1
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Tourigny DS, Altieri B, Secener KA, Sbiera S, Schauer MP, Arampatzi P, Herterich S, Sauer S, Fassnacht M, Ronchi CL. Cellular landscape of adrenocortical carcinoma at single-nuclei resolution. Mol Cell Endocrinol 2024; 590:112272. [PMID: 38759836 DOI: 10.1016/j.mce.2024.112272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Adrenocortical carcinoma (ACC) is a rare yet devastating tumour of the adrenal gland with a molecular pathology that remains incompletely understood. To gain novel insights into the cellular landscape of ACC, we generated single-nuclei RNA sequencing (snRNA-seq) data sets from twelve ACC tumour samples and analysed these alongside snRNA-seq data sets from normal adrenal glands (NAGs). We find the ACC tumour microenvironment to be relatively devoid of immune cells compared to NAG tissues, consistent with known high tumour purity values for ACC as an immunologically "cold" tumour. Our analysis identifies three separate groups of ACC samples that are characterised by different relative compositions of adrenocortical cell types. These include cell populations that are specifically enriched in the most clinically aggressive and hormonally active tumours, displaying hallmarks of reorganised cell mechanobiology and dysregulated steroidogenesis, respectively. We also identified and validated a population of mitotically active adrenocortical cells that strongly overexpress genes POLQ, DIAPH3 and EZH2 to support tumour expansion alongside an LGR4+ progenitor-like or cell-of-origin candidate for adrenocortical carcinogenesis. Trajectory inference suggests the fate adopted by malignant adrenocortical cells upon differentiation is associated with the copy number or allelic balance state of the imprinted DLK1/MEG3 genomic locus, which we verified by assessing bulk tumour DNA methylation status. In conclusion, our results therefore provide new insights into the clinical and cellular heterogeneity of ACC, revealing how genetic perturbations to healthy adrenocortical renewal and zonation provide a molecular basis for disease pathogenesis.
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Affiliation(s)
- David S Tourigny
- School of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Barbara Altieri
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Kerim A Secener
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany; Institute of Biochemistry, Department of Biology, Chemistry and Pharmacy, Free University Berlin, Berlin, 14195, Germany
| | - Silviu Sbiera
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Marc P Schauer
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany; Center for Cellular Immunotherapy, Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, 97080, Germany
| | | | - Sabine Herterich
- Central Laboratory, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
| | - Martin Fassnacht
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Cristina L Ronchi
- Institute of Metabolism and System Research, University of Birmingham, Birmingham, B15 2TT, UK; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham, B15 2GW, UK.
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2
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Howe JR, Chan CL, Lee D, Blanquart M, Romero HK, Zadina AN, Lemieux ME, Mills F, Desplats PA, Tye KM, Root CM. Control of innate olfactory valence by segregated cortical amygdala circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600895. [PMID: 38979308 PMCID: PMC11230396 DOI: 10.1101/2024.06.26.600895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Animals perform innate behaviors that are stereotyped responses to specific evolutionarily relevant stimuli in the absence of prior learning or experience. These behaviors can be reduced to an axis of valence, whereby specific odors evoke approach or avoidance. The cortical amygdala (plCoA) mediates innate attraction and aversion to odor. However, little is known about how this brain area gives rise to behaviors of opposing motivational valence. Here, we sought to define the circuit features of plCoA that give rise to innate olfactory behaviors of valence. We characterized the physiology, gene expression, and projections of this structure, identifying a divergent, topographic organization that selectively controls innate attraction and avoidance to odor. First, we examined odor-evoked responses in these areas and found sparse encoding of odor identity, but not valence. We next considered a topographic organization and found that optogenetic stimulation of the anterior and posterior domains of plCoA elicits attraction and avoidance, respectively, suggesting a functional axis for valence. Using single cell and spatial RNA sequencing, we identified the molecular cell types in plCoA, revealing an anteroposterior gradient in cell types, whereby anterior glutamatergic neurons preferentially express Slc17a6 and posterior neurons express Slc17a7 . Activation of these respective cell types recapitulates appetitive and aversive valence behaviors, and chemogenetic inhibition reveals partial necessity for valence responses to innate appetitive or aversive odors. Finally, we identified topographically organized circuits defined by projections, whereby anterior neurons preferentially project to medial amygdala, and posterior neurons preferentially project to nucleus accumbens, which are respectively sufficient and necessary for innate negative and positive olfactory valence. Together, these data advance our understanding of how the olfactory system generates stereotypic, hardwired attraction and avoidance, and supports a model whereby distinct, topographically distributed plCoA populations direct innate olfactory valence responses by signaling to divergent valence-specific targets, linking upstream olfactory identity to downstream valence behaviors, through a population code. This represents a novel circuit motif in which valence encoding is represented not by the firing properties of individual neurons, but by population level identity encoding that is routed through divergent targets to mediate distinct valence.
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3
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Currey L, Mitchell B, Al-Khalily M, McElnea SJ, Kozulin P, Harkins D, Pelenyi A, Fenlon L, Suarez R, Kurniawan ND, Burne TH, Harris L, Thor S, Piper M. Polycomb repressive complex 2 is critical for mouse cortical glutamatergic neuron development. Cereb Cortex 2024; 34:bhae268. [PMID: 38960704 PMCID: PMC11221884 DOI: 10.1093/cercor/bhae268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 07/05/2024] Open
Abstract
The Polycomb Repressive Complex 2 (PRC2) regulates corticogenesis, yet the consequences of mutations to this epigenetic modifier in the mature brain are poorly defined. Importantly, PRC2 core genes are haploinsufficient and causative of several human neurodevelopmental disorders. To address the role of PRC2 in mature cortical structure and function, we conditionally deleted the PRC2 gene Eed from the developing mouse dorsal telencephalon. Adult homozygotes displayed smaller forebrain structures. Single-nucleus transcriptomics revealed that glutamatergic neurons were particularly affected, exhibiting dysregulated gene expression profiles, accompanied by aberrations in neuronal morphology and connectivity. Remarkably, homozygous mice performed well on challenging cognitive tasks. In contrast, while heterozygous mice did not exhibit clear anatomical or behavioral differences, they displayed dysregulation of neuronal genes and altered neuronal morphology that was strikingly different from homozygous phenotypes. Collectively, these data reveal how alterations to PRC2 function shape the mature brain and reveal a dose-specific role for PRC2 in determining glutamatergic neuron identity.
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Affiliation(s)
- Laura Currey
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Benjamin Mitchell
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Majd Al-Khalily
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - Sarah-Jayne McElnea
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Kozulin
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Danyon Harkins
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alexandra Pelenyi
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Laura Fenlon
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rodrigo Suarez
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nyoman D Kurniawan
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - Thomas H Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD 4076, Australia
| | - Lachlan Harris
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Cancer Neuroscience Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Stefan Thor
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
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4
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Yang GN, Sun YBY, Roberts PK, Moka H, Sung MK, Gardner-Russell J, El Wazan L, Toussaint B, Kumar S, Machin H, Dusting GJ, Parfitt GJ, Davidson K, Chong EW, Brown KD, Polo JM, Daniell M. Exploring Single-cell RNA sequencing as a decision-making tool in the clinical management of Fuchs' Endothelial Corneal Dystrophy. Prog Retin Eye Res 2024:101286. [PMID: 38969166 DOI: 10.1016/j.preteyeres.2024.101286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/14/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has enabled the identification of novel gene signatures and cell heterogeneity in numerous tissues and diseases. Here we review the use of this technology for Fuchs' Endothelial Corneal Dystrophy (FECD). FECD is the most common indication for corneal endothelial transplantation worldwide. FECD is challenging to manage because it is genetically heterogenous, can be autosomal dominant or sporadic, and progress at different rates. Single-cell RNA sequencing has enabled the discovery of several FECD subtypes, each with associated gene signatures, and cell heterogeneity. Current FECD treatments are mainly surgical, with various Rho kinase (ROCK) inhibitors used to promote endothelial cell metabolism and proliferation following surgery. A range of emerging therapies for FECD including cell therapies, gene therapies, tissue engineered scaffolds, and pharmaceuticals are in preclinical and clinical trials. Unlike conventional disease management methods based on clinical presentations and family history, targeting FECD using scRNA-seq based precision-medicine has the potential to pinpoint the disease subtypes, mechanisms, stages, severities, and help clinicians in making the best decision for surgeries and the applications of therapeutics. In this review, we first discuss the feasibility and potential of using scRNA-seq in clinical diagnostics for FECD, highlight advances from the latest clinical treatments and emerging therapies for FECD, integrate scRNA-seq results and clinical notes from our FECD patients and discuss the potential of applying alternative therapies to manage these cases clinically.
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Affiliation(s)
- Gink N Yang
- Centre for Eye Research Australia, level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Yu B Y Sun
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Philip Ke Roberts
- Department of Ophthalmology, Medical University Vienna, 18-20 Währinger Gürtel, Vienna, Austria
| | - Hothri Moka
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, United Kingdom
| | - Min K Sung
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, United Kingdom
| | - Jesse Gardner-Russell
- Centre for Eye Research Australia, level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Layal El Wazan
- Centre for Eye Research Australia, level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Bridget Toussaint
- Centre for Eye Research Australia, level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Satheesh Kumar
- Centre for Eye Research Australia, level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Heather Machin
- Centre for Eye Research Australia, level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Lions Eye Donation Service, level 7, Smorgon Family Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia
| | - Gregory J Dusting
- Centre for Eye Research Australia, level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Geraint J Parfitt
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, United Kingdom
| | - Kathryn Davidson
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Elaine W Chong
- Centre for Eye Research Australia, level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Department of Ophthalmology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Karl D Brown
- Centre for Eye Research Australia, level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Jose M Polo
- Department of Ophthalmology, Medical University Vienna, 18-20 Währinger Gürtel, Vienna, Austria
| | - Mark Daniell
- Centre for Eye Research Australia, level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Lions Eye Donation Service, level 7, Smorgon Family Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia.
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5
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O'Shea TM, Ao Y, Wang S, Ren Y, Cheng AL, Kawaguchi R, Shi Z, Swarup V, Sofroniew MV. Derivation and transcriptional reprogramming of border-forming wound repair astrocytes after spinal cord injury or stroke in mice. Nat Neurosci 2024:10.1038/s41593-024-01684-6. [PMID: 38907165 DOI: 10.1038/s41593-024-01684-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 05/15/2024] [Indexed: 06/23/2024]
Abstract
Central nervous system (CNS) lesions become surrounded by neuroprotective borders of newly proliferated reactive astrocytes; however, fundamental features of these cells are poorly understood. Here we show that following spinal cord injury or stroke, 90% and 10% of border-forming astrocytes derive, respectively, from proliferating local astrocytes and oligodendrocyte progenitor cells in adult mice of both sexes. Temporal transcriptome analysis, single-nucleus RNA sequencing and immunohistochemistry show that after focal CNS injury, local mature astrocytes dedifferentiate, proliferate and become transcriptionally reprogrammed to permanently altered new states, with persisting downregulation of molecules associated with astrocyte-neuron interactions and upregulation of molecules associated with wound healing, microbial defense and interactions with stromal and immune cells. These wound repair astrocytes share morphologic and transcriptional features with perimeningeal limitans astrocytes and are the predominant source of neuroprotective borders that re-establish CNS integrity around lesions by separating neural parenchyma from stromal and immune cells as occurs throughout the healthy CNS.
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Affiliation(s)
- Timothy M O'Shea
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
| | - Yan Ao
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Shinong Wang
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Yilong Ren
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, PR China
| | - Amy L Cheng
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Riki Kawaguchi
- Departments of Psychiatry and Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Zechuan Shi
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA, USA
| | - Michael V Sofroniew
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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6
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Wang H, Liu J, Zhu P, Shi L, Liu Y, Yang X, Yang X. Single-nucleus transcriptome reveals cell dynamic response of liver during the late chick embryonic development. Poult Sci 2024; 103:103979. [PMID: 38941785 DOI: 10.1016/j.psj.2024.103979] [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: 03/18/2024] [Revised: 05/29/2024] [Accepted: 06/10/2024] [Indexed: 06/30/2024] Open
Abstract
The late embryonic development of the liver, a major metabolic organ, remains poorly characterized at single cell resolution. Here, we used single-nucleus RNA-sequencing (snRNA-seq) to characterize the chicken liver cells at 2 embryonic development time points (E14 and D1). We uncovered 8 cell types including hepatocytes, endothelial cells, hepatic stellate cells, erythrocytes, cholangiocytes, kupffer cells, mesothelial cells, and lymphocytes. And we discovered significant differences in the abundance of different cell types between E14 and D1. Moreover, we characterized the heterogeneity of hepatocytes, endothelial cells, and mesenchymal cells based on the gene regulatory networks of each clusters. Trajectory analyses revealed 128 genes associated with hepatocyte development and function, including apolipoprotein genes involved hepatic lipid metabolism and NADH dehydrogenase subunits involved hepatic oxidative phosphorylation. Furthermore, we identified the differentially expressed genes (DEGs) between E14 and D1 at the cellular levels, which contribute to changes in liver development and function. These DEGs were significantly enriched in PPAR signaling pathways and lipid metabolism related pathways. Our results presented the single-cell mapping of chick embryonic liver at late stages of development and demonstrated the metabolic changes across the 2 age stages at the cellular level, which can help to further study the molecular development mechanism of embryonic liver.
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Affiliation(s)
- Huimei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Jiongyan Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Pinhui Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Lin Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Xin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
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7
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Aulston BD, Gimse K, Bazick HO, Kramar EA, Pizzo DP, Parra-Rivas LA, Sun J, Branes-Guerrero K, Checka N, Bagheri N, Satyadev N, Carlson-Stevermer J, Saito T, Saido TC, Audhya A, Wood MA, Zylka MJ, Saha K, Roy S. Long term rescue of Alzheimer's deficits in vivo by one-time gene-editing of App C-terminus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.598099. [PMID: 38895278 PMCID: PMC11185791 DOI: 10.1101/2024.06.08.598099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Gene-editing technologies promise to create a new class of therapeutics that can achieve permanent correction with a single intervention. Besides eliminating mutant alleles in familial disease, gene-editing can also be used to favorably manipulate upstream pathophysiologic events and alter disease-course in wider patient populations, but few such feasible therapeutic avenues have been reported. Here we use CRISPR-Cas9 to edit the last exon of amyloid precursor protein (App), relevant for Alzheimer's disease (AD). Our strategy effectively eliminates an endocytic (YENPTY) motif at APP C-terminus, while preserving the N-terminus and compensatory APP-homologues. This manipulation favorably alters events along the amyloid-pathway - inhibiting toxic APP-β-cleavage fragments (including Aβ) and upregulating neuroprotective APP-α-cleavage products. AAV-driven editing ameliorates neuropathologic, electrophysiologic, and behavioral deficits in an AD knockin mouse model. Effects persist for many months, and no abnormalities are seen in WT mice even after germline App-editing; underlining overall efficacy and safety. Pathologic alterations in the glial-transcriptome of App-KI mice, as seen by single nuclei RNA-sequencing (sNuc-Seq), are also normalized by App C-terminus editing. Our strategy takes advantage of innate transcriptional rules that render terminal exons insensitive to nonsense-decay, and the upstream manipulation is expected to be effective for all forms of AD. These studies offer a path for a one-time disease-modifying treatment for AD.
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Affiliation(s)
- Brent D. Aulston
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Kirstan Gimse
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53715, USA; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Hannah O. Bazick
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eniko A. Kramar
- Department of Neurobiology and Behavior, School of Biological Sciences University of California, Irvine 92697-2695, USA
| | - Donald P. Pizzo
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Leonardo A. Parra-Rivas
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Jichao Sun
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
- Present address: Department of Geriatrics and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People’s Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Kristen Branes-Guerrero
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
- Present address: Eli Lilly Pharmaceuticals, Indianapolis, IN, USA
| | - Nidhi Checka
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Neda Bagheri
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Nihal Satyadev
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
- Present address: Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Jared Carlson-Stevermer
- Synthego Corporation, 3696 Haven Ave Suite A, Redwood City, CA 94063
- Present address: Serotiny Inc., 329 Oyster Point Boulevard, 3rd Floor, South San Francisco, CA 94080
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
| | - Takaomi C. Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Marcelo A. Wood
- Department of Neurobiology and Behavior, School of Biological Sciences University of California, Irvine 92697-2695, USA
| | - Mark J. Zylka
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Krishanu Saha
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53715, USA; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Subhojit Roy
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
- Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
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8
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Kumari P, Kaur M, Dindhoria K, Ashford B, Amarasinghe SL, Thind AS. Advances in long-read single-cell transcriptomics. Hum Genet 2024:10.1007/s00439-024-02678-x. [PMID: 38787419 DOI: 10.1007/s00439-024-02678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited in their ability to provide complete transcript coverage, resolve isoforms, and identify novel transcripts. The scRNA-Seq protocols developed for long-read sequencing platforms overcome these limitations by enabling the characterization of full-length transcripts. Long-read scRNA-Seq techniques initially suffered from comparatively poor accuracy compared to short read scRNA-Seq. However, with improvements in accuracy, accessibility, and cost efficiency, long-reads are gaining popularity in the field of scRNA-Seq. This review details the advances in long-read scRNA-Seq, with an emphasis on library preparation protocols and downstream bioinformatics analysis tools.
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Affiliation(s)
- Pallawi Kumari
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Manmeet Kaur
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Kiran Dindhoria
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Bruce Ashford
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia
| | - Shanika L Amarasinghe
- Monash Biomedical Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Walter and Eliza Hall Institute of Medical Research, 1G, Royal Parade, Parkville, VIC, 3025, Australia
| | - Amarinder Singh Thind
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia.
- The School of Chemistry and Molecular Bioscience (SCMB), University of Wollongong, Loftus St, Wollongong, NSW, 2500, Australia.
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9
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Jiang A, You L, Handley RR, Hawkins V, Reid SJ, Jacobsen JC, Patassini S, Rudiger SR, Mclaughlan CJ, Kelly JM, Verma PJ, Bawden CS, Gusella JF, MacDonald ME, Waldvogel HJ, Faull RLM, Lehnert K, Snell RG. Single nuclei RNA-seq reveals a medium spiny neuron glutamate excitotoxicity signature prior to the onset of neuronal death in an ovine Huntington's disease model. Hum Mol Genet 2024:ddae087. [PMID: 38776957 DOI: 10.1093/hmg/ddae087] [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: 03/07/2024] [Revised: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Huntington's disease (HD) is a neurodegenerative genetic disorder caused by an expansion in the CAG repeat tract of the huntingtin (HTT) gene resulting in behavioural, cognitive, and motor defects. Current knowledge of disease pathogenesis remains incomplete, and no disease course-modifying interventions are in clinical use. We have previously reported the development and characterisation of the OVT73 transgenic sheep model of HD. The 73 polyglutamine repeat is somatically stable and therefore likely captures a prodromal phase of the disease with an absence of motor symptomatology even at 5-years of age and no detectable striatal cell loss. To better understand the disease-initiating events we have undertaken a single nuclei transcriptome study of the striatum of an extensively studied cohort of 5-year-old OVT73 HD sheep and age matched wild-type controls. We have identified transcriptional upregulation of genes encoding N-methyl-D-aspartate (NMDA), α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and kainate receptors in medium spiny neurons, the cell type preferentially lost early in HD. Further, we observed an upregulation of astrocytic glutamate uptake transporters and medium spiny neuron GABAA receptors, which may maintain glutamate homeostasis. Taken together, these observations support the glutamate excitotoxicity hypothesis as an early neurodegeneration cascade-initiating process but the threshold of toxicity may be regulated by several protective mechanisms. Addressing this biochemical defect early may prevent neuronal loss and avoid the more complex secondary consequences precipitated by cell death.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, 131 Dong'an Road, Shanghai 200032, China
- Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, 130 Dong'an Road, Shanghai 200032, China
| | - Renee R Handley
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Victoria Hawkins
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Suzanne J Reid
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Jessie C Jacobsen
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Stefano Patassini
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Skye R Rudiger
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, 129 Holland Road, Adelaide, SA 5350, Australia
| | - Clive J Mclaughlan
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, 129 Holland Road, Adelaide, SA 5350, Australia
| | - Jennifer M Kelly
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, 129 Holland Road, Adelaide, SA 5350, Australia
| | - Paul J Verma
- Aquatic and Livestock Sciences, South Australian Research and Development Institute, 129 Holland Road, Adelaide, SA 5350, Australia
| | - C Simon Bawden
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, 129 Holland Road, Adelaide, SA 5350, Australia
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, United States
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States
- Department of Neurology, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, United States
| | - Henry J Waldvogel
- Department of Anatomy and Medical Imaging, Centre for Brain Research, Faculty of Medical and Health Science, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
| | - Richard L M Faull
- Department of Anatomy and Medical Imaging, Centre for Brain Research, Faculty of Medical and Health Science, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Russell G Snell
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
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10
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Kim J, Vanrobaeys Y, Davatolhagh MF, Kelvington B, Chatterjee S, Ferri SL, Angelakos C, Mills AA, Fuccillo MV, Nickl-Jockschat T, Abel T. A chromosome region linked to neurodevelopmental disorders acts in distinct neuronal circuits in males and females to control locomotor behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594746. [PMID: 38952795 PMCID: PMC11216371 DOI: 10.1101/2024.05.17.594746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Biological sex shapes the manifestation and progression of neurodevelopmental disorders (NDDs). These disorders often demonstrate male-specific vulnerabilities; however, the identification of underlying mechanisms remains a significant challenge in the field. Hemideletion of the 16p11.2 region (16p11.2 del/+) is associated with NDDs, and mice modeling 16p11.2 del/+ exhibit sex-specific striatum-related phenotypes relevant to NDDs. Striatal circuits, crucial for locomotor control, consist of two distinct pathways: the direct and indirect pathways originating from D1 dopamine receptor (D1R) and D2 dopamine receptor (D2R) expressing spiny projection neurons (SPNs), respectively. In this study, we define the impact of 16p11.2 del/+ on striatal circuits in male and female mice. Using snRNA-seq, we identify sex- and cell type-specific transcriptomic changes in the D1- and D2-SPNs of 16p11.2 del/+ mice, indicating distinct transcriptomic signatures in D1-SPNs and D2-SPNs in males and females, with a ∼5-fold greater impact in males. Further pathway analysis reveals differential gene expression changes in 16p11.2 del/+ male mice linked to synaptic plasticity in D1- and D2-SPNs and GABA signaling pathway changes in D1-SPNs. Consistent with our snRNA-seq study revealing changes in GABA signaling pathways, we observe distinct changes in miniature inhibitory postsynaptic currents (mIPSCs) in D1- and D2-SPNs from 16p11.2 del/+ male mice. Behaviorally, we utilize conditional genetic approaches to introduce the hemideletion selectively in either D1- or D2-SPNs and find that conditional hemideletion of genes in the 16p11.2 region in D2-SPNs causes hyperactivity in male mice, but hemideletion in D1-SPNs does not. Within the striatum, hemideletion of genes in D2-SPNs in the dorsal lateral striatum leads to hyperactivity in males, demonstrating the importance of this striatal region. Interestingly, conditional 16p11.2 del/+ within the cortex drives hyperactivity in both sexes. Our work reveals that a locus linked to NDDs acts in different striatal circuits, selectively impacting behavior in a sex- and cell type-specific manner, providing new insight into male vulnerability for NDDs. Highlights - 16p11.2 hemideletion (16p11.2 del/+) induces sex- and cell type-specific transcriptomic signatures in spiny projection neurons (SPNs). - Transcriptomic changes in GABA signaling in D1-SPNs align with changes in inhibitory synapse function. - 16p11.2 del/+ in D2-SPNs causes hyperactivity in males but not females. - 16p11.2 del/+ in D2-SPNs in the dorsal lateral striatum drives hyperactivity in males. - 16p11.2 del/+ in cortex drives hyperactivity in both sexes. Graphic abstract
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11
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Hoo R, Ruiz-Morales ER, Kelava I, Rawat M, Mazzeo CI, Tuck E, Sancho-Serra C, Chelaghma S, Predeus AV, Murray S, Fernandez-Antoran D, Waller RF, Álvarez-Errico D, Lee MCS, Vento-Tormo R. Acute response to pathogens in the early human placenta at single-cell resolution. Cell Syst 2024; 15:425-444.e9. [PMID: 38703772 DOI: 10.1016/j.cels.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/01/2023] [Accepted: 04/16/2024] [Indexed: 05/06/2024]
Abstract
The placenta is a selective maternal-fetal barrier that provides nourishment and protection from infections. However, certain pathogens can attach to and even cross the placenta, causing pregnancy complications with potential lifelong impacts on the child's health. Here, we profiled at the single-cell level the placental responses to three pathogens associated with intrauterine complications-Plasmodium falciparum, Listeria monocytogenes, and Toxoplasma gondii. We found that upon exposure to the pathogens, all placental lineages trigger inflammatory responses that may compromise placental function. Additionally, we characterized the responses of fetal macrophages known as Hofbauer cells (HBCs) to each pathogen and propose that they are the probable niche for T. gondii. Finally, we revealed how P. falciparum adapts to the placental microenvironment by modulating protein export into the host erythrocyte and nutrient uptake pathways. Altogether, we have defined the cellular networks and signaling pathways mediating acute placental inflammatory responses that could contribute to pregnancy complications.
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Affiliation(s)
- Regina Hoo
- Wellcome Sanger Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Iva Kelava
- Wellcome Sanger Institute, Cambridge, UK
| | - Mukul Rawat
- Wellcome Sanger Institute, Cambridge, UK; Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | | | | | | | - Sara Chelaghma
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - David Fernandez-Antoran
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Marcus C S Lee
- Wellcome Sanger Institute, Cambridge, UK; Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK.
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
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12
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Scheper M, Sørensen FNF, Ruffolo G, Gaeta A, Lissner LJ, Anink JJ, Korshunova I, Jansen FE, Riney K, van Hecke W, Mühlebner A, Khodosevich K, Schubert D, Palma E, Mills JD, Aronica E. Impaired GABAergic regulation and developmental immaturity in interneurons derived from the medial ganglionic eminence in the tuberous sclerosis complex. Acta Neuropathol 2024; 147:80. [PMID: 38714540 PMCID: PMC11076412 DOI: 10.1007/s00401-024-02737-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/10/2024]
Abstract
GABAergic interneurons play a critical role in maintaining neural circuit balance, excitation-inhibition regulation, and cognitive function modulation. In tuberous sclerosis complex (TSC), GABAergic neuron dysfunction contributes to disrupted network activity and associated neurological symptoms, assumingly in a cell type-specific manner. This GABAergic centric study focuses on identifying specific interneuron subpopulations within TSC, emphasizing the unique characteristics of medial ganglionic eminence (MGE)- and caudal ganglionic eminence (CGE)-derived interneurons. Using single-nuclei RNA sequencing in TSC patient material, we identify somatostatin-expressing (SST+) interneurons as a unique and immature subpopulation in TSC. The disrupted maturation of SST+ interneurons may undergo an incomplete switch from excitatory to inhibitory GABAergic signaling during development, resulting in reduced inhibitory properties. Notably, this study reveals markers of immaturity specifically in SST+ interneurons, including an abnormal NKCC1/KCC2 ratio, indicating an imbalance in chloride homeostasis crucial for the postsynaptic consequences of GABAergic signaling as well as the downregulation of GABAA receptor subunits, GABRA1, and upregulation of GABRA2. Further exploration of SST+ interneurons revealed altered localization patterns of SST+ interneurons in TSC brain tissue, concentrated in deeper cortical layers, possibly linked to cortical dyslamination. In the epilepsy context, our research underscores the diverse cell type-specific roles of GABAergic interneurons in shaping seizures, advocating for precise therapeutic considerations. Moreover, this study illuminates the potential contribution of SST+ interneurons to TSC pathophysiology, offering insights for targeted therapeutic interventions.
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Affiliation(s)
- Mirte Scheper
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
| | - Frederik N F Sørensen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Gabriele Ruffolo
- Department of Physiology and Pharmacology, University of Rome Sapienza, 00185, Rome, Italy
- IRCCS San Raffaele Roma, 00163, Rome, Italy
| | - Alessandro Gaeta
- Department of Physiology and Pharmacology, University of Rome Sapienza, 00185, Rome, Italy
| | - Lilian J Lissner
- Department of Physiology and Pharmacology, University of Rome Sapienza, 00185, Rome, Italy
| | - Jasper J Anink
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Irina Korshunova
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Floor E Jansen
- Department of Child Neurology, Brain Center University Medical Center, Member of ERN EpiCare, 3584 BA, Utrecht, The Netherlands
| | - Kate Riney
- Faculty of Medicine, The University of Queensland, St Lucia, QLD, 4067, Australia
- Neurosciences Unit, Queensland Children's Hospital, South Brisbane, QLD, 4101, Australia
| | - Wim van Hecke
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Angelika Mühlebner
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Dirk Schubert
- Department of Cognitive Neurosciences, Radboudumc, Donders Institute for Brain Cognition and Behaviour, 6525 HR, Nijmegen, The Netherlands
| | - Eleonora Palma
- Department of Physiology and Pharmacology, University of Rome Sapienza, 00185, Rome, Italy
- IRCCS San Raffaele Roma, 00163, Rome, Italy
| | - James D Mills
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Bucks, SL9 0RJ, UK
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands
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13
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Al-Dalahmah O, Lam M, McInvale JJ, Qu W, Nguyen T, Mun JY, Kwon S, Ifediora N, Mahajan A, Humala N, Winters T, Angeles E, Jakubiak KA, Kühn R, Kim YA, De Rosa MC, Doege CA, Paryani F, Flowers X, Dovas A, Mela A, Lu H, DeTure MA, Vonsattel JP, Wszolek ZK, Dickson DW, Kuhlmann T, Zaehres H, Schöler HR, Sproul AA, Siegelin MD, De Jager PL, Goldman JE, Menon V, Canoll P, Hargus G. Osteopontin drives neuroinflammation and cell loss in MAPT-N279K frontotemporal dementia patient neurons. Cell Stem Cell 2024; 31:676-693.e10. [PMID: 38626772 DOI: 10.1016/j.stem.2024.03.013] [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: 04/04/2023] [Revised: 01/07/2024] [Accepted: 03/19/2024] [Indexed: 05/05/2024]
Abstract
Frontotemporal dementia (FTD) is an incurable group of early-onset dementias that can be caused by the deposition of hyperphosphorylated tau in patient brains. However, the mechanisms leading to neurodegeneration remain largely unknown. Here, we combined single-cell analyses of FTD patient brains with a stem cell culture and transplantation model of FTD. We identified disease phenotypes in FTD neurons carrying the MAPT-N279K mutation, which were related to oxidative stress, oxidative phosphorylation, and neuroinflammation with an upregulation of the inflammation-associated protein osteopontin (OPN). Human FTD neurons survived less and elicited an increased microglial response after transplantation into the mouse forebrain, which we further characterized by single nucleus RNA sequencing of microdissected grafts. Notably, downregulation of OPN in engrafted FTD neurons resulted in improved engraftment and reduced microglial infiltration, indicating an immune-modulatory role of OPN in patient neurons, which may represent a potential therapeutic target in FTD.
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Affiliation(s)
- Osama Al-Dalahmah
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Matti Lam
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julie J McInvale
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Wenhui Qu
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Trang Nguyen
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Jeong-Yeon Mun
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Sam Kwon
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Nkechime Ifediora
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Aayushi Mahajan
- Department of Neurosurgery, Columbia University, New York, NY 10032, USA
| | - Nelson Humala
- Department of Neurosurgery, Columbia University, New York, NY 10032, USA
| | - Tristan Winters
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Ellen Angeles
- Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Kelly A Jakubiak
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Rebekka Kühn
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Yoon A Kim
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Maria Caterina De Rosa
- Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Claudia A Doege
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Fahad Paryani
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xena Flowers
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Athanassios Dovas
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Angeliki Mela
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Hong Lu
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Michael A DeTure
- Department of Neuroscience, The Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Jean Paul Vonsattel
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Zbigniew K Wszolek
- Department of Neurology, The Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, The Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Tanja Kuhlmann
- Institute of Neuropathology, University Hospital Münster, Münster 48149, Germany
| | - Holm Zaehres
- Institute of Anatomy, Ruhr University Bochum, Medical Faculty, Bochum 44801, Germany; Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Andrew A Sproul
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Markus D Siegelin
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Philip L De Jager
- Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA; Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - James E Goldman
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Vilas Menon
- Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA; Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter Canoll
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Gunnar Hargus
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease & the Aging Brain, Columbia University, New York, NY 10032, USA.
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14
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Fancy NN, Smith AM, Caramello A, Tsartsalis S, Davey K, Muirhead RCJ, McGarry A, Jenkyns MH, Schneegans E, Chau V, Thomas M, Boulger S, Cheung TKD, Adair E, Papageorgopoulou M, Willumsen N, Khozoie C, Gomez-Nicola D, Jackson JS, Matthews PM. Characterisation of premature cell senescence in Alzheimer's disease using single nuclear transcriptomics. Acta Neuropathol 2024; 147:78. [PMID: 38695952 PMCID: PMC11065703 DOI: 10.1007/s00401-024-02727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/28/2024] [Indexed: 05/05/2024]
Abstract
Aging is associated with cell senescence and is the major risk factor for AD. We characterized premature cell senescence in postmortem brains from non-diseased controls (NDC) and donors with Alzheimer's disease (AD) using imaging mass cytometry (IMC) and single nuclear RNA (snRNA) sequencing (> 200,000 nuclei). We found increases in numbers of glia immunostaining for galactosidase beta (> fourfold) and p16INK4A (up to twofold) with AD relative to NDC. Increased glial expression of genes related to senescence was associated with greater β-amyloid load. Prematurely senescent microglia downregulated phagocytic pathways suggesting reduced capacity for β-amyloid clearance. Gene set enrichment and pseudo-time trajectories described extensive DNA double-strand breaks (DSBs), mitochondrial dysfunction and ER stress associated with increased β-amyloid leading to premature senescence in microglia. We replicated these observations with independent AD snRNA-seq datasets. Our results describe a burden of senescent glia with AD that is sufficiently high to contribute to disease progression. These findings support the hypothesis that microglia are a primary target for senolytic treatments in AD.
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Affiliation(s)
- Nurun N Fancy
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Amy M Smith
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- Centre for Brain Research and Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Alessia Caramello
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Stergios Tsartsalis
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Karen Davey
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- UK Dementia Research Institute Centre, King's College London, London, UK
| | - Robert C J Muirhead
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- UK Dementia Research Institute Centre, King's College London, London, UK
| | - Aisling McGarry
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Marion H Jenkyns
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Eleonore Schneegans
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Vicky Chau
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Michael Thomas
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Sam Boulger
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - To Ka Dorcas Cheung
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Emily Adair
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Marianna Papageorgopoulou
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Nanet Willumsen
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Combiz Khozoie
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Diego Gomez-Nicola
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Johanna S Jackson
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Paul M Matthews
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK.
- UK Dementia Research Institute Centre, Imperial College London, London, UK.
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15
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Renaut S, Saavedra Armero V, Boudreau DK, Gaudreault N, Desmeules P, Thériault S, Mathieu P, Joubert P, Bossé Y. Single-cell and single-nucleus RNA-sequencing from paired normal-adenocarcinoma lung samples provide both common and discordant biological insights. PLoS Genet 2024; 20:e1011301. [PMID: 38814983 PMCID: PMC11166281 DOI: 10.1371/journal.pgen.1011301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/11/2024] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Whether single-cell RNA-sequencing (scRNA-seq) captures the same biological information as single-nucleus RNA-sequencing (snRNA-seq) remains uncertain and likely to be context-dependent. Herein, a head-to-head comparison was performed in matched normal-adenocarcinoma human lung samples to assess biological insights derived from scRNA-seq versus snRNA-seq and better understand the cellular transition that occurs from normal to tumoral tissue. Here, the transcriptome of 160,621 cells/nuclei was obtained. In non-tumor lung, cell type proportions varied widely between scRNA-seq and snRNA-seq with a predominance of immune cells in the former (81.5%) and epithelial cells (69.9%) in the later. Similar results were observed in adenocarcinomas, in addition to an overall increase in cell type heterogeneity and a greater prevalence of copy number variants in cells of epithelial origin, which suggests malignant assignment. The cell type transition that occurs from normal lung tissue to adenocarcinoma was not always concordant whether cells or nuclei were examined. As expected, large differential expression of the whole-cell and nuclear transcriptome was observed, but cell-type specific changes of paired normal and tumor lung samples revealed a set of common genes in the cells and nuclei involved in cancer-related pathways. In addition, we showed that the ligand-receptor interactome landscape of lung adenocarcinoma was largely different whether cells or nuclei were evaluated. Immune cell depletion in fresh specimens partly mitigated the difference in cell type composition observed between cells and nuclei. However, the extra manipulations affected cell viability and amplified the transcriptional signatures associated with stress responses. In conclusion, research applications focussing on mapping the immune landscape of lung adenocarcinoma benefit from scRNA-seq in fresh samples, whereas snRNA-seq of frozen samples provide a low-cost alternative to profile more epithelial and cancer cells, and yield cell type proportions that more closely match tissue content.
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Affiliation(s)
- Sébastien Renaut
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Victoria Saavedra Armero
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Dominique K. Boudreau
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Nathalie Gaudreault
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Patrice Desmeules
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Sébastien Thériault
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Patrick Mathieu
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec–Université Laval, Quebec City, Canada
- Department of Molecular Medicine, Université Laval, Quebec City, Canada
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16
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Akindehin S, Liskiewicz A, Liskiewicz D, Bernecker M, Garcia-Caceres C, Drucker DJ, Finan B, Grandl G, Gutgesell R, Hofmann SM, Khalil A, Liu X, Cota P, Bakhti M, Czarnecki O, Bastidas-Ponce A, Lickert H, Kang L, Maity G, Novikoff A, Parlee S, Pathak E, Schriever SC, Sterr M, Ussar S, Zhang Q, DiMarchi R, Tschöp MH, Pfluger PT, Douros JD, Müller TD. Loss of GIPR in LEPR cells impairs glucose control by GIP and GIP:GLP-1 co-agonism without affecting body weight and food intake in mice. Mol Metab 2024; 83:101915. [PMID: 38492844 PMCID: PMC10973979 DOI: 10.1016/j.molmet.2024.101915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
OBJECTIVE The glucose-dependent insulinotropic polypeptide (GIP) decreases body weight via central GIP receptor (GIPR) signaling, but the underlying mechanisms remain largely unknown. Here, we assessed whether GIP regulates body weight and glucose control via GIPR signaling in cells that express the leptin receptor (Lepr). METHODS Hypothalamic, hindbrain, and pancreatic co-expression of Gipr and Lepr was assessed using single cell RNAseq analysis. Mice with deletion of Gipr in Lepr cells were generated and metabolically characterized for alterations in diet-induced obesity (DIO), glucose control and leptin sensitivity. Long-acting single- and dual-agonists at GIPR and GLP-1R were further used to assess drug effects on energy and glucose metabolism in DIO wildtype (WT) and Lepr-Gipr knock-out (KO) mice. RESULTS Gipr and Lepr show strong co-expression in the pancreas, but not in the hypothalamus and hindbrain. DIO Lepr-Gipr KO mice are indistinguishable from WT controls related to body weight, food intake and diet-induced leptin resistance. Acyl-GIP and the GIPR:GLP-1R co-agonist MAR709 remain fully efficacious to decrease body weight and food intake in DIO Lepr-Gipr KO mice. Consistent with the demonstration that Gipr and Lepr highly co-localize in the endocrine pancreas, including the β-cells, we find the superior glycemic effect of GIPR:GLP-1R co-agonism over single GLP-1R agonism to vanish in Lepr-Gipr KO mice. CONCLUSIONS GIPR signaling in cells/neurons that express the leptin receptor is not implicated in the control of body weight or food intake, but is of crucial importance for the superior glycemic effects of GIPR:GLP-1R co-agonism relative to single GLP-1R agonism.
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Affiliation(s)
- Seun Akindehin
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Helmholtz Diabetes School, Helmholtz Diabetes Center, Munich, Germany
| | - Arkadiusz Liskiewicz
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Poland
| | - Daniela Liskiewicz
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute of Physiotherapy and Health Sciences, Academy of Physical Education, Katowice, Poland
| | - Miriam Bernecker
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Helmholtz Diabetes School, Helmholtz Diabetes Center, Munich, Germany; Neurobiology of Diabetes Research Unit, Germany
| | - Cristina Garcia-Caceres
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Daniel J Drucker
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Brian Finan
- Novo Nordisk Research Center Indianapolis, Indianapolis, IN, USA
| | - Gerald Grandl
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Robert Gutgesell
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Susanna M Hofmann
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany; Medical Clinic and Polyclinic IV, Ludwig-Maximilians University of München, Munich, Germany
| | - Ahmed Khalil
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Xue Liu
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Perla Cota
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Mostafa Bakhti
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Oliver Czarnecki
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Aimée Bastidas-Ponce
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Heiko Lickert
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Lingru Kang
- German Center for Diabetes Research (DZD), Neuherberg, Germany; RU Adipocytes & Metabolism, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
| | - Gandhari Maity
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Aaron Novikoff
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Sebastian Parlee
- Novo Nordisk Research Center Indianapolis, Indianapolis, IN, USA
| | - Ekta Pathak
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; Neurobiology of Diabetes Research Unit, Germany
| | - Sonja C Schriever
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; Neurobiology of Diabetes Research Unit, Germany
| | - Michael Sterr
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Siegfried Ussar
- German Center for Diabetes Research (DZD), Neuherberg, Germany; RU Adipocytes & Metabolism, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
| | - Qian Zhang
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Richard DiMarchi
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Matthias H Tschöp
- Division of Metabolic Diseases, Department of Medicine, Technical University Munich, Munich, Germany; Helmholtz Munich, Neuherberg, Germany
| | - Paul T Pfluger
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; Neurobiology of Diabetes Research Unit, Germany; Division of Neurobiology of Diabetes, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Timo D Müller
- Institute for Diabetes and Obesity, Helmholtz Munich, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology, Ludgwig-Maximilians-University Munich, Germany.
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Xie G, Toledo MP, Hu X, Yong HJ, Sanchez PS, Liu C, Naji A, Irianto J, Wang YJ. NKX2-2 based nuclei sorting on frozen human archival pancreas enables the enrichment of islet endocrine populations for single-nucleus RNA sequencing. BMC Genomics 2024; 25:427. [PMID: 38689254 PMCID: PMC11059690 DOI: 10.1186/s12864-024-10335-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Current approaches to profile the single-cell transcriptomics of human pancreatic endocrine cells almost exclusively rely on freshly isolated islets. However, human islets are limited in availability. Furthermore, the extensive processing steps during islet isolation and subsequent single cell dissolution might alter gene expressions. In this work, we report the development of a single-nucleus RNA sequencing (snRNA-seq) approach with targeted islet cell enrichment for endocrine-population focused transcriptomic profiling using frozen archival pancreatic tissues without islet isolation. RESULTS We cross-compared five nuclei isolation protocols and selected the citric acid method as the best strategy to isolate nuclei with high RNA integrity and low cytoplasmic contamination from frozen archival human pancreata. We innovated fluorescence-activated nuclei sorting based on the positive signal of NKX2-2 antibody to enrich nuclei of the endocrine population from the entire nuclei pool of the pancreas. Our sample preparation procedure generated high-quality single-nucleus gene-expression libraries while preserving the endocrine population diversity. In comparison with single-cell RNA sequencing (scRNA-seq) library generated with live cells from freshly isolated human islets, the snRNA-seq library displayed comparable endocrine cellular composition and cell type signature gene expression. However, between these two types of libraries, differential enrichments of transcripts belonging to different functional classes could be observed. CONCLUSIONS Our work fills a technological gap and helps to unleash frozen archival pancreatic tissues for molecular profiling targeting the endocrine population. This study opens doors to retrospective mappings of endocrine cell dynamics in pancreatic tissues of complex histopathology. We expect that our protocol is applicable to enrich nuclei for transcriptomics studies from various populations in different types of frozen archival tissues.
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Affiliation(s)
- Gengqiang Xie
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Maria Pilar Toledo
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Xue Hu
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Hyo Jeong Yong
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Pamela Sandoval Sanchez
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Chengyang Liu
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ali Naji
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Jerome Irianto
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Yue J Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA.
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18
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Yaghmaeian Salmani B, Lahti L, Gillberg L, Jacobsen JK, Mantas I, Svenningsson P, Perlmann T. Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model. eLife 2024; 12:RP89482. [PMID: 38587883 PMCID: PMC11001297 DOI: 10.7554/elife.89482] [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: 04/09/2024] Open
Abstract
Midbrain dopamine (mDA) neurons comprise diverse cells with unique innervation targets and functions. This is illustrated by the selective sensitivity of mDA neurons of the substantia nigra compacta (SNc) in patients with Parkinson's disease, while those in the ventral tegmental area (VTA) are relatively spared. Here, we used single nuclei RNA sequencing (snRNA-seq) of approximately 70,000 mouse midbrain cells to build a high-resolution atlas of mouse mDA neuron diversity at the molecular level. The results showed that differences between mDA neuron groups could best be understood as a continuum without sharp differences between subtypes. Thus, we assigned mDA neurons to several 'territories' and 'neighborhoods' within a shifting gene expression landscape where boundaries are gradual rather than discrete. Based on the enriched gene expression patterns of these territories and neighborhoods, we were able to localize them in the adult mouse midbrain. Moreover, because the underlying mechanisms for the variable sensitivities of diverse mDA neurons to pathological insults are not well understood, we analyzed surviving neurons after partial 6-hydroxydopamine (6-OHDA) lesions to unravel gene expression patterns that correlate with mDA neuron vulnerability and resilience. Together, this atlas provides a basis for further studies on the neurophysiological role of mDA neurons in health and disease.
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Affiliation(s)
| | - Laura Lahti
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
| | - Linda Gillberg
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
| | - Jesper Kjaer Jacobsen
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
- Department of Neurology, Karolinska University HospitalStockholmSweden
| | - Ioannis Mantas
- Department of Clinical Neuroscience, Karolinska InstitutetStockholmSweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska InstitutetStockholmSweden
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
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19
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Fiorini MR, Dilliott AA, Thomas RA, Farhan SMK. Transcriptomics of Human Brain Tissue in Parkinson's Disease: a Comparison of Bulk and Single-cell RNA Sequencing. Mol Neurobiol 2024:10.1007/s12035-024-04124-5. [PMID: 38578357 DOI: 10.1007/s12035-024-04124-5] [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: 10/11/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
Parkinson's disease (PD) is a chronic and progressive neurodegenerative disease leading to motor dysfunction and, in some cases, dementia. Transcriptome analysis is one promising approach for characterizing PD and other neurodegenerative disorders by informing how specific disease events influence gene expression and contribute to pathogenesis. With the emergence of single-cell and single-nucleus RNA sequencing (scnRNA-seq) technologies, the transcriptional landscape of neurodegenerative diseases can now be described at the cellular level. As the application of scnRNA-seq is becoming routine, it calls to question how results at a single-cell resolution compare to those obtained from RNA sequencing of whole tissues (bulk RNA-seq), whether the findings are compatible, and how the assays are complimentary for unraveling the elusive transcriptional changes that drive neurodegenerative disease. Herein, we review the studies that have leveraged RNA-seq technologies to investigate PD. Through the integration of bulk and scnRNA-seq findings from human, post-mortem brain tissue, we use the PD literature as a case study to evaluate the compatibility of the results generated from each assay and demonstrate the complementarity of the sequencing technologies. Finally, through the lens of the PD transcriptomic literature, we evaluate the current feasibility of bulk and scnRNA-seq technologies to illustrate the necessity of both technologies for achieving a comprehensive insight into the mechanism by which gene expression promotes neurodegenerative disease. We conclude that the continued application of both assays will provide the greatest insight into neurodegenerative disease pathology, providing both cell-specific and whole-tissue level information.
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Affiliation(s)
- Michael R Fiorini
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Allison A Dilliott
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Rhalena A Thomas
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada.
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.
| | - Sali M K Farhan
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.
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20
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Shen Y, Shao M, Hao ZZ, Huang M, Xu N, Liu S. Multimodal Nature of the Single-cell Primate Brain Atlas: Morphology, Transcriptome, Electrophysiology, and Connectivity. Neurosci Bull 2024; 40:517-532. [PMID: 38194157 PMCID: PMC11003949 DOI: 10.1007/s12264-023-01160-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/23/2023] [Indexed: 01/10/2024] Open
Abstract
Primates exhibit complex brain structures that augment cognitive function. The neocortex fulfills high-cognitive functions through billions of connected neurons. These neurons have distinct transcriptomic, morphological, and electrophysiological properties, and their connectivity principles vary. These features endow the primate brain atlas with a multimodal nature. The recent integration of next-generation sequencing with modified patch-clamp techniques is revolutionizing the way to census the primate neocortex, enabling a multimodal neuronal atlas to be established in great detail: (1) single-cell/single-nucleus RNA-seq technology establishes high-throughput transcriptomic references, covering all major transcriptomic cell types; (2) patch-seq links the morphological and electrophysiological features to the transcriptomic reference; (3) multicell patch-clamp delineates the principles of local connectivity. Here, we review the applications of these technologies in the primate neocortex and discuss the current advances and tentative gaps for a comprehensive understanding of the primate neocortex.
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Affiliation(s)
- Yuhui Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mingting Shao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhao-Zhe Hao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mengyao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Nana Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, 510080, China.
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21
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Tsartsalis S, Sleven H, Fancy N, Wessely F, Smith AM, Willumsen N, Cheung TKD, Rokicki MJ, Chau V, Ifie E, Khozoie C, Ansorge O, Yang X, Jenkyns MH, Davey K, McGarry A, Muirhead RCJ, Debette S, Jackson JS, Montagne A, Owen DR, Miners JS, Love S, Webber C, Cader MZ, Matthews PM. A single nuclear transcriptomic characterisation of mechanisms responsible for impaired angiogenesis and blood-brain barrier function in Alzheimer's disease. Nat Commun 2024; 15:2243. [PMID: 38472200 DOI: 10.1038/s41467-024-46630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Brain perfusion and blood-brain barrier (BBB) integrity are reduced early in Alzheimer's disease (AD). We performed single nucleus RNA sequencing of vascular cells isolated from AD and non-diseased control brains to characterise pathological transcriptional signatures responsible for this. We show that endothelial cells (EC) are enriched for expression of genes associated with susceptibility to AD. Increased β-amyloid is associated with BBB impairment and a dysfunctional angiogenic response related to a failure of increased pro-angiogenic HIF1A to increased VEGFA signalling to EC. This is associated with vascular inflammatory activation, EC senescence and apoptosis. Our genomic dissection of vascular cell risk gene enrichment provides evidence for a role of EC pathology in AD and suggests that reducing vascular inflammatory activation and restoring effective angiogenesis could reduce vascular dysfunction contributing to the genesis or progression of early AD.
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Affiliation(s)
- Stergios Tsartsalis
- Department of Brain Sciences, Imperial College London, London, UK
- Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Hannah Sleven
- Nuffield Department of Clinical Neurosciences, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Road, University of Oxford, Oxford, UK
| | - Nurun Fancy
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Frank Wessely
- UK Dementia Research Institute Centre, Cardiff University, Cardiff, UK
| | - Amy M Smith
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- Centre for Brain Research and Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Nanet Willumsen
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - To Ka Dorcas Cheung
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Michal J Rokicki
- UK Dementia Research Institute Centre, Cardiff University, Cardiff, UK
| | - Vicky Chau
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Eseoghene Ifie
- Neuropathology Unit, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Combiz Khozoie
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Olaf Ansorge
- Neuropathology Unit, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Xin Yang
- Department of Brain Sciences, Imperial College London, London, UK
- St Edmund Hall, University of Oxford, Oxford, UK
| | - Marion H Jenkyns
- Department of Brain Sciences, Imperial College London, London, UK
| | - Karen Davey
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Aisling McGarry
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Robert C J Muirhead
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Stephanie Debette
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, Team ELEANOR, UMR 1219, 33000, Bordeaux, France
| | - Johanna S Jackson
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Axel Montagne
- Centre for Clinical Brain Sciences, and UK Dementia Research Institute, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - David R Owen
- Department of Brain Sciences, Imperial College London, London, UK
| | - J Scott Miners
- Dementia Research Group, University of Bristol, Bristol, UK
| | - Seth Love
- Dementia Research Group, University of Bristol, Bristol, UK
| | - Caleb Webber
- UK Dementia Research Institute Centre, Cardiff University, Cardiff, UK
| | - M Zameel Cader
- Nuffield Department of Clinical Neurosciences, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Road, University of Oxford, Oxford, UK
| | - Paul M Matthews
- Department of Brain Sciences, Imperial College London, London, UK.
- UK Dementia Research Institute Centre, Imperial College London, London, UK.
- St Edmund Hall, University of Oxford, Oxford, UK.
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22
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Tukker AM, Bowman AB. Application of Single Cell Gene Expression Technologies to Neurotoxicology. CURRENT OPINION IN TOXICOLOGY 2024; 37:100458. [PMID: 38617035 PMCID: PMC11008280 DOI: 10.1016/j.cotox.2023.100458] [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] [Indexed: 04/16/2024]
Abstract
Neurotoxicological research faces the challenge of linking biological changes resulting from exposures to neuronal function. An additional challenge is understanding cell-type specific differences and selective vulnerabilities of distinct neuronal populations to toxic insults. Single cell RNA-sequencing (scRNA-seq) allows for measurement of the transcriptome of individual cells. This makes it a valuable tool for validating and characterizing cell types present in multicell type samples in complex tissue or cell culture models, but also for understanding how different cell types respond to toxic insults. Pathway analysis of differentially expressed genes can provide in depth insights into underlying cell type-specific mechanisms of neurotoxicity. Toxicological data often has to be translated to outcomes for human health which requires an understanding of inter-species differences. Transcriptomic data aids in understanding these differences, including understanding developmental timelines of different species. We believe that scRNA-seq holds exciting promises for future neurotoxicological research.
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Affiliation(s)
- Anke M Tukker
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | - Aaron B Bowman
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
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23
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Vukic M, Chouaref J, Della Chiara V, Dogan S, Ratner F, Hogenboom JZM, Epp TA, Chawengsaksophak K, Vonk KKD, Breukel C, Ariyurek Y, San Leon Granado D, Kloet SL, Daxinger L. CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses. SCIENCE ADVANCES 2024; 10:eadk3384. [PMID: 38335290 PMCID: PMC10857554 DOI: 10.1126/sciadv.adk3384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
Disruption of cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting the deposition of H3K9 trimethylation (H3K9me3). CDCA7-associated aberrant DNA hypomethylation translated to localized, tissue-specific transcriptional dysregulation that affected large gene clusters. In the brain, we identify CDCA7 as a transcriptional repressor and epigenetic regulator of clustered protocadherin isoform choice. Increased protocadherin isoform expression frequency is accompanied by DNA methylation loss, gain of H3K4 trimethylation (H3K4me3), and increased binding of the transcriptional regulator CCCTC-binding factor (CTCF). Overall, our in vivo work identifies a key role for CDCA7 in safeguarding tissue-specific expression of gene clusters via the DNA methylation pathway.
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Affiliation(s)
- Maja Vukic
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Jihed Chouaref
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Serkan Dogan
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Fallon Ratner
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Trevor A. Epp
- Laboratory of Cell Differentiation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- CZ-OPENSCREEN, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kallayanee Chawengsaksophak
- Laboratory of Cell Differentiation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kelly K. D. Vonk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Cor Breukel
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Susan L. Kloet
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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24
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Lei Y, Liang X, Sun Y, Yao T, Gong H, Chen Z, Gao Y, Wang H, Wang R, Huang Y, Yang T, Yu M, Liu L, Yi CX, Wu QF, Kong X, Xu X, Liu S, Zhang Z, Liu T. Region-specific transcriptomic responses to obesity and diabetes in macaque hypothalamus. Cell Metab 2024; 36:438-453.e6. [PMID: 38325338 DOI: 10.1016/j.cmet.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/27/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024]
Abstract
The hypothalamus plays a crucial role in the progression of obesity and diabetes; however, its structural complexity and cellular heterogeneity impede targeted treatments. Here, we profiled the single-cell and spatial transcriptome of the hypothalamus in obese and sporadic type 2 diabetic macaques, revealing primate-specific distributions of clusters and genes as well as spatial region, cell-type-, and gene-feature-specific changes. The infundibular (INF) and paraventricular nuclei (PVN) are most susceptible to metabolic disruption, with the PVN being more sensitive to diabetes. In the INF, obesity results in reduced synaptic plasticity and energy sensing capability, whereas diabetes involves molecular reprogramming associated with impaired tanycytic barriers, activated microglia, and neuronal inflammatory response. In the PVN, cellular metabolism and neural activity are suppressed in diabetic macaques. Spatial transcriptomic data reveal microglia's preference for the parenchyma over the third ventricle in diabetes. Our findings provide a comprehensive view of molecular changes associated with obesity and diabetes.
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Affiliation(s)
- Ying Lei
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Xian Liang
- State Key Laboratory of Genetic Engineering, Department of Endocrinology and Metabolism, Human Phenome Institute, Institute of Metabolism and Integrative Biology, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yunong Sun
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Ting Yao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University School of Medicine, Xi'an, Shanxi 710063, China
| | - Hongyu Gong
- School of Life Sciences, Institues of Biomedical Sciences, Inner Mongolia University, Hohhot 010000, China
| | - Zhenhua Chen
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanqing Gao
- Jiangsu Provincial Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Hui Wang
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ru Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Yunqi Huang
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Tao Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Miao Yu
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Longqi Liu
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Chun-Xia Yi
- Department of Endocrinology and Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, the Netherlands
| | - Qing-Feng Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xingxing Kong
- School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Xun Xu
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China.
| | - Shiping Liu
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China.
| | - Zhi Zhang
- State Key Laboratory of Genetic Engineering, Department of Endocrinology and Metabolism, Human Phenome Institute, Institute of Metabolism and Integrative Biology, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Tiemin Liu
- State Key Laboratory of Genetic Engineering, Department of Endocrinology and Metabolism, Human Phenome Institute, Institute of Metabolism and Integrative Biology, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; School of Life Sciences, Fudan University, Shanghai 200438, China; School of Life Sciences, Institues of Biomedical Sciences, Inner Mongolia University, Hohhot 010000, China.
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25
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He Z, Chen Q, Wang K, Lin J, Peng Y, Zhang J, Yan X, Jie Y. Single-cell transcriptomics analysis of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. Eur J Neurosci 2024; 59:333-357. [PMID: 38221677 DOI: 10.1111/ejn.16242] [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: 05/17/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024]
Abstract
Single-cell transcriptomics analysis is an advanced technology that can describe the intracellular transcriptome in complex tissues. It profiles and analyses datasets by single-cell RNA sequencing. Neurodegenerative diseases are identified by the abnormal apoptosis of neurons in the brain with few or no effective therapy strategies at present, which has been a growing healthcare concern and brought a great burden to society. The transcriptome of individual cells provides deep insights into previously unforeseen cellular heterogeneity and gene expression differences in neurodegenerative disorders. It detects multiple cell subsets and functional changes during pathological progression, which deepens the understanding of the molecular underpinnings and cellular basis of neurodegenerative diseases. Furthermore, the transcriptome analysis of immune cells shows the regulation of immune response. Different subtypes of immune cells and their interaction are found to contribute to disease progression. This finding enables the discovery of novel targets and biomarkers for early diagnosis. In this review, we emphasize the principles of the technology, and its recent progress in the study of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. The application of single-cell transcriptomics analysis in neurodegenerative disorders would help explore the pathogenesis of these diseases and develop novel therapeutic methods.
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Affiliation(s)
- Ziping He
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Qianqian Chen
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Kaiyue Wang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiang Lin
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Yilin Peng
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Jinlong Zhang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
| | - Xisheng Yan
- Department of Cardiovascular Medicine, Wuhan Third Hospital & Tongren Hospital of Wuhan University, Wuhan, China
| | - Yan Jie
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
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26
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Yang S, Liu C, Jiang M, Liu X, Geng L, Zhang Y, Sun S, Wang K, Yin J, Ma S, Wang S, Belmonte JCI, Zhang W, Qu J, Liu GH. A single-nucleus transcriptomic atlas of primate liver aging uncovers the pro-senescence role of SREBP2 in hepatocytes. Protein Cell 2024; 15:98-120. [PMID: 37378670 PMCID: PMC10833472 DOI: 10.1093/procel/pwad039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Aging increases the risk of liver diseases and systemic susceptibility to aging-related diseases. However, cell type-specific changes and the underlying mechanism of liver aging in higher vertebrates remain incompletely characterized. Here, we constructed the first single-nucleus transcriptomic landscape of primate liver aging, in which we resolved cell type-specific gene expression fluctuation in hepatocytes across three liver zonations and detected aberrant cell-cell interactions between hepatocytes and niche cells. Upon in-depth dissection of this rich dataset, we identified impaired lipid metabolism and upregulation of chronic inflammation-related genes prominently associated with declined liver functions during aging. In particular, hyperactivated sterol regulatory element-binding protein (SREBP) signaling was a hallmark of the aged liver, and consequently, forced activation of SREBP2 in human primary hepatocytes recapitulated in vivo aging phenotypes, manifesting as impaired detoxification and accelerated cellular senescence. This study expands our knowledge of primate liver aging and informs the development of diagnostics and therapeutic interventions for liver aging and associated diseases.
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Affiliation(s)
- Shanshan Yang
- 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
- Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Chengyu 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
| | - Mengmeng Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 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, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Lingling Geng
- 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
| | - Yiyuan Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, 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, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Kang Wang
- 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
| | - Jian Yin
- 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
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, 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
| | | | - 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
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Jing Qu
- 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
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Guang-Hui Liu
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 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
- Xuanwu Hospital Capital Medical University, Beijing 100053, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
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27
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Swaminath S, Russell AB. The use of single-cell RNA-seq to study heterogeneity at varying levels of virus-host interactions. PLoS Pathog 2024; 20:e1011898. [PMID: 38236826 PMCID: PMC10796064 DOI: 10.1371/journal.ppat.1011898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
The outcome of viral infection depends on the diversity of the infecting viral population and the heterogeneity of the cell population that is infected. Until almost a decade ago, the study of these dynamic processes during viral infection was challenging and limited to certain targeted measurements. Presently, with the use of single-cell sequencing technology, the complex interface defined by the interactions of cells with infecting virus can now be studied across the breadth of the transcriptome in thousands of individual cells simultaneously. In this review, we will describe the use of single-cell RNA sequencing (scRNA-seq) to study the heterogeneity of viral infections, ranging from individual virions to the immune response between infected individuals. In addition, we highlight certain key experimental limitations and methodological decisions that are critical to analyzing scRNA-seq data at each scale.
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Affiliation(s)
- Sharmada Swaminath
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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28
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Wang JH, Wu C, Lian YN, Cao XW, Wang ZY, Dong JJ, Wu Q, Liu L, Sun L, Chen W, Chen WJ, Zhang Z, Zhuo M, Li XY. Single-cell RNA sequencing uncovers the cell type-dependent transcriptomic changes in the retrosplenial cortex after peripheral nerve injury. Cell Rep 2023; 42:113551. [PMID: 38048224 DOI: 10.1016/j.celrep.2023.113551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/14/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
The retrosplenial cortex (RSC) is a vital area for storing remote memory and has recently been found to undergo broad changes after peripheral nerve injury. However, little is known about the role of RSC in pain regulation. Here, we examine the involvement of RSC in the pain of mice with nerve injury. Notably, reducing the activities of calcium-/calmodulin-dependent protein kinase type II-positive splenial neurons chemogenetically increases paw withdrawal threshold and extends thermal withdrawal latency in mice with nerve injury. The single-cell or single-nucleus RNA-sequencing results predict enhanced excitatory synaptic transmissions in RSC induced by nerve injury. Local infusion of 1-naphthyl acetyl spermine into RSC to decrease the excitatory synaptic transmissions relieves pain and induces conditioned place preference. Our data indicate that RSC is critical for regulating physiological and neuropathic pain. The cell type-dependent transcriptomic information would help understand the molecular basis of neuropathic pain.
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Affiliation(s)
- Jing-Hua Wang
- Department of Psychiatry of the Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain, Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Cheng Wu
- Department of Psychiatry of the Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain, Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang 314400, China; Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh EH8 9JU, UK
| | - Yan-Na Lian
- Department of Psychiatry of the Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain, Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiao-Wen Cao
- Department of Psychiatry of the Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain, Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zi-Yue Wang
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain, Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jia-Jun Dong
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang 314400, China
| | - Qin Wu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang 314400, China
| | - Li Liu
- Core Facilities of the School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Li Sun
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain, Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wei Chen
- Department of Psychiatry, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Wen-Juan Chen
- Department of Psychiatry, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Zhi Zhang
- Key Laboratory of Brain Functions and Diseases, School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Min Zhuo
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xiang-Yao Li
- Department of Psychiatry of the Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain, Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang 314400, China; Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh EH8 9JU, UK.
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29
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Zhu JH, Guan XC, Yi LL, Xu H, Li QY, Cheng WJ, Xie YX, Li WZ, Zhao HY, Wei HJ, Zhao SM. Single-nucleus transcriptome sequencing reveals hepatic cell atlas in pigs. BMC Genomics 2023; 24:770. [PMID: 38087243 PMCID: PMC10717992 DOI: 10.1186/s12864-023-09765-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND As the largest substantive organ of animals, the liver plays an essential role in the physiological processes of digestive metabolism and immune defense. However, the cellular composition of the pig liver remains poorly understood. This investigation used single-nucleus RNA sequencing technology to identify cell types from liver tissues of pigs, providing a theoretical basis for further investigating liver cell types in pigs. RESULTS The analysis revealed 13 cells clusters which were further identified 7 cell types including endothelial cells, T cells, hepatocytes, Kupffer cells, stellate cells, B cells, and cholangiocytes. The dominant cell types were endothelial cells, T cells and hepatocytes in the liver tissue of Dahe pigs and Dahe black pigs, which accounts for about 85.76% and 82.74%, respectively. The number of endothelial cells was higher in the liver tissue of Dahe pigs compared to Dahe black pigs, while the opposite tendency was observed for T cells. Moreover, functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic endothelial cells were significantly enriched in the protein processing in endoplasmic reticulum, MAPK signaling pathway, and FoxO signaling pathway. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic T cells were significantly enriched in the thyroid hormone signaling pathway, B cell receptor signaling pathway, and focal adhesion. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic hepatocytes were significantly enriched in the metabolic pathways. CONCLUSIONS In summary, this study provides a comprehensive cell atlas of porcine hepatic tissue. The number, gene expression level and functional characteristics of each cell type in pig liver tissue varied between breeds.
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Affiliation(s)
- Jun-Hong Zhu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuan-Cheng Guan
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Lan-Lan Yi
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong Xu
- School of Public Finance and Economics, Yunnan University of Finance and Economics, Kunming, 650221, China
| | - Qiu-Yan Li
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Wen-Jie Cheng
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Yu-Xiao Xie
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- College of Biology and Agriculture, Zunyi Normal University, Zunyi, 563006, China
| | - Wei-Zhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Ye Zhao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Jiang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China.
| | - Su-Mei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China.
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
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30
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Huang D, Zuo Y, Zhang C, Sun G, Jing Y, Lei J, Ma S, Sun S, Lu H, Cai Y, Zhang W, Gao F, Peng Xiang A, Belmonte JCI, Liu GH, Qu J, Wang S. A single-nucleus transcriptomic atlas of primate testicular aging reveals exhaustion of the spermatogonial stem cell reservoir and loss of Sertoli cell homeostasis. Protein Cell 2023; 14:888-907. [PMID: 36929025 PMCID: PMC10691849 DOI: 10.1093/procel/pwac057] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
The testis is pivotal for male reproduction, and its progressive functional decline in aging is associated with infertility. However, the regulatory mechanism underlying primate testicular aging remains largely elusive. Here, we resolve the aging-related cellular and molecular alterations of primate testicular aging by establishing a single-nucleus transcriptomic atlas. Gene-expression patterns along the spermatogenesis trajectory revealed molecular programs associated with attrition of spermatogonial stem cell reservoir, disturbed meiosis and impaired spermiogenesis along the sequential continuum. Remarkably, Sertoli cell was identified as the cell type most susceptible to aging, given its deeply perturbed age-associated transcriptional profiles. Concomitantly, downregulation of the transcription factor Wilms' Tumor 1 (WT1), essential for Sertoli cell homeostasis, was associated with accelerated cellular senescence, disrupted tight junctions, and a compromised cell identity signature, which altogether may help create a hostile microenvironment for spermatogenesis. Collectively, our study depicts in-depth transcriptomic traits of non-human primate (NHP) testicular aging at single-cell resolution, providing potential diagnostic biomarkers and targets for therapeutic interventions against testicular aging and age-related male reproductive diseases.
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Grants
- 2022M712216 National Key Research and Development Program of China
- 81921006, 82125011, 92149301, 92168201, 91949209, 92049304, 92049116, 32121001, 82192863, 82122024, 82071588, 32000500, 31900523, 82201714, 82271600, 82201727 National Natural Science Foundation of China
- 11000022T000000461062 Beijing-affiliated Medical Research
- CAS-WX2021SF-0301, CAS-WX2021SF-0101, CAS-WX2022SDC-XK14 Youth Innovation Promotion Association
- CAS-WX2021SF-0301 Youth Innovation Promotion Association
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Affiliation(s)
- Daoyuan Huang
- Advanced Innovation Center for Human Brain Protection, 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
| | - Yuesheng Zuo
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Chen Zhang
- The Fifth People’s Hospital of Chongqing, Chongqing 400062, China
| | - Guoqiang Sun
- 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
| | - Ying Jing
- 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
| | - Jinghui Lei
- Advanced Innovation Center for Human Brain Protection, 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
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- Aging Biomarker Consortium, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
| | - Huifen Lu
- Advanced Innovation Center for Human Brain Protection, 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
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
- Sino-Danish Center for Education and Research, Beijing 101408, China
- Aging Biomarker Consortium, China
| | - Fei Gao
- 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
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510000, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510000, China
| | | | - Guang-Hui Liu
- Advanced Innovation Center for Human Brain Protection, 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
- 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
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- Aging Biomarker Consortium, China
| | - Jing Qu
- 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
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem cell and Regeneration, CAS, Beijing 100101, China
- Aging Biomarker Consortium, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, 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
- Aging Biomarker Consortium, China
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31
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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). Front Cell Neurosci 2023; 17:1256619. [PMID: 38094513 PMCID: PMC10716316 DOI: 10.3389/fncel.2023.1256619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/11/2023] [Indexed: 12/20/2023] Open
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 NSForest 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, 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 within 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)
- Ely Cheikh Boussaty
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Neil Tedeschi
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Mark Novotny
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Yuzuru Ninoyu
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Eric Du
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Clara Draf
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Uri Manor
- Department of Cell and Developmental Biology, University of California San Diego, Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, CA, United States
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA, United States
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
| | - Rick Friedman
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
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32
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Cao J, Li W, Li J, Mazid MA, Li C, Jiang Y, Jia W, Wu L, Liao Z, Sun S, Song W, Fu J, Wang Y, Lu Y, Xu Y, Nie Y, Bian X, Gao C, Zhang X, Zhang L, Shang S, Li Y, Fu L, Liu H, Lai J, Wang Y, Yuan Y, Jin X, Li Y, Liu C, Lai Y, Shi X, Maxwell PH, Xu X, Liu L, Poo M, Wang X, Sun Q, Esteban MA, Liu Z. Live birth of chimeric monkey with high contribution from embryonic stem cells. Cell 2023; 186:4996-5014.e24. [PMID: 37949056 DOI: 10.1016/j.cell.2023.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 07/18/2023] [Accepted: 10/03/2023] [Indexed: 11/12/2023]
Abstract
A formal demonstration that mammalian pluripotent stem cells possess preimplantation embryonic cell-like (naive) pluripotency is the generation of chimeric animals through early embryo complementation with homologous cells. Whereas such naive pluripotency has been well demonstrated in rodents, poor chimerism has been achieved in other species including non-human primates due to the inability of the donor cells to match the developmental state of the host embryos. Here, we have systematically tested various culture conditions for establishing monkey naive embryonic stem cells and optimized the procedures for chimeric embryo culture. This approach generated an aborted fetus and a live chimeric monkey with high donor cell contribution. A stringent characterization pipeline demonstrated that donor cells efficiently (up to 90%) incorporated into various tissues (including the gonads and placenta) of the chimeric monkeys. Our results have major implications for the study of primate naive pluripotency and genetic engineering of non-human primates.
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Affiliation(s)
- Jing Cao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jie Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Md Abdul Mazid
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Chunyang Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu Jiang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenqi Jia
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Wu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zhaodi Liao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiyu Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weixiang Song
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiqiang Fu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Lu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuting Xu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanhong Nie
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyan Bian
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Changshan Gao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaotong Zhang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liansheng Zhang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shenshen Shang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunpan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lixin Fu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Junjian Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yang Wang
- BGI-Research, Hangzhou 310030, China
| | - Yue Yuan
- BGI-Research, Hangzhou 310030, China
| | - Xin Jin
- BGI-Research, Shenzhen 518083, China; School of Medicine, South China University of Technology, Guangzhou, China
| | - Yan Li
- BGI-Research, Shenzhen 518083, China
| | | | - Yiwei Lai
- BGI-Research, Hangzhou 310030, China
| | | | - Patrick H Maxwell
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 0ST, United Kingdom
| | - Xun Xu
- BGI-Research, Hangzhou 310030, China; BGI-Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China
| | | | - Muming Poo
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Qiang Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Miguel A Esteban
- BGI-Research, Hangzhou 310030, China; Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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33
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Rodríguez-Montes L, Ovchinnikova S, Yuan X, Studer T, Sarropoulos I, Anders S, Kaessmann H, Cardoso-Moreira M. Sex-biased gene expression across mammalian organ development and evolution. Science 2023; 382:eadf1046. [PMID: 37917687 PMCID: PMC7615307 DOI: 10.1126/science.adf1046] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 09/18/2023] [Indexed: 11/04/2023]
Abstract
Sexually dimorphic traits are common among mammals and are specified during development through the deployment of sex-specific genetic programs. Because little is known about these programs, we investigated them using a resource of gene expression profiles in males and females throughout the development of five organs in five mammals (human, mouse, rat, rabbit, and opossum) and a bird (chicken). We found that sex-biased gene expression varied considerably across organs and species and was often cell-type specific. Sex differences increased abruptly around sexual maturity instead of increasing gradually during organ development. Finally, sex-biased gene expression evolved rapidly at the gene level, with differences between organs in the evolutionary mechanisms used, but more slowly at the cellular level, with the same cell types being sexually dimorphic across species.
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Affiliation(s)
- Leticia Rodríguez-Montes
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | | | - Xuefei Yuan
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Tania Studer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Simon Anders
- BioQuant, Heidelberg University, D-69120 Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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34
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Li Z, Gu H, Xu X, Tian Y, Huang X, Du Y. Unveiling the novel immune and molecular signatures of ovarian cancer: insights and innovations from single-cell sequencing. Front Immunol 2023; 14:1288027. [PMID: 38022625 PMCID: PMC10654630 DOI: 10.3389/fimmu.2023.1288027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Ovarian cancer is a highly heterogeneous and lethal malignancy with limited treatment options. Over the past decade, single-cell sequencing has emerged as an advanced biological technology capable of decoding the landscape of ovarian cancer at the single-cell resolution. It operates at the level of genes, transcriptomes, proteins, epigenomes, and metabolisms, providing detailed information that is distinct from bulk sequencing methods, which only offer average data for specific lesions. Single-cell sequencing technology provides detailed insights into the immune and molecular mechanisms underlying tumor occurrence, development, drug resistance, and immune escape. These insights can guide the development of innovative diagnostic markers, therapeutic strategies, and prognostic indicators. Overall, this review provides a comprehensive summary of the diverse applications of single-cell sequencing in ovarian cancer. It encompasses the identification and characterization of novel cell subpopulations, the elucidation of tumor heterogeneity, the investigation of the tumor microenvironment, the analysis of mechanisms underlying metastasis, and the integration of innovative approaches such as organoid models and multi-omics analysis.
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Affiliation(s)
- Zhongkang Li
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Haihan Gu
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaotong Xu
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanpeng Tian
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xianghua Huang
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanfang Du
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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35
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Yang S, Chen D, Xie L, Zou X, Xiao Y, Rao L, Yao T, Zhang Q, Cai L, Huang F, Yang B, Huang L. Developmental dynamics of the single nucleus regulatory landscape of pig hippocampus. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2614-2628. [PMID: 37428306 DOI: 10.1007/s11427-022-2345-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/14/2023] [Indexed: 07/11/2023]
Abstract
The hippocampus is a brain region associated with memory, learning and spatial navigation, its aging-related dysfunction is a common sign of Alzheimer's disease. Pig is a good model for human neurodegenerative disease, but our understanding of the regulatory program of the pig hippocampus and its cross-species conservation in humans remains limited. Here, we profiled chromatin accessibility in 33,409 high-quality nuclei and gene expression in 8,122 high-quality nuclei of the pig hippocampus at four postnatal stages. We identified 510,908 accessible chromatin regions (ACRs) in 12 major cell types, among which progenitor cells such as neuroblasts and oligodendrocyte progenitor cells showed a dynamic decrease from early to later developmental stages. We revealed significant enrichment of transposable elements in cell type-specific ACRs, particularly in neuroblasts. We identified oligodendrocytes as the most prominent cell type with the greatest number of genes that showed significant changes during the development. We identified ACRs and key transcription factors underlying the trajectory of neurogenesis (such as POU3F3 and EGR1) and oligodendrocyte differentiation (RXRA and FOXO6). We examined 27 Alzheimer's disease-related genes in our data and found that 15 showed cell type-specific activity (TREM2, RIN3 and CLU), and 15 genes displayed age-associated dynamic activity (BIN1, RABEP1 and APOE). We intersected our data with human genome-wide association study results to detect neurological disease-associated cell types. The present study provides a single nucleus-accessible chromatin landscape of the pig hippocampus at different developmental stages and is helpful for the exploration of pigs as a biomedical model in human neurodegenerative diseases.
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Affiliation(s)
- Siyu Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dong Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lei Xie
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaoxiao Zou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yanyuan Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lin Rao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tianxiong Yao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qing Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Liping Cai
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Fei Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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36
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Gruber T, Lechner F, Murat C, Contreras RE, Sanchez-Quant E, Miok V, Makris K, Le Thuc O, González-García I, García-Clave E, Althammer F, Krabichler Q, DeCamp LM, Jones RG, Lutter D, Williams RH, Pfluger PT, Müller TD, Woods SC, Pospisilik JA, Martinez-Jimenez CP, Tschöp MH, Grinevich V, García-Cáceres C. High-calorie diets uncouple hypothalamic oxytocin neurons from a gut-to-brain satiation pathway via κ-opioid signaling. Cell Rep 2023; 42:113305. [PMID: 37864798 PMCID: PMC10636643 DOI: 10.1016/j.celrep.2023.113305] [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: 08/04/2022] [Revised: 08/21/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023] Open
Abstract
Oxytocin-expressing paraventricular hypothalamic neurons (PVNOT neurons) integrate afferent signals from the gut, including cholecystokinin (CCK), to adjust whole-body energy homeostasis. However, the molecular underpinnings by which PVNOT neurons orchestrate gut-to-brain feeding control remain unclear. Here, we show that mice undergoing selective ablation of PVNOT neurons fail to reduce food intake in response to CCK and develop hyperphagic obesity on a chow diet. Notably, exposing wild-type mice to a high-fat/high-sugar (HFHS) diet recapitulates this insensitivity toward CCK, which is linked to diet-induced transcriptional and electrophysiological aberrations specifically in PVNOT neurons. Restoring OT pathways in diet-induced obese (DIO) mice via chemogenetics or polypharmacology sufficiently re-establishes CCK's anorexigenic effects. Last, by single-cell profiling, we identify a specialized PVNOT neuronal subpopulation with increased κ-opioid signaling under an HFHS diet, which restrains their CCK-evoked activation. In sum, we document a (patho)mechanism by which PVNOT signaling uncouples a gut-brain satiation pathway under obesogenic conditions.
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Affiliation(s)
- Tim Gruber
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49506, USA; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49506, USA.
| | - Franziska Lechner
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Cahuê Murat
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Raian E Contreras
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Eva Sanchez-Quant
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, Neuherberg, Germany
| | - Viktorian Miok
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Konstantinos Makris
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ophélia Le Thuc
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Ismael González-García
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Elena García-Clave
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | | | - Quirin Krabichler
- Department of Neuropeptide Research in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Lisa M DeCamp
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49506, USA
| | - Russell G Jones
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49506, USA
| | - Dominik Lutter
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Rhiannan H Williams
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute for Neurogenomics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Paul T Pfluger
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Research Unit NeuroBiology of Diabetes, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Neurobiology of Diabetes, TUM School of Medicine, Technical University Munich, 80333 Munich, Germany
| | - Timo D Müller
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Department of Pharmacology and Experimental Therapy, Institute for Experimental and Clinical Pharmacology and Toxicology, Eberhard Karls Hospitals and Clinics, Tübingen, Germany
| | - Stephen C Woods
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
| | - John Andrew Pospisilik
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49506, USA; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49506, USA
| | - Celia P Martinez-Jimenez
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49506, USA; TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Matthias H Tschöp
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Division of Metabolic Diseases, Department of Medicine, Technische Universität, Munich, Germany
| | - Valery Grinevich
- Department of Neuropeptide Research in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; Center for Neuroinflammation and Cardiometabolic Diseases, Georgia State University, Atlanta, GA, USA.
| | - Cristina García-Cáceres
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, 80336 Munich, Germany.
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Niu Y, Cheng Y, Miao Z, Xu J, Jiang H, Yan J. Inhibitory neuron map of sevoflurane induced neurotoxicity model in young primates. Front Cell Neurosci 2023; 17:1252782. [PMID: 38026701 PMCID: PMC10643782 DOI: 10.3389/fncel.2023.1252782] [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: 07/04/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Sevoflurane, one of the most commonly used anesthetic agents in children, may induce neuronal dysfunction and cognitive impairment. Exposure to sevoflurane might induce an imbalance between neural excitation and inhibition which could be a mechanism behind anesthesia-induced cognitive and affective dysfunctions. However, the underlying mechanisms remain unclear. Methods In this study, we used two rhesus macaques in the control group, and one rhesus macaques in the anesthesia group. We employed single-nucleus RNA sequencing (snRNA-seq) technology to explore alterations in distinct types of inhibitory neurons involved in the long-term cognitive impairment caused by sevoflurane in young macaques. Results Following sevoflurane treatment, an upregulation was observed in the SST+ inhibitory neuron in the LHX6+ neighborhood in the hippocampus of rhesus macaques. This alteration might impact brain development by influencing interneuron migration and maturation. Additionally, we proposed a novel classification of inhibitory neurons, defined by CNR1 and LHX6 applicable to both humans and macaques. Discussion Our study proposed a novel classification of inhibitory neurons defined by LHX6 and CNR1, relevant in macaques and humans. We also provide evidence that sevoflurane upregulated the SST+ inhibitory neuron in the LHX6+ neighborhood in the hippocampus of rhesus macaques, which may underlie the potential neurotoxic effects induced by general anesthetics. Our results also offer a more reliable approach for studying the structure and function of the human brain.
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Affiliation(s)
| | | | | | | | | | - Jia Yan
- Department of Anesthesiology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Jing J, Hu M, Ngodup T, Ma Q, Lau SNN, Ljungberg C, McGinley MJ, Trussell LO, Jiang X. Comprehensive analysis of cellular specializations that initiate parallel auditory processing pathways in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.539065. [PMID: 37293040 PMCID: PMC10245571 DOI: 10.1101/2023.05.15.539065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The cochlear nuclear complex (CN) is the starting point for all central auditory processing and comprises a suite of neuronal cell types that are highly specialized for neural coding of acoustic signals. To examine how their striking functional specializations are determined at the molecular level, we performed single-nucleus RNA sequencing of the mouse CN to molecularly define all constituent cell types and related them to morphologically- and electrophysiologically-defined neurons using Patch-seq. We reveal an expanded set of molecular cell types encompassing all previously described major types and discover new subtypes both in terms of topographic and cell-physiologic properties. Our results define a complete cell-type taxonomy in CN that reconciles anatomical position, morphological, physiological, and molecular criteria. This high-resolution account of cellular heterogeneity and specializations from the molecular to the circuit level illustrates molecular underpinnings of functional specializations and enables genetic dissection of auditory processing and hearing disorders with unprecedented specificity.
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Affiliation(s)
- Junzhan Jing
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Ming Hu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Tenzin Ngodup
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | - Qianqian Ma
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shu-Ning Natalie Lau
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Cecilia Ljungberg
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew J. McGinley
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Laurence O. Trussell
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | - Xiaolong Jiang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, USA
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Yang L, Wang X, Zheng JX, Xu ZR, Li LC, Xiong YL, Zhou BC, Gao J, Xu CR. Determination of key events in mouse hepatocyte maturation at the single-cell level. Dev Cell 2023; 58:1996-2010.e6. [PMID: 37557173 DOI: 10.1016/j.devcel.2023.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 02/10/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
Hepatocytes, the liver's predominant cells, perform numerous essential biological functions. However, crucial events and regulators during hepatocyte maturation require in-depth investigation. In this study, we performed single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) to explore the precise hepatocyte development process in mice. We defined three maturation stages of postnatal hepatocytes, each of which establishes specific metabolic functions and exhibits distinct proliferation rates. Hepatic zonation is gradually formed during hepatocyte maturation. Hepatocytes or their nuclei with distinct ploidies exhibit zonation preferences in distribution and asynchrony in maturation. Moreover, by combining gene regulatory network analysis with in vivo genetic manipulation, we identified critical maturation- and zonation-related transcription factors. This study not only delineates the comprehensive transcriptomic profiles of hepatocyte maturation but also presents a paradigm to identify genes that function in the development of hepatocyte maturation and zonation by combining genetic manipulation and measurement of coordinates in a single-cell developmental trajectory.
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Affiliation(s)
- Li Yang
- Department of Human Anatomy, Histology, and Embryology, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xin Wang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jia-Xi Zheng
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Zi-Ran Xu
- PKU-Tsinghua-NIBS Graduate Program, Peking University, Beijing 100871, China
| | - Lin-Chen Li
- Department of Human Anatomy, Histology, and Embryology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yu-Long Xiong
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Bi-Chen Zhou
- Department of Human Anatomy, Histology, and Embryology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Jie Gao
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Cheng-Ran Xu
- Department of Human Anatomy, Histology, and Embryology, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; State Key Laboratory of Female Fertility Promotion, Peking University, Beijing 100191, China.
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Salamon I, Park Y, Miškić T, Kopić J, Matteson P, Page NF, Roque A, McAuliffe GW, Favate J, Garcia-Forn M, Shah P, Judaš M, Millonig JH, Kostović I, De Rubeis S, Hart RP, Krsnik Ž, Rasin MR. Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex. Nat Commun 2023; 14:6025. [PMID: 37758766 PMCID: PMC10533865 DOI: 10.1038/s41467-023-41730-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Abnormalities in neocortical and synaptic development are linked to neurodevelopmental disorders. However, the molecular and cellular mechanisms governing initial synapse formation in the prenatal neocortex remain poorly understood. Using polysome profiling coupled with snRNAseq on human cortical samples at various fetal phases, we identify human mRNAs, including those encoding synaptic proteins, with finely controlled translation in distinct cell populations of developing frontal neocortices. Examination of murine and human neocortex reveals that the RNA binding protein and translational regulator, CELF4, is expressed in compartments enriched in initial synaptogenesis: the marginal zone and the subplate. We also find that Celf4/CELF4-target mRNAs are encoded by risk genes for adverse neurodevelopmental outcomes translating into synaptic proteins. Surprisingly, deleting Celf4 in the forebrain disrupts the balance of subplate synapses in a sex-specific fashion. This highlights the significance of RNA binding proteins and mRNA translation in evolutionarily advanced synaptic development, potentially contributing to sex differences.
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Affiliation(s)
- Iva Salamon
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Rutgers University, School of Graduate Studies, New Brunswick, NJ, 08854, USA
| | - Yongkyu Park
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Terezija Miškić
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - Janja Kopić
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - Paul Matteson
- Center for Advanced Biotechnology and Medicine, Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Nicholas F Page
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Alfonso Roque
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Geoffrey W McAuliffe
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - John Favate
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Marta Garcia-Forn
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Miloš Judaš
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - James H Millonig
- Center for Advanced Biotechnology and Medicine, Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Ivica Kostović
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Željka Krsnik
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia.
| | - Mladen-Roko Rasin
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
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Stevenson ME, Bieri G, Kaletsky R, St Ange J, Remesal L, Pratt KJB, Zhou S, Weng Y, Murphy CT, Villeda SA. Neuronal activation of G αq EGL-30/GNAQ late in life rejuvenates cognition across species. Cell Rep 2023; 42:113151. [PMID: 37713310 PMCID: PMC10627507 DOI: 10.1016/j.celrep.2023.113151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/10/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023] Open
Abstract
Loss of cognitive function with age is devastating. EGL-30/GNAQ and Gαq signaling pathways are highly conserved between C. elegans and mammals, and murine Gnaq is enriched in hippocampal neurons and declines with age. We found that activation of EGL-30 in aged worms triples memory span, and GNAQ gain of function significantly improved memory in aged mice: GNAQ(gf) in hippocampal neurons of 24-month-old mice (equivalent to 70- to 80-year-old humans) rescued age-related impairments in well-being and memory. Single-nucleus RNA sequencing revealed increased expression of genes regulating synaptic function, axon guidance, and memory in GNAQ-treated mice, and worm orthologs of these genes were required for long-term memory extension in worms. These experiments demonstrate that C. elegans is a powerful model to identify mammalian regulators of memory, leading to the identification of a pathway that improves memory in extremely old mice. To our knowledge, this is the oldest age at which an intervention has improved age-related cognitive decline.
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Affiliation(s)
- Morgan E Stevenson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gregor Bieri
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar Aging Research Institute, San Francisco, CA 94143, USA
| | - Rachel Kaletsky
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan St Ange
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - L Remesal
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar Aging Research Institute, San Francisco, CA 94143, USA
| | - Karishma J B Pratt
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar Aging Research Institute, San Francisco, CA 94143, USA
| | - Shiyi Zhou
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yifei Weng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Coleen T Murphy
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Saul A Villeda
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar Aging Research Institute, San Francisco, CA 94143, USA.
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Fan LY, Yang J, Liu RY, Kong Y, Guo GY, Xu YM. Integrating single-nucleus sequence profiling to reveal the transcriptional dynamics of Alzheimer's disease, Parkinson's disease, and multiple sclerosis. J Transl Med 2023; 21:649. [PMID: 37735671 PMCID: PMC10515258 DOI: 10.1186/s12967-023-04516-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD), Parkinson's disease (PD), and multiple sclerosis (MS) are three nervous system diseases that partially overlap clinically and genetically. However, bulk RNA-sequencing did not accurately detect the core pathogenic molecules in them. The availability of high-quality single cell RNA-sequencing data of post-mortem brain collections permits the generation of a large-scale gene expression in different cells in human brain, focusing on the molecular features and relationships between diseases and genes. We integrated single-nucleus RNA-sequencing (snRNA-seq) datasets of human brains with AD, PD, and MS to identify transcriptomic commonalities and distinctions among them. METHODS The snRNA-seq datasets were downloaded from Gene Expression Omnibus (GEO) database. The Seurat package was used for snRNA-seq data processing. The uniform manifold approximation and projection (UMAP) were utilized for cluster identification. The FindMarker function in Seurat was used to identify the differently expressed genes. Functional enrichment analysis was carried out using the Gene Set Enrichment Analysis (GSEA) and Gene ontology (GO). The protein-protein interaction (PPI) analysis of differentially expressed genes (DEGs) was analyzed using STRING database ( http://string-db.org ). SCENIC analysis was performed using utilizing pySCENIC (v0.10.0) based on the hg19-tss-centered-10 kb-10species databases. The analysis of potential therapeutic drugs was analyzed on Connectivity Map ( https://clue.io ). RESULTS The gene regulatory network analysis identified several hub genes regulated in AD, PD, and MS, in which HSPB1 and HSPA1A were key molecules. These upregulated HSP family genes interact with ribosome genes in AD and MS, and with immunomodulatory genes in PD. We further identified several transcriptional regulators (SPI1, CEBPA, TFE3, GRHPR, and TP53) of the hub genes, which has important implications for uncovering the molecular crosstalk among AD, PD, and MS. Arctigenin was identified as a potential therapeutic drug for AD, PD, and MS. CONCLUSIONS Together, the integrated snRNA-seq data and findings have significant implications for unraveling the shared and unique molecular crosstalk among AD, PD, and MS. HSPB1 and HSPA1A as promising targets involved in the pathological mechanisms of neurodegenerative diseases. Additionally, the identification of arctigenin as a potential therapeutic drug for AD, PD, and MS further highlights its potential in treating these neurological disorders. These discoveries lay the groundwork for future research and interventions to enhance our understanding and treatment of AD, PD, and MS.
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Affiliation(s)
- Li-Yuan Fan
- Department of Neurology, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Jing Yang
- Department of Neurology, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Ruo-Yu Liu
- Department of Neurology, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Ying Kong
- Department of Neurology, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Guang-Yu Guo
- Department of Neurology, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China.
| | - Yu-Ming Xu
- Department of Neurology, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China.
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Niu M, Cao W, Wang Y, Zhu Q, Luo J, Wang B, Zheng H, Weitz DA, Zong C. Droplet-based transcriptome profiling of individual synapses. Nat Biotechnol 2023; 41:1332-1344. [PMID: 36646931 DOI: 10.1038/s41587-022-01635-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/06/2022] [Indexed: 01/17/2023]
Abstract
Synapses are crucial structures that mediate signal transmission between neurons in complex neural circuits and display considerable morphological and electrophysiological heterogeneity. So far we still lack a high-throughput method to profile the molecular heterogeneity among individual synapses. In the present study, we develop a droplet-based single-cell (sc) total-RNA-sequencing platform, called Multiple-Annealing-and-Tailing-based Quantitative scRNA-seq in Droplets, for transcriptome profiling of individual neurites, primarily composed of synaptosomes. In the synaptosome transcriptome, or 'synaptome', profiling of both mouse and human brain samples, we detect subclusters among synaptosomes that are associated with neuronal subtypes and characterize the landscape of transcript splicing that occurs within synapses. We extend synaptome profiling to synaptopathy in an Alzheimer's disease (AD) mouse model and discover AD-associated synaptic gene expression changes that cannot be detected by single-nucleus transcriptome profiling. Overall, our results show that this platform provides a high-throughput, single-synaptosome transcriptome profiling tool that will facilitate future discoveries in neuroscience.
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Affiliation(s)
- Muchun Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Wenjian Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston, TX, USA
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, China
| | - Yongcheng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Wyss Institute of Bioinspired Engineering, Harvard University, Cambridge, MA, USA
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Qiangyuan Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, China
| | - Jiayi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Baiping Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Hui Zheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - David A Weitz
- Wyss Institute of Bioinspired Engineering, Harvard University, Cambridge, MA, USA.
- Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- McNair Medical Institute, Baylor College of Medicine, Houston, TX, USA.
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Daniels RR, Taylor RS, Robledo D, Macqueen DJ. Single cell genomics as a transformative approach for aquaculture research and innovation. REVIEWS IN AQUACULTURE 2023; 15:1618-1637. [PMID: 38505116 PMCID: PMC10946576 DOI: 10.1111/raq.12806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/21/2024]
Abstract
Single cell genomics encompasses a suite of rapidly maturing technologies that measure the molecular profiles of individual cells within target samples. These approaches provide a large up-step in biological information compared to long-established 'bulk' methods that profile the average molecular profiles of all cells in a sample, and have led to transformative advances in understanding of cellular biology, particularly in humans and model organisms. The application of single cell genomics is fast expanding to non-model taxa, including aquaculture species, where numerous research applications are underway with many more envisaged. In this review, we highlight the potential transformative applications of single cell genomics in aquaculture research, considering barriers and potential solutions to the broad uptake of these technologies. Focusing on single cell transcriptomics, we outline considerations for experimental design, including the essential requirement to obtain high quality cells/nuclei for sequencing in ectothermic aquatic species. We further outline data analysis and bioinformatics considerations, tailored to studies with the under-characterized genomes of aquaculture species, where our knowledge of cellular heterogeneity and cell marker genes is immature. Overall, this review offers a useful source of knowledge for researchers aiming to apply single cell genomics to address biological challenges faced by the global aquaculture sector though an improved understanding of cell biology.
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Affiliation(s)
- Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Richard S. Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
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Yang HJ, Seo SI, Lee J, Huh CW, Kim JS, Park JC, Kim H, Shin H, Shin CM, Park CH, Lee SK. Sample Collection Methods in Upper Gastrointestinal Research. J Korean Med Sci 2023; 38:e255. [PMID: 37582502 PMCID: PMC10427214 DOI: 10.3346/jkms.2023.38.e255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/16/2023] [Indexed: 08/17/2023] Open
Abstract
In recent years, significant translational research advances have been made in the upper gastrointestinal (GI) research field. Endoscopic evaluation is a reasonable option for acquiring upper GI tissue for research purposes because it has minimal risk and can be applied to unresectable gastric cancer. The optimal number of biopsy samples and sample storage is crucial and might influence results. Furthermore, the methods for sample acquisition can be applied differently according to the research purpose; however, there have been few reports on methods for sample collection from endoscopic biopsies. In this review, we suggested a protocol for collecting study samples for upper GI research, including microbiome, DNA, RNA, protein, single-cell RNA sequencing, and organoid culture, through a comprehensive literature review. For microbiome analysis, one or two pieces of biopsied material obtained using standard endoscopic forceps may be sufficient. Additionally, 5 mL of gastric fluid and 3-4 mL of saliva is recommended for microbiome analyses. At least one gastric biopsy tissue is necessary for most DNA or RNA analyses, while proteomics analysis may require at least 2-3 biopsy tissues. Single cell-RNA sequencing requires at least 3-5 tissues and additional 1-2 tissues, if possible. For successful organoid culture, multiple sampling is necessary to improve the quality of specimens.
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Affiliation(s)
- Hyo-Joon Yang
- Division of Gastroenterology, Department of Internal Medicine and Gastrointestinal Cancer Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung In Seo
- Division of Gastroenterology, Department of Internal Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Jin Lee
- Department of Internal Medicine, Inje University College of Medicine, Haeundae Paik Hospital, Busan, Korea
| | - Cheal Wung Huh
- Division of Gastroenterology, Department of Internal Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, Korea
| | - Joon Sung Kim
- Division of Gastroenterology, Department of Internal Medicine, College of Medicine, Incheon St. Mary's Hospital, The Catholic University of Korea, Incheon, Korea
| | - Jun Chul Park
- Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Hyunki Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Hakdong Shin
- Department of Food Science and Biotechnology, Sejong University, Seoul, Korea
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Chan Hyuk Park
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea.
| | - Sang Kil Lee
- Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea.
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Chen C, Ge Y, Lu L. Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1185377. [PMID: 37636094 PMCID: PMC10453814 DOI: 10.3389/fpls.2023.1185377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023]
Abstract
Single-cell and spatial transcriptomics have diverted researchers' attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research.
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Affiliation(s)
- Ce Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yining Ge
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lingli Lu
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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van den Oord EJCG, Aberg KA. Fine-grained cell-type specific association studies with human bulk brain data using a large single-nucleus RNA sequencing based reference panel. Sci Rep 2023; 13:13004. [PMID: 37563216 PMCID: PMC10415334 DOI: 10.1038/s41598-023-39864-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Brain disorders are leading causes of disability worldwide. Gene expression studies provide promising opportunities to better understand their etiology but it is critical that expression is studied on a cell-type level. Cell-type specific association studies can be performed with bulk expression data using statistical methods that capitalize on cell-type proportions estimated with the help of a reference panel. To create a fine-grained reference panel for the human prefrontal cortex, we performed an integrated analysis of the seven largest single nucleus RNA-seq studies. Our panel included 17 cell-types that were robustly detected across all studies, subregions of the prefrontal cortex, and sex and age groups. To estimate the cell-type proportions, we used an empirical Bayes estimator that substantially outperformed three estimators recommended previously after a comprehensive evaluation of methods to estimate cell-type proportions from brain transcriptome data. This is important as being able to precisely estimate the cell-type proportions may avoid unreliable results in downstream analyses particularly for the multiple cell-types that had low abundances. Transcriptome-wide association studies performed with permuted bulk expression data showed that it is possible to perform transcriptome-wide association studies for even the rarest cell-types without an increased risk of false positives.
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Affiliation(s)
- Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, McGuire Hall, Room 216A, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA.
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, McGuire Hall, Room 216A, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA
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Lischetti U, Tastanova A, Singer F, Grob L, Carrara M, Cheng PF, Martínez Gómez JM, Sella F, Haunerdinger V, Beisel C, Levesque MP. Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma. Commun Biol 2023; 6:830. [PMID: 37563418 PMCID: PMC10415364 DOI: 10.1038/s42003-023-05182-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
Multi-omics profiling by CITE-seq bridges the RNA-protein gap in single-cell analysis but has been largely applied to liquid biopsies. Applying CITE-seq to clinically relevant solid biopsies to characterize healthy tissue and the tumor microenvironment is an essential next step in single-cell translational studies. In this study, gating of cell populations based on their transcriptome signatures for use in cell type-specific ridge plots allowed identification of positive antibody signals and setting of manual thresholds. Next, we compare five skin dissociation protocols by taking into account dissociation efficiency, captured cell type heterogeneity and recovered surface proteome. To assess the effect of enzymatic digestion on transcriptome and epitope expression in immune cell populations, we analyze peripheral blood mononuclear cells (PBMCs) with and without dissociation. To further assess the RNA-protein gap, RNA-protein we perform codetection and correlation analyses on thresholded protein values. Finally, in a proof-of-concept study, using protein abundance analysis on selected surface markers in a cohort of healthy skin, primary, and metastatic melanoma we identify CD56 surface marker expression on metastatic melanoma cells, which was further confirmed by multiplex immunohistochemistry. This work provides practical guidelines for processing and analysis of clinically relevant solid tissue biopsies for biomarker discovery.
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Affiliation(s)
- Ulrike Lischetti
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
- Department of Biomedicine, University Hospital Basel, University of Basel, 4031, Basel, Switzerland
| | - Aizhan Tastanova
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - Franziska Singer
- ETH Zurich, NEXUS Personalized Health Technologies, Wagistrasse 18, 8952, Schlieren, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Linda Grob
- ETH Zurich, NEXUS Personalized Health Technologies, Wagistrasse 18, 8952, Schlieren, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Matteo Carrara
- ETH Zurich, NEXUS Personalized Health Technologies, Wagistrasse 18, 8952, Schlieren, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Phil F Cheng
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julia M Martínez Gómez
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Sella
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Veronika Haunerdinger
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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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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