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Zhu R, Pan X, Wang S, Qiu Z, Gu C, Yao X, Li W. Updated skin transcriptomic atlas depicted by reciprocal contribution of single-nucleus RNA sequencing and single-cell RNA sequencing. J Dermatol Sci 2023; 111:22-31. [PMID: 37407342 DOI: 10.1016/j.jdermsci.2023.06.005] [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: 02/12/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of skin biology, but its utility is restricted by the requirement of fresh samples, inadequate dissociation-induced cell loss or death, and activation during tissue digestion. Single-nucleus RNA sequencing (snRNA-seq) can use frozen, hard-to-dissociate materials, which might be a promising method to circumvent the limitations of scRNA-seq for the skin tissue. OBJECTIVE To profile skin cells using snRNA-seq in parallel with scRNA-seq. METHODS We performed snRNA-seq in parallel with scRNA-seq for the bisected skin sample of one person and integrated previously published scRNA-seq data for analysis. We comparatively analyzed the differences in cell proportions and gene expression between the two methods. The differentiation trajectories of keratinocytes and fibroblasts were analyzed by Slingshot analysis. RESULTS snRNA-seq was less susceptible to contamination from mitochondrial and ribosomal RNA, and exhibited a greater capacity to detect transcription factors. snRNA-seq identified more spatially and functionally relevant keratinocyte clusters that constitute cell trajectories with expected differentiation dynamics. Novel markers, e.g., LYPD3, EMP2, and CSTB, were revealed for different differentiation stages of keratinocytes, and NFIB and GRHL1 were identified as transcription factors involving in the proliferation and functional differentiation of keratinocytes. Fibroblasts were found in a state of activation in scRNA-seq. And scRNA-seq detected a greater number of immune cells. CONCLUSIONS We generated an updated atlas of the skin transcriptome based on the reciprocal contribution of scRNA-seq and snRNA-seq.
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Affiliation(s)
- Ronghui Zhu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Xiaoyu Pan
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Shangshang Wang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Zhuoqiong Qiu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Chaoying Gu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Xu Yao
- Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Wei Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China.
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Wu J, Li Y, Huang Y, Liu L, Zhang H, Nagy C, Tan X, Cheng K, Liu Y, Pu J, Wang H, Wu Q, Perry SW, Turecki G, Wong ML, Licinio J, Zheng P, Xie P. Integrating spatial and single-nucleus transcriptomic data elucidates microglial-specific responses in female cynomolgus macaques with depressive-like behaviors. Nat Neurosci 2023; 26:1352-1364. [PMID: 37443281 DOI: 10.1038/s41593-023-01379-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/12/2023] [Indexed: 07/15/2023]
Abstract
Major depressive disorder represents a serious public health challenge worldwide; however, the underlying cellular and molecular mechanisms are mostly unknown. Here, we profile the dorsolateral prefrontal cortex of female cynomolgus macaques with social stress-associated depressive-like behaviors using single-nucleus RNA-sequencing and spatial transcriptomics. We find gene expression changes associated with depressive-like behaviors mostly in microglia, and we report a pro-inflammatory microglia subpopulation enriched in the depressive-like condition. Single-nucleus RNA-sequencing data result in the identification of six enriched gene modules associated with depressive-like behaviors, and these modules are further resolved by spatial transcriptomics. Gene modules associated with huddle and sit alone behaviors are expressed in neurons and oligodendrocytes of the superficial cortical layer, while gene modules associated with locomotion and amicable behaviors are enriched in microglia and astrocytes in mid-to-deep cortical layers. The depressive-like behavior associated microglia subpopulation is enriched in deep cortical layers. In summary, our findings show cell-type and cortical layer-specific gene expression changes and identify one microglia subpopulation associated with depressive-like behaviors in female non-human primates.
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Affiliation(s)
- Jing Wu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Yifan Li
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Yu Huang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Lanxiang Liu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Hanping Zhang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Corina Nagy
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, Quebec, Canada
| | - Xunmin Tan
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Ke Cheng
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yiyun Liu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Juncai Pu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haiyang Wang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
| | - Qingyuan Wu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Neurology, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Seth W Perry
- Department of Psychiatry, College of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Ma-Li Wong
- Department of Psychiatry, College of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Julio Licinio
- Department of Psychiatry, College of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Peng Zheng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Jinfeng Laboratory, Chongqing, China.
| | - Peng Xie
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Jinfeng Laboratory, Chongqing, China.
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Hobson BD, Stanley AT, De Los Santos MB, Culbertson B, Mosharov EV, Sims PA, Sulzer D. Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain. Brain Behav Immun 2023; 111:277-291. [PMID: 37100211 PMCID: PMC10460506 DOI: 10.1016/j.bbi.2023.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/28/2023] [Accepted: 04/23/2023] [Indexed: 04/28/2023] Open
Abstract
Dysregulated inflammation within the central nervous system (CNS) contributes to neuropathology in infectious, autoimmune, and neurodegenerative disease. With the exception of microglia, major histocompatibility complex (MHC) proteins are virtually undetectable in the mature, healthy central nervous system (CNS). Neurons have generally been considered incapable of antigen presentation, and although interferon gamma (IFN-γ) can elicit neuronal MHC class I (MHC-I) expression and antigen presentation in vitro, it has been unclear whether similar responses occur in vivo. Here we directly injected IFN-γ into the ventral midbrain of mature mice and analyzed gene expression profiles of specific CNS cell types. We found that IFN-γ upregulated MHC-I and associated mRNAs in ventral midbrain microglia, astrocytes, oligodendrocytes, and GABAergic, glutamatergic, and dopaminergic neurons. The core set of IFN-γ-induced genes and their response kinetics were similar in neurons and glia, but with a lower amplitude of expression in neurons. A diverse repertoire of genes was upregulated in glia, particularly microglia, which were the only cells to undergo cellular proliferation and express MHC classII (MHC-II) and associated genes. To determine if neurons respond directly via cell-autonomous IFN-γ receptor (IFNGR) signaling, we produced mutant mice with a deletion of the IFN-γ-binding domain of IFNGR1 in dopaminergic neurons, which resulted in a complete loss of dopaminergic neuronal responses to IFN-γ. Our results demonstrate that IFN-γ induces neuronal IFNGR signaling and upregulation of MHC-I and related genes in vivo, although the expression level is low compared to oligodendrocytes, astrocytes, and microglia.
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Affiliation(s)
- Benjamin D Hobson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Adrien T Stanley
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Mark B De Los Santos
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Bruce Culbertson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Eugene V Mosharov
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, United States; Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
| | - David Sulzer
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Pharmacology, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
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54
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Zhang H, Li J, Yu Y, Ren J, Liu Q, Bao Z, Sun S, Liu X, Ma S, Liu Z, Yan K, Wu Z, Fan Y, Sun X, Zhang Y, Ji Q, Cheng F, Wei PH, Ma X, Zhang S, Xie Z, Niu Y, Wang YJ, Han JDJ, Jiang T, Zhao G, Ji W, Izpisua Belmonte JC, Wang S, Qu J, Zhang W, Liu GH. Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging. Cell Rep 2023; 42:112593. [PMID: 37261950 DOI: 10.1016/j.celrep.2023.112593] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/10/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
The primate frontal lobe (FL) is sensitive to aging-related neurocognitive decline. However, the aging-associated molecular mechanisms remain unclear. Here, using physiologically aged non-human primates (NHPs), we depicted a comprehensive landscape of FL aging with multidimensional profiling encompassing bulk and single-nucleus transcriptomes, quantitative proteome, and DNA methylome. Conjoint analysis across these molecular and neuropathological layers underscores nuclear lamina and heterochromatin erosion, resurrection of endogenous retroviruses (ERVs), activated pro-inflammatory cyclic GMP-AMP synthase (cGAS) signaling, and cellular senescence in post-mitotic neurons of aged NHP and human FL. Using human embryonic stem-cell-derived neurons recapitulating cellular aging in vitro, we verified the loss of B-type lamins inducing resurrection of ERVs as an initiating event of the aging-bound cascade in post-mitotic neurons. Of significance, these aging-related cellular and molecular changes can be alleviated by abacavir, a nucleoside reverse transcriptase inhibitor, either through direct treatment of senescent human neurons in vitro or oral administration to aged mice.
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Affiliation(s)
- Hui Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yu
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China; Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Liu
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zhaoshi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; Chinese Glioma Genome Atlas Network & Asian Glioma Genome Atlas Network, Beijing 100070, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Cheng
- University of Chinese Academy of Sciences, Beijing 100049, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng-Hu Wei
- Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China; MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xibo Ma
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiqiang Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Zhengwei Xie
- Peking University International Cancer Institute, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yan-Jiang Wang
- Department of Neurology, Daping Hospital, Third Military Medical University, Chongqing 400042, China; State Key Laboratory of Trauma, Burn and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, China
| | - Tao Jiang
- Beijing Neurosurgical Institute, Beijing 100070, China; Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China; Chinese Glioma Genome Atlas Network & Asian Glioma Genome Atlas Network, Beijing 100070, China
| | - Guoguang Zhao
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Clinical Research Center for Epilepsy Capital Medical University, Beijing 100053, China; Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | | | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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Grosch M, Schraft L, Chan A, Küchenhoff L, Rapti K, Ferreira AM, Kornienko J, Li S, Radke MH, Krämer C, Clauder-Münster S, Perlas E, Backs J, Gotthardt M, Dieterich C, van den Hoogenhof MMG, Grimm D, Steinmetz LM. Striated muscle-specific base editing enables correction of mutations causing dilated cardiomyopathy. Nat Commun 2023; 14:3714. [PMID: 37349314 PMCID: PMC10287752 DOI: 10.1038/s41467-023-39352-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/08/2023] [Indexed: 06/24/2023] Open
Abstract
Dilated cardiomyopathy is the second most common cause for heart failure with no cure except a high-risk heart transplantation. Approximately 30% of patients harbor heritable mutations which are amenable to CRISPR-based gene therapy. However, challenges related to delivery of the editing complex and off-target concerns hamper the broad applicability of CRISPR agents in the heart. We employ a combination of the viral vector AAVMYO with superior targeting specificity of heart muscle tissue and CRISPR base editors to repair patient mutations in the cardiac splice factor Rbm20, which cause aggressive dilated cardiomyopathy. Using optimized conditions, we repair >70% of cardiomyocytes in two Rbm20 knock-in mouse models that we have generated to serve as an in vivo platform of our editing strategy. Treatment of juvenile mice restores the localization defect of RBM20 in 75% of cells and splicing of RBM20 targets including TTN. Three months after injection, cardiac dilation and ejection fraction reach wild-type levels. Single-nuclei RNA sequencing uncovers restoration of the transcriptional profile across all major cardiac cell types and whole-genome sequencing reveals no evidence for aberrant off-target editing. Our study highlights the potential of base editors combined with AAVMYO to achieve gene repair for treatment of hereditary cardiac diseases.
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Affiliation(s)
- Markus Grosch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Laura Schraft
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Adrian Chan
- Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Leonie Küchenhoff
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Kleopatra Rapti
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Anne-Maud Ferreira
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Kornienko
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Shengdi Li
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Michael H Radke
- Translational Cardiology and Functional Genomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Chiara Krämer
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, BioQuant, University of Heidelberg, Heidelberg, Germany
| | | | - Emerald Perlas
- Epigenetics and Neurobiology Unit, EMBL Rome, Monterotondo, Italy
| | - Johannes Backs
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Institute of Experimental Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Gotthardt
- Translational Cardiology and Functional Genomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Dieterich
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Maarten M G van den Hoogenhof
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Institute of Experimental Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Dirk Grimm
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, BioQuant, University of Heidelberg, Heidelberg, Germany
- German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany.
- Stanford Genome Technology Center, Palo Alto, CA, USA.
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56
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Orozco LD, Owen LA, Hofmann J, Stockwell AD, Tao J, Haller S, Mukundan VT, Clarke C, Lund J, Sridhar A, Mayba O, Barr JL, Zavala RA, Graves EC, Zhang C, Husami N, Finley R, Au E, Lillvis JH, Farkas MH, Shakoor A, Sherva R, Kim IK, Kaminker JS, Townsend MJ, Farrer LA, Yaspan BL, Chen HH, DeAngelis MM. A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration. CELL GENOMICS 2023; 3:100302. [PMID: 37388919 PMCID: PMC10300496 DOI: 10.1016/j.xgen.2023.100302] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/21/2023] [Accepted: 03/22/2023] [Indexed: 07/01/2023]
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness, affecting 200 million people worldwide. To identify genes that could be targeted for treatment, we created a molecular atlas at different stages of AMD. Our resource is comprised of RNA sequencing (RNA-seq) and DNA methylation microarrays from bulk macular retinal pigment epithelium (RPE)/choroid of clinically phenotyped normal and AMD donor eyes (n = 85), single-nucleus RNA-seq (164,399 cells), and single-nucleus assay for transposase-accessible chromatin (ATAC)-seq (125,822 cells) from the retina, RPE, and choroid of 6 AMD and 7 control donors. We identified 23 genome-wide significant loci differentially methylated in AMD, over 1,000 differentially expressed genes across different disease stages, and an AMD Müller state distinct from normal or gliosis. Chromatin accessibility peaks in genome-wide association study (GWAS) loci revealed putative causal genes for AMD, including HTRA1 and C6orf223. Our systems biology approach uncovered molecular mechanisms underlying AMD, including regulators of WNT signaling, FRZB and TLE2, as mechanistic players in disease.
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Affiliation(s)
- Luz D. Orozco
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Leah A. Owen
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Jeffrey Hofmann
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Amy D. Stockwell
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Jianhua Tao
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Susan Haller
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Vineeth T. Mukundan
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Christine Clarke
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Jessica Lund
- Departments of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Akshayalakshmi Sridhar
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Oleg Mayba
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Julie L. Barr
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Rylee A. Zavala
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Elijah C. Graves
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Charles Zhang
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Nadine Husami
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Robert Finley
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Elizabeth Au
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - John H. Lillvis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Michael H. Farkas
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Akbar Shakoor
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
| | - Richard Sherva
- Department of Medicine, Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye & Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Joshua S. Kaminker
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Michael J. Townsend
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Lindsay A. Farrer
- Department of Medicine, Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Brian L. Yaspan
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Hsu-Hsin Chen
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Margaret M. DeAngelis
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
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Boussaty EC, Tedeschi N, Novotny M, Ninoyu Y, Du E, Draf C, Zhang Y, Manor U, Scheuermann RH, Friedman R. Cochlear transcriptome analysis of an outbred mouse population (CFW). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528661. [PMID: 36824745 PMCID: PMC9948975 DOI: 10.1101/2023.02.15.528661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Age-related hearing loss (ARHL) is the most common cause of hearing loss and one of the most prevalent conditions affecting the elderly worldwide. Despite evidence from our lab and others about its polygenic nature, little is known about the specific genes, cell types and pathways involved in ARHL, impeding the development of therapeutic interventions. In this manuscript, we describe, for the first time, the complete cell-type specific transcriptome of the aging mouse cochlea using snRNA-seq in an outbred mouse model in relation to auditory threshold variation. Cochlear cell types were identified using unsupervised clustering and annotated via a three-tiered approach - first by linking to expression of known marker genes, then using the NS-Forest algorithm to select minimum cluster-specific marker genes and reduce dimensional feature space for statistical comparison of our clusters with existing publicly-available data sets on the gEAR website (https://umgear.org/), and finally, by validating and refining the annotations using Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) and the cluster-specific marker genes as probes. We report on 60 unique cell-types expanding the number of defined cochlear cell types by more than two times. Importantly, we show significant specific cell type increases and decreases associated with loss of hearing acuity implicating specific subsets of hair cell subtypes, ganglion cell subtypes, and cell subtypes withing the stria vascularis in this model of ARHL. These results provide a view into the cellular and molecular mechanisms responsible for age-related hearing loss and pathways for therapeutic targeting.
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Affiliation(s)
| | | | | | - Yuzuru Ninoyu
- Department of Otolaryngology, University of California, San Diego, CA
| | - Eric Du
- Department of Otolaryngology, University of California, San Diego, CA
| | - Clara Draf
- Department of Otolaryngology, University of California, San Diego, CA
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA
| | - Uri Manor
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, CA, United States
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA
- Department of Pathology, University of California, San Diego, CA
| | - Rick Friedman
- Department of Otolaryngology, University of California, San Diego, CA
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Chen H, Ding J, Xue H, Tang X, Yan Y, Xie Y. SnRNA-Seq analysis reveals ten hub genes associated with alveolar epithelial cell injury during pulmonary acute respiratory distress syndrome. Heliyon 2023; 9:e17160. [PMID: 37389073 PMCID: PMC10300320 DOI: 10.1016/j.heliyon.2023.e17160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 07/01/2023] Open
Abstract
Background Alveolar epithelial cell injury is a key factor in the occurrence and development of pulmonary acute respiratory distress syndrome (ARDSp). Yet the gene expression profile of alveolar epithelial cells of patients with ARDSp remains unclear. Methods We analyzed single nuclear RNA sequencing (snRNA-Seq) data from autopsy lung tissues of both ARDSp patients and healthy donors. Sequence data for type 2 alveolar epithelizal cells (AT2) were extracted by the Seurat package. Differentially expressed genes (DEGs) in AT2 were identified by the criteria |log2FC| ≥ 0.25 and P < 0.05 with DESeq2. A protein interaction network was constructed using Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software to identify hub genes. We then constructed an ARDSp rat model through induction by lipopolysaccharide (LPS) airway instillation. Left lung RNA was extracted and sequenced via Illumina Hiseq platforms. Analysis of the rat RNA sequencing data was then used to verify hub genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on the identified hub genes. Results In AT2, a total of 289 genes were identified as differentially expressed between those from ARDSp patients and healthy donors, and these included 190 upregulated and 99 downregulated genes. Ten hub genes were further identified (RPS27A, ACTG1, CAV1, HSP90AA1, HSPA5, CCND1, ITGA3, B2M, NEDD4L, and SEMA5A). There was a similar expression trend of HSPA5 between rat RNA and snRNA sequencing data. Discussion ARDSp altered the gene expression profile of AT2. The identified hub genes were enriched in biological processes mainly involved in cell growth and transformation. Relatedly, ferroptosis and autophagy are possibly involved in AT2 injury during ARDSp. These novel insights into ARDSp may aid the discovery of potential targets for the diagnosis and treatment of ARDSp.
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Affiliation(s)
- Haoran Chen
- Kangda College of Nanjing Medical University, Zip Code 222000, Lianyungang City, Jiangsu Province, China
| | - Jinqiu Ding
- The Institute of Emergency Medicine of Lianyungang, 222000, Lianyungang City, Jiangsu Province, China
| | - Haoyue Xue
- Department of Emergency and Critical Care Medicine, Lianyungang Clinical College of Xuzhou Medical University, No. 6 Zhenhua Road, Zip Code 222000, Lianyungang City, Jiangsu Province, China
| | - Xinyi Tang
- Department of Emergency and Critical Care Medicine, Lianyungang Clinical College of Nanjing Medical University, No. 6 Zhenhua Road, Zip Code 222000, Lianyungang City, Jiangsu Province, China
| | - Yao Yan
- Department of Emergency Medicine, Lianyungang Clinical College of Nanjing Medical University, The First People’s Hospital of Lianyungang City, Zip Code 222000, Lianyungang City, Jiangsu Province, China
- Department of Critical Care Medicine, The Second People’s Hospital of Lianyungang City, Zip Code 222000, Lianyungang City, Jiangsu Province, China
| | - Yongpeng Xie
- Department of Emergency and Critical Care Medicine, Lianyungang Clinical College of Nanjing Medical University, No. 6 Zhenhua Road, Zip Code 222000, Lianyungang City, Jiangsu Province, China
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Sant P, Rippe K, Mallm JP. Approaches for single-cell RNA sequencing across tissues and cell types. Transcription 2023; 14:127-145. [PMID: 37062951 PMCID: PMC10807473 DOI: 10.1080/21541264.2023.2200721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/30/2023] [Indexed: 04/18/2023] Open
Abstract
Single-cell sequencing of RNA (scRNA-seq) has advanced our understanding of cellular heterogeneity and signaling in developmental biology and disease. A large number of complementary assays have been developed to profile transcriptomes of individual cells, also in combination with other readouts, such as chromatin accessibility or antibody-based analysis of protein surface markers. As scRNA-seq technologies are advancing fast, it is challenging to establish robust workflows and up-to-date protocols that are best suited to address the large range of research questions. Here, we review scRNA-seq techniques from mRNA end-counting to total RNA in relation to their specific features and outline the necessary sample preparation steps and quality control measures. Based on our experience in dealing with the continuously growing portfolio from the perspective of a central single-cell facility, we aim to provide guidance on how workflows can be best automatized and share our experience in coping with the continuous expansion of scRNA-seq techniques.
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Affiliation(s)
- Pooja Sant
- Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Karsten Rippe
- Division Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
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60
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Kim B, Kim D, Schulmann A, Patel Y, Caban-Rivera C, Kim P, Jambhale A, Johnson KR, Feng N, Xu Q, Kang SJ, Mandal A, Kelly M, Akula N, McMahon FJ, Lipska B, Marenco S, Auluck PK. Cellular Diversity in Human Subgenual Anterior Cingulate and Dorsolateral Prefrontal Cortex by Single-Nucleus RNA-Sequencing. J Neurosci 2023; 43:3582-3597. [PMID: 37037607 PMCID: PMC10184745 DOI: 10.1523/jneurosci.0830-22.2023] [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: 04/29/2022] [Revised: 02/27/2023] [Accepted: 03/15/2023] [Indexed: 04/12/2023] Open
Abstract
Regional cellular heterogeneity is a fundamental feature of the human neocortex; however, details of this heterogeneity are still undefined. We used single-nucleus RNA-sequencing to examine cell-specific transcriptional features in the dorsolateral PFC (DLPFC) and the subgenual anterior cingulate cortex (sgACC), regions implicated in major psychiatric disorders. Droplet-based nuclei-capture and library preparation were performed on replicate samples from 8 male donors without history of psychiatric or neurologic disorder. Unsupervised clustering identified major neural cell classes. Subsequent iterative clustering of neurons further revealed 20 excitatory and 22 inhibitory subclasses. Inhibitory cells were consistently more abundant in the sgACC and excitatory neuron subclusters exhibited considerable variability across brain regions. Excitatory cell subclasses also exhibited greater within-class transcriptional differences between the two regions. We used these molecular definitions to determine which cell classes might be enriched in loci carrying a genetic signal in genome-wide association studies or for differentially expressed genes in mental illness. We found that the heritable signals of psychiatric disorders were enriched in neurons and that, while the gene expression changes detected in bulk-RNA-sequencing studies were dominated by glial cells, some alterations could be identified in specific classes of excitatory and inhibitory neurons. Intriguingly, only two excitatory cell classes exhibited concomitant region-specific enrichment for both genome-wide association study loci and transcriptional dysregulation. In sum, by detailing the molecular and cellular diversity of the DLPFC and sgACC, we were able to generate hypotheses on regional and cell-specific dysfunctions that may contribute to the development of mental illness.SIGNIFICANCE STATEMENT Dysfunction of the subgenual anterior cingulate cortex has been implicated in mood disorders, particularly major depressive disorder, and the dorsolateral PFC, a subsection of the PFC involved in executive functioning, has been implicated in schizophrenia. Understanding the cellular composition of these regions is critical to elucidating the neurobiology underlying psychiatric and neurologic disorders. We studied cell type diversity of the subgenual anterior cingulate cortex and dorsolateral PFC of humans with no neuropsychiatric illness using a clustering analysis of single-nuclei RNA-sequencing data. Defining the transcriptomic profile of cellular subpopulations in these cortical regions is a first step to demystifying the cellular and molecular pathways involved in psychiatric disorders.
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Affiliation(s)
- Billy Kim
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Dowon Kim
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Anton Schulmann
- Human Genetics Branch, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Yash Patel
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Carolina Caban-Rivera
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Paul Kim
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Ananya Jambhale
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Kory R Johnson
- Information Technology and Bioinformatics Program, National Institute of Neurological Disorders and Stroke-Intramural Research Program, Bethesda, Maryland 20892
| | - Ningping Feng
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Qing Xu
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Sun Jung Kang
- Genetic Epidemiology Research Branch, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Ajeet Mandal
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Michael Kelly
- CCR Single Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, Maryland 20892
| | - Nirmala Akula
- Human Genetics Branch, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Francis J McMahon
- Human Genetics Branch, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Barbara Lipska
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Stefano Marenco
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
| | - Pavan K Auluck
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, Maryland 20892
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Alldred MJ, Ginsberg SD. Microisolation of Spatially Characterized Single Populations of Neurons for RNA Sequencing from Mouse and Postmortem Human Brain Tissues. J Clin Med 2023; 12:3304. [PMID: 37176744 PMCID: PMC10179294 DOI: 10.3390/jcm12093304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/28/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Single-cell and single-population RNA sequencing (RNA-seq) is a rapidly evolving new field of intense investigation. Recent studies indicate unique transcriptomic profiles are derived based on the spatial localization of neurons within circuits and regions. Individual neuronal subtypes can have vastly different transcriptomic fingerprints, well beyond the basic excitatory neuron and inhibitory neuron designations. To study single-population gene expression profiles of spatially characterized neurons, we have developed a methodology combining laser capture microdissection (LCM), RNA purification of single populations of neurons, and subsequent library preparation for downstream applications, including RNA-seq. LCM provides the benefit of isolating single neurons characterized by morphology or via transmitter-identified and/or receptor immunoreactivity and enables spatial localization within the sample. We utilize unfixed human postmortem and mouse brain tissue that is frozen to preserve RNA quality in order to isolate the desired neurons of interest. Microisolated neurons are then pooled for RNA purification utilizing as few as 250 individual neurons from a tissue section, precluding extraneous nonspecific tissue contaminants. Library preparation is performed from picogram RNA quantities extracted from LCM-captured neurons. Single-population RNA-seq analysis demonstrates that microisolated neurons from both postmortem human and mouse brain tissues are viable for transcriptomic profiling, including differential gene expression assessment and bioinformatic pathway inquiry.
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Affiliation(s)
- Melissa J. Alldred
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Stephen D. Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
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Al-Dalahmah O, Argenziano MG, Kannan A, Mahajan A, Furnari J, Paryani F, Boyett D, Save A, Humala N, Khan F, Li J, Lu H, Sun Y, Tuddenham JF, Goldberg AR, Dovas A, Banu MA, Sudhakar T, Bush E, Lassman AB, McKhann GM, Gill BJA, Youngerman B, Sisti MB, Bruce JN, Sims PA, Menon V, Canoll P. Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states. Nat Commun 2023; 14:2586. [PMID: 37142563 PMCID: PMC10160047 DOI: 10.1038/s41467-023-38186-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
Glioblastoma (GBM) diffusely infiltrates the brain and intermingles with non-neoplastic brain cells, including astrocytes, neurons and microglia/myeloid cells. This complex mixture of cell types forms the biological context for therapeutic response and tumor recurrence. We used single-nucleus RNA sequencing and spatial transcriptomics to determine the cellular composition and transcriptional states in primary and recurrent glioma and identified three compositional 'tissue-states' defined by cohabitation patterns between specific subpopulations of neoplastic and non-neoplastic brain cells. These tissue-states correlated with radiographic, histopathologic, and prognostic features and were enriched in distinct metabolic pathways. Fatty acid biosynthesis was enriched in the tissue-state defined by the cohabitation of astrocyte-like/mesenchymal glioma cells, reactive astrocytes, and macrophages, and was associated with recurrent GBM and shorter survival. Treating acute slices of GBM with a fatty acid synthesis inhibitor depleted the transcriptional signature of this pernicious tissue-state. These findings point to therapies that target interdependencies in the GBM microenvironment.
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Affiliation(s)
- Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Michael G Argenziano
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Adithya Kannan
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Julia Furnari
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Fahad Paryani
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Deborah Boyett
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Akshay Save
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Nelson Humala
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Fatima Khan
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - Juncheng Li
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - Hong Lu
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - Yu Sun
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - John F Tuddenham
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Alexander R Goldberg
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - Athanassios Dovas
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA
| | - Matei A Banu
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Tejaswi Sudhakar
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Erin Bush
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Andrew B Lassman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Guy M McKhann
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Brian J A Gill
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Brett Youngerman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Michael B Sisti
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Jeffrey N Bruce
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Neurological Surgery, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Peter A Sims
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA
| | - Vilas Menon
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, 10032, USA.
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons (VP&S), New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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63
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Pregizer S, Vreven T, Mathur M, Robinson LN. Multi-omic single cell sequencing: Overview and opportunities for kidney disease therapeutic development. Front Mol Biosci 2023; 10:1176856. [PMID: 37091871 PMCID: PMC10113659 DOI: 10.3389/fmolb.2023.1176856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
Single cell sequencing technologies have rapidly advanced in the last decade and are increasingly applied to gain unprecedented insights by deconstructing complex biology to its fundamental unit, the individual cell. First developed for measurement of gene expression, single cell sequencing approaches have evolved to allow simultaneous profiling of multiple additional features, including chromatin accessibility within the nucleus and protein expression at the cell surface. These multi-omic approaches can now further be applied to cells in situ, capturing the spatial context within which their biology occurs. To extract insights from these complex datasets, new computational tools have facilitated the integration of information across different data types and the use of machine learning approaches. Here, we summarize current experimental and computational methods for generation and integration of single cell multi-omic datasets. We focus on opportunities for multi-omic single cell sequencing to augment therapeutic development for kidney disease, including applications for biomarkers, disease stratification and target identification.
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Arutyunyan A, Roberts K, Troulé K, Wong FCK, Sheridan MA, Kats I, Garcia-Alonso L, Velten B, Hoo R, Ruiz-Morales ER, Sancho-Serra C, Shilts J, Handfield LF, Marconato L, Tuck E, Gardner L, Mazzeo CI, Li Q, Kelava I, Wright GJ, Prigmore E, Teichmann SA, Bayraktar OA, Moffett A, Stegle O, Turco MY, Vento-Tormo R. Spatial multiomics map of trophoblast development in early pregnancy. Nature 2023; 616:143-151. [PMID: 36991123 PMCID: PMC10076224 DOI: 10.1038/s41586-023-05869-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 02/21/2023] [Indexed: 03/31/2023]
Abstract
The relationship between the human placenta-the extraembryonic organ made by the fetus, and the decidua-the mucosal layer of the uterus, is essential to nurture and protect the fetus during pregnancy. Extravillous trophoblast cells (EVTs) derived from placental villi infiltrate the decidua, transforming the maternal arteries into high-conductance vessels1. Defects in trophoblast invasion and arterial transformation established during early pregnancy underlie common pregnancy disorders such as pre-eclampsia2. Here we have generated a spatially resolved multiomics single-cell atlas of the entire human maternal-fetal interface including the myometrium, which enables us to resolve the full trajectory of trophoblast differentiation. We have used this cellular map to infer the possible transcription factors mediating EVT invasion and show that they are preserved in in vitro models of EVT differentiation from primary trophoblast organoids3,4 and trophoblast stem cells5. We define the transcriptomes of the final cell states of trophoblast invasion: placental bed giant cells (fused multinucleated EVTs) and endovascular EVTs (which form plugs inside the maternal arteries). We predict the cell-cell communication events contributing to trophoblast invasion and placental bed giant cell formation, and model the dual role of interstitial EVTs and endovascular EVTs in mediating arterial transformation during early pregnancy. Together, our data provide a comprehensive analysis of postimplantation trophoblast differentiation that can be used to inform the design of experimental models of the human placenta in early pregnancy.
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Affiliation(s)
- Anna Arutyunyan
- Wellcome Sanger Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | | | | | - Megan A Sheridan
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ilia Kats
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Britta Velten
- Wellcome Sanger Institute, Cambridge, UK
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Regina Hoo
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | | | | | - Luca Marconato
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Lucy Gardner
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Qian Li
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Iva Kelava
- Wellcome Sanger Institute, Cambridge, UK
| | - Gavin J Wright
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, UK
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | | | - Ashley Moffett
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Oliver Stegle
- Wellcome Sanger Institute, Cambridge, UK.
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
| | - Margherita Y Turco
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
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65
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Butto T, Mungikar K, Baumann P, Winter J, Lutz B, Gerber S. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing. Cells 2023; 12:cells12071051. [PMID: 37048124 PMCID: PMC10093037 DOI: 10.3390/cells12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.
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Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Peter Baumann
- Faculty of Biology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center Mainz, 55128 Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
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66
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Drenckhahn JD, Nicin L, Akhouaji S, Krück S, Blank AE, Schänzer A, Yörüker U, Jux C, Tombor L, Abplanalp W, John D, Zeiher AM, Dimmeler S, Rupp S. Cardiomyocyte hyperplasia and immaturity but not hypertrophy are characteristic features of patients with RASopathies. J Mol Cell Cardiol 2023; 178:22-35. [PMID: 36948385 DOI: 10.1016/j.yjmcc.2023.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/11/2023] [Accepted: 03/14/2023] [Indexed: 03/24/2023]
Abstract
AIMS RASopathies are caused by mutations in genes that alter the MAP kinase pathway and are marked by several malformations with cardiovascular disorders as the predominant cause of mortality. Mechanistic insights in the underlying pathogenesis in affected cardiac tissue are rare. The aim of the study was to assess the impact of RASopathy causing mutations on the human heart. METHODS AND RESULTS Using single cell approaches and histopathology we analyzed cardiac tissue from children with different RASopathy-associated mutations compared to age-matched dilated cardiomyopathy (DCM) and control hearts. The volume of cardiomyocytes was reduced in RASopathy conditions compared to controls and DCM patients, and the estimated number of cardiomyocytes per heart was ~4-10 times higher. Single nuclei RNA sequencing of a 13-year-old RASopathy patient (carrying a PTPN11 c.1528C > G mutation) revealed that myocardial cell composition and transcriptional patterns were similar to <1 year old DCM hearts. Additionally, immaturity of cardiomyocytes is shown by an increased MYH6/MYH7 expression ratio and reduced expression of genes associated with fatty acid metabolism. In the patient with the PTPN11 mutation activation of the MAP kinase pathway was not evident in cardiomyocytes, whereas increased phosphorylation of PDK1 and its downstream kinase Akt was detected. CONCLUSION In conclusion, an immature cardiomyocyte differentiation status appears to be preserved in juvenile RASopathy patients. The increased mass of the heart in such patients is due to an increase in cardiomyocyte number (hyperplasia) but not an enlargement of individual cardiomyocytes (hypertrophy).
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Affiliation(s)
- Jörg-Detlef Drenckhahn
- Department of Pediatric Cardiology, Intensive Care Medicine and Congenital Heart Disease, Justus Liebig University Giessen, Giessen, Germany
| | - Luka Nicin
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Sara Akhouaji
- Department of Pediatric Cardiology, Intensive Care Medicine and Congenital Heart Disease, Justus Liebig University Giessen, Giessen, Germany
| | - Svenja Krück
- Department of Pediatric Cardiology, Intensive Care Medicine and Congenital Heart Disease, Justus Liebig University Giessen, Giessen, Germany
| | - Anna Eva Blank
- Department of Pediatric Cardiology, Intensive Care Medicine and Congenital Heart Disease, Justus Liebig University Giessen, Giessen, Germany
| | - Anne Schänzer
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| | - Uygar Yörüker
- Department of Pediatric Cardiac Surgery, University Hospital Giessen, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Jux
- Department of Pediatric Cardiology, Intensive Care Medicine and Congenital Heart Disease, Justus Liebig University Giessen, Giessen, Germany
| | - Lukas Tombor
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany; German Center for Cardiovascular Research, RheinMain, Frankfurt, Germany
| | - Wesley Abplanalp
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany; German Center for Cardiovascular Research, RheinMain, Frankfurt, Germany
| | - David John
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany; German Center for Cardiovascular Research, RheinMain, Frankfurt, Germany
| | - Andreas M Zeiher
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany; German Center for Cardiovascular Research, RheinMain, Frankfurt, Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany; Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany; German Center for Cardiovascular Research, RheinMain, Frankfurt, Germany
| | - Stefan Rupp
- Department of Pediatric Cardiology, Intensive Care Medicine and Congenital Heart Disease, Justus Liebig University Giessen, Giessen, Germany.
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67
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The gut microbiome modulates the transformation of microglial subtypes. Mol Psychiatry 2023; 28:1611-1621. [PMID: 36914812 DOI: 10.1038/s41380-023-02017-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023]
Abstract
Clinical and animal studies have shown that gut microbiome disturbances can affect neural function and behaviors via the microbiota-gut-brain axis, and may be implicated in the pathogenesis of several brain diseases. However, exactly how the gut microbiome modulates nervous system activity remains obscure. Here, using a single-cell nucleus sequencing approach, we sought to characterize the cell type-specific transcriptomic changes in the prefrontal cortex and hippocampus derived from germ-free (GF), specific pathogen free, and colonized-GF mice. We found that the absence of gut microbiota resulted in cell-specific transcriptomic changes. Furthermore, microglia transcriptomes were preferentially influenced, which could be effectively reversed by microbial colonization. Significantly, the gut microbiome modulated the mutual transformation of microglial subpopulations in the two regions. Cross-species analysis showed that the transcriptome changes of these microglial subpopulations were mainly associated with Alzheimer's disease (AD) and major depressive disorder (MDD), which were further supported by animal behavioral tests. Our findings demonstrate that gut microbiota mainly modulate the mutual transformation of microglial subtypes, which may lead to new insights into the pathogenesis of AD and MDD.
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68
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Olsen TR, Talla P, Furnari J, Bruce JN, Canoll P, Zha S, Sims PA. Scalable co-sequencing of RNA and DNA from individual nuclei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527940. [PMID: 36798358 PMCID: PMC9934633 DOI: 10.1101/2023.02.09.527940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution. However, existing tools lack the throughput required for comprehensive analysis of complex tumors and tissues. We introduce a highly scalable method for jointly profiling DNA and expression following nucleosome depletion (DEFND-seq). In DEFND-seq, nuclei are nucleosome-depleted, tagmented, and separated into individual droplets for mRNA and genomic DNA barcoding. Once nuclei have been depleted of nucleosomes, subsequent steps can be performed using the widely available 10x Genomics droplet microfluidic technology and commercial kits without experimental modification. We demonstrate the production of high-complexity mRNA and gDNA sequencing libraries from thousands of individual nuclei from both cell lines and archived surgical specimens for associating gene expression phenotypes with both copy number and single nucleotide variants.
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Affiliation(s)
- Timothy R Olsen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Pranay Talla
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Julia Furnari
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032
| | - Jeffrey N Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032
| | - Peter Canoll
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032
| | - Shan Zha
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032
- Institute for Cancer Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
- Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, 10032
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032
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69
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Murdock MH, Tsai LH. Insights into Alzheimer's disease from single-cell genomic approaches. Nat Neurosci 2023; 26:181-195. [PMID: 36593328 PMCID: PMC10155598 DOI: 10.1038/s41593-022-01222-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/28/2022] [Indexed: 01/03/2023]
Abstract
Alzheimer's disease (AD) is an age-related disease pathologically defined by the deposition of amyloid plaques and neurofibrillary tangles in the brain parenchyma. Single-cell profiling has shown that Alzheimer's dementia involves the complex interplay of virtually every major brain cell type. Here, we highlight cell-type-specific molecular perturbations in AD. We discuss how genomic information from single cells expands existing paradigms of AD pathogenesis and highlight new opportunities for therapeutic interventions.
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Affiliation(s)
- Mitchell H Murdock
- Department of Brain and Cognitive Sciences, The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
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70
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Wiseman JA, Dragunow M, I-H Park T. Cell Type-Specific Nuclei Markers: The Need for Human Brain Research to Go Nuclear. Neuroscientist 2023; 29:41-61. [PMID: 34459315 DOI: 10.1177/10738584211037351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Identifying and interrogating cell type-specific populations within the heterogeneous milieu of the human brain is paramount to resolving the processes of normal brain homeostasis and the pathogenesis of neurological disorders. While brain cell type-specific markers are well established, most are localized on cellular membranes or within the cytoplasm, with limited literature describing those found in the nucleus. Due to the complex cytoarchitecture of the human brain, immunohistochemical studies require well-defined cell-specific nuclear markers for more precise and efficient quantification of the cellular populations. Furthermore, efficient nuclear markers are required for cell type-specific purification and transcriptomic interrogation of archived human brain tissue through nuclei isolation-based RNA sequencing. To sate the growing demand for robust cell type-specific nuclear markers, we thought it prudent to comprehensively review the current literature to identify and consolidate a novel series of robust cell type-specific nuclear markers that can assist researchers across a range of neuroscientific disciplines. The following review article collates and discusses several key and prospective cell type-specific nuclei markers for each of the major human brain cell types; it then concludes by discussing the potential applications of cell type-specific nuclear workflows and the power of nuclear-based neuroscientific research.
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Affiliation(s)
- James A Wiseman
- Department of Pharmacology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Mike Dragunow
- Department of Pharmacology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Neurosurgical Research Unit, The Centre for Brain Research, University of Auckland, Auckland, New Zealand.,Hugh Green Biobank, The Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Thomas I-H Park
- Department of Pharmacology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
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71
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Li M, Chen X, Yang Q, Cao S, Wyler S, Yuan R, Zhang L, Liao M, Lv M, Wang F, Guo Y, Zhou J, Zhang L, Xie X, Liang W. Single-nucleus profiling of adult mice sub-ventricular zone after blast-related traumatic brain injury. Sci Data 2023; 10:13. [PMID: 36604452 PMCID: PMC9814753 DOI: 10.1038/s41597-022-01925-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Explosive blast-related traumatic brain injuries (bTBI) are common in war zones and urban terrorist attacks. These bTBIs often result in complex neuropathologic damage and neurologic complications. However, there is still a lack of specific strategies for diagnosing and/or treating bTBIs. The sub-ventricular zone (SVZ), which undergoes adult neurogenesis, is critical for the neurological maintenance and repair after brain injury. However, the cellular responses and mechanisms that trigger and modulate these activities in the pathophysiological processes following bTBI remain poorly understood. Here we employ single-nucleus RNA-sequencing (snRNA-seq) of the SVZ from mice subjected to a bTBI. This data-set, including 15272 cells (7778 bTBI and 7494 control) representing all SVZ cell types and is ideally suited for exploring the mechanisms underlying the pathogenesis of bTBIs. Additionally, it can serve as a reference for future studies regarding the diagnosis and treatment of bTBIs.
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Affiliation(s)
- Manrui Li
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, Shanghai, 200000, China
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xiameng Chen
- Department of Forensic Pathology and Forensic Clinical Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Qiuyun Yang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shuqiang Cao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Steven Wyler
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | | | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Feng Wang
- Department of Medical Oncology, Cancer Center, Sichuan University, Chengdu, 610041, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Jihong Zhou
- Army Medical University, Chongqing, 404000, China.
| | - Lin Zhang
- Sichuan University, Chengdu, 610041, China.
| | - Xiaoqi Xie
- Department of Critical Care Medicine, Sichuan University, Chengdu, 610041, China.
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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72
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van den Oord EJCG, Xie LY, Zhao M, Aberg KA, Clark SL. A single-nucleus transcriptomics study of alcohol use disorder in the nucleus accumbens. Addict Biol 2023; 28:e13250. [PMID: 36577731 DOI: 10.1111/adb.13250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/29/2022] [Accepted: 10/13/2022] [Indexed: 11/14/2022]
Abstract
Gene expression studies offer promising opportunities to better understand the processes underlying alcohol use disorder (AUD). As cell types differ in their function, gene expression profiles will typically vary across cell types. When studying bulk tissue, failure to account for this cellular diversity has a detrimental impact on the ability to detect disease associations. We therefore assayed the transcriptomes of 32,531 individual nuclei extracted from the nucleus accumbens (NAc) of nine donors with AUD and nine controls (72% male). Our study identified 17 clearly delineated cell types. We detected 26 transcriptome-wide significant differentially expressed genes (DEGs) that mainly involved medium spiny neurons with both D1-type and D2-type dopamine receptors, microglia (MGL) and oligodendrocytes. A higher than expected number of DEGs replicated in an existing single nucleus gene expression study of alcohol dependence in the prefrontal cortex (enrichment ratio 1.91, p value 0.019) with two genes remaining significant after a Bonferroni correction. Our most compelling result involved CD53 in MGL that replicated in the same cell type in the prefrontal cortex and was previously implicated in studies of DNA methylation, bulk gene expression and genetic variants. Several DEGs were previously reported to be associated with AUD (e.g., PER1 and MGAT5). The DEGs for MSN.3 seemed involved in neurodegeneration, disruption of circadian rhythms, alterations in glucose metabolism and changes in synaptic plasticity. For MGL, the DEGs implicated neuroinflammation and immune-related processes and for OLI, disruptions in myelination. This identification of the specific cell-types from which the association signals originate will be key for designing proper follow-up experiments and, eventually, novel clinical interventions.
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Affiliation(s)
- Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Lin Y Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Shaunna L Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, College Station, Texas, USA
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73
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Kim N, Kang H, Jo A, Yoo SA, Lee HO. Perspectives on single-nucleus RNA sequencing in different cell types and tissues. J Pathol Transl Med 2023; 57:52-59. [PMID: 36623812 PMCID: PMC9846005 DOI: 10.4132/jptm.2022.12.19] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Single-cell RNA sequencing has become a powerful and essential tool for delineating cellular diversity in normal tissues and alterations in disease states. For certain cell types and conditions, there are difficulties in isolating intact cells for transcriptome profiling due to their fragility, large size, tight interconnections, and other factors. Single-nucleus RNA sequencing (snRNA-seq) is an alternative or complementary approach for cells that are difficult to isolate. In this review, we will provide an overview of the experimental and analysis steps of snRNA-seq to understand the methods and characteristics of general and tissue-specific snRNA-seq data. Knowing the advantages and limitations of snRNA-seq will increase its use and improve the biological interpretation of the data generated using this technique.
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Affiliation(s)
- Nayoung Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea
| | - Huiram Kang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea
| | - Areum Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea
| | - Seung-Ah Yoo
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea,Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul,
Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul,
Korea,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul,
Korea,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul,
Korea
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74
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Palmer CR, Chun J. Extraction and Purification of Single Nuclei from Frozen Human Brain Tissue. Methods Mol Biol 2023; 2561:31-42. [PMID: 36399263 DOI: 10.1007/978-1-0716-2655-9_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] [Indexed: 06/16/2023]
Abstract
Resolving the complexity of the human brain at the level of single cells is essential to gaining an understanding of the immense diversity of cell types and functional states in both healthy and diseased brains. To exploit fully the technologies available for such studies, one must extract and isolate pure nuclei from unfixed postmortem tissue while preserving the molecules to be interrogated. Currently, nuclei are necessary substitutes for individual brain cells, since myriad cell types/sub-types constituting the human brain are embedded within the neuropil-a complex milieu of interconnected cells, processes, and synapses-which precludes intact and selective isolation of single brain cells. Here, we describe a protocol for the extraction and purification of intact single nuclei from frozen human brain tissue along with modifications to accommodate numerous downstream analyses, particularly for transcriptomic applications.
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Affiliation(s)
- Carter R Palmer
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, La Jolla, CA, USA
| | - Jerold Chun
- Translational Neuroscience Initiative, Neuroscience Drug Discovery, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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75
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Murat F, Mbengue N, Winge SB, Trefzer T, Leushkin E, Sepp M, Cardoso-Moreira M, Schmidt J, Schneider C, Mößinger K, Brüning T, Lamanna F, Belles MR, Conrad C, Kondova I, Bontrop R, Behr R, Khaitovich P, Pääbo S, Marques-Bonet T, Grützner F, Almstrup K, Schierup MH, Kaessmann H. The molecular evolution of spermatogenesis across mammals. Nature 2023; 613:308-316. [PMID: 36544022 PMCID: PMC9834047 DOI: 10.1038/s41586-022-05547-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Abstract
The testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1-6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and include seven primates. We find that the rapid evolution of the testis was driven by accelerated fixation rates of gene expression changes, amino acid substitutions and new genes in late spermatogenic stages, probably facilitated by reduced pleiotropic constraints, haploid selection and transcriptionally permissive chromatin. We identify temporal expression changes of individual genes across species and conserved expression programs controlling ancestral spermatogenic processes. Genes predominantly expressed in spermatogonia (germ cells fuelling spermatogenesis) and Sertoli (somatic support) cells accumulated on X chromosomes during evolution, presumably owing to male-beneficial selective forces. Further work identified transcriptomal differences between X- and Y-bearing spermatids and uncovered that meiotic sex-chromosome inactivation (MSCI) also occurs in monotremes and hence is common to mammalian sex-chromosome systems. Thus, the mechanism of meiotic silencing of unsynapsed chromatin, which underlies MSCI, is an ancestral mammalian feature. Our study illuminates the molecular evolution of spermatogenesis and associated selective forces, and provides a resource for investigating the biology of the testis across mammals.
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Affiliation(s)
- Florent Murat
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany. .,INRAE, LPGP, Rennes, France.
| | - Noe Mbengue
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
| | - Sofia Boeg Winge
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Timo Trefzer
- Berlin Institute of Health at Charité, University of Medicine Berlin, Corporate Member of the Free University of Berlin, Humboldt-University of Berlin, Berlin, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Julia Schmidt
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Celine Schneider
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Katharina Mößinger
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Thoomke Brüning
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Francesco Lamanna
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Christian Conrad
- Berlin Institute of Health at Charité, University of Medicine Berlin, Corporate Member of the Free University of Berlin, Humboldt-University of Berlin, Berlin, Germany
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, the Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, the Netherlands
| | - Rüdiger Behr
- German Primate Center (DPZ), Platform Degenerative Diseases, Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Miquel Crusafont Catalan Institute of Paleontology, Autonomous University of Barcelona, Barcelona, Spain
| | - Frank Grützner
- The Robinson Research Institute, School of Biological Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Henrik Kaessmann
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
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76
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Madissoon E, Oliver AJ, Kleshchevnikov V, Wilbrey-Clark A, Polanski K, Richoz N, Ribeiro Orsi A, Mamanova L, Bolt L, Elmentaite R, Pett JP, Huang N, Xu C, He P, Dabrowska M, Pritchard S, Tuck L, Prigmore E, Perera S, Knights A, Oszlanczi A, Hunter A, Vieira SF, Patel M, Lindeboom RGH, Campos LS, Matsuo K, Nakayama T, Yoshida M, Worlock KB, Nikolić MZ, Georgakopoulos N, Mahbubani KT, Saeb-Parsy K, Bayraktar OA, Clatworthy MR, Stegle O, Kumasaka N, Teichmann SA, Meyer KB. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche. Nat Genet 2023; 55:66-77. [PMID: 36543915 PMCID: PMC9839452 DOI: 10.1038/s41588-022-01243-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new 'gland-associated immune niche' has implications for respiratory health.
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Affiliation(s)
- Elo Madissoon
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Amanda J Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | | | - Nathan Richoz
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, UK
| | - Ana Ribeiro Orsi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - J Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Andrew Knights
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Agnes Oszlanczi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Adam Hunter
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sara F Vieira
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Lia S Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Nikitas Georgakopoulos
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | | | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, UK
| | - Oliver Stegle
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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77
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Liu CY, Chen HH. Large-Scale Single-Nucleus RNA Sequencing Compatible with Complex Archived Samples. Methods Mol Biol 2022; 2560:333-346. [PMID: 36481908 DOI: 10.1007/978-1-0716-2651-1_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transcriptome profiling at single-cell resolution allows us to identify and assess functional cell types and cellular states, including those within degenerating ocular tissues in retinitis pigmentosa. The technology is particularly valuable when studying tissues with high cellular heterogeneity, or when specific cell types are of interest. In this chapter, we introduce a detailed protocol of a medium-throughput single-nucleus RNA sequencing technique that utilizes frozen tissue as input sample. This protocol can be executed by any researcher with basic training in molecular biology techniques. With this protocol, a single experimenter can easily process two samples per day up to cDNA amplification, and library preparations can be done in batches of 8. Routinely we can obtain ~20 K nuclei per eye from 3 to 4 library preparations.
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Affiliation(s)
- Chao-Yu Liu
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu-Hsin Chen
- Department of Biomarker Discovery OMNI, Genentech , South San Francisco, CA, United States.
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78
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Oh JM, An M, Son DS, Choi J, Cho YB, Yoo CE, Park WY. Comparison of cell type distribution between single-cell and single-nucleus RNA sequencing: enrichment of adherent cell types in single-nucleus RNA sequencing. Exp Mol Med 2022; 54:2128-2134. [PMID: 36460793 PMCID: PMC9794763 DOI: 10.1038/s12276-022-00892-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 08/23/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Abstract
Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) is an effective technique for estimating the cellular composition and transcriptional profiles of individual cells from fresh tissue. Single-nucleus RNA sequencing (snRNA-seq) is necessary to perform this type of analysis in frozen or difficult-to-dissociate tissues, which cannot be subjected to scRNA-seq. This difference in the state of tissues leads to variation in cell-type distributions among each platform. To identify the characteristics of these methods and their differences, scRNA-seq and snRNA-seq were performed in parallel for colon and liver tissues. The two platforms revealed similar diversity but different proportions of cell types in matched tissues. The proportions of epithelial cells in the colon and hepatocytes in the liver were relatively high in snRNA-seq and that of immune cells was relatively high in scRNA-seq. This difference could be explained by variations in the expression scores of adhesion genes due to the disruption of the cytoplasmic contents during scRNA-seq. The enrichment of epithelial cells in the colon resulted in a discrepancy in the differentiation of epithelial cells. This enrichment was also well matched with the images of hematoxylin and eosin staining and the estimated distribution of cell types in bulk RNA sequencing. These results showed that snRNA-seq could be used to analyze tissues that cannot be subjected to scRNA-seq and provides more information in specific cell type analysis.
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Affiliation(s)
- Jin-Mi Oh
- grid.414964.a0000 0001 0640 5613Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Minae An
- grid.414964.a0000 0001 0640 5613Innovative Institute for Precision Medicine, Samsung Medical Center, Seoul, Korea
| | - Dae-Soon Son
- grid.256753.00000 0004 0470 5964School of Big Data Science, Data Science Convergence Research Center, Hallym University, Chuncheon, 24252 Korea
| | - Jinhyuk Choi
- grid.222754.40000 0001 0840 2678Department of Legal Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Yong Beom Cho
- grid.414964.a0000 0001 0640 5613Department of Surgery, Sungkyunkwan University, Samsung Medical Center, Seoul, Korea ,grid.264381.a0000 0001 2181 989XDepartment of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Chang Eun Yoo
- grid.414964.a0000 0001 0640 5613Basic Research Support Center, Samsung Research Institute for Future Medicine/Samsung Medical Center, Seoul, Korea
| | - Woong-Yang Park
- grid.414964.a0000 0001 0640 5613Samsung Genome Institute, Samsung Medical Center, Seoul, Korea ,grid.264381.a0000 0001 2181 989XDepartment of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea ,Geninus Inc, Seoul, Korea ,grid.264381.a0000 0001 2181 989XDepartment of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
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79
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Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material. Front Zool 2022; 19:27. [DOI: 10.1186/s12983-022-00472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Recent technological advances opened the opportunity to simultaneously study gene expression for thousands of individual cells on a genome-wide scale. The experimental accessibility of such single-cell RNA sequencing (scRNAseq) approaches allowed gaining insights into the cell type composition of heterogeneous tissue samples of animal model systems and emerging models alike. A major prerequisite for a successful application of the method is the dissociation of complex tissues into individual cells, which often requires large amounts of input material and harsh mechanical, chemical and temperature conditions. However, the availability of tissue material may be limited for small animals, specific organs, certain developmental stages or if samples need to be acquired from collected specimens. Therefore, we evaluated different dissociation protocols to obtain single cells from small tissue samples of Drosophila melanogaster eye-antennal imaginal discs.
Results
We show that a combination of mechanical and chemical dissociation resulted in sufficient high-quality cells. As an alternative, we tested protocols for the isolation of single nuclei, which turned out to be highly efficient for fresh and frozen tissue samples. Eventually, we performed scRNAseq and single-nuclei RNA sequencing (snRNAseq) to show that the best protocols for both methods successfully identified relevant cell types. At the same time, snRNAseq resulted in less artificial gene expression that is caused by rather harsh dissociation conditions needed to obtain single cells for scRNAseq. A direct comparison of scRNAseq and snRNAseq data revealed that both datasets share biologically relevant genes among the most variable genes, and we showed differences in the relative contribution of the two approaches to identified cell types.
Conclusion
We present two dissociation protocols that allow isolating single cells and single nuclei, respectively, from low input material. Both protocols resulted in extraction of high-quality RNA for subsequent scRNAseq or snRNAseq applications. If tissue availability is limited, we recommend the snRNAseq procedure of fresh or frozen tissue samples as it is perfectly suited to obtain thorough insights into cellular diversity of complex tissue.
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80
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Pratt KJB, Shea JM, Remesal-Gomez L, Bieri G, Smith LK, Couthouis J, Chen CP, Roy IJ, Gontier G, Villeda SA. Loss of neuronal Tet2 enhances hippocampal-dependent cognitive function. Cell Rep 2022; 41:111612. [PMID: 36351399 PMCID: PMC10032941 DOI: 10.1016/j.celrep.2022.111612] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/04/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022] Open
Abstract
DNA methylation has emerged as a critical modulator of neuronal plasticity and cognitive function. Notwithstanding, the role of enzymes that demethylate DNA remain to be fully explored. Here, we report that loss of ten-eleven translocation methylcytosine dioxygenase 2 (Tet2), which catalyzes oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), in adult neurons enhances cognitive function. In the adult mouse hippocampus, we detected an enrichment of Tet2 in neurons. Viral-mediated neuronal overexpression and RNA interference of Tet2 altered dendritic complexity and synaptic-plasticity-related gene expression in vitro. Overexpression of neuronal Tet2 in adult hippocampus, and loss of Tet2 in adult glutamatergic neurons, resulted in differential hydroxymethylation associated with genes involved in synaptic transmission. Functionally, overexpression of neuronal Tet2 impaired hippocampal-dependent memory, while loss of neuronal Tet2 enhanced memory. Ultimately, these data identify neuronal Tet2 as a molecular target to boost cognitive function.
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Affiliation(s)
- Karishma J B Pratt
- Department of Anatomy, University of California San Francisco, 513 Parnassus Avenue, Box 0452, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jeremy M Shea
- Department of Anatomy, University of California San Francisco, 513 Parnassus Avenue, Box 0452, San Francisco, CA 94143, USA
| | - Laura Remesal-Gomez
- Department of Anatomy, University of California San Francisco, 513 Parnassus Avenue, Box 0452, San Francisco, CA 94143, USA
| | - Gregor Bieri
- Department of Anatomy, University of California San Francisco, 513 Parnassus Avenue, Box 0452, San Francisco, CA 94143, USA
| | - Lucas K Smith
- Department of Anatomy, University of California San Francisco, 513 Parnassus Avenue, Box 0452, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Julien Couthouis
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher P Chen
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Irena J Roy
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Geraldine Gontier
- Department of Anatomy, University of California San Francisco, 513 Parnassus Avenue, Box 0452, San Francisco, CA 94143, USA.
| | - Saul A Villeda
- Department of Anatomy, University of California San Francisco, 513 Parnassus Avenue, Box 0452, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA 94143, USA; Department of Physical Therapy and Rehabilitation Science, San Francisco, CA 94143, USA; Bakar Aging Research Institute, San Francisco, CA 94143, USA.
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81
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Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex. Nat Commun 2022; 13:6747. [PMID: 36347848 PMCID: PMC9643508 DOI: 10.1038/s41467-022-34413-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Single cell approaches have increased our knowledge about the cell type composition of the non-human primate (NHP), but a detailed characterization of area-specific regulatory features remains outstanding. We generated single-cell transcriptomic and chromatin accessibility (single-cell ATAC) data of 358,237 cells from prefrontal cortex (PFC), primary motor cortex (M1) and primary visual cortex (V1) of adult female cynomolgus monkey brain, and integrated this dataset with Stereo-seq (spatial enhanced resolution omics-sequencing) of the corresponding cortical areas to assign topographic information to molecular states. We identified area-specific chromatin accessible sites and their targeted genes, including the cell type-specific transcriptional regulatory network associated with excitatory neurons heterogeneity. We reveal calcium ion transport and axon guidance genes related to specialized functions of PFC and M1, identified the similarities and differences between adult macaque and human oligodendrocyte trajectories, and mapped the genetic variants and gene perturbations of human diseases to NHP cortical cells. This resource establishes a transcriptomic and chromatin accessibility combinatory regulatory landscape at a single-cell and spatially resolved resolution in NHP cortex.
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82
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Osborne LM, Payne JL, Sherer ML, Sabunciyan S. Altered extracellular mRNA communication in postpartum depression is associated with decreased autophagy. Mol Psychiatry 2022; 27:4526-4535. [PMID: 36138128 DOI: 10.1038/s41380-022-01794-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/29/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022]
Abstract
We investigated whether extracellular RNA communication, which is a recently discovered mode of intercellular communication that is involved in a variety of important biological processes including pregnancy, is associated with postpartum depression (PPD). Extracellular RNA communication is increased during pregnancy and is involved in embryo implantation, uterine spiral artery remodeling, parturition, preterm birth, immunity, and the inflammatory response. Since immune anomalies are associated with PPD, we characterized the mRNA content of extracellular vesicles (EV) in a cohort of prospectively collected blood plasma samples at six time-points throughout pregnancy and the postpartum (2nd trimester, 3rd trimester, 2 weeks postpartum, 6 weeks postpartum, 3 months postpartum, and 6 months postpartum) in an academic medical setting from women who went on to develop PPD (N = 7, defined as euthymic in pregnancy with postpartum-onset depressive symptoms assessed by Edinburgh Postnatal Depression Scale ≥13 at any postpartum time point) and matched unaffected controls (N = 7, defined as euthymic throughout pregnancy and postpartum). Blood samples were available for all participants at the T2 and W6 timepoints, with fewer samples available at other time points. This analysis revealed that EV mRNA levels during pregnancy and the postpartum period were extensively altered in women who went on to develop PPD. Gene set enrichment analysis revealed that mRNAs associated with autophagy were decreased in PPD cases. In contrast, EV mRNAs from ribosomes and mitochondria, two organelles that are selectively targeted by autophagy, were elevated in PPD cases. Cellular deconvolution analysis discovered that EV mRNAs associated with PPD originated from monocytes and macrophages. Quantitative PCR analysis for four relevant genes in another cohort replicated these findings and confirmed that extracellular RNA levels are altered in PPD. We demonstrate that EV mRNA communication is robustly altered during pregnancy and the postpartum period in women who go on to develop PPD. Our work also establishes a direct link between reduced autophagy and PPD in patient samples. These data warrant investigating the feasibility of developing EV mRNA based biomarkers and therapeutic agents for PPD.
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Affiliation(s)
- Lauren M Osborne
- Department of Obstetrics & Gynecology, Weill Cornell Medicine, New York, New York, USA.,Department of Psychiatry, Weill Cornell Medicine, New York, New York, USA
| | - Jennifer L Payne
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA, USA
| | - Morgan L Sherer
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sarven Sabunciyan
- Department of Pediatrics, Stanley Division, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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83
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Single-cell transcriptomics in planaria: new tools allow new insights into cellular and evolutionary features. Biochem Soc Trans 2022; 50:1237-1246. [DOI: 10.1042/bst20210825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]
Abstract
Single-cell transcriptomics has revolutionised biology allowing the quantification of gene expression in individual cells. Since each single cell contains cell type specific mRNAs, these techniques enable the classification of cell identities. Therefore, single cell methods have been used to explore the repertoire of cell types (the single cell atlas) of different organisms, including freshwater planarians. Nowadays, planarians are one of the most prominent animal models in single cell biology. They have been studied at the single cell level for over a decade using most of the available single cell methodological approaches. These include plate-based methods, such as qPCR, nanodroplet methods and in situ barcoding methods. Because of these studies, we now have a very good picture of planarian cell types and their differentiation trajectories. Planarian regenerative properties and other characteristics, such as their developmental plasticity and their capacity to reproduce asexually, ensure that another decade of single cell biology in planarians is yet to come. Here, we review these characteristics, the new biological insights that have been obtained by single-cell transcriptomics and outline the perspectives for the future.
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84
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Cuevas-Diaz Duran R, González-Orozco JC, Velasco I, Wu JQ. Single-cell and single-nuclei RNA sequencing as powerful tools to decipher cellular heterogeneity and dysregulation in neurodegenerative diseases. Front Cell Dev Biol 2022; 10:884748. [PMID: 36353512 PMCID: PMC9637968 DOI: 10.3389/fcell.2022.884748] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 10/06/2022] [Indexed: 08/10/2023] Open
Abstract
Neurodegenerative diseases affect millions of people worldwide and there are currently no cures. Two types of common neurodegenerative diseases are Alzheimer's (AD) and Parkinson's disease (PD). Single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq) have become powerful tools to elucidate the inherent complexity and dynamics of the central nervous system at cellular resolution. This technology has allowed the identification of cell types and states, providing new insights into cellular susceptibilities and molecular mechanisms underlying neurodegenerative conditions. Exciting research using high throughput scRNA-seq and snRNA-seq technologies to study AD and PD is emerging. Herein we review the recent progress in understanding these neurodegenerative diseases using these state-of-the-art technologies. We discuss the fundamental principles and implications of single-cell sequencing of the human brain. Moreover, we review some examples of the computational and analytical tools required to interpret the extensive amount of data generated from these assays. We conclude by highlighting challenges and limitations in the application of these technologies in the study of AD and PD.
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Affiliation(s)
| | | | - Iván Velasco
- Instituto de Fisiología Celular—Neurociencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suárez”, Mexico City, Mexico
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, United States
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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85
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Michelotti TC, Kisby BR, Flores LS, Tegeler AP, Fokar M, Crasto C, Menarim BC, Loux SC, Strieder-Barboza C. Single-nuclei analysis reveals depot-specific transcriptional heterogeneity and depot-specific cell types in adipose tissue of dairy cows. Front Cell Dev Biol 2022; 10:1025240. [PMID: 36313560 PMCID: PMC9616121 DOI: 10.3389/fcell.2022.1025240] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Adipose tissue (AT) is an endocrine organ with a central role on whole-body energy metabolism and development of metabolic diseases. Single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, respectively) analyses in mice and human AT have revealed vast cell heterogeneity and functionally distinct subtypes that are potential therapeutic targets to metabolic disease. In periparturient dairy cows, AT goes through intensive remodeling and its dysfunction is associated with metabolic disease pathogenesis and decreased productive performance. The contributions of depot-specific cells and subtypes to the development of diseases in dairy cows remain to be studied. Our objective was to elucidate differences in cellular diversity of visceral (VAT) and subcutaneous (SAT) AT in dairy cows at the single-nuclei level. We collected matched SAT and VAT samples from three dairy cows and performed snRNA-seq analysis. We identified distinct cell types including four major mature adipocytes (AD) and three stem and progenitor cells (ASPC) subtypes, along with endothelial cells (EC), mesothelial cells (ME), immune cells, and pericytes and smooth muscle cells. All major cell types were present in both SAT and VAT, although a strong VAT-specificity was observed for ME, which were basically absent in SAT. One ASPC subtype was defined as adipogenic (PPARG+) while the other two had a fibro-adipogenic profile (PDGFRA+). We identified vascular and lymphatic EC subtypes, and different immune cell types and subtypes in both SAT and VAT, i.e., macrophages, monocytes, T cells, and natural killer cells. Not only did VAT show a greater proportion of immune cells, but these visceral immune cells had greater activation of pathways related to immune and inflammatory response, and complement cascade in comparison with SAT. There was a substantial contrast between depots for gene expression of complement cascade, which were greatly expressed by VAT cell subtypes compared to SAT, indicating a pro-inflammatory profile in VAT. Unprecedently, our study demonstrated cell-type and depot-specific heterogeneity in VAT and SAT of dairy cows. A better understanding of depot-specific molecular and cellular features of SAT and VAT will aid in the development of AT-targeted strategies to prevent and treat metabolic disease in dairy cows, especially during the periparturient period.
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Affiliation(s)
- Tainara C. Michelotti
- Department of Veterinary Sciences, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, United States
| | - Brent R. Kisby
- Department of Pharmacology and Neuroscience, Texas Tech University Health Science Center, Lubbock, TX, United States
| | - Lauryn S. Flores
- Department of Veterinary Sciences, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, United States
| | - Alexandra P. Tegeler
- Department of Veterinary Sciences, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, United States
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
| | - Chiquito Crasto
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
- Department of Computer Science, Whitacre College of Engineering, Texas Tech University, Lubbock, TX, United States
- Department of University Studies, Texas Tech University, Lubbock, TX, United States
| | - Bruno C. Menarim
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States
| | - Shavahn C. Loux
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States
| | - Clarissa Strieder-Barboza
- Department of Veterinary Sciences, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, United States
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
- *Correspondence: Clarissa Strieder-Barboza,
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86
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Sardoo AM, Zhang S, Ferraro TN, Keck TM, Chen Y. Decoding brain memory formation by single-cell RNA sequencing. Brief Bioinform 2022; 23:6713514. [PMID: 36156112 PMCID: PMC9677489 DOI: 10.1093/bib/bbac412] [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: 05/18/2022] [Revised: 07/10/2022] [Accepted: 08/25/2022] [Indexed: 12/14/2022] Open
Abstract
To understand how distinct memories are formed and stored in the brain is an important and fundamental question in neuroscience and computational biology. A population of neurons, termed engram cells, represents the physiological manifestation of a specific memory trace and is characterized by dynamic changes in gene expression, which in turn alters the synaptic connectivity and excitability of these cells. Recent applications of single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) are promising approaches for delineating the dynamic expression profiles in these subsets of neurons, and thus understanding memory-specific genes, their combinatorial patterns and regulatory networks. The aim of this article is to review and discuss the experimental and computational procedures of sc/snRNA-seq, new studies of molecular mechanisms of memory aided by sc/snRNA-seq in human brain diseases and related mouse models, and computational challenges in understanding the regulatory mechanisms underlying long-term memory formation.
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Affiliation(s)
- Atlas M Sardoo
- Department of Biological & Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA
| | - Shaoqiang Zhang
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin 300387, China
| | - Thomas N Ferraro
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Thomas M Keck
- Department of Biological & Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA,Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, USA
| | - Yong Chen
- Corresponding author. Yong Chen, Department of Biological and Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA. Tel.: +1 856 256 4500; E-mail:
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87
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Le H, Peng B, Uy J, Carrillo D, Zhang Y, Aevermann BD, Scheuermann RH. Machine learning for cell type classification from single nucleus RNA sequencing data. PLoS One 2022; 17:e0275070. [PMID: 36149937 PMCID: PMC9506651 DOI: 10.1371/journal.pone.0275070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022] Open
Abstract
With the advent of single cell/nucleus RNA sequencing (sc/snRNA-seq), the field of cell phenotyping is now a data-driven exercise providing statistical evidence to support cell type/state categorization. However, the task of classifying cells into specific, well-defined categories with the empirical data provided by sc/snRNA-seq remains nontrivial due to the difficulty in determining specific differences between related cell types with close transcriptional similarities, resulting in challenges with matching cell types identified in separate experiments. To investigate possible approaches to overcome these obstacles, we explored the use of supervised machine learning methods-logistic regression, support vector machines, random forests, neural networks, and light gradient boosting machine (LightGBM)-as approaches to classify cell types using snRNA-seq datasets from human brain middle temporal gyrus (MTG) and human kidney. Classification accuracy was evaluated using an F-beta score weighted in favor of precision to account for technical artifacts of gene expression dropout. We examined the impact of hyperparameter optimization and feature selection methods on F-beta score performance. We found that the best performing model for granular cell type classification in both datasets is a multinomial logistic regression classifier and that an effective feature selection step was the most influential factor in optimizing the performance of the machine learning pipelines.
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Affiliation(s)
- Huy Le
- Department of Bioengineering, University of California, San Diego, CA, United States of America
| | - Beverly Peng
- Department of Bioengineering, University of California, San Diego, CA, United States of America
| | - Janelle Uy
- Department of Bioengineering, University of California, San Diego, CA, United States of America
| | - Daniel Carrillo
- Department of Bioengineering, University of California, San Diego, CA, United States of America
| | - Yun Zhang
- Department of informatics, J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Brian D. Aevermann
- Department of informatics, J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Richard H. Scheuermann
- Department of informatics, J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Pathology, University of California, San Diego, CA, United States of America
- La Jolla Institute for Immunology, San Diego, CA, United States of America
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88
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Otero-Garcia M, Mahajani SU, Wakhloo D, Tang W, Xue YQ, Morabito S, Pan J, Oberhauser J, Madira AE, Shakouri T, Deng Y, Allison T, He Z, Lowry WE, Kawaguchi R, Swarup V, Cobos I. Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer's disease. Neuron 2022; 110:2929-2948.e8. [PMID: 35882228 PMCID: PMC9509477 DOI: 10.1016/j.neuron.2022.06.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 03/08/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023]
Abstract
Tau aggregation in neurofibrillary tangles (NFTs) is closely associated with neurodegeneration and cognitive decline in Alzheimer's disease (AD). However, the molecular signatures that distinguish between aggregation-prone and aggregation-resistant cell states are unknown. We developed methods for the high-throughput isolation and transcriptome profiling of single somas with NFTs from the human AD brain, quantified the susceptibility of 20 neocortical subtypes for NFT formation and death, and identified both shared and cell-type-specific signatures. NFT-bearing neurons shared a marked upregulation of synaptic transmission-related genes, including a core set of 63 genes enriched for synaptic vesicle cycling. Oxidative phosphorylation and mitochondrial dysfunction were highly cell-type dependent. Apoptosis was only modestly enriched, and the susceptibilities of NFT-bearing and NFT-free neurons for death were highly similar. Our analysis suggests that NFTs represent cell-type-specific responses to stress and synaptic dysfunction. We provide a resource for biomarker discovery and the investigation of tau-dependent and tau-independent mechanisms of neurodegeneration.
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Affiliation(s)
- Marcos Otero-Garcia
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sameehan U Mahajani
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Debia Wakhloo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Weijing Tang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yue-Qiang Xue
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samuel Morabito
- Mathematical, Computational and Systems Biology Program, University of California, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Jie Pan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jane Oberhauser
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Angela E Madira
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tamara Shakouri
- Department of Pathology, University of California, Los Angeles, CA 90095, USA
| | - Yongning Deng
- Department of Pathology, University of California, Los Angeles, CA 90095, USA; Department of Neurology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Thomas Allison
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
| | - Zihuai He
- Department Neurology and Neurological Sciences and Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - William E Lowry
- Department of Molecular Cell and Developmental Biology, Broad Center for Regenerative Medicine and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Riki Kawaguchi
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Vivek Swarup
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA; Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Inma Cobos
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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89
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Cheung V, Chung P, Feinberg EH. Transcriptional profiling of mouse projection neurons with VECTORseq. STAR Protoc 2022; 3:101625. [PMID: 36035788 PMCID: PMC9405111 DOI: 10.1016/j.xpro.2022.101625] [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: 11/28/2022] Open
Abstract
Existing techniques for transcriptional profiling of projection neurons could be applied to only one neuronal population per experiment. To increase throughput, we developed VECTORseq, which repurposes retrogradely infecting viruses to deliver multiplexable RNA barcodes, enabling projection anatomy to be read out in single-cell datasets. In this protocol, we describe the delivery of viral barcodes to mouse brain to label different projection neurons. We then detail single-cell or nuclei isolation for sequencing, followed by the analysis of single-cell sequencing data. For complete details on the use and execution of this protocol, please refer to Cheung et al. (2021).
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Affiliation(s)
- Victoria Cheung
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Philip Chung
- Department of Anesthesiology & Pain Medicine, University of Washington, Seattle, WA 98195, USA
| | - Evan H Feinberg
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94158, USA.
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90
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Almeida D, Turecki G. Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection. Methods 2022; 207:3-10. [PMID: 36064002 DOI: 10.1016/j.ymeth.2022.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The transcriptome of a cell constitutes an essential piece of cellular identity and contributes to the multifaceted complexity and heterogeneity of cell-types within the mammalian brain. Thus, while a wealth of studies have investigated transcriptomic alterations underlying the pathophysiology of diseases of the brain, their use of bulk-tissue homogenates makes it difficult to tease apart whether observed differences are explained by disease state or cellular composition. Cell-type-specific enrichment strategies are, therefore, crucial in the context of gene expression profiling. Laser capture microdissection (LCM) is one such strategy that allows for the capture of specific cell-types, or regions of interest, under microscopic visualization. In this review, we focus on using LCM for cell-type specific gene expression profiling in post-mortem human brain samples. We begin with a discussion of various LCM systems, followed by a walk-through of each step in the LCM to gene expression profiling workflow and a description of some of the limitations associated with LCM. Throughout the review, we highlight important considerations when using LCM with post-mortem human brain samples. Whenever applicable, commercially available kits that have proven successful in the context of LCM with post-mortem human brain samples are described.
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Affiliation(s)
- Daniel Almeida
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3; Department of Psychiatry, McGill University, Montreal, QC, Canada, H3A 1A1.
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91
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Park SHE, Ortiz AK, Konopka G. Corticogenesis across species at single-cell resolution. Dev Neurobiol 2022; 82:517-532. [PMID: 35932776 PMCID: PMC9481703 DOI: 10.1002/dneu.22896] [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: 01/22/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 11/07/2022]
Abstract
The neocortex (or pallium) consists of diverse cell types that are organized in a highly species-specific manner under strict spatiotemporal control during development. Many of the cell types are present transiently throughout development but contribute to permanent species-specific cortical features that are acquired through evolution. Therefore, capturing cell type-specific biological information has always been an important quest in the field of neurodevelopment. The progress in achieving fine cellular resolution has been slow due to technical challenges. However, with recent advancements in single-cell and multi-omics technologies, many laboratories have begun to successfully interrogate cellular and molecular mechanisms driving corticogenesis at single-cell resolution. In this review, we provide summarized results from many primary publications and several in-depth review articles that utilize or address single-cell genomics techniques to understand important topics, such as cellular and molecular mechanisms governing cortical progenitor proliferation, cell lineage progression, neuronal specification, and arealization, across multiple gyrencephalic (i.e., human and non-human primates) and lissencephalic species (i.e., mouse, reptiles, and songbirds). We also examine findings from recent studies involving epigenomic and posttranscriptional regulation of corticogenesis. In the discussion section, we provide our insights on the challenges the field currently faces as well as promising future applications of single cell technologies.
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Affiliation(s)
- Seon Hye E Park
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ana K Ortiz
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, USA
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92
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Sozzi E, Nilsson F, Kajtez J, Parmar M, Fiorenzano A. Generation of Human Ventral Midbrain Organoids Derived from Pluripotent Stem Cells. Curr Protoc 2022; 2:e555. [PMID: 36121202 DOI: 10.1002/cpz1.555] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder worldwide and is caused by the degeneration and loss of dopamine (DA) neurons in the ventral midbrain (VM). The focal and progressive degeneration of DA neurons in the VM makes PD a particularly attractive target for cell-based therapies. Human pluripotent stem cells (hPSCs) offer unprecedented opportunities to model the development and functional properties of human DA neurons in a dish. The use of human in vitro models based on hPSCs has empowered studies of VM development and provided access to neurons expressing a particular disease-specific phenotype. Currently, hPSC differentiation is most routinely carried out in monolayer cultures, which do not properly recapitulate cell-cell interactions and the structural complexity of the brain. Moreover, 2D cultures are challenging to maintain long term, as the cells tend to detach from the plate and lose their functional characteristics. This precludes the possibility of mimicking later phases of DA neurogenesis and recreating the complexity of functional neural circuitries. Here, we describe protocols showing how to maintain hPSCs in an undifferentiated state and how to then drive these hPSCs into 3D regionalized VM organoids. After long-term culture, these VM organoids exhibit mature and post-mitotic molecular features, including neuromelanin pigments similar to those released in primate VMs. We also report a protocol describing how to efficiently perform immunohistochemistry and how to detect neuromelanin-containing DA neurons in VM organoids. Together, these protocols provide a 3D in vitro platform that can be used to better understand the molecular mechanisms underlying DA neuron function and disease and may serve as a powerful tool for designing more targeted disease-modifying therapies. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Human pluripotent stem cell culture Basic Protocol 2: hPS cell differentiation for the generation of human ventral midbrain organoids Basic Protocol 3: Characterization of ventral midbrain organoids.
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Affiliation(s)
- Edoardo Sozzi
- Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, Lund Stem Cell Center, Department of Experimental Medical Science, Lund University, Sweden
| | - Fredrik Nilsson
- Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, Lund Stem Cell Center, Department of Experimental Medical Science, Lund University, Sweden
| | - Janko Kajtez
- Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, Lund Stem Cell Center, Department of Experimental Medical Science, Lund University, Sweden
| | - Malin Parmar
- Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, Lund Stem Cell Center, Department of Experimental Medical Science, Lund University, Sweden
| | - Alessandro Fiorenzano
- Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, Lund Stem Cell Center, Department of Experimental Medical Science, Lund University, Sweden
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93
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Almazán A, Çevrim Ç, Musser JM, Averof M, Paris M. Crustacean leg regeneration restores complex microanatomy and cell diversity. SCIENCE ADVANCES 2022; 8:eabn9823. [PMID: 36001670 PMCID: PMC9401613 DOI: 10.1126/sciadv.abn9823] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Animals can regenerate complex organs, yet this process frequently results in imprecise replicas of the original structure. In the crustacean Parhyale, embryonic and regenerating legs differ in gene expression dynamics but produce apparently similar mature structures. We examine the fidelity of Parhyale leg regeneration using complementary approaches to investigate microanatomy, sensory function, cellular composition, and cell molecular profiles. We find that regeneration precisely replicates the complex microanatomy and spatial distribution of external sensory organs and restores their sensory function. Single-nuclei sequencing shows that regenerated and uninjured legs are indistinguishable in terms of cell-type composition and transcriptional profiles. This remarkable fidelity highlights the ability of organisms to achieve identical outcomes via distinct processes.
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Affiliation(s)
- Alba Almazán
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Centre National de la Recherche Scientifique (CNRS), École Normale Supérieure de Lyon and Université Claude Bernard Lyon 1, 69007 Lyon, France
| | - Çağrı Çevrim
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Centre National de la Recherche Scientifique (CNRS), École Normale Supérieure de Lyon and Université Claude Bernard Lyon 1, 69007 Lyon, France
| | - Jacob M. Musser
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Michalis Averof
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Centre National de la Recherche Scientifique (CNRS), École Normale Supérieure de Lyon and Université Claude Bernard Lyon 1, 69007 Lyon, France
| | - Mathilde Paris
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Centre National de la Recherche Scientifique (CNRS), École Normale Supérieure de Lyon and Université Claude Bernard Lyon 1, 69007 Lyon, France
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94
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Bergmann T, Liu Y, Skov J, Mogus L, Lee J, Pfisterer U, Handfield LF, Asenjo-Martinez A, Lisa-Vargas I, Seemann SE, Lee JTH, Patikas N, Kornum BR, Denham M, Hyttel P, Witter MP, Gorodkin J, Pers TH, Hemberg M, Khodosevich K, Hall VJ. Production of human entorhinal stellate cell-like cells by forward programming shows an important role of Foxp1 in reprogramming. Front Cell Dev Biol 2022; 10:976549. [PMID: 36046338 PMCID: PMC9420913 DOI: 10.3389/fcell.2022.976549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Stellate cells are principal neurons in the entorhinal cortex that contribute to spatial processing. They also play a role in the context of Alzheimer's disease as they accumulate Amyloid beta early in the disease. Producing human stellate cells from pluripotent stem cells would allow researchers to study early mechanisms of Alzheimer's disease, however, no protocols currently exist for producing such cells. In order to develop novel stem cell protocols, we characterize at high resolution the development of the porcine medial entorhinal cortex by tracing neuronal and glial subtypes from mid-gestation to the adult brain to identify the transcriptomic profile of progenitor and adult stellate cells. Importantly, we could confirm the robustness of our data by extracting developmental factors from the identified intermediate stellate cell cluster and implemented these factors to generate putative intermediate stellate cells from human induced pluripotent stem cells. Six transcription factors identified from the stellate cell cluster including RUNX1T1, SOX5, FOXP1, MEF2C, TCF4, EYA2 were overexpressed using a forward programming approach to produce neurons expressing a unique combination of RELN, SATB2, LEF1 and BCL11B observed in stellate cells. Further analyses of the individual transcription factors led to the discovery that FOXP1 is critical in the reprogramming process and omission of RUNX1T1 and EYA2 enhances neuron conversion. Our findings contribute not only to the profiling of cell types within the developing and adult brain's medial entorhinal cortex but also provides proof-of-concept for using scRNAseq data to produce entorhinal intermediate stellate cells from human pluripotent stem cells in-vitro.
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Affiliation(s)
- Tobias Bergmann
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yong Liu
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jonathan Skov
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Leo Mogus
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Julie Lee
- Novo Nordisk Foundation Center for Stem Cell Research, DanStem University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulrich Pfisterer
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Andrea Asenjo-Martinez
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Irene Lisa-Vargas
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stefan E. Seemann
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jimmy Tsz Hang Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nikolaos Patikas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Birgitte Rahbek Kornum
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mark Denham
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Poul Hyttel
- Disease, Stem Cells and Embryology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Menno P. Witter
- Kavli Institute for Systems Neuroscience, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tune H. Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vanessa Jane Hall
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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95
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Oxytocin-based therapies for treatment of Prader-Willi and Schaaf-Yang syndromes: evidence, disappointments, and future research strategies. Transl Psychiatry 2022; 12:318. [PMID: 35941105 PMCID: PMC9360032 DOI: 10.1038/s41398-022-02054-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/23/2022] [Accepted: 07/01/2022] [Indexed: 11/09/2022] Open
Abstract
The prosocial neuropeptide oxytocin is being developed as a potential treatment for various neuropsychiatric disorders including autism spectrum disorder (ASD). Early studies using intranasal oxytocin in patients with ASD yielded encouraging results and for some time, scientists and affected families placed high hopes on the use of intranasal oxytocin for behavioral therapy in ASD. However, a recent Phase III trial obtained negative results using intranasal oxytocin for the treatment of behavioral symptoms in children with ASD. Given the frequently observed autism-like behavioral phenotypes in Prader-Willi and Schaaf-Yang syndromes, it is unclear whether oxytocin treatment represents a viable option to treat behavioral symptoms in these diseases. Here we review the latest findings on intranasal OT treatment, Prader-Willi and Schaaf-Yang syndromes, and propose novel research strategies for tailored oxytocin-based therapies for affected individuals. Finally, we propose the critical period theory, which could explain why oxytocin-based treatment seems to be most efficient in infants, but not adolescents.
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96
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Lin H, Ma X, Sun Y, Peng H, Wang Y, Thomas SS, Hu Z. Decoding the transcriptome of denervated muscle at single-nucleus resolution. J Cachexia Sarcopenia Muscle 2022; 13:2102-2117. [PMID: 35726356 PMCID: PMC9398230 DOI: 10.1002/jcsm.13023] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 02/18/2022] [Accepted: 05/09/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Skeletal muscle exhibits remarkable plasticity under both physiological and pathological conditions. One major manifestation of this plasticity is muscle atrophy that is an adaptive response to catabolic stimuli. Because the heterogeneous transcriptome responses to catabolism in different types of muscle cells are not fully characterized, we applied single-nucleus RNA sequencing (snRNA-seq) to unveil muscle atrophy related transcriptional changes at single nucleus resolution. METHODS Using a sciatic denervation mouse model of muscle atrophy, snRNA-seq was performed to generate single-nucleus transcriptional profiles of the gastrocnemius muscle from normal and denervated mice. Various bioinformatics analyses, including unsupervised clustering, functional enrichment analysis, trajectory analysis, regulon inference, metabolic signature characterization and cell-cell communication prediction, were applied to illustrate the transcriptome changes of the individual cell types. RESULTS A total of 29 539 muscle nuclei (normal vs. denervation: 15 739 vs. 13 800) were classified into 13 nuclear types according to the known cell markers. Among these, the type IIb myonuclei were further divided into two subgroups, which we designated as type IIb1 and type IIb2 myonuclei. In response to denervation, the proportion of type IIb2 myonuclei increased sharply (78.12% vs. 38.45%, P < 0.05). Concomitantly, trajectory analysis revealed that denervated type IIb2 myonuclei clearly deviated away from the normal type IIb2 myonuclei, indicating that this subgroup underwent robust transcriptional reprogramming upon denervation. Signature genes in denervated type IIb2 myonuclei included Runx1, Gadd45a, Igfn1, Robo2, Dlg2, and Sh3d19 (P < 0.001). The gene regulatory network analysis captured a group of atrophy-related regulons (Foxo3, Runx1, Elk4, and Bhlhe40) whose activities were enhanced (P < 0.01), especially in the type IIb2 myonuclei. The metabolic landscape in the myonuclei showed that most of the metabolic pathways were down-regulated by denervation (P < 0.001), while some of the metabolic signalling, such as glutathione metabolism, was specifically activated in the denervated type IIb2 myonulei. We also investigated the transcriptomic alterations in the type I myofibres, muscle stem cells, fibro-adipogenic progenitors, macrophages, endothelial cells and pericytes and characterized their signature responses to denervation. By predicting the cell-cell interactions, we observed that the communications between myofibres and muscle resident cells were diminished by denervation. CONCLUSIONS Our results define the myonuclear transition, metabolic remodelling, and gene regulation networks reprogramming associated with denervation-induced muscle atrophy and illustrate the molecular basis of the heterogeneity and plasticity of muscle cells in response to catabolism. These results provide a useful resource for exploring the molecular mechanism of muscle atrophy.
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Affiliation(s)
- Hongchun Lin
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Nephrology Division, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xinxin Ma
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Yuxiang Sun
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hui Peng
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanlin Wang
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Sandhya Sara Thomas
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Zhaoyong Hu
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
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97
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Abstract
The single-cell revolution in the field of genomics is in full bloom, with clever new molecular biology tricks appearing regularly that allow researchers to explore new modalities or scale up their projects to millions of cells and beyond. Techniques abound to measure RNA expression, DNA alterations, protein abundance, chromatin accessibility, and more, all with single-cell resolution and often in combination. Despite such a rapidly changing technology landscape, there are several fundamental principles that are applicable to the majority of experimental workflows to help users avoid pitfalls and exploit the advantages of the chosen platform. In this overview article, we describe a variety of popular single-cell genomics technologies and address some common questions pertaining to study design, sample preparation, quality control, and sequencing strategy. As the majority of relevant publications currently revolve around single-cell RNA-seq, we will prioritize this genomics modality in our discussion. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Claire Regan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
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98
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Hardwick SA, Hu W, Joglekar A, Fan L, Collier PG, Foord C, Balacco J, Lanjewar S, Sampson MM, Koopmans F, Prjibelski AD, Mikheenko A, Belchikov N, Jarroux J, Lucas AB, Palkovits M, Luo W, Milner TA, Ndhlovu LC, Smit AB, Trojanowski JQ, Lee VMY, Fedrigo O, Sloan SA, Tombácz D, Ross ME, Jarvis E, Boldogkői Z, Gan L, Tilgner HU. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nat Biotechnol 2022; 40:1082-1092. [PMID: 35256815 PMCID: PMC9287170 DOI: 10.1038/s41587-022-01231-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/20/2022] [Indexed: 12/11/2022]
Abstract
Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhibit coordinated and highly cell-type-specific inclusion. We found two distinct combination patterns: those distinguishing neural cell types, enriched in TSS-exon, exon-polyadenylation-site and non-adjacent exon pairs, and those with multiple configurations within one cell type, enriched in adjacent exon pairs. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons, implying that coordination can be rapidly established during evolution. SnISOr-Seq enables cell-type-specific long-read isoform analysis in human brain and in any frozen or hard-to-dissociate sample.
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Affiliation(s)
- Simon A Hardwick
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Li Fan
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Paul G Collier
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Careen Foord
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | | | - Samantha Lanjewar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Frank Koopmans
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - Andrey D Prjibelski
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Natan Belchikov
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Medicine, New York, NY, USA
| | - Julien Jarroux
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | | | - Miklós Palkovits
- Human Brain Tissue Bank, Semmelweis University, Budapest, Hungary
| | - Wenjie Luo
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Virginia M Y Lee
- Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | | | - Steven A Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | | | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Li Gan
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA.
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99
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Garcia-Alonso L, Lorenzi V, Mazzeo CI, Alves-Lopes JP, Roberts K, Sancho-Serra C, Engelbert J, Marečková M, Gruhn WH, Botting RA, Li T, Crespo B, van Dongen S, Kiselev VY, Prigmore E, Herbert M, Moffett A, Chédotal A, Bayraktar OA, Surani A, Haniffa M, Vento-Tormo R. Single-cell roadmap of human gonadal development. Nature 2022; 607:540-547. [PMID: 35794482 PMCID: PMC9300467 DOI: 10.1038/s41586-022-04918-4] [Citation(s) in RCA: 111] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/30/2022] [Indexed: 01/09/2023]
Abstract
Gonadal development is a complex process that involves sex determination followed by divergent maturation into either testes or ovaries1. Historically, limited tissue accessibility, a lack of reliable in vitro models and critical differences between humans and mice have hampered our knowledge of human gonadogenesis, despite its importance in gonadal conditions and infertility. Here, we generated a comprehensive map of first- and second-trimester human gonads using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy. We extracted human-specific regulatory programmes that control the development of germline and somatic cell lineages by profiling equivalent developmental stages in mice. In both species, we define the somatic cell states present at the time of sex specification, including the bipotent early supporting population that, in males, upregulates the testis-determining factor SRY and sPAX8s, a gonadal lineage located at the gonadal-mesonephric interface. In females, we resolve the cellular and molecular events that give rise to the first and second waves of granulosa cells that compartmentalize the developing ovary to modulate germ cell differentiation. In males, we identify human SIGLEC15+ and TREM2+ fetal testicular macrophages, which signal to somatic cells outside and inside the developing testis cords, respectively. This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, which can guide in vitro gonadogenesis.
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Affiliation(s)
| | | | | | - João Pedro Alves-Lopes
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, UK
| | | | | | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Magda Marečková
- Wellcome Sanger Institute, Cambridge, UK
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Wolfram H Gruhn
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tong Li
- Wellcome Sanger Institute, Cambridge, UK
| | - Berta Crespo
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | | | | | - Mary Herbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ashley Moffett
- University of Cambridge Centre for Trophoblast Research, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
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100
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Baratta AM, Brandner AJ, Plasil SL, Rice RC, Farris SP. Advancements in Genomic and Behavioral Neuroscience Analysis for the Study of Normal and Pathological Brain Function. Front Mol Neurosci 2022; 15:905328. [PMID: 35813067 PMCID: PMC9259865 DOI: 10.3389/fnmol.2022.905328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Psychiatric and neurological disorders are influenced by an undetermined number of genes and molecular pathways that may differ among afflicted individuals. Functionally testing and characterizing biological systems is essential to discovering the interrelationship among candidate genes and understanding the neurobiology of behavior. Recent advancements in genetic, genomic, and behavioral approaches are revolutionizing modern neuroscience. Although these tools are often used separately for independent experiments, combining these areas of research will provide a viable avenue for multidimensional studies on the brain. Herein we will briefly review some of the available tools that have been developed for characterizing novel cellular and animal models of human disease. A major challenge will be openly sharing resources and datasets to effectively integrate seemingly disparate types of information and how these systems impact human disorders. However, as these emerging technologies continue to be developed and adopted by the scientific community, they will bring about unprecedented opportunities in our understanding of molecular neuroscience and behavior.
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Affiliation(s)
- Annalisa M. Baratta
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Adam J. Brandner
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sonja L. Plasil
- Department of Pharmacology & Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rachel C. Rice
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sean P. Farris
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Sean P. Farris,
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