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Xu J, Jia Z, Zhao X, Wang L, Jin G, Li Z, Yin N, Li Y, Peng M. BCOR and ZC3H12A suppress a core stemness program in exhausted CD8+ T cells. J Exp Med 2025; 222:e20241133. [PMID: 40327039 PMCID: PMC12054362 DOI: 10.1084/jem.20241133] [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: 07/02/2024] [Revised: 11/25/2024] [Accepted: 04/16/2025] [Indexed: 05/07/2025] Open
Abstract
In chronic viral infections, sustained CD8+ T cell response relies on TCF1+ precursor-exhausted T cells (TPEX) exhibiting stem-like properties. TPEX self-renew and respond to PD-1 blockade, underscoring their paramount importance. However, strategies for effectively augmenting TPEX remain limited. Here, we demonstrate that ZC3H12A deficiency initiates a stemness program in TPEX but also increases cell death, whereas BCOR deficiency predominantly promotes TPEX proliferation. Consequently, co-targeting of both BCOR and ZC3H12A imparts exceptional stemness and functionality to TPEX, thereby enhancing viral control. Mechanistically, BCOR and ZC3H12A collaboratively suppress a core stemness program in TPEX characterized by heightened expression of ∼216 factors. While TCF1 plays a role, this core stemness program relies on novel factors, including PDZK1IP1, IFIT3, PIM2, LTB, and POU2F2. Crucially, overexpressing POU2F2 robustly boosts TPEX and enhances antiviral immunity. Thus, a core stemness program exists in exhausted T cells, jointly repressed by BCOR and ZC3H12A, robustly controlling TPEX differentiation and providing new targets for addressing T cell exhaustion.
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Affiliation(s)
- Jing Xu
- State Key Laboratory of Molecular Oncology, Institute for Immunology, Beijing Key Laboratory of Immunological Research of Allergy, School of Basic Medical Sciences, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zeran Jia
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- IDG/McGovern Institute for Brain Research, State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Xiaocui Zhao
- State Key Laboratory of Molecular Oncology, Institute for Immunology, Beijing Key Laboratory of Immunological Research of Allergy, School of Basic Medical Sciences, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lixia Wang
- State Key Laboratory of Molecular Oncology, Institute for Immunology, Beijing Key Laboratory of Immunological Research of Allergy, School of Basic Medical Sciences, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Gang Jin
- State Key Laboratory of Molecular Oncology, Institute for Immunology, Beijing Key Laboratory of Immunological Research of Allergy, School of Basic Medical Sciences, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zhuoyang Li
- State Key Laboratory of Molecular Oncology, Institute for Immunology, Beijing Key Laboratory of Immunological Research of Allergy, School of Basic Medical Sciences, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Na Yin
- State Key Laboratory of Molecular Oncology, Institute for Immunology, Beijing Key Laboratory of Immunological Research of Allergy, School of Basic Medical Sciences, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yinqing Li
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- IDG/McGovern Institute for Brain Research, State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Min Peng
- State Key Laboratory of Molecular Oncology, Institute for Immunology, Beijing Key Laboratory of Immunological Research of Allergy, School of Basic Medical Sciences, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
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2
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Kim S, Shin JJ, Kang M, Yang Y, Cho YS, Paik H, Kim J, Yi Y, Lee S, Koo HY, Bok J, Bae YC, Kim JY, Kim E. Alternatively spliced mini-exon B in PTPδ regulates excitatory synapses through cell-type-specific trans-synaptic PTPδ-IL1RAP interaction. Nat Commun 2025; 16:4415. [PMID: 40360498 PMCID: PMC12075705 DOI: 10.1038/s41467-025-59685-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 04/30/2025] [Indexed: 05/15/2025] Open
Abstract
PTPδ, encoded by PTPRD, is implicated in various neurological, psychiatric, and neurodevelopmental disorders, but the underlying mechanisms remain unclear. PTPδ trans-synaptically interacts with multiple postsynaptic adhesion molecules, which involves its extracellular alternatively spliced mini-exons, meA and meB. While PTPδ-meA functions have been studied in vivo, PTPδ-meB has not been studied. Here, we report that, unlike homozygous PTPδ-meA-mutant mice, homozygous PTPδ-meB-mutant (Ptprd-meB-/-) mice show markedly reduced early postnatal survival. Heterozygous Ptprd-meB+/- male mice show behavioral abnormalities and decreased excitatory synaptic density and transmission in dentate gyrus granule cells (DG-GCs). Proteomic analyses identify decreased postsynaptic density levels of IL1RAP, a known trans-synaptic partner of meB-containing PTPδ. Accordingly, IL1RAP-mutant mice show decreased excitatory synaptic transmission in DG-GCs. Ptprd-meB+/- DG interneurons with minimal IL1RAP expression show increased excitatory synaptic density and transmission. Therefore, PTPδ-meB is important for survival, synaptic, and behavioral phenotypes and regulates excitatory synapses in cell-type-specific and IL1RAP-dependent manners.
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Affiliation(s)
- Seoyeong Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea
| | - Jae Jin Shin
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea
| | - Muwon Kang
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea
| | - Yeji Yang
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea
- Digital Omics Research Center, Korea Basic Science Institute (KBSI), Ochang, 28119, Korea
| | - Yi Sul Cho
- Department of Anatomy and Neurobiology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea
| | - Hyojung Paik
- Center for Biomedical Computing, Korea Institute of Science and Technology Information (KISTI), Daejeon, 34141, Korea
| | - Jimin Kim
- Center for Biomedical Computing, Korea Institute of Science and Technology Information (KISTI), Daejeon, 34141, Korea
| | - Yunho Yi
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Suho Lee
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea
| | - Hei Yeun Koo
- Department of Anatomy, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Jinwoong Bok
- Department of Anatomy, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Yong Chul Bae
- Department of Anatomy and Neurobiology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea
| | - Jin Young Kim
- Digital Omics Research Center, Korea Basic Science Institute (KBSI), Ochang, 28119, Korea
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea.
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea.
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3
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Zhang B, Yue D, Han B, Bao D, Zhang X, Hao X, Lin X, Lindsey K, Zhu L, Jin S, Wang M, Xu H, Du M, Yu Y, Zhang X, Yang X. RAPID LEAF FALLING 1 facilitates chemical defoliation and mechanical harvesting in cotton. MOLECULAR PLANT 2025; 18:765-782. [PMID: 40158208 DOI: 10.1016/j.molp.2025.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 02/02/2025] [Accepted: 03/25/2025] [Indexed: 04/02/2025]
Abstract
Chemical defoliation stands as the ultimate tool in enabling the mechanical harvest of cotton, offering economic and environmental advantages. However, the underlying molecular mechanism that triggers leaf abscission through defoliant remains unsolved. In this study, we meticulously constructed a transcriptomic atlas through single-nucleus mRNA sequencing (snRNA-seq) of the abscission zone (AZ) from cotton petiole. We identified two newly-formed cell types, abscission cells and protection layer cells in cotton petiole AZ after defoliant treatment. GhRLF1 (RAPID LEAF FALLING 1), as one of the members of the cytokinin oxidase/dehydrogenase (CKX) gene family, was further characterized as a key marker gene unique to the abscission cells following defoliant treatment. Overexpression of GhRLF1 resulted in reduced cytokinin accumulation and accelerated leaf abscission. Conversely, CRISPR/Cas9-mediated loss of GhRLF1 function appeared to delay this process. Its interacting regulators, GhWRKY70, acting as "Pioneer" activator, and GhMYB108, acting as "Successor" activator, orchestrate a sequential modulation of GhWRKY70/GhMYB108-GhRLF1-CTK (cytokinin) within the AZ to regulate cotton leaf abscission. GhRLF1 not only regulates leaf abscission but also reduces cotton yield. Consequently, transgenic lines that exhibit rapid leaf falling and require less defoliant but show unaffected cotton yield were developed for mechanical harvesting. This was achieved using a defoliant-induced petiole-specific promoter, proPER21, to drive GhRLF1 (proPER21::RLF1). This pioneering biotechnology offers a new strategy for the chemical defoliation of machine-harvested cotton, ensuring stable production and reducing leaf debris in harvested cotton, thereby enhancing environmental sustainability.
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Affiliation(s)
- Bing Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Bei Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Danfan Bao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Xiao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Xuyang Hao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Xin Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Keith Lindsey
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Haijiang Xu
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, P.R. China
| | - Mingwei Du
- College of Agriculture and Biotechnology, China Agricultural University, Beijing 100193, P.R. China
| | - Yu Yu
- Xinjiang Academy of Agriculture and Reclamation Science, Cotton Institute, Shihezi 832000, Xinjiang, P.R. China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China.
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China.
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4
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Yagishita H, Sasaki T. Integrating physiological and transcriptomic analyses at the single-neuron level. Neurosci Res 2025; 214:69-74. [PMID: 38821412 DOI: 10.1016/j.neures.2024.05.003] [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: 05/12/2024] [Revised: 04/30/2024] [Accepted: 05/12/2024] [Indexed: 06/02/2024]
Abstract
Neurons generate various spike patterns to execute different functions. Understanding how these physiological neuronal spike patterns are related to their molecular characteristics is a long-standing issue in neuroscience. Herein, we review the results of recent studies that have addressed this issue by integrating physiological and transcriptomic techniques. A sequence of experiments, including in vivo recording and/or labeling, brain tissue slicing, cell collection, and transcriptomic analysis, have identified the gene expression profiles of brain neurons at the single-cell level, with activity patterns recorded in living animals. Although these techniques are still in the early stages, this methodological idea is principally applicable to various brain regions and neuronal activity patterns. Accumulating evidence will contribute to a deeper understanding of neuronal characteristics by integrating insights from molecules to cells, circuits, and behaviors.
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Affiliation(s)
- Haruya Yagishita
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-Ku, Sendai 980-8578, Japan
| | - Takuya Sasaki
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-Ku, Sendai 980-8578, Japan.
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5
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Spitzer A, Johnson KC, Nomura M, Garofano L, Nehar-Belaid D, Darnell NG, Greenwald AC, Bussema L, Oh YT, Varn FS, D'Angelo F, Gritsch S, Anderson KJ, Migliozzi S, Gonzalez Castro LN, Chowdhury T, Robine N, Reeves C, Park JB, Lipsa A, Hertel F, Golebiewska A, Niclou SP, Nusrat L, Kellet S, Das S, Moon HE, Paek SH, Bielle F, Laurenge A, Di Stefano AL, Mathon B, Picca A, Sanson M, Tanaka S, Saito N, Ashley DM, Keir ST, Ligon KL, Huse JT, Yung WKA, Lasorella A, Iavarone A, Verhaak RGW, Tirosh I, Suvà ML. Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics. Nat Genet 2025; 57:1168-1178. [PMID: 40346362 PMCID: PMC12081298 DOI: 10.1038/s41588-025-02168-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 03/17/2025] [Indexed: 05/11/2025]
Abstract
The evolution of isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) after standard-of-care therapy remains poorly understood. Here we analyzed matched primary and recurrent GBMs from 59 patients using single-nucleus RNA sequencing and bulk DNA sequencing, assessing the longitudinal evolution of the GBM ecosystem across layers of cellular and molecular heterogeneity. The most consistent change was a lower malignant cell fraction at recurrence and a reciprocal increase in glial and neuronal cell types in the tumor microenvironment (TME). The predominant malignant cell state differed between most matched pairs, but no states were exclusive or highly enriched in either time point, nor was there a consistent longitudinal trajectory across the cohort. Nevertheless, specific trajectories were enriched in subsets of patients. Changes in malignant state abundances mirrored changes in TME composition and baseline profiles, reflecting the co-evolution of the GBM ecosystem. Our study provides a blueprint of GBM's diverse longitudinal trajectories and highlights the treatment and TME modifiers that shape them.
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Affiliation(s)
- Avishay Spitzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Oncology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kevin C Johnson
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Masashi Nomura
- Department of Pathology and Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Luciano Garofano
- Department of Public Health Sciences, Division of Biostatistics and Bioinformatics, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | | | - Noam Galili Darnell
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alissa C Greenwald
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lillian Bussema
- Department of Pathology and Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Young Taek Oh
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Frederick S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Fulvio D'Angelo
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
- Department of Neurological Surgery, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Simon Gritsch
- Department of Pathology and Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin J Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Simona Migliozzi
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - L Nicolas Gonzalez Castro
- Department of Pathology and Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tamrin Chowdhury
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Nicolas Robine
- Department of Computational Biology, New York Genome Center, New York City, NY, USA
| | - Catherine Reeves
- Department of Sequencing Operations, New York Genome Center, New York City, NY, USA
| | - Jong Bae Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Republic of Korea
| | - Anuja Lipsa
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Frank Hertel
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
- University of Luxembourg Faculty of Science, Technology and Medicine, Luxembourg, Luxembourg
| | - Labeeba Nusrat
- Division of Neurosurgery, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Sorcha Kellet
- Division of Neurosurgery, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Sunit Das
- Division of Neurosurgery, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Hyo-Eun Moon
- Department of Neurosurgery, Cancer Research Institute, Hypoxia/Ischemia Disease Institute, Seoul National University, Seoul, Republic of Korea
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute, Hypoxia/Ischemia Disease Institute, Seoul National University, Seoul, Republic of Korea
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon-si, Republic of Korea
| | - Franck Bielle
- Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM-Paris Brain Institute, Equipe labellisée LNCC, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Neuropathology, Paris, France
| | - Alice Laurenge
- Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM-Paris Brain Institute, Equipe labellisée LNCC, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Neuro-oncology, Paris, France
| | - Anna Luisa Di Stefano
- Neurology Department, Foch Hospital, Suresnes, France
- Neurosurgery Unit, Ospedali Riuniti di Livorno, Livorno, Italy
| | - Bertrand Mathon
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Neurosurgery, Paris, France
| | - Alberto Picca
- Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM-Paris Brain Institute, Equipe labellisée LNCC, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Neuro-oncology, Paris, France
| | - Marc Sanson
- Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM-Paris Brain Institute, Equipe labellisée LNCC, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Neuro-oncology, Paris, France
- Brain Tumor Bank Onconeurotek (ONT), AP-HP, Paris, France
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - David M Ashley
- Department of Neurosurgery, The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | - Stephen T Keir
- Department of Neurosurgery, The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jason T Huse
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - W K Alfred Yung
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Lasorella
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA.
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA.
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA.
- Department of Neurological Surgery, University of Miami, Miller School of Medicine, Miami, FL, USA.
| | - Roel G W Verhaak
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.
- Department of Neurosurgery, Amsterdam University Medical Center, Amsterdam, the Netherlands.
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Mario L Suvà
- Department of Pathology and Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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6
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Nomura M, Spitzer A, Johnson KC, Garofano L, Nehar-Belaid D, Galili Darnell N, Greenwald AC, Bussema L, Oh YT, Varn FS, D'Angelo F, Gritsch S, Anderson KJ, Migliozzi S, Gonzalez Castro LN, ChowdhFury T, Robine N, Reeves C, Park JB, Lipsa A, Hertel F, Golebiewska A, Niclou SP, Nusrat L, Kellet S, Das S, Moon HE, Paek SH, Bielle F, Laurenge A, Di Stefano AL, Mathon B, Picca A, Sanson M, Tanaka S, Saito N, Ashley DM, Keir ST, Ligon KL, Huse JT, Yung WKA, Lasorella A, Verhaak RGW, Iavarone A, Suvà ML, Tirosh I. The multilayered transcriptional architecture of glioblastoma ecosystems. Nat Genet 2025; 57:1155-1167. [PMID: 40346361 PMCID: PMC12081307 DOI: 10.1038/s41588-025-02167-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 03/17/2025] [Indexed: 05/11/2025]
Abstract
In isocitrate dehydrogenase wildtype glioblastoma (GBM), cellular heterogeneity across and within tumors may drive therapeutic resistance. Here we analyzed 121 primary and recurrent GBM samples from 59 patients using single-nucleus RNA sequencing and bulk tumor DNA sequencing to characterize GBM transcriptional heterogeneity. First, GBMs can be classified by their broad cellular composition, encompassing malignant and nonmalignant cell types. Second, in each cell type we describe the diversity of cellular states and their pathway activation, particularly an expanded set of malignant cell states, including glial progenitor cell-like, neuronal-like and cilia-like. Third, the remaining variation between GBMs highlights three baseline gene expression programs. These three layers of heterogeneity are interrelated and partially associated with specific genetic aberrations, thereby defining three stereotypic GBM ecosystems. This work provides an unparalleled view of the multilayered transcriptional architecture of GBM. How this architecture evolves during disease progression is addressed in the companion manuscript by Spitzer et al.
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Affiliation(s)
- Masashi Nomura
- Department of Pathology and Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Avishay Spitzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Oncology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kevin C Johnson
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Luciano Garofano
- Department of Public Health Sciences, Division of Biostatistics and Bioinformatics, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | | | - Noam Galili Darnell
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alissa C Greenwald
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lillian Bussema
- Department of Pathology and Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Young Taek Oh
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Frederick S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Fulvio D'Angelo
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
- Department of Neurological Surgery, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Simon Gritsch
- Department of Pathology and Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin J Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Simona Migliozzi
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - L Nicolas Gonzalez Castro
- Department of Pathology and Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tamrin ChowdhFury
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Nicolas Robine
- Department of Computational Biology, New York Genome Center, New York, NY, USA
| | - Catherine Reeves
- Department of Sequencing Operations, New York Genome Center, New York, NY, USA
| | - Jong Bae Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Republic of Korea
| | - Anuja Lipsa
- NORLUX Neuro-Oncology laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Frank Hertel
- NORLUX Neuro-Oncology laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anna Golebiewska
- NORLUX Neuro-Oncology laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Simone P Niclou
- NORLUX Neuro-Oncology laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
- University of Luxembourg; Faculty of Science, Technology and Medicine, Esch-sur-Alzette, Luxembourg
| | - Labeeba Nusrat
- Division of Neurosurgery, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Sorcha Kellet
- Division of Neurosurgery, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Sunit Das
- Division of Neurosurgery, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Hyo Eun Moon
- Department of Neurosurgery, Cancer Research Institute, Hypoxia Ischemia Disease Institute, Seoul National University, Seoul, Republic of Korea
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute, Hypoxia Ischemia Disease Institute, Seoul National University, Seoul, Republic of Korea
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon-si, Republic of Korea
| | - Franck Bielle
- Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM-Paris Brain Institute, Equipe Labellisée LNCC, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Neuropathology, Paris, France
| | - Alice Laurenge
- Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM-Paris Brain Institute, Equipe Labellisée LNCC, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Neuro-oncology, Paris, France
| | - Anna Luisa Di Stefano
- Neurology Department, Foch Hospital, Suresnes, France
- Neurosurgery Unit, Ospedali Riuniti di Livorno, Livorno, Italy
| | - Bertrand Mathon
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Neurosurgery, Paris, France
| | - Alberto Picca
- Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM-Paris Brain Institute, Equipe Labellisée LNCC, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Neuro-oncology, Paris, France
| | - Marc Sanson
- Sorbonne Université, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM-Paris Brain Institute, Equipe Labellisée LNCC, Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Neuro-oncology, Paris, France
- AP-HP, Brain Tumor Bank Onconeurotek (ONT), Paris, France
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - David M Ashley
- Department of Neurosurgery, The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | - Stephen T Keir
- Department of Neurosurgery, The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jason T Huse
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - W K Alfred Yung
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Lasorella
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA.
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA.
| | - Roel G W Verhaak
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.
- Department of Neurosurgery, Amsterdam University Medical Center, Amsterdam, the Netherlands.
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA.
- Department of Neurological Surgery, University of Miami, Miller School of Medicine, Miami, FL, USA.
| | - Mario L Suvà
- Department of Pathology and Krantz Family Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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7
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Zeppilli S, Gurrola AO, Demetci P, Brann DH, Pham TM, Attey R, Zilkha N, Kimchi T, Datta SR, Singh R, Tosches MA, Crombach A, Fleischmann A. Single-cell genomics of the mouse olfactory cortex reveals contrasts with neocortex and ancestral signatures of cell type evolution. Nat Neurosci 2025; 28:937-948. [PMID: 40200010 DOI: 10.1038/s41593-025-01924-3] [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: 09/10/2023] [Accepted: 02/19/2025] [Indexed: 04/10/2025]
Abstract
Understanding the molecular logic of cortical cell-type diversity can illuminate cortical circuit function and evolution. Here, we performed single-nucleus transcriptome and chromatin accessibility analyses to compare neurons across three- to six-layered cortical areas of adult mice and across tetrapod species. We found that, in contrast to the six-layered neocortex, glutamatergic neurons of the three-layered mouse olfactory (piriform) cortex displayed continuous rather than discrete variation in transcriptomic profiles. Subsets of piriform and neocortical glutamatergic cells with conserved transcriptomic profiles were distinguished by distinct, area-specific epigenetic states. Furthermore, we identified a prominent population of immature neurons in piriform cortex and observed that, in contrast to the neocortex, piriform cortex exhibited divergence between glutamatergic cells in laboratory versus wild-derived mice. Finally, we showed that piriform neurons displayed greater transcriptomic similarity to cortical neurons of turtles, lizards and salamanders than to those of the neocortex. In summary, despite over 200 million years of coevolution alongside the neocortex, olfactory cortex neurons retain molecular signatures of ancestral cortical identity.
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Affiliation(s)
- Sara Zeppilli
- Department of Neuroscience and Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Alonso O Gurrola
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Pinar Demetci
- Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - David H Brann
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Tuan M Pham
- Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Robin Attey
- Department of Neuroscience and Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Noga Zilkha
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Kimchi
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sandeep R Datta
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ritambhara Singh
- Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Maria A Tosches
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Anton Crombach
- Inria Centre de Lyon, Villeurbanne, France.
- INSA-Lyon, CNRS, UCBL, LIRIS, UMR5205, Villeurbanne, France.
- INSA-Lyon, CITI, UR3720, Villeurbanne, France.
| | - Alexander Fleischmann
- Department of Neuroscience and Carney Institute for Brain Science, Brown University, Providence, RI, USA.
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8
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Wang YM, Wang WC, Pan Y, Zeng L, Wu J, Wang ZB, Zhuang XL, Li ML, Cooper DN, Wang S, Shao Y, Wang LM, Fan YY, He Y, Hu XT, Wu DD. Regional and aging-specific cellular architecture of non-human primate brains. Genome Med 2025; 17:41. [PMID: 40296047 PMCID: PMC12038948 DOI: 10.1186/s13073-025-01469-x] [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: 01/19/2024] [Accepted: 04/08/2025] [Indexed: 04/30/2025] Open
Abstract
BACKGROUND Deciphering the functionality and dynamics of brain networks across different regions and age groups in non-human primates (NHPs) is crucial for understanding the evolution of human cognition as well as the processes underlying brain pathogenesis. However, systemic delineation of the cellular composition and molecular connections among multiple brain regions and their alterations induced by aging in NHPs remain largely unresolved. METHODS In this study, we performed single-nucleus RNA sequencing on 39 samples collected from 10 brain regions of two young and two aged rhesus macaques using the DNBelab C4 system. Validation of protein expression of signatures specific to particular cell types, brain regions, and aging was conducted through a series of immunofluorescence and immunohistochemistry staining experiments. Loss-of-function experiments mediated by short hairpin RNA (shRNA) targeting two age-related genes (i.e., VSNL1 and HPCAL4) were performed in U251 glioma cells to verify their aging effects. Senescence-associated beta-galactosidase (SA-β-gal) staining and quantitative PCR (qPCR) of senescence marker genes were employed to assess cellular senescence in U251 cells. RESULTS We have established a large-scale cell atlas encompassing over 330,000 cells for the rhesus macaque brain. Our analysis identified numerous gene expression signatures that were specific to particular cell types, subtypes, brain regions, and aging. These datasets greatly expand our knowledge of primate brain organization and highlight the potential involvement of specific molecular and cellular components in both the regionalization and functional integrity of the brain. Our analysis also disclosed extensive transcriptional alterations and cell-cell connections across brain regions in the aging macaques. Finally, by examining the heritability enrichment of human complex traits and diseases, we determined that neurological traits were significantly enriched in neuronal cells and multiple regions with aging-relevant gene expression signatures, while immune-related traits exhibited pronounced enrichment in microglia. CONCLUSIONS Taken together, our study presents a valuable resource for investigating the cellular and molecular architecture of the primate nervous system, thereby expanding our understanding of the mechanisms underlying brain function, aging, and disease.
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Affiliation(s)
- Yun-Mei Wang
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wen-Chao Wang
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, 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, 650201, 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, 650107, Yunnan, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yongzhang Pan
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Zeng
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jing Wu
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, 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, 650201, 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, 650107, Yunnan, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zheng-Bo Wang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Yunnan Key Laboratory of Primate Biomedical Research, Kunming, 650107, China
| | - Xiao-Lin Zhuang
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ming-Li Li
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sheng Wang
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yong Shao
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Li-Min Wang
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, 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, 650201, 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, 650107, Yunnan, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ying-Yin Fan
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, 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, 650201, 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, 650107, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yonghan He
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xin-Tian Hu
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, 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, 650201, 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, 650107, Yunnan, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, 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, 650107, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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9
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Islam MR, Jackson B, Naomi MT, Schatz B, Tan N, Murdock M, Park DS, Amorim DR, Jiang X, Pineda SS, Adaikkan C, Fernandez Avalos V, Geigenmuller U, Firenze RM, Kellis M, Boyden ES, Tsai LH. Multisensory gamma stimulation enhances adult neurogenesis and improves cognitive function in male mice with Down Syndrome. PLoS One 2025; 20:e0317428. [PMID: 40273201 PMCID: PMC12021272 DOI: 10.1371/journal.pone.0317428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Accepted: 12/27/2024] [Indexed: 04/26/2025] Open
Affiliation(s)
- Md Rezaul Islam
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Brennan Jackson
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Maeesha Tasnim Naomi
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Brooke Schatz
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Noah Tan
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Mitchell Murdock
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Dong Shin Park
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Daniela Rodrigues Amorim
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Xueqiao Jiang
- Departments of Biological Engineering and Brain and Cognitive Sciences, McGovern Institute, Cambridge, Massachusetts, United States of America
| | - S. Sebastian Pineda
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Chinnakkaruppan Adaikkan
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Vanesa Fernandez Avalos
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ute Geigenmuller
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rosalind Mott Firenze
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Edward S. Boyden
- Departments of Biological Engineering and Brain and Cognitive Sciences, McGovern Institute, Cambridge, Massachusetts, United States of America
- Koch Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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10
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Zhai D, Zheng M, Huang C, Wang X, Shi Y. RyR2-mediated calcium signaling regulates T-cell activation and Th1 differentiation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2025:vkaf046. [PMID: 40249873 DOI: 10.1093/jimmun/vkaf046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Accepted: 02/27/2025] [Indexed: 04/20/2025]
Abstract
T helper cell differentiation is one of the key developmental events in the peripheral immune regulations, resulting in better adaptation to the nature of infection and inflammation. While it is known that several factors are involved in this differentiation, including subsets of antigen-presenting cells, cytokine environment, and metabolic activation, how calcium signaling plays a role in this event has remained elusive and sometimes controversial. In this report, we show that ER membrane Ca2+ ion channel ryanodine receptor 2 (RyR2) may be an important regulator in this event. RyR2-deficient T cells show greater retention of Ca2+ in the ER and have reduced SOCE activation, leading a delayed entry of NFAT2 into the nuclei. This delay causes a significant bias toward Th1 both in cytokine profiles and in T-bet expression, likely as a result of increased Il12rb2 and Stat4 expression. Interestingly, such a bias permits better host protection against intracellular Listeria Monocytogenes infection. Our work suggests the possibility that RyR2 may be regulated in T-cell activation for biased Th polarization, which may provide a target for fine-tuning T-cell differentiation in future clinical settings.
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Affiliation(s)
- Di Zhai
- Institute for Immunology, and School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Mingke Zheng
- Institute for Immunology, and School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Cheng Huang
- Institute for Immunology, and School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Xiaobo Wang
- Institute for Immunology, and School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Yan Shi
- Institute for Immunology, and School of Basic Medical Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
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11
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Ernst KJ, Okonechnikov K, Bageritz J, Perera AA, Mallm JP, Wittmann A, Maaß KK, Leible S, Boutros M, Pfister SM, Zuckermann M, Jones DTW. A simplified preparation method for single-nucleus RNA-sequencing using long-term frozen brain tumor tissues. Sci Rep 2025; 15:12849. [PMID: 40229354 PMCID: PMC11997191 DOI: 10.1038/s41598-025-97053-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 04/02/2025] [Indexed: 04/16/2025] Open
Abstract
Single-cell RNA-sequencing has provided intriguing new insights into research areas such as developmental processes and tumor heterogeneity. Most approaches, however, rely on the availability of fresh surgical specimens, thereby dramatically reducing the ability to profile particularly rare tissue types. Here, we optimized a method to isolate intact nuclei from long-term frozen pediatric glioma tissues. We performed a technical comparison between different single-nucleus RNA-sequencing (snRNA-seq) systems and applied the established nucleus isolation method to analyze frozen primary glioma tissues. The results show that our fast, simple and low-cost nuclear isolation protocol provides intact nuclei, which can be used in both droplet- and plate-based single-cell sequencing platforms - allowing the identification of distinct tumor cell populations and infiltrating microglia. Additional optimization to include shorter RNA fragments in the 3' sequencing library improved gene detection and cell type annotation. Taken together, the method dramatically increases the potential of studying rare tumor entities and is specifically tailored for using frozen brain tumor tissue.
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Affiliation(s)
- Kati J Ernst
- Division of Pediatric Glioma Research, Hopp Children'S Cancer Center Heidelberg (Kitz), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, Hopp Children'S Cancer Center Heidelberg (Kitz), Heidelberg, Germany
| | - Josephine Bageritz
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ashwyn A Perera
- Division of Pediatric Glioma Research, Hopp Children'S Cancer Center Heidelberg (Kitz), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single-Cell Open Lab; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea Wittmann
- Division of Pediatric Glioma Research, Hopp Children'S Cancer Center Heidelberg (Kitz), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kendra K Maaß
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, Hopp Children'S Cancer Center Heidelberg (Kitz), Heidelberg, Germany
| | - Svenja Leible
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, Hopp Children'S Cancer Center Heidelberg (Kitz), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marc Zuckermann
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, Hopp Children'S Cancer Center Heidelberg (Kitz), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Glioma Research, Hopp Children'S Cancer Center Heidelberg (Kitz), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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12
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Mostafa M, Disouky A, Lazarov O. Therapeutic modulation of neurogenesis to improve hippocampal plasticity and cognition in aging and Alzheimer's disease. Neurotherapeutics 2025; 22:e00580. [PMID: 40180804 PMCID: PMC12047516 DOI: 10.1016/j.neurot.2025.e00580] [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: 12/11/2024] [Revised: 03/14/2025] [Accepted: 03/17/2025] [Indexed: 04/05/2025] Open
Abstract
Alzheimer's disease is characterized by progressive memory loss and cognitive decline. The hippocampal formation is the most vulnerable brain area in Alzheimer's disease. Neurons in layer II of the entorhinal cortex and the CA1 region of the hippocampus are lost at early stages of the disease. A unique feature of the hippocampus is the formation of new neurons that incorporate in the dentate gyrus of the hippocampus. New neurons form synapses with neurons in layer II of the entorhinal cortex and with the CA3 region. Immature and new neurons are characterized by high level of plasticity. They play important roles in learning and memory. Hippocampal neurogenesis is impaired early in mouse models of Alzheimer's disease and in human patients. In fact, neurogenesis is compromised in mild cognitive impairment (MCI), suggesting that rescuing neurogenesis may restore hippocampal plasticity and attenuate neuronal vulnerability and memory loss. This review will discuss the current understanding of therapies that target neurogenesis or modulate it, for the treatment of Alzheimer's disease.
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Affiliation(s)
- Mostafa Mostafa
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Ahmed Disouky
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Orly Lazarov
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, 60612, USA.
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13
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Ritchie EM, Acar D, Zhong S, Pu Q, Li Y, Zheng B, Jin Y. Translatome analysis reveals cellular network in DLK-dependent hippocampal glutamatergic neuron degeneration. eLife 2025; 13:RP101173. [PMID: 40067879 PMCID: PMC11896613 DOI: 10.7554/elife.101173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2025] Open
Abstract
The conserved MAP3K12/Dual Leucine Zipper Kinase (DLK) plays versatile roles in neuronal development, axon injury and stress responses, and neurodegeneration, depending on cell-type and cellular contexts. Emerging evidence implicates abnormal DLK signaling in several neurodegenerative diseases. However, our understanding of the DLK-dependent gene network in the central nervous system remains limited. Here, we investigated the roles of DLK in hippocampal glutamatergic neurons using conditional knockout and induced overexpression mice. We found that dorsal CA1 and dentate gyrus neurons are vulnerable to elevated expression of DLK, while CA3 neurons appear less vulnerable. We identified the DLK-dependent translatome that includes conserved molecular signatures and displays cell-type specificity. Increasing DLK signaling is associated with disruptions to microtubules, potentially involving STMN4. Additionally, primary cultured hippocampal neurons expressing different levels of DLK show altered neurite outgrowth, axon specification, and synapse formation. The identification of translational targets of DLK in hippocampal glutamatergic neurons has relevance to our understanding of selective neuron vulnerability under stress and pathological conditions.
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Affiliation(s)
- Erin M Ritchie
- Department of Neurobiology, School of Biological Sciences, University of California San DiegoLa JollaUnited States
- Biomedical Sciences Graduate Program, School of Medicine, University of California San DiegoLa JollaUnited States
| | - Dilan Acar
- Department of Neurobiology, School of Biological Sciences, University of California San DiegoLa JollaUnited States
| | - Siming Zhong
- Department of Neurobiology, School of Biological Sciences, University of California San DiegoLa JollaUnited States
| | - Qianyi Pu
- Department of Neurobiology, School of Biological Sciences, University of California San DiegoLa JollaUnited States
| | - Yunbo Li
- Department of Neurobiology, School of Biological Sciences, University of California San DiegoLa JollaUnited States
| | - Binhai Zheng
- Department of Neurosciences, School of Medicine, University of California San DiegoLa JollaUnited States
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California San DiegoLa JollaUnited States
- Department of Neurosciences, School of Medicine, University of California San DiegoLa JollaUnited States
- Kavli Institute for Brain and Mind, University of California San DiegoLa JollaUnited States
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14
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Suo Z, Xiao T, Qu Y, Zheng Y, Xu W, Zhou B, Yang J, Yu J, Zheng H, Ni C. Aged hippocampal single-cell atlas screening unveils disrupted neuroglial system in postoperative cognitive impairment. Aging Cell 2025; 24:e14406. [PMID: 39540334 PMCID: PMC11896209 DOI: 10.1111/acel.14406] [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: 06/08/2024] [Revised: 10/08/2024] [Accepted: 10/23/2024] [Indexed: 11/16/2024] Open
Abstract
Glia-neuron interaction is a crucial feature in aged hippocampus during the occurrence of postoperative cognitive impairment. However, the regulatory effects of microglia, astrocytes, and oligodendrocytes in this glia-neuron interaction, the potential mechanisms and gene targets are still to be elucidated. Here, single-cell RNA sequencing was performed to detect the perioperative genomic expression characteristics of neuroglial system in the hippocampus of aged mice, and to investigate the potential cross-cellular mechanisms and valuable treatment options for glia-neuron interaction-related cognitive impairment. We found that postoperative neurons and glia cells exhibited protein dysmetabolism and mitochondrial electron misrouting. Impaired autophagy and circadian rhythm worsened microglia activation/neuroinflammation, and exacerbated these metabolic alterations. Reactive microglia also aggravated astrocyte and oligodendrocyte cytotoxicity through the PGD2/DP and complement pathways, altering glutamate level and synaptic function via the "tripartite synapses" model, and affecting neuronal myelination. Ligand-receptor communication also indicated these synaptic and axonal dysfunctions via enhanced MDK and PTN pathways. Additionally, we found that anesthetic dexmedetomidine hold therapeutic potential within the disrupted neuroglial system. It enhanced neuronal metabolic rebalance (Atf3-related) and reduced neuroinflammation from a multicellular perspective, therefore improving postoperative cognitive impairment. Together, our study proposes an aged hippocampal cell atlas and provides insights into the role of disrupted glia-neuron cycle in postoperative cognitive impairment. Our findings also elucidate the therapeutic potential and mechanism of dexmedetomidine intervention.
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Affiliation(s)
- Zizheng Suo
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yinyin Qu
- Department of AnesthesiologyPeking University Third HospitalBeijingChina
| | - Yuxiang Zheng
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Wenjie Xu
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Bowen Zhou
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jing Yang
- Department of AnesthesiologyPeking University Third HospitalBeijingChina
| | - Jie Yu
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hui Zheng
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Cheng Ni
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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15
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Chan JC, Salvo GD, Cunningham AM, Dutta S, Brindley EA, Wan E, Zhang C, Maze I. Persistent dopamine-dependent remodeling of the neural transcriptome in response to pregnancy and postpartum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.20.639313. [PMID: 40060435 PMCID: PMC11888212 DOI: 10.1101/2025.02.20.639313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
Pregnancy and postpartum experiences represent transformative physiological states that impose lasting demands on the maternal body and brain, resulting in lifelong neural adaptations. However, the precise molecular mechanisms driving these persistent alterations remain poorly understood. Here, we used brain-wide transcriptomic profiling to define the molecular landscape of parity-induced neural plasticity, identifying the dorsal hippocampus (dHpc) as a key site of transcriptional remodeling. Combining single-cell RNA sequencing with a maternal-pup separation paradigm, we additionally demonstrated that chronic postpartum stress significantly disrupts dHpc adaptations by altering dopamine dynamics, leading to dysregulated transcription, altered cellular plasticity, and impaired behavior. We further established the sufficiency of dopamine modulation in the regulation of these parity-induced adaptations via chemogenetic suppression of dopamine release into dHpc, which recapitulated key transcriptional and behavioral features of parity in virgin females. In sum, our findings establish dopamine as a central regulator of parity-induced neuroadaptations, revealing a fundamental transcriptional mechanism by which female reproductive experiences remodel the maternal brain to sustain long-term behavioral adaptations.
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Affiliation(s)
- Jennifer C Chan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Giuseppina Di Salvo
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Ashley M Cunningham
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sohini Dutta
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elizabeth A Brindley
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ethan Wan
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Cindy Zhang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ian Maze
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Howard Hughes Medical Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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16
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Wu YE, De Luca R, Broadhurst RY, Venner A, Sohn LT, Bandaru SS, Schwalbe DC, Campbell J, Arrigoni E, Fuller PM. Suprachiasmatic Neuromedin-S Neurons Regulate Arousal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.22.639648. [PMID: 40027719 PMCID: PMC11870627 DOI: 10.1101/2025.02.22.639648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Mammalian circadian rhythms, which orchestrate the daily temporal structure of biological processes, including the sleep-wake cycle, are primarily regulated by the circadian clock in the hypothalamic suprachiasmatic nucleus (SCN). The SCN clock is also implicated in providing an arousal 'signal,' particularly during the wake-maintenance zone (WMZ) of our biological day, essential for sustaining normal levels of wakefulness in the presence of mounting sleep pressure. Here we identify a role for SCN Neuromedin-S (SCN NMS ) neurons in regulating the level of arousal, especially during the WMZ. We used chemogenetic and optogenetic methods to activate SCN NMS neurons in vivo, which potently drove wakefulness. Fiber photometry confirmed the wake-active profile of SCN NM neurons. Genetically ablating SCN NMS neurons disrupted the sleep-wake cycle, reducing wakefulness during the dark period and abolished the circadian rhythm of body temperature. SCN NMS neurons target the dorsomedial hypothalamic nucleus (DMH), and photostimulation of their terminals within the DMH rapidly produces arousal from sleep. Pre-synaptic inputs to SCN NMS neurons were also identified, including regions known to influence SCN clock regulation. Unexpectedly, we discovered strong input from the preoptic area (POA), which itself receives substantial inhibitory input from the DMH, forming a possible arousal-promoting circuit (SCN->DMH->POA->SCN). Finally, we analyzed the transcriptional profile of SCN NMS neurons via single-nuclei RNA-Seq, revealing three distinct subtypes. Our findings link molecularly-defined SCN neurons to sleep-wake patterns, body temperature rhythms, and arousal control. Significance Statement Our study's findings provide a cellular and neurobiological understanding of how Neuromedin-S (NMS)-containing SCN neurons contribute to regulating circadian rhythms, sleep-wake patterns, body temperature, and arousal control in mammals. This research illuminates the circuit, cellular, and synaptic mechanisms through which SCN neurons regulate daily cycles of wakefulness and sleep, with implications for understanding and potentially manipulating these processes in health and disease.
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Affiliation(s)
- Yu-Er Wu
- Department of Neurological Surgery, University of California, Davis School of Medicine; Davis, CA 95618, USA
- Department of Neurology, Division of Sleep Medicine, and Program in Neuroscience Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA 02215, USA
| | - Roberto De Luca
- Department of Neurology, Division of Sleep Medicine, and Program in Neuroscience Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA 02215, USA
| | - Rebecca Y. Broadhurst
- Department of Neurology, Division of Sleep Medicine, and Program in Neuroscience Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA 02215, USA
| | - Anne Venner
- Department of Neurology, Division of Sleep Medicine, and Program in Neuroscience Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA 02215, USA
| | - Lauren T. Sohn
- Department of Neurology, Division of Sleep Medicine, and Program in Neuroscience Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA 02215, USA
| | - Sathyajit S. Bandaru
- Department of Neurology, Division of Sleep Medicine, and Program in Neuroscience Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA 02215, USA
| | - Dana C. Schwalbe
- Department of Biology, University of Virginia; Charlottesville, VA 22904, USA
| | - John Campbell
- Department of Biology, University of Virginia; Charlottesville, VA 22904, USA
| | - Elda Arrigoni
- Department of Neurology, Division of Sleep Medicine, and Program in Neuroscience Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA 02215, USA
| | - Patrick M Fuller
- Department of Neurological Surgery, University of California, Davis School of Medicine; Davis, CA 95618, USA
- Department of Neurology, Division of Sleep Medicine, and Program in Neuroscience Beth Israel Deaconess Medical Center, Harvard Medical School; Boston, MA 02215, USA
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17
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Bartholome O, Neirinckx V, De La Brassinne O, Desloovere J, Van Den Ackerveken P, Raedt R, Rogister B. Synaptic Vesicle Glycoprotein 2A Knockout in Parvalbumin and Somatostatin Interneurons Drives Seizures in the Postnatal Mouse Brain. J Neurosci 2025; 45:e1169242024. [PMID: 39753304 PMCID: PMC11841765 DOI: 10.1523/jneurosci.1169-24.2024] [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: 06/19/2024] [Revised: 11/15/2024] [Accepted: 12/10/2024] [Indexed: 02/21/2025] Open
Abstract
Synaptic vesicle glycoprotein 2A (SV2A) is a presynaptic protein targeted by the antiseizure drug levetiracetam. One or more of the three SV2 genes is expressed in all neurons and is essential to normal neurotransmission. Loss of SV2A results in a seizure phenotype in mice and mutations in humans are also linked to congenital seizures. How SV2A action impacts the epileptic phenotype remains unclear, especially among the diverse neuronal populations that regulate network excitability. This study explored how brain structure and function are affected by SV2A conditional knock-out (SV2A-cKO) in specific neural cell subtypes. We show that SV2A-cKO in all neurons of the postnatal brain triggers lethal seizures, suggesting that the seizures observed in earlier knock-out models were not due to aberrant brain development. Similar lethal seizures are detected in mice in which the loss of SV2A is limited to GABAergic neurons, whereas loss in excitatory neurons produces no noticeable phenotype. No apparent gender difference was ever observed. Further investigation revealed that SV2A-cKO in different GABAergic interneuron populations induces seizure, with variable timescales and severity. Most notably SV2A-cKO in parvalbumin interneurons (PV+) leads to lethal seizures in young animals, while SV2A-cKO in somatostatin (SST) inhibitory neurons results in seizures that were scarcely observed only in adult mice. These results support the crucial role SV2A plays in PV and SST interneurons and suggest that the action of levetiracetam may be due largely to effects on a subset of GABAergic interneurons.
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Affiliation(s)
- Odile Bartholome
- Nervous System Disorders and Therapy, GIGA Institute, University of Liège, Liège 4000, Belgium
| | - Virginie Neirinckx
- Nervous System Disorders and Therapy, GIGA Institute, University of Liège, Liège 4000, Belgium
| | - Orianne De La Brassinne
- Nervous System Disorders and Therapy, GIGA Institute, University of Liège, Liège 4000, Belgium
| | | | | | | | - Bernard Rogister
- Nervous System Disorders and Therapy, GIGA Institute, University of Liège, Liège 4000, Belgium
- Neurology Department, CHU, Academic Hospital, University of Liège, Liège 4000 Belgium
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18
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Zhou Y, Su Y, Yang Q, Li J, Hong Y, Gao T, Zhong Y, Ma X, Jin M, Liu X, Yuan N, Kennedy BC, Wang L, Yan L, Viaene AN, Helbig I, Kessler SK, Kleinman JE, Hyde TM, Nauen DW, Liu C, Liu Z, Shen Z, Li C, Xu S, He J, Weinberger DR, Ming GL, Song H. Comparative molecular landscapes of immature neurons in the mammalian dentate gyrus across species reveal special features in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.16.638557. [PMID: 40027814 PMCID: PMC11870590 DOI: 10.1101/2025.02.16.638557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Immature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity, learning and memory, but their evolutionary changes across species and specialized features in humans remain poorly understood. Here we performed machine learning-augmented analysis of published single-cell RNA-sequencing datasets and identified macaque imGCs with transcriptome-wide immature neuronal characteristics. Our cross-species comparisons among humans, monkeys, pigs, and mice showed few shared (such as DPYSL5), but mostly species-specific gene expression in imGCs that converged onto common biological processes regulating neuronal development. We further identified human-specific transcriptomic features of imGCs and demonstrated functional roles of human imGC-enriched expression of a family of proton-transporting vacuolar-type ATPase subtypes in development of imGCs derived from human pluripotent stem cells. Our study reveals divergent gene expression patterns but convergent biological processes in the molecular characteristics of imGCs across species, highlighting the importance of conducting independent molecular and functional analyses for adult neurogenesis in different species.
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Affiliation(s)
- Yi Zhou
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Yijing Su
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Oral Medicine, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qian Yang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiaqi Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Yan Hong
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Taosha Gao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yanqing Zhong
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xueting Ma
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Mengmeng Jin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Xinglan Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Nini Yuan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Benjamin C. Kennedy
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lizhou Wang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Longying Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Angela N. Viaene
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sudha K. Kessler
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, The Solomon H. Snyder Department of Neuroscience, Department of Neurology, and Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, The Solomon H. Snyder Department of Neuroscience, Department of Neurology, and Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David W. Nauen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cirong Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Zhen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Zhiming Shen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Chao Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Shengjin Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Jie He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, The Solomon H. Snyder Department of Neuroscience, Department of Neurology, and Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Guo-li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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19
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Saunders RA, Allen WE, Pan X, Sandhu J, Lu J, Lau TK, Smolyar K, Sullivan ZA, Dulac C, Weissman JS, Zhuang X. A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.11.18.624217. [PMID: 39605605 PMCID: PMC11601512 DOI: 10.1101/2024.11.18.624217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect the genetic control of diverse cellular and tissue phenotypes in vivo. Here, we develop paired imaging and sequencing methods to construct large-scale, multi-modal genotype-phenotypes maps in tissue with pooled genetic perturbations. Using imaging, we identify genetic perturbations in individual cells while simultaneously measuring their gene expression and subcellular morphology. Using single-cell sequencing, we measure transcriptomic responses to the same genetic perturbations. We apply this approach to study hundreds of genetic perturbations in the mouse liver. Our study reveals regulators of hepatocyte zonation and liver unfolded protein response, as well as distinct pathways that cause hepatocyte steatosis. Our approach enables new ways of interrogating the genetic basis of complex cellular and organismal physiology and provides crucial training data for emerging machine-learning models of cellular function.
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Affiliation(s)
- Reuben A. Saunders
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Whitehead Institute, Cambridge, MA 02139, USA
- University of California, San Francisco, San Francisco, CA 94158, USA
- Present address: Society of Fellows, Harvard University, MA 02138, USA
- These authors contributed equally
| | - William E. Allen
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Society of Fellows, Harvard University, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Present address: Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305; Arc Institute, Palo Alto, CA 94304
- These authors contributed equally
- Lead contact
| | - Xingjie Pan
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Lead AI Scientist
| | - Jaspreet Sandhu
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Whitehead Institute, Cambridge, MA 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jiaqi Lu
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas K. Lau
- Department of Statistics, Stanford University, Stanford, CA 94305
| | - Karina Smolyar
- Whitehead Institute, Cambridge, MA 02139, USA
- Department of Biology, MIT, Cambridge, MA 02139 USA
| | - Zuri A. Sullivan
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Catherine Dulac
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jonathan S. Weissman
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Whitehead Institute, Cambridge, MA 02139, USA
- Department of Biology, MIT, Cambridge, MA 02139 USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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20
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Lantz C, Becker A, DeBerge M, Filipp M, Glinton K, Ananthakrishnan A, Urbanczyk J, Cetlin M, Alzamroon A, Abdel-Latif A, Spite M, Ge ZD, Thorp EB. Early-age efferocytosis directs macrophage arachidonic acid metabolism for tissue regeneration. Immunity 2025; 58:344-361.e7. [PMID: 39938482 PMCID: PMC11839170 DOI: 10.1016/j.immuni.2024.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/20/2024] [Accepted: 11/21/2024] [Indexed: 02/14/2025]
Abstract
In response to organ injury in adults, macrophages often promote scarring, yet during early life, they are required for tissue regeneration. To elucidate the mechanisms underlying age-associated regeneration, we compared the macrophage injury response in newborn versus adult hearts. Single-cell analysis revealed an accumulation of tissue-resident macrophages in neonates that were selectively polarized for apoptotic cell recognition and uptake (efferocytosis). Ablation of the apoptotic cell recognition receptor Mertk in newborns prevented cardiac regeneration. These findings could be attributed to reprogramming of macrophage gene expression that was required for biosynthesis of the eicosanoid thromboxane A2, which unexpectedly activated parenchymal cell proliferation. Markers of thromboxane A2 production were suppressed in adult macrophages after efferocytosis. Moreover, macrophage-neighboring neonatal cardiomyocytes expressed the thromboxane A2 receptor, whose activation induced a metabolic shift that supported cellular proliferation. Our data reveal a fundamental age-defined macrophage response in which lipid mitogens produced during efferocytosis support receptor-mediated tissue regeneration.
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Affiliation(s)
- Connor Lantz
- Department of Pathology, Feinberg School of Medicine, Chicago, IL 60611, USA; Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA.
| | - Amanda Becker
- Department of Pediatrics, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Matthew DeBerge
- Department of Pathology, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mallory Filipp
- Department of Pathology, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kristofor Glinton
- Department of Pathology, Feinberg School of Medicine, Chicago, IL 60611, USA
| | | | - Jessica Urbanczyk
- Department of Pathology, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Madeline Cetlin
- Department of Pathology, Feinberg School of Medicine, Chicago, IL 60611, USA
| | | | | | - Matthew Spite
- Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zhi-Dong Ge
- Department of Pathology, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Edward B Thorp
- Department of Pathology, Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Chicago, IL 60611, USA; Heart Center, Stanley Manne Children's Research Institute, Ann & Robert Lurie Children's Hospital, Chicago, IL 60611, USA; Comprehensive Transplant Center, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA.
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21
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Simmons SK, Adiconis X, Haywood N, Parker J, Lin Z, Liao Z, Tuncali I, Al’Khafaji AM, Shin A, Jagadeesh K, Gosik K, Gatzen M, Smith JT, El Kodsi DN, Kuras Y, Baecher-Allan C, Serrano GE, Beach TG, Garimella K, Rozenblatt-Rosen O, Regev A, Dong X, Scherzer CR, Levin JZ. Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.13.607784. [PMID: 39185246 PMCID: PMC11343128 DOI: 10.1101/2024.08.13.607784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool for understanding gene function across diverse cells. Recently, this has included the use of allele-specific expression (ASE) analysis to better understand how variation in the human genome affects RNA expression at the single-cell level. We reasoned that because intronic reads are more prevalent in single-nucleus RNA-Seq (snRNA-Seq), and introns are under lower purifying selection and thus enriched for genetic variants, that snRNA-seq should facilitate single-cell analysis of ASE. Here we demonstrate how experimental and computational choices can improve the results of allelic imbalance analysis. We explore how experimental choices, such as RNA source, read length, sequencing depth, genotyping, etc., impact the power of ASE-based methods. We developed a new suite of computational tools to process and analyze scRNA-seq and snRNA-seq for ASE. As hypothesized, we extracted more ASE information from reads in intronic regions than those in exonic regions and show how read length can be set to increase power. Additionally, hybrid selection improved our power to detect allelic imbalance in genes of interest. We also explored methods to recover allele-specific isoform expression levels from both long- and short-read snRNA-seq. To further investigate ASE in the context of human disease, we applied our methods to a Parkinson's disease cohort of 94 individuals and show that ASE analysis had more power than eQTL analysis to identify significant SNP/gene pairs in our direct comparison of the two methods. Overall, we provide an end-to-end experimental and computational approach for future studies.
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Affiliation(s)
- Sean K. Simmons
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xian Adiconis
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathan Haywood
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacob Parker
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Stephen & Denise Adams Center for Parkinson’s Disease Research of Yale School of Medicine, New Haven, CT 06510, USA
| | - Zechuan Lin
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Stephen & Denise Adams Center for Parkinson’s Disease Research of Yale School of Medicine, New Haven, CT 06510, USA
| | - Zhixiang Liao
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Precision Neurology Program of Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Idil Tuncali
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Precision Neurology Program of Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aziz M. Al’Khafaji
- Broad Clinical Labs, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Asa Shin
- Broad Clinical Labs, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karthik Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kirk Gosik
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Gatzen
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan T. Smith
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel N. El Kodsi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Precision Neurology Program of Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yuliya Kuras
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Precision Neurology Program of Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Clare Baecher-Allan
- Dept. of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Geidy E. Serrano
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Thomas G. Beach
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Kiran Garimella
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Present address: Genentech, South San Francisco, CA 94080, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Present address: Genentech, South San Francisco, CA 94080, USA
| | - Xianjun Dong
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Stephen & Denise Adams Center for Parkinson’s Disease Research of Yale School of Medicine, New Haven, CT 06510, USA
| | - Clemens R. Scherzer
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Stephen & Denise Adams Center for Parkinson’s Disease Research of Yale School of Medicine, New Haven, CT 06510, USA
| | - Joshua Z. Levin
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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22
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2025; 68:5-102. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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23
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Shi R, Chen H, Zhang W, Leak RK, Lou D, Chen K, Chen J. Single-cell RNA sequencing in stroke and traumatic brain injury: Current achievements, challenges, and future perspectives on transcriptomic profiling. J Cereb Blood Flow Metab 2024:271678X241305914. [PMID: 39648853 PMCID: PMC11626557 DOI: 10.1177/0271678x241305914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 10/19/2024] [Accepted: 11/06/2024] [Indexed: 12/10/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a high-throughput transcriptomic approach with the power to identify rare cells, discover new cellular subclusters, and describe novel genes. scRNA-seq can simultaneously reveal dynamic shifts in cellular phenotypes and heterogeneities in cellular subtypes. Since the publication of the first protocol on scRNA-seq in 2009, this evolving technology has continued to improve, through the use of cell-specific barcodes, adoption of droplet-based systems, and development of advanced computational methods. Despite induction of the cellular stress response during the tissue dissociation process, scRNA-seq remains a popular technology, and commercially available scRNA-seq methods have been applied to the brain. Recent advances in spatial transcriptomics now allow the researcher to capture the positional context of transcriptional activity, strengthening our knowledge of cellular organization and cell-cell interactions in spatially intact tissues. A combination of spatial transcriptomic data with proteomic, metabolomic, or chromatin accessibility data is a promising direction for future research. Herein, we provide an overview of the workflow, data analyses methods, and pros and cons of scRNA-seq technology. We also summarize the latest achievements of scRNA-seq in stroke and acute traumatic brain injury, and describe future applications of scRNA-seq and spatial transcriptomics.
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Affiliation(s)
- Ruyu Shi
- Department of Human Genetics, School of Public Health, University of Pittsburgh, USA
| | - Huaijun Chen
- Pittsburgh Institute of Brain Disorders & Recovery and Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
- Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA, USA
| | - Wenting Zhang
- Pittsburgh Institute of Brain Disorders & Recovery and Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
- Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA, USA
| | - Rehana K Leak
- Graduate School of Pharmaceutical Sciences, School of Pharmacy, Duquesne University, Pittsburgh, PA, USA
| | - Dequan Lou
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kong Chen
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jun Chen
- Pittsburgh Institute of Brain Disorders & Recovery and Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
- Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA, USA
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24
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Grant MT, Nelvagal HR, Tecos M, Hamed A, Swanson K, Cooper JD, Vrecenak JD. Cellular trafficking and fate mapping of cells within the nervous system after in utero hematopoietic cell transplantation. Commun Biol 2024; 7:1624. [PMID: 39638879 PMCID: PMC11621337 DOI: 10.1038/s42003-024-06847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 09/05/2024] [Indexed: 12/07/2024] Open
Abstract
In utero hematopoietic cell transplantation (IUHCT) utilizes fetal immune tolerance to achieve durable chimerism without conditioning or immunosuppression during a unique window in fetal development. Though donor cells have been observed within the nervous system following in utero injection, the timeline and distribution of cellular trafficking across the blood-brain barrier following IUHCT is not well understood. We injected 20 × 106 adult bone marrow mononuclear cells intravenously at gestational age (GA) 12-17 days and found that donor cells were maximally concentrated in the brain with treatment between GA 13-14. Donor cell engraftment persisted within the brain at every timepoint analyzed and concentrated within the hindbrain with significantly more grafted cells than in the forebrain. Additionally, transplanted cells terminally differentiated into various nervous system cellular morphologies and also populated the enteric nervous system. This study is the first to document the timeline and distribution of donor cell trafficking into the immune-protected nervous system and serves as a foundation for the application of IUHCT to treat neurogenetic diseases.
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Affiliation(s)
- Matthew T Grant
- Washington University in St. Louis School of Medicine, Department of Surgery, Division of Pediatric Surgery, St. Louis, MO, USA
| | - Hemanth Ramesh Nelvagal
- Washington University in St. Louis School of Medicine, Department of Pediatrics, Division of Genetics and Genomics, St. Louis, MO, USA
- University College London, School of Pharmacy, Department of Pharmacology, London, UK
| | - Maria Tecos
- Washington University in St. Louis School of Medicine, Department of Surgery, Division of Pediatric Surgery, St. Louis, MO, USA
| | - Amal Hamed
- Washington University in St. Louis School of Medicine, Department of Surgery, Division of Pediatric Surgery, St. Louis, MO, USA
| | - Kerry Swanson
- Washington University in St. Louis School of Medicine, Department of Surgery, Division of Pediatric Surgery, St. Louis, MO, USA
| | - Jonathan D Cooper
- Washington University in St. Louis School of Medicine, Department of Pediatrics, Division of Genetics and Genomics, St. Louis, MO, USA
| | - Jesse D Vrecenak
- Washington University in St. Louis School of Medicine, Department of Surgery, Division of Pediatric Surgery, St. Louis, MO, USA.
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25
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Ament SA, Campbell RR, Lobo MK, Receveur JP, Agrawal K, Borjabad A, Byrareddy SN, Chang L, Clarke D, Emani P, Gabuzda D, Gaulton KJ, Giglio M, Giorgi FM, Gok B, Guda C, Hadas E, Herb BR, Hu W, Huttner A, Ishmam MR, Jacobs MM, Kelschenbach J, Kim DW, Lee C, Liu S, Liu X, Madras BK, Mahurkar AA, Mash DC, Mukamel EA, Niu M, O'Connor RM, Pagan CM, Pang APS, Pillai P, Repunte-Canonigo V, Ruzicka WB, Stanley J, Tickle T, Tsai SYA, Wang A, Wills L, Wilson AM, Wright SN, Xu S, Yang J, Zand M, Zhang L, Zhang J, Akbarian S, Buch S, Cheng CS, Corley MJ, Fox HS, Gerstein M, Gummuluru S, Heiman M, Ho YC, Kellis M, Kenny PJ, Kluger Y, Milner TA, Moore DJ, Morgello S, Ndhlovu LC, Rana TM, Sanna PP, Satterlee JS, Sestan N, Spector SA, Spudich S, Tilgner HU, Volsky DJ, White OR, Williams DW, Zeng H. The single-cell opioid responses in the context of HIV (SCORCH) consortium. Mol Psychiatry 2024; 29:3950-3961. [PMID: 38879719 PMCID: PMC11609103 DOI: 10.1038/s41380-024-02620-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 05/12/2024] [Accepted: 05/17/2024] [Indexed: 06/19/2024]
Abstract
Substance use disorders (SUD) and drug addiction are major threats to public health, impacting not only the millions of individuals struggling with SUD, but also surrounding families and communities. One of the seminal challenges in treating and studying addiction in human populations is the high prevalence of co-morbid conditions, including an increased risk of contracting a human immunodeficiency virus (HIV) infection. Of the ~15 million people who inject drugs globally, 17% are persons with HIV. Conversely, HIV is a risk factor for SUD because chronic pain syndromes, often encountered in persons with HIV, can lead to an increased use of opioid pain medications that in turn can increase the risk for opioid addiction. We hypothesize that SUD and HIV exert shared effects on brain cell types, including adaptations related to neuroplasticity, neurodegeneration, and neuroinflammation. Basic research is needed to refine our understanding of these affected cell types and adaptations. Studying the effects of SUD in the context of HIV at the single-cell level represents a compelling strategy to understand the reciprocal interactions among both conditions, made feasible by the availability of large, extensively-phenotyped human brain tissue collections that have been amassed by the Neuro-HIV research community. In addition, sophisticated animal models that have been developed for both conditions provide a means to precisely evaluate specific exposures and stages of disease. We propose that single-cell genomics is a uniquely powerful technology to characterize the effects of SUD and HIV in the brain, integrating data from human cohorts and animal models. We have formed the Single-Cell Opioid Responses in the Context of HIV (SCORCH) consortium to carry out this strategy.
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Affiliation(s)
- Seth A Ament
- University of Maryland School of Medicine, Baltimore, MD, USA.
| | | | - Mary Kay Lobo
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | | | - Linda Chang
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Dana Gabuzda
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Michelle Giglio
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | - Eran Hadas
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian R Herb
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Wen Hu
- Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | - Cheyu Lee
- University of California Irvine, Irvine, CA, USA
| | - Shuhui Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiaokun Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Anup A Mahurkar
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Meng Niu
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | | | - Piya Pillai
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - W Brad Ruzicka
- McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | | | | | | | - Allen Wang
- University of California San Diego, La Jolla, CA, USA
| | - Lauren Wills
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Siwei Xu
- University of California Irvine, Irvine, CA, USA
| | | | - Maryam Zand
- University of California San Diego, La Jolla, CA, USA
| | - Le Zhang
- Yale School of Medicine, New Haven, CT, USA
| | - Jing Zhang
- University of California Irvine, Irvine, CA, USA
| | | | - Shilpa Buch
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | - Howard S Fox
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | - Myriam Heiman
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ya-Chi Ho
- Yale School of Medicine, New Haven, CT, USA
| | - Manolis Kellis
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul J Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - David J Moore
- University of California San Diego, La Jolla, CA, USA
| | - Susan Morgello
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Tariq M Rana
- University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | - David J Volsky
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Owen R White
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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26
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Webster AN, Becker JJ, Li C, Schwalbe DC, Kerspern D, Karolczak EO, Bundon CB, Onoharigho RA, Crook M, Jalil M, Godschall EN, Dame EG, Dawer A, Belmont-Rausch DM, Pers TH, Lutas A, Habib N, Güler AD, Krashes MJ, Campbell JN. Molecular connectomics reveals a glucagon-like peptide 1-sensitive neural circuit for satiety. Nat Metab 2024; 6:2354-2373. [PMID: 39627618 DOI: 10.1038/s42255-024-01168-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 10/17/2024] [Indexed: 12/11/2024]
Abstract
Liraglutide and other glucagon-like peptide 1 receptor agonists (GLP-1RAs) are effective weight loss drugs, but how they suppress appetite remains unclear. One potential mechanism is by activating neurons that inhibit the hunger-promoting Agouti-related peptide (AgRP) neurons of the arcuate hypothalamus (Arc). To identify these afferents, we developed a method combining rabies-based connectomics with single-nucleus transcriptomics. Here, we identify at least 21 afferent subtypes of AgRP neurons in the mouse mediobasal and paraventricular hypothalamus, which are predicted by our method. Among these are thyrotropin-releasing hormone (TRH)+ Arc (TRHArc) neurons, inhibitory neurons that express the Glp1r gene and are activated by the GLP-1RA liraglutide. Activating TRHArc neurons inhibits AgRP neurons and feeding, probably in an AgRP neuron-dependent manner. Silencing TRHArc neurons causes overeating and weight gain and attenuates liraglutide's effect on body weight. Our results demonstrate a widely applicable method for molecular connectomics, comprehensively identify local inputs to AgRP neurons and reveal a circuit through which GLP-1RAs suppress appetite.
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Affiliation(s)
- Addison N Webster
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Jordan J Becker
- Section on Motivational Processes Underlying Appetite, Diabetes, Endocrinology & Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Chia Li
- Section on Motivational Processes Underlying Appetite, Diabetes, Endocrinology & Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Dana C Schwalbe
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Damien Kerspern
- Section on Motivational Processes Underlying Appetite, Diabetes, Endocrinology & Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Eva O Karolczak
- Section on Motivational Processes Underlying Appetite, Diabetes, Endocrinology & Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | | | | | - Maisie Crook
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Maira Jalil
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Emily G Dame
- Section on Motivational Processes Underlying Appetite, Diabetes, Endocrinology & Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Adam Dawer
- Section on Motivational Processes Underlying Appetite, Diabetes, Endocrinology & Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | | | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Lutas
- Section on Motivational Processes Underlying Appetite, Diabetes, Endocrinology & Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Naomi Habib
- Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ali D Güler
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Michael J Krashes
- Section on Motivational Processes Underlying Appetite, Diabetes, Endocrinology & Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
| | - John N Campbell
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA.
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
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27
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Niu Y, Chen X, Zhang Y, Ge Y, Gao J, Huang T. Decoding neuronal genes in stroke-induced pain: insights from single-nucleus sequencing in mice. BMC Neurol 2024; 24:459. [PMID: 39581982 PMCID: PMC11587673 DOI: 10.1186/s12883-024-03965-w] [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: 03/04/2024] [Accepted: 11/19/2024] [Indexed: 11/26/2024] Open
Abstract
BACKGROUND The role of neurons in central post-stroke pain (CPSP) following thalamic hemorrhage remains unclear. This study aimed to identify key genes associated with post-thalamic hemorrhage pain and to explore their functions in neurons. Single-nucleus RNA sequencing (snRNA-seq) data from a mouse model was used for this analysis. METHODS First, snRNA-seq data were analyzed to identify cell types associated with CPSP induced by thalamic hemorrhage. Differentially expressed genes (DEGs) in neurons were then screened between control and model groups, followed by the construction of a protein-protein interaction (PPI) network for the DEGs. CytoNCA was used to assess node connectivity in the PPI network, and the top 5 key genes were identified. Subsequently, transcription factor (TF)-mRNA and miRNA-mRNA networks were constructed, and small-molecule drugs potentially targeting these key genes were predicted. Finally, the expression differences of key genes in neurons were compared between the model and control groups. RESULTS A total of 13 cell clusters were identified, categorized into 8 cell types: T cells, endothelial cells, monocytes, neural progenitor cells (NPCs), microglia, astrocytes, neurons, and oligodendrocytes. A total of 228 DEGs were detected in neurons when comparing the model group with the control group. The PPI network of the DEGs consisted of 126 nodes and 209 edges, identifying the top 5 key genes: Dlgap1, Cacna1c, Gria2, Hsp90ab1, and Gapdh. The miRNA-mRNA network included 68 miRNA-mRNA pairs, 62 miRNAs, and 5 mRNAs, while the TF-mRNA network consisted of 66 TF-mRNA pairs, 56 TFs, and 5 mRNAs. Drug prediction identified 110 small-molecule drugs (e.g., purpurogallin, nifedipine, and novobiocin) potentially targeting these key genes. Additionally, Cacna1c were significantly upregulated in model mice. CONCLUSION This study identified the role of key genes in thalamic hemorrhage-induced CPSP through snRNA-seq, providing a scientific basis for further exploration of the molecular mechanisms underlying CPSP.
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Affiliation(s)
- Yan Niu
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province, 221004, P. R. China
- Department of Anesthesiology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 Nan Tong Western Road, Yangzhou, Jiangsu Province, 225001, P. R. China
- Yangzhou Key Laboratory of Anaesthesiology, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou, Jiangsu Province, 225001, P. R. China
| | - Xiaoping Chen
- Department of Anesthesiology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 Nan Tong Western Road, Yangzhou, Jiangsu Province, 225001, P. R. China
- Yangzhou Key Laboratory of Anaesthesiology, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou, Jiangsu Province, 225001, P. R. China
| | - Yang Zhang
- Department of Anesthesiology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 Nan Tong Western Road, Yangzhou, Jiangsu Province, 225001, P. R. China
- Yangzhou Key Laboratory of Anaesthesiology, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou, Jiangsu Province, 225001, P. R. China
| | - Yali Ge
- Department of Anesthesiology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 Nan Tong Western Road, Yangzhou, Jiangsu Province, 225001, P. R. China
- Yangzhou Key Laboratory of Anaesthesiology, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou, Jiangsu Province, 225001, P. R. China
| | - Ju Gao
- Department of Anesthesiology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 Nan Tong Western Road, Yangzhou, Jiangsu Province, 225001, P. R. China.
- Yangzhou Key Laboratory of Anaesthesiology, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou, Jiangsu Province, 225001, P. R. China.
| | - Tianfeng Huang
- Department of Anesthesiology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 Nan Tong Western Road, Yangzhou, Jiangsu Province, 225001, P. R. China.
- Yangzhou Key Laboratory of Anaesthesiology, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou, Jiangsu Province, 225001, P. R. China.
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28
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Hou M, Zhang J, Wang Q, Zhao R, Cao Y, Chen Y, Wang K, Ding N, Qi Y, Sun X, Zhang Y, Li J. Single-Nucleus RNA Sequencing Reveals the Transcriptome Profiling of Ovarian Cells in Adolescent Cyprinus carpio. Animals (Basel) 2024; 14:3263. [PMID: 39595315 PMCID: PMC11591389 DOI: 10.3390/ani14223263] [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: 09/23/2024] [Revised: 10/27/2024] [Accepted: 11/12/2024] [Indexed: 11/28/2024] Open
Abstract
The common carp (Cyprinus carpio) is a crucial freshwater species cultivated worldwide for food consumption. Female carp have better growth performance than males, which fascinates scholars to uncover the mechanism of gonadal differentiation and produce mono-sex populations. However, the mechanism of ovarian development at single-cell resolution is limited. Here, we conducted single-nucleus RNA sequencing in adolescent common carp ovaries. Our study obtained transcriptional profiles of 13,155 nuclei and revealed 13 distinct cell clusters in the ovaries, including three subtypes of germ cells and four subtypes of granulosa cells. We subsequently performed pseudotime trajectory analysis to delineate potential mechanisms underlying the development of germ cells and granulosa cells. We identified 1250 dynamic expression genes in germ cells and 1815 in granulosa cells (q-value < 0.01), including zp3, eif4a2 and aspm in germ cells and fshr and esr1 in granulosa cells. The functional annotation showed that dynamic expression genes in germ cells were involved in sperm-egg recognition and some terms related to meiosis, such as sister chromatid segregation and homologous recombination. Genes expressed dynamically in granulosa cells were related to the TGF-β signaling pathway, response to gonadotropin, and development of primary female sexual characteristics. In addition, the dynamic genes expressed in granulosa cells might relate to the complex communication between different cell types. In summary, our study provided a transcriptome profile of common carp ovaries at single-nucleus resolution, and we further revealed the potential cell type-specific mechanisms underlying oogenesis and the differentiation of granulosa cells, which will facilitate breeding all-female common carp populations.
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Affiliation(s)
- Mingxi Hou
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (J.Z.); (Q.W.); (R.Z.); (Y.C.); (N.D.); (X.S.); (Y.Z.)
| | - Jin Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (J.Z.); (Q.W.); (R.Z.); (Y.C.); (N.D.); (X.S.); (Y.Z.)
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (J.Z.); (Q.W.); (R.Z.); (Y.C.); (N.D.); (X.S.); (Y.Z.)
| | - Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (J.Z.); (Q.W.); (R.Z.); (Y.C.); (N.D.); (X.S.); (Y.Z.)
| | - Yiming Cao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (J.Z.); (Q.W.); (R.Z.); (Y.C.); (N.D.); (X.S.); (Y.Z.)
| | - Yingjie Chen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; (Y.C.); (K.W.); (Y.Q.)
| | - Kaikuo Wang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; (Y.C.); (K.W.); (Y.Q.)
| | - Ning Ding
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (J.Z.); (Q.W.); (R.Z.); (Y.C.); (N.D.); (X.S.); (Y.Z.)
- Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingjie Qi
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; (Y.C.); (K.W.); (Y.Q.)
| | - Xiaoqing Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (J.Z.); (Q.W.); (R.Z.); (Y.C.); (N.D.); (X.S.); (Y.Z.)
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (J.Z.); (Q.W.); (R.Z.); (Y.C.); (N.D.); (X.S.); (Y.Z.)
| | - Jiongtang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (J.Z.); (Q.W.); (R.Z.); (Y.C.); (N.D.); (X.S.); (Y.Z.)
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29
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Seeler S, Arnarsson K, Dreßen M, Krane M, Doppler SA. Beyond the Heartbeat: Single-Cell Omics Redefining Cardiovascular Research. Curr Cardiol Rep 2024; 26:1183-1196. [PMID: 39158785 DOI: 10.1007/s11886-024-02117-3] [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] [Accepted: 08/07/2024] [Indexed: 08/20/2024]
Abstract
PURPOSE OF REVIEW This review aims to explore recent advances in single-cell omics techniques as applied to various regions of the human heart, illuminating cellular diversity, regulatory networks, and disease mechanisms. We examine the contributions of single-cell transcriptomics, genomics, proteomics, epigenomics, and spatial transcriptomics in unraveling the complexity of cardiac tissues. RECENT FINDINGS Recent strides in single-cell omics technologies have revolutionized our understanding of the heart's cellular composition, cell type heterogeneity, and molecular dynamics. These advancements have elucidated pathological conditions as well as the cellular landscape in heart development. We highlight emerging applications of integrated single-cell omics, particularly for cardiac regeneration, disease modeling, and precision medicine, and emphasize the transformative potential of these technologies to advance cardiovascular research and clinical practice.
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Affiliation(s)
- Sabine Seeler
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
| | - Kristjan Arnarsson
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
| | - Martina Dreßen
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Division of Cardiac Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Stefanie A Doppler
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany.
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany.
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30
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Bonine N, Zanzani V, Van Hemelryk A, Vanneste B, Zwicker C, Thoné T, Roelandt S, Bekaert SL, Koster J, Janoueix-Lerosey I, Thirant C, Van Haver S, Roberts SS, Mus LM, De Wilde B, Van Roy N, Everaert C, Speleman F, Vermeirssen V, Scott CL, De Preter K. NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors. Cell Rep 2024; 43:114804. [PMID: 39368085 DOI: 10.1016/j.celrep.2024.114804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/11/2024] [Accepted: 09/12/2024] [Indexed: 10/07/2024] Open
Abstract
Neuroblastoma, a rare embryonic tumor arising from neural crest development, is responsible for 15% of pediatric cancer-related deaths. Recently, several single-cell transcriptome studies were performed on neuroblastoma patient samples to investigate the cell of origin and tumor heterogeneity. However, these individual studies involved a small number of tumors and cells, limiting the conclusions that could be drawn. To overcome this limitation, we integrated seven single-cell or single-nucleus datasets into a harmonized cell atlas covering 362,991 cells across 61 patients. We use this atlas to decipher the transcriptional landscape of neuroblastoma at single-cell resolution, revealing associations between transcriptomic profiles and clinical outcomes within the tumor compartment. In addition, we characterize the complex immune-cell landscape and uncover considerable heterogeneity among tumor-associated macrophages. Finally, we showcase the utility of our atlas as a resource by expanding it with additional data and using it as a reference for data-driven cell-type annotation.
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Affiliation(s)
- Noah Bonine
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Vittorio Zanzani
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory for Computational Biology, Integromics and Gene Regulation (CBIGR), Ghent University, Ghent, Belgium
| | - Annelies Van Hemelryk
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Bavo Vanneste
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Christian Zwicker
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Tinne Thoné
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Sofie Roelandt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Sarah-Lee Bekaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jan Koster
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Isabelle Janoueix-Lerosey
- Inserm U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
| | - Cécile Thirant
- Inserm U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
| | - Stéphane Van Haver
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen S Roberts
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Liselot M Mus
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bram De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Nadine Van Roy
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Celine Everaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Frank Speleman
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Vanessa Vermeirssen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory for Computational Biology, Integromics and Gene Regulation (CBIGR), Ghent University, Ghent, Belgium
| | - Charlotte L Scott
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium.
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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31
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Verstappe B, Scott CL. Implementing distinct spatial proteogenomic technologies: opportunities, challenges, and key considerations. Clin Exp Immunol 2024; 218:151-162. [PMID: 39133142 PMCID: PMC11482502 DOI: 10.1093/cei/uxae077] [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: 03/29/2024] [Revised: 06/11/2024] [Accepted: 08/09/2024] [Indexed: 08/13/2024] Open
Abstract
Our ability to understand the cellular complexity of tissues has been revolutionized in recent years with significant advances in proteogenomic technologies including those enabling spatial analyses. This has led to numerous consortium efforts, such as the human cell atlas initiative which aims to profile all cells in the human body in healthy and diseased contexts. The availability of such information will subsequently lead to the identification of novel biomarkers of disease and of course therapeutic avenues. However, before such an atlas of any given healthy or diseased tissue can be generated, several factors should be considered including which specific techniques are optimal for the biological question at hand. In this review, we aim to highlight some of the considerations we believe to be important in the experimental design and analysis process, with the goal of helping to navigate the rapidly changing landscape of technologies available.
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Affiliation(s)
- Bram Verstappe
- Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Ghent, Belgium
| | - Charlotte L Scott
- Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Ghent, Belgium
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Castletroy, Co. Limerick, Ireland
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32
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Chen ZK, Quintanilla L, Su Y, Sheehy RN, Simon JM, Luo YJ, Li YD, Chen Z, Asrican B, Tart DS, Farmer WT, Ming GL, Song H, Song J. Septo-dentate gyrus cholinergic circuits modulate function and morphogenesis of adult neural stem cells through granule cell intermediaries. Proc Natl Acad Sci U S A 2024; 121:e2405117121. [PMID: 39312657 PMCID: PMC11459179 DOI: 10.1073/pnas.2405117121] [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: 03/15/2024] [Accepted: 07/17/2024] [Indexed: 09/25/2024] Open
Abstract
Cholinergic neurons in the basal forebrain play a crucial role in regulating adult hippocampal neurogenesis (AHN). However, the circuit and molecular mechanisms underlying cholinergic modulation of AHN, especially the initial stages of this process related to the generation of newborn progeny from quiescent radial neural stem cells (rNSCs), remain unclear. Here, we report that stimulation of the cholinergic circuits projected from the diagonal band of Broca (DB) to the dentate gyrus (DG) neurogenic niche promotes proliferation and morphological development of rNSCs, resulting in increased neural stem/progenitor pool and rNSCs with longer radial processes and larger busy heads. Interestingly, DG granule cells (GCs) are required for DB-DG cholinergic circuit-dependent modulation of proliferation and morphogenesis of rNSCs. Furthermore, single-nucleus RNA sequencing of DG reveals cell type-specific transcriptional changes in response to cholinergic circuit stimulation, with GCs (among all the DG niche cells) exhibiting the most extensive transcriptional changes. Our findings shed light on how the DB-DG cholinergic circuits orchestrate the key niche components to support neurogenic function and morphogenesis of rNSCs at the circuit and molecular levels.
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Affiliation(s)
- Ze-Ka Chen
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Luis Quintanilla
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Neuroscience Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Yijing Su
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Oral Medicine, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ryan N. Sheehy
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Pharmacology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jeremy M. Simon
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Yan-Jia Luo
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Ya-Dong Li
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Zhe Chen
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Brent Asrican
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Dalton S. Tart
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - W. Todd Farmer
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Juan Song
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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De Rijk P, Watzeels T, Küçükali F, Van Dongen J, Faura J, Willems P, De Deyn L, Duchateau L, Grones C, Eekhout T, De Pooter T, Joris G, Rombauts S, De Rybel B, Rademakers R, Van Breusegem F, Strazisar M, Sleegers K, De Coster W. Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing. Bioinformatics 2024; 40:btae549. [PMID: 39254601 PMCID: PMC11419950 DOI: 10.1093/bioinformatics/btae549] [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: 04/23/2024] [Revised: 08/29/2024] [Accepted: 09/06/2024] [Indexed: 09/11/2024] Open
Abstract
MOTIVATION Existing nanopore single-cell data analysis tools showed severe limitations in handling current data sizes. RESULTS We introduce scywalker, an innovative and scalable package developed to comprehensively analyze long-read sequencing data of full-length single-cell or single-nuclei cDNA. We developed novel scalable methods for cell barcode demultiplexing and single-cell isoform calling and quantification and incorporated these in an easily deployable package. Scywalker streamlines the entire analysis process, from sequenced fragments in FASTQ format to demultiplexed pseudobulk isoform counts, into a single command suitable for execution on either server or cluster. Scywalker includes data quality control, cell type identification, and an interactive report. Assessment of datasets from the human brain, Arabidopsis leaves, and previously benchmarked data from mixed cell lines demonstrate excellent correlation with short-read analyses at both the cell-barcoding and gene quantification levels. At the isoform level, we show that scywalker facilitates the direct identification of cell-type-specific expression of novel isoforms. AVAILABILITY AND IMPLEMENTATION Scywalker is available on github.com/derijkp/scywalker under the GNU General Public License (GPL) and at https://zenodo.org/records/13359438/files/scywalker-0.108.0-Linux-x86_64.tar.gz.
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Affiliation(s)
- Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Universiteitsplein 1, Antwerp, 2610, Belgium
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Tijs Watzeels
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
- Complex Genetics of Alzheimer’s Disease Group, VIB Center for Molecular Neurology, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Fahri Küçükali
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
- Complex Genetics of Alzheimer’s Disease Group, VIB Center for Molecular Neurology, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Jasper Van Dongen
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
- Complex Genetics of Alzheimer’s Disease Group, VIB Center for Molecular Neurology, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Júlia Faura
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Zwijnaarde, 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 71, Zwijnaarde, 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
- VIB Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, Ghent, 9052, Belgium
| | - Lara De Deyn
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
- Complex Genetics of Alzheimer’s Disease Group, VIB Center for Molecular Neurology, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Lena Duchateau
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
- Complex Genetics of Alzheimer’s Disease Group, VIB Center for Molecular Neurology, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Carolin Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Zwijnaarde, 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 71, Zwijnaarde, 9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Zwijnaarde, 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 71, Zwijnaarde, 9052, Belgium
- VIB Single Cell Core, VIB, Technologiepark-Zwijnaarde 71, Ghent, 9052, Belgium
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Universiteitsplein 1, Antwerp, 2610, Belgium
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Geert Joris
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Universiteitsplein 1, Antwerp, 2610, Belgium
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Zwijnaarde, 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 71, Zwijnaarde, 9052, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Zwijnaarde, 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 71, Zwijnaarde, 9052, Belgium
| | - Rosa Rademakers
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Zwijnaarde, 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 71, Zwijnaarde, 9052, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Universiteitsplein 1, Antwerp, 2610, Belgium
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Kristel Sleegers
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
- Complex Genetics of Alzheimer’s Disease Group, VIB Center for Molecular Neurology, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Wouter De Coster
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Universiteitsplein 1, Antwerp, 2610, Belgium
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Green GS, Fujita M, Yang HS, Taga M, Cain A, McCabe C, Comandante-Lou N, White CC, Schmidtner AK, Zeng L, Sigalov A, Wang Y, Regev A, Klein HU, Menon V, Bennett DA, Habib N, De Jager PL. Cellular communities reveal trajectories of brain ageing and Alzheimer's disease. Nature 2024; 633:634-645. [PMID: 39198642 PMCID: PMC11877878 DOI: 10.1038/s41586-024-07871-6] [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: 02/22/2023] [Accepted: 07/24/2024] [Indexed: 09/01/2024]
Abstract
Alzheimer's disease (AD) has recently been associated with diverse cell states1-11, yet when and how these states affect the onset of AD remains unclear. Here we used a data-driven approach to reconstruct the dynamics of the brain's cellular environment and identified a trajectory leading to AD that is distinct from other ageing-related effects. First, we built a comprehensive cell atlas of the aged prefrontal cortex from 1.65 million single-nucleus RNA-sequencing profiles sampled from 437 older individuals, and identified specific glial and neuronal subpopulations associated with AD-related traits. Causal modelling then prioritized two distinct lipid-associated microglial subpopulations-one drives amyloid-β proteinopathy while the other mediates the effect of amyloid-β on tau proteinopathy-as well as an astrocyte subpopulation that mediates the effect of tau on cognitive decline. To model the dynamics of cellular environments, we devised the BEYOND methodology, which identified two distinct trajectories of brain ageing, each defined by coordinated progressive changes in certain cellular communities that lead to (1) AD dementia or (2) alternative brain ageing. Thus, we provide a cellular foundation for a new perspective on AD pathophysiology that informs personalized therapeutic development, targeting different cellular communities for individuals on the path to AD or to alternative brain ageing.
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Affiliation(s)
- Gilad Sahar Green
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Masashi Fujita
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Hyun-Sik Yang
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Mariko Taga
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Anael Cain
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Natacha Comandante-Lou
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Anna K Schmidtner
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lu Zeng
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Alina Sigalov
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Yangling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, San Francisco, CA, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA.
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Naomi Habib
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Chen X, Huang Y, Huang L, Huang Z, Hao ZZ, Xu L, Xu N, Li Z, Mou Y, Ye M, You R, Zhang X, Liu S, Miao Z. A brain cell atlas integrating single-cell transcriptomes across human brain regions. Nat Med 2024; 30:2679-2691. [PMID: 39095595 PMCID: PMC11405287 DOI: 10.1038/s41591-024-03150-z] [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: 07/31/2023] [Accepted: 06/24/2024] [Indexed: 08/04/2024]
Abstract
While single-cell technologies have greatly advanced our comprehension of human brain cell types and functions, studies including large numbers of donors and multiple brain regions are needed to extend our understanding of brain cell heterogeneity. Integrating atlas-level single-cell data presents a chance to reveal rare cell types and cellular heterogeneity across brain regions. Here we present the Brain Cell Atlas, a comprehensive reference atlas of brain cells, by assembling single-cell data from 70 human and 103 mouse studies of the brain throughout major developmental stages across brain regions, covering over 26.3 million cells or nuclei from both healthy and diseased tissues. Using machine-learning based algorithms, the Brain Cell Atlas provides a consensus cell type annotation, and it showcases the identification of putative neural progenitor cells and a cell subpopulation of PCDH9high microglia in the human brain. We demonstrate the gene regulatory difference of PCDH9high microglia between hippocampus and prefrontal cortex and elucidate the cell-cell communication network. The Brain Cell Atlas presents an atlas-level integrative resource for comparing brain cells in different environments and conditions within the Human Cell Atlas.
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Affiliation(s)
- Xinyue Chen
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Yin Huang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Liangfeng Huang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Ziliang Huang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 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, China
| | - Lahong Xu
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 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, China
| | - Zhi Li
- Department of Neurosurgery/Neuro-oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yonggao Mou
- Department of Neurosurgery/Neuro-oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Mingli Ye
- Tsinghua Fuzhou Institute for Data Technology, Fuzhou, China
| | - Renke You
- Tsinghua Fuzhou Institute for Data Technology, Fuzhou, China
| | - Xuegong Zhang
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing, China
- School of Medicine, Tsinghua University, Beijing, China
- School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 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, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, China.
| | - Zhichao Miao
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China.
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou International Bio Island, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou International Bio Island, Guangzhou, China.
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36
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Zhu S, Kubota N, Wang S, Wang T, Xiao G, Hoshida Y. STIE: Single-cell level deconvolution, convolution, and clustering in in situ capturing-based spatial transcriptomics. Nat Commun 2024; 15:7559. [PMID: 39214995 PMCID: PMC11364663 DOI: 10.1038/s41467-024-51728-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
In in situ capturing-based spatial transcriptomics, spots of the same size and printed at fixed locations cannot precisely capture the randomly-located single cells, therefore inherently failing to profile transcriptome at the single-cell level. To this end, we present STIE, an Expectation Maximization algorithm that aligns the spatial transcriptome to its matched histology image-based nuclear morphology and recovers missing cells from ~70% gap area, thereby achieving the real single-cell level and whole-slide scale deconvolution, convolution, and clustering for both low- and high-resolution spots. STIE characterizes cell-type-specific gene expression and demonstrates outperforming concordance with true cell-type-specific transcriptomic signatures than the other spot- and subspot-level methods. Furthermore, STIE reveals the single-cell level insights, for instance, lower actual spot resolution than its reported spot size, unbiased evaluation of cell type colocalization, superior power of high-resolution spot in distinguishing nuanced cell types, and spatial cell-cell interactions at the single-cell level other than spot level.
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Affiliation(s)
- Shijia Zhu
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
- Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Naoto Kubota
- Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shidan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yujin Hoshida
- Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Peng R, Zhang L, Xie Y, Guo S, Cao X, Yang M. Spatial multi-omics analysis of the microenvironment in traumatic spinal cord injury: a narrative review. Front Immunol 2024; 15:1432841. [PMID: 39267742 PMCID: PMC11390538 DOI: 10.3389/fimmu.2024.1432841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/22/2024] [Indexed: 09/15/2024] Open
Abstract
Traumatic spinal cord injury (tSCI) is a severe injury to the central nervous system that is categorized into primary and secondary injuries. Among them, the local microenvironmental imbalance in the spinal cord caused by secondary spinal cord injury includes accumulation of cytokines and chemokines, reduced angiogenesis, dysregulation of cellular energy metabolism, and dysfunction of immune cells at the site of injury, which severely impedes neurological recovery from spinal cord injury (SCI). In recent years, single-cell techniques have revealed the heterogeneity of multiple immune cells at the genomic, transcriptomic, proteomic, and metabolomic levels after tSCI, further deepening our understanding of the mechanisms underlying tSCI. However, spatial information about the tSCI microenvironment, such as cell location and cell-cell interactions, is lost in these approaches. The application of spatial multi-omics technology can solve this problem by combining the data obtained from immunohistochemistry and multiparametric analysis to reveal the changes in the microenvironment at different times of secondary injury after SCI. In this review, we systematically review the progress of spatial multi-omics techniques in the study of the microenvironment after SCI, including changes in the immune microenvironment and discuss potential future therapeutic strategies.
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Affiliation(s)
- Run Peng
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China
| | - Liang Zhang
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China
| | - Yongqi Xie
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China
| | - Shuang Guo
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China
- Department of Rehabilitation, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xinqi Cao
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China
| | - Mingliang Yang
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation, Research Center, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
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38
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Hildebrandt F, Iturritza MU, Zwicker C, Vanneste B, Van Hul N, Semle E, Quin J, Pascini T, Saarenpää S, He M, Andersson ER, Scott CL, Vega-Rodriguez J, Lundeberg J, Ankarklev J. Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution. Nat Commun 2024; 15:7105. [PMID: 39160174 PMCID: PMC11333755 DOI: 10.1038/s41467-024-51418-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
Upon infecting its vertebrate host, the malaria parasite initially invades the liver where it undergoes massive replication, whilst remaining clinically silent. The coordination of host responses across the complex liver tissue during malaria infection remains unexplored. Here, we perform spatial transcriptomics in combination with single-nuclei RNA sequencing over multiple time points to delineate host-pathogen interactions across Plasmodium berghei-infected liver tissues. Our data reveals significant changes in spatial gene expression in the malaria-infected tissues. These include changes related to lipid metabolism in the proximity to sites of Plasmodium infection, distinct inflammation programs between lobular zones, and regions with enrichment of different inflammatory cells, which we term 'inflammatory hotspots'. We also observe significant upregulation of genes involved in inflammation in the control liver tissues of mice injected with mosquito salivary gland components. However, this response is considerably delayed compared to that observed in P. berghei-infected mice. Our study establishes a benchmark for investigating transcriptome changes during host-parasite interactions in tissues, it provides informative insights regarding in vivo study design linked to infection and offers a useful tool for the discovery and validation of de novo intervention strategies aimed at malaria liver stage infection.
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Affiliation(s)
- Franziska Hildebrandt
- Molecular Biosciences, the Wenner Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, SE-106 91, Stockholm, Sweden.
| | - Miren Urrutia Iturritza
- Molecular Biosciences, the Wenner Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, SE-106 91, Stockholm, Sweden
| | - Christian Zwicker
- Department of Biomedical Molecular Biology, Faculty of Sciences, Ghent University, Ghent, Belgium
- Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, Ghent, 9052, Belgium
| | - Bavo Vanneste
- Department of Biomedical Molecular Biology, Faculty of Sciences, Ghent University, Ghent, Belgium
- Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, Ghent, 9052, Belgium
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, Ghent, 9052, Belgium
| | - Noémi Van Hul
- Department of Cell and Molecular Biology, Karolinska Institutet Stockholm, SE-171 77, Solna, Sweden
| | - Elisa Semle
- Molecular Biosciences, the Wenner Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, SE-106 91, Stockholm, Sweden
| | - Jaclyn Quin
- Molecular Biosciences, the Wenner Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, SE-106 91, Stockholm, Sweden
| | - Tales Pascini
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12735 Twinbrook Parkway, Rm 2E20A, Rockville, MD, 20852, USA
| | - Sami Saarenpää
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Tomtebodavägen 23a, SE-171 65, Solna, Sweden
| | - Mengxiao He
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Tomtebodavägen 23a, SE-171 65, Solna, Sweden
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet Stockholm, SE-171 77, Solna, Sweden
| | - Charlotte L Scott
- Department of Biomedical Molecular Biology, Faculty of Sciences, Ghent University, Ghent, Belgium
- Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Technologiepark-Zwijnaarde 71, Ghent, 9052, Belgium
| | - Joel Vega-Rodriguez
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12735 Twinbrook Parkway, Rm 2E20A, Rockville, MD, 20852, USA
| | - Joakim Lundeberg
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Tomtebodavägen 23a, SE-171 65, Solna, Sweden
| | - Johan Ankarklev
- Molecular Biosciences, the Wenner Gren Institute, Stockholm University, Svante Arrhenius Väg 20C, SE-106 91, Stockholm, Sweden.
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Methi A, Islam MR, Kaurani L, Sakib MS, Krüger DM, Pena T, Burkhardt S, Liebetanz D, Fischer A. A Single-Cell Transcriptomic Analysis of the Mouse Hippocampus After Voluntary Exercise. Mol Neurobiol 2024; 61:5628-5645. [PMID: 38217668 PMCID: PMC11249425 DOI: 10.1007/s12035-023-03869-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/29/2023] [Indexed: 01/15/2024]
Abstract
Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms, we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after 4 weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-κB, Wnt/β-catenin, Notch, and retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important resource dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline.
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Affiliation(s)
- Aditi Methi
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Md Rezaul Islam
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Lalit Kaurani
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - M Sadman Sakib
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Dennis M Krüger
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Tonatiuh Pena
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Susanne Burkhardt
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - David Liebetanz
- Department of Neurology, University Medical Center, Göttingen, Germany
| | - André Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany.
- Department for Psychiatry and Psychotherapy, University Medical Center of Göttingen, Georg-August University, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
- DZHK (German Center for Cardiovascular Research), Partner Site, Göttingen, Germany.
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Gomez-Murcia V, Launay A, Carvalho K, Burgard A, Meriaux C, Caillierez R, Eddarkaoui S, Kilinc D, Siedlecki-Wullich D, Besegher M, Bégard S, Thiroux B, Jung M, Nebie O, Wisztorski M, Déglon N, Montmasson C, Bemelmans AP, Hamdane M, Lebouvier T, Vieau D, Fournier I, Buee L, Lévi S, Lopes LV, Boutillier AL, Faivre E, Blum D. Neuronal A2A receptor exacerbates synapse loss and memory deficits in APP/PS1 mice. Brain 2024; 147:2691-2705. [PMID: 38964748 PMCID: PMC11292904 DOI: 10.1093/brain/awae113] [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: 11/30/2023] [Revised: 02/20/2024] [Accepted: 03/21/2024] [Indexed: 07/06/2024] Open
Abstract
Early pathological upregulation of adenosine A2A receptors (A2ARs), one of the caffeine targets, by neurons is thought to be involved in the development of synaptic and memory deficits in Alzheimer's disease (AD) but mechanisms remain ill-defined. To tackle this question, we promoted a neuronal upregulation of A2AR in the hippocampus of APP/PS1 mice developing AD-like amyloidogenesis. Our findings revealed that the early upregulation of A2AR in the presence of an ongoing amyloid pathology exacerbates memory impairments of APP/PS1 mice. These behavioural changes were not linked to major change in the development of amyloid pathology but rather associated with increased phosphorylated tau at neuritic plaques. Moreover, proteomic and transcriptomic analyses coupled with quantitative immunofluorescence studies indicated that neuronal upregulation of the receptor promoted both neuronal and non-neuronal autonomous alterations, i.e. enhanced neuroinflammatory response but also loss of excitatory synapses and impaired neuronal mitochondrial function, presumably accounting for the detrimental effect on memory. Overall, our results provide compelling evidence that neuronal A2AR dysfunction, as seen in the brain of patients, contributes to amyloid-related pathogenesis and underscores the potential of A2AR as a relevant therapeutic target for mitigating cognitive impairments in this neurodegenerative disorder.
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Affiliation(s)
- Victoria Gomez-Murcia
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Agathe Launay
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Kévin Carvalho
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Anaëlle Burgard
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), University of Strasbourg, F-67000 Strasbourg, France
- UMR7364–Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), CNRS, F-67000 Strasbourg, France
| | - Céline Meriaux
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Raphaëlle Caillierez
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Sabiha Eddarkaoui
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Devrim Kilinc
- Inserm U1167, LabEx DISTALZ, Université de Lille, Institut Pasteur de Lille, CHU Lille, F-59000 Lille, France
| | - Dolores Siedlecki-Wullich
- Inserm U1167, LabEx DISTALZ, Université de Lille, Institut Pasteur de Lille, CHU Lille, F-59000 Lille, France
| | - Mélanie Besegher
- Plateformes Lilloises en Biologie et Santé (PLBS)–UAR 2014–US 41, CNRS, Inserm, Université de Lille, Institut Pasteur de Lille, CHU Lille, F-59000 Lille, France
| | - Séverine Bégard
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Bryan Thiroux
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Matthieu Jung
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), University of Strasbourg, CNRS UMR7104, Inserm U1258—GenomEast Platform, F-67400 Illkirch, France
| | - Ouada Nebie
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Maxence Wisztorski
- Inserm U1192, Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), Université de Lille, Lille F-59000, France
| | - Nicole Déglon
- Laboratory of Cellular and Molecular Neurotherapies (LCMN), Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Neuroscience Research Center (CRN), 1011 Lausanne, Switzerland
| | - Claire Montmasson
- Institut du Fer à Moulin, Inserm UMR-S 1270, Sorbonne Université, F-75005 Paris, France
| | - Alexis-Pierre Bemelmans
- Laboratoire des Maladies Neurodégénératives: mécanismes, thérapies, imagerie, Université Paris-Saclay, CEA, CNRS, F-92265 Fontenay-aux-Roses, France
| | - Malika Hamdane
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Thibaud Lebouvier
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
- Memory Clinic, CHU Lille, F-59000 Lille, France
| | - Didier Vieau
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Isabelle Fournier
- Inserm U1192, Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), Université de Lille, Lille F-59000, France
| | - Luc Buee
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - Sabine Lévi
- Institut du Fer à Moulin, Inserm UMR-S 1270, Sorbonne Université, F-75005 Paris, France
| | - Luisa V Lopes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina de Lisboa, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Anne-Laurence Boutillier
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), University of Strasbourg, F-67000 Strasbourg, France
- UMR7364–Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), CNRS, F-67000 Strasbourg, France
| | - Emilie Faivre
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
| | - David Blum
- UMR-S1172 Lille Neuroscience & Cognition (LilNCog), University of Lille, Inserm, CHU Lille, F-59000 Lille, France
- Alzheimer & Tauopathies Team, LabEx DISTALZ, University of Lille, F-59000 Lille, France
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41
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Schwalbe DC, Stornetta DS, Abraham-Fan RJ, Souza GMPR, Jalil M, Crook ME, Campbell JN, Abbott SBG. Molecular Organization of Autonomic, Respiratory, and Spinally-Projecting Neurons in the Mouse Ventrolateral Medulla. J Neurosci 2024; 44:e2211232024. [PMID: 38918066 PMCID: PMC11293450 DOI: 10.1523/jneurosci.2211-23.2024] [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: 11/28/2023] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
The ventrolateral medulla (VLM) is a crucial region in the brain for visceral and somatic control, serving as a significant source of synaptic input to the spinal cord. Experimental studies have shown that gene expression in individual VLM neurons is predictive of their function. However, the molecular and cellular organization of the VLM has remained uncertain. This study aimed to create a comprehensive dataset of VLM cells using single-cell RNA sequencing in male and female mice. The dataset was enriched with targeted sequencing of spinally-projecting and adrenergic/noradrenergic VLM neurons. Based on differentially expressed genes, the resulting dataset of 114,805 VLM cells identifies 23 subtypes of neurons, excluding those in the inferior olive, and five subtypes of astrocytes. Spinally-projecting neurons were found to be abundant in seven subtypes of neurons, which were validated through in situ hybridization. These subtypes included adrenergic/noradrenergic neurons, serotonergic neurons, and neurons expressing gene markers associated with premotor neurons in the ventromedial medulla. Further analysis of adrenergic/noradrenergic neurons and serotonergic neurons identified nine and six subtypes, respectively, within each class of monoaminergic neurons. Marker genes that identify the neural network responsible for breathing were concentrated in two subtypes of neurons, delineated from each other by markers for excitatory and inhibitory neurons. These datasets are available for public download and for analysis with a user-friendly interface. Collectively, this study provides a fine-scale molecular identification of cells in the VLM, forming the foundation for a better understanding of the VLM's role in vital functions and motor control.
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Affiliation(s)
- Dana C Schwalbe
- Departments of Biology, University of Virginia, Charlottesville, Virginia 22904
| | | | | | | | - Maira Jalil
- Departments of Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Maisie E Crook
- Departments of Biology, University of Virginia, Charlottesville, Virginia 22904
| | - John N Campbell
- Departments of Biology, University of Virginia, Charlottesville, Virginia 22904
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Rasetto NB, Giacomini D, Berardino AA, Waichman TV, Beckel MS, Di Bella DJ, Brown J, Davies-Sala MG, Gerhardinger C, Lie DC, Arlotta P, Chernomoretz A, Schinder AF. Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus. SCIENCE ADVANCES 2024; 10:eadp6039. [PMID: 39028813 PMCID: PMC11259177 DOI: 10.1126/sciadv.adp6039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/13/2024] [Indexed: 07/21/2024]
Abstract
The adult hippocampus generates new granule cells (aGCs) with functional capabilities that convey unique forms of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like cells (RGLs) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to study aGC differentiation using single-nuclei RNA sequencing. Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple immature stages bearing increasing levels of effector genes supporting growth, excitability, and synaptogenesis. Analysis of differential gene expression, pseudo-time trajectory, and transcription factors (TFs) revealed critical transitions defining four cellular states: quiescent RGLs, proliferative progenitors, immature aGCs, and mature aGCs. Becoming mature aGCs involved a transcriptional switch that shuts down pathways promoting cell growth, such SoxC TFs, to activate programs that likely control neuronal homeostasis. aGCs overexpressing Sox4 or Sox11 remained immature. Our results unveil precise molecular mechanisms driving adult RGLs through the pathway of neuronal differentiation.
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Affiliation(s)
- Natalí B. Rasetto
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
| | - Damiana Giacomini
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
| | - Ariel A. Berardino
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
| | - Tomás Vega Waichman
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
| | - Maximiliano S. Beckel
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
| | - Daniela J. Di Bella
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Juliana Brown
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - M. Georgina Davies-Sala
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
| | - Chiara Gerhardinger
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dieter Chichung Lie
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Paola Arlotta
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ariel Chernomoretz
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
- University of Buenos Aires, School of Science, Phys Dept and INFINA (CONICET-UBA), Buenos Aires, Argentina
| | - Alejandro F. Schinder
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
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43
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Sorek G, Haim Y, Chalifa-Caspi V, Lazarescu O, Ziv-Agam M, Hagemann T, Nono Nankam PA, Blüher M, Liberty IF, Dukhno O, Kukeev I, Yeger-Lotem E, Rudich A, Levin L. sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human adipose tissues. iScience 2024; 27:110368. [PMID: 39071890 PMCID: PMC11277759 DOI: 10.1016/j.isci.2024.110368] [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: 08/21/2023] [Revised: 02/27/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024] Open
Abstract
Deconvolution algorithms mostly rely on single-cell RNA-sequencing (scRNA-seq) data applied onto bulk RNA-sequencing (bulk RNA-seq) to estimate tissues' cell-type composition, with performance accuracy validated on deposited databases. Adipose tissues' cellular composition is highly variable, and adipocytes can only be captured by single-nucleus RNA-sequencing (snRNA-seq). Here we report the development of sNucConv, a Scaden deep-learning-based deconvolution tool, trained using 5 hSAT and 7 hVAT snRNA-seq-based data corrected by (i) snRNA-seq/bulk RNA-seq highly correlated genes and (ii) individual cell-type regression models. Applying sNucConv on our bulk RNA-seq data resulted in cell-type proportion estimation of 15 and 13 cell types, with accuracy of R = 0.93 (range: 0.76-0.97) and R = 0.95 (range: 0.92-0.98) for hVAT and hSAT, respectively. This performance level was further validated on an independent set of samples (5 hSAT; 5 hVAT). The resulting model was depot specific, reflecting depot differences in gene expression patterns. Jointly, sNucConv provides proof-of-concept for producing validated deconvolution models for tissues un-amenable to scRNA-seq.
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Affiliation(s)
- Gil Sorek
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yulia Haim
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Vered Chalifa-Caspi
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Or Lazarescu
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maya Ziv-Agam
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tobias Hagemann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Pamela Arielle Nono Nankam
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Idit F. Liberty
- Soroka University Medical Center, and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Oleg Dukhno
- Soroka University Medical Center, and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ivan Kukeev
- Soroka University Medical Center, and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Assaf Rudich
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Webster AN, Becker JJ, Li C, Schwalbe DC, Kerspern D, Karolczak EO, Bundon C, Onoharigho RA, Crook M, Jalil M, Godschall EN, Dame EG, Dawer A, Belmont-Rausch DM, Pers TH, Lutas A, Habib N, Guler AD, Krashes MJ, Campbell JN. Molecular Connectomics Reveals a Glucagon-Like Peptide 1 Sensitive Neural Circuit for Satiety. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.31.564990. [PMID: 37961449 PMCID: PMC10635031 DOI: 10.1101/2023.10.31.564990] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Liraglutide and other agonists of the glucagon-like peptide 1 receptor (GLP-1RAs) are effective weight loss drugs, but how they suppress appetite remains unclear. One potential mechanism is by activating neurons which inhibit hunger-promoting Agouti-related peptide (AgRP) neurons of the arcuate hypothalamus (Arc). To identify these afferents, we developed a method combining rabies-based connectomics with single-nuclei transcriptomics. Applying this method to AgRP neurons predicted at least 21 afferent subtypes in the mouse mediobasal and paraventricular hypothalamus. Among these are Trh+ Arc neurons, inhibitory neurons which express the Glp1r gene and are activated by the GLP-1RA liraglutide. Activating Trh+ Arc neurons inhibits AgRP neurons and feeding in an AgRP neuron-dependent manner. Silencing Trh+ Arc neurons causes over-eating and weight gain and attenuates liraglutide's effect on body weight. Our results demonstrate a widely applicable method for molecular connectomics, comprehensively identify local inputs to AgRP neurons, and reveal a circuit through which GLP-1RAs suppress appetite.
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Wen Y, Yang H, Hong Y. Transcriptomic Approaches to Cardiomyocyte-Biomaterial Interactions: A Review. ACS Biomater Sci Eng 2024; 10:4175-4194. [PMID: 38934720 DOI: 10.1021/acsbiomaterials.4c00303] [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] [Indexed: 06/28/2024]
Abstract
Biomaterials, essential for supporting, enhancing, and repairing damaged tissues, play a critical role in various medical applications. This Review focuses on the interaction of biomaterials and cardiomyocytes, emphasizing the unique significance of transcriptomic approaches in understanding their interactions, which are pivotal in cardiac bioengineering and regenerative medicine. Transcriptomic approaches serve as powerful tools to investigate how cardiomyocytes respond to biomaterials, shedding light on the gene expression patterns, regulatory pathways, and cellular processes involved in these interactions. Emerging technologies such as bulk RNA-seq, single-cell RNA-seq, single-nucleus RNA-seq, and spatial transcriptomics offer promising avenues for more precise and in-depth investigations. Longitudinal studies, pathway analyses, and machine learning techniques further improve the ability to explore the complex regulatory mechanisms involved. This review also discusses the challenges and opportunities of utilizing transcriptomic techniques in cardiomyocyte-biomaterial research. Although there are ongoing challenges such as costs, cell size limitation, sample differences, and complex analytical process, there exist exciting prospects in comprehensive gene expression analyses, biomaterial design, cardiac disease treatment, and drug testing. These multimodal methodologies have the capacity to deepen our understanding of the intricate interaction network between cardiomyocytes and biomaterials, potentially revolutionizing cardiac research with the aim of promoting heart health, and they are also promising for studying interactions between biomaterials and other cell types.
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Affiliation(s)
- Yufeng Wen
- Department of Bioengineering, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Huaxiao Yang
- Department of Biomedical Engineering, University of North Texas, Denton, Texas 76207, United States
| | - Yi Hong
- Department of Bioengineering, University of Texas at Arlington, Arlington, Texas 76019, United States
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46
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Mahat DB, Tippens ND, Martin-Rufino JD, Waterton SK, Fu J, Blatt SE, Sharp PA. Single-cell nascent RNA sequencing unveils coordinated global transcription. Nature 2024; 631:216-223. [PMID: 38839954 PMCID: PMC11222150 DOI: 10.1038/s41586-024-07517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Transcription is the primary regulatory step in gene expression. Divergent transcription initiation from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers1,2. Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity in cell populations3. However, fundamental questions about the temporal regulation of transcription and enhancer-gene coordination remain unanswered, primarily because of the absence of a single-cell perspective on active transcription. In this study, we present scGRO-seq-a new single-cell nascent RNA sequencing assay that uses click chemistry-and unveil coordinated transcription throughout the genome. We demonstrate the episodic nature of transcription and the co-transcription of functionally related genes. scGRO-seq can estimate burst size and frequency by directly quantifying transcribing RNA polymerases in individual cells and can leverage replication-dependent non-polyadenylated histone gene transcription to elucidate cell cycle dynamics. The single-nucleotide spatial and temporal resolution of scGRO-seq enables the identification of networks of enhancers and genes. Our results suggest that the bursting of transcription at super-enhancers precedes bursting from associated genes. By imparting insights into the dynamic nature of global transcription and the origin and propagation of transcription signals, we demonstrate the ability of scGRO-seq to investigate the mechanisms of transcription regulation and the role of enhancers in gene expression.
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Affiliation(s)
- Dig B Mahat
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nathaniel D Tippens
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Sean K Waterton
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Jiayu Fu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Sarah E Blatt
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Exact Sciences, Madison, WI, USA
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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47
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Kuo A, Hansen KD, Hicks SC. Quantification and statistical modeling of droplet-based single-nucleus RNA-sequencing data. Biostatistics 2024; 25:801-817. [PMID: 37257175 PMCID: PMC11247185 DOI: 10.1093/biostatistics/kxad010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 03/22/2023] [Accepted: 04/19/2023] [Indexed: 06/02/2023] Open
Abstract
In complex tissues containing cells that are difficult to dissociate, single-nucleus RNA-sequencing (snRNA-seq) has become the preferred experimental technology over single-cell RNA-sequencing (scRNA-seq) to measure gene expression. To accurately model these data in downstream analyses, previous work has shown that droplet-based scRNA-seq data are not zero-inflated, but whether droplet-based snRNA-seq data follow the same probability distributions has not been systematically evaluated. Using pseudonegative control data from nuclei in mouse cortex sequenced with the 10x Genomics Chromium system and mouse kidney sequenced with the DropSeq system, we found that droplet-based snRNA-seq data follow a negative binomial distribution, suggesting that parametric statistical models applied to scRNA-seq are transferable to snRNA-seq. Furthermore, we found that the quantification choices in adapting quantification mapping strategies from scRNA-seq to snRNA-seq can play a significant role in downstream analyses and biological interpretation. In particular, reference transcriptomes that do not include intronic regions result in significantly smaller library sizes and incongruous cell type classifications. We also confirmed the presence of a gene length bias in snRNA-seq data, which we show is present in both exonic and intronic reads, and investigate potential causes for the bias.
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Affiliation(s)
- Albert Kuo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
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48
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De Jonghe J, Opzoomer JW, Vilas-Zornoza A, Crane P, Nilges BS, Vicari M, Lee H, Lara-Astiaso D, Gross T, Morf J, Schneider K, Cudini J, Ramos-Mucci L, Mooijman D, Tiklová K, Salas SM, Langseth CM, Kashikar ND, Roberts CES, Lundeberg J, Nilsson M, Shalek AK, Cribbs AP, Taylor-King JP. A community effort to track commercial single-cell and spatial 'omic technologies and business trends. Nat Biotechnol 2024; 42:1017-1023. [PMID: 39020213 DOI: 10.1038/s41587-024-02305-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Affiliation(s)
| | - James W Opzoomer
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, London, UK
- Relation Therapeutics, London, UK
| | | | | | | | - Marco Vicari
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Hower Lee
- spatialist AB, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - David Lara-Astiaso
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Hematology, University of Cambridge, Cambridge, UK
| | | | - Jörg Morf
- Skyhawk Therapeutics, Basel, Switzerland
| | | | | | | | | | - Katarína Tiklová
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Sergio Marco Salas
- spatialist AB, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Christoffer Mattsson Langseth
- spatialist AB, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | | | - Charles E S Roberts
- Relation Therapeutics, London, UK
- ARK Investment Management, St. Petersburg, FL, USA
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Alex K Shalek
- Relation Therapeutics, London, UK
- Institute for Medical Engineering and Science, Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Adam P Cribbs
- Caeruleus Genomics, Oxford, UK
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK
- Oxford Centre for Translational Myeloma Research University of Oxford, Oxford, UK
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49
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Vogel JW, Alexander-Bloch AF, Wagstyl K, Bertolero MA, Markello RD, Pines A, Sydnor VJ, Diaz-Papkovich A, Hansen JY, Evans AC, Bernhardt B, Misic B, Satterthwaite TD, Seidlitz J. Deciphering the functional specialization of whole-brain spatiomolecular gradients in the adult brain. Proc Natl Acad Sci U S A 2024; 121:e2219137121. [PMID: 38861593 PMCID: PMC11194492 DOI: 10.1073/pnas.2219137121] [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: 11/08/2022] [Accepted: 04/27/2024] [Indexed: 06/13/2024] Open
Abstract
Cortical arealization arises during neurodevelopment from the confluence of molecular gradients representing patterned expression of morphogens and transcription factors. However, whether similar gradients are maintained in the adult brain remains unknown. Here, we uncover three axes of topographic variation in gene expression in the adult human brain that specifically capture previously identified rostral-caudal, dorsal-ventral, and medial-lateral axes of early developmental patterning. The interaction of these spatiomolecular gradients i) accurately reconstructs the position of brain tissue samples, ii) delineates known functional territories, and iii) can model the topographical variation of diverse cortical features. The spatiomolecular gradients are distinct from canonical cortical axes differentiating the primary sensory cortex from the association cortex, but radiate in parallel with the axes traversed by local field potentials along the cortex. We replicate all three molecular gradients in three independent human datasets as well as two nonhuman primate datasets and find that each gradient shows a distinct developmental trajectory across the lifespan. The gradients are composed of several well-known transcription factors (e.g., PAX6 and SIX3), and a small set of genes shared across gradients are strongly enriched for multiple diseases. Together, these results provide insight into the developmental sculpting of functionally distinct brain regions, governed by three robust transcriptomic axes embedded within brain parenchyma.
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Affiliation(s)
- Jacob W. Vogel
- Department of Clinical Sciences Malmö, SciLifeLab, Lund University, Lund, Sweden202 13
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA19104
| | - Aaron F. Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA19104
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Penn-Children’s Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA19104
| | - Konrad Wagstyl
- Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, LondonWC1N 3AR, United Kingdom
| | - Maxwell A. Bertolero
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA19104
| | - Ross D. Markello
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QCH3A 2B4, Canada
| | - Adam Pines
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA94305
| | - Valerie J. Sydnor
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA19104
| | - Alex Diaz-Papkovich
- Quantitative Life Sciences, McGill University, Montreal, QCH3A 1E3, Canada
- McGill Genome Centre, McGill University, Montreal, QCH3A 0G1, Canada
| | - Justine Y. Hansen
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QCH3A 2B4, Canada
| | - Alan C. Evans
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QCH3A 2B4, Canada
| | - Boris Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QCH3A 2B4, Canada
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QCH3A 2B4, Canada
| | - Theodore D. Satterthwaite
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA19104
- Penn-Children’s Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA19104
| | - Jakob Seidlitz
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA19104
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Penn-Children’s Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA19104
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50
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He J, Huo X, Pei G, Jia Z, Yan Y, Yu J, Qu H, Xie Y, Yuan J, Zheng Y, Hu Y, Shi M, You K, Li T, Ma T, Zhang MQ, Ding S, Li P, Li Y. Dual-role transcription factors stabilize intermediate expression levels. Cell 2024; 187:2746-2766.e25. [PMID: 38631355 DOI: 10.1016/j.cell.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Precise control of gene expression levels is essential for normal cell functions, yet how they are defined and tightly maintained, particularly at intermediate levels, remains elusive. Here, using a series of newly developed sequencing, imaging, and functional assays, we uncover a class of transcription factors with dual roles as activators and repressors, referred to as condensate-forming level-regulating dual-action transcription factors (TFs). They reduce high expression but increase low expression to achieve stable intermediate levels. Dual-action TFs directly exert activating and repressing functions via condensate-forming domains that compartmentalize core transcriptional unit selectively. Clinically relevant mutations in these domains, which are linked to a range of developmental disorders, impair condensate selectivity and dual-action TF activity. These results collectively address a fundamental question in expression regulation and demonstrate the potential of level-regulating dual-action TFs as powerful effectors for engineering controlled expression levels.
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Affiliation(s)
- Jinnan He
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiangru Huo
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Zeran Jia
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yiming Yan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawei Yu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Haozhi Qu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yunxin Xie
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Junsong Yuan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yuan Zheng
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yanyan Hu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Minglei Shi
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kaiqiang You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tianhua Ma
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Michael Q Zhang
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China; Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas, TX 75080-3021, USA
| | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China.
| | - Yinqing Li
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
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