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Zeng Z, Ma Y, Hu L, Tan B, Liu P, Wang Y, Xing C, Xiong Y, Du H. OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing. Nat Commun 2024; 15:5983. [PMID: 39013860 PMCID: PMC11252408 DOI: 10.1038/s41467-024-50194-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/28/2024] [Indexed: 07/18/2024] Open
Abstract
Single-cell sequencing is frequently affected by "omission" due to limitations in sequencing throughput, yet bulk RNA-seq may contain these ostensibly "omitted" cells. Here, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping communities. This approach effectively interpolates and restores the continuity of "omitted" cells within single-cell RNA sequencing datasets. Furthermore, OmicVerse provides an extensive toolkit for both bulk and single cell RNA-seq analysis, offering seamless access to diverse methodologies, streamlining computational processes, fostering exquisite data visualization, and facilitating the extraction of significant biological insights to advance scientific research.
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Affiliation(s)
- Zehua Zeng
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China.
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, China.
| | - Yuqing Ma
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province, China
- Institute of Biopharmaceutics and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province, China
| | - Lei Hu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Bowen Tan
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing, China
| | - Peng Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Yixuan Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Cencan Xing
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China.
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, China.
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-Sen University, Guangzhou, Guangdong, China.
| | - Hongwu Du
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China.
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, China.
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2
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Duc Nguyen H, Ardeshir A, Fonseca VA, Kim WK. Cluster of differentiation molecules in the metabolic syndrome. Clin Chim Acta 2024; 561:119819. [PMID: 38901629 DOI: 10.1016/j.cca.2024.119819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
Metabolic syndrome (MetS) represents a significant public health concern due to its association with an increased risk of cardiovascular disease, type 2 diabetes, and other serious health conditions. Despite extensive research, the underlying molecular mechanisms contributing to MetS pathogenesis remain elusive. This review aims to provide a comprehensive overview of the molecular mechanisms linking MetS and cluster of differentiation (CD) markers, which play critical roles in immune regulation and cellular signaling. Through an extensive literature review with a systematic approach, we examine the involvement of various CD markers in MetS development and progression, including their roles in adipose tissue inflammation, insulin resistance, dyslipidemia, and hypertension. Additionally, we discuss potential therapeutic strategies targeting CD markers for the management of MetS. By synthesizing current evidence, this review contributes to a deeper understanding of the complex interplay between immune dysregulation and metabolic dysfunction in MetS, paving the way for the development of novel therapeutic interventions.
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Affiliation(s)
- Hai Duc Nguyen
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Amir Ardeshir
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Vivian A Fonseca
- Department Endocrinology Metabolism & Diabetes, Tulane University School of Medicine, New Orleans, LA, USA
| | - Woong-Ki Kim
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA.
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3
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Diemler CA, MacLean M, Heuer SE, Hewes AA, Marola OJ, Libby RT, Howell GR. Microglia depletion leads to increased susceptibility to ocular hypertension-dependent glaucoma. Front Aging Neurosci 2024; 16:1396443. [PMID: 39015474 PMCID: PMC11250491 DOI: 10.3389/fnagi.2024.1396443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/07/2024] [Indexed: 07/18/2024] Open
Abstract
In recent years, microglia have been highlighted for playing integral roles in neurodegenerative diseases, like glaucoma. To better understand the role of microglia during chronic ocular hypertension, we depleted microglia from aged (9-12 months old) DBA/2 J (D2) mice, which exhibit age-related increases in intraocular pressure, using a dietary CSF1R antagonist, PLX5622. Retinal ganglion cell (RGC) somas were counted, and optic nerve cross-sections stained and assessed for glaucomatous damage. Sustained administration of dietary PLX5622 significantly reduced the numbers of retinal microglia. Dietary PLX5622 did not lead to changes in intraocular pressure in D2 or normotensive DBA/2 J-Gpnmb+ (D2-Gpnmb+ ) control mice. While PLX5622-treated D2-Gpnmb+ did not develop optic nerve damage, PLX5622-treated D2 mice showed a significant increase in moderate-to-severe optic nerve damage compared to D2 mice fed a control diet. In conclusion, global reduction of microglia exacerbated glaucomatous neurodegeneration in D2 mice suggesting microglia play an overall beneficial role in protecting from ocular hypertension associated RGC loss.
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Affiliation(s)
- Cory A. Diemler
- The Jackson Laboratory, Bar Harbor, ME, United States
- Graduate School of Biological Sciences and Engineering, University of Maine, Orono, ME, United States
| | | | - Sarah E. Heuer
- The Jackson Laboratory, Bar Harbor, ME, United States
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, United States
| | | | | | - Richard T. Libby
- Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY, United States
| | - Gareth R. Howell
- The Jackson Laboratory, Bar Harbor, ME, United States
- Graduate School of Biological Sciences and Engineering, University of Maine, Orono, ME, United States
- Flaum Eye Institute, University of Rochester Medical Center, Rochester, NY, United States
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4
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Chadarevian JP, Hasselmann J, Lahian A, Capocchi JK, Escobar A, Lim TE, Le L, Tu C, Nguyen J, Kiani Shabestari S, Carlen-Jones W, Gandhi S, Bu G, Hume DA, Pridans C, Wszolek ZK, Spitale RC, Davtyan H, Blurton-Jones M. Therapeutic potential of human microglia transplantation in a chimeric model of CSF1R-related leukoencephalopathy. Neuron 2024:S0896-6273(24)00370-2. [PMID: 38897209 DOI: 10.1016/j.neuron.2024.05.023] [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: 11/15/2023] [Revised: 04/18/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Microglia replacement strategies are increasingly being considered for the treatment of primary microgliopathies like adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP). However, available mouse models fail to recapitulate the diverse neuropathologies and reduced microglia numbers observed in patients. In this study, we generated a xenotolerant mouse model lacking the fms-intronic regulatory element (FIRE) enhancer within Csf1r, which develops nearly all the hallmark pathologies associated with ALSP. Remarkably, transplantation of human induced pluripotent stem cell (iPSC)-derived microglial (iMG) progenitors restores a homeostatic microglial signature and prevents the development of axonal spheroids, white matter abnormalities, reactive astrocytosis, and brain calcifications. Furthermore, transplantation of CRISPR-corrected ALSP-patient-derived iMG reverses pre-existing spheroids, astrogliosis, and calcification pathologies. Together with the accompanying study by Munro and colleagues, our results demonstrate the utility of FIRE mice to model ALSP and provide compelling evidence that iMG transplantation could offer a promising new therapeutic strategy for ALSP and perhaps other microglia-associated neurological disorders.
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Affiliation(s)
- Jean Paul Chadarevian
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA, USA; Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - Jonathan Hasselmann
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - Alina Lahian
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA, USA; Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - Joia K Capocchi
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA
| | - Adrian Escobar
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - Tau En Lim
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - Lauren Le
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA
| | - Christina Tu
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - Jasmine Nguyen
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA
| | - Sepideh Kiani Shabestari
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - William Carlen-Jones
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA
| | - Sunil Gandhi
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA, USA
| | - Guojun Bu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - David A Hume
- Mater Research Institute, University of Queensland, Brisbane, QLD, Australia
| | - Clare Pridans
- University of Edinburgh, University of Edinburgh Center for Inflammation Research, Edinburgh, UK
| | | | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Hayk Davtyan
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.
| | - Mathew Blurton-Jones
- Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA, USA; Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.
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5
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Hwang M, Bergmann CC. Neurotropic murine coronavirus mediated demyelination: Factors dampening pathogenesis. J Neuroimmunol 2024; 393:578382. [PMID: 38850674 DOI: 10.1016/j.jneuroim.2024.578382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/12/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
Virus infections and autoimmune responses are implicated as primary triggers of demyelinating diseases. Specifically, the association of Epstein-Barr virus (EBV) infection with development of multiple sclerosis (MS) has re-ignited an interest in virus induced autoimmune responses to CNS antigens. Nevertheless, demyelination may also be caused by immune mediated bystander pathology in an attempt to control direct infection in the CNS. Tissue damage as a result of anti-viral responses or low level viral persistence may lead to immune activation manifesting in demyelinating lesions, axonal damage and clinical symptoms. This review focuses on the neurotropic mouse coronavirus induced demyelination model to highlight how immune responses activated during the acute phase pave the way to dampen pathology and promote repair. We specifically discuss the role of immune dampening factors programmed cell death ligand 1 (PD-L1) and interleukin (IL)-10, as well as microglia and triggering receptor expressed on myeloid cells 2 (Trem2), in limiting demyelination independent of viral persistence.
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Affiliation(s)
- Mihyun Hwang
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA; Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Cornelia C Bergmann
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA; Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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