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Matuleviciute R, Akinluyi ET, Muntslag TAO, Dewing JM, Long KR, Vernon AC, Tremblay ME, Menassa DA. Microglial contribution to the pathology of neurodevelopmental disorders in humans. Acta Neuropathol 2023; 146:663-683. [PMID: 37656188 PMCID: PMC10564830 DOI: 10.1007/s00401-023-02629-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
Microglia are the brain's resident macrophages, which guide various developmental processes crucial for brain maturation, activity, and plasticity. Microglial progenitors enter the telencephalic wall by the 4th postconceptional week and colonise the fetal brain in a manner that spatiotemporally tracks key neurodevelopmental processes in humans. However, much of what we know about how microglia shape neurodevelopment comes from rodent studies. Multiple differences exist between human and rodent microglia warranting further focus on the human condition, particularly as microglia are emerging as critically involved in the pathological signature of various cognitive and neurodevelopmental disorders. In this article, we review the evidence supporting microglial involvement in basic neurodevelopmental processes by focusing on the human species. We next concur on the neuropathological evidence demonstrating whether and how microglia contribute to the aetiology of two neurodevelopmental disorders: autism spectrum conditions and schizophrenia. Next, we highlight how recent technologies have revolutionised our understanding of microglial biology with a focus on how these tools can help us elucidate at unprecedented resolution the links between microglia and neurodevelopmental disorders. We conclude by reviewing which current treatment approaches have shown most promise towards targeting microglia in neurodevelopmental disorders and suggest novel avenues for future consideration.
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Affiliation(s)
- Rugile Matuleviciute
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Elizabeth T Akinluyi
- Division of Medical Sciences, University of Victoria, Victoria, Canada
- Department of Pharmacology and Therapeutics, Afe Babalola University, Ado Ekiti, Nigeria
| | - Tim A O Muntslag
- Princess Maxima Centre for Paediatric Oncology, Utrecht, The Netherlands
| | | | - Katherine R Long
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Anthony C Vernon
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - David A Menassa
- Department of Neuropathology & The Queen's College, University of Oxford, Oxford, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden.
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52
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Griffin A, Chen M, Tiwari VK. Dissection of cellular disruptions in autism spectrum disorder comorbidities. Eur J Neurosci 2023; 58:3921-3931. [PMID: 37807181 DOI: 10.1111/ejn.16155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/29/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023]
Abstract
Up to 80% of children with autism spectrum disorder have at least one other neuropsychiatric comorbidity. The causes of such disorders are highly genetic, yet many studies fail to take analysis further than risk gene discovery to see cellular and mechanistic changes occurring. Therefore, the goal of this study was to unveil novel gene expression signatures involved in important neurodevelopmental processes that, when disrupted, lead to each of the autism comorbidities of interest. We achieved this by analysing a single-nuclei RNA sequencing dataset with prefrontal cortex samples from autism spectrum disorder plus comorbidities for differentially expressed genes. The highest number of alterations was seen in excitatory neurons, which also showed differential population and cell-cell interactions across disorders and an increase in expression of genes involved in neurodevelopmental pathways. Interestingly, the group without comorbidities displayed an increase in neuron-neuron interactions yet a decrease in population number, suggesting a major rewiring of neuronal connections. Further analysis of the topmost significant genes from this cell type in developing prefrontal cortex datasets revealed interesting expression trajectories corresponding to important time points during corticogenesis. This further identified four novel candidate genes that show a potential link to developmental pathways that may contribute to autism and its comorbidities when dysregulated. The study provides a better understanding of co-occurring conditions at a transcriptomic and cell-type level and thereby aid future research in providing earlier diagnosis, care and intervention.
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Affiliation(s)
- Aoife Griffin
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queen's University Belfast, UK
| | - Mei Chen
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queen's University Belfast, UK
| | - Vijay K Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queen's University Belfast, UK
- Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark
- Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
- Danish Institute for Advanced Study (DIAS), Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
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Mulligan MR, Bicknell LS. The molecular genetics of nELAVL in brain development and disease. Eur J Hum Genet 2023; 31:1209-1217. [PMID: 37697079 PMCID: PMC10620143 DOI: 10.1038/s41431-023-01456-z] [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: 07/06/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Embryonic development requires tight control of gene expression levels, activity, and localisation. This control is coordinated by multiple levels of regulation on DNA, RNA and protein. RNA-binding proteins (RBPs) are recognised as key regulators of post-transcriptional gene regulation, where their binding controls splicing, polyadenylation, nuclear export, mRNA stability, translation rate and decay. In brain development, the ELAVL family of RNA binding proteins undertake essential functions across spatiotemporal windows to help regulate and specify transcriptomic programmes for cell specialisation. Despite their recognised importance in neural tissues, their molecular roles and connections to pathology are less explored. Here we provide an overview of the neuronal ELAVL family, noting commonalities and differences amongst different species, their molecular characteristics, and roles in the cell. We bring together the available molecular genetics evidence to link different ELAVL proteins to phenotypes and disease, in both the brain and beyond, including ELAVL2, which is the least studied ELAVL family member. We find that ELAVL-related pathology shares a common neurological theme, but different ELAVL proteins are more strongly connected to different phenotypes, reflecting their specialised expression across time and space.
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Affiliation(s)
- Meghan R Mulligan
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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Bai F, Huang L, Deng J, Long Z, Hao X, Chen P, Wu G, Wen H, Deng Q, Bao X, Huang J, Yang M, Li D, Ren Y, Zhang M, Xiong Y, Li H. Prelimbic area to lateral hypothalamus circuit drives social aggression. iScience 2023; 26:107718. [PMID: 37810230 PMCID: PMC10551839 DOI: 10.1016/j.isci.2023.107718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/06/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
Controlling aggression is a vital skill in social species such as rodents and humans and has been associated with the medial prefrontal cortex (mPFC). In this study, we showed that during aggressive behavior, the activity of GABAergic neurons in the prelimbic area (PL) of the mPFC was significantly suppressed. Specific activation of GABAergic PL neurons significantly curbed male-to-male aggression and inhibited conditioned place preference (CPP) for aggression-paired contexts, whereas specific inhibition of GABAergic PL neurons brought about the opposite effect. Moreover, GABAergic projections from PL neurons to the lateral hypothalamus (LH) orexinergic neurons mediated aggressive behavior. Finally, directly modulated LH-orexinergic neurons influence aggressive behavior. These results suggest that GABAergic PL-orexinergic LH projection is an important control circuit for intermale aggressive behavior, both of which could be targets for curbing aggression.
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Affiliation(s)
- Fuhai Bai
- Department of Anesthesiology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Lu Huang
- Department of Anesthesiology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Jiao Deng
- Department of Anesthesiology and Perioperative Medicine, Xijing Hospital, Air Force Medical University, Xi’an, Shaanxi 710032, China
| | - Zonghong Long
- Department of Anesthesiology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Xianglin Hao
- Department of Pathology, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Penghui Chen
- Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, Army Medical University, Chongqing 400038, China
| | - Guangyan Wu
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Huizhong Wen
- Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, Army Medical University, Chongqing 400038, China
| | - Qiangting Deng
- Editorial Office of Journal of Army Medical University, Chongqing 400038, China
| | - Xiaohang Bao
- Department of Anesthesiology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Jing Huang
- Department of Anesthesiology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Ming Yang
- Department of Anesthesiology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Defeng Li
- Clinical Medical Research Center, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Yukun Ren
- Department of Anesthesiology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Min Zhang
- Department of Anesthesiology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Ying Xiong
- Department of Neurobiology, Chongqing Key Laboratory of Neurobiology, Army Medical University, Chongqing 400038, China
| | - Hong Li
- Department of Anesthesiology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
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Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ, de la Torre-Ubieta L. Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534016. [PMID: 36993726 PMCID: PMC10055310 DOI: 10.1101/2023.03.25.534016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders, yet the role of cell-type-specific splicing or transcript-isoform diversity during human brain development has not been systematically investigated. Here, we leveraged single-molecule long-read sequencing to deeply profile the full-length transcriptome of the germinal zone (GZ) and cortical plate (CP) regions of the developing human neocortex at tissue and single-cell resolution. We identified 214,516 unique isoforms, of which 72.6% are novel (unannotated in Gencode-v33), and uncovered a substantial contribution of transcript-isoform diversity, regulated by RNA binding proteins, in defining cellular identity in the developing neocortex. We leveraged this comprehensive isoform-centric gene annotation to re-prioritize thousands of rare de novo risk variants and elucidate genetic risk mechanisms for neuropsychiatric disorders. One-Sentence Summary A cell-specific atlas of gene isoform expression helps shape our understanding of brain development and disease. Structured Abstract INTRODUCTION: The development of the human brain is regulated by precise molecular and genetic mechanisms driving spatio-temporal and cell-type-specific transcript expression programs. Alternative splicing, a major mechanism increasing transcript diversity, is highly prevalent in the human brain, influences many aspects of brain development, and has strong links to neuropsychiatric disorders. Despite this, the cell-type-specific transcript-isoform diversity of the developing human brain has not been systematically investigated.RATIONALE: Understanding splicing patterns and isoform diversity across the developing neocortex has translational relevance and can elucidate genetic risk mechanisms in neurodevelopmental disorders. However, short-read sequencing, the prevalent technology for transcriptome profiling, is not well suited to capturing alternative splicing and isoform diversity. To address this, we employed third-generation long-read sequencing, which enables capture and sequencing of complete individual RNA molecules, to deeply profile the full-length transcriptome of the germinal zone (GZ) and cortical plate (CP) regions of the developing human neocortex at tissue and single-cell resolution.RESULTS: We profiled microdissected GZ and CP regions of post-conception week (PCW) 15-17 human neocortex in bulk and at single-cell resolution across six subjects using high-fidelity long-read sequencing (PacBio IsoSeq). We identified 214,516 unique isoforms, of which 72.6% were novel (unannotated in Gencode), and >7,000 novel exons, expanding the proteome by 92,422 putative proteoforms. We uncovered thousands of isoform switches during cortical neurogenesis predicted to impact RNA regulatory domains or protein structure and implicating previously uncharacterized RNA-binding proteins in cellular identity and neuropsychiatric disease. At the single-cell level, early-stage excitatory neurons exhibited the greatest isoform diversity, and isoform-centric single-cell clustering led to the identification of previously uncharacterized cell states. We systematically assessed the contribution of transcriptomic features, and localized cell and spatio-temporal transcript expression signatures across neuropsychiatric disorders, revealing predominant enrichments in dynamic isoform expression and utilization patterns and that the number and complexity of isoforms per gene is strongly predictive of disease. Leveraging this resource, we re-prioritized thousands of rare de novo risk variants associated with autism spectrum disorders (ASD), intellectual disability (ID), and neurodevelopmental disorders (NDDs), more broadly, to potentially more severe consequences and revealed a larger proportion of cryptic splice variants with the expanded transcriptome annotation provided in this study.CONCLUSION: Our study offers a comprehensive landscape of isoform diversity in the human neocortex during development. This extensive cataloging of novel isoforms and splicing events sheds light on the underlying mechanisms of neurodevelopmental disorders and presents an opportunity to explore rare genetic variants linked to these conditions. The implications of our findings extend beyond fundamental neuroscience, as they provide crucial insights into the molecular basis of developmental brain disorders and pave the way for targeted therapeutic interventions. To facilitate exploration of this dataset we developed an online portal ( https://sciso.gandallab.org/ ).
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Smeland OB, Kutrolli G, Bahrami S, Fominykh V, Parker N, Hindley GFL, Rødevand L, Jaholkowski P, Tesfaye M, Parekh P, Elvsåshagen T, Grotzinger AD, Steen NE, van der Meer D, O’Connell KS, Djurovic S, Dale AM, Shadrin AA, Frei O, Andreassen OA. The shared genetic risk architecture of neurological and psychiatric disorders: a genome-wide analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.21.23292993. [PMID: 37503175 PMCID: PMC10371109 DOI: 10.1101/2023.07.21.23292993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
While neurological and psychiatric disorders have historically been considered to reflect distinct pathogenic entities, recent findings suggest shared pathobiological mechanisms. However, the extent to which these heritable disorders share genetic influences remains unclear. Here, we performed a comprehensive analysis of GWAS data, involving nearly 1 million cases across ten neurological diseases and ten psychiatric disorders, to compare their common genetic risk and biological underpinnings. Using complementary statistical tools, we demonstrate widespread genetic overlap across the disorders, even in the absence of genetic correlations. This indicates that a large set of common variants impact risk of multiple neurological and psychiatric disorders, but with divergent effect sizes. Furthermore, biological interrogation revealed a range of biological processes associated with neurological diseases, while psychiatric disorders consistently implicated neuronal biology. Altogether, the study indicates that neurological and psychiatric disorders share key etiological aspects, which has important implications for disease classification, precision medicine, and clinical practice.
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Affiliation(s)
- Olav B. Smeland
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Gleda Kutrolli
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Shahram Bahrami
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Vera Fominykh
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Nadine Parker
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Guy F. L. Hindley
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Psychosis Studies, Institute of Psychiatry, Psychology and Neurosciences, King’s College London, London, United Kingdom
| | - Linn Rødevand
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Piotr Jaholkowski
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Markos Tesfaye
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychiatry, St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Pravesh Parekh
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Torbjørn Elvsåshagen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Neurology, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
| | - Andrew D. Grotzinger
- Department of Psychology and Neuroscience, University of Colorado at Boulder, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA
| | | | | | - Nils Eiel Steen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dennis van der Meer
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, The Netherlands
| | - Kevin S. O’Connell
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anders M. Dale
- Multimodal Imaging Laboratory, University of California San Diego, La Jolla, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, USA
- Department of Neurosciences, University of California San Diego, La Jolla, USA
- Department of Radiology, University of California, San Diego, La Jolla, USA
| | - Alexey A. Shadrin
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Oleksandr Frei
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ole A. Andreassen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
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Zhong J, Han C, Chen P, Liu R. SGAE: single-cell gene association entropy for revealing critical states of cell transitions during embryonic development. Brief Bioinform 2023; 24:bbad366. [PMID: 37833841 DOI: 10.1093/bib/bbad366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 10/15/2023] Open
Abstract
The critical point or pivotal threshold of cell transition occurs in early embryonic development when cell differentiation culminates in its transition to specific cell fates, at which the cell population undergoes an abrupt and qualitative shift. Revealing such critical points of cell transitions can track cellular heterogeneity and shed light on the molecular mechanisms of cell differentiation. However, precise detection of critical state transitions proves challenging when relying on single-cell RNA sequencing data due to their inherent sparsity, noise, and heterogeneity. In this study, diverging from conventional methods like differential gene analysis or static techniques that emphasize classification of cell types, an innovative computational approach, single-cell gene association entropy (SGAE), is designed for the analysis of single-cell RNA-seq data and utilizes gene association information to reveal critical states of cell transitions. More specifically, through the translation of gene expression data into local SGAE scores, the proposed SGAE can serve as an index to quantitatively assess the resilience and critical properties of genetic regulatory networks, consequently detecting the signal of cell transitions. Analyses of five single-cell datasets for embryonic development demonstrate that the SGAE method achieves better performance in facilitating the characterization of a critical phase transition compared with other existing methods. Moreover, the SGAE value can effectively discriminate cellular heterogeneity over time and performs well in the temporal clustering of cells. Besides, biological functional analysis also indicates the effectiveness of the proposed approach.
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Affiliation(s)
- Jiayuan Zhong
- School of Mathematics and Big Data, Foshan University, Foshan 528000, China
| | - Chongyin Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510640, China
| | - Pei Chen
- School of Mathematics, South China University of Technology, Guangzhou 510640, China
| | - Rui Liu
- School of Mathematics, South China University of Technology, Guangzhou 510640, China
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58
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Sun MA, Yang R, Liu H, Wang W, Song X, Hu B, Reynolds N, Roso K, Chen LH, Greer PK, Keir ST, McLendon RE, Cheng SY, Bigner DD, Ashley DM, Pirozzi CJ, He Y. Repurposing Clemastine to Target Glioblastoma Cell Stemness. Cancers (Basel) 2023; 15:4619. [PMID: 37760589 PMCID: PMC10526458 DOI: 10.3390/cancers15184619] [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: 08/13/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Brain tumor-initiating cells (BTICs) and tumor cell plasticity promote glioblastoma (GBM) progression. Here, we demonstrate that clemastine, an over-the-counter drug for treating hay fever and allergy symptoms, effectively attenuated the stemness and suppressed the propagation of primary BTIC cultures bearing PDGFRA amplification. These effects on BTICs were accompanied by altered gene expression profiling indicative of their more differentiated states, resonating with the activity of clemastine in promoting the differentiation of normal oligodendrocyte progenitor cells (OPCs) into mature oligodendrocytes. Functional assays for pharmacological targets of clemastine revealed that the Emopamil Binding Protein (EBP), an enzyme in the cholesterol biosynthesis pathway, is essential for BTIC propagation and a target that mediates the suppressive effects of clemastine. Finally, we showed that a neural stem cell-derived mouse glioma model displaying predominantly proneural features was similarly susceptible to clemastine treatment. Collectively, these results identify pathways essential for maintaining the stemness and progenitor features of GBMs, uncover BTIC dependency on EBP, and suggest that non-oncology, low-toxicity drugs with OPC differentiation-promoting activity can be repurposed to target GBM stemness and aid in their treatment.
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Affiliation(s)
- Michael A. Sun
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
- Pathology Graduate Program, Duke University Medical Center, Durham, NC 27710, USA
| | - Rui Yang
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Heng Liu
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
- Pathology Graduate Program, Duke University Medical Center, Durham, NC 27710, USA
| | - Wenzhe Wang
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiao Song
- The Ken & Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (X.S.); (B.H.); (S.-Y.C.)
| | - Bo Hu
- The Ken & Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (X.S.); (B.H.); (S.-Y.C.)
| | - Nathan Reynolds
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kristen Roso
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lee H. Chen
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Paula K. Greer
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Stephen T. Keir
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Neurosurgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Roger E. McLendon
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Shi-Yuan Cheng
- The Ken & Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (X.S.); (B.H.); (S.-Y.C.)
| | - Darell D. Bigner
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Neurosurgery, Duke University Medical Center, Durham, NC 27710, USA
| | - David M. Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Neurosurgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher J. Pirozzi
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Yiping He
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA; (M.A.S.); (R.Y.); (H.L.); (W.W.); (N.R.); (K.R.); (L.H.C.); (P.K.G.); (S.T.K.); (R.E.M.); (D.D.B.); (D.M.A.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
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Nano PR, Fazzari E, Azizad D, Nguyen CV, Wang S, Kan RL, Wick B, Haeussler M, Bhaduri A. A Meta-Atlas of the Developing Human Cortex Identifies Modules Driving Cell Subtype Specification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557406. [PMID: 37745597 PMCID: PMC10515829 DOI: 10.1101/2023.09.12.557406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Human brain development requires the generation of hundreds of diverse cell types, a process targeted by recent single-cell transcriptomic profiling efforts. Through a meta-analysis of seven of these published datasets, we have generated 225 meta-modules - gene co-expression networks that can describe mechanisms underlying cortical development. Several meta-modules have potential roles in both establishing and refining cortical cell type identities, and we validated their spatiotemporal expression in primary human cortical tissues. These include meta-module 20, associated with FEZF2+ deep layer neurons. Half of meta-module 20 genes are putative FEZF2 targets, including TSHZ3, a transcription factor associated with neurodevelopmental disorders. Human cortical organoid experiments validated that both factors are necessary for deep layer neuron specification. Importantly, subtle manipulations of these factors drive slight changes in meta-module activity that cascade into strong differences in cell fate - demonstrating how of our meta-atlas can engender further mechanistic analyses of cortical fate specification.
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Muñoz EM, Martínez Cerdeño V. Editorial: Transcription regulation - Brain development and homeostasis - A finely tuned and orchestrated scenario in physiology and pathology, volume II. Front Mol Neurosci 2023; 16:1280573. [PMID: 37736114 PMCID: PMC10509287 DOI: 10.3389/fnmol.2023.1280573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Affiliation(s)
- Estela M. Muñoz
- Institute of Histology and Embryology of Mendoza (IHEM), National University of Cuyo (UNCuyo), National Scientific and Technical Research Council (CONICET), Mendoza, Argentina
| | - Verónica Martínez Cerdeño
- Department of Pathology and Laboratory Medicine, Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children of Northern California, and MIND Institute at the UC Davis Medical Center, University of California Davis School of Medicine, Sacramento, CA, United States
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Stevelink R, Campbell C, Chen S, Abou-Khalil B, Adesoji OM, Afawi Z, Amadori E, Anderson A, Anderson J, Andrade DM, Annesi G, Auce P, Avbersek A, Bahlo M, Baker MD, Balagura G, Balestrini S, Barba C, Barboza K, Bartolomei F, Bast T, Baum L, Baumgartner T, Baykan B, Bebek N, Becker AJ, Becker F, Bennett CA, Berghuis B, Berkovic SF, Beydoun A, Bianchini C, Bisulli F, Blatt I, Bobbili DR, Borggraefe I, Bosselmann C, Braatz V, Bradfield JP, Brockmann K, Brody LC, Buono RJ, Busch RM, Caglayan H, Campbell E, Canafoglia L, Canavati C, Cascino GD, Castellotti B, Catarino CB, Cavalleri GL, Cerrato F, Chassoux F, Cherny SS, Cheung CL, Chinthapalli K, Chou IJ, Chung SK, Churchhouse C, Clark PO, Cole AJ, Compston A, Coppola A, Cosico M, Cossette P, Craig JJ, Cusick C, Daly MJ, Davis LK, de Haan GJ, Delanty N, Depondt C, Derambure P, Devinsky O, Di Vito L, Dlugos DJ, Doccini V, Doherty CP, El-Naggar H, Elger CE, Ellis CA, Eriksson JG, Faucon A, Feng YCA, Ferguson L, Ferraro TN, Ferri L, Feucht M, Fitzgerald M, Fonferko-Shadrach B, Fortunato F, Franceschetti S, Franke A, French JA, Freri E, Gagliardi M, Gambardella A, Geller EB, Giangregorio T, Gjerstad L, Glauser T, Goldberg E, Goldman A, Granata T, Greenberg DA, Guerrini R, Gupta N, Haas KF, Hakonarson H, Hallmann K, Hassanin E, Hegde M, Heinzen EL, Helbig I, Hengsbach C, Heyne HO, Hirose S, Hirsch E, Hjalgrim H, Howrigan DP, Hucks D, Hung PC, Iacomino M, Imbach LL, Inoue Y, Ishii A, Jamnadas-Khoda J, Jehi L, Johnson MR, Kälviäinen R, Kamatani Y, Kanaan M, Kanai M, Kantanen AM, Kara B, Kariuki SM, Kasperavičiūte D, Kasteleijn-Nolst Trenite D, Kato M, Kegele J, Kesim Y, Khoueiry-Zgheib N, King C, Kirsch HE, Klein KM, Kluger G, Knake S, Knowlton RC, Koeleman BPC, Korczyn AD, Koupparis A, Kousiappa I, Krause R, Krenn M, Krestel H, Krey I, Kunz WS, Kurki MI, Kurlemann G, Kuzniecky R, Kwan P, Labate A, Lacey A, Lal D, Landoulsi Z, Lau YL, Lauxmann S, Leech SL, Lehesjoki AE, Lemke JR, Lerche H, Lesca G, Leu C, Lewin N, Lewis-Smith D, Li GHY, Li QS, Licchetta L, Lin KL, Lindhout D, Linnankivi T, Lopes-Cendes I, Lowenstein DH, Lui CHT, Madia F, Magnusson S, Marson AG, May P, McGraw CM, Mei D, Mills JL, Minardi R, Mirza N, Møller RS, Molloy AM, Montomoli M, Mostacci B, Muccioli L, Muhle H, Müller-Schlüter K, Najm IM, Nasreddine W, Neale BM, Neubauer B, Newton CRJC, Nöthen MM, Nothnagel M, Nürnberg P, O’Brien TJ, Okada Y, Ólafsson E, Oliver KL, Özkara C, Palotie A, Pangilinan F, Papacostas SS, Parrini E, Pato CN, Pato MT, Pendziwiat M, Petrovski S, Pickrell WO, Pinsky R, Pippucci T, Poduri A, Pondrelli F, Powell RHW, Privitera M, Rademacher A, Radtke R, Ragona F, Rau S, Rees MI, Regan BM, Reif PS, Rhelms S, Riva A, Rosenow F, Ryvlin P, Saarela A, Sadleir LG, Sander JW, Sander T, Scala M, Scattergood T, Schachter SC, Schankin CJ, Scheffer IE, Schmitz B, Schoch S, Schubert-Bast S, Schulze-Bonhage A, Scudieri P, Sham P, Sheidley BR, Shih JJ, Sills GJ, Sisodiya SM, Smith MC, Smith PE, Sonsma ACM, Speed D, Sperling MR, Stefansson H, Stefansson K, Steinhoff BJ, Stephani U, Stewart WC, Stipa C, Striano P, Stroink H, Strzelczyk A, Surges R, Suzuki T, Tan KM, Taneja RS, Tanteles GA, Taubøll E, Thio LL, Thomas GN, Thomas RH, Timonen O, Tinuper P, Todaro M, Topaloğlu P, Tozzi R, Tsai MH, Tumiene B, Turkdogan D, Unnsteinsdóttir U, Utkus A, Vaidiswaran P, Valton L, van Baalen A, Vetro A, Vining EPG, Visscher F, von Brauchitsch S, von Wrede R, Wagner RG, Weber YG, Weckhuysen S, Weisenberg J, Weller M, Widdess-Walsh P, Wolff M, Wolking S, Wu D, Yamakawa K, Yang W, Yapıcı Z, Yücesan E, Zagaglia S, Zahnert F, Zara F, Zhou W, Zimprich F, Zsurka G, Zulfiqar Ali Q. GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture. Nat Genet 2023; 55:1471-1482. [PMID: 37653029 PMCID: PMC10484785 DOI: 10.1038/s41588-023-01485-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
Epilepsy is a highly heritable disorder affecting over 50 million people worldwide, of which about one-third are resistant to current treatments. Here we report a multi-ancestry genome-wide association study including 29,944 cases, stratified into three broad categories and seven subtypes of epilepsy, and 52,538 controls. We identify 26 genome-wide significant loci, 19 of which are specific to genetic generalized epilepsy (GGE). We implicate 29 likely causal genes underlying these 26 loci. SNP-based heritability analyses show that common variants explain between 39.6% and 90% of genetic risk for GGE and its subtypes. Subtype analysis revealed markedly different genetic architectures between focal and generalized epilepsies. Gene-set analyses of GGE signals implicate synaptic processes in both excitatory and inhibitory neurons in the brain. Prioritized candidate genes overlap with monogenic epilepsy genes and with targets of current antiseizure medications. Finally, we leverage our results to identify alternate drugs with predicted efficacy if repurposed for epilepsy treatment.
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Chao S, Zhang F, Yan H, Wang L, Zhang L, Wang Z, Xue R, Wang L, Wu Z, Jiang B, Shi G, Xue Y, Du J, Bu P. Targeting intratumor heterogeneity suppresses colorectal cancer chemoresistance and metastasis. EMBO Rep 2023; 24:e56416. [PMID: 37338390 PMCID: PMC10398666 DOI: 10.15252/embr.202256416] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/09/2023] [Accepted: 05/25/2023] [Indexed: 06/21/2023] Open
Abstract
Intratumor heterogeneity (ITH) is a barrier to effective therapy. However, it is largely unknown how ITH is established at the onset of tumor progression, such as in colorectal cancer (CRC). Here, we integrate single-cell RNA-seq and functional validation to show that asymmetric division of CRC stem-like cells (CCSC) is critical for early ITH establishment. We find that CCSC-derived xenografts contain seven cell subtypes, including CCSCs, that dynamically change during CRC xenograft progression. Furthermore, three of the subtypes are generated by asymmetric division of CCSCs. They are functionally distinct and appear at the early stage of xenografts. In particular, we identify a chemoresistant and an invasive subtype, and investigate the regulators that control their generation. Finally, we show that targeting the regulators influences cell subtype composition and CRC progression. Our findings demonstrate that asymmetric division of CCSCs contributes to the early establishment of ITH. Targeting asymmetric division may alter ITH and benefit CRC therapy.
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Affiliation(s)
- Shanshan Chao
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Fei Zhang
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Huiwen Yan
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of MedicineDuke UniversityDurhamNCUSA
| | - Liwen Zhang
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Zhi Wang
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Ruixin Xue
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Lei Wang
- Laboratory Animal Research Center, Institute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Zhenzhen Wu
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Bing Jiang
- Nanozyme Medical Center, School of Basic Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Guizhi Shi
- Laboratory Animal Research Center, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- Aviation General Hospital of BeijingMedical University and Beijing Institute of Translational Medicine, University of Chinese Academy of SciencesBeijingChina
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Junfeng Du
- Department of General Surgery, The 7 Medical CenterChinese PLA General HospitalBeijingChina
- The 2 School of Clinical MedicineSouthern Medical UniversityGuangdongChina
- Medical Department of General Surgery, The 1 Medical CenterChinese PLA General HospitalBeijingChina
| | - Pengcheng Bu
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
- Center for Excellence in BiomacromoleculesChinese Academy of SciencesBeijingChina
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63
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Teng P, Li Y, Ku L, Wang F, Goldsmith DR, Wen Z, Yao B, Feng Y. The human lncRNA GOMAFU suppresses neuronal interferon response pathways affected in neuropsychiatric diseases. Brain Behav Immun 2023; 112:175-187. [PMID: 37301236 PMCID: PMC10527610 DOI: 10.1016/j.bbi.2023.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 05/26/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play multifaceted roles in regulating brain gene networks. LncRNA abnormalities are thought to underlie the complex etiology of numerous neuropsychiatric disorders. One example is the human lncRNA gene GOMAFU, which is found dysregulated in schizophrenia (SCZ) postmortem brains and harbors genetic variants that contribute to the risk of SCZ. However, transcriptome-wide biological pathways regulated by GOMAFU have not been determined. How GOMAFU dysregulation contributes to SCZ pathogenesis remains elusive. Here we report that GOMAFU is a novel suppressor of human neuronal interferon (IFN) response pathways that are hyperactive in the postmortem SCZ brains. We analyzed recently released transcriptomic profiling datasets in clinically relevant brain areas derived from multiple SCZ cohorts and found brain region-specific dysregulation of GOMAFU. Using CRISPR-Cas9 to delete the GOMAFU promoter in a human neural progenitor cell model, we identified transcriptomic alterations caused by GOMAFU deficiency in pathways commonly affected in postmortem brains of SCZ and autism spectrum disorder (ASD), with the most striking effects on upregulation of numerous genes underlying IFN signaling. In addition, expression levels of GOMAFU target genes in the IFN pathway are differentially affected in SCZ brain regions and negatively associated with GOMAFU alterations. Furthermore, acute exposure to IFN-γ causes a rapid decline of GOMAFU and activation of a subclass of GOMAFU targets in stress and immune response pathways that are affected in SCZ brains, which form a highly interactive molecular network. Together, our studies unveiled the first evidence of lncRNA-governed neuronal response pathways to IFN challenge and suggest that GOMAFU dysregulation may mediate environmental risks and contribute to etiological neuroinflammatory responses by brain neurons of neuropsychiatric diseases.
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Affiliation(s)
- Peng Teng
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, United States
| | - Yangping Li
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, United States
| | - Li Ku
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, United States
| | - Feng Wang
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, United States
| | - David R Goldsmith
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States; Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States; Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, United States.
| | - Yue Feng
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, United States.
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64
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Park SHE, Kulkarni A, Konopka G. FOXP1 orchestrates neurogenesis in human cortical basal radial glial cells. PLoS Biol 2023; 21:e3001852. [PMID: 37540706 PMCID: PMC10431666 DOI: 10.1371/journal.pbio.3001852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 08/16/2023] [Accepted: 06/21/2023] [Indexed: 08/06/2023] Open
Abstract
During cortical development, human basal radial glial cells (bRGCs) are highly capable of sustained self-renewal and neurogenesis. Selective pressures on this cell type may have contributed to the evolution of the human neocortex, leading to an increase in cortical size. bRGCs have enriched expression for Forkhead Box P1 (FOXP1), a transcription factor implicated in neurodevelopmental disorders (NDDs) such as autism spectrum disorder. However, the cell type-specific roles of FOXP1 in bRGCs during cortical development remain unexplored. Here, we examine the requirement for FOXP1 gene expression regulation underlying the production of bRGCs using human brain organoids. We examine a developmental time point when FOXP1 expression is highest in the cortical progenitors, and the bRGCs, in particular, begin to actively produce neurons. With the loss of FOXP1, we show a reduction in the number of bRGCs, as well as reduced proliferation and differentiation of the remaining bRGCs, all of which lead to reduced numbers of excitatory cortical neurons over time. Using single-nuclei RNA sequencing and cell trajectory analysis, we uncover a role for FOXP1 in directing cortical progenitor proliferation and differentiation by regulating key signaling pathways related to neurogenesis and NDDs. Together, these results demonstrate that FOXP1 regulates human-specific features in early cortical development.
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Affiliation(s)
- Seon Hye E. Park
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ashwinikumar Kulkarni
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, Texas, United States of America
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65
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Wu J, Li Y, Huang Y, Liu L, Zhang H, Nagy C, Tan X, Cheng K, Liu Y, Pu J, Wang H, Wu Q, Perry SW, Turecki G, Wong ML, Licinio J, Zheng P, Xie P. Integrating spatial and single-nucleus transcriptomic data elucidates microglial-specific responses in female cynomolgus macaques with depressive-like behaviors. Nat Neurosci 2023; 26:1352-1364. [PMID: 37443281 DOI: 10.1038/s41593-023-01379-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/12/2023] [Indexed: 07/15/2023]
Abstract
Major depressive disorder represents a serious public health challenge worldwide; however, the underlying cellular and molecular mechanisms are mostly unknown. Here, we profile the dorsolateral prefrontal cortex of female cynomolgus macaques with social stress-associated depressive-like behaviors using single-nucleus RNA-sequencing and spatial transcriptomics. We find gene expression changes associated with depressive-like behaviors mostly in microglia, and we report a pro-inflammatory microglia subpopulation enriched in the depressive-like condition. Single-nucleus RNA-sequencing data result in the identification of six enriched gene modules associated with depressive-like behaviors, and these modules are further resolved by spatial transcriptomics. Gene modules associated with huddle and sit alone behaviors are expressed in neurons and oligodendrocytes of the superficial cortical layer, while gene modules associated with locomotion and amicable behaviors are enriched in microglia and astrocytes in mid-to-deep cortical layers. The depressive-like behavior associated microglia subpopulation is enriched in deep cortical layers. In summary, our findings show cell-type and cortical layer-specific gene expression changes and identify one microglia subpopulation associated with depressive-like behaviors in female non-human primates.
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Affiliation(s)
- Jing Wu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Yifan Li
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Yu Huang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Lanxiang Liu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Hanping Zhang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Corina Nagy
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, Quebec, Canada
| | - Xunmin Tan
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Ke Cheng
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yiyun Liu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Juncai Pu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haiyang Wang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Qingyuan Wu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Seth W Perry
- Department of Psychiatry, College of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Ma-Li Wong
- Department of Psychiatry, College of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Julio Licinio
- Department of Psychiatry, College of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Peng Zheng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Jinfeng Laboratory, Chongqing, China.
| | - Peng Xie
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Jinfeng Laboratory, Chongqing, China.
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66
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Zhong G, Choi YA, Shen Y. VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants. Commun Biol 2023; 6:774. [PMID: 37491581 PMCID: PMC10368729 DOI: 10.1038/s42003-023-05155-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 07/18/2023] [Indexed: 07/27/2023] Open
Abstract
Rare or de novo variants have substantial contribution to human diseases, but the statistical power to identify risk genes by rare variants is generally low due to rarity of genotype data. Previous studies have shown that risk genes usually have high expression in relevant cell types, although for many conditions the identity of these cell types are largely unknown. Recent efforts in single cell atlas in human and model organisms produced large amount of gene expression data. Here we present VBASS, a Bayesian method that integrates single-cell expression and de novo variant (DNV) data to improve power of disease risk gene discovery. VBASS models disease risk prior as a function of expression profiles, approximated by deep neural networks. It learns the weights of neural networks and parameters of Gamma-Poisson likelihood models of DNV counts jointly from expression and genetics data. On simulated data, VBASS shows proper error rate control and better power than state-of-the-art methods. We applied VBASS to published datasets and identified more candidate risk genes with supports from literature or data from independent cohorts. VBASS can be generalized to integrate other types of functional genomics data in statistical genetics analysis.
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Affiliation(s)
- Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Yoolim A Choi
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
- JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA.
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Niu RZ, Feng WQ, Yu QS, Shi LL, Qin QM, Liu J. Integrated analysis of plasma proteome and cortex single-cell transcriptome reveals the novel biomarkers during cortical aging. Front Aging Neurosci 2023; 15:1063861. [PMID: 37539343 PMCID: PMC10394382 DOI: 10.3389/fnagi.2023.1063861] [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: 10/07/2022] [Accepted: 06/26/2023] [Indexed: 08/05/2023] Open
Abstract
Background With the increase of age, multiple physiological functions of people begin gradually degenerating. Regardless of natural aging or pathological aging, the decline in cognitive function is one of the most obvious features in the process of brain aging. Brain aging is a key factor for several neuropsychiatric disorders and for most neurodegenerative diseases characterized by onset typically occurring late in life and with worsening of symptoms over time. Therefore, the early prevention and intervention of aging progression are particularly important. Since there is no unified conclusion about the plasma diagnostic biomarkers of brain aging, this paper innovatively employed the combined multi-omics analysis to delineate the plasma markers of brain aging. Methods In order to search for specific aging markers in plasma during cerebral cortex aging, we used multi-omics analysis to screen out differential genes/proteins by integrating two prefrontal cortex (PFC) single-nucleus transcriptome sequencing (snRNA-seq) datasets and one plasma proteome sequencing datasets. Then plasma samples were collected from 20 young people and 20 elder people to verify the selected differential genes/proteins with ELISA assay. Results We first integrated snRNA-seq data of the post-mortem human PFC and generated profiles of 65,064 nuclei from 14 subjects across adult (44-58 years), early-aging (69-79 years), and late-aging (85-94 years) stages. Seven major cell types were classified based on established markers, including oligodendrocyte, excitatory neurons, oligodendrocyte progenitor cells, astrocytes, microglia, inhibitory neurons, and endotheliocytes. A total of 93 cell-specific genes were identified to be significantly associated with age. Afterward, plasma proteomics data from 2,925 plasma proteins across 4,263 young adults to nonagenarians (18-95 years old) were combined with the outcomes from snRNA-seq data to obtain 12 differential genes/proteins (GPC5, CA10, DGKB, ST6GALNAC5, DSCAM, IL1RAPL2, TMEM132C, VCAN, APOE, PYH1R, CNTN2, SPOCK3). Finally, we verified the 12 differential genes by ELISA and found that the expression trends of five biomarkers (DSCAM, CNTN2, IL1RAPL2, CA10, GPC5) were correlated with brain aging. Conclusion Five differentially expressed proteins (DSCAM, CNTN2, IL1RAPL2, CA10, GPC5) can be considered as one of the screening indicators of brain aging, and provide a scientific basis for clinical diagnosis and intervention.
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68
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Singh AK, Amar I, Ramadasan H, Kappagantula KS, Chavali S. Proteins with amino acid repeats constitute a rapidly evolvable and human-specific essentialome. Cell Rep 2023; 42:112811. [PMID: 37453061 DOI: 10.1016/j.celrep.2023.112811] [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: 01/11/2023] [Revised: 05/30/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Protein products of essential genes, indispensable for organismal survival, are highly conserved and bring about fundamental functions. Interestingly, proteins that contain amino acid homorepeats that tend to evolve rapidly are enriched in eukaryotic essentialomes. Why are proteins with hypermutable homorepeats enriched in conserved and functionally vital essential proteins? We solve this functional versus evolutionary paradox by demonstrating that human essential proteins with homorepeats bring about crosstalk across biological processes through high interactability and have distinct regulatory functions affecting expansive global regulation. Importantly, essential proteins with homorepeats rapidly diverge with the amino acid substitutions frequently affecting functional sites, likely facilitating rapid adaptability. Strikingly, essential proteins with homorepeats influence human-specific embryonic and brain development, implying that the presence of homorepeats could contribute to the emergence of human-specific processes. Thus, we propose that homorepeat-containing essential proteins affecting species-specific traits can be potential intervention targets across pathologies, including cancers and neurological disorders.
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Affiliation(s)
- Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Ishita Amar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Harikrishnan Ramadasan
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Keertana S Kappagantula
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India.
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69
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Alves VC, Figueiro-Silva J, Ferrer I, Carro E. Epigenetic silencing of OR and TAS2R genes expression in human orbitofrontal cortex at early stages of sporadic Alzheimer's disease. Cell Mol Life Sci 2023; 80:196. [PMID: 37405535 PMCID: PMC10322771 DOI: 10.1007/s00018-023-04845-1] [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: 12/16/2022] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023]
Abstract
Modulation of brain olfactory (OR) and taste receptor (TASR) expression was recently reported in neurological diseases. However, there is still limited evidence of these genes' expression in the human brain and the transcriptional regulation mechanisms involved remain elusive. We explored the possible expression and regulation of selected OR and TASR in the human orbitofrontal cortex (OFC) of sporadic Alzheimer's disease (AD) and non-demented control specimens using quantitative real-time RT-PCR and ELISA. Global H3K9me3 amounts were measured on OFC total histone extracts, and H3K9me3 binding at each chemoreceptor locus was examined through native chromatin immunoprecipitation. To investigate the potential interactome of the repressive histone mark H3K9me3 in OFC specimens, native nuclear complex co-immunoprecipitation (Co-IP) was combined with reverse phase-liquid chromatography coupled to mass spectrometry analysis. Interaction between H3K9me3 and MeCP2 was validated by reciprocal Co-IP, and global MeCP2 levels were quantitated. We found that OR and TAS2R genes are expressed and markedly downregulated in OFC at early stages of sporadic AD, preceding the progressive reduction in their protein levels and the appearance of AD-associated neuropathology. The expression pattern did not follow disease progression suggesting transcriptional regulation through epigenetic mechanisms. We discovered an increase of OFC global H3K9me3 levels and a substantial enrichment of this repressive signature at ORs and TAS2Rs proximal promoter at early stages of AD, ultimately lost at advanced stages. We revealed the interaction between H3K9me3 and MeCP2 at early stages and found that MeCP2 protein is increased in sporadic AD. Findings suggest MeCP2 might be implicated in OR and TAS2R transcriptional regulation through interaction with H3K9me3, and as an early event, it may uncover a novel etiopathogenetic mechanism of sporadic AD.
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Affiliation(s)
- Victoria Cunha Alves
- Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- PhD Program in Neuroscience, Autonoma de Madrid University, Madrid, Spain
| | - Joana Figueiro-Silva
- Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
| | - Isidre Ferrer
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Institute of Neuropathology, Bellvitge University Hospital-IDIBELL, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Eva Carro
- Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Present Address: Neurobiology of Alzheimer’s Disease Unit, Functional Unit for Research Into Chronic Diseases, Instituto de Salud Carlos III, Madrid, Spain
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70
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Liu R, Dong W, Xiong D, Hu L, Zhang H, Yuan X, Tang Z, Fu F, Yang X, Wu X. Single-cell RNA-sequencing identifies various proportions of excitatory and inhibitory neurons in cultured human fetal brain cortical tissues. Front Neurosci 2023; 17:1177747. [PMID: 37449269 PMCID: PMC10338112 DOI: 10.3389/fnins.2023.1177747] [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: 03/11/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Cortical neural progenitor cells possess the capacity to differentiate into both excitatory and inhibitory neurons. However, the precise proportions in which these progenitor cells differentiate remain unclear. Methods Human fetal prefrontal cortical tissues were collected at various fetal stages and cultured in vitro. Bulk and single-cell RNA sequencing techniques were employed to analyze the resulting neuronal cell types, cell proportions, and the expression levels of cell-type marker genes. Results The culture of fetal prefrontal cortex tissues obtained at gestation weeks 11 and 20 predominantly consisted of excitatory and inhibitory neurons, respectively. This abrupt transition in cell proportions was primarily driven by the differential lineage specificity of neural progenitors in the fetal cortical tissues at distinct stages of fetal brain development. Additionally, it was observed that the transcriptional profiles of cultured fetal cortical tissues were strongly influenced by the presence of FGF2. Discussion This study presents a novel strategy to obtain excitatory and inhibitory neuronal cells from the culture of fetal cortical tissues. The findings shed light on the mechanisms underlying neurogenesis and provide an approach that might contribute to future research investigating the pathophysiology of various neural disorders.
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Affiliation(s)
- Rong Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wei Dong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Dan Xiong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lanqi Hu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Haoran Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoping Yuan
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhonghui Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xin Yang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xia Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
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71
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Zhang H, Li J, Yu Y, Ren J, Liu Q, Bao Z, Sun S, Liu X, Ma S, Liu Z, Yan K, Wu Z, Fan Y, Sun X, Zhang Y, Ji Q, Cheng F, Wei PH, Ma X, Zhang S, Xie Z, Niu Y, Wang YJ, Han JDJ, Jiang T, Zhao G, Ji W, Izpisua Belmonte JC, Wang S, Qu J, Zhang W, Liu GH. Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging. Cell Rep 2023; 42:112593. [PMID: 37261950 DOI: 10.1016/j.celrep.2023.112593] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/10/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
The primate frontal lobe (FL) is sensitive to aging-related neurocognitive decline. However, the aging-associated molecular mechanisms remain unclear. Here, using physiologically aged non-human primates (NHPs), we depicted a comprehensive landscape of FL aging with multidimensional profiling encompassing bulk and single-nucleus transcriptomes, quantitative proteome, and DNA methylome. Conjoint analysis across these molecular and neuropathological layers underscores nuclear lamina and heterochromatin erosion, resurrection of endogenous retroviruses (ERVs), activated pro-inflammatory cyclic GMP-AMP synthase (cGAS) signaling, and cellular senescence in post-mitotic neurons of aged NHP and human FL. Using human embryonic stem-cell-derived neurons recapitulating cellular aging in vitro, we verified the loss of B-type lamins inducing resurrection of ERVs as an initiating event of the aging-bound cascade in post-mitotic neurons. Of significance, these aging-related cellular and molecular changes can be alleviated by abacavir, a nucleoside reverse transcriptase inhibitor, either through direct treatment of senescent human neurons in vitro or oral administration to aged mice.
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Affiliation(s)
- Hui Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yu
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China; Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Liu
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zhaoshi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; Chinese Glioma Genome Atlas Network & Asian Glioma Genome Atlas Network, Beijing 100070, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Cheng
- University of Chinese Academy of Sciences, Beijing 100049, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng-Hu Wei
- Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China; MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xibo Ma
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiqiang Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Zhengwei Xie
- Peking University International Cancer Institute, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yan-Jiang Wang
- Department of Neurology, Daping Hospital, Third Military Medical University, Chongqing 400042, China; State Key Laboratory of Trauma, Burn and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Tao Jiang
- Beijing Neurosurgical Institute, Beijing 100070, China; Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; Chinese Glioma Genome Atlas Network & Asian Glioma Genome Atlas Network, Beijing 100070, China
| | - Guoguang Zhao
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Clinical Research Center for Epilepsy Capital Medical University, Beijing 100053, China; Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | | | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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Sebastian R, Jin K, Pavon N, Bansal R, Potter A, Song Y, Babu J, Gabriel R, Sun Y, Aronow B, Pak C. Schizophrenia-associated NRXN1 deletions induce developmental-timing- and cell-type-specific vulnerabilities in human brain organoids. Nat Commun 2023; 14:3770. [PMID: 37355690 PMCID: PMC10290702 DOI: 10.1038/s41467-023-39420-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/13/2023] [Indexed: 06/26/2023] Open
Abstract
De novo mutations and copy number deletions in NRXN1 (2p16.3) pose a significant risk for schizophrenia (SCZ). It is unclear how NRXN1 deletions impact cortical development in a cell type-specific manner and disease background modulates these phenotypes. Here, we leveraged human pluripotent stem cell-derived forebrain organoid models carrying NRXN1 heterozygous deletions in isogenic and SCZ patient genetic backgrounds and conducted single-cell transcriptomic analysis over the course of brain organoid development from 3 weeks to 3.5 months. Intriguingly, while both deletions similarly impacted molecular pathways associated with ubiquitin-proteasome system, alternative splicing, and synaptic signaling in maturing glutamatergic and GABAergic neurons, SCZ-NRXN1 deletions specifically perturbed developmental trajectories of early neural progenitors and accumulated disease-specific transcriptomic signatures. Using calcium imaging, we found that both deletions led to long-lasting changes in spontaneous and synchronous neuronal networks, implicating synaptic dysfunction. Our study reveals developmental-timing- and cell-type-dependent actions of NRXN1 deletions in unique genetic contexts.
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Affiliation(s)
- Rebecca Sebastian
- Graduate Program in Neuroscience & Behavior, UMass Amherst, Amherst, MA, 01003, USA
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Narciso Pavon
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Ruby Bansal
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Andrew Potter
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Yoonjae Song
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Juliana Babu
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Rafael Gabriel
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Yubing Sun
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA, 01003, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, 45256, USA
| | - ChangHui Pak
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA.
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Zeng B, Liu Z, Lu Y, Zhong S, Qin S, Huang L, Zeng Y, Li Z, Dong H, Shi Y, Yang J, Dai Y, Ma Q, Sun L, Bian L, Han D, Chen Y, Qiu X, Wang W, Marín O, Wu Q, Wang Y, Wang X. The single-cell and spatial transcriptional landscape of human gastrulation and early brain development. Cell Stem Cell 2023; 30:851-866.e7. [PMID: 37192616 PMCID: PMC10241223 DOI: 10.1016/j.stem.2023.04.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 05/18/2023]
Abstract
The emergence of the three germ layers and the lineage-specific precursor cells orchestrating organogenesis represent fundamental milestones during early embryonic development. We analyzed the transcriptional profiles of over 400,000 cells from 14 human samples collected from post-conceptional weeks (PCW) 3 to 12 to delineate the dynamic molecular and cellular landscape of early gastrulation and nervous system development. We described the diversification of cell types, the spatial patterning of neural tube cells, and the signaling pathways likely involved in transforming epiblast cells into neuroepithelial cells and then into radial glia. We resolved 24 clusters of radial glial cells along the neural tube and outlined differentiation trajectories for the main classes of neurons. Lastly, we identified conserved and distinctive features across species by comparing early embryonic single-cell transcriptomic profiles between humans and mice. This comprehensive atlas sheds light on the molecular mechanisms underlying gastrulation and early human brain development.
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Affiliation(s)
- Bo Zeng
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; Changping Laboratory, Beijing 102206, China
| | - Zeyuan Liu
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; Changping Laboratory, Beijing 102206, China
| | - Yufeng Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Suijuan Zhong
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; Changping Laboratory, Beijing 102206, China
| | - Shenyue Qin
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Luwei Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Zeng
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Zixiao Li
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China; Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing 100069, China
| | - Hao Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingchao Shi
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Guangdong Institute of Intelligence Science and Technology, Guangdong 519031, China
| | - Jialei Yang
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China; Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Yalun Dai
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China; Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Qiang Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Le Sun
- Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Lihong Bian
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Dan Han
- Department of Obstetrics & Gynecology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Youqiao Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Xin Qiu
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China; Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Wei Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK.
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; Changping Laboratory, Beijing 102206, China.
| | - Yongjun Wang
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China; Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing 100069, China.
| | - Xiaoqun Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute of Brain Disorders, Capital Medical University, Beijing 100069, China; Guangdong Institute of Intelligence Science and Technology, Guangdong 519031, China; Changping Laboratory, Beijing 102206, China; New Cornerstone Science Laboratory, Beijing Normal University, Beijing 100875, China.
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74
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El-Danaf RN, Rajesh R, Desplan C. Temporal regulation of neural diversity in Drosophila and vertebrates. Semin Cell Dev Biol 2023; 142:13-22. [PMID: 35623984 DOI: 10.1016/j.semcdb.2022.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
Abstract
The generation of neuronal diversity involves temporal patterning mechanisms by which a given progenitor sequentially produces multiple cell types. Several parallels are evident between the brain development programs of Drosophila and vertebrates, such as the successive emergence of specific cell types and the use of combinations of transcription factors to specify cell fates. Furthermore, cell-extrinsic cues such as hormones and signaling pathways have also been shown to be regulatory modules of temporal patterning. Recently, transcriptomic and epigenomic studies using large single-cell sequencing datasets have provided insights into the transcriptional dynamics of neurogenesis in the Drosophila and mammalian central nervous systems. We review these commonalities in the specification of neuronal identity and highlight the conserved or convergent strategies of brain development by discussing temporal patterning mechanisms found in flies and vertebrates.
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Affiliation(s)
- Rana N El-Danaf
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Raghuvanshi Rajesh
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Claude Desplan
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates; Department of Biology, New York University, New York, NY 10003, USA.
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75
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Fernández-Moya SM, Ganesh AJ, Plass M. Neural cell diversity in the light of single-cell transcriptomics. Transcription 2023; 14:158-176. [PMID: 38229529 PMCID: PMC10807474 DOI: 10.1080/21541264.2023.2295044] [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: 06/27/2023] [Accepted: 11/10/2023] [Indexed: 01/18/2024] Open
Abstract
The development of highly parallel and affordable high-throughput single-cell transcriptomics technologies has revolutionized our understanding of brain complexity. These methods have been used to build cellular maps of the brain, its different regions, and catalog the diversity of cells in each of them during development, aging and even in disease. Now we know that cellular diversity is way beyond what was previously thought. Single-cell transcriptomics analyses have revealed that cell types previously considered homogeneous based on imaging techniques differ depending on several factors including sex, age and location within the brain. The expression profiles of these cells have also been exploited to understand which are the regulatory programs behind cellular diversity and decipher the transcriptional pathways driving them. In this review, we summarize how single-cell transcriptomics have changed our view on the cellular diversity in the human brain, and how it could impact the way we study neurodegenerative diseases. Moreover, we describe the new computational approaches that can be used to study cellular differentiation and gain insight into the functions of individual cell populations under different conditions and their alterations in disease.
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Affiliation(s)
- Sandra María Fernández-Moya
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, L’Hospitalet del Llobregat, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P- CMR[C], Barcelona, L’Hospitalet del Llobregat, Spain
| | - Akshay Jaya Ganesh
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, L’Hospitalet del Llobregat, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P- CMR[C], Barcelona, L’Hospitalet del Llobregat, Spain
| | - Mireya Plass
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, L’Hospitalet del Llobregat, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P- CMR[C], Barcelona, L’Hospitalet del Llobregat, Spain
- Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
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76
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Sant P, Rippe K, Mallm JP. Approaches for single-cell RNA sequencing across tissues and cell types. Transcription 2023; 14:127-145. [PMID: 37062951 PMCID: PMC10807473 DOI: 10.1080/21541264.2023.2200721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/30/2023] [Indexed: 04/18/2023] Open
Abstract
Single-cell sequencing of RNA (scRNA-seq) has advanced our understanding of cellular heterogeneity and signaling in developmental biology and disease. A large number of complementary assays have been developed to profile transcriptomes of individual cells, also in combination with other readouts, such as chromatin accessibility or antibody-based analysis of protein surface markers. As scRNA-seq technologies are advancing fast, it is challenging to establish robust workflows and up-to-date protocols that are best suited to address the large range of research questions. Here, we review scRNA-seq techniques from mRNA end-counting to total RNA in relation to their specific features and outline the necessary sample preparation steps and quality control measures. Based on our experience in dealing with the continuously growing portfolio from the perspective of a central single-cell facility, we aim to provide guidance on how workflows can be best automatized and share our experience in coping with the continuous expansion of scRNA-seq techniques.
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Affiliation(s)
- Pooja Sant
- Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Karsten Rippe
- Division Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
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77
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Seeker LA, Bestard-Cuche N, Jäkel S, Kazakou NL, Bøstrand SMK, Wagstaff LJ, Cholewa-Waclaw J, Kilpatrick AM, Van Bruggen D, Kabbe M, Baldivia Pohl F, Moslehi Z, Henderson NC, Vallejos CA, La Manno G, Castelo-Branco G, Williams A. Brain matters: unveiling the distinct contributions of region, age, and sex to glia diversity and CNS function. Acta Neuropathol Commun 2023; 11:84. [PMID: 37217978 PMCID: PMC10204264 DOI: 10.1186/s40478-023-01568-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 05/24/2023] Open
Abstract
The myelinated white matter tracts of the central nervous system (CNS) are essential for fast transmission of electrical impulses and are often differentially affected in human neurodegenerative diseases across CNS region, age and sex. We hypothesize that this selective vulnerability is underpinned by physiological variation in white matter glia. Using single nucleus RNA sequencing of human post-mortem white matter samples from the brain, cerebellum and spinal cord and subsequent tissue-based validation we found substantial glial heterogeneity with tissue region: we identified region-specific oligodendrocyte precursor cells (OPCs) that retain developmental origin markers into adulthood, distinguishing them from mouse OPCs. Region-specific OPCs give rise to similar oligodendrocyte populations, however spinal cord oligodendrocytes exhibit markers such as SKAP2 which are associated with increased myelin production and we found a spinal cord selective population particularly equipped for producing long and thick myelin sheaths based on the expression of genes/proteins such as HCN2. Spinal cord microglia exhibit a more activated phenotype compared to brain microglia, suggesting that the spinal cord is a more pro-inflammatory environment, a difference that intensifies with age. Astrocyte gene expression correlates strongly with CNS region, however, astrocytes do not show a more activated state with region or age. Across all glia, sex differences are subtle but the consistent increased expression of protein-folding genes in male donors hints at pathways that may contribute to sex differences in disease susceptibility. These findings are essential to consider for understanding selective CNS pathologies and developing tailored therapeutic strategies.
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Affiliation(s)
- Luise A Seeker
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Bioquarter, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Nadine Bestard-Cuche
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Bioquarter, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Sarah Jäkel
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Bioquarter, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
- Institute for Stroke and Dementia Research, Klinikum Der Universität München, Ludwig-Maximilians-Universität, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Nina-Lydia Kazakou
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Bioquarter, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Sunniva M K Bøstrand
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Bioquarter, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Laura J Wagstaff
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Bioquarter, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Justyna Cholewa-Waclaw
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Bioquarter, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Alastair M Kilpatrick
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Bioquarter, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - David Van Bruggen
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Mukund Kabbe
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Fabio Baldivia Pohl
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Zahra Moslehi
- Laboratory of Neurodevelopmental Systems Biology, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Catalina A Vallejos
- MRC Human Genetics Unit, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Alan Turing Institute, 96 Euston Road, London, NW1 2DB, UK
| | - Gioele La Manno
- Laboratory of Neurodevelopmental Systems Biology, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Goncalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Stockholm Node, 171 77, Stockholm, Sweden
| | - Anna Williams
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh Bioquarter, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK.
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78
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Piwecka M, Rajewsky N, Rybak-Wolf A. Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease. Nat Rev Neurol 2023:10.1038/s41582-023-00809-y. [PMID: 37198436 DOI: 10.1038/s41582-023-00809-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2023] [Indexed: 05/19/2023]
Abstract
In the past decade, single-cell technologies have proliferated and improved from their technically challenging beginnings to become common laboratory methods capable of determining the expression of thousands of genes in thousands of cells simultaneously. The field has progressed by taking the CNS as a primary research subject - the cellular complexity and multiplicity of neuronal cell types provide fertile ground for the increasing power of single-cell methods. Current single-cell RNA sequencing methods can quantify gene expression with sufficient accuracy to finely resolve even subtle differences between cell types and states, thus providing a great tool for studying the molecular and cellular repertoire of the CNS and its disorders. However, single-cell RNA sequencing requires the dissociation of tissue samples, which means that the interrelationships between cells are lost. Spatial transcriptomic methods bypass tissue dissociation and retain this spatial information, thereby allowing gene expression to be assessed across thousands of cells within the context of tissue structural organization. Here, we discuss how single-cell and spatially resolved transcriptomics have been contributing to unravelling the pathomechanisms underlying brain disorders. We focus on three areas where we feel these new technologies have provided particularly useful insights: selective neuronal vulnerability, neuroimmune dysfunction and cell-type-specific treatment response. We also discuss the limitations and future directions of single-cell and spatial RNA sequencing technologies.
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Affiliation(s)
- Monika Piwecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
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79
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Schafer ST, Mansour AA, Schlachetzki JCM, Pena M, Ghassemzadeh S, Mitchell L, Mar A, Quang D, Stumpf S, Ortiz IS, Lana AJ, Baek C, Zaghal R, Glass CK, Nimmerjahn A, Gage FH. An in vivo neuroimmune organoid model to study human microglia phenotypes. Cell 2023; 186:2111-2126.e20. [PMID: 37172564 PMCID: PMC10284271 DOI: 10.1016/j.cell.2023.04.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 12/18/2022] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
Microglia are specialized brain-resident macrophages that play crucial roles in brain development, homeostasis, and disease. However, until now, the ability to model interactions between the human brain environment and microglia has been severely limited. To overcome these limitations, we developed an in vivo xenotransplantation approach that allows us to study functionally mature human microglia (hMGs) that operate within a physiologically relevant, vascularized immunocompetent human brain organoid (iHBO) model. Our data show that organoid-resident hMGs gain human-specific transcriptomic signatures that closely resemble their in vivo counterparts. In vivo two-photon imaging reveals that hMGs actively engage in surveilling the human brain environment, react to local injuries, and respond to systemic inflammatory cues. Finally, we demonstrate that the transplanted iHBOs developed here offer the unprecedented opportunity to study functional human microglia phenotypes in health and disease and provide experimental evidence for a brain-environment-induced immune response in a patient-specific model of autism with macrocephaly.
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Affiliation(s)
- Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Psychiatry and Psychotherapy, School of Medicine, Technical University of Munich, 81675 Munich, Germany; Center for Organoid Systems, Technical University of Munich, 85748 Garching, Germany; TranslaTUM - Organoid Hub, Technical University of Munich, 81675 Munich, Germany.
| | - Abed AlFatah Mansour
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Medical Neurobiology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Monique Pena
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Psychiatry and Psychotherapy, School of Medicine, Technical University of Munich, 81675 Munich, Germany; Center for Organoid Systems, Technical University of Munich, 85748 Garching, Germany; TranslaTUM - Organoid Hub, Technical University of Munich, 81675 Munich, Germany
| | - Saeed Ghassemzadeh
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Lisa Mitchell
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Amanda Mar
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daphne Quang
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sarah Stumpf
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Irene Santisteban Ortiz
- Department of Psychiatry and Psychotherapy, School of Medicine, Technical University of Munich, 81675 Munich, Germany; Center for Organoid Systems, Technical University of Munich, 85748 Garching, Germany; TranslaTUM - Organoid Hub, Technical University of Munich, 81675 Munich, Germany
| | - Addison J Lana
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Clara Baek
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Raghad Zaghal
- Department of Medical Neurobiology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Axel Nimmerjahn
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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80
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Rukh S, Meechan DW, Maynard TM, Lamantia AS. Out of Line or Altered States? Neural Progenitors as a Target in a Polygenic Neurodevelopmental Disorder. Dev Neurosci 2023; 46:1-21. [PMID: 37231803 DOI: 10.1159/000530898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
The genesis of a mature complement of neurons is thought to require, at least in part, precursor cell lineages in which neural progenitors have distinct identities recognized by exclusive expression of one or a few molecular markers. Nevertheless, limited progenitor types distinguished by specific markers and lineal progression through such subclasses cannot easily yield the magnitude of neuronal diversity in most regions of the nervous system. The late Verne Caviness, to whom this edition of Developmental Neuroscience is dedicated, recognized this mismatch. In his pioneering work on the histogenesis of the cerebral cortex, he acknowledged the additional flexibility required to generate multiple classes of cortical projection and interneurons. This flexibility may be accomplished by establishing cell states in which levels rather than binary expression or repression of individual genes vary across each progenitor's shared transcriptome. Such states may reflect local, stochastic signaling via soluble factors or coincidence of cell surface ligand/receptor pairs in subsets of neighboring progenitors. This probabilistic, rather than determined, signaling could modify transcription levels via multiple pathways within an apparently uniform population of progenitors. Progenitor states, therefore, rather than lineal relationships between types may underlie the generation of neuronal diversity in most regions of the nervous system. Moreover, mechanisms that influence variation required for flexible progenitor states may be targets for pathological changes in a broad range of neurodevelopmental disorders, especially those with polygenic origins.
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Affiliation(s)
- Shah Rukh
- Fralin Biomedical Research Institute, Virginia Tech Carilion School of Medicine, Roanoke, Virginia, USA
| | - Daniel W Meechan
- Fralin Biomedical Research Institute, Virginia Tech Carilion School of Medicine, Roanoke, Virginia, USA
| | - Thomas M Maynard
- Fralin Biomedical Research Institute, Virginia Tech Carilion School of Medicine, Roanoke, Virginia, USA
| | - Anthony-Samuel Lamantia
- Fralin Biomedical Research Institute, Virginia Tech Carilion School of Medicine, Roanoke, Virginia, USA
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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81
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Murtaj V, Butti E, Martino G, Panina-Bordignon P. Endogenous neural stem cells characterization using omics approaches: Current knowledge in health and disease. Front Cell Neurosci 2023; 17:1125785. [PMID: 37091923 PMCID: PMC10113633 DOI: 10.3389/fncel.2023.1125785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Neural stem cells (NSCs), an invaluable source of neuronal and glial progeny, have been widely interrogated in the last twenty years, mainly to understand their therapeutic potential. Most of the studies were performed with cells derived from pluripotent stem cells of either rodents or humans, and have mainly focused on their potential in regenerative medicine. High-throughput omics technologies, such as transcriptomics, epigenetics, proteomics, and metabolomics, which exploded in the past decade, represent a powerful tool to investigate the molecular mechanisms characterizing the heterogeneity of endogenous NSCs. The transition from bulk studies to single cell approaches brought significant insights by revealing complex system phenotypes, from the molecular to the organism level. Here, we will discuss the current literature that has been greatly enriched in the “omics era”, successfully exploring the nature and function of endogenous NSCs and the process of neurogenesis. Overall, the information obtained from omics studies of endogenous NSCs provides a sharper picture of NSCs function during neurodevelopment in healthy and in perturbed environments.
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Affiliation(s)
- Valentina Murtaj
- Division of Neuroscience, San Raffaele Vita-Salute University, Milan, Italy
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Erica Butti
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Gianvito Martino
- Division of Neuroscience, San Raffaele Vita-Salute University, Milan, Italy
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Paola Panina-Bordignon
- Division of Neuroscience, San Raffaele Vita-Salute University, Milan, Italy
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
- *Correspondence: Paola Panina-Bordignon
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82
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Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O, Jarvis ED, Sheynkman G, Korkin D, Ross ME, Tilgner HU. Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.02.535281. [PMID: 37066387 PMCID: PMC10103983 DOI: 10.1101/2023.04.02.535281] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
RNA isoforms influence cell identity and function. Until recently, technological limitations prevented a genome-wide appraisal of isoform influence on cell identity in various parts of the brain. Using enhanced long-read single-cell isoform sequencing, we comprehensively analyze RNA isoforms in multiple mouse brain regions, cell subtypes, and developmental timepoints from postnatal day 14 (P14) to adult (P56). For 75% of genes, full-length isoform expression varies along one or more axes of phenotypic origin, underscoring the pervasiveness of isoform regulation across multiple scales. As expected, splicing varies strongly between cell types. However, certain gene classes including neurotransmitter release and reuptake as well as synapse turnover, harbor significant variability in the same cell type across anatomical regions, suggesting differences in network activity may influence cell-type identity. Glial brain-region specificity in isoform expression includes strong poly(A)-site regulation, whereas neurons have stronger TSS regulation. Furthermore, developmental patterns of cell-type specific splicing are especially pronounced in the murine adolescent transition from P21 to P28. The same cell type traced across development shows more isoform variability than across adult anatomical regions, indicating a coordinated modulation of functional programs dictating neural development. As most cell-type specific exons in P56 mouse hippocampus behave similarly in newly generated data from human hippocampi, these principles may be extrapolated to human brain. However, human brains have evolved additional cell-type specificity in splicing, suggesting gain-of-function isoforms. Taken together, we present a detailed single-cell atlas of full-length brain isoform regulation across development and anatomical regions, providing a previously unappreciated degree of isoform variability across multiple scales of the brain.
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Affiliation(s)
- Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | | | - Oleksandr Narykov
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, the Rockefeller University, New York, NY
| | - Erich D Jarvis
- Vertebrate Genome Lab, the Rockefeller University, New York, NY
- Laboratory of Neurogenetics of Language, the Rockefeller University, New York, NY
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
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83
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Shen X, Li M, Shao K, Li Y, Ge Z. Post-ischemic inflammatory response in the brain: Targeting immune cell in ischemic stroke therapy. Front Mol Neurosci 2023; 16:1076016. [PMID: 37078089 PMCID: PMC10106693 DOI: 10.3389/fnmol.2023.1076016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
An ischemic stroke occurs when the blood supply is obstructed to the vascular basin, causing the death of nerve cells and forming the ischemic core. Subsequently, the brain enters the stage of reconstruction and repair. The whole process includes cellular brain damage, inflammatory reaction, blood–brain barrier destruction, and nerve repair. During this process, the proportion and function of neurons, immune cells, glial cells, endothelial cells, and other cells change. Identifying potential differences in gene expression between cell types or heterogeneity between cells of the same type helps to understand the cellular changes that occur in the brain and the context of disease. The recent emergence of single-cell sequencing technology has promoted the exploration of single-cell diversity and the elucidation of the molecular mechanism of ischemic stroke, thus providing new ideas and directions for the diagnosis and clinical treatment of ischemic stroke.
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Affiliation(s)
- Xueyang Shen
- Department of Neurology, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Mingming Li
- Department of Neurology, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
- Gansu Provincial Neurology Clinical Medical Research Center, The Second Hospital of Lanzhou University, Lanzhou, China
- Expert Workstation of Academician Wang Longde, The Second Hospital of Lanzhou University, Lanzhou, China
| | - Kangmei Shao
- Department of Neurology, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
| | - Yongnan Li
- Department of Cardiac Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
- Yongnan Li,
| | - Zhaoming Ge
- Department of Neurology, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
- Gansu Provincial Neurology Clinical Medical Research Center, The Second Hospital of Lanzhou University, Lanzhou, China
- Expert Workstation of Academician Wang Longde, The Second Hospital of Lanzhou University, Lanzhou, China
- *Correspondence: Zhaoming Ge,
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84
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Wu BS, Ge YJ, Zhang W, Chen SD, Xiang ST, Zhang YR, Ou YN, Jiang YC, Tan L, Cheng W, Suckling J, Feng JF, Yu JT, Mao Y. Genome-wide association study of cerebellar white matter microstructure and genetic overlap with common brain disorders. Neuroimage 2023; 269:119928. [PMID: 36740028 DOI: 10.1016/j.neuroimage.2023.119928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/12/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The cerebellum is recognized as being involved in neurocognitive and motor functions with communication with extra-cerebellar regions relying on the white matter integrity of the cerebellar peduncles. However, the genetic determinants of cerebellar white matter integrity remain largely unknown. METHODS We conducted a genome-wide association analysis of cerebellar white matter microstructure using diffusion tensor imaging data from 25,415 individuals from UK Biobank. The integrity of cerebellar white matter microstructure was measured as fractional anisotropy (FA) and mean diffusivity (MD). Identification of independent genomic loci, functional annotation, and tissue and cell-type analysis were conducted with FUMA. The linkage disequilibrium score regression (LDSC) was used to calculate genetic correlations between cerebellar white matter microstructure and regional brain volumes and brain-related traits. Furthermore, the conditional/conjunctional false discovery rate (condFDR/conjFDR) framework was employed to identify the shared genetic basis between cerebellar white matter microstructure and common brain disorders. RESULTS We identified 11 genetic loci (P < 8.3 × 10-9) and 86 genes associated with cerebellar white matter microstructure. Further functional enrichment analysis implicated the involvement of GABAergic neurons and cholinergic pathways. Significant polygenetic overlap between cerebellar white matter tracts and their anatomically connected or adjacent brain regions was detected. In addition, we report the overall genetic correlation and specific loci shared between cerebellar white matter microstructural integrity and brain-related traits, including movement, cognitive, psychiatric, and cerebrovascular categories. CONCLUSIONS Collectively, this study represents a step forward in understanding the genetics of cerebellar white matter microstructure and its shared genetic etiology with common brain disorders.
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Affiliation(s)
- Bang-Sheng Wu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Jun Ge
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Wei Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Shi-Dong Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shi-Tong Xiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Ya-Ru Zhang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ya-Nan Ou
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Yu-Chao Jiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Wei Cheng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China; Fudan ISTBI-ZJNU Algorithm Centre for Brain-Inspired Intelligence, Zhejiang Normal University, Jinhua, China; Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - John Suckling
- Department of Psychiatry, Brain Mapping Unit, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Jian-Feng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; Department of Computer Science, University of Warwick, Coventry CV4 7AL, UK
| | - Jin-Tai Yu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Ying Mao
- Department of Neurosurgery and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
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85
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Chang C, Zuo H, Li Y. Recent advances in deciphering hippocampus complexity using single-cell transcriptomics. Neurobiol Dis 2023; 179:106062. [PMID: 36878328 DOI: 10.1016/j.nbd.2023.106062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023] Open
Abstract
Single-cell and single-nucleus RNA sequencing (scRNA-seq and snRNA-seq) technologies have emerged as revolutionary and powerful tools, which have helped in achieving significant progress in biomedical research over the last decade. scRNA-seq and snRNA-seq resolve heterogeneous cell populations from different tissues and help reveal the function and dynamics at the single-cell level. The hippocampus is an essential component for cognitive functions, including learning, memory, and emotion regulation. However, the molecular mechanisms underlying the activity of hippocampus have not been fully elucidated. The development of scRNA-seq and snRNA-seq technologies provides strong support for attaining an in-depth understanding of hippocampal cell types and gene expression regulation from the single-cell transcriptome profiling perspective. This review summarizes the applications of scRNA-seq and snRNA-seq in the hippocampus to further expand our knowledge of the molecular mechanisms related to hippocampal development, health, and diseases.
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Affiliation(s)
- Chenxu Chang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hongyan Zuo
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Yang Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
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86
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Zoabi S, Andreyanov M, Heinrich R, Ron S, Carmi I, Gutfreund Y, Berlin S. A custom-made AAV1 variant (AAV1-T593K) enables efficient transduction of Japanese quail neurons in vitro and in vivo. Commun Biol 2023; 6:337. [PMID: 36977781 PMCID: PMC10050006 DOI: 10.1038/s42003-023-04712-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The widespread use of rodents in neuroscience has prompted the development of optimized viral variants for transduction of brain cells, in vivo. However, many of the viruses developed are less efficient in other model organisms, with birds being among the most resistant to transduction by current viral tools. Resultantly, the use of genetically-encoded tools and methods in avian species is markedly lower than in rodents; likely holding the field back. We sought to bridge this gap by developing custom viruses towards the transduction of brain cells of the Japanese quail. We first develop a protocol for culturing primary neurons and glia from quail embryos, followed by characterization of cultures via immunostaining, single cell mRNA sequencing, patch clamp electrophysiology and calcium imaging. We then leveraged the cultures for the rapid screening of various viruses, only to find that all yielded poor to no infection of cells in vitro. However, few infected neurons were obtained by AAV1 and AAV2. Scrutiny of the sequence of the AAV receptor found in quails led us to rationally design a custom-made AAV variant (AAV1-T593K; AAV1*) that exhibits improved transduction efficiencies in vitro and in vivo (14- and five-fold, respectively). Together, we present unique culturing method, transcriptomic profiles of quail's brain cells and a custom-tailored AAV1 for transduction of quail neurons in vitro and in vivo.
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Affiliation(s)
- Shaden Zoabi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Michael Andreyanov
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Ronit Heinrich
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Shaked Ron
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Ido Carmi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Yoram Gutfreund
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Shai Berlin
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel.
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87
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Regal JA, Guerra García ME, Jain V, Chandramohan V, Ashley DM, Gregory SG, Thompson EM, López GY, Reitman ZJ. Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population. Acta Neuropathol Commun 2023; 11:50. [PMID: 36966348 PMCID: PMC10039537 DOI: 10.1186/s40478-023-01548-3] [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: 12/18/2022] [Accepted: 03/06/2023] [Indexed: 03/27/2023] Open
Abstract
Gangliogliomas are brain tumors composed of neuron-like and macroglia-like components that occur in children and young adults. Gangliogliomas are often characterized by a rare population of immature astrocyte-appearing cells expressing CD34, a marker expressed in the neuroectoderm (neural precursor cells) during embryogenesis. New insights are needed to refine tumor classification and to identify therapeutic approaches. We evaluated five gangliogliomas with single nucleus RNA-seq, cellular indexing of transcriptomes and epitopes by sequencing, and/or spatially-resolved RNA-seq. We uncovered a population of CD34+ neoplastic cells with mixed neuroectodermal, immature astrocyte, and neuronal markers. Gene regulatory network interrogation in these neuroectoderm-like cells revealed control of transcriptional programming by TCF7L2/MEIS1-PAX6 and SOX2, similar to that found during neuroectodermal/neural development. Developmental trajectory analyses place neuroectoderm-like tumor cells as precursor cells that give rise to neuron-like and macroglia-like neoplastic cells. Spatially-resolved transcriptomics revealed a neuroectoderm-like tumor cell niche with relative lack of vascular and immune cells. We used these high resolution results to deconvolute clinically-annotated transcriptomic data, confirming that CD34+ cell-associated gene programs associate with gangliogliomas compared to other glial brain tumors. Together, these deep transcriptomic approaches characterized a ganglioglioma cellular hierarchy-confirming CD34+ neuroectoderm-like tumor precursor cells, controlling transcription programs, cell signaling, and associated immune cell states. These findings may guide tumor classification, diagnosis, prognostication, and therapeutic investigations.
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Affiliation(s)
- Joshua A Regal
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA
| | | | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27710, USA
| | | | - David M Ashley
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27710, USA
| | - Eric M Thompson
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
| | - Giselle Y López
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
- Department of Pathology, Duke University, Durham, NC, 27710, USA
| | - Zachary J Reitman
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA.
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA.
- Department of Pathology, Duke University, Durham, NC, 27710, USA.
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88
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Ren T, Chen C, Danilov AV, Liu S, Guan X, Du S, Wu X, Sherman MH, Spellman PT, Coussens LM, Adey AC, Mills GB, Wu LY, Xia Z. Supervised learning of high-confidence phenotypic subpopulations from single-cell data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533712. [PMID: 36993424 PMCID: PMC10055361 DOI: 10.1101/2023.03.23.533712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Accurately identifying phenotype-relevant cell subsets from heterogeneous cell populations is crucial for delineating the underlying mechanisms driving biological or clinical phenotypes. Here, by deploying a learning with rejection strategy, we developed a novel supervised learning framework called PENCIL to identify subpopulations associated with categorical or continuous phenotypes from single-cell data. By embedding a feature selection function into this flexible framework, for the first time, we were able to select informative features and identify cell subpopulations simultaneously, which enables the accurate identification of phenotypic subpopulations otherwise missed by methods incapable of concurrent gene selection. Furthermore, the regression mode of PENCIL presents a novel ability for supervised phenotypic trajectory learning of subpopulations from single-cell data. We conducted comprehensive simulations to evaluate PENCIĽs versatility in simultaneous gene selection, subpopulation identification and phenotypic trajectory prediction. PENCIL is fast and scalable to analyze 1 million cells within 1 hour. Using the classification mode, PENCIL detected T-cell subpopulations associated with melanoma immunotherapy outcomes. Moreover, when applied to scRNA-seq of a mantle cell lymphoma patient with drug treatment across multiple time points, the regression mode of PENCIL revealed a transcriptional treatment response trajectory. Collectively, our work introduces a scalable and flexible infrastructure to accurately identify phenotype-associated subpopulations from single-cell data.
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Affiliation(s)
- Tao Ren
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Canping Chen
- Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | | | - Susan Liu
- Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Xiangnan Guan
- Department of Oncology Biomarker Development, Genentech Inc, South San Francisco, CA, USA
| | - Shunyi Du
- Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Xiwei Wu
- City of Hope National Medical Center, Duarte, CA, USA
| | - Mara H. Sherman
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Paul T. Spellman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Lisa M. Coussens
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Andrew C. Adey
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Gordon B. Mills
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Ling-Yun Wu
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Xia
- Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
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89
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De Kleijn KMA, Zuure WA, Straasheijm KR, Martens MB, Avramut MC, Koning RI, Martens GJM. Human cortical spheroids with a high diversity of innately developing brain cell types. Stem Cell Res Ther 2023; 14:50. [PMID: 36959625 PMCID: PMC10035191 DOI: 10.1186/s13287-023-03261-3] [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: 06/03/2022] [Accepted: 02/28/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Three-dimensional (3D) human brain spheroids are instrumental to study central nervous system (CNS) development and (dys)function. Yet, in current brain spheroid models the limited variety of cell types hampers an integrated exploration of CNS (disease) mechanisms. METHODS Here we report a 5-month culture protocol that reproducibly generates H9 embryonic stem cell-derived human cortical spheroids (hCSs) with a large cell-type variety. RESULTS We established the presence of not only neuroectoderm-derived neural progenitor populations, mature excitatory and inhibitory neurons, astrocytes and oligodendrocyte (precursor) cells, but also mesoderm-derived microglia and endothelial cell populations in the hCSs via RNA-sequencing, qPCR, immunocytochemistry and transmission electron microscopy. Transcriptomic analysis revealed resemblance between the 5-months-old hCSs and dorsal frontal rather than inferior regions of human fetal brains of 19-26 weeks of gestational age. Pro-inflammatory stimulation of the generated hCSs induced a neuroinflammatory response, offering a proof-of-principle of the applicability of the spheroids. CONCLUSIONS Our protocol provides a 3D human brain cell model containing a wide variety of innately developing neuroectoderm- as well as mesoderm-derived cell types, furnishing a versatile platform for comprehensive examination of intercellular CNS communication and neurological disease mechanisms.
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Affiliation(s)
- Kim M A De Kleijn
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Centre for Neuroscience, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands.
- NeuroDrug Research Ltd, 6525ED, Nijmegen, The Netherlands.
| | - Wieteke A Zuure
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Centre for Neuroscience, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands
| | | | | | - M Cristina Avramut
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300RC, Leiden, The Netherlands
| | - Roman I Koning
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300RC, Leiden, The Netherlands
| | - Gerard J M Martens
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Centre for Neuroscience, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands
- NeuroDrug Research Ltd, 6525ED, Nijmegen, The Netherlands
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90
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Huang Y, Wang Q, Peng Y, Du W, Wang Q, Qi J, Hao Z, Wang Y. Spatiotemporal expression patterns of genes coding for plasmalemmal chloride transporters and channels in neurological diseases. Mol Brain 2023; 16:30. [PMID: 36934242 PMCID: PMC10024392 DOI: 10.1186/s13041-023-01018-w] [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: 08/22/2022] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
Neuronal voltage changes which are dependent on chloride transporters and channels are involved in forming neural functions during early development and maintaining their stability until adulthood. The intracellular chloride concentration maintains a steady state, which is delicately regulated by various genes coding for chloride transporters and channels (GClTC) on the plasmalemma; however, the synergistic effect of these genes in central nervous system disorders remains unclear. In this study, we first defined 10 gene clusters with similar temporal expression patterns, and identified 41 GClTC related to brain developmental process. Then, we found 4 clusters containing 22 GClTC were enriched for the neuronal functions. The GClTC from different clusters presented distinct cell type preferences and anatomical heterogeneity. We also observed strong correlations between clustered genes and diseases, most of which were nervous system disorders. Finally, we found that one of the most well-known GClTC, SLC12A2, had a more profound effect on glial cell-related diseases than on neuron-related diseases, which was in accordance with our observation that SLC12A2 was mainly expressed in oligodendrocytes during brain development. Our findings provide a more comprehensive understanding of the temporal and spatial expression characteristics of GClTC, which can help us understand the complex roles of GClTC in the development of the healthy human brain and the etiology of brain disorders.
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Affiliation(s)
- Yanruo Huang
- Department of Anesthesiology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Qihang Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunsong Peng
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Hefei, 230026, China
- Medical Imaging Department, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wenjie Du
- Department of Anesthesiology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Qi Wang
- Department of Anesthesiology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jiangtao Qi
- Department of Anesthesiology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Zijian Hao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China.
| | - Yingwei Wang
- Department of Anesthesiology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
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91
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Bo T, Li J, Hu G, Zhang G, Wang W, Lv Q, Zhao S, Ma J, Qin M, Yao X, Wang M, Wang GZ, Wang Z. Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys. Nat Commun 2023; 14:1499. [PMID: 36932104 PMCID: PMC10023667 DOI: 10.1038/s41467-023-37246-w] [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: 08/08/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Integrative analyses of transcriptomic and neuroimaging data have generated a wealth of information about biological pathways underlying regional variability in imaging-derived brain phenotypes in humans, but rarely in nonhuman primates due to the lack of a comprehensive anatomically-defined atlas of brain transcriptomics. Here we generate complementary bulk RNA-sequencing dataset of 819 samples from 110 brain regions and single-nucleus RNA-sequencing dataset, and neuroimaging data from 162 cynomolgus macaques, to examine the link between brain-wide gene expression and regional variation in morphometry. We not only observe global/regional expression profiles of macaque brain comparable to human but unravel a dorsolateral-ventromedial gradient of gene assemblies within the primate frontal lobe. Furthermore, we identify a set of 971 protein-coding and 34 non-coding genes consistently associated with cortical thickness, specially enriched for neurons and oligodendrocytes. These data provide a unique resource to investigate nonhuman primate models of human diseases and probe cross-species evolutionary mechanisms.
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Affiliation(s)
- Tingting Bo
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Clinical Neuroscience Center, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ganlu Hu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Ge Zhang
- Department of Medical Imaging, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, China
| | - Wei Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qian Lv
- School of Psychological and Cognitive Sciences; Beijing Key Laboratory of Behavior and Mental Health; IDG/McGovern Institute for Brain Research; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shaoling Zhao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjie Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meng Qin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiaohui Yao
- Qingdao Innovation and Development Center, Harbin Engineering University, Qingdao, Shandong, China
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Meiyun Wang
- Department of Medical Imaging, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, China.
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Zheng Wang
- School of Psychological and Cognitive Sciences; Beijing Key Laboratory of Behavior and Mental Health; IDG/McGovern Institute for Brain Research; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- School of Biomedical Engineering, Hainan University, Haikou, Hainan, China.
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92
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Xu Y, Zhang T, Zhou Q, Hu M, Qi Y, Xue Y, Nie Y, Wang L, Bao Z, Shi W. A single-cell transcriptome atlas profiles early organogenesis in human embryos. Nat Cell Biol 2023; 25:604-615. [PMID: 36928764 DOI: 10.1038/s41556-023-01108-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
The early window of human embryogenesis is largely a black box for developmental biologists. Here we probed the cellular diversity of 4-6 week human embryos when essentially all organs are just laid out. On the basis of over 180,000 single-cell transcriptomes, we generated a comprehensive atlas of 313 clusters in 18 developmental systems, which were annotated with a collection of ontology and markers from 157 publications. Together with spatial transcriptome on embryonic sections, we characterized the molecule and spatial architecture of previously unappreciated cell types. Combined with data from other vertebrates, the rich information shed light on spatial patterning of axes, systemic temporal regulation of developmental progression and potential human-specific regulation. Our study provides a compendium of early progenitor cells of human organs, which can serve as the root of lineage analysis in organogenesis.
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Affiliation(s)
- Yichi Xu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Tengjiao Zhang
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qin Zhou
- Traditional Chinese Medicine Hospital of Kunshan, Suzhou, China
| | - Mengzhu Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yao Qi
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yifang Xue
- Traditional Chinese Medicine Hospital of Kunshan, Suzhou, China
| | - Yuxiao Nie
- School of Pharmacy, Fudan University, Shanghai, China
| | - Lihui Wang
- Traditional Chinese Medicine Hospital of Kunshan, Suzhou, China
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.
| | - Weiyang Shi
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University, Shanghai, China.
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93
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Wightman DP, Savage JE, Tissink E, Romero C, Jansen IE, Posthuma D. The genetic overlap between Alzheimer’s disease, amyotrophic lateral sclerosis, Lewy body dementia, and Parkinson’s disease. Neurobiol Aging 2023; 127:99-112. [PMID: 37045620 DOI: 10.1016/j.neurobiolaging.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/23/2023] [Accepted: 03/03/2023] [Indexed: 03/13/2023]
Abstract
Neurodegenerative diseases are a group of disorders characterized by neuronal cell death causing a variety of physical and mental problems. While these disorders can be characterized by their phenotypic presentation within the nervous system, their aetiologies differ to varying degrees. The majority of previous genetic evidence for overlap between neurodegenerative diseases has been pairwise. In this study, we aimed to identify overlap between the 4 investigated neurodegenerative disorders (Alzheimer's disease, amyotrophic lateral sclerosis, Lewy body dementia, and Parkinson's disease) at the variant, gene, genomic locus, gene-set, cell, or tissue level, with specific interest in overlap between 3 or more diseases. Using local genetic correlation, we found 2 loci (TMEM175 and HLA) that were shared across 3 disorders. We also highlighted genes, genomic loci, gene sets, cell types, and tissue types which may be important to 2 or more disorders by analyzing the association of variants with a common factor estimated from the 4 disorders. Our study successfully highlighted genetic loci and tissues associated with 2 or more neurodegenerative diseases.
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94
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Kang H, Liu Q, Seim I, Zhang W, Li H, Gao H, Lin W, Lin M, Zhang P, Zhang Y, Gao H, Wang Y, Qin Y, Liu M, Dong L, Yang Z, Zhang Y, Han L, Fan G, Li S. A genome and single-nucleus cerebral cortex transcriptome atlas of the short-finned pilot whale Globicephala macrorhynchus. Mol Ecol Resour 2023. [PMID: 36826393 DOI: 10.1111/1755-0998.13775] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Cetaceans (dolphins, whales, and porpoises) have large and anatomically sophisticated brains. To expand our understanding of the cellular makeup of cetacean brains and the similarities and divergence between the brains of cetaceans and terrestrial mammals, we report a short-finned pilot whale (Globicephala macrorhynchus) single-nucleus transcriptome atlas. To achieve this goal, we assembled a chromosome-scale reference genome spanning 2.25 Gb on 22 chromosomes and profiled the gene expression of five major anatomical cortical regions of the short-finned pilot whale by single-nucleus RNA-sequencing (snRNA-seq). We identified six major cell lineages in the cerebral cortex (excitatory neurons, inhibitory neurons, oligodendrocytes, oligodendrocyte precursor cells, astrocytes, and endothelial cells), eight molecularly distinct subclusters of excitatory neurons, and four subclusters of inhibitory neurons. Finally, a comparison of snRNA-seq data from the short-finned pilot whale, human, and rhesus macaque revealed a broadly conserved cellular makeup of brain cell types. Our study provides genomic resources and molecular insights into cetacean brain evolution.
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Affiliation(s)
- Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qun Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, Qingdao, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenwei Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hanbo Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Haiyu Gao
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhi Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Mingli Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | | | - Yang Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Yating Qin
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Mingming Liu
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Lijun Dong
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Zixin Yang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Lei Han
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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95
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Sha Z, Schijven D, Fisher SE, Francks C. Genetic architecture of the white matter connectome of the human brain. SCIENCE ADVANCES 2023; 9:eadd2870. [PMID: 36800424 PMCID: PMC9937579 DOI: 10.1126/sciadv.add2870] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
White matter tracts form the structural basis of large-scale brain networks. We applied brain-wide tractography to diffusion images from 30,810 adults (U.K. Biobank) and found significant heritability for 90 node-level and 851 edge-level network connectivity measures. Multivariate genome-wide association analyses identified 325 genetic loci, of which 80% had not been previously associated with brain metrics. Enrichment analyses implicated neurodevelopmental processes including neurogenesis, neural differentiation, neural migration, neural projection guidance, and axon development, as well as prenatal brain expression especially in stem cells, astrocytes, microglia, and neurons. The multivariate association profiles implicated 31 loci in connectivity between core regions of the left-hemisphere language network. Polygenic scores for psychiatric, neurological, and behavioral traits also showed significant multivariate associations with structural connectivity, each implicating distinct sets of brain regions with trait-relevant functional profiles. This large-scale mapping study revealed common genetic contributions to variation in the structural connectome of the human brain.
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Affiliation(s)
- Zhiqiang Sha
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Dick Schijven
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Simon E. Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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96
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Zhou YN, Jiang L, Zhang Y, Zhou CN, Yang H, He Q, Wang YY, Xiao Q, Huang DJ, Luo YM, Tang Y, Chao FL. Anti-LINGO-1 antibody protects neurons and synapses in the medial prefrontal cortex of APP/PS1 transgenic mice. Neurosci Res 2023:S0168-0102(23)00039-1. [PMID: 36804877 DOI: 10.1016/j.neures.2023.02.005] [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: 11/28/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
The medial prefrontal cortex (mPFC), one of the most vulnerable brain regions in Alzheimer's disease (AD), plays a critical role in cognition. Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein-1 (LINGO-1) negatively affects nerve growth in the central nervous system; however, its role in the pathological damage to the mPFC remains to be studied in AD. In this study, an anti-LINGO-1 antibody was administered to 10-month-old APP/PS1 mice, and behavioral tests, stereological methods, immunohistochemistry and immunofluorescence were used to answer this question. Our results revealed that LINGO-1 was highly expressed in the neurons of the mPFC of AD mice, and the anti-LINGO-1 antibody improved prefrontal cortex-related function and reduced the protein level of LINGO-1, atrophy of the volume, Aβ deposition and massive losses of synapses and neurons in the mPFC of AD mice. Antagonizing LINGO-1 could effectively alleviate the pathological damage in the mPFC of AD mice, which might be an important structural basis for improving prefrontal cortex-related function. Abnormal expression of LINGO-1 in the mPFC may be one of the key targets of AD, and the effect initiated by the anti-LINGO-1 antibody may provide an important basis in the search for drugs for the prevention and treatment of AD.
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Affiliation(s)
- Yu-Ning Zhou
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Lin Jiang
- Experimental Teaching Management Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Yi Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China
| | - Chun-Ni Zhou
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Hao Yang
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Qi He
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Yi-Ying Wang
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Qian Xiao
- Department of Radioactive Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Du-Juan Huang
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Yan-Min Luo
- Department of Physiology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China
| | - Yong Tang
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China.
| | - Feng-Lei Chao
- Department of Histology and Embryology, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China; Laboratory of Stem Cell and Tissue Engineering, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, PR China.
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97
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Molecular and cellular evolution of the amygdala across species analyzed by single-nucleus transcriptome profiling. Cell Discov 2023; 9:19. [PMID: 36788214 PMCID: PMC9929086 DOI: 10.1038/s41421-022-00506-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/24/2022] [Indexed: 02/16/2023] Open
Abstract
The amygdala, or an amygdala-like structure, is found in the brains of all vertebrates and plays a critical role in survival and reproduction. However, the cellular architecture of the amygdala and how it has evolved remain elusive. Here, we generated single-nucleus RNA-sequencing data for more than 200,000 cells in the amygdala of humans, macaques, mice, and chickens. Abundant neuronal cell types from different amygdala subnuclei were identified in all datasets. Cross-species analysis revealed that inhibitory neurons and inhibitory neuron-enriched subnuclei of the amygdala were well-conserved in cellular composition and marker gene expression, whereas excitatory neuron-enriched subnuclei were relatively divergent. Furthermore, LAMP5+ interneurons were much more abundant in primates, while DRD2+ inhibitory neurons and LAMP5+SATB2+ excitatory neurons were dominant in the human central amygdalar nucleus (CEA) and basolateral amygdalar complex (BLA), respectively. We also identified CEA-like neurons and their species-specific distribution patterns in chickens. This study highlights the extreme cell-type diversity in the amygdala and reveals the conservation and divergence of cell types and gene expression patterns across species that may contribute to species-specific adaptations.
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98
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Cui Z, Gong Y, Luo X, Zheng N, Tan S, Liu S, Li Y, Wang Q, Sun F, Hu M, Pan W, Yang X. β-Glucan alleviates goal-directed behavioral deficits in mice infected with Toxoplasma gondii. Parasit Vectors 2023; 16:65. [PMID: 36782332 PMCID: PMC9926625 DOI: 10.1186/s13071-023-05686-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Toxoplasma gondii (T. gondii) is a neuroinvasive parasite causing neuroinflammation, which in turn is associated with a higher risk for several psycho-behavioral disorders. There is an urgent need to identify drugs capable of improving cognitive deficits induced by T. gondii infection. β-Glucan, an active ingredient in mushrooms, could significantly enhance immunity. However, the effects of β-glucan against neuroinflammation and cognitive decline induced by T. gondii infection remain unknown. The present study aimed to investigate the neuroprotective effect of β-glucan on goal-directed behavior of mice chronically infected by T. gondii Wh6 strain. METHODS A mice model of chronic T. gondii Wh6 infection was established by infecting mice by oral gavage with 10 cysts of T. gondii Wh6. Intraperitoneal injection of β-glucan was manipulated 2 weeks before T. gondii infection. Performance of the infected mice on the Y-maze test and temporal order memory (TOM) test was used to assess the goal-directed behavior. Golgi-Cox staining, transmission electron microscopy, immunofluorescence, real-time PCR and western blot assays were used to detect prefrontal cortex-associated pathological change and neuroinflammation. RESULTS The administration of β-glucan significantly prevented T. gondii Wh6-induced goal-directed behavioral impairment as assessed behaviorally by the Y-maze test and TOM test. In the prefrontal cortex, β-glucan was able to counter T. gondii Wh6-induced degeneration of neurites, impairment of synaptic ultrastructure and decrease of pre- and postsynaptic protein levels. Also, β-glucan significantly prevented the hyperactivation of pro-inflammatory microglia and astrocytes, as well as the upregulation of proinflammatory cytokines caused by chronic T. gondii Wh6 infection. CONCLUSIONS This study revealed that β-glucan prevents goal-directed behavioral impairment induced by chronic T. gondii infection in mice. These findings suggest that β-glucan may be an effective drug candidate to prevent T. gondii-associated psycho-behavioral disorders including goal-directed behavioral injury.
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Affiliation(s)
- Zeyu Cui
- grid.417303.20000 0000 9927 0537Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China ,grid.417303.20000 0000 9927 0537The Second Clinical Medical College, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Yuying Gong
- grid.417303.20000 0000 9927 0537Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Xiaotong Luo
- grid.417303.20000 0000 9927 0537Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China ,grid.417303.20000 0000 9927 0537The Second Clinical Medical College, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Niuyi Zheng
- grid.417303.20000 0000 9927 0537Department of Anatomy, Basic Medical College, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Shimin Tan
- grid.417303.20000 0000 9927 0537Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China ,grid.417303.20000 0000 9927 0537The Second Clinical Medical College, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Shuxi Liu
- grid.417303.20000 0000 9927 0537Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China ,grid.417303.20000 0000 9927 0537The First Clinical Medical College, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Youwei Li
- grid.417303.20000 0000 9927 0537Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China ,grid.417303.20000 0000 9927 0537The Second Clinical Medical College, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Qingling Wang
- grid.417303.20000 0000 9927 0537Department of Pathology, Basic Medical College, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Fenfen Sun
- grid.417303.20000 0000 9927 0537Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Minmin Hu
- grid.417303.20000 0000 9927 0537Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Wei Pan
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
| | - Xiaoying Yang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
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99
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An NA, Zhang J, Mo F, Luan X, Tian L, Shen QS, Li X, Li C, Zhou F, Zhang B, Ji M, Qi J, Zhou WZ, Ding W, Chen JY, Yu J, Zhang L, Shu S, Hu B, Li CY. De novo genes with an lncRNA origin encode unique human brain developmental functionality. Nat Ecol Evol 2023; 7:264-278. [PMID: 36593289 PMCID: PMC9911349 DOI: 10.1038/s41559-022-01925-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 10/04/2022] [Indexed: 01/03/2023]
Abstract
Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant in general, yet how and why this all-or-nothing transition to functionality happens remains unclear. Here, in 74 human/hominoid-specific de novo genes, we identified distinctive U1 elements and RNA splice-related sequences accounting for RNA nuclear export, differentiating mRNAs from lncRNAs, and driving the origin of de novo genes from lncRNA loci. The polymorphic sites facilitating the lncRNA-mRNA conversion through regulating nuclear export are selectively constrained, maintaining a boundary that differentiates mRNAs from lncRNAs. The functional new genes actively passing through it thus showed a mode of pre-adaptive origin, in that they acquire functions along with the achievement of their coding potential. As a proof of concept, we verified the regulations of splicing and U1 recognition on the nuclear export efficiency of one of these genes, the ENSG00000205704, in human neural progenitor cells. Notably, knock-out or over-expression of this gene in human embryonic stem cells accelerates or delays the neuronal maturation of cortical organoids, respectively. The transgenic mice with ectopically expressed ENSG00000205704 showed enlarged brains with cortical expansion. We thus demonstrate the key roles of nuclear export in de novo gene origin. These newly originated genes should reflect the novel uniqueness of human brain development.
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Affiliation(s)
- Ni A An
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jie Zhang
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuke Luan
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Lu Tian
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xiangshang Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chunqiong Li
- Chinese Institute for Brain Research, Beijing, China
| | - Fanqi Zhou
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Boya Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingjun Ji
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jianhuan Qi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wanqiu Ding
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Shaokun Shu
- Peking University International Cancer Institute, Beijing, China
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.
- Chinese Institute for Brain Research, Beijing, China.
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100
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Murdock MH, Tsai LH. Insights into Alzheimer's disease from single-cell genomic approaches. Nat Neurosci 2023; 26:181-195. [PMID: 36593328 PMCID: PMC10155598 DOI: 10.1038/s41593-022-01222-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/28/2022] [Indexed: 01/03/2023]
Abstract
Alzheimer's disease (AD) is an age-related disease pathologically defined by the deposition of amyloid plaques and neurofibrillary tangles in the brain parenchyma. Single-cell profiling has shown that Alzheimer's dementia involves the complex interplay of virtually every major brain cell type. Here, we highlight cell-type-specific molecular perturbations in AD. We discuss how genomic information from single cells expands existing paradigms of AD pathogenesis and highlight new opportunities for therapeutic interventions.
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Affiliation(s)
- Mitchell H Murdock
- Department of Brain and Cognitive Sciences, The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
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