affiliation(s)
- Maolei Gong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Ruoxi Shi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yijun Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Jinpeng Ke
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Hong-Zhen Du
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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