1
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Nussinov R, Yavuz BR, Jang H. Single cell spatial biology over developmental time can decipher pediatric brain pathologies. Neurobiol Dis 2024; 199:106597. [PMID: 38992777 DOI: 10.1016/j.nbd.2024.106597] [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: 03/27/2024] [Revised: 06/18/2024] [Accepted: 07/07/2024] [Indexed: 07/13/2024] Open
Abstract
Pediatric low grade brain tumors and neurodevelopmental disorders share proteins, signaling pathways, and networks. They also share germline mutations and an impaired prenatal differentiation origin. They may differ in the timing of the events and proliferation. We suggest that their pivotal distinct, albeit partially overlapping, outcomes relate to the cell states, which depend on their spatial location, and timing of gene expression during brain development. These attributes are crucial as the brain develops sequentially, and single-cell spatial organization influences cell state, thus function. Our underlying premise is that the root cause in neurodevelopmental disorders and pediatric tumors is impaired prenatal differentiation. Data related to pediatric brain tumors, neurodevelopmental disorders, brain cell (sub)types, locations, and timing of expression in the developing brain are scant. However, emerging single cell technologies, including transcriptomic, spatial biology, spatial high-resolution imaging performed over the brain developmental time, could be transformational in deciphering brain pathologies thereby pharmacology.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Bengi Ruken Yavuz
- Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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2
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Zhao Z, Shuai Y, Wu Y, Xu X, Li M, Wu D. Age-dependent functional development pattern in neonatal brain: An fMRI-based brain entropy study. Neuroimage 2024; 297:120669. [PMID: 38852805 DOI: 10.1016/j.neuroimage.2024.120669] [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: 12/11/2023] [Revised: 04/01/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024] Open
Abstract
The relationship between brain entropy (BEN) and early brain development has been established through animal studies. However, it remains unclear whether the BEN can be used to identify age-dependent functional changes in human neonatal brains and the genetic underpinning of the new neuroimaging marker remains to be elucidated. In this study, we analyzed resting-state fMRI data from the Developing Human Connectome Project, including 280 infants who were scanned at 37.5-43.5 weeks postmenstrual age. The BEN maps were calculated for each subject, and a voxel-wise analysis was conducted using a general linear model to examine the effects of age, sex, and preterm birth on BEN. Additionally, we evaluated the correlation between regional BEN and gene expression levels. Our results demonstrated that the BEN in the sensorimotor-auditory and association cortices, along the 'S-A' axis, was significantly positively correlated with postnatal age (PNA), and negatively correlated with gestational age (GA), respectively. Meanwhile, the BEN in the right rolandic operculum correlated significantly with both GA and PNA. Preterm-born infants exhibited increased BEN values in widespread cortical areas, particularly in the visual-motor cortex, when compared to term-born infants. Moreover, we identified five BEN-related genes (DNAJC12, FIG4, STX12, CETN2, and IRF2BP2), which were involved in protein folding, synaptic vesicle transportation and cell division. These findings suggest that the fMRI-based BEN can serve as an indicator of age-dependent brain functional development in human neonates, which may be influenced by specific genes.
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Affiliation(s)
- Zhiyong Zhao
- Department of Radiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yifan Shuai
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Yihan Wu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Xinyi Xu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Mingyang Li
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Dan Wu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China.
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3
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Villoch-Fernandez J, Martínez-García N, Martín-López M, Maeso-Alonso L, López-Ferreras L, Vazquez-Jimenez A, Muñoz-Hidalgo L, Garcia-Romero N, Sanchez JM, Fernandez A, Ayuso-Sacido A, Marques MM, Marin MC. A novel TAp73-inhibitory compound counteracts stemness features of glioblastoma stem cells. Mol Oncol 2024. [PMID: 39090849 DOI: 10.1002/1878-0261.13694] [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: 12/11/2023] [Revised: 05/01/2024] [Accepted: 06/19/2024] [Indexed: 08/04/2024] Open
Abstract
Glioblastoma (GB) is the most common and fatal type of primary malignant brain tumor for which effective therapeutics are still lacking. GB stem cells, with tumor-initiating and self-renewal capacity, are mostly responsible for GB malignancy, representing a crucial target for therapies. The TP73 gene, which is highly expressed in GB, gives rise to the TAp73 isoform, a pleiotropic protein that regulates neural stem cell biology; however, its role in cancer has been highly controversial. We inactivated TP73 in human GB stem cells and revealed that TAp73 is required for their stemness potential, acting as a regulator of the transcriptional stemness signatures, highlighting TAp73 as a possible therapeutic target. As proof of concept, we identified a novel natural compound with TAp73-inhibitory capacity, which was highly effective against GB stem cells. The treatment reduced GB stem cell-invasion capacity and stem features, at least in part by TAp73 repression. Our data are consistent with a novel paradigm in which hijacking of p73-regulated neurodevelopmental programs, including neural stemness, might sustain tumor progression, pointing out TAp73 as a therapeutic strategy for GB.
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Affiliation(s)
| | - Nicole Martínez-García
- Instituto de Biomedicina y Departamento de Producción Animal, Universidad de León, Spain
| | | | - Laura Maeso-Alonso
- Instituto de Biomedicina y Departamento de Biología Molecular, Universidad de León, Spain
| | - Lorena López-Ferreras
- Instituto de Biomedicina y Departamento de Biología Molecular, Universidad de León, Spain
| | | | - Lisandra Muñoz-Hidalgo
- Department of Pathology, Faculty of Medicine and Odontology, Universidad de Valencia, Spain
| | - Noemí Garcia-Romero
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, Madrid, Spain
| | | | | | - Angel Ayuso-Sacido
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, Madrid, Spain
| | - Margarita M Marques
- Instituto de Desarrollo Ganadero y Sanidad Animal y Departamento de Producción Animal, Universidad de León, Spain
| | - Maria C Marin
- Instituto de Biomedicina y Departamento de Biología Molecular, Universidad de León, Spain
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4
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Morales-Vicente DA, Tahira AC, Woellner-Santos D, Amaral MS, Berzoti-Coelho MG, Verjovski-Almeida S. The Human Developing Cerebral Cortex Is Characterized by an Elevated De Novo Expression of Long Noncoding RNAs in Excitatory Neurons. Mol Biol Evol 2024; 41:msae123. [PMID: 38913688 PMCID: PMC11221658 DOI: 10.1093/molbev/msae123] [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: 11/23/2023] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
The outstanding human cognitive capacities are computed in the cerebral cortex, a mammalian-specific brain region and the place of massive biological innovation. Long noncoding RNAs have emerged as gene regulatory elements with higher evolutionary turnover than mRNAs. The many long noncoding RNAs identified in neural tissues make them candidates for molecular sources of cerebral cortex evolution and disease. Here, we characterized the genomic and cellular shifts that occurred during the evolution of the long noncoding RNA repertoire expressed in the developing cerebral cortex and explored putative roles for these long noncoding RNAs in the evolution of the human brain. Using transcriptomics and comparative genomics, we comprehensively annotated the cortical transcriptomes of humans, rhesus macaques, mice, and chickens and classified human cortical long noncoding RNAs into evolutionary groups as a function of their predicted minimal ages. Long noncoding RNA evolutionary groups showed differences in expression levels, splicing efficiencies, transposable element contents, genomic distributions, and transcription factor binding to their promoters. Furthermore, older long noncoding RNAs showed preferential expression in germinative zones, outer radial glial cells, and cortical inhibitory (GABAergic) neurons. In comparison, younger long noncoding RNAs showed preferential expression in cortical excitatory (glutamatergic) neurons, were enriched in primate and human-specific gene co-expression modules, and were dysregulated in neurodevelopmental disorders. These results suggest different evolutionary routes for older and younger cortical long noncoding RNAs, highlighting old long noncoding RNAs as a possible source of molecular evolution of conserved developmental programs; conversely, we propose that the de novo expression of primate- and human-specific young long noncoding RNAs is a putative source of molecular evolution and dysfunction of cortical excitatory neurons, warranting further investigation.
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Affiliation(s)
- David A Morales-Vicente
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Ana C Tahira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
| | - Daisy Woellner-Santos
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Murilo S Amaral
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
| | - Maria G Berzoti-Coelho
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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5
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Ferreira AFF, Ulrich H, Feng ZP, Sun HS, Britto LR. Neurodegeneration and glial morphological changes are both prevented by TRPM2 inhibition during the progression of a Parkinson's disease mouse model. Exp Neurol 2024; 377:114780. [PMID: 38649091 DOI: 10.1016/j.expneurol.2024.114780] [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: 01/17/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Parkinson's disease (PD) is a neurodegenerative disease characterized by dopaminergic neuron death and neuroinflammation. Emerging evidence points to the involvement of the transient receptor potential melastatin 2 (TRPM2) channel in neuron death and glial activation in several neurodegenerative diseases. However, the involvement of TRPM2 in PD and specifically its relation to the neuroinflammation aspect of the disease remains poorly understood. Here, we hypothesized that AG490, a TRPM2 inhibitor, can be used as a treatment in a mouse model of PD. Mice underwent stereotaxic surgery for 6-hydroxydopamine (6-OHDA) administration in the right striatum. Motor behavioral tests (apomorphine, cylinder, and rotarod) were performed on day 3 post-injection to confirm the PD model induction. AG490 was then daily injected i.p. between days 3 to 6 after surgery. On day 6, motor behavior was assessed again. Substantia nigra (SNc) and striatum (CPu) were collected for immunohistochemistry, immunoblotting, and RT-qPCR analysis on day 7. Our results revealed that AG490 post-treatment reduced motor behavior impairment and nigrostriatal neurodegeneration. In addition, the compound prevented TRPM2 upregulation and changes of the Akt/GSK-3β/caspase-3 signaling pathway. The TRPM2 inhibition also avoids the glial morphology changes observed in the PD group. Remarkably, the morphometrical analysis revealed that the ameboid-shaped microglia, found in 6-OHDA-injected animals, were no longer present in the AG490-treated group. These results indicate that AG490 treatment can reduce dopaminergic neuronal death and suppress neuroinflammation in a PD mouse model. Inhibition of TRPM2 by AG490 could then represent a potential therapeutical strategy to be evaluated for PD treatment.
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Affiliation(s)
- Ana Flavia F Ferreira
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada.
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Zhong-Ping Feng
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Hong-Shuo Sun
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada; Department of Surgery, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Luiz Roberto Britto
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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6
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Ganglberger F, Kargl D, Töpfer M, Hernandez-Lallement J, Lawless N, Fernandez-Albert F, Haubensak W, Bühler K. BrainTACO: an explorable multi-scale multi-modal brain transcriptomic and connectivity data resource. Commun Biol 2024; 7:730. [PMID: 38877144 PMCID: PMC11178817 DOI: 10.1038/s42003-024-06355-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/20/2024] [Indexed: 06/16/2024] Open
Abstract
Exploring the relationships between genes and brain circuitry can be accelerated by joint analysis of heterogeneous datasets from 3D imaging data, anatomical data, as well as brain networks at varying scales, resolutions, and modalities. Generating an integrated view, beyond the individual resources' original purpose, requires the fusion of these data to a common space, and a visualization that bridges the gap across scales. However, despite ever expanding datasets, few platforms for integration and exploration of this heterogeneous data exist. To this end, we present the BrainTACO (Brain Transcriptomic And Connectivity Data) resource, a selection of heterogeneous, and multi-scale neurobiological data spatially mapped onto a common, hierarchical reference space, combined via a holistic data integration scheme. To access BrainTACO, we extended BrainTrawler, a web-based visual analytics framework for spatial neurobiological data, with comparative visualizations of multiple resources. This enables gene expression dissection of brain networks with, to the best of our knowledge, an unprecedented coverage and allows for the identification of potential genetic drivers of connectivity in both mice and humans that may contribute to the discovery of dysconnectivity phenotypes. Hence, BrainTACO reduces the need for time-consuming manual data aggregation often required for computational analyses in script-based toolboxes, and supports neuroscientists by directly leveraging the data instead of preparing it.
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Affiliation(s)
- Florian Ganglberger
- Biomedical Image Informatics, VRVis Research Center, Vienna, Austria
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma, Biberach an der Riss, Germany
| | - Dominic Kargl
- Department of Neuronal Cell Biology, Vienna Medical University, Vienna, Austria
| | - Markus Töpfer
- Biomedical Image Informatics, VRVis Research Center, Vienna, Austria
| | - Julien Hernandez-Lallement
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma, Biberach an der Riss, Germany
| | - Nathan Lawless
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma, Biberach an der Riss, Germany
| | - Francesc Fernandez-Albert
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma, Biberach an der Riss, Germany
| | - Wulf Haubensak
- Department of Neuronal Cell Biology, Vienna Medical University, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Katja Bühler
- Biomedical Image Informatics, VRVis Research Center, Vienna, Austria.
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7
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Singh A, Del-Valle-Anton L, de Juan Romero C, Zhang Z, Ortuño EF, Mahesh A, Espinós A, Soler R, Cárdenas A, Fernández V, Lusby R, Tiwari VK, Borrell V. Gene regulatory landscape of cerebral cortex folding. SCIENCE ADVANCES 2024; 10:eadn1640. [PMID: 38838158 DOI: 10.1126/sciadv.adn1640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/02/2024] [Indexed: 06/07/2024]
Abstract
Folding of the cerebral cortex is a key aspect of mammalian brain development and evolution, and defects are linked to severe neurological disorders. Primary folding occurs in highly stereotyped patterns that are predefined in the cortical germinal zones by a transcriptomic protomap. The gene regulatory landscape governing the emergence of this folding protomap remains unknown. We characterized the spatiotemporal dynamics of gene expression and active epigenetic landscape (H3K27ac) across prospective folds and fissures in ferret. Our results show that the transcriptomic protomap begins to emerge at early embryonic stages, and it involves cell-fate signaling pathways. The H3K27ac landscape reveals developmental cell-fate restriction and engages known developmental regulators, including the transcription factor Cux2. Manipulating Cux2 expression in cortical progenitors changed their proliferation and the folding pattern in ferret, caused by selective transcriptional changes as revealed by single-cell RNA sequencing analyses. Our findings highlight the key relevance of epigenetic mechanisms in defining the patterns of cerebral cortex folding.
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Affiliation(s)
- Aditi Singh
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK
| | - Lucia Del-Valle-Anton
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Camino de Juan Romero
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Ziyi Zhang
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK
| | - Eduardo Fernández Ortuño
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Arun Mahesh
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK
- Institute for Molecular Medicine, University of Southern Denmark, Odense M, Denmark
| | - Alexandre Espinós
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Rafael Soler
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Adrián Cárdenas
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Virginia Fernández
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
| | - Ryan Lusby
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK
| | - Vijay K Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK
- Institute for Molecular Medicine, University of Southern Denmark, Odense M, Denmark
- Danish Institute for Advanced Study (DIAS), Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant 03550, Spain
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8
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Zhang L, Xiong Z, Xiao M. A Review of the Application of Spatial Transcriptomics in Neuroscience. Interdiscip Sci 2024; 16:243-260. [PMID: 38374297 DOI: 10.1007/s12539-024-00603-4] [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: 10/10/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Since spatial transcriptomics can locate and distinguish the gene expression of functional genes in special regions and tissue, it is important for us to investigate the brain development, the development mechanism of brain diseases, and the relationship between brain structure and function in Neuroscience (or Brain science). While previous studies have introduced the crucial spatial transcriptomic techniques and data analysis methods, there are few studies to comprehensively overview the key methods, data resources, and technological applications of spatial transcriptomics in Neuroscience. For these reasons, we first investigate several common spatial transcriptomic data analysis approaches and data resources. Second, we introduce the applications of the spatial transcriptomic data analysis approaches in Neuroscience. Third, we summarize the integrating spatial transcriptomics with other technologies in Neuroscience. Finally, we discuss the challenges and future research directions of spatial transcriptomics in Neuroscience.
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Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Zhenqi Xiong
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Ming Xiao
- College of Computer Science, Sichuan University, Chengdu, 610065, China.
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9
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Wu T, Wang L, Jian C, Zhang Z, Zeng R, Mi B, Liu G, Zhang Y, Shi C. A distinct "repair" role of regulatory T cells in fracture healing. Front Med 2024; 18:516-537. [PMID: 38491211 DOI: 10.1007/s11684-023-1024-8] [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: 04/17/2023] [Accepted: 07/20/2023] [Indexed: 03/18/2024]
Abstract
Regulatory T cells (Tregs) suppress immune responses and inflammation. Here, we described the distinct nonimmunological role of Tregs in fracture healing. The recruitment from the circulation pool, peripheral induction, and local expansion rapidly enriched Tregs in the injured bone. The Tregs in the injured bone displayed superiority in direct osteogenesis over Tregs from lymphoid organs. Punctual depletion of Tregs compromised the fracture healing process, which leads to increased bone nonunion. In addition, bone callus Tregs showed unique T-cell receptor repertoires. Amphiregulin was the most overexpressed protein in bone callus Tregs, and it can directly facilitate the proliferation and differentiation of osteogenic precursor cells by activation of phosphatidylinositol 3-kinase/protein kinase B signaling pathways. The results of loss- and gain-function studies further evidenced that amphiregulin can reverse the compromised healing caused by Treg dysfunction. Tregs also enriched in patient bone callus and amphiregulin can promote the osteogenesis of human pre-osteoblastic cells. Our findings indicate the distinct and nonredundant role of Tregs in fracture healing, which will provide a new therapeutic target and strategy in the clinical treatment of fractures.
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Affiliation(s)
- Tingting Wu
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan, 430022, China
| | - Lulu Wang
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan, 430022, China
| | - Chen Jian
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan, 430022, China
| | - Zhenhe Zhang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ruiyin Zeng
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bobin Mi
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Guohui Liu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yu Zhang
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan, 430022, China
| | - Chen Shi
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan, 430022, China.
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10
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McCluskey KE, Stovell KM, Law K, Kostyanovskaya E, Schmidt J, Exner CRT, Dea J, Brimble E, State MW, Willsey AJ, Willsey HR. Autism gene variants disrupt enteric neuron migration and cause gastrointestinal dysmotility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.593642. [PMID: 38854068 PMCID: PMC11160671 DOI: 10.1101/2024.05.28.593642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The comorbidity of autism spectrum disorders and severe gastrointestinal symptoms is well-established, yet the molecular underpinnings remain unknown. The identification of high-confidence large-effect autism risk genes offers the opportunity to identify convergent, underlying biology by studying these genes in the context of the gastrointestinal system. Here we show that the expression of these genes is enriched in human prenatal gut neurons as well as their migratory progenitors, suggesting that the development and/or function of these neurons may be disrupted by autism-associated pathogenic variants, leading to gastrointestinal dysfunction. Here we document the prevalence of gastrointestinal issues in patients with large-effect variants in sixteen of these genes, highlighting dysmotility, consistent with potential enteric neuron dysfunction. Using the high-throughput diploid frog Xenopus tropicalis , we individually target five of these genes ( SYNGAP1, CHD8, SCN2A, CHD2 , and DYRK1A ) and observe disrupted enteric neuronal progenitor migration for each. More extensive analysis of DYRK1A reveals that perturbation causes gut dysmotility in vivo , which can be ameliorated by treatment with a selective serotonin reuptake inhibitor (escitalopram) or a serotonin receptor 6 agonist, identified by in vivo drug screening. This work suggests that atypical development of enteric neurons contributes to the gastrointestinal distress commonly seen in individuals with autism and that increasing serotonin signaling may be a productive therapeutic avenue.
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11
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Greenwald AC, Darnell NG, Hoefflin R, Simkin D, Mount CW, Gonzalez Castro LN, Harnik Y, Dumont S, Hirsch D, Nomura M, Talpir T, Kedmi M, Goliand I, Medici G, Laffy J, Li B, Mangena V, Keren-Shaul H, Weller M, Addadi Y, Neidert MC, Suvà ML, Tirosh I. Integrative spatial analysis reveals a multi-layered organization of glioblastoma. Cell 2024; 187:2485-2501.e26. [PMID: 38653236 PMCID: PMC11088502 DOI: 10.1016/j.cell.2024.03.029] [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: 06/16/2023] [Revised: 01/11/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Glioma contains malignant cells in diverse states. Here, we combine spatial transcriptomics, spatial proteomics, and computational approaches to define glioma cellular states and uncover their organization. We find three prominent modes of organization. First, gliomas are composed of small local environments, each typically enriched with one major cellular state. Second, specific pairs of states preferentially reside in proximity across multiple scales. This pairing of states is consistent across tumors. Third, these pairwise interactions collectively define a global architecture composed of five layers. Hypoxia appears to drive the layers, as it is associated with a long-range organization that includes all cancer cell states. Accordingly, tumor regions distant from any hypoxic/necrotic foci and tumors that lack hypoxia such as low-grade IDH-mutant glioma are less organized. In summary, we provide a conceptual framework for the organization of cellular states in glioma, highlighting hypoxia as a long-range tissue organizer.
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Affiliation(s)
- Alissa C Greenwald
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Galili Darnell
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rouven Hoefflin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dor Simkin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Christopher W Mount
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - L Nicolas Gonzalez Castro
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Yotam Harnik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sydney Dumont
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dana Hirsch
- Immunohistochemistry Unit, Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Masashi Nomura
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tom Talpir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Kedmi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Goliand
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Gioele Medici
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julie Laffy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Baoguo Li
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Vamsi Mangena
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hadas Keren-Shaul
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Weller
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Yoseph Addadi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Marian C Neidert
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Neurosurgery, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Mario L Suvà
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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12
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Lee MK, Azizgolshani N, Shapiro JA, Nguyen LN, Kolling FW, Zanazzi GJ, Frost HR, Christensen BC. Identifying tumor type and cell type-specific gene expression alterations in pediatric central nervous system tumors. Nat Commun 2024; 15:3634. [PMID: 38688897 PMCID: PMC11061189 DOI: 10.1038/s41467-024-47712-8] [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: 02/18/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
Central nervous system (CNS) tumors are the leading cause of pediatric cancer death, and these patients have an increased risk for developing secondary neoplasms. Due to the low prevalence of pediatric CNS tumors, major advances in targeted therapies have been lagging compared to other adult tumors. We collect single nuclei RNA-seq data from 84,700 nuclei of 35 pediatric CNS tumors and three non-tumoral pediatric brain tissues and characterize tumor heterogeneity and transcriptomic alterations. We distinguish cell subpopulations associated with specific tumor types including radial glial cells in ependymomas and oligodendrocyte precursor cells in astrocytomas. In tumors, we observe pathways important in neural stem cell-like populations, a cell type previously associated with therapy resistance. Lastly, we identify transcriptomic alterations among pediatric CNS tumor types compared to non-tumor tissues, while accounting for cell type effects on gene expression. Our results suggest potential tumor type and cell type-specific targets for pediatric CNS tumor treatment. Here we address current gaps in understanding single nuclei gene expression profiles of previously under-investigated tumor types and enhance current knowledge of gene expression profiles of single cells of various pediatric CNS tumors.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Joshua A Shapiro
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA, USA
| | - Lananh N Nguyen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - George J Zanazzi
- Dartmouth Cancer Center, Lebanon, NH, USA
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Hildreth Robert Frost
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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13
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Baig S, Nadaf J, Allache R, Le PU, Luo M, Djedid A, Nkili-Meyong A, Safisamghabadi M, Prat A, Antel J, Guiot MC, Petrecca K. Identity and nature of neural stem cells in the adult human subventricular zone. iScience 2024; 27:109342. [PMID: 38495819 PMCID: PMC10940989 DOI: 10.1016/j.isci.2024.109342] [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: 10/03/2023] [Revised: 12/26/2023] [Accepted: 02/22/2024] [Indexed: 03/19/2024] Open
Abstract
The existence of neural stem cells (NSCs) in adult human brain neurogenic regions remains unresolved. To address this, we created a cell atlas of the adult human subventricular zone (SVZ) derived from fresh neurosurgical samples using single-cell transcriptomics. We discovered 2 adult radial glia (RG)-like populations, aRG1 and aRG2. aRG1 shared features with fetal early RG (eRG) and aRG2 were transcriptomically similar to fetal outer RG (oRG). We also captured early neuronal and oligodendrocytic NSC states. We found that the biological programs driven by their transcriptomes support their roles as early lineage NSCs. Finally, we show that these NSCs have the potential to transition between states and along lineage trajectories. These data reveal that multipotent NSCs reside in the adult human SVZ.
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Affiliation(s)
- Salma Baig
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Javad Nadaf
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Redouane Allache
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Phuong U. Le
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Michael Luo
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Annisa Djedid
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Andriniaina Nkili-Meyong
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Maryam Safisamghabadi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Alex Prat
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC H2X0A9, Canada
| | - Jack Antel
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Marie-Christine Guiot
- Department of Neuropathology, Montreal Neurological Institute-Hospital, McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
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14
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Shen Y, Shao M, Hao ZZ, Huang M, Xu N, Liu S. Multimodal Nature of the Single-cell Primate Brain Atlas: Morphology, Transcriptome, Electrophysiology, and Connectivity. Neurosci Bull 2024; 40:517-532. [PMID: 38194157 PMCID: PMC11003949 DOI: 10.1007/s12264-023-01160-4] [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: 03/22/2023] [Accepted: 09/23/2023] [Indexed: 01/10/2024] Open
Abstract
Primates exhibit complex brain structures that augment cognitive function. The neocortex fulfills high-cognitive functions through billions of connected neurons. These neurons have distinct transcriptomic, morphological, and electrophysiological properties, and their connectivity principles vary. These features endow the primate brain atlas with a multimodal nature. The recent integration of next-generation sequencing with modified patch-clamp techniques is revolutionizing the way to census the primate neocortex, enabling a multimodal neuronal atlas to be established in great detail: (1) single-cell/single-nucleus RNA-seq technology establishes high-throughput transcriptomic references, covering all major transcriptomic cell types; (2) patch-seq links the morphological and electrophysiological features to the transcriptomic reference; (3) multicell patch-clamp delineates the principles of local connectivity. Here, we review the applications of these technologies in the primate neocortex and discuss the current advances and tentative gaps for a comprehensive understanding of the primate neocortex.
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Affiliation(s)
- Yuhui Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mingting Shao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhao-Zhe Hao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mengyao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Nana Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, 510080, China.
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15
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Perez-Corredor P, Vanderleest TE, Vacano GN, Sanchez JS, Villalba-Moreno ND, Marino C, Krasemann S, Mendivil-Perez MA, Aguillón D, Jiménez-Del-Río M, Baena A, Sepulveda-Falla D, Lopera F, Quiroz YT, Arboleda-Velasquez JF, Mazzarino RC. APOE3 Christchurch modulates β-catenin/Wnt signaling in iPS cell-derived cerebral organoids from Alzheimer's cases. Front Mol Neurosci 2024; 17:1373568. [PMID: 38571814 PMCID: PMC10987717 DOI: 10.3389/fnmol.2024.1373568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 02/22/2024] [Indexed: 04/05/2024] Open
Abstract
A patient with the PSEN1 E280A mutation and homozygous for APOE3 Christchurch (APOE3Ch) displayed extreme resistance to Alzheimer's disease (AD) cognitive decline and tauopathy, despite having a high amyloid burden. To further investigate the differences in biological processes attributed to APOE3Ch, we generated induced pluripotent stem (iPS) cell-derived cerebral organoids from this resistant case and a non-protected control, using CRISPR/Cas9 gene editing to modulate APOE3Ch expression. In the APOE3Ch cerebral organoids, we observed a protective pattern from early tau phosphorylation. ScRNA sequencing revealed regulation of Cadherin and Wnt signaling pathways by APOE3Ch, with immunostaining indicating elevated β-catenin protein levels. Further in vitro reporter assays unexpectedly demonstrated that ApoE3Ch functions as a Wnt3a signaling enhancer. This work uncovered a neomorphic molecular mechanism of protection of ApoE3 Christchurch, which may serve as the foundation for the future development of protected case-inspired therapeutics targeting AD and tauopathies.
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Affiliation(s)
- Paula Perez-Corredor
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology at Harvard Medical School, Boston, MA, United States
| | - Timothy E. Vanderleest
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology at Harvard Medical School, Boston, MA, United States
| | | | - Justin S. Sanchez
- Massachusetts General Hospital and Department of Neurology at Harvard Medical School, Boston, MA, United States
| | - Nelson D. Villalba-Moreno
- Molecular Neuropathology of Alzheimer’s Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Marino
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology at Harvard Medical School, Boston, MA, United States
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - David Aguillón
- The Neuroscience Group of Antioquia, University of Antioquia, Medellín, Colombia
| | | | - Ana Baena
- The Neuroscience Group of Antioquia, University of Antioquia, Medellín, Colombia
| | - Diego Sepulveda-Falla
- Molecular Neuropathology of Alzheimer’s Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Francisco Lopera
- The Neuroscience Group of Antioquia, University of Antioquia, Medellín, Colombia
| | - Yakeel T. Quiroz
- Massachusetts General Hospital and Department of Neurology at Harvard Medical School, Boston, MA, United States
- The Neuroscience Group of Antioquia, University of Antioquia, Medellín, Colombia
- Massachusetts General Hospital and Department of Psychiatry at Harvard Medical School, Boston, MA, United States
| | - Joseph F. Arboleda-Velasquez
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology at Harvard Medical School, Boston, MA, United States
| | - Randall C. Mazzarino
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology at Harvard Medical School, Boston, MA, United States
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16
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Fan Q, Wang H, Gu T, Liu H, Deng P, Li B, Yang H, Mao Y, Shao Z. Modeling the precise interaction of glioblastoma with human brain region-specific organoids. iScience 2024; 27:109111. [PMID: 38390494 PMCID: PMC10882168 DOI: 10.1016/j.isci.2024.109111] [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: 07/21/2023] [Revised: 09/18/2023] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
Glioblastoma is a highly aggressive malignant tumor of the central nervous system, but the interaction between glioblastoma and different types of neurons remains unclear. Here, we established a co-culture model in vitro using 3D printed molds with microchannels, in which glioblastoma organoids (GB), dorsal forebrain organoids (DO, mainly composed of excitatory neurons), and ventral forebrain organoids (VO, mainly composed of inhibitory neurons) were assembled. Our results indicate that DO has a greater impact on altered gene expression profiles of GB, resulting in increased invasive potential. GB cells preferentially invaded DO along axons, whereas this phenomenon was not observed in VO. Furthermore, GB cells selectively inhibited neurite outgrowth in DOs and reduced the expression of the vesicular GABA transporter (VGAT), leading to neuronal hyperexcitability. By revealing how glioblastoma interacts with brain cells, our study provides a more comprehensive understanding of this disease.
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Affiliation(s)
- Qi Fan
- Institutes for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Fudan University, Shanghai, China
| | - Hanze Wang
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Tianyi Gu
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 201203, China
| | - Huihui Liu
- Institutes for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Fudan University, Shanghai, China
| | - Peng Deng
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Bo Li
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Hui Yang
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhicheng Shao
- Institutes for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Fudan University, Shanghai, China
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17
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Ball G, Oldham S, Kyriakopoulou V, Williams LZJ, Karolis V, Price A, Hutter J, Seal ML, Alexander-Bloch A, Hajnal JV, Edwards AD, Robinson EC, Seidlitz J. Molecular signatures of cortical expansion in the human fetal brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580198. [PMID: 38405710 PMCID: PMC10888819 DOI: 10.1101/2024.02.13.580198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The third trimester of human gestation is characterised by rapid increases in brain volume and cortical surface area. A growing catalogue of cells in the prenatal brain has revealed remarkable molecular diversity across cortical areas.1,2 Despite this, little is known about how this translates into the patterns of differential cortical expansion observed in humans during the latter stages of gestation. Here we present a new resource, μBrain, to facilitate knowledge translation between molecular and anatomical descriptions of the prenatal developing brain. Built using generative artificial intelligence, μBrain is a three-dimensional cellular-resolution digital atlas combining publicly-available serial sections of the postmortem human brain at 21 weeks gestation3 with bulk tissue microarray data, sampled across 29 cortical regions and 5 transient tissue zones.4 Using μBrain, we evaluate the molecular signatures of preferentially-expanded cortical regions during human gestation, quantified in utero using magnetic resonance imaging (MRI). We find that differences in the rates of expansion across cortical areas during gestation respect anatomical and evolutionary boundaries between cortical types5 and are founded upon extended periods of upper-layer cortical neuron migration that continue beyond mid-gestation. We identify a set of genes that are upregulated from mid-gestation and highly expressed in rapidly expanding neocortex, which are implicated in genetic disorders with cognitive sequelae. Our findings demonstrate a spatial coupling between areal differences in the timing of neurogenesis and rates of expansion across the neocortical sheet during the prenatal epoch. The μBrain atlas is available from: https://garedaba.github.io/micro-brain/ and provides a new tool to comprehensively map early brain development across domains, model systems and resolution scales.
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Affiliation(s)
- G Ball
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - S Oldham
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Australia
| | - V Kyriakopoulou
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - L Z J Williams
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - V Karolis
- Centre for the Developing Brain, King's College London, London, UK
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - A Price
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - J Hutter
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - M L Seal
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - A Alexander-Bloch
- Department of Child and Adolescent Psychiatry and Behavioral Sciences, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA
| | - J V Hajnal
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - A D Edwards
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - E C Robinson
- Centre for the Developing Brain, King's College London, London, UK
- School of Biomedical Engineering & Imaging Science, King's College London, London, UK
| | - J Seidlitz
- Department of Child and Adolescent Psychiatry and Behavioral Sciences, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA
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18
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Monnier L, Cournède PH. A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization. PLoS Comput Biol 2024; 20:e1011880. [PMID: 38386700 PMCID: PMC10914288 DOI: 10.1371/journal.pcbi.1011880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 03/05/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technology produces an unprecedented resolution at the level of a unique cell, raising great hopes in medicine. Nevertheless, scRNA-seq data suffer from high variations due to the experimental conditions, called batch effects, preventing any aggregated downstream analysis. Adversarial Information Factorization provides a robust batch-effect correction method that does not rely on prior knowledge of the cell types nor a specific normalization strategy while being adapted to any downstream analysis task. It compares to and even outperforms state-of-the-art methods in several scenarios: low signal-to-noise ratio, batch-specific cell types with few cells, and a multi-batches dataset with imbalanced batches and batch-specific cell types. Moreover, it best preserves the relative gene expression between cell types, yielding superior differential expression analysis results. Finally, in a more complex setting of a Leukemia cohort, our method preserved most of the underlying biological information for each patient while aligning the batches, improving the clustering metrics in the aggregated dataset.
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Affiliation(s)
- Lily Monnier
- Paris-Saclay University, CentraleSupélec, Laboratory of Mathematics and Computer Science (MICS), Gif-sur-Yvette, France
| | - Paul-Henry Cournède
- Paris-Saclay University, CentraleSupélec, Laboratory of Mathematics and Computer Science (MICS), Gif-sur-Yvette, France
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19
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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20
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Pang Z, Cravatt BF, Ye L. Deciphering Drug Targets and Actions with Single-Cell and Spatial Resolution. Annu Rev Pharmacol Toxicol 2024; 64:507-526. [PMID: 37722721 DOI: 10.1146/annurev-pharmtox-033123-123610] [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] [Indexed: 09/20/2023]
Abstract
Recent advances in chemical, molecular, and genetic approaches have provided us with an unprecedented capacity to identify drug-target interactions across the whole proteome and genome. Meanwhile, rapid developments of single-cell and spatial omics technologies are revolutionizing our understanding of the molecular architecture of biological systems. However, a significant gap remains in how we align our understanding of drug actions, traditionally based on molecular affinities, with the in vivo cellular and spatial tissue heterogeneity revealed by these newer techniques. Here, we review state-of-the-art methods for profiling drug-target interactions and emerging multiomics tools to delineate the tissue heterogeneity at single-cell resolution. Highlighting the recent technical advances enabling high-resolution, multiplexable in situ small-molecule drug imaging (clearing-assisted tissue click chemistry, or CATCH), we foresee the integration of single-cell and spatial omics platforms, data, and concepts into the future framework of defining and understanding in vivo drug-target interactions and mechanisms of actions.
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Affiliation(s)
- Zhengyuan Pang
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California, USA;
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA;
| | - Li Ye
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California, USA;
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
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21
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Yang YT, Gan Z, Zhang J, Zhao X, Yang Y, Han S, Wu W, Zhao XM. STAB2: an updated spatio-temporal cell atlas of the human and mouse brain. Nucleic Acids Res 2024; 52:D1033-D1041. [PMID: 37904591 PMCID: PMC10767951 DOI: 10.1093/nar/gkad955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
The brain is constituted of heterogeneous types of neuronal and non-neuronal cells, which are organized into distinct anatomical regions, and show precise regulation of gene expression during development, aging and function. In the current database release, STAB2 provides a systematic cellular map of the human and mouse brain by integrating recently published large-scale single-cell and single-nucleus RNA-sequencing datasets from diverse regions and across lifespan. We applied a hierarchical strategy of unsupervised clustering on the integrated single-cell transcriptomic datasets to precisely annotate the cell types and subtypes in the human and mouse brain. Currently, STAB2 includes 71 and 61 different cell subtypes defined in the human and mouse brain, respectively. It covers 63 subregions and 15 developmental stages of human brain, and 38 subregions and 30 developmental stages of mouse brain, generating a comprehensive atlas for exploring spatiotemporal transcriptomic dynamics in the mammalian brain. We also augmented web interfaces for querying and visualizing the gene expression in specific cell types. STAB2 is freely available at https://mai.fudan.edu.cn/stab2.
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Affiliation(s)
- Yucheng T Yang
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang 313000, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, Zhejiang 313000, China
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Ziquan Gan
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Jinglong Zhang
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Xingzhong Zhao
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Yifan Yang
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Shuwen Han
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang 313000, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, Zhejiang 313000, China
| | - Wei Wu
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang 313000, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, Zhejiang 313000, China
| | - Xing-Ming Zhao
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang 313000, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, Zhejiang 313000, China
- Institute of Science and Technology for Brain‐Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai 200032, China
- International Human Phenome Institutes (Shanghai), Shanghai 200433, China
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22
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Wang J, Yu J, Wang M, Zhang L, Yang K, Du X, Wu J, Wang X, Li F, Qiu Z. Discovery and Validation of Novel Genes in a Large Chinese Autism Spectrum Disorder Cohort. Biol Psychiatry 2023; 94:792-803. [PMID: 37393044 DOI: 10.1016/j.biopsych.2023.06.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 06/02/2023] [Accepted: 06/20/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a neurodevelopmental disorder that causes impairments in social communication and stereotypical behaviors, often accompanied by developmental delay or intellectual disability. A growing body of evidence suggests that ASD is highly heritable, and genetic studies have defined numerous risk genes. However, most studies have been conducted with individuals of European and Hispanic ancestry, and there is a lack of genetic analyses of ASD in the East Asian population. METHODS We performed whole-exome sequencing on 772 Chinese ASD trios and combined the data with a previous study of 369 Chinese ASD trios, identifying de novo variants in 1141 ASD trios. We used single-cell RNA sequencing analysis to identify the cell types in which ASD-related genes were enriched. In addition, we validated the function of a candidate high-functioning autism gene in mouse models using genetic approaches. RESULTS Our findings showed that ASD without developmental delay or intellectual disability carried fewer disruptive de novo variants than ASD with developmental delay or intellectual disability. Moreover, we identified 9 novel ASD candidate genes that were not present in the current ASD gene database. We further validated one such novel ASD candidate gene, SLC35G1, by showing that mice harboring a heterozygous deletion of Slc35g1 exhibited defects in interactive social behaviors. CONCLUSIONS Our work nominates novel ASD candidate genes and emphasizes the importance of genome-wide genetic studies with ASD cohorts of different ancestries to reveal the comprehensive genetic architecture of ASD.
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Affiliation(s)
- Jincheng Wang
- Department of Developmental and Behavioural Pediatric & Child Primary Care, Brain and Behavioural Research Unit of Shanghai Institute for Pediatric Research, Institute of Autism, and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juehua Yu
- Department of Developmental and Behavioural Pediatric & Child Primary Care, Brain and Behavioural Research Unit of Shanghai Institute for Pediatric Research, Institute of Autism, and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengdi Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lingli Zhang
- Department of Developmental and Behavioural Pediatric & Child Primary Care, Brain and Behavioural Research Unit of Shanghai Institute for Pediatric Research, Institute of Autism, and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kan Yang
- Department of Developmental and Behavioural Pediatric & Child Primary Care, Brain and Behavioural Research Unit of Shanghai Institute for Pediatric Research, Institute of Autism, and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiujuan Du
- Department of Developmental and Behavioural Pediatric & Child Primary Care, Brain and Behavioural Research Unit of Shanghai Institute for Pediatric Research, Institute of Autism, and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaoqun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Fei Li
- Department of Developmental and Behavioural Pediatric & Child Primary Care, Brain and Behavioural Research Unit of Shanghai Institute for Pediatric Research, Institute of Autism, and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Zilong Qiu
- Department of Developmental and Behavioural Pediatric & Child Primary Care, Brain and Behavioural Research Unit of Shanghai Institute for Pediatric Research, Institute of Autism, and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; Songjiang Research Institute, Songjiang District Central Hospital, and Institute of Autism, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Clinical Neuroscience Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
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23
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Tian Y, Xu G, Zhang J, Chen K, Liu S. Nodal properties of the resting-state brain functional network in childhood and adolescence. J Neuroimaging 2023; 33:1015-1023. [PMID: 37735776 DOI: 10.1111/jon.13155] [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: 05/31/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND AND PURPOSE Changes in the topological properties of brain functional network nodes during childhood and adolescence can provide more detailed and intuitive information on the rules of brain development. This study aims to explore the characteristics of nodal attributes in child and adolescent brain functional networks and analyze the correlation between nodal attributes in different brain regions and age. METHODS Forty-two healthy volunteers aged 6-18 years who were right-handed primary and middle school students were recruited, and the subgroup analysis included children (6-12 years, n = 19) and adolescents (13-18 years, n = 23). Resting-state functional magnetic resonance imaging data were collected using a 3.0 Tesla MRI scanner. The topological properties of the functional brain network were analyzed using graph theory. RESULTS Compared with the children group, the degree centrality and nodal efficiency of multiple brain regions in the adolescent group were significantly increased, and the nodal shortest path was reduced (q<0.05, false discovery rate corrected). These brain regions were widely distributed in the whole brain and significantly correlated with age. Compared with the children group, reduced degree centralities were observed in the left dorsolateral fusiform gyrus, left rostral cuneus gyrus, and right medial superior occipital gyrus. CONCLUSION The transmission efficiency of the brain's core network gradually increased, and the subnetwork function gradually improved in children and adolescents with age. The functional development of each brain area in the occipital visual cortex was uneven and there was functional differentiation within the occipital visual cortex.
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Affiliation(s)
- Yu Tian
- Department of Radiology, the Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Radiology, the Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Gaoqiang Xu
- Department of Radiology, the Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jing Zhang
- Department of Radiology, the Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Kuntao Chen
- Department of Radiology, the Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
| | - Songjiang Liu
- Department of Radiology, the Affiliated Hospital of Zunyi Medical University, Zunyi, China
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24
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Konopka G, Bhaduri A. Functional genomics and systems biology in human neuroscience. Nature 2023; 623:274-282. [PMID: 37938705 DOI: 10.1038/s41586-023-06686-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/27/2023] [Indexed: 11/09/2023]
Abstract
Neuroscience research has entered a phase of key discoveries in the realm of neurogenomics owing to strong financial and intellectual support for resource building and tool development. The previous challenge of tissue heterogeneity has been met with the application of techniques that can profile individual cells at scale. Moreover, the ability to perturb genes, gene regulatory elements and neuronal activity in a cell-type-specific manner has been integrated with gene expression studies to uncover the functional underpinnings of the genome at a systems level. Although these insights have necessarily been grounded in model systems, we now have the opportunity to apply these approaches in humans and in human tissue, thanks to advances in human genetics, brain imaging and tissue collection. We acknowledge that there will probably always be limits to the extent to which we can apply the genomic tools developed in model systems to human neuroscience; however, as we describe in this Perspective, the neuroscience field is now primed with an optimal foundation for tackling this ambitious challenge. The application of systems-level network analyses to these datasets will facilitate a deeper appreciation of human neurogenomics that cannot otherwise be achieved from directly observable phenomena.
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Affiliation(s)
- Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
- Peter O'Donnell Jr Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA.
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25
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Yuan B, Wang M, Wu X, Cheng P, Zhang R, Zhang R, Yu S, Zhang J, Du Y, Wang X, Qiu Z. Identification of de novo Mutations in the Chinese Autism Spectrum Disorder Cohort via Whole-Exome Sequencing Unveils Brain Regions Implicated in Autism. Neurosci Bull 2023; 39:1469-1480. [PMID: 36881370 PMCID: PMC10533446 DOI: 10.1007/s12264-023-01037-6] [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: 09/19/2022] [Accepted: 10/30/2022] [Indexed: 03/08/2023] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder characterized by deficits in social interactions and repetitive behaviors. Although hundreds of ASD risk genes, implicated in synaptic formation and transcriptional regulation, have been identified through human genetic studies, the East Asian ASD cohorts are still under-represented in genome-wide genetic studies. Here, we applied whole-exome sequencing to 369 ASD trios including probands and unaffected parents of Chinese origin. Using a joint-calling analytical pipeline based on GATK toolkits, we identified numerous de novo mutations including 55 high-impact variants and 165 moderate-impact variants, as well as de novo copy number variations containing known ASD-related genes. Importantly, combined with single-cell sequencing data from the developing human brain, we found that the expression of genes with de novo mutations was specifically enriched in the pre-, post-central gyrus (PRC, PC) and banks of the superior temporal (BST) regions in the human brain. By further analyzing the brain imaging data with ASD and healthy controls, we found that the gray volume of the right BST in ASD patients was significantly decreased compared to healthy controls, suggesting the potential structural deficits associated with ASD. Finally, we found a decrease in the seed-based functional connectivity between BST/PC/PRC and sensory areas, the insula, as well as the frontal lobes in ASD patients. This work indicated that combinatorial analysis with genome-wide screening, single-cell sequencing, and brain imaging data reveal the brain regions contributing to the etiology of ASD.
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Affiliation(s)
- Bo Yuan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Mengdi Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinran Wu
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Peipei Cheng
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Ran Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ran Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Shunying Yu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Jie Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.
| | - Yasong Du
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China.
| | - Xiaoqun Wang
- Beijing Normal University, Beijing, 100875, China.
| | - Zilong Qiu
- Songjiang Research Institute, Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China.
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200032, China.
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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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27
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Zhuang XL, Zhang JJ, Shao Y, Ye Y, Chen CY, Zhou L, Wang ZB, Luo X, Su B, Yao YG, Cooper DN, Hu BX, Wang L, Qi XG, Lin J, Zhang GJ, Wang W, Sheng N, Wu DD. Integrative Omics Reveals Rapidly Evolving Regulatory Sequences Driving Primate Brain Evolution. Mol Biol Evol 2023; 40:msad173. [PMID: 37494289 PMCID: PMC10404817 DOI: 10.1093/molbev/msad173] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
Although the continual expansion of the brain during primate evolution accounts for our enhanced cognitive capabilities, the drivers of brain evolution have scarcely been explored in these ancestral nodes. Here, we performed large-scale comparative genomic, transcriptomic, and epigenomic analyses to investigate the evolutionary alterations acquired by brain genes and provide comprehensive listings of innovatory genetic elements along the evolutionary path from ancestral primates to human. The regulatory sequences associated with brain-expressed genes experienced rapid change, particularly in the ancestor of the Simiiformes. Extensive comparisons of single-cell and bulk transcriptomic data between primate and nonprimate brains revealed that these regulatory sequences may drive the high expression of certain genes in primate brains. Employing in utero electroporation into mouse embryonic cortex, we show that the primate-specific brain-biased gene BMP7 was recruited, probably in the ancestor of the Simiiformes, to regulate neuronal proliferation in the primate ventricular zone. Our study provides a comprehensive listing of genes and regulatory changes along the brain evolution lineage of ancestral primates leading to human. These data should be invaluable for future functional studies that will deepen our understanding not only of the genetic basis of human brain evolution but also of inherited disease.
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Affiliation(s)
- Xiao-Lin Zhuang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jin-Jin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yaxin Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chun-Yan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Center of Evolutionary & Organismal Biology, and Women’s Hospital at Zhejiang University School of Medicine, Hangzhou, Guangdong, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Guangdong, China
| | - Zheng-bo Wang
- Yunnan Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yong-Gang Yao
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, Wales, UK
| | - Ben-Xia Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lu Wang
- College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Xiao-Guang Qi
- College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Jiangwei Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Guo-Jie Zhang
- Center of Evolutionary & Organismal Biology, and Women’s Hospital at Zhejiang University School of Medicine, Hangzhou, Guangdong, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Guangdong, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Nengyin Sheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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Voss AJ, Lanjewar SN, Sampson MM, King A, Hill EJ, Sing A, Sojka C, Bhatia TN, Spangle JM, Sloan SA. Identification of ligand-receptor pairs that drive human astrocyte development. Nat Neurosci 2023; 26:1339-1351. [PMID: 37460808 PMCID: PMC11046429 DOI: 10.1038/s41593-023-01375-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/08/2023] [Indexed: 08/05/2023]
Abstract
Extrinsic signaling between diverse cell types is crucial for nervous system development. Ligand binding is a key driver of developmental processes. Nevertheless, it remains a significant challenge to disentangle which and how extrinsic signals act cooperatively to affect changes in recipient cells. In the developing human brain, cortical progenitors transition from neurogenesis to gliogenesis in a stereotyped sequence that is in part influenced by extrinsic ligands. Here we used published transcriptomic data to identify and functionally test five ligand-receptor pairs that synergistically drive human astrogenesis. We validate the synergistic contributions of TGFβ2, NLGN1, TSLP, DKK1 and BMP4 ligands on astrocyte development in both hCOs and primary fetal tissue. We confirm that the cooperative capabilities of these five ligands are greater than their individual capacities. Additionally, we discovered that their combinatorial effects converge in part on the mTORC1 signaling pathway, resulting in transcriptomic and morphological features of astrocyte development. Our data-driven framework can leverage single-cell and bulk genomic data to generate and test functional hypotheses surrounding cell-cell communication regulating neurodevelopmental processes.
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Affiliation(s)
- Anna J Voss
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Samantha N Lanjewar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Maureen M Sampson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alexia King
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Emily J Hill
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Anson Sing
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Caitlin Sojka
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Tarun N Bhatia
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer M Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Steven A Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
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Proshchina A, Kharlamova A, Krivova Y, Godovalova O, Otlyga D, Gulimova V, Otlyga E, Junemann O, Sonin G, Saveliev S. Neuromorphological Atlas of Human Prenatal Brain Development: White Paper. Life (Basel) 2023; 13:life13051182. [PMID: 37240827 DOI: 10.3390/life13051182] [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: 03/29/2023] [Revised: 05/06/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Recent morphological data on human brain development are quite fragmentary. However, they are highly requested for a number of medical practices, educational programs, and fundamental research in the fields of embryology, cytology and histology, neurology, physiology, path anatomy, neonatology, and others. This paper provides the initial information on the new online Human Prenatal Brain Development Atlas (HBDA). The Atlas will start with forebrain annotated hemisphere maps, based on human fetal brain serial sections at the different stages of prenatal ontogenesis. Spatiotemporal changes in the regional-specific immunophenotype profiles will also be demonstrated on virtual serial sections. The HBDA can serve as a reference database for the neurological research, which provides opportunity to compare the data obtained by noninvasive techniques, such as neurosonography, X-ray computed tomography and magnetic resonance imaging, functional magnetic resonance imaging, 3D high-resolution phase-contrast computed tomography visualization techniques, as well as spatial transcriptomics data. It could also become a database for the qualitative and quantitative analysis of individual variability in the human brain. Systemized data on the mechanisms and pathways of prenatal human glio- and neurogenesis could also contribute to the search for new therapy methods for a large spectrum of neurological pathologies, including neurodegenerative and cancer diseases. The preliminary data are now accessible on the special HBDA website.
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Affiliation(s)
- Alexandra Proshchina
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Tsurupi Street, 3, 117418 Moscow, Russia
| | - Anastasia Kharlamova
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Tsurupi Street, 3, 117418 Moscow, Russia
| | - Yuliya Krivova
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Tsurupi Street, 3, 117418 Moscow, Russia
| | - Olga Godovalova
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Tsurupi Street, 3, 117418 Moscow, Russia
| | - Dmitriy Otlyga
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Tsurupi Street, 3, 117418 Moscow, Russia
| | - Victoria Gulimova
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Tsurupi Street, 3, 117418 Moscow, Russia
| | - Ekaterina Otlyga
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Tsurupi Street, 3, 117418 Moscow, Russia
| | - Olga Junemann
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Tsurupi Street, 3, 117418 Moscow, Russia
| | - Gleb Sonin
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Tsurupi Street, 3, 117418 Moscow, Russia
| | - Sergey Saveliev
- Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Tsurupi Street, 3, 117418 Moscow, Russia
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30
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Pieczonka K, Khazaei M, Fehlings MG. Promoting the Differentiation of Neural Progenitor Cells into Oligodendrocytes through the Induction of Olig2 Expression: A Transcriptomic Study Using RNA-seq Analysis. Cells 2023; 12:cells12091252. [PMID: 37174652 PMCID: PMC10177465 DOI: 10.3390/cells12091252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
Oligodendrocytes are the myelinating cells of the central nervous system that facilitate efficient signal transduction. The loss of these cells and the associated myelin sheath can lead to profound functional deficits. Moreover, oligodendrocytes also play key roles in mediating glial-neuronal interactions, which further speaks to their importance in health and disease. Neural progenitor cells (NPCs) are a promising source of cells for the treatment of oligodendrocyte-related neurological diseases due to their ability to differentiate into a variety of cell types, including oligodendrocytes. However, the efficiency of oligodendrocyte differentiation is often low. In this study, we induced the expression of the Olig2 transcription factor in tripotent NPCs using a doxycycline-inducible promoter, such that the extent of oligodendrocyte differentiation could be carefully regulated. We characterized the differentiation profile and the transcriptome of these inducible oligodendrogenic NPCs (ioNPCs) using a combination of qRT-PCR, immunocytochemistry and RNA sequencing with gene ontology (GO) and gene set enrichment analysis (GSEA). Our results show that the ioNPCs differentiated into a significantly greater proportion of oligodendrocytes than the NPCs. The induction of Olig2 expression was also associated with the upregulation of genes involved in oligodendrocyte development and function, as well as the downregulation of genes involved in other cell lineages. The GO and GSEA analyses further corroborated the oligodendrocyte specification of the ioNPCs.
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Affiliation(s)
- Katarzyna Pieczonka
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mohamad Khazaei
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Michael G Fehlings
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada
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31
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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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32
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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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33
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Liu P, Guo L, Yu X, Liu P, Yu Y, Kong X, Yu X, Zephania HM, Liu P, Huang Y. Identification of region-specific amino acid signatures for doxorubicin-induced chemo brain. Amino Acids 2023; 55:325-336. [PMID: 36604337 DOI: 10.1007/s00726-022-03231-8] [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: 08/10/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023]
Abstract
Doxorubicin (DOX) is a cornerstone of chemotherapy for solid tumors and leukemias. DOX-induced cognitive impairment, termed chemo brain, has been reported in cancer survivors, whereas its mechanism remains poorly understood. Here we initially evaluated the cognitive impairments of mice treated with clinically relevant, long-term, low-dosage of DOX. Using HILIC-MS/MS-based targeted metabolomics, we presented the changes of 21 amino acids across six anatomical brain regions of mice with DOX-induced chemo brain. By mapping the altered amino acids to the human metabolic network, we constructed an amino acid-based network module for each brain region. We identified phenylalanine, tyrosine, methionine, and γ-aminobutyric acid as putative signatures of three regions (hippocampus, prefrontal cortex, and neocortex) highly associated with cognition. Relying on the reported mouse brain metabolome atlas, we found that DOX might perturb the amino acid homeostasis in multiple brain regions, similar to the changes in the aging brain. Correlation analysis suggested the possible indirect neurotoxicity of DOX that altered the brain levels of phenylalanine, tyrosine, and methionine by causing metabolic disorders in the liver and kidney. In summary, we revealed the region-specific amino acid signatures as actionable targets for DOX-induced chemo brain, which might provide safer treatment and improve the quality of life among cancer survivors.
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Affiliation(s)
- Peijia Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150001, China
| | - Linling Guo
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Nanjing, 210009, China
| | - Xinyue Yu
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Nanjing, 210009, China
| | - Peipei Liu
- Department of Pharmacology, School of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin, 150001, China
| | - Yan Yu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150001, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150001, China
| | - Xiaxia Yu
- Department of Pharmacy, Affiliated Zhongda Hospital, School of Medicine, Southeast University, 87 Dingjia Bridge, Nanjing, 210009, China
| | - Hove Mzingaye Zephania
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Nanjing, 210009, China
| | - Peifang Liu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150001, China.
| | - Yin Huang
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Nanjing, 210009, China.
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34
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Guo J, Zheng W, Liu Y, Zhou M, Shi Y, Lei M, Zhang C, Liu Z. Long non-coding RNA DLX6-AS1 is the key mediator of glomerular podocyte injury and albuminuria in diabetic nephropathy by targeting the miR-346/GSK-3β signaling pathway. Cell Death Dis 2023; 14:172. [PMID: 36854759 PMCID: PMC9975222 DOI: 10.1038/s41419-023-05695-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 03/02/2023]
Abstract
Progressive albuminuria is the primary clinical symptom of diabetic nephropathy (DN), leading to a gradual decline in kidney function. DLX6-AS1 was the first reported long non-coding RNA (lncRNA) to participate in organogenesis and play crucial roles in the brain or neural cell development. Herein, we investigated the DLX6-AS1 (Dlx6-os1 in mice) role in DN pathogenesis. We found that DLX6-AS1 expression in DN patients correlated with the extent of albuminuria. Dlx6-os1 overexpression induced cellular damage and inflammatory responses in cultured podocytes through miR-346-mediated regulation of the GSK-3β pathway. In various established diabetic and newly developed knockout mouse models, Dlx6-os1 knockdown/knockout significantly reduced podocyte injury and albuminuria. The Dlx6-os1 effects were remarkably modulated by miR-346 mimics or mutants and significantly diminished in podocyte-specific GSK-3β-knockout mice. Thus, DLX6-AS1 (Dlx6-os1) promotes DN development by accelerating podocyte injury and inflammation through the upregulation of the GSK-3β pathway, providing a novel molecular target for DN therapy.
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Affiliation(s)
- Jia Guo
- Nephrology Research Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
- Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, P. R. China.
- Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, P. R. China.
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, P. R. China.
| | - Wen Zheng
- Nephrology Research Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, P. R. China
| | - Yong Liu
- Nephrology Research Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, P. R. China
| | - Mengwen Zhou
- Nephrology Research Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, P. R. China
| | - Yan Shi
- Nephrology Research Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, P. R. China
| | - Min Lei
- Nephrology Research Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, P. R. China
| | - Chaojie Zhang
- Nephrology Research Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China
- Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, P. R. China
| | - Zhangsuo Liu
- Nephrology Research Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, P. R. China.
- Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, P. R. China.
- Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, P. R. China.
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, P. R. China.
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Lee MK, Azizgolshani N, Shapiro JA, Nguyen LN, Kolling FW, Zanazzi GJ, Frost HR, Christensen BC. Tumor type and cell type-specific gene expression alterations in diverse pediatric central nervous system tumors identified using single nuclei RNA-seq. RESEARCH SQUARE 2023:rs.3.rs-2517703. [PMID: 36865335 PMCID: PMC9980204 DOI: 10.21203/rs.3.rs-2517703/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Central nervous system (CNS) tumors are the leading cause of pediatric cancer death, and these patients have an increased risk for developing secondary neoplasms. Due to the low prevalence of pediatric CNS tumors, major advances in targeted therapies have been lagging compared to other adult tumors. We collected single nuclei RNA-seq data from 35 pediatric CNS tumors and three non-tumoral pediatric brain tissues (84,700 nuclei) and characterized tumor heterogeneity and transcriptomic alterations. We distinguished cell subpopulations associated with specific tumor types including radial glial cells in ependymomas and oligodendrocyte precursor cells in astrocytomas. In tumors, we observed pathways important in neural stem cell-like populations, a cell type previously associated with therapy resistance. Lastly, we identified transcriptomic alterations among pediatric CNS tumor types compared to non-tumor tissues, while accounting for cell type effects on gene expression. Our results suggest potential tumor type and cell type-specific targets for pediatric CNS tumor treatment. In this study, we address current gaps in understanding single nuclei gene expression profiles of previously uninvestigated tumor types and enhance current knowledge of gene expression profiles of single cells of various pediatric CNS tumors.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Cardiothoracic Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Joshua A Shapiro
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA, USA
| | - Lananh N Nguyen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - George J Zanazzi
- Dartmouth Cancer Center, Lebanon, NH, USA
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Hildreth Robert Frost
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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36
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Ito M, Fujii N, Kohara S, Hori S, Tanaka M, Wittwer C, Kikuchi K, Iijima T, Kakimoto Y, Hirabayashi K, Kurotaki D, Jessen HJ, Saiardi A, Nagata E. Inositol pyrophosphate profiling reveals regulatory roles of IP6K2-dependent enhanced IP 7 metabolism in the enteric nervous system. J Biol Chem 2023; 299:102928. [PMID: 36681123 PMCID: PMC9957762 DOI: 10.1016/j.jbc.2023.102928] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/20/2023] Open
Abstract
Inositol pyrophosphates regulate diverse physiological processes; to better understand their functional roles, assessing their tissue-specific distribution is important. Here, we profiled inositol pyrophosphate levels in mammalian organs using an originally designed liquid chromatography-mass spectrometry (LC-MS) protocol and discovered that the gastrointestinal tract (GIT) contained the highest levels of diphosphoinositol pentakisphosphate (IP7) and its precursor inositol hexakisphosphate (IP6). Although their absolute levels in the GIT are diet dependent, elevated IP7 metabolism still exists under dietary regimens devoid of exogenous IP7. Of the major GIT cells, enteric neurons selectively express the IP7-synthesizing enzyme IP6K2. We found that IP6K2-knockout mice exhibited significantly impaired IP7 metabolism in the various organs including the proximal GIT. In addition, our LC-MS analysis displayed that genetic ablation of IP6K2 significantly impaired IP7 metabolism in the gut and duodenal muscularis externa containing myenteric plexus. Whole transcriptome analysis of duodenal muscularis externa further suggested that IP6K2 inhibition significantly altered expression levels of the gene sets associated with mature neurons, neural progenitor/stem cells, and glial cells, as well as of certain genes modulating neuronal differentiation and functioning, implying critical roles of the IP6K2-IP7 axis in developmental and functional regulation of the enteric nervous system. These results collectively reveal an unexpected role of mammalian IP7-a highly active IP6K2-IP7 pathway is conducive to the enteric nervous system.
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Affiliation(s)
- Masatoshi Ito
- Support Center for Medical Research and Education, Tokai University, Isehara, Japan.
| | - Natsuko Fujii
- Department of Neurology, Tokai University School of Medicine, Isehara, Japan
| | - Saori Kohara
- Department of Neurology, Tokai University School of Medicine, Isehara, Japan
| | - Shuho Hori
- Support Center for Medical Research and Education, Tokai University, Isehara, Japan
| | - Masayuki Tanaka
- Support Center for Medical Research and Education, Tokai University, Isehara, Japan
| | | | - Kenta Kikuchi
- Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takatoshi Iijima
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Yu Kakimoto
- Department of Forensic Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Kenichi Hirabayashi
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Daisuke Kurotaki
- Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Eiichiro Nagata
- Department of Neurology, Tokai University School of Medicine, Isehara, Japan.
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37
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Investigation of early molecular alterations in tauopathy with generative adversarial networks. Sci Rep 2023; 13:732. [PMID: 36639689 PMCID: PMC9839697 DOI: 10.1038/s41598-023-28081-6] [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: 05/06/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
The recent advances in deep learning-based approaches hold great promise for unravelling biological mechanisms, discovering biomarkers, and predicting gene function. Here, we deployed a deep generative model for simulating the molecular progression of tauopathy and dissecting its early features. We applied generative adversarial networks (GANs) for bulk RNA-seq analysis in a mouse model of tauopathy (TPR50-P301S). The union set of differentially expressed genes from four comparisons (two phenotypes with two time points) was used as input training data. We devised four-way transition curves for a virtual simulation of disease progression, clustered and grouped the curves by patterns, and identified eight distinct pattern groups showing different biological features from Gene Ontology enrichment analyses. Genes that were upregulated in early tauopathy were associated with vasculature development, and these changes preceded immune responses. We confirmed significant disease-associated differences in the public human data for the genes of the different pattern groups. Validation with weighted gene co-expression network analysis suggested that our GAN-based approach can be used to detect distinct patterns of early molecular changes during disease progression, which may be extremely difficult in in vivo experiments. The generative model is a valid systematic approach for exploring the sequential cascades of mechanisms and targeting early molecular events related to dementia.
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38
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Mazzarino RC, Perez-Corredor P, Vanderleest TE, Vacano GN, Sanchez JS, Villalba-Moreno ND, Krausemann S, Mendivil-Perez MA, Aguillón D, Jimenez-Del-Río M, Baena A, Sepulveda-Falla D, Lopera FJ, Quiroz YT, Arboleda-Velasquez JF. APOE3 Christchurch modulates tau phosphorylation and β-catenin/Wnt/Cadherin signaling in induced pluripotent stem cell-derived cerebral organoids from Alzheimer's cases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523290. [PMID: 36712026 PMCID: PMC9882052 DOI: 10.1101/2023.01.11.523290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia among older adults. APOE3 Christchurch (R136S, APOE3Ch ) variant homozygosity was reported in an individual with extreme resistance to autosomal dominant AD due to the PSEN1 E280A mutation. This subject had a delayed clinical age at onset and resistance to tauopathy and neurodegeneration despite extremely high amyloid plaque burden. We established induced pluripotent stem (iPS) cell-derived cerebral organoids from this resistant case and from a non-protected kindred control (with PSEN1 E280A and APOE3/3 ). We used CRISPR/Cas9 gene editing to successfully remove the APOE3Ch to wild type in iPS cells from the protected case and to introduce the APOE3Ch as homozygote in iPS cells from the non-protected case to examine causality. We found significant reduction of tau phosphorylation (pTau 202/205 and pTau396) in cerebral organoids with the APOE3Ch variant, consistent with the strikingly reduced tau pathology found in the resistant case. We identified Cadherin and Wnt pathways as signaling mechanisms regulated by the APOE3Ch variant through single cell RNA sequencing in cerebral organoids. We also identified elevated β-catenin protein, a regulator of tau phosphorylation, as a candidate mediator of APOE3Ch resistance to tauopathy. Our findings show that APOE3Ch is necessary and sufficient to confer resistance to tauopathy in an experimental ex-vivo model establishing a foundation for the development of novel, protected case-inspired therapeutics for tauopathies, including Alzheimer's.
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39
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Singh A, Tiwari VK. Transcriptional networks of transient cell states during human prefrontal cortex development. Front Mol Neurosci 2023; 16:1126438. [PMID: 37138706 PMCID: PMC10150774 DOI: 10.3389/fnmol.2023.1126438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/15/2023] [Indexed: 05/05/2023] Open
Abstract
The human brain is divided into various anatomical regions that control and coordinate unique functions. The prefrontal cortex (PFC) is a large brain region that comprises a range of neuronal and non-neuronal cell types, sharing extensive interconnections with subcortical areas, and plays a critical role in cognition and memory. A timely appearance of distinct cell types through embryonic development is crucial for an anatomically perfect and functional brain. Direct tracing of cell fate development in the human brain is not possible, but single-cell transcriptome sequencing (scRNA-seq) datasets provide the opportunity to dissect cellular heterogeneity and its molecular regulators. Here, using scRNA-seq data of human PFC from fetal stages, we elucidate distinct transient cell states during PFC development and their underlying gene regulatory circuitry. We further identified that distinct intermediate cell states consist of specific gene regulatory modules essential to reach terminal fate using discrete developmental paths. Moreover, using in silico gene knock-out and over-expression analysis, we validated crucial gene regulatory components during the lineage specification of oligodendrocyte progenitor cells. Our study illustrates unique intermediate states and specific gene interaction networks that warrant further investigation for their functional contribution to typical brain development and discusses how this knowledge can be harvested for therapeutic intervention in challenging neurodevelopmental disorders.
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Affiliation(s)
- Aditi Singh
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University, Belfast, United Kingdom
| | - Vijay K. Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University, Belfast, United Kingdom
- Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark
- Danish Institute for Advanced Study (DIAS), Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
- *Correspondence: Vijay K. Tiwari, ;
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40
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Ramos SI, Mussa ZM, Falk EN, Pai B, Giotti B, Allette K, Cai P, Dekio F, Sebra R, Beaumont KG, Tsankov AM, Tsankova NM. An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics. Nat Commun 2022; 13:7671. [PMID: 36509746 PMCID: PMC9744747 DOI: 10.1038/s41467-022-34975-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/10/2022] [Indexed: 12/14/2022] Open
Abstract
Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas of over 200,000 nuclei derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples from 17 to 41 gestational weeks, and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors.
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Affiliation(s)
- Susana I Ramos
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zarmeen M Mussa
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elisa N Falk
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Balagopal Pai
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimaada Allette
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Peiwen Cai
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Fumiko Dekio
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kristin G Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nadejda M Tsankova
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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41
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Herring CA, Simmons RK, Freytag S, Poppe D, Moffet JJD, Pflueger J, Buckberry S, Vargas-Landin DB, Clément O, Echeverría EG, Sutton GJ, Alvarez-Franco A, Hou R, Pflueger C, McDonald K, Polo JM, Forrest ARR, Nowak AK, Voineagu I, Martelotto L, Lister R. Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution. Cell 2022; 185:4428-4447.e28. [PMID: 36318921 DOI: 10.1016/j.cell.2022.09.039] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 07/19/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
Human brain development is underpinned by cellular and molecular reconfigurations continuing into the third decade of life. To reveal cell dynamics orchestrating neural maturation, we profiled human prefrontal cortex gene expression and chromatin accessibility at single-cell resolution from gestation to adulthood. Integrative analyses define the dynamic trajectories of each cell type, revealing major gene expression reconfiguration at the prenatal-to-postnatal transition in all cell types followed by continuous reconfiguration into adulthood and identifying regulatory networks guiding cellular developmental programs, states, and functions. We uncover links between expression dynamics and developmental milestones, characterize the diverse timing of when cells acquire adult-like states, and identify molecular convergence from distinct developmental origins. We further reveal cellular dynamics and their regulators implicated in neurological disorders. Finally, using this reference, we benchmark cell identities and maturation states in organoid models. Together, this captures the dynamic regulatory landscape of human cortical development.
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Affiliation(s)
- Charles A Herring
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Rebecca K Simmons
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Saskia Freytag
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Joel J D Moffet
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Dulce B Vargas-Landin
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Olivier Clément
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Enrique Goñi Echeverría
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Gavin J Sutton
- School of Biotechnology and Biomolecular Sciences, Cellular Genomics Futures Institute, and the RNA Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alba Alvarez-Franco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Rui Hou
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Christian Pflueger
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Kerrie McDonald
- Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jose M Polo
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3000, Australia
| | - Alistair R R Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Anna K Nowak
- Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, Cellular Genomics Futures Institute, and the RNA Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Luciano Martelotto
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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42
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Liao J, Qian J, Fang Y, Chen Z, Zhuang X, Zhang N, Shao X, Hu Y, Yang P, Cheng J, Hu Y, Yu L, Yang H, Zhang J, Lu X, Shao L, Wu D, Gao Y, Chen H, Fan X. De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution. Nat Commun 2022; 13:6498. [PMID: 36310179 PMCID: PMC9618574 DOI: 10.1038/s41467-022-34271-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 10/19/2022] [Indexed: 12/25/2022] Open
Abstract
Uncovering the tissue molecular architecture at single-cell resolution could help better understand organisms' biological and pathological processes. However, bulk RNA-seq can only measure gene expression in cell mixtures, without revealing the transcriptional heterogeneity and spatial patterns of single cells. Herein, we introduce Bulk2Space ( https://github.com/ZJUFanLab/bulk2space ), a deep learning framework-based spatial deconvolution algorithm that can simultaneously disclose the spatial and cellular heterogeneity of bulk RNA-seq data using existing single-cell and spatial transcriptomics references. The use of bulk transcriptomics to validate Bulk2Space unveils, in particular, the spatial variance of immune cells in different tumor regions, the molecular and spatial heterogeneity of tissues during inflammation-induced tumorigenesis, and spatial patterns of novel genes in different cell types. Moreover, Bulk2Space is utilized to perform spatial deconvolution analysis on bulk transcriptome data from two different mouse brain regions derived from our in-house developed sequencing approach termed Spatial-seq. We have not only reconstructed the hierarchical structure of the mouse isocortex but also further annotated cell types that were not identified by original methods in the mouse hypothalamus.
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Affiliation(s)
- Jie Liao
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Jingyang Qian
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Yin Fang
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China
| | - Zhuo Chen
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China
| | - Xiang Zhuang
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China
| | - Ningyu Zhang
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China
| | - Xin Shao
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China
| | - Yining Hu
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Penghui Yang
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Junyun Cheng
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- Innovation Center in Zhejiang University, State Key Laboratory of Component-Based Chinese Medicine, 310058, Hangzhou, China
| | - Yang Hu
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- Innovation Center in Zhejiang University, State Key Laboratory of Component-Based Chinese Medicine, 310058, Hangzhou, China
| | - Lingqi Yu
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Haihong Yang
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China
| | - Jinlu Zhang
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China
| | - Xiaoyan Lu
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
- Innovation Center in Zhejiang University, State Key Laboratory of Component-Based Chinese Medicine, 310058, Hangzhou, China
| | - Li Shao
- Institute of Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, 310015, Hangzhou, China
| | - Dan Wu
- College of Biomedical Engineering and Instrument Science, Zhejiang University, 310013, Hangzhou, China
| | - Yue Gao
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, 100850, Beijing, China.
| | - Huajun Chen
- College of Computer Science and Technology, Zhejiang University, 310027, Hangzhou, China.
- Hangzhou Innovation Center, Zhejiang University, 310058, Hangzhou, China.
| | - Xiaohui Fan
- College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China.
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, 314100, Jiaxing, China.
- Innovation Center in Zhejiang University, State Key Laboratory of Component-Based Chinese Medicine, 310058, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, China.
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43
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Yan H, Wang R, Ma S, Huang D, Wang S, Ren J, Lu C, Chen X, Lu X, Zheng Z, Zhang W, Qu J, Zhou Y, Liu GH. Lineage Landscape: a comprehensive database that records lineage commitment across species. Nucleic Acids Res 2022; 51:D1061-D1066. [PMID: 36305824 PMCID: PMC9825468 DOI: 10.1093/nar/gkac951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/23/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023] Open
Abstract
Commitment to specific cell lineages is critical for mammalian embryonic development. Lineage determination, differentiation, maintenance, and organogenesis result in diverse life forms composed of multiple cell types. To understand the formation and maintenance of living individuals, including human beings, a comprehensive database that integrates multi-omic information underlying lineage differentiation across multiple species is urgently needed. Here, we construct Lineage Landscape, a database that compiles, analyzes and visualizes transcriptomic and epigenomic information related to lineage development in a collection of species. This landscape draws together datasets that capture the ongoing changes in cell lineages from classic model organisms to human beings throughout embryonic, fetal, adult, and aged stages, providing comprehensive, open-access information that is useful to researchers of a broad spectrum of life science disciplines. Lineage Landscape contains single-cell gene expression and bulk transcriptomic, DNA methylation, histone modifications, and chromatin accessibility profiles. Using this database, users can explore genes of interest that exhibit dynamic expression patterns at the transcriptional or epigenetic levels at different stages of lineage development. Lineage Landscape currently includes over 6.6 million cells, 15 million differentially expressed genes and 36 million data entries across 10 species and 34 organs. Lineage Landscape is free to access, browse, search, and download at http://data.iscr.ac.cn/lineage/#/home.
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Affiliation(s)
| | | | | | | | | | | | - Changfa Lu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xin Chen
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyong Lu
- University of Chinese Academy of Sciences, Beijing 100049, China,China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zikai Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China,China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiqi Zhang
- Correspondence may also be addressed to Weiqi Zhang. Tel: +86 10 8409 7838;
| | - Jing Qu
- Correspondence may also be addressed to Jing Qu. Tel: +86 10 6480 7768;
| | - Yuanchun Zhou
- Correspondence may also be addressed to Yuanchun Zhou. Tel: +86 10 5881 2561;
| | - Guang-Hui Liu
- To whom correspondence should be addressed. Tel: +86 10 6480 7583;
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44
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Qian X, DeGennaro EM, Talukdar M, Akula SK, Lai A, Shao DD, Gonzalez D, Marciano JH, Smith RS, Hylton NK, Yang E, Bazan JF, Barrett L, Yeh RC, Hill RS, Beck SG, Otani A, Angad J, Mitani T, Posey JE, Pehlivan D, Calame D, Aydin H, Yesilbas O, Parks KC, Argilli E, England E, Im K, Taranath A, Scott HS, Barnett CP, Arts P, Sherr EH, Lupski JR, Walsh CA. Loss of non-motor kinesin KIF26A causes congenital brain malformations via dysregulated neuronal migration and axonal growth as well as apoptosis. Dev Cell 2022; 57:2381-2396.e13. [PMID: 36228617 PMCID: PMC10585591 DOI: 10.1016/j.devcel.2022.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/13/2022] [Accepted: 09/20/2022] [Indexed: 01/16/2023]
Abstract
Kinesins are canonical molecular motors but can also function as modulators of intracellular signaling. KIF26A, an unconventional kinesin that lacks motor activity, inhibits growth-factor-receptor-bound protein 2 (GRB2)- and focal adhesion kinase (FAK)-dependent signal transduction, but its functions in the brain have not been characterized. We report a patient cohort with biallelic loss-of-function variants in KIF26A, exhibiting a spectrum of congenital brain malformations. In the developing brain, KIF26A is preferentially expressed during early- and mid-gestation in excitatory neurons. Combining mice and human iPSC-derived organoid models, we discovered that loss of KIF26A causes excitatory neuron-specific defects in radial migration, localization, dendritic and axonal growth, and apoptosis, offering a convincing explanation of the disease etiology in patients. Single-cell RNA sequencing in KIF26A knockout organoids revealed transcriptional changes in MAPK, MYC, and E2F pathways. Our findings illustrate the pathogenesis of KIF26A loss-of-function variants and identify the surprising versatility of this non-motor kinesin.
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Affiliation(s)
- Xuyu Qian
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen M DeGennaro
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maya Talukdar
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Shyam K Akula
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard, MIT MD/PhD Program, Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Abbe Lai
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Diane D Shao
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dilenny Gonzalez
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jack H Marciano
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Richard S Smith
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Norma K Hylton
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard, MIT MD/PhD Program, Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Edward Yang
- Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Radiology, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Lee Barrett
- Department of Neurobiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca C Yeh
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha G Beck
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aoi Otani
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jolly Angad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey
| | - Osman Yesilbas
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Faculty of Medicine, Karadeniz Technical University, Trabzon 61080, Turkey
| | - Kendall C Parks
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emanuela Argilli
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eleina England
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiho Im
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ajay Taranath
- Department of Medical Imaging, South Australia Medical Imaging, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia; Australian Genomics, Parkville, VIC, Australia
| | - Christopher P Barnett
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Pediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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45
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Massimo M, Long KR. Orchestrating human neocortex development across the scales; from micro to macro. Semin Cell Dev Biol 2022; 130:24-36. [PMID: 34583893 DOI: 10.1016/j.semcdb.2021.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/27/2021] [Accepted: 09/10/2021] [Indexed: 10/20/2022]
Abstract
How our brains have developed to perform the many complex functions that make us human has long remained a question of great interest. Over the last few decades, many scientists from a wide range of fields have tried to answer this question by aiming to uncover the mechanisms that regulate the development of the human neocortex. They have approached this on different scales, focusing microscopically on individual cells all the way up to macroscopically imaging entire brains within living patients. In this review we will summarise these key findings and how they fit together.
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Affiliation(s)
- Marco Massimo
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom; MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, United Kingdom
| | - Katherine R Long
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom; MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, United Kingdom.
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46
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Zhou QJ, Liu X, Zhang L, Wang R, Yin T, Li X, Li G, He Y, Ding Z, Ma P, Wang SZ, Mao B, Zhang S, Wang GD. A single-nucleus transcriptomic atlas of the dog hippocampus reveals the potential relationship between specific cell types and domestication. Natl Sci Rev 2022; 9:nwac147. [PMID: 36569494 PMCID: PMC9772819 DOI: 10.1093/nsr/nwac147] [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: 03/16/2022] [Revised: 06/28/2022] [Accepted: 07/09/2022] [Indexed: 12/27/2022] Open
Abstract
The process of domestication has led to dramatic differences in behavioral traits between domestic dogs and gray wolves. Whole-genome research found that a class of putative positively selected genes were related to various aspects of learning and memory, such as long-term potentiation and long-term depression. In this study, we constructed a single-nucleus transcriptomic atlas of the dog hippocampus to illustrate its cell types, cell lineage and molecular features. Using the transcriptomes of 105 057 nuclei from the hippocampus of a Beagle dog, we identified 26 cell clusters and a putative trajectory of oligodendrocyte development. Comparative analysis revealed a significant convergence between dog differentially expressed genes (DEGs) and putative positively selected genes (PSGs). Forty putative PSGs were DEGs in glutamatergic neurons, especially in Cluster 14, which is related to the regulation of nervous system development. In summary, this study provides a blueprint to understand the cellular mechanism of dog domestication.
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Affiliation(s)
| | | | | | - Rong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China,College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Tingting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiaolu Li
- Genomic Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Guimei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yuqi He
- Genomic Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Zhaoli Ding
- Genomic Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Shi-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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47
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Lewis JD, Acosta H, Tuulari JJ, Fonov VS, Collins DL, Scheinin NM, Lehtola SJ, Rosberg A, Lidauer K, Ukharova E, Saunavaara J, Parkkola R, Lähdesmäki T, Karlsson L, Karlsson H. Allometry in the corpus callosum in neonates: Sexual dimorphism. Hum Brain Mapp 2022; 43:4609-4619. [PMID: 35722945 PMCID: PMC9491283 DOI: 10.1002/hbm.25977] [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: 04/15/2022] [Revised: 05/23/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022] Open
Abstract
The corpus callosum (CC) is the largest fiber tract in the human brain, allowing interhemispheric communication by connecting homologous areas of the two cerebral hemispheres. In adults, CC size shows a robust allometric relationship with brain size, with larger brains having larger callosa, but smaller brains having larger callosa relative to brain size. Such an allometric relationship has been shown in both males and females, with no significant difference between the sexes. But there is some evidence that there are alterations in these allometric relationships during development. However, it is currently not known whether there is sexual dimorphism in these allometric relationships from birth, or if it only develops later. We study this in neonate data. Our results indicate that there are already sex differences in these allometric relationships in neonates: male neonates show the adult‐like allometric relationship between CC size and brain size; however female neonates show a significantly more positive allometry between CC size and brain size than either male neonates or female adults. The underlying cause of this sexual dimorphism is unclear; but the existence of this sexual dimorphism in neonates suggests that sex‐differences in lateralization have prenatal origins.
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Affiliation(s)
- John D Lewis
- Montreal Neurological Institute and Hospital, McGill University, Quebec, Canada
| | - Henriette Acosta
- Department of Psychiatry and Psychotherapy, Philipps University of Marburg, Marburg, Germany.,FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland
| | - Jetro J Tuulari
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Turku Collegium for Science and Medicine and Technology, University of Turku, Turku, Finland.,Department of Future Technologies, University of Turku, Turku, Finland.,Department of Psychiatry, University of Turku and Turku University Hospital, Turku, Finland
| | - Vladimir S Fonov
- Montreal Neurological Institute and Hospital, McGill University, Quebec, Canada
| | - D Louis Collins
- Montreal Neurological Institute and Hospital, McGill University, Quebec, Canada
| | - Noora M Scheinin
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Department of Psychiatry, University of Turku and Turku University Hospital, Turku, Finland
| | - Satu J Lehtola
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland
| | - Aylin Rosberg
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Department of Radiology, University of Turku and Turku University Hospital, Turku, Finland
| | - Kristian Lidauer
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland
| | - Elena Ukharova
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Department of Neuroscience and Biomedical Engineering, Aalto University School of Science, Espoo, Finland
| | - Jani Saunavaara
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Department of Medical Physics, Turku University Hospital, Turku, Finland
| | - Riitta Parkkola
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Department of Radiology, University of Turku and Turku University Hospital, Turku, Finland
| | - Tuire Lähdesmäki
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Department of Pediatric Neurology, University of Turku and Turku University Hospital, Turku, Finland
| | - Linnea Karlsson
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Department of Psychiatry, University of Turku and Turku University Hospital, Turku, Finland.,Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland.,Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Hasse Karlsson
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Department of Psychiatry, University of Turku and Turku University Hospital, Turku, Finland
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48
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Wu C, Liu Y, Wei D, Tao L, Yuan L, Jing T, Wang B. Gene Coexpression Network Characterizing Microenvironmental Heterogeneity and Intercellular Communication in Pancreatic Ductal Adenocarcinoma: Implications of Prognostic Significance and Therapeutic Target. Front Oncol 2022; 12:840474. [PMID: 35719923 PMCID: PMC9198606 DOI: 10.3389/fonc.2022.840474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/26/2022] [Indexed: 11/20/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is characterized by intensive stromal involvement and heterogeneity. Pancreatic cancer cells interact with the surrounding tumor microenvironment (TME), leading to tumor development, unfavorable prognosis, and therapy resistance. Herein, we aim to clarify a gene network indicative of TME features and find a vulnerability for combating pancreatic cancer. Methods Single-cell RNA sequencing data processed by the Seurat package were used to retrieve cell component marker genes (CCMGs). The correlation networks/modules of CCMGs were determined by WGCNA. Neural network and risk score models were constructed for prognosis prediction. Cell–cell communication analysis was achieved by NATMI software. The effect of the ITGA2 inhibitor was evaluated in vivo by using a KrasG12D-driven murine pancreatic cancer model. Results WGCNA categorized CCMGs into eight gene coexpression networks. TME genes derived from the significant networks were able to stratify PDAC samples into two main TME subclasses with diverse prognoses. Furthermore, we generated a neural network model and risk score model that robustly predicted the prognosis and therapeutic outcomes. A functional enrichment analysis of hub genes governing gene networks revealed a crucial role of cell junction molecule–mediated intercellular communication in PDAC malignancy. The pharmacological inhibition of ITGA2 counteracts the cancer-promoting microenvironment and ameliorates pancreatic lesions in vivo. Conclusion By utilizing single-cell data and WGCNA to deconvolute the bulk transcriptome, we exploited novel PDAC prognosis–predicting strategies. Targeting the hub gene ITGA2 attenuated tumor development in a PDAC mouse model. These findings may provide novel insights into PDAC therapy.
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Affiliation(s)
- Chengsi Wu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yizhen Liu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Yizhen Liu, ; Tiantian Jing, ; Boshi Wang,
| | - Dianhui Wei
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Tao
- Emergency Department, 305 Hospital of People’s Liberation Army, Beijing, China
| | - Lili Yuan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tiantian Jing
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Yizhen Liu, ; Tiantian Jing, ; Boshi Wang,
| | - Boshi Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Yizhen Liu, ; Tiantian Jing, ; Boshi Wang,
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49
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Willsey HR, Willsey AJ, Wang B, State MW. Genomics, convergent neuroscience and progress in understanding autism spectrum disorder. Nat Rev Neurosci 2022; 23:323-341. [PMID: 35440779 PMCID: PMC10693992 DOI: 10.1038/s41583-022-00576-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/31/2022]
Abstract
More than a hundred genes have been identified that, when disrupted, impart large risk for autism spectrum disorder (ASD). Current knowledge about the encoded proteins - although incomplete - points to a very wide range of developmentally dynamic and diverse biological processes. Moreover, the core symptoms of ASD involve distinctly human characteristics, presenting challenges to interpreting evolutionarily distant model systems. Indeed, despite a decade of striking progress in gene discovery, an actionable understanding of pathobiology remains elusive. Increasingly, convergent neuroscience approaches have been recognized as an important complement to traditional uses of genetics to illuminate the biology of human disorders. These methods seek to identify intersection among molecular-level, cellular-level and circuit-level functions across multiple risk genes and have highlighted developing excitatory neurons in the human mid-gestational prefrontal cortex as an important pathobiological nexus in ASD. In addition, neurogenesis, chromatin modification and synaptic function have emerged as key potential mediators of genetic vulnerability. The continued expansion of foundational 'omics' data sets, the application of higher-throughput model systems and incorporating developmental trajectories and sex differences into future analyses will refine and extend these results. Ultimately, a systems-level understanding of ASD genetic risk holds promise for clarifying pathobiology and advancing therapeutics.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA.
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50
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Xu X, Zhang M, Zhang X, Liu Y, Cai L, Zhang Q, Chen Q, Lin L, Lin S, Song Y, Zhu Z, Yang C. Decoding Expression Dynamics of Protein and Transcriptome at the Single-Cell Level in Paired Picoliter Chambers. Anal Chem 2022; 94:8164-8173. [PMID: 35650660 DOI: 10.1021/acs.analchem.1c05312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simultaneous analysis of mRNAs and proteins at the single-cell level provides information about the dynamics and correlations of gene and protein expressions in individual cells, enabling a comprehensive study of cellular heterogeneity and expression patterns. Here, we present a platform for about 1000 cellular indexing of mRNAs and membrane proteins, named multi-Paired-seq, with high cell utilization, accurate molecular measurement, and low cost. Based on hydrodynamic differential flow resistance, multi-Paired-seq largely improves cell utilization in the percentage of cells measured in population (>95%). Combined with the pump/valve structure, cell-free antibodies and mRNAs can be removed completely for highly accurate detection (R = 0.96) of protein copies. The picoliter reaction chambers allow high detection sensitivity for both mRNA transcripts and protein copies and low sequencing cost. Using multi-Paired-seq, three clusters of known breast cancer cell types are identified according to multimodal measurements, and the expression correlations between mRNAs and proteins under altered conditions are quantified. Multi-Paired-seq provides multimodal measurements at the single-cell level, which offers a new tool for cell biology, developmental biology, drug discovery, and precision medicine.
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Affiliation(s)
- Xing Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Mingxia Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China.,Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Xuebing Zhang
- Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Yilong Liu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Linfeng Cai
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qianqian Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qin Chen
- Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Li Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shichao Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yanling Song
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chaoyong Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
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