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Matsuo K, Nshihara H. Rebuilding insight into the pathophysiology of Alzheimer's disease through new blood-brain barrier models. Neural Regen Res 2024; 19:1954-1960. [PMID: 38227521 DOI: 10.4103/1673-5374.390978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/01/2023] [Indexed: 01/17/2024] Open
Abstract
The blood-brain barrier is a unique function of the microvasculature in the brain parenchyma that maintains homeostasis in the central nervous system. Blood-brain barrier breakdown is a common pathology in various neurological diseases, such as Alzheimer's disease, stroke, multiple sclerosis, and Parkinson's disease. Traditionally, it has been considered a consequence of neuroinflammation or neurodegeneration, but recent advanced imaging techniques and detailed studies in animal models show that blood-brain barrier breakdown occurs early in the disease process and may precede neuronal loss. Thus, the blood-brain barrier is attractive as a potential therapeutic target for neurological diseases that lack effective therapeutics. To elucidate the molecular mechanism underlying blood-brain barrier breakdown and translate them into therapeutic strategies for neurological diseases, there is a growing demand for experimental models of human origin that allow for functional assessments. Recently, several human induced pluripotent stem cell-derived blood-brain barrier models have been established and various in vitro blood-brain barrier models using microdevices have been proposed. Especially in the Alzheimer's disease field, the human evidence for blood-brain barrier dysfunction has been demonstrated and human induced pluripotent stem cell-derived blood-brain barrier models have suggested the putative molecular mechanisms of pathological blood-brain barrier. In this review, we summarize recent evidence of blood-brain barrier dysfunction in Alzheimer's disease from pathological analyses, imaging studies, animal models, and stem cell sources. Additionally, we discuss the potential future directions for blood-brain barrier research.
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Affiliation(s)
- Kinya Matsuo
- Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Hideaki Nshihara
- Department of Neurotherapeutics, Yamaguchi University, Ube, Japan
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2
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Tung YT, Chen YC, Derr K, Wilson K, Song MJ, Ferrer M. A 3D Bioprinted Human Neurovascular Unit Model of Glioblastoma Tumor Growth. Adv Healthc Mater 2024; 13:e2302831. [PMID: 38394389 DOI: 10.1002/adhm.202302831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/29/2024] [Indexed: 02/25/2024]
Abstract
A 3D bioprinted neurovascular unit (NVU) model is developed to study glioblastoma (GBM) tumor growth in a brain-like microenvironment. The NVU model includes human primary astrocytes, pericytes and brain microvascular endothelial cells, and patient-derived glioblastoma cells (JHH-520) are used for this study. Fluorescence reporters are used with confocal high content imaging to quantitate real-time microvascular network formation and tumor growth. Extensive validation of the NVU-GBM model includes immunostaining for brain relevant cellular markers and extracellular matrix components; single cell RNA sequencing (scRNAseq) to establish physiologically relevant transcriptomics changes; and secretion of NVU and GBM-relevant cytokines. The scRNAseq reveals changes in gene expression and cytokines secretion associated with wound healing/angiogenesis, including the appearance of an endothelial mesenchymal transition cell population. The NVU-GBM model is used to test 18 chemotherapeutics and anti-cancer drugs to assess the pharmacological relevance of the model and robustness for high throughput screening.
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Affiliation(s)
- Yen-Ting Tung
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Yu-Chi Chen
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Kristy Derr
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Kelli Wilson
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Min Jae Song
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
| | - Marc Ferrer
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA
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3
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Matsui Y, Togayachi A, Sakamoto K, Angata K, Kadomatsu K, Nishihara S. Integrated Systems Analysis Deciphers Transcriptome and Glycoproteome Links in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.25.573290. [PMID: 38234803 PMCID: PMC10793412 DOI: 10.1101/2023.12.25.573290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Glycosylation is increasingly recognized as a potential therapeutic target in Alzheimer's disease. In recent years, evidence of Alzheimer's disease-specific glycoproteins has been established. However, the mechanisms underlying their dysregulation, including tissue- and cell-type specificity, are not fully understood. We aimed to explore the upstream regulators of aberrant glycosylation by integrating multiple data sources using a glycogenomics approach. We identified dysregulation of the glycosyltransferase PLOD3 in oligodendrocytes as an upstream regulator of cerebral vessels and found that it is involved in COL4A5 synthesis, which is strongly correlated with amyloid fiber formation. Furthermore, COL4A5 has been suggested to interact with astrocytes via extracellular matrix receptors as a ligand. This study suggests directions for new therapeutic strategies for Alzheimer's disease targeting glycosyltransferases.
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Affiliation(s)
- Yusuke Matsui
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Biomedical and Health Informatics Unit, Department of Integrated Health Science, Nagoya University Graduate School of Medicine, Daiko-minami, Higashi-ku, Nagoya, 461-8673, Japan
| | - Akira Togayachi
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Kazuma Sakamoto
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kiyohiko Angata
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Kenji Kadomatsu
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Shoko Nishihara
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
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Rajput P, Brookshier A, Kothari S, Eckstein L, Chang H, Liska S, Lamb J, Sances S, Lyden P. Differential Vulnerability and Response to Injury among Brain Cell Types Comprising the Neurovascular Unit. J Neurosci 2024; 44:e1093222024. [PMID: 38548341 PMCID: PMC11140689 DOI: 10.1523/jneurosci.1093-22.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 02/29/2024] [Accepted: 03/11/2024] [Indexed: 05/31/2024] Open
Abstract
The neurovascular unit (NVU) includes multiple different cell types, including neurons, astrocytes, endothelial cells, and pericytes, which respond to insults on very different time or dose scales. We defined differential vulnerability among these cell types, using response to two different insults: oxygen-glucose deprivation (OGD) and thrombin-mediated cytotoxicity. We found that neurons are most vulnerable, followed by endothelial cells and astrocytes. After temporary focal cerebral ischemia in male rats, we found significantly more injured neurons, compared with astrocytes in the ischemic area, consistent with differential vulnerability in vivo. We sought to illustrate different and shared mechanisms across all cell types during response to insult. We found that gene expression profiles in response to OGD differed among the cell types, with a paucity of gene responses shared by all types. All cell types activated genes relating to autophagy, apoptosis, and necroptosis, but the specific genes differed. Astrocytes and endothelial cells also activated pathways connected to DNA repair and antiapoptosis. Taken together, the data support the concept of differential vulnerability in the NVU and suggest that different elements of the unit will evolve from salvageable to irretrievable on different time scales while residing in the same brain region and receiving the same (ischemic) blood flow. Future work will focus on the mechanisms of these differences. These data suggest future stroke therapy development should target different elements of the NVU differently.
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Affiliation(s)
- Padmesh Rajput
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of USC, Los Angeles, California 90089-2821
| | - Allison Brookshier
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of USC, Los Angeles, California 90089-2821
| | - Shweta Kothari
- Chinook Therapeutics, Inc., Vancouver, British Columbia V5T 4T5, Canada
- Cedars-Sinai Medical Center, Los Angeles, California 90048
| | - Lillie Eckstein
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of USC, Los Angeles, California 90089-2821
| | - Heather Chang
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of USC, Los Angeles, California 90089-2821
| | - Sophie Liska
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of USC, Los Angeles, California 90089-2821
| | - Jessica Lamb
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of USC, Los Angeles, California 90089-2821
| | - Samuel Sances
- Cedars-Sinai Medical Center, Los Angeles, California 90048
| | - Patrick Lyden
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of USC, Los Angeles, California 90089-2821
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Buonfiglioli A, Kübler R, Missall R, Jong RD, Chan S, Haage V, Wendt S, Lin AJ, Mattei D, Graziani M, Latour B, Gigase F, Nygaard HB, De Jager PL, De Witte LD. A microglia-containing cerebral organoid model to study early life immune challenges. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595814. [PMID: 38826204 PMCID: PMC11142229 DOI: 10.1101/2024.05.24.595814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Prenatal infections and activation of the maternal immune system have been proposed to contribute to causing neurodevelopmental disorders (NDDs), chronic conditions often linked to brain abnormalities. Microglia are the resident immune cells of the brain and play a key role in neurodevelopment. Disruption of microglial functions can lead to brain abnormalities and increase the risk of developing NDDs. How the maternal as well as the fetal immune system affect human neurodevelopment and contribute to NDDs remains unclear. An important reason for this knowledge gap is the fact that the impact of exposure to prenatal risk factors has been challenging to study in the human context. Here, we characterized a model of cerebral organoids (CO) with integrated microglia (COiMg). These organoids express typical microglial markers and respond to inflammatory stimuli. The presence of microglia influences cerebral organoid development, including cell density and neural differentiation, and regulates the expression of several ciliated mesenchymal cell markers. Moreover, COiMg and organoids without microglia show similar but also distinct responses to inflammatory stimuli. Additionally, IFN-γ induced significant transcriptional and structural changes in the cerebral organoids, that appear to be regulated by the presence of microglia. Specifically, interferon-gamma (IFN-γ) was found to alter the expression of genes linked to autism. This model provides a valuable tool to study how inflammatory perturbations and microglial presence affect neurodevelopmental processes.
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Le Grand Q, Tsuchida A, Koch A, Imtiaz MA, Aziz NA, Vigneron C, Zago L, Lathrop M, Dubrac A, Couffinhal T, Crivello F, Matthews PM, Mishra A, Breteler MMB, Tzourio C, Debette S. Diffusion imaging genomics provides novel insight into early mechanisms of cerebral small vessel disease. Mol Psychiatry 2024:10.1038/s41380-024-02604-7. [PMID: 38811690 DOI: 10.1038/s41380-024-02604-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024]
Abstract
Cerebral small vessel disease (cSVD) is a leading cause of stroke and dementia. Genetic risk loci for white matter hyperintensities (WMH), the most common MRI-marker of cSVD in older age, were recently shown to be significantly associated with white matter (WM) microstructure on diffusion tensor imaging (signal-based) in young adults. To provide new insights into these early changes in WM microstructure and their relation with cSVD, we sought to explore the genetic underpinnings of cutting-edge tissue-based diffusion imaging markers across the adult lifespan. We conducted a genome-wide association study of neurite orientation dispersion and density imaging (NODDI) markers in young adults (i-Share study: N = 1 758, (mean[range]) 22.1[18-35] years), with follow-up in young middle-aged (Rhineland Study: N = 714, 35.2[30-40] years) and late middle-aged to older individuals (UK Biobank: N = 33 224, 64.3[45-82] years). We identified 21 loci associated with NODDI markers across brain regions in young adults. The most robust association, replicated in both follow-up cohorts, was with Neurite Density Index (NDI) at chr5q14.3, a known WMH locus in VCAN. Two additional loci were replicated in UK Biobank, at chr17q21.2 with NDI, and chr19q13.12 with Orientation Dispersion Index (ODI). Transcriptome-wide association studies showed associations of STAT3 expression in arterial and adipose tissue (chr17q21.2) with NDI, and of several genes at chr19q13.12 with ODI. Genetic susceptibility to larger WMH volume, but not to vascular risk factors, was significantly associated with decreased NDI in young adults, especially in regions known to harbor WMH in older age. Individually, seven of 25 known WMH risk loci were associated with NDI in young adults. In conclusion, we identified multiple novel genetic risk loci associated with NODDI markers, particularly NDI, in early adulthood. These point to possible early-life mechanisms underlying cSVD and to processes involving remyelination, neurodevelopment and neurodegeneration, with a potential for novel approaches to prevention.
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Affiliation(s)
- Quentin Le Grand
- University of Bordeaux, INSERM, Bordeaux Population Health research center, UMR1219, F-33000, Bordeaux, France
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ami Tsuchida
- University of Bordeaux, INSERM, Bordeaux Population Health research center, UMR1219, F-33000, Bordeaux, France
- University of Bordeaux, Institute of Neurodegenerative Diseases, UMR5293, Neurofunctional Imaging Group, F-33000, Bordeaux, France
- CNRS, Institute of Neurodegenerative Diseases, UMR5293, Neurofunctional Imaging Group, F-33000, Bordeaux, France
- CEA, Institute of Neurodegenerative Diseases, UMR5293, Neurofunctional Imaging Group, F-33000, Bordeaux, France
| | - Alexandra Koch
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Mohammed-Aslam Imtiaz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - N Ahmad Aziz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Chloé Vigneron
- University of Bordeaux, INSERM, Bordeaux Population Health research center, UMR1219, F-33000, Bordeaux, France
| | - Laure Zago
- University of Bordeaux, Institute of Neurodegenerative Diseases, UMR5293, Neurofunctional Imaging Group, F-33000, Bordeaux, France
- CNRS, Institute of Neurodegenerative Diseases, UMR5293, Neurofunctional Imaging Group, F-33000, Bordeaux, France
- CEA, Institute of Neurodegenerative Diseases, UMR5293, Neurofunctional Imaging Group, F-33000, Bordeaux, France
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada; Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, QC, H3A 0G1, Canada
| | - Alexandre Dubrac
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, QC, Canada
- Département d'Ophtalmologie, Université de Montréal, Montréal, QC, Canada
| | - Thierry Couffinhal
- University of Bordeaux, INSERM, Biologie des maladies cardiovasculaires, U1034, F-33600, Pessac, France
| | - Fabrice Crivello
- University of Bordeaux, Institute of Neurodegenerative Diseases, UMR5293, Neurofunctional Imaging Group, F-33000, Bordeaux, France
- CNRS, Institute of Neurodegenerative Diseases, UMR5293, Neurofunctional Imaging Group, F-33000, Bordeaux, France
- CEA, Institute of Neurodegenerative Diseases, UMR5293, Neurofunctional Imaging Group, F-33000, Bordeaux, France
| | - Paul M Matthews
- UK Dementia Research Institute and Department of Brain Sciences, Imperial College, London, UK
| | - Aniket Mishra
- University of Bordeaux, INSERM, Bordeaux Population Health research center, UMR1219, F-33000, Bordeaux, France
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Christophe Tzourio
- University of Bordeaux, INSERM, Bordeaux Population Health research center, UMR1219, F-33000, Bordeaux, France
- Bordeaux University Hospital, Department of Medical Informatics, F-33000, Bordeaux, France
| | - Stéphanie Debette
- University of Bordeaux, INSERM, Bordeaux Population Health research center, UMR1219, F-33000, Bordeaux, France.
- Bordeaux University Hospital, Department of Neurology, Institute for Neurodegenerative Diseases, F-33000, Bordeaux, France.
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7
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Sullivan JM, Bagnell AM, Alevy J, Avila EM, Mihaljević L, Saavedra-Rivera PC, Kong L, Huh JS, McCray BA, Aisenberg WH, Zuberi AR, Bogdanik L, Lutz CM, Qiu Z, Quinlan KA, Searson PC, Sumner CJ. Gain-of-function mutations of TRPV4 acting in endothelial cells drive blood-CNS barrier breakdown and motor neuron degeneration in mice. Sci Transl Med 2024; 16:eadk1358. [PMID: 38776392 DOI: 10.1126/scitranslmed.adk1358] [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: 08/03/2023] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
Blood-CNS barrier disruption is a hallmark of numerous neurological disorders, yet whether barrier breakdown is sufficient to trigger neurodegenerative disease remains unresolved. Therapeutic strategies to mitigate barrier hyperpermeability are also limited. Dominant missense mutations of the cation channel transient receptor potential vanilloid 4 (TRPV4) cause forms of hereditary motor neuron disease. To gain insights into the cellular basis of these disorders, we generated knock-in mouse models of TRPV4 channelopathy by introducing two disease-causing mutations (R269C and R232C) into the endogenous mouse Trpv4 gene. TRPV4 mutant mice exhibited weakness, early lethality, and regional motor neuron loss. Genetic deletion of the mutant Trpv4 allele from endothelial cells (but not neurons, glia, or muscle) rescued these phenotypes. Symptomatic mutant mice exhibited focal disruptions of blood-spinal cord barrier (BSCB) integrity, associated with a gain of function of mutant TRPV4 channel activity in neural vascular endothelial cells (NVECs) and alterations of NVEC tight junction structure. Systemic administration of a TRPV4-specific antagonist abrogated channel-mediated BSCB impairments and provided a marked phenotypic rescue of symptomatic mutant mice. Together, our findings show that mutant TRPV4 channels can drive motor neuron degeneration in a non-cell autonomous manner by precipitating focal breakdown of the BSCB. Further, these data highlight the reversibility of TRPV4-mediated BSCB impairments and identify a potential therapeutic strategy for patients with TRPV4 mutations.
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Affiliation(s)
- Jeremy M Sullivan
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anna M Bagnell
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jonathan Alevy
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elvia Mena Avila
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Ljubica Mihaljević
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Lingling Kong
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jennifer S Huh
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Brett A McCray
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William H Aisenberg
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | - Zhaozhu Qiu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Katharina A Quinlan
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Peter C Searson
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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8
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Porkoláb G, Mészáros M, Szecskó A, Vigh JP, Walter FR, Figueiredo R, Kálomista I, Hoyk Z, Vizsnyiczai G, Gróf I, Jan JS, Gosselet F, Pirity MK, Vastag M, Hudson N, Campbell M, Veszelka S, Deli MA. Synergistic induction of blood-brain barrier properties. Proc Natl Acad Sci U S A 2024; 121:e2316006121. [PMID: 38748577 PMCID: PMC11126970 DOI: 10.1073/pnas.2316006121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/05/2024] [Indexed: 05/27/2024] Open
Abstract
Blood-brain barrier (BBB) models derived from human stem cells are powerful tools to improve our understanding of cerebrovascular diseases and to facilitate drug development for the human brain. Yet providing stem cell-derived endothelial cells with the right signaling cues to acquire BBB characteristics while also retaining their vascular identity remains challenging. Here, we show that the simultaneous activation of cyclic AMP and Wnt/β-catenin signaling and inhibition of the TGF-β pathway in endothelial cells robustly induce BBB properties in vitro. To target this interaction, we present a small-molecule cocktail named cARLA, which synergistically enhances barrier tightness in a range of BBB models across species. Mechanistically, we reveal that the three pathways converge on Wnt/β-catenin signaling to mediate the effect of cARLA via the tight junction protein claudin-5. We demonstrate that cARLA shifts the gene expressional profile of human stem cell-derived endothelial cells toward the in vivo brain endothelial signature, with a higher glycocalyx density and efflux pump activity, lower rates of endocytosis, and a characteristic endothelial response to proinflammatory cytokines. Finally, we illustrate how cARLA can improve the predictive value of human BBB models regarding the brain penetration of drugs and targeted nanoparticles. Due to its synergistic effect, high reproducibility, and ease of use, cARLA has the potential to advance drug development for the human brain by improving BBB models across laboratories.
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Affiliation(s)
- Gergő Porkoláb
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
- Doctoral School of Biology, University of Szeged, SzegedH-6720, Hungary
| | - Mária Mészáros
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
| | - Anikó Szecskó
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
- Doctoral School of Biology, University of Szeged, SzegedH-6720, Hungary
| | - Judit P. Vigh
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
- Doctoral School of Biology, University of Szeged, SzegedH-6720, Hungary
| | - Fruzsina R. Walter
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
| | | | - Ildikó Kálomista
- In Vitro Metabolism Laboratory, Gedeon Richter, BudapestH-1103, Hungary
| | - Zsófia Hoyk
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
| | - Gaszton Vizsnyiczai
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
| | - Ilona Gróf
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
| | - Jeng-Shiung Jan
- Department of Chemical Engineering, National Cheng Kung University, Tainan70101, Taiwan
| | - Fabien Gosselet
- Laboratoire de la Barriére Hémato-Encéphalique, Université d’Artois, Lens62307, France
| | - Melinda K. Pirity
- Institute of Genetics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
| | - Monika Vastag
- In Vitro Metabolism Laboratory, Gedeon Richter, BudapestH-1103, Hungary
| | - Natalie Hudson
- Smurfit Institute of Genetics, Trinity College Dublin, DublinD02 VF25, Ireland
| | - Matthew Campbell
- Smurfit Institute of Genetics, Trinity College Dublin, DublinD02 VF25, Ireland
| | - Szilvia Veszelka
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
| | - Mária A. Deli
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, SzegedH-6726, Hungary
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9
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Wojtas AM, Dammer EB, Guo Q, Ping L, Shantaraman A, Duong DM, Yin L, Fox EJ, Seifar F, Lee EB, Johnson ECB, Lah JJ, Levey AI, Levites Y, Rangaraju S, Golde TE, Seyfried NT. Proteomic changes in the human cerebrovasculature in Alzheimer's disease and related tauopathies linked to peripheral biomarkers in plasma and cerebrospinal fluid. Alzheimers Dement 2024. [PMID: 38713744 DOI: 10.1002/alz.13821] [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: 01/25/2024] [Revised: 02/21/2024] [Accepted: 03/02/2024] [Indexed: 05/09/2024]
Abstract
INTRODUCTION Cerebrovascular dysfunction is a pathological hallmark of Alzheimer's disease (AD). Nevertheless, detecting cerebrovascular changes within bulk tissues has limited our ability to characterize proteomic alterations from less abundant cell types. METHODS We conducted quantitative proteomics on bulk brain tissues and isolated cerebrovasculature from the same individuals, encompassing control (N = 28), progressive supranuclear palsy (PSP) (N = 18), and AD (N = 21) cases. RESULTS Protein co-expression network analysis identified unique cerebrovascular modules significantly correlated with amyloid plaques, cerebrovascular amyloid angiopathy (CAA), and/or tau pathology. The protein products within AD genetic risk loci were concentrated within cerebrovascular modules. The overlap between differentially abundant proteins in AD cerebrospinal fluid (CSF) and plasma with cerebrovascular network highlighted a significant increase of matrisome proteins, SMOC1 and SMOC2, in CSF, plasma, and brain. DISCUSSION These findings enhance our understanding of cerebrovascular deficits in AD, shedding light on potential biomarkers associated with CAA and vascular dysfunction in neurodegenerative diseases.
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Affiliation(s)
- Aleksandra M Wojtas
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Qi Guo
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ananth Shantaraman
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Edward J Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Fatemeh Seifar
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Edward B Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Pennsylvania, USA
| | - Erik C B Johnson
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James J Lah
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Allan I Levey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yona Levites
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Srikant Rangaraju
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Todd E Golde
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
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10
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Enström A, Carlsson R, Buizza C, Lewi M, Paul G. Pericyte-Specific Secretome Profiling in Hypoxia Using TurboID in a Multicellular in Vitro Spheroid Model. Mol Cell Proteomics 2024; 23:100782. [PMID: 38705386 DOI: 10.1016/j.mcpro.2024.100782] [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: 08/22/2023] [Revised: 04/09/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024] Open
Abstract
Cellular communication within the brain is imperative for maintaining homeostasis and mounting effective responses to pathological triggers like hypoxia. However, a comprehensive understanding of the precise composition and dynamic release of secreted molecules has remained elusive, confined primarily to investigations using isolated monocultures. To overcome these limitations, we utilized the potential of TurboID, a non-toxic biotin ligation enzyme, to capture and enrich secreted proteins specifically originating from human brain pericytes in spheroid cocultures with human endothelial cells and astrocytes. This approach allowed us to characterize the pericyte secretome within a more physiologically relevant multicellular setting encompassing the constituents of the blood-brain barrier. Through a combination of mass spectrometry and multiplex immunoassays, we identified a wide spectrum of different secreted proteins by pericytes. Our findings demonstrate that the pericytes secretome is profoundly shaped by their intercellular communication with other blood-brain barrier-residing cells. Moreover, we identified substantial differences in the secretory profiles between hypoxic and normoxic pericytes. Mass spectrometry analysis showed that hypoxic pericytes in coculture increase their release of signals related to protein secretion, mTOR signaling, and the complement system, while hypoxic pericytes in monocultures showed an upregulation in proliferative pathways including G2M checkpoints, E2F-, and Myc-targets. In addition, hypoxic pericytes show an upregulation of proangiogenic proteins such as VEGFA but display downregulation of canonical proinflammatory cytokines such as CXCL1, MCP-1, and CXCL6. Understanding the specific composition of secreted proteins in the multicellular brain microvasculature is crucial for advancing our knowledge of brain homeostasis and the mechanisms underlying pathology. This study has implications for the identification of targeted therapeutic strategies aimed at modulating microvascular signaling in brain pathologies associated with hypoxia.
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Affiliation(s)
- Andreas Enström
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Robert Carlsson
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Carolina Buizza
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Marvel Lewi
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Gesine Paul
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden; Department of Neurology, Scania University Hospital, Lund, Sweden; Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
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11
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Dobner S, Tóth F, de Rooij LPMH. A high-resolution view of the heterogeneous aging endothelium. Angiogenesis 2024; 27:129-145. [PMID: 38324119 PMCID: PMC11021252 DOI: 10.1007/s10456-023-09904-6] [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: 08/21/2023] [Accepted: 12/28/2023] [Indexed: 02/08/2024]
Abstract
Vascular endothelial cell (EC) aging has a strong impact on tissue perfusion and overall cardiovascular health. While studies confined to the investigation of aging-associated vascular readouts in one or a few tissues have already drastically expanded our understanding of EC aging, single-cell omics and other high-resolution profiling technologies have started to illuminate the intricate molecular changes underlying endothelial aging across diverse tissues and vascular beds at scale. In this review, we provide an overview of recent insights into the heterogeneous adaptations of the aging vascular endothelium. We address critical questions regarding tissue-specific and universal responses of the endothelium to the aging process, EC turnover dynamics throughout lifespan, and the differential susceptibility of ECs to acquiring aging-associated traits. In doing so, we underscore the transformative potential of single-cell approaches in advancing our comprehension of endothelial aging, essential to foster the development of future innovative therapeutic strategies for aging-associated vascular conditions.
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Affiliation(s)
- Sarah Dobner
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fanni Tóth
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Laura P M H de Rooij
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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12
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Katdare KA, Kjar A, O’Brown NM, Neal EH, Sorets AG, Shostak A, Romero-Fernandez W, Kwiatkowski AJ, Mlouk K, Kim H, Cowell RP, Schwensen KR, Horner KB, Wilson JT, Schrag MS, Megason SG, Lippmann ES. IQGAP2 regulates blood-brain barrier immune dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.07.527394. [PMID: 38645082 PMCID: PMC11030232 DOI: 10.1101/2023.02.07.527394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Brain endothelial cells (BECs) play an important role in maintaining central nervous system (CNS) homeostasis through blood-brain barrier (BBB) functions. BECs express low baseline levels of adhesion receptors, which limits entry of leukocytes. However, the molecular mediators governing this phenotype remain mostly unclear. Here, we explored how infiltration of immune cells across the BBB is influenced by the scaffold protein IQ motif containing GTPase activating protein 2 (IQGAP2). In mice and zebrafish, we demonstrate that loss of Iqgap2 increases infiltration of peripheral leukocytes into the CNS under homeostatic and inflammatory conditions. Using single-cell RNA sequencing and immunohistology, we further show that BECs from mice lacking Iqgap2 exhibit a profound inflammatory signature, including extensive upregulation of adhesion receptors and antigen-processing machinery. Human tissue analyses also reveal that Alzheimer's disease is associated with reduced hippocampal IQGAP2. Overall, our results implicate IQGAP2 as an essential regulator of BBB immune privilege and immune cell entry into the CNS.
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Affiliation(s)
- Ketaki A. Katdare
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Andrew Kjar
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - Emma H. Neal
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Alexander G. Sorets
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Alena Shostak
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Kate Mlouk
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Hyosung Kim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Rebecca P. Cowell
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Katrina R. Schwensen
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kensley B. Horner
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - John T. Wilson
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Matthew S. Schrag
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sean G. Megason
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ethan S. Lippmann
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
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13
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Deng YT, Wu BS, Yang L, He XY, Kang JJ, Liu WS, Li ZY, Wu XR, Zhang YR, Chen SD, Ge YJ, Huang YY, Feng JF, Zhu Y, Dong Q, Mao Y, Cheng W, Yu JT. Large-scale whole-exome sequencing of neuropsychiatric diseases and traits in 350,770 adults. Nat Hum Behav 2024:10.1038/s41562-024-01861-4. [PMID: 38589703 DOI: 10.1038/s41562-024-01861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
While numerous genomic loci have been identified for neuropsychiatric conditions, the contribution of protein-coding variants has yet to be determined. Here we conducted a large-scale whole-exome-sequencing study to interrogate the impact of protein-coding variants on 46 neuropsychiatric diseases and 23 traits in 350,770 adults from the UK Biobank. Twenty new genes were associated with neuropsychiatric diseases through coding variants, among which 16 genes had impacts on the longitudinal risks of diseases. Thirty new genes were associated with neuropsychiatric traits, with SYNGAP1 showing pleiotropic effects across cognitive function domains. Pairwise estimation of genetic correlations at the coding-variant level highlighted shared genetic associations among pairs of neurodegenerative diseases and mental disorders. Lastly, a comprehensive multi-omics analysis suggested that alterations in brain structures, blood proteins and inflammation potentially contribute to the gene-phenotype linkages. Overall, our findings characterized a compendium of protein-coding variants for future research on the biology and therapeutics of neuropsychiatric phenotypes.
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Affiliation(s)
- Yue-Ting Deng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bang-Sheng Wu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liu Yang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao-Yu He
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ju-Jiao Kang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Wei-Shi Liu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ze-Yu Li
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Xin-Rui Wu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ya-Ru Zhang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shi-Dong Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Jun Ge
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Yuan Huang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian-Feng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
- Department of Computer Science, University of Warwick, Coventry, UK
| | - Ying Zhu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Qiang Dong
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital Fudan University, Shanghai, China
| | - Wei Cheng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China.
- Fudan ISTBI-ZJNU Algorithm Centre for Brain-inspired Intelligence, Zhejiang Normal University, Zhejiang, China.
| | - Jin-Tai Yu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
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14
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Wasielewska JM, Szostak K, McInnes LE, Quek H, Chaves JCS, Liddell JR, Koistinaho J, Oikari LE, Donnelly PS, White AR. Patient-Derived Blood-Brain Barrier Model for Screening Copper Bis(thiosemicarbazone) Complexes as Potential Therapeutics in Alzheimer's Disease. ACS Chem Neurosci 2024; 15:1432-1455. [PMID: 38477556 DOI: 10.1021/acschemneuro.3c00743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Abstract
Alzheimer's disease (AD) is the most prevalent cause of dementia characterized by a progressive cognitive decline. Addressing neuroinflammation represents a promising therapeutic avenue to treat AD; however, the development of effective antineuroinflammatory compounds is often hindered by their limited blood-brain barrier (BBB) permeability. Consequently, there is an urgent need for accurate, preclinical AD patient-specific BBB models to facilitate the early identification of immunomodulatory drugs capable of efficiently crossing the human AD BBB. This study presents a unique approach to BBB drug permeability screening as it utilizes the familial AD patient-derived induced brain endothelial-like cell (iBEC)-based model, which exhibits increased disease relevance and serves as an improved BBB drug permeability assessment tool when compared to traditionally employed in vitro models. To demonstrate its utility as a small molecule drug candidate screening platform, we investigated the effects of diacetylbis(N(4)-methylthiosemicarbazonato)copper(II) (CuII(atsm)) and a library of metal bis(thiosemicarbazone) complexes─a class of compounds exhibiting antineuroinflammatory therapeutic potential in neurodegenerative disorders. By evaluating the toxicity, cellular accumulation, and permeability of those compounds in the AD patient-derived iBEC, we have identified 3,4-hexanedione bis(N(4)-methylthiosemicarbazonato)copper(II) (CuII(dtsm)) as a candidate with good transport across the AD BBB. Furthermore, we have developed a multiplex approach where AD patient-derived iBEC were combined with immune modulators TNFα and IFNγ to establish an in vitro model representing the characteristic neuroinflammatory phenotype at the patient's BBB. Here, we observed that treatment with CuII(dtsm) not only reduced the expression of proinflammatory cytokine genes but also reversed the detrimental effects of TNFα and IFNγ on the integrity and function of the AD iBEC monolayer. This suggests a novel pathway through which copper bis(thiosemicarbazone) complexes may exert neurotherapeutic effects on AD by mitigating BBB neuroinflammation and related BBB integrity impairment. Together, the presented model provides an effective and easily scalable in vitro BBB platform for screening AD drug candidates. Its improved translational potential makes it a valuable tool for advancing the development of metal-based compounds aimed at modulating neuroinflammation in AD.
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Affiliation(s)
- Joanna M Wasielewska
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- Faculty of Medicine, University of Queensland, Herston, QLD 4006, Australia
| | - Kathryn Szostak
- School of Chemistry, Bio21 Institute for Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Lachlan E McInnes
- School of Chemistry, Bio21 Institute for Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hazel Quek
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- School of Biomedical Science, University of Queensland, St. Lucia, QLD 4067, Australia
| | - Juliana C S Chaves
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Jeffrey R Liddell
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jari Koistinaho
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, University of Helsinki, Helsinki 00014,Finland
- Neuroscience Centre, Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Lotta E Oikari
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Paul S Donnelly
- School of Chemistry, Bio21 Institute for Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Anthony R White
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- School of Biomedical Science, University of Queensland, St. Lucia, QLD 4067, Australia
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15
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Ji H, Han Y, Danyang Jie, Yue Li, Hailan Yang, Sun H, You C, Xiao A, Liu Y. Decoding the biology and clinical implication of neutrophils in intracranial aneurysm. Ann Clin Transl Neurol 2024; 11:958-972. [PMID: 38317016 PMCID: PMC11021671 DOI: 10.1002/acn3.52014] [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: 08/20/2023] [Revised: 10/08/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024] Open
Abstract
OBJECTIVE Abundant neutrophils have been identified in both ruptured and unruptured intracranial aneurysm (IA) domes, with their function and clinical implication being poorly characterized. MATERIALS AND METHODS We employed single-cell RNA sequencing (scRNA-Seq) datasets of both human and murine model, and external bulk mRNA sequencing datasets to thoroughly explore the features and functional heterogeneous of neutrophils infiltrating the IA dome. RESULTS We found that both unruptured and ruptured IA dome contain a substantial population of neutrophils, characterized by FCGR3B, G0S2, CSF3R, and CXCR2. These cells exhibited heterogeneity in terms of function and differentiation. Despite similar transcriptional activation, neutrophils in IA dome expressed a repertoire of gene programs that mimicked transcriptomic alterations observed from bone marrow to peripheral blood, showing self-similarity. In addition, the recruitment of neutrophils in unruptured IA was primarily mediated by monocytes/macrophages, and once ruptured, both neutrophils, and a specific subset of inflammatory smooth muscle cells (SMCs) were involved in the process. The receiver operator characteristic curve (ROC) analysis indicated that distinct neutrophil subclusters were associated with IA formation and rupture, respectively. By reviewing current studies, we found that neutrophils play a detrimental role to IA wall integrity through secreting specific ligands, ferroptosis driven by ALOX5AP and PTGS2, and the formation of neutrophil extracellular traps (NETs) mediated by PADI4. INTERPRETATION This study delineated the biology and potential clinical implications of neutrophils in IA dome and provided a reliable basis for future researches.
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Affiliation(s)
- Hang Ji
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Yujing Han
- Plevic Floor Disorders Centre, West China Tianfu HospitalSichuan UniversityNo. 3966, Tianfu AvenueChengduSichuanChina
| | - Danyang Jie
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Yue Li
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Hailan Yang
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Haogeng Sun
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Chao You
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Anqi Xiao
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Yi Liu
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
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16
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Bejarano L, Kauzlaric A, Lamprou E, Lourenco J, Fournier N, Ballabio M, Colotti R, Maas R, Galland S, Massara M, Soukup K, Lilja J, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA. Interrogation of endothelial and mural cells in brain metastasis reveals key immune-regulatory mechanisms. Cancer Cell 2024; 42:378-395.e10. [PMID: 38242126 DOI: 10.1016/j.ccell.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/11/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Brain metastasis (BrM) is a common malignancy, predominantly originating from lung, melanoma, and breast cancers. The vasculature is a key component of the BrM tumor microenvironment with critical roles in regulating metastatic seeding and progression. However, the heterogeneity of the major BrM vascular components, namely endothelial and mural cells, is still poorly understood. We perform single-cell and bulk RNA-sequencing of sorted vascular cell types and detect multiple subtypes enriched specifically in BrM compared to non-tumor brain, including previously unrecognized immune regulatory subtypes. We integrate the human data with mouse models, creating a platform to interrogate vascular targets for the treatment of BrM. We find that the CD276 immune checkpoint molecule is significantly upregulated in the BrM vasculature, and anti-CD276 blocking antibodies prolonged survival in preclinical trials. This study provides important insights into the complex interactions between the vasculature, immune cells, and cancer cells, with translational relevance for designing therapeutic interventions.
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Affiliation(s)
- Leire Bejarano
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Annamaria Kauzlaric
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eleni Lamprou
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Joao Lourenco
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nadine Fournier
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michelle Ballabio
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Roberto Colotti
- In Vivo Imaging Facility (IVIF), University of Lausanne, Lausanne, Switzerland
| | - Roeltje Maas
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Sabine Galland
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Matteo Massara
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Klara Soukup
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Johanna Lilja
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Jean-Philippe Brouland
- Department of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Andreas F Hottinger
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Roy T Daniel
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Monika E Hegi
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Johanna A Joyce
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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17
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Ji H, Li Y, Sun H, Chen R, Zhou R, Yang Y, Wang R, You C, Xiao A, Yi L. Decoding the Cell Atlas and Inflammatory Features of Human Intracranial Aneurysm Wall by Single-Cell RNA Sequencing. J Am Heart Assoc 2024; 13:e032456. [PMID: 38390814 PMCID: PMC10944067 DOI: 10.1161/jaha.123.032456] [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: 11/28/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND Intracranial aneurysm (IA) is common and occasionally results in life-threatening hemorrhagic strokes. However, the cell architecture and inflammation in the IA dome remain less understood. METHODS AND RESULTS Single-cell RNA sequencing was performed on ruptured and unruptured human IA domes for delineating the cell atlas, gene expression perturbations, and inflammation features. Two external bulk mRNA sequencing-based data sets and serological results of 126 patients were collected for validation. As a result, a total of 21 332 qualified cells were captured. Vascular cells, including endothelial cells, smooth muscle cells, fibroblasts, and pericytes, were assigned in extremely sparse numbers (4.84%), and were confirmed by immunofluorescence staining. Pericytes, characterized by ABCC9 and HIGD1B, were identified in the IA dome for the first time. Abundant immune cells were identified, with the proportion of monocytes/macrophages and neutrophils being remarkably higher in ruptured IA. The lymphocyte compartment was also thoroughly categorized. By leveraging external data sets and machine learning algorithms, macrophages were robustly associated with IA rupture, irrespective of their polarization status. The single nucleotide polymorphism rs2280543, which is identified in East Asian populations, was associated with macrophage metabolic reprogramming through regulating TALDO1 expression. CONCLUSIONS This study provides insights into the cellular architecture and inflammatory features in the IA dome and may enlighten novel therapeutics for unruptured IA.
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Affiliation(s)
- Hang Ji
- Department of Neurosurgery, West China HospitalSichuan UniversityChengduChina
| | - Yue Li
- Department of Neurosurgery, West China HospitalSichuan UniversityChengduChina
| | - Haogeng Sun
- Department of Neurosurgery, West China HospitalSichuan UniversityChengduChina
| | - Ruiqi Chen
- Department of Neurosurgery, West China HospitalSichuan UniversityChengduChina
| | - Ran Zhou
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China HospitalSichuan UniversityChengduChina
| | - Yongbo Yang
- Department of Neurosurgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Rong Wang
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Chao You
- Department of Neurosurgery, West China HospitalSichuan UniversityChengduChina
| | - Anqi Xiao
- Department of Neurosurgery, West China HospitalSichuan UniversityChengduChina
| | - Liu Yi
- Department of Neurosurgery, West China HospitalSichuan UniversityChengduChina
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18
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Fei CJ, Li ZY, Ning J, Yang L, Wu BS, Kang JJ, Liu WS, He XY, You J, Chen SD, Yu H, Huang ZL, Feng JF, Yu JT, Cheng W. Exome sequencing identifies genes associated with sleep-related traits. Nat Hum Behav 2024; 8:576-589. [PMID: 38177695 DOI: 10.1038/s41562-023-01785-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024]
Abstract
Sleep is vital for human health and has a moderate heritability. Previous genome-wide association studies have limitations in capturing the role of rare genetic variants in sleep-related traits. Here we conducted a large-scale exome-wide association study of eight sleep-related traits (sleep duration, insomnia symptoms, chronotype, daytime sleepiness, daytime napping, ease of getting up in the morning, snoring and sleep apnoea) among 450,000 participants from UK Biobank. We identified 22 new genes associated with chronotype (ADGRL4, COL6A3, CLK4 and KRTAP3-3), daytime sleepiness (ST3GAL1 and ANKRD12), daytime napping (PLEKHM1, ANKRD12 and ZBTB21), snoring (WDR59) and sleep apnoea (13 genes). Notably, 20 of these genes were confirmed to be significantly associated with sleep disorders in the FinnGen cohort. Enrichment analysis revealed that these discovered genes were enriched in circadian rhythm and central nervous system neurons. Phenotypic association analysis showed that ANKRD12 was associated with cognition and inflammatory traits. Our results demonstrate the value of large-scale whole-exome analysis in understanding the genetic architecture of sleep-related traits and potential biological mechanisms.
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Affiliation(s)
- Chen-Jie Fei
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ze-Yu Li
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Jing Ning
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liu Yang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bang-Sheng Wu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ju-Jiao Kang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Wei-Shi Liu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao-Yu He
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jia You
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Shi-Dong Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Huan Yu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi-Li Huang
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Jian-Feng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
- Department of Computer Science, University of Warwick, Coventry, UK
| | - Jin-Tai Yu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Wei Cheng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China.
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19
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Kwok AJ, Lu J, Huang J, Ip BY, Mok VCT, Lai HM, Ko H. High-resolution omics of vascular ageing and inflammatory pathways in neurodegeneration. Semin Cell Dev Biol 2024; 155:30-49. [PMID: 37380595 DOI: 10.1016/j.semcdb.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: 04/29/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
High-resolution omics, particularly single-cell and spatial transcriptomic profiling, are rapidly enhancing our comprehension of the normal molecular diversity of gliovascular cells, as well as their age-related changes that contribute to neurodegeneration. With more omic profiling studies being conducted, it is becoming increasingly essential to synthesise valuable information from the rapidly accumulating findings. In this review, we present an overview of the molecular features of neurovascular and glial cells that have been recently discovered through omic profiling, with a focus on those that have potentially significant functional implications and/or show cross-species differences between human and mouse, and that are linked to vascular deficits and inflammatory pathways in ageing and neurodegenerative disorders. Additionally, we highlight the translational applications of omic profiling, and discuss omic-based strategies to accelerate biomarker discovery and facilitate disease course-modifying therapeutics development for neurodegenerative conditions.
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Affiliation(s)
- Andrew J Kwok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jianning Lu
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junzhe Huang
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bonaventure Y Ip
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hei Ming Lai
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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20
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Crouch EE, Diafos LN, Valenzuela EJ, Wedderburn-Pugh K, Birrueta JO, Caston J, Joseph T, Andrews MG, Bhaduri A, Huang EJ. Profiling human brain vascular cells using single-cell transcriptomics and organoids. Nat Protoc 2024; 19:603-628. [PMID: 38102365 DOI: 10.1038/s41596-023-00929-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/13/2023] [Indexed: 12/17/2023]
Abstract
Angiogenesis and neurogenesis are functionally interconnected during brain development. However, the study of the vasculature has trailed other brain cell types because they are delicate and of low abundance. Here we describe a protocol extension to purify prenatal human brain endothelial and mural cells with FACS and utilize them in downstream applications, including transcriptomics, culture and organoid transplantation. This approach is simple, efficient and generates high yields from small amounts of tissue. When the experiment is completed within a 24 h postmortem interval, these healthy cells produce high-quality data in single-cell transcriptomics experiments. These vascular cells can be cultured, passaged and expanded for many in vitro assays, including Matrigel vascular tube formation, microfluidic chambers and metabolic measurements. Under these culture conditions, primary vascular cells maintain expression of cell-type markers for at least 3 weeks. Finally, we describe how to use primary vascular cells for transplantation into cortical organoids, which captures key features of neurovascular interactions in prenatal human brain development. In terms of timing, tissue processing and staining requires ~3 h, followed by an additional 3 h of FACS. The transplant procedure of primary, FACS-purified vascular cells into cortical organoids requires an additional 2 h. The time required for different transcriptomic and epigenomic protocols can vary based on the specific application, and we offer strategies to mitigate batch effects and optimize data quality. In sum, this vasculo-centric approach offers an integrated platform to interrogate neurovascular interactions and human brain vascular development.
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Affiliation(s)
- Elizabeth E Crouch
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
- Biomedical Science Graduate Program, University of California San Francisco, San Francisco, CA, USA.
| | - Loukas N Diafos
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Edward J Valenzuela
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Kaylee Wedderburn-Pugh
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Biomedical Science Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Janeth Ochoa Birrueta
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Jaela Caston
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Biomedical Science Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Tara Joseph
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Madeline G Andrews
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco (UCSF), San Francisco, CA, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Aparna Bhaduri
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Eric J Huang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
- Biomedical Science Graduate Program, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- Pathology Service 113B, San Francisco Veterans Affairs Healthcare System, San Francisco, CA, USA.
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21
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Gastfriend BD, Snyder ME, Holt HE, Daneman R, Palecek SP, Shusta EV. Notch3 directs differentiation of brain mural cells from human pluripotent stem cell-derived neural crest. SCIENCE ADVANCES 2024; 10:eadi1737. [PMID: 38306433 PMCID: PMC10836734 DOI: 10.1126/sciadv.adi1737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/04/2024] [Indexed: 02/04/2024]
Abstract
Brain mural cells regulate development and function of the blood-brain barrier and control blood flow. Existing in vitro models of human brain mural cells have low expression of key mural cell genes, including NOTCH3. Thus, we asked whether activation of Notch3 signaling in hPSC-derived neural crest could direct the differentiation of brain mural cells with an improved transcriptional profile. Overexpression of the Notch3 intracellular domain (N3ICD) induced expression of mural cell markers PDGFRβ, TBX2, FOXS1, KCNJ8, SLC6A12, and endogenous Notch3. The resulting N3ICD-derived brain mural cells produced extracellular matrix, self-assembled with endothelial cells, and had functional KATP channels. ChIP-seq revealed that Notch3 serves as a direct input to relatively few genes in the context of this differentiation process. Our work demonstrates that activation of Notch3 signaling is sufficient to direct the differentiation of neural crest to mural cells and establishes a developmentally relevant differentiation protocol.
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Affiliation(s)
- Benjamin D Gastfriend
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Margaret E Snyder
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hope E Holt
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Richard Daneman
- Departments of Neurosciences and Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI 53706, USA
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22
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Punzon-Jimenez P, Machado-Lopez A, Perez-Moraga R, Llera-Oyola J, Grases D, Galvez-Viedma M, Sibai M, Satorres-Perez E, Lopez-Agullo S, Badenes R, Ferrer-Gomez C, Porta-Pardo E, Roson B, Simon C, Mas A. Effect of aging on the human myometrium at single-cell resolution. Nat Commun 2024; 15:945. [PMID: 38296945 PMCID: PMC10830479 DOI: 10.1038/s41467-024-45143-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024] Open
Abstract
Age-associated myometrial dysfunction can prompt complications during pregnancy and labor, which is one of the factors contributing to the 7.8-fold increase in maternal mortality in women over 40. Using single-cell/single-nucleus RNA sequencing and spatial transcriptomics, we have constructed a cellular atlas of the aging myometrium from 186,120 cells across twenty perimenopausal and postmenopausal women. We identify 23 myometrial cell subpopulations, including contractile and venous capillary cells as well as immune-modulated fibroblasts. Myometrial aging leads to fewer contractile capillary cells, a reduced level of ion channel expression in smooth muscle cells, and impaired gene expression in endothelial, smooth muscle, fibroblast, perivascular, and immune cells. We observe altered myometrial cell-to-cell communication as an aging hallmark, which associated with the loss of 25 signaling pathways, including those related to angiogenesis, tissue repair, contractility, immunity, and nervous system regulation. These insights may contribute to a better understanding of the complications faced by older individuals during pregnancy and labor.
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Affiliation(s)
- Paula Punzon-Jimenez
- Carlos Simon Foundation, Valencia, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain
| | - Alba Machado-Lopez
- Carlos Simon Foundation, Valencia, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Raul Perez-Moraga
- Carlos Simon Foundation, Valencia, Spain
- R&D Department, Igenomix, Valencia, Spain
| | | | - Daniela Grases
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | | | - Mustafa Sibai
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | | | | | - Rafael Badenes
- Department of Surgery, University of Valencia, Valencia, Spain
- Hospital Clinico Universitario, Valencia, Spain
| | | | | | - Beatriz Roson
- Carlos Simon Foundation, Valencia, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Carlos Simon
- Carlos Simon Foundation, Valencia, Spain.
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain.
- Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA, USA.
| | - Aymara Mas
- Carlos Simon Foundation, Valencia, Spain.
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.
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23
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Xu X, Zhang C, Tang G, Wang N, Feng Y. Single-cell transcriptome profiling highlights the role of APP in blood vessels in assessing the risk of patients with proliferative diabetic retinopathy developing Alzheimer's disease. Front Cell Dev Biol 2024; 11:1328979. [PMID: 38328307 PMCID: PMC10847282 DOI: 10.3389/fcell.2023.1328979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/29/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction: The incidence of diabetic retinopathy (DR) has been found to be associated with the risk of developing Alzheimer's disease (AD). In addition to the common properties of neurodegeneration, their progressions are involved with abnormal vascular functions. However, the interactions between them have not been fully understood. This study aimed to investigate the key factor for the underlying interactions and shared signaling pathways in the vasculature of DR and AD. Methods: We retrieved single-cell RNA sequencing (scRNA-seq) data regarding human fibrovascular membrane (FVM) of proliferative diabetic retinopathy (PDR) and human hippocampus vessels of AD from the NCBI-GEO database. GSEA analysis was performed to analyze AD-related genes in endothelial cells and pericytes of PDR. CellChat was used for predicting cell-cell communication and the signaling pathway. Results: The data suggested that amyloid-beta precursor protein (APP) signaling was found crucial in the vasculature of PDR and AD. Endothelial cells and pericytes could pose influences on other cells mainly via APP signaling in PDR. The endothelial cells were mainly coordinated with macrophages in the hippocampus vasculature of AD via APP signaling. The bulk RNA-seq in mice with PDR validated that the expression of APP gene had a significant correlation with that of the AD genome-wide association studies (GWAS) gene. Discussion: Our study demonstrates that the vasculopathy of PDR and AD is likely to share a common signaling pathway, of which the APP-related pathway is a potential target.
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Affiliation(s)
| | | | | | | | - Yibin Feng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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24
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Wojtas AM, Dammer EB, Guo Q, Ping L, Shantaraman A, Duong DM, Yin L, Fox EJ, Seifar F, Lee EB, Johnson ECB, Lah JJ, Levey AI, Levites Y, Rangaraju S, Golde TE, Seyfried NT. Proteomic Changes in the Human Cerebrovasculature in Alzheimer's Disease and Related Tauopathies Linked to Peripheral Biomarkers in Plasma and Cerebrospinal Fluid. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.10.24301099. [PMID: 38260316 PMCID: PMC10802758 DOI: 10.1101/2024.01.10.24301099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Dysfunction of the neurovascular unit stands as a significant pathological hallmark of Alzheimer's disease (AD) and age-related neurodegenerative diseases. Nevertheless, detecting vascular changes in the brain within bulk tissues has proven challenging, limiting our ability to characterize proteomic alterations from less abundant cell types. To address this challenge, we conducted quantitative proteomic analyses on both bulk brain tissues and cerebrovascular-enriched fractions from the same individuals, encompassing cognitively unimpaired control, progressive supranuclear palsy (PSP), and AD cases. Protein co-expression network analysis identified modules unique to the cerebrovascular fractions, specifically enriched with pericytes, endothelial cells, and smooth muscle cells. Many of these modules also exhibited significant correlations with amyloid plaques, cerebral amyloid angiopathy (CAA), and/or tau pathology in the brain. Notably, the protein products within AD genetic risk loci were found concentrated within modules unique to the vascular fractions, consistent with a role of cerebrovascular deficits in the etiology of AD. To prioritize peripheral AD biomarkers associated with vascular dysfunction, we assessed the overlap between differentially abundant proteins in AD cerebrospinal fluid (CSF) and plasma with a vascular-enriched network modules in the brain. This analysis highlighted matrisome proteins, SMOC1 and SMOC2, as being increased in CSF, plasma, and brain. Immunohistochemical analysis revealed SMOC1 deposition in both parenchymal plaques and CAA in the AD brain, whereas SMOC2 was predominantly localized to CAA. Collectively, these findings significantly enhance our understanding of the involvement of cerebrovascular abnormalities in AD, shedding light on potential biomarkers and molecular pathways associated with CAA and vascular dysfunction in neurodegenerative diseases.
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Affiliation(s)
- Aleksandra M. Wojtas
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B. Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Qi Guo
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Ananth Shantaraman
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M. Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Edward J. Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Fatemeh Seifar
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Edward B. Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, PA, USA
| | - Erik C. B. Johnson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I. Levey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Yona Levites
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Todd E. Golde
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
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25
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Flotho M, Amand J, Hirsch P, Grandke F, Wyss-Coray T, Keller A, Kern F. ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution. Nucleic Acids Res 2024; 52:D1089-D1096. [PMID: 37941147 PMCID: PMC10767845 DOI: 10.1093/nar/gkad990] [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: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023] Open
Abstract
The molecular causes and mechanisms of neurodegenerative diseases remain poorly understood. A growing number of single-cell studies have implicated various neural, glial, and immune cell subtypes to affect the mammalian central nervous system in many age-related disorders. Integrating this body of transcriptomic evidence into a comprehensive and reproducible framework poses several computational challenges. Here, we introduce ZEBRA, a large single-cell and single-nucleus RNA-seq database. ZEBRA integrates and normalizes gene expression and metadata from 33 studies, encompassing 4.2 million human and mouse brain cells sampled from 39 brain regions. It incorporates samples from patients with neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, and Multiple sclerosis, as well as samples from relevant mouse models. We employed scVI, a deep probabilistic auto-encoder model, to integrate the samples and curated both cell and sample metadata for downstream analysis. ZEBRA allows for cell-type and disease-specific markers to be explored and compared between sample conditions and brain regions, a cell composition analysis, and gene-wise feature mappings. Our comprehensive molecular database facilitates the generation of data-driven hypotheses, enhancing our understanding of mammalian brain function during aging and disease. The data sets, along with an interactive database are freely available at https://www.ccb.uni-saarland.de/zebra.
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Affiliation(s)
- Matthias Flotho
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123 Saarbrücken, Germany
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jérémy Amand
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123 Saarbrücken, Germany
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Pascal Hirsch
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Friederike Grandke
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
| | - Andreas Keller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123 Saarbrücken, Germany
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123 Saarbrücken, Germany
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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26
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Yeung SHS, Lee RHS, Cheng GWY, Ma IWT, Kofler J, Kent C, Ma F, Herrup K, Fornage M, Arai K, Tse KH. White matter hyperintensity genetic risk factor TRIM47 regulates autophagy in brain endothelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.566359. [PMID: 38187529 PMCID: PMC10769267 DOI: 10.1101/2023.12.18.566359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
White matter hyperintensity (WMH) is strongly correlated with age-related dementia and hypertension, but its pathogenesis remains obscure. GWAS identified TRIM47 at 17q25 locus as a top genetic risk factor for WMH formation. TRIM family is a class of E3 ubiquitin ligase with pivotal functions in autophagy, which is critical for brain endothelial cell (ECs) remodeling during hypertension. We hypothesize that TRIM47 regulates autophagy and its loss-of-function disturbs cerebrovasculature. Based on transcriptomics and immunohistochemistry, TRIM47 is found selectively expressed by brain ECs in human and mouse, and its transcription is upregulated by artificially-induced autophagy while downregulated in hypertension-like conditions. Using in silico simulation, immunocytochemistry and super-resolution microscopy, we identified the highly conserved binding site between TRIM47 and the LIR (LC3-interacting region) motif of LC3B. Importantly, pharmacological autophagy induction increased Trim47 expression on mouse ECs (b.End3) culture, while silencing Trim47 significantly increased autophagy with ULK1 phosphorylation induction, transcription and vacuole formation. Together, we confirm that TRIM47 is an endogenous inhibitor of autophagy in brain ECs, and such TRIM47-mediated regulation connects genetic and physiological risk factors for WMH formation but warrants further investigation. SUMMARY STATEMENT TRIM47, top genetic risk factor for white matter hyperintensity formation, is a negative regulator of autophagy in brain endothelial cells and implicates a novel cellular mechanism for age-related cerebrovascular changes.
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27
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van Splunder H, Villacampa P, Martínez-Romero A, Graupera M. Pericytes in the disease spotlight. Trends Cell Biol 2024; 34:58-71. [PMID: 37474376 PMCID: PMC10777571 DOI: 10.1016/j.tcb.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/01/2023] [Accepted: 06/09/2023] [Indexed: 07/22/2023]
Abstract
Pericytes are known as the mural cells in small-caliber vessels that interact closely with the endothelium. Pericytes play a key role in vasculature formation and homeostasis, and when dysfunctional contribute to vasculature-related diseases such as diabetic retinopathy and neurodegenerative conditions. In addition, significant extravascular roles of pathological pericytes are being discovered with relevant implications for cancer and fibrosis. Pericyte research is challenged by the lack of consistent molecular markers and clear discrimination criteria versus other (mural) cells. However, advances in single-cell approaches are uncovering and clarifying mural cell identities, biological functions, and ontogeny across organs. We discuss the latest developments in pericyte pathobiology to inform future research directions and potential outcomes.
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Affiliation(s)
- Hielke van Splunder
- Endothelial Pathobiology and Microenviroment Group, Josep Carreras Leukemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Pilar Villacampa
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), Carrer de la Feixa Llarga s/n, 08907 l'Hospitalet de Llobregat, Barcelona, Spain
| | - Anabel Martínez-Romero
- Endothelial Pathobiology and Microenviroment Group, Josep Carreras Leukemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Mariona Graupera
- Endothelial Pathobiology and Microenviroment Group, Josep Carreras Leukemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain; Institución Catalana de Investigación y Estudios Avanzados (ICREA), Passeig de Lluís Companys 23, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Avenida de Monforte de Lemos 5, 28029 Madrid, Spain.
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28
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Kim JS, Haimon Z, Boura-Halfon S, Jung S. Translatome Profiling of Tissue-Resident Macrophages Using the RiboTag Approach. Methods Mol Biol 2024; 2713:253-267. [PMID: 37639128 DOI: 10.1007/978-1-0716-3437-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Global gene expression profiling has provided valuable insights into the specific contributions of different cell types to various physiological processes. Notably though, both bulk and single-cell transcriptomics require the prior retrieval of the cells from their tissue context to be analyzed. Isolation protocols for tissue macrophages are, however, notoriously inefficient and, moreover, prone to introduce considerable bias and artifacts. Here, we will discuss a valuable alternative, originally introduced by Amieux and colleagues. This so-called RiboTag approach allows, in combination with respective macrophage-specific Cre transgenic lines, to retrieve macrophage translatomes from crude tissue extracts. We will review our experience with this ingenious method, focusing on the study of brain macrophages, including microglia and border-associated cells. We will elaborate on the advantages of the RiboTag approach that render it a valuable complement to standard cell sorting-based profiling strategies, especially for the investigation of tissue macrophages.
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Affiliation(s)
- Jung-Seok Kim
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Zhana Haimon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sigalit Boura-Halfon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Jung
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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29
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Tijms BM, Vromen EM, Mjaavatten O, Holstege H, Reus LM, van der Lee S, Wesenhagen KEJ, Lorenzini L, Vermunt L, Venkatraghavan V, Tesi N, Tomassen J, den Braber A, Goossens J, Vanmechelen E, Barkhof F, Pijnenburg YAL, van der Flier WM, Teunissen CE, Berven FS, Visser PJ. Cerebrospinal fluid proteomics in patients with Alzheimer's disease reveals five molecular subtypes with distinct genetic risk profiles. NATURE AGING 2024; 4:33-47. [PMID: 38195725 PMCID: PMC10798889 DOI: 10.1038/s43587-023-00550-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Alzheimer's disease (AD) is heterogenous at the molecular level. Understanding this heterogeneity is critical for AD drug development. Here we define AD molecular subtypes using mass spectrometry proteomics in cerebrospinal fluid, based on 1,058 proteins, with different levels in individuals with AD (n = 419) compared to controls (n = 187). These AD subtypes had alterations in protein levels that were associated with distinct molecular processes: subtype 1 was characterized by proteins related to neuronal hyperplasticity; subtype 2 by innate immune activation; subtype 3 by RNA dysregulation; subtype 4 by choroid plexus dysfunction; and subtype 5 by blood-brain barrier impairment. Each subtype was related to specific AD genetic risk variants, for example, subtype 1 was enriched with TREM2 R47H. Subtypes also differed in clinical outcomes, survival times and anatomical patterns of brain atrophy. These results indicate molecular heterogeneity in AD and highlight the need for personalized medicine.
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Affiliation(s)
- Betty M Tijms
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands.
| | - Ellen M Vromen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Olav Mjaavatten
- Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Henne Holstege
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Lianne M Reus
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sven van der Lee
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Kirsten E J Wesenhagen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Luigi Lorenzini
- Department of Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neuroimaging, Amsterdam, the Netherlands
| | - Lisa Vermunt
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Neurochemistry Laboratory, Department of Laboratory Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Vikram Venkatraghavan
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Niccoló Tesi
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Jori Tomassen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Anouk den Braber
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | | | | | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Epidemiology & Data Science, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Charlotte E Teunissen
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Neurochemistry Laboratory, Department of Laboratory Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Frode S Berven
- Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
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30
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Maden SK, Kwon SH, Huuki-Myers LA, Collado-Torres L, Hicks SC, Maynard KR. Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets. Genome Biol 2023; 24:288. [PMID: 38098055 PMCID: PMC10722720 DOI: 10.1186/s13059-023-03123-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
Deconvolution of cell mixtures in "bulk" transcriptomic samples from homogenate human tissue is important for understanding disease pathologies. However, several experimental and computational challenges impede transcriptomics-based deconvolution approaches using single-cell/nucleus RNA-seq reference atlases. Cells from the brain and blood have substantially different sizes, total mRNA, and transcriptional activities, and existing approaches may quantify total mRNA instead of cell type proportions. Further, standards are lacking for the use of cell reference atlases and integrative analyses of single-cell and spatial transcriptomics data. We discuss how to approach these key challenges with orthogonal "gold standard" datasets for evaluating deconvolution methods.
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Affiliation(s)
- Sean K Maden
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Louise A Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Leonardo Collado-Torres
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA.
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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31
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Al-Thani M, Goodwin-Trotman M, Bell S, Patel K, Fleming LK, Vilain C, Abramowicz M, Allan SM, Wang T, Cader MZ, Horsburgh K, Van Agtmael T, Sinha S, Markus HS, Granata A. A novel human iPSC model of COL4A1/A2 small vessel disease unveils a key pathogenic role of matrix metalloproteinases. Stem Cell Reports 2023; 18:2386-2399. [PMID: 37977146 PMCID: PMC10724071 DOI: 10.1016/j.stemcr.2023.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Cerebral small vessel disease (SVD) affects the small vessels in the brain and is a leading cause of stroke and dementia. Emerging evidence supports a role of the extracellular matrix (ECM), at the interface between blood and brain, in the progression of SVD pathology, but this remains poorly characterized. To address ECM role in SVD, we developed a co-culture model of mural and endothelial cells using human induced pluripotent stem cells from patients with COL4A1/A2 SVD-related mutations. This model revealed that these mutations induce apoptosis, migration defects, ECM remodeling, and transcriptome changes in mural cells. Importantly, these mural cell defects exert a detrimental effect on endothelial cell tight junctions through paracrine actions. COL4A1/A2 models also express high levels of matrix metalloproteinases (MMPs), and inhibiting MMP activity partially rescues the ECM abnormalities and mural cell phenotypic changes. These data provide a basis for targeting MMP as a therapeutic opportunity in SVD.
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Affiliation(s)
- Maha Al-Thani
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge and Royal Papworth Hospital, Cambridge, UK
| | - Mary Goodwin-Trotman
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge and Royal Papworth Hospital, Cambridge, UK
| | - Steven Bell
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge and Royal Papworth Hospital, Cambridge, UK
| | - Krushangi Patel
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge and Royal Papworth Hospital, Cambridge, UK
| | - Lauren K Fleming
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Catheline Vilain
- Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Bruxelles, Belgium
| | - Marc Abramowicz
- Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Bruxelles, Belgium
| | - Stuart M Allan
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Tao Wang
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, The University of Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - M Zameel Cader
- Nuffield Department of Clinical Neurosciences, Kavli Institute of Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Road, University of Oxford, Oxford, UK
| | - Karen Horsburgh
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Tom Van Agtmael
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Sanjay Sinha
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Hugh S Markus
- Department of Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alessandra Granata
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge and Royal Papworth Hospital, Cambridge, UK.
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32
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Haqqani AS, Mianoor Z, Star AT, Detcheverry FE, Delaney CE, Stanimirovic DB, Hamel E, Badhwar A. Proteome Profiling of Brain Vessels in a Mouse Model of Cerebrovascular Pathology. BIOLOGY 2023; 12:1500. [PMID: 38132326 PMCID: PMC10740654 DOI: 10.3390/biology12121500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Cerebrovascular pathology that involves altered protein levels (or signaling) of the transforming growth factor beta (TGFβ) family has been associated with various forms of age-related dementias, including Alzheimer disease (AD) and vascular cognitive impairment and dementia (VCID). Transgenic mice overexpressing TGFβ1 in the brain (TGF mice) recapitulate VCID-associated cerebrovascular pathology and develop cognitive deficits in old age or when submitted to comorbid cardiovascular risk factors for dementia. We characterized the cerebrovascular proteome of TGF mice using mass spectrometry (MS)-based quantitative proteomics. Cerebral arteries were surgically removed from 6-month-old-TGF and wild-type mice, and proteins were extracted and analyzed by gel-free nanoLC-MS/MS. We identified 3602 proteins in brain vessels, with 20 demonstrating significantly altered levels in TGF mice. For total and/or differentially expressed proteins (p ≤ 0.01, ≥ 2-fold change), using multiple databases, we (a) performed protein characterization, (b) demonstrated the presence of their RNA transcripts in both mouse and human cerebrovascular cells, and (c) demonstrated that several of these proteins were present in human extracellular vesicles (EVs) circulating in blood. Finally, using human plasma, we demonstrated the presence of several of these proteins in plasma and plasma EVs. Dysregulated proteins point to perturbed brain vessel vasomotricity, remodeling, and inflammation. Given that blood-isolated EVs are novel, attractive, and a minimally invasive biomarker discovery platform for age-related dementias, several proteins identified in this study can potentially serve as VCID markers in humans.
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Affiliation(s)
- Arsalan S. Haqqani
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada; (A.S.H.); (A.T.S.); (C.E.D.); (D.B.S.)
| | - Zainab Mianoor
- Multiomics Investigation of Neurodegenerative Diseases (MIND) Laboratory, 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada; (Z.M.); (F.E.D.)
- Département de Pharmacologie et Physiologie, Institut de Génie Biomédical, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montreal, QC H3T 1J4, Canada
- Centre de Recherche de l’Institut Universitaire de Gériatrie (CRIUGM), 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada
| | - Alexandra T. Star
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada; (A.S.H.); (A.T.S.); (C.E.D.); (D.B.S.)
| | - Flavie E. Detcheverry
- Multiomics Investigation of Neurodegenerative Diseases (MIND) Laboratory, 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada; (Z.M.); (F.E.D.)
- Département de Pharmacologie et Physiologie, Institut de Génie Biomédical, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montreal, QC H3T 1J4, Canada
- Centre de Recherche de l’Institut Universitaire de Gériatrie (CRIUGM), 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada
| | - Christie E. Delaney
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada; (A.S.H.); (A.T.S.); (C.E.D.); (D.B.S.)
| | - Danica B. Stanimirovic
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada; (A.S.H.); (A.T.S.); (C.E.D.); (D.B.S.)
| | - Edith Hamel
- Laboratory of Cerebrovascular Research, Montreal Neurological Institute, McGill University, 3801 Rue University, Montreal, QC H3A 2B4, Canada;
| | - AmanPreet Badhwar
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada; (A.S.H.); (A.T.S.); (C.E.D.); (D.B.S.)
- Multiomics Investigation of Neurodegenerative Diseases (MIND) Laboratory, 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada; (Z.M.); (F.E.D.)
- Département de Pharmacologie et Physiologie, Institut de Génie Biomédical, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montreal, QC H3T 1J4, Canada
- Centre de Recherche de l’Institut Universitaire de Gériatrie (CRIUGM), 4545 Chemin Queen Mary, Montreal, QC H3W 1W4, Canada
- Laboratory of Cerebrovascular Research, Montreal Neurological Institute, McGill University, 3801 Rue University, Montreal, QC H3A 2B4, Canada;
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Holl D, Göritz C. Decoding fibrosis in the human central nervous system. Am J Physiol Cell Physiol 2023; 325:C1415-C1420. [PMID: 37811731 DOI: 10.1152/ajpcell.00243.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
Recent advancements in human tissue analyses and animal models have revealed that fibrotic scarring is a common response to various lesions in the central nervous system (CNS). Perivascular cells within the brain or spinal cord give rise to stromal fibroblasts that form fibrotic scar tissue. In this review, we summarize the current understanding of fibrotic scar formation in different CNS lesions and evaluate published human single-cell gene expression datasets to gather information on perivascular cells. Specifically, we highlight the classification of pericytes and fibroblast subtypes and compare the marker expression of perivascular cells across different datasets.
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Affiliation(s)
- Daniel Holl
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christian Göritz
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Stellenbosch Institute for Advanced Study, Wallenberg Centre, Stellenbosch, South Africa
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34
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Liu W, You J, Ge Y, Wu B, Zhang Y, Chen S, Zhang Y, Huang S, Ma L, Feng J, Cheng W, Yu J. Association of biological age with health outcomes and its modifiable factors. Aging Cell 2023; 22:e13995. [PMID: 37723992 PMCID: PMC10726867 DOI: 10.1111/acel.13995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
Identifying the clinical implications and modifiable and unmodifiable factors of aging requires the measurement of biological age (BA) and age gap. Leveraging the biomedical traits involved with physical measures, biochemical assays, genomic data, and cognitive functions from the healthy participants in the UK Biobank, we establish an integrative BA model consisting of multi-dimensional indicators. Accelerated aging (age gap >3.2 years) at baseline is associated incident circulatory diseases, related chronic disorders, all-cause, and cause-specific mortality. We identify 35 modifiable factors for age gap (p < 4.81 × 10-4 ), where pulmonary functions, body mass, hand grip strength, basal metabolic rate, estimated glomerular filtration rate, and C-reactive protein show the most significant associations. Genetic analyses replicate the possible associations between age gap and health-related outcomes and further identify CST3 as an essential gene for biological aging, which is highly expressed in the brain and is associated with immune and metabolic traits. Our study profiles the landscape of biological aging and provides insights into the preventive strategies and therapeutic targets for aging.
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Affiliation(s)
- Wei‐Shi Liu
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Jia You
- Institute of Science and Technology for Brain‐Inspired Intelligence, Fudan UniversityShanghaiChina
- Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence (Fudan University), Ministry of EducationShanghaiChina
| | - Yi‐Jun Ge
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Bang‐Sheng Wu
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Yi Zhang
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Shi‐Dong Chen
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Ya‐Ru Zhang
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Shu‐Yi Huang
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Ling‐Zhi Ma
- Department of Neurology, Qingdao Municipal HospitalQingdao UniversityQingdaoChina
| | - Jian‐Feng Feng
- Institute of Science and Technology for Brain‐Inspired Intelligence, Fudan UniversityShanghaiChina
- Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence (Fudan University), Ministry of EducationShanghaiChina
- Department of Computer ScienceUniversity of WarwickCoventryUK
| | - Wei Cheng
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
- Institute of Science and Technology for Brain‐Inspired Intelligence, Fudan UniversityShanghaiChina
- Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence (Fudan University), Ministry of EducationShanghaiChina
- Fudan ISTBI—ZJNU Algorithm Centre for Brain‐Inspired IntelligenceZhejiang Normal UniversityJinhuaChina
- Shanghai Medical College and Zhongshan Hosptital Immunotherapy Technology Transfer CenterShanghaiChina
| | - Jin‐Tai Yu
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
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35
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Wakid M, Almeida D, Aouabed Z, Rahimian R, Davoli MA, Yerko V, Leonova-Erko E, Richard V, Zahedi R, Borchers C, Turecki G, Mechawar N. Universal method for the isolation of microvessels from frozen brain tissue: A proof-of-concept multiomic investigation of the neurovasculature. Brain Behav Immun Health 2023; 34:100684. [PMID: 37822873 PMCID: PMC10562768 DOI: 10.1016/j.bbih.2023.100684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
The neurovascular unit, comprised of vascular cell types that collectively regulate cerebral blood flow to meet the needs of coupled neurons, is paramount for the proper function of the central nervous system. The neurovascular unit gatekeeps blood-brain barrier properties, which experiences impairment in several central nervous system diseases associated with neuroinflammation and contributes to pathogenesis. To better understand function and dysfunction at the neurovascular unit and how it may confer inflammatory processes within the brain, isolation and characterization of the neurovascular unit is needed. Here, we describe a singular, standardized protocol to enrich and isolate microvessels from archived snap-frozen human and frozen mouse cerebral cortex using mechanical homogenization and centrifugation-separation that preserves the structural integrity and multicellular composition of microvessel fragments. For the first time, microvessels are isolated from postmortem ventromedial prefrontal cortex tissue and are comprehensively investigated as a structural unit using both RNA sequencing and Liquid Chromatography with tandem mass spectrometry (LC-MS/MS). Both the transcriptome and proteome are obtained and compared, demonstrating that the isolated brain microvessel is a robust model for the NVU and can be used to generate highly informative datasets in both physiological and disease contexts.
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Affiliation(s)
- Marina Wakid
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, Quebec, Canada
| | - Daniel Almeida
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, Quebec, Canada
| | - Zahia Aouabed
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
| | - Reza Rahimian
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
| | | | - Volodymyr Yerko
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
| | - Elena Leonova-Erko
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
| | - Vincent Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - René Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Christoph Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, Quebec, Canada
- Department of Psychiatry, McGill University, Montréal, Quebec, Canada
| | - Naguib Mechawar
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, Quebec, Canada
- Department of Psychiatry, McGill University, Montréal, Quebec, Canada
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36
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Cleuren A, Molema G. Organotypic heterogeneity in microvascular endothelial cell responses in sepsis-a molecular treasure trove and pharmacological Gordian knot. Front Med (Lausanne) 2023; 10:1252021. [PMID: 38020105 PMCID: PMC10665520 DOI: 10.3389/fmed.2023.1252021] [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: 07/03/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
In the last decades, it has become evident that endothelial cells (ECs) in the microvasculature play an important role in the pathophysiology of sepsis-associated multiple organ dysfunction syndrome (MODS). Studies on how ECs orchestrate leukocyte recruitment, control microvascular integrity and permeability, and regulate the haemostatic balance have provided a wealth of knowledge and potential molecular targets that could be considered for pharmacological intervention in sepsis. Yet, this information has not been translated into effective treatments. As MODS affects specific vascular beds, (organotypic) endothelial heterogeneity may be an important contributing factor to this lack of success. On the other hand, given the involvement of ECs in sepsis, this heterogeneity could also be leveraged for therapeutic gain to target specific sites of the vasculature given its full accessibility to drugs. In this review, we describe current knowledge that defines heterogeneity of organ-specific microvascular ECs at the molecular level and elaborate on studies that have reported EC responses across organ systems in sepsis patients and animal models of sepsis. We discuss hypothesis-driven, single-molecule studies that have formed the basis of our understanding of endothelial cell engagement in sepsis pathophysiology, and include recent studies employing high-throughput technologies. The latter deliver comprehensive data sets to describe molecular signatures for organotypic ECs that could lead to new hypotheses and form the foundation for rational pharmacological intervention and biomarker panel development. Particularly results from single cell RNA sequencing and spatial transcriptomics studies are eagerly awaited as they are expected to unveil the full spatiotemporal signature of EC responses to sepsis. With increasing awareness of the existence of distinct sepsis subphenotypes, and the need to develop new drug regimen and companion diagnostics, a better understanding of the molecular pathways exploited by ECs in sepsis pathophysiology will be a cornerstone to halt the detrimental processes that lead to MODS.
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Affiliation(s)
- Audrey Cleuren
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Grietje Molema
- Department Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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37
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Sato Y, Asahi T, Kataoka K. Integrative single-cell RNA-seq analysis of vascularized cerebral organoids. BMC Biol 2023; 21:245. [PMID: 37940920 PMCID: PMC10634128 DOI: 10.1186/s12915-023-01711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/25/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Cerebral organoids are three-dimensional in vitro cultured brains that mimic the function and structure of the human brain. One of the major challenges for cerebral organoids is the lack of functional vasculature. Without perfusable vessels, oxygen and nutrient supplies may be insufficient for long-term culture, hindering the investigation of the neurovascular interactions. Recently, several strategies for the vascularization of human cerebral organoids have been reported. However, the generalizable trends and variability among different strategies are unclear due to the lack of a comprehensive characterization and comparison of these vascularization strategies. In this study, we aimed to explore the effect of different vascularization strategies on the nervous system and vasculature in human cerebral organoids. RESULTS We integrated single-cell RNA sequencing data of multiple vascularized and vascular organoids and fetal brains from publicly available datasets and assessed the protocol-dependent and culture-day-dependent effects on the cell composition and transcriptomic profiles in neuronal and vascular cells. We revealed the similarities and uniqueness of multiple vascularization strategies and demonstrated the transcriptomic effects of vascular induction on neuronal and mesodermal-like cell populations. Moreover, our data suggested that the interaction between neurons and mesodermal-like cell populations is important for the cerebrovascular-specific profile of endothelial-like cells. CONCLUSIONS This study highlights the current challenges to vascularization strategies in human cerebral organoids and offers a benchmark for the future fabrication of vascularized organoids.
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Affiliation(s)
- Yuya Sato
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Toru Asahi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Comprehensive Research Organization, Waseda University, Tokyo, Japan.
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan.
| | - Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan.
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38
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Kearns NA, Iatrou A, Flood DJ, De Tissera S, Mullaney ZM, Xu J, Gaiteri C, Bennett DA, Wang Y. Dissecting the human leptomeninges at single-cell resolution. Nat Commun 2023; 14:7036. [PMID: 37923721 PMCID: PMC10624900 DOI: 10.1038/s41467-023-42825-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023] Open
Abstract
Emerging evidence shows that the meninges conduct essential immune surveillance and immune defense at the brain border, and the dysfunction of meningeal immunity contributes to aging and neurodegeneration. However, no study exists on the molecular properties of cell types within human leptomeninges. Here, we provide single nuclei profiling of dissected postmortem leptomeninges from aged individuals. We detect diverse cell types, including unique meningeal endothelial, mural, and fibroblast subtypes. For immune cells, we show that most T cells express CD8 and bear characteristics of tissue-resident memory T cells. We also identify distinct subtypes of border-associated macrophages (BAMs) that display differential gene expressions from microglia and express risk genes for Alzheimer's Disease (AD), as nominated by genome-wide association studies (GWAS). We discover cell-type-specific differentially expressed genes in individuals with Alzheimer's dementia, particularly in fibroblasts and BAMs. Indeed, when cultured, leptomeningeal cells display the signature of ex vivo AD fibroblasts upon amyloid-β treatment. We further explore ligand-receptor interactions within the leptomeningeal niche and computationally infer intercellular communications in AD. Thus, our study establishes a molecular map of human leptomeningeal cell types, providing significant insight into the border immune and fibrotic responses in AD.
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Affiliation(s)
- Nicola A Kearns
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Artemis Iatrou
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, 02478, USA
| | - Daniel J Flood
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Sashini De Tissera
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Zachary M Mullaney
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Jishu Xu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
- Department of Psychiatry, Upstate Medical University, Syracuse, NY, 13210, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA.
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA.
- Rush Graduate College, Rush University, Chicago IL, 60612, USA.
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39
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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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40
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Zarodniuk M, Steele A, Lu X, Li J, Datta M. CNS tumor stroma transcriptomics identify perivascular fibroblasts as predictors of immunotherapy resistance in glioblastoma patients. NPJ Genom Med 2023; 8:35. [PMID: 37884531 PMCID: PMC10603041 DOI: 10.1038/s41525-023-00381-w] [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: 07/05/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Excessive deposition of extracellular matrix (ECM) is a hallmark of solid tumors; however, it remains poorly understood which cellular and molecular components contribute to the formation of ECM stroma in central nervous system (CNS) tumors. Here, we undertake a pan-CNS analysis of retrospective gene expression datasets to characterize inter- and intra-tumoral heterogeneity of ECM remodeling signatures in both adult and pediatric CNS disease. We find that CNS lesions - glioblastoma in particular - can be divided into two ECM-based subtypes (ECMhi and ECMlo) that are influenced by the presence of perivascular stromal cells resembling cancer-associated fibroblasts (CAFs). Ligand-receptor network analysis predicts that perivascular fibroblasts activate signaling pathways responsible for recruitment of tumor-associated macrophages and promotion of cancer stemness. Our analysis reveals that perivascular fibroblasts are correlated with unfavorable response to immune checkpoint blockade in glioblastoma and poor patient survival across a subset of CNS tumors. We provide insights into new stroma-driven mechanisms underlying immune evasion and immunotherapy resistance in CNS tumors like glioblastoma, and discuss how targeting these perivascular fibroblasts may prove an effective approach to improving treatment response and patient survival in a variety of CNS tumors.
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Affiliation(s)
- Maksym Zarodniuk
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Alexander Steele
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Xin Lu
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, USA
| | - Meenal Datta
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, USA.
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41
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Zhao N, Chung TD, Guo Z, Jamieson JJ, Liang L, Linville RM, Pessell AF, Wang L, Searson PC. The influence of physiological and pathological perturbations on blood-brain barrier function. Front Neurosci 2023; 17:1289894. [PMID: 37937070 PMCID: PMC10626523 DOI: 10.3389/fnins.2023.1289894] [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: 09/06/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023] Open
Abstract
The blood-brain barrier (BBB) is located at the interface between the vascular system and the brain parenchyma, and is responsible for communication with systemic circulation and peripheral tissues. During life, the BBB can be subjected to a wide range of perturbations or stresses that may be endogenous or exogenous, pathological or therapeutic, or intended or unintended. The risk factors for many diseases of the brain are multifactorial and involve perturbations that may occur simultaneously (e.g., two-hit model for Alzheimer's disease) and result in different outcomes. Therefore, it is important to understand the influence of individual perturbations on BBB function in isolation. Here we review the effects of eight perturbations: mechanical forces, temperature, electromagnetic radiation, hypoxia, endogenous factors, exogenous factors, chemical factors, and pathogens. While some perturbations may result in acute or chronic BBB disruption, many are also exploited for diagnostic or therapeutic purposes. The resultant outcome on BBB function depends on the dose (or magnitude) and duration of the perturbation. Homeostasis may be restored by self-repair, for example, via processes such as proliferation of affected cells or angiogenesis to create new vasculature. Transient or sustained BBB dysfunction may result in acute or pathological symptoms, for example, microhemorrhages or hypoperfusion. In more extreme cases, perturbations may lead to cytotoxicity and cell death, for example, through exposure to cytotoxic plaques.
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Affiliation(s)
- Nan Zhao
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, United States
| | - Tracy D. Chung
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Zhaobin Guo
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, United States
| | - John J. Jamieson
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Lily Liang
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Raleigh M. Linville
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Alex F. Pessell
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Linus Wang
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Peter C. Searson
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, United States
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42
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Hou L, Xiong X, Park Y, Boix C, James B, Sun N, He L, Patel A, Zhang Z, Molinie B, Van Wittenberghe N, Steelman S, Nusbaum C, Aguet F, Ardlie KG, Kellis M. Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease. Nat Genet 2023; 55:1665-1676. [PMID: 37770633 PMCID: PMC10562256 DOI: 10.1038/s41588-023-01509-5] [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: 06/25/2022] [Accepted: 08/22/2023] [Indexed: 09/30/2023]
Abstract
Genetic variants associated with complex traits are primarily noncoding, and their effects on gene-regulatory activity remain largely uncharacterized. To address this, we profile epigenomic variation of histone mark H3K27ac across 387 brain, heart, muscle and lung samples from Genotype-Tissue Expression (GTEx). We annotate 282 k active regulatory elements (AREs) with tissue-specific activity patterns. We identify 2,436 sex-biased AREs and 5,397 genetically influenced AREs associated with 130 k genetic variants (haQTLs) across tissues. We integrate genetic and epigenomic variation to provide mechanistic insights for disease-associated loci from 55 genome-wide association studies (GWAS), by revealing candidate tissues of action, driver SNPs and impacted AREs. Lastly, we build ARE-gene linking scores based on genetics (gLink scores) and demonstrate their unique ability to prioritize SNP-ARE-gene circuits. Overall, our epigenomic datasets, computational integration and mechanistic predictions provide valuable resources and important insights for understanding the molecular basis of human diseases/traits such as schizophrenia.
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Affiliation(s)
- Lei Hou
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xushen Xiong
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Yongjin Park
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Carles Boix
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Benjamin James
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Na Sun
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Liang He
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aman Patel
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Zhizhuo Zhang
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Benoit Molinie
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Scott Steelman
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chad Nusbaum
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - François Aguet
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Manolis Kellis
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Zhang L, Jia Z, Wu Q, Bai T, Wang B, Hu X, Li T, Liu X, Fu J, Chen Y, Ding X, Liu Z, Xu Z, Zhou H. Alleviating symptoms of neurodegenerative disorders by astrocyte-specific overexpression of TMEM164 in mice. Nat Metab 2023; 5:1787-1802. [PMID: 37679556 DOI: 10.1038/s42255-023-00887-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/08/2023] [Indexed: 09/09/2023]
Abstract
Neuroinflammatory microglia secrete cytokines to induce neurotoxic reactive astrocytes, which are one of the major causes of neuronal death. However, the intrinsic key regulators underlying neurotoxic reactive astrocytes induction are unknown. Here we show that the transmembrane protein 164 (TMEM164) is an early-response intrinsic factor that regulates neurotoxic astrocyte reactivity. TMEM164 overexpression inhibits the induction of neurotoxic reactive astrocytes, maintains normal astrocytic functions and suppresses neurotoxic reactive astrocyte-mediated neuronal death by decreasing the secretion of neurotoxic saturated lipids. Adeno-associated virus-mediated, astrocyte-specific TMEM164 overexpression in male and female mice prevents the induction of neurotoxic reactive astrocytes, dopaminergic neuronal loss and motor deficits in a Parkinson's disease model. Notably, brain-wide astrocyte-specific TMEM164 overexpression prevents the induction of neurotoxic reactive astrocytes, amyloid β deposition, neurodegeneration and memory decline in the 5XFAD Alzheimer's disease mouse model, suggesting that TMEM164 could serve as a potential therapeutic target for neurodegenerative disorders.
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Affiliation(s)
- Liansheng Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Zhiheng Jia
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qiang Wu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Tao Bai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Bo Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xinde Hu
- Genemagic Biosciences, Shanghai, China
| | - Tianwen Li
- Fudan University Huashan Hospital, Department of Neurosurgery, National Center for Neurological Disorders, National Key Laboratory for Medical Neurobiology, Shanghai Key Library of Brain Function and Regeneration, Institutes of Brain Science, MOE Frontiers Center for Brain Science, Shanghai Medical College-Fudan University, Shanghai, China
| | - Xingyu Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Jiqiang Fu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yuelei Chen
- Stem Cell Bank/Stem Cell Core Facility, Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoyan Ding
- Stem Cell Bank/Stem Cell Core Facility, Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Zhen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Zhengzheng Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Haibo Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
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44
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Jones HE, Coelho-Santos V, Bonney SK, Abrams KA, Shih AY, Siegenthaler JA. Meningeal origins and dynamics of perivascular fibroblast development on the mouse cerebral vasculature. Development 2023; 150:dev201805. [PMID: 37756588 PMCID: PMC10565218 DOI: 10.1242/dev.201805] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Perivascular fibroblasts (PVFs) are a fibroblast-like cell type that reside on large-diameter blood vessels in the adult meninges and central nervous system (CNS). PVFs contribute to fibrosis following injury but their homeostatic functions are not defined. PVFs were previously shown to be absent from most brain regions at birth and are only detected postnatally within the cerebral cortex. However, the origin, timing and cellular mechanisms of PVF development are not known. We used Col1a1-GFP and Col1a2-CreERT2 transgenic mice to track PVF development postnatally. Using lineage tracing and in vivo imaging we show that brain PVFs originate from the meninges and are first seen on parenchymal cerebrovasculature at postnatal day (P) 5. After P5, PVF coverage of the cerebrovasculature expands via local cell proliferation and migration from the meninges. Finally, we show that PVFs and perivascular macrophages develop concurrently. These findings provide the first complete timeline for PVF development in the brain, enabling future work into how PVF development is coordinated with cell types and structures in and around the perivascular spaces to support normal CNS vascular function.
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Affiliation(s)
- Hannah E. Jones
- Department of Pediatrics, Section of Developmental Biology, University of Colorado, Aurora, CO 80045, USA
- Cell Biology, Stem Cells and Development Graduate Program, University of Colorado, Aurora, CO 80045, USA
| | - Vanessa Coelho-Santos
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Stephanie K. Bonney
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Kelsey A. Abrams
- Department of Pediatrics, Section of Developmental Biology, University of Colorado, Aurora, CO 80045, USA
- Cell Biology, Stem Cells and Development Graduate Program, University of Colorado, Aurora, CO 80045, USA
| | - Andy Y. Shih
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Julie A. Siegenthaler
- Department of Pediatrics, Section of Developmental Biology, University of Colorado, Aurora, CO 80045, USA
- Cell Biology, Stem Cells and Development Graduate Program, University of Colorado, Aurora, CO 80045, USA
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45
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Sun N, Victor MB, Park YP, Xiong X, Scannail AN, Leary N, Prosper S, Viswanathan S, Luna X, Boix CA, James BT, Tanigawa Y, Galani K, Mathys H, Jiang X, Ng AP, Bennett DA, Tsai LH, Kellis M. Human microglial state dynamics in Alzheimer's disease progression. Cell 2023; 186:4386-4403.e29. [PMID: 37774678 PMCID: PMC10644954 DOI: 10.1016/j.cell.2023.08.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/21/2023] [Accepted: 08/29/2023] [Indexed: 10/01/2023]
Abstract
Altered microglial states affect neuroinflammation, neurodegeneration, and disease but remain poorly understood. Here, we report 194,000 single-nucleus microglial transcriptomes and epigenomes across 443 human subjects and diverse Alzheimer's disease (AD) pathological phenotypes. We annotate 12 microglial transcriptional states, including AD-dysregulated homeostatic, inflammatory, and lipid-processing states. We identify 1,542 AD-differentially-expressed genes, including both microglia-state-specific and disease-stage-specific alterations. By integrating epigenomic, transcriptomic, and motif information, we infer upstream regulators of microglial cell states, gene-regulatory networks, enhancer-gene links, and transcription-factor-driven microglial state transitions. We demonstrate that ectopic expression of our predicted homeostatic-state activators induces homeostatic features in human iPSC-derived microglia-like cells, while inhibiting activators of inflammation can block inflammatory progression. Lastly, we pinpoint the expression of AD-risk genes in microglial states and differential expression of AD-risk genes and their regulators during AD progression. Overall, we provide insights underlying microglial states, including state-specific and AD-stage-specific microglial alterations at unprecedented resolution.
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Affiliation(s)
- Na Sun
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matheus B Victor
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yongjin P Park
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pathology and Laboratory Medicine, Department of Statistics, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Xushen Xiong
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aine Ni Scannail
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Noelle Leary
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shaniah Prosper
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Soujanya Viswanathan
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xochitl Luna
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carles A Boix
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin T James
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yosuke Tanigawa
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kyriaki Galani
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hansruedi Mathys
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Xueqiao Jiang
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ayesha P Ng
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Li-Huei Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Jing K, Xu Y, Yang Y, Yin P, Ning D, Huang G, Deng Y, Chen G, Li G, Tian SZ, Zheng M. ScSmOP: a universal computational pipeline for single-cell single-molecule multiomics data analysis. Brief Bioinform 2023; 24:bbad343. [PMID: 37779245 DOI: 10.1093/bib/bbad343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/24/2023] [Accepted: 09/10/2023] [Indexed: 10/03/2023] Open
Abstract
Single-cell multiomics techniques have been widely applied to detect the key signature of cells. These methods have achieved a single-molecule resolution and can even reveal spatial localization. These emerging methods provide insights elucidating the features of genomic, epigenomic and transcriptomic heterogeneity in individual cells. However, they have given rise to new computational challenges in data processing. Here, we describe Single-cell Single-molecule multiple Omics Pipeline (ScSmOP), a universal pipeline for barcode-indexed single-cell single-molecule multiomics data analysis. Essentially, the C language is utilized in ScSmOP to set up spaced-seed hash table-based algorithms for barcode identification according to ligation-based barcoding data and synthesis-based barcoding data, followed by data mapping and deconvolution. We demonstrate high reproducibility of data processing between ScSmOP and published pipelines in comprehensive analyses of single-cell omics data (scRNA-seq, scATAC-seq, scARC-seq), single-molecule chromatin interaction data (ChIA-Drop, SPRITE, RD-SPRITE), single-cell single-molecule chromatin interaction data (scSPRITE) and spatial transcriptomic data from various cell types and species. Additionally, ScSmOP shows more rapid performance and is a versatile, efficient, easy-to-use and robust pipeline for single-cell single-molecule multiomics data analysis.
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Affiliation(s)
- Kai Jing
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yewen Xu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yang Yang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Pengfei Yin
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Duo Ning
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guangyu Huang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuqing Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Gengzhan Chen
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Simon Zhongyuan Tian
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Meizhen Zheng
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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47
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Sneha NP, Dharshini SAP, Taguchi YH, Gromiha MM. Investigating Neuron Degeneration in Huntington's Disease Using RNA-Seq Based Transcriptome Study. Genes (Basel) 2023; 14:1801. [PMID: 37761940 PMCID: PMC10530489 DOI: 10.3390/genes14091801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/02/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (HTT) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the key brain region responsible for executing motor/movement activities. Investigating patient and control samples from the BA4 region will provide a deeper understanding of the genes responsible for neuron degeneration and help to identify potential markers. Previous studies have focused on overall differential gene expression and associated biological functions. In this study, we illustrate the relationship between variants and differentially expressed genes/transcripts. We identified variants and their associated genes along with the quantification of genes and transcripts. We also predicted the effect of variants on various regulatory activities and found that many variants are regulating gene expression. Variants affecting miRNA and its targets are also highlighted in our study. Co-expression network studies revealed the role of novel genes. Function interaction network analysis unveiled the importance of genes involved in vesicle-mediated transport. From this unified approach, we propose that genes expressed in immune cells are crucial for reducing neuron death in HD.
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Affiliation(s)
- Nela Pragathi Sneha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
| | - S. Akila Parvathy Dharshini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
| | - Y.-h. Taguchi
- Department of Physics, Chuo University, Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan;
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
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48
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Fu J, Liang H, Yuan P, Wei Z, Zhong P. Brain pericyte biology: from physiopathological mechanisms to potential therapeutic applications in ischemic stroke. Front Cell Neurosci 2023; 17:1267785. [PMID: 37780206 PMCID: PMC10536258 DOI: 10.3389/fncel.2023.1267785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Pericytes play an indispensable role in various organs and biological processes, such as promoting angiogenesis, regulating microvascular blood flow, and participating in immune responses. Therefore, in this review, we will first introduce the discovery and development of pericytes, identification methods and functional characteristics, then focus on brain pericytes, on the one hand, to summarize the functions of brain pericytes under physiological conditions, mainly discussing from the aspects of stem cell characteristics, contractile characteristics and paracrine characteristics; on the other hand, to summarize the role of brain pericytes under pathological conditions, mainly taking ischemic stroke as an example. Finally, we will discuss and analyze the application and development of pericytes as therapeutic targets, providing the research basis and direction for future microvascular diseases, especially ischemic stroke treatment.
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Affiliation(s)
- Jiaqi Fu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Department of Neurology, Shidong Hospital, Yangpu District, Shanghai, China
| | - Huazheng Liang
- Monash Suzhou Research Institute, Suzhou, Jiangsu, China
| | - Ping Yuan
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhenyu Wei
- Department of Neurology, Shidong Hospital, Yangpu District, Shanghai, China
| | - Ping Zhong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Department of Neurology, Shidong Hospital, Yangpu District, Shanghai, China
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49
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Paryani F, Kwon JS, Ng CW, Madden N, Ofori K, Tang A, Lu H, Li J, Mahajan A, Davidson SM, Basile A, McHugh C, Vonsattel JP, Hickman R, Zody M, Houseman DE, Goldman JE, Yoo AS, Menon V, Al-Dalahmah O. Multi-OMIC analysis of Huntington disease reveals a neuroprotective astrocyte state. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556867. [PMID: 37745577 PMCID: PMC10515780 DOI: 10.1101/2023.09.08.556867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Huntington disease (HD) is an incurable neurodegenerative disease characterized by neuronal loss and astrogliosis. One hallmark of HD is the selective neuronal vulnerability of striatal medium spiny neurons. To date, the underlying mechanisms of this selective vulnerability have not been fully defined. Here, we employed a multi-omic approach including single nucleus RNAseq (snRNAseq), bulk RNAseq, lipidomics, HTT gene CAG repeat length measurements, and multiplexed immunofluorescence on post-mortem brain tissue from multiple brain regions of HD and control donors. We defined a signature of genes that is driven by CAG repeat length and found it enriched in astrocytic and microglial genes. Moreover, weighted gene correlation network analysis showed loss of connectivity of astrocytic and microglial modules in HD and identified modules that correlated with CAG-repeat length which further implicated inflammatory pathways and metabolism. We performed lipidomic analysis of HD and control brains and identified several lipid species that correlate with HD grade, including ceramides and very long chain fatty acids. Integration of lipidomics and bulk transcriptomics identified a consensus gene signature that correlates with HD grade and HD lipidomic abnormalities and implicated the unfolded protein response pathway. Because astrocytes are critical for brain lipid metabolism and play important roles in regulating inflammation, we analyzed our snRNAseq dataset with an emphasis on astrocyte pathology. We found two main astrocyte types that spanned multiple brain regions; these types correspond to protoplasmic astrocytes, and fibrous-like - CD44-positive, astrocytes. HD pathology was differentially associated with these cell types in a region-specific manner. One protoplasmic astrocyte cluster showed high expression of metallothionein genes, the depletion of this cluster positively correlated with the depletion of vulnerable medium spiny neurons in the caudate nucleus. We confirmed that metallothioneins were increased in cingulate HD astrocytes but were unchanged or even decreased in caudate astrocytes. We combined existing genome-wide association studies (GWAS) with a GWA study conducted on HD patients from the original Venezuelan cohort and identified a single-nucleotide polymorphism in the metallothionein gene locus associated with delayed age of onset. Functional studies found that metallothionein overexpressing astrocytes are better able to buffer glutamate and were neuroprotective of patient-derived directly reprogrammed HD MSNs as well as against rotenone-induced neuronal death in vitro. Finally, we found that metallothionein-overexpressing astrocytes increased the phagocytic activity of microglia in vitro and increased the expression of genes involved in fatty acid binding. Together, we identified an astrocytic phenotype that is regionally-enriched in less vulnerable brain regions that can be leveraged to protect neurons in HD.
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Affiliation(s)
- Fahad Paryani
- Department of Neurology, Columbia University Irving Medical Center
| | - Ji-Sun Kwon
- Washington University School of Medicine in St. Louis
| | - Chris W Ng
- Massachusetts Institute of Technology, Department of Biological Engineering
| | - Nacoya Madden
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Kenneth Ofori
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Alice Tang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Hong Lu
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Juncheng Li
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Aayushi Mahajan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Shawn M. Davidson
- Princeton University, Lewis-Sigler Institute for Integrative Genomics
| | | | | | - Jean Paul Vonsattel
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Richard Hickman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | | | - David E. Houseman
- Massachusetts Institute of Technology, Department of Biological Engineering
| | - James E. Goldman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Andrew S. Yoo
- Washington University School of Medicine in St. Louis
| | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center
| | - Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
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Pozojevic J, Spielmann M. Single-Cell Sequencing in Neurodegenerative Disorders. Mol Diagn Ther 2023; 27:553-561. [PMID: 37552451 PMCID: PMC10435411 DOI: 10.1007/s40291-023-00668-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 08/09/2023]
Abstract
Neurodegenerative disorders are typically characterized by late onset progressive damage to specific (sub)populations of cells of the nervous system that are essential for mobility, coordination, strength, sensation, and cognition. Addressing this selective cellular vulnerability has become feasible with the emergence of single-cell-omics technologies, which now represent the state-of-the-art approach to profile heterogeneity of complex tissues including human post-mortem brain at unprecedented resolution. In this review, we briefly recapitulate the experimental workflow of single-cell RNA sequencing and summarize the recent knowledge acquired with it in the most common neurodegenerative diseases: Parkinson's, Alzheimer's, Huntington's disease, and multiple sclerosis. We also discuss the possibility of applying single-cell approaches in the diagnostics and therapy of neurodegenerative disorders, as well as the limitations. While we are currently at the point of deeply exploring the transcriptomic changes in the affected cells, further technological developments hold a promise of manipulating the affected pathways once we understand them better.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Human Genetics, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, 23562, Lübeck, Germany
| | - Malte Spielmann
- Institute of Human Genetics, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, 23562, Lübeck, Germany.
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, 23562, Lübeck, Germany.
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