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Shang Y, Wang Z, Xi L, Wang Y, Liu M, Feng Y, Wang J, Wu Q, Xiang X, Chen M, Ding Y. Droplet-based single-cell sequencing: Strategies and applications. Biotechnol Adv 2024:108454. [PMID: 39271031 DOI: 10.1016/j.biotechadv.2024.108454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 08/22/2024] [Accepted: 09/10/2024] [Indexed: 09/15/2024]
Abstract
Notable advancements in single-cell omics technologies have not only addressed longstanding challenges but also enabled unprecedented studies of cellular heterogeneity with unprecedented resolution and scale. These strides have led to groundbreaking insights into complex biological systems, paving the way for a more profound comprehension of human biology and diseases. The droplet microfluidic technology has become a crucial component in many single-cell sequencing workflows in terms of throughput, cost-effectiveness, and automation. Utilizing a microfluidic chip to encapsulate and profile individual cells within droplets has significantly improved single-cell research. Therefore, this review aims to comprehensively elaborate the droplet microfluidics-assisted omics methods from a single-cell perspective. The strategies for using droplet microfluidics in the realms of genomics, epigenomics, transcriptomics, and proteomics analyses are first introduced. On this basis, the focus then turns to the latest applications of this technology in different sequencing patterns, including mono- and multi-omics. Finally, the challenges and further perspectives of droplet-based single-cell sequencing in both foundational research and commercial applications are discussed.
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Affiliation(s)
- Yuting Shang
- Department of Food Science & Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhengzheng Wang
- Department of Food Science & Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Liqing Xi
- Department of Food Science & Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yantao Wang
- Department of Food Science & Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Meijing Liu
- Department of Food Science & Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ying Feng
- Department of Food Science & Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou 510432, China
| | - Qingping Wu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xinran Xiang
- Fujian Key Laboratory of Aptamers Technology, Fuzhou General Clinical Medical School (the 900th Hospital), Fujian Medical University, Fuzhou 350001, China; Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, China.
| | - Moutong Chen
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Yu Ding
- Department of Food Science & Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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Huang T, Guo Y, Xie W, Yin J, Zhang Y, Chen W, Huang D, Li P. Brain border-derived CXCL2 + neutrophils drive NET formation and impair vascular reperfusion following ischemic stroke. CNS Neurosci Ther 2024; 30:e14916. [PMID: 39135337 PMCID: PMC11319398 DOI: 10.1111/cns.14916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND The brain border compartments harbor a diverse population of immune cells and serve as invasion sites for leukocyte influx into the brain following CNS injury. However, how brain-border myeloid cells affect stroke pathology remains poorly characterized. METHODS AND RESULTS Here, we showed that ischemic stroke-induced expansion of CXCL2+ neutrophils, which exhibit highly proinflammatory features. We tracked CXCL2+ neutrophils in vivo by utilizing a photoconvertible Kik-GR mouse (fluorescent proteins Kikume Green Red, Kik-GR) and found that brain-infiltrating CXCL2+ neutrophils following ischemic stroke were mainly derived from the brain border rather than the periphery. We demonstrated that CXCL2 neutralization inhibited the formation and releasing of neutrophil extracellular traps (NETs) from in vitro cultured primary neutrophils. Furthermore, CXCL2-neutralizing antibody treatment reduced brain infarcts and improved vascular reperfusion at day 3 postischemic stroke. CONCLUSIONS Collectively, brain border-derived CXCL2+ neutrophil expansion may impair vascular reperfusion by releasing NETs following ischemic stroke.
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Affiliation(s)
- Tingting Huang
- Department of Anesthesiology, Clinical Research Center, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Key Laboratory of Anesthesiology, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
| | - Yunlu Guo
- Department of Anesthesiology, Clinical Research Center, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Key Laboratory of Anesthesiology, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
| | - Wanqing Xie
- Department of Anesthesiology, Clinical Research Center, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Key Laboratory of Anesthesiology, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
| | - Jiemin Yin
- Department of Anesthesiology, Clinical Research Center, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Key Laboratory of Anesthesiology, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
| | - Yueman Zhang
- Department of Anesthesiology, Clinical Research Center, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Key Laboratory of Anesthesiology, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
| | - Weijie Chen
- Department of Anesthesiology, Clinical Research Center, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Key Laboratory of Anesthesiology, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
| | - Dan Huang
- Department of Anesthesiology, Clinical Research Center, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Key Laboratory of Anesthesiology, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
| | - Peiying Li
- Department of Anesthesiology, Clinical Research Center, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Key Laboratory of Anesthesiology, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
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3
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Trzebanski S, Kim JS, Larossi N, Raanan A, Kancheva D, Bastos J, Haddad M, Solomon A, Sivan E, Aizik D, Kralova JS, Gross-Vered M, Boura-Halfon S, Lapidot T, Alon R, Movahedi K, Jung S. Classical monocyte ontogeny dictates their functions and fates as tissue macrophages. Immunity 2024; 57:1225-1242.e6. [PMID: 38749446 DOI: 10.1016/j.immuni.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 12/29/2023] [Accepted: 04/18/2024] [Indexed: 06/14/2024]
Abstract
Classical monocytes (CMs) are ephemeral myeloid immune cells that circulate in the blood. Emerging evidence suggests that CMs can have distinct ontogeny and originate from either granulocyte-monocyte- or monocyte-dendritic-cell progenitors (GMPs or MDPs). Here, we report surface markers that allowed segregation of murine GMP- and MDP-derived CMs, i.e., GMP-Mo and MDP-Mo, as well as their functional characterization, including fate definition following adoptive cell transfer. GMP-Mo and MDP-Mo yielded an equal increase in homeostatic CM progeny, such as blood-resident non-classical monocytes and gut macrophages; however, these cells differentially seeded various other selected tissues, including the dura mater and lung. Specifically, GMP-Mo and MDP-Mo differentiated into distinct interstitial lung macrophages, linking CM dichotomy to previously reported pulmonary macrophage heterogeneity. Collectively, we provide evidence for the existence of two functionally distinct CM subsets in the mouse that differentially contribute to peripheral tissue macrophage populations in homeostasis and following challenge.
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Affiliation(s)
- Sébastien Trzebanski
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jung-Seok Kim
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Niss Larossi
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ayala Raanan
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Daliya Kancheva
- Brain and Systems Immunology Laboratory, Brussels Center for Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jonathan Bastos
- Brain and Systems Immunology Laboratory, Brussels Center for Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Montaser Haddad
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Aryeh Solomon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ehud Sivan
- MICC Cell Observatory Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan Aizik
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Mor Gross-Vered
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sigalit Boura-Halfon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tsvee Lapidot
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ronen Alon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kiavash Movahedi
- Brain and Systems Immunology Laboratory, Brussels Center for Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Steffen Jung
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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4
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Wang L, Zheng J, Zhao S, Wan Y, Wang M, Bosco DB, Kuan CY, Richardson JR, Wu LJ. CCR2 + monocytes replenish border-associated macrophages in the diseased mouse brain. Cell Rep 2024; 43:114120. [PMID: 38625796 PMCID: PMC11105166 DOI: 10.1016/j.celrep.2024.114120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 02/06/2024] [Accepted: 03/30/2024] [Indexed: 04/18/2024] Open
Abstract
Border-associated macrophages (BAMs) are tissue-resident macrophages that reside at the border of the central nervous system (CNS). Since BAMs originate from yolk sac progenitors that do not persist after birth, the means by which this population of cells is maintained is not well understood. Using two-photon microscopy and multiple lineage-tracing strategies, we determine that CCR2+ monocytes are significant contributors to BAM populations following disruptions of CNS homeostasis in adult mice. After BAM depletion, while the residual BAMs possess partial self-repopulation capability, the CCR2+ monocytes are a critical source of the repopulated BAMs. In addition, we demonstrate the existence of CCR2+ monocyte-derived long-lived BAMs in a brain compression model and in a sepsis model after the initial disruption of homeostasis. Our study reveals that the short-lived CCR2+ monocytes transform into long-lived BAM-like cells at the CNS border and subsequently contribute to BAM populations.
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Affiliation(s)
- Lingxiao Wang
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Jiaying Zheng
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Shunyi Zhao
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Yushan Wan
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Meijie Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Dale B Bosco
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chia-Yi Kuan
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jason R Richardson
- Department of Environmental Health Science, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL 33199, USA
| | - Long-Jun Wu
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA; Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Center for Neuroimmunology and Glial Biology, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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5
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Zhou C, Xu H, Luo J. Meningeal lymphatic vasculature, a general target for glioblastoma therapy? FUNDAMENTAL RESEARCH 2024; 4:267-269. [PMID: 38933521 PMCID: PMC11197748 DOI: 10.1016/j.fmre.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/19/2022] [Accepted: 04/03/2023] [Indexed: 06/28/2024] Open
Abstract
Glioblastoma (GBM) causes nearly universal mortality as a result of the failure of conventional therapies including surgical resection, targeted radiation therapy, and chemotherapy. An increasingly important treatment option is combining immunotherapy with other therapies in both preclinical and clinical studies. The central nervous system (CNS) has been historically considered an immune privileged area, but increasing evidence, including the recent rediscovery of meningeal lymphatic vessels (MLVs), has overturned this notion. MLVs are populated by multiple immune cells and connect the CNS to the periphery by draining cerebrospinal fluid with soluble CNS antigens and immune cells into cervical lymph nodes. In the past few years, more and more studies have indicated that MLVs are involved in the regulation of inflammation and the immune response in the pathogenesis of various CNS diseases including GBM. Here, we explore the critical interlinkages between MLVs and GBM therapies including chemotherapy, radiotherapy and immunotherapy, and propose the meningeal lymphatic vasculature as a general target for GBM therapy.
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Affiliation(s)
| | | | - Jincai Luo
- Laboratory of Vascular Biology, Institute of Molecular Medicine, College of Future Technology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
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6
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Srinivasan S, Kancheva D, De Ren S, Saito T, Jans M, Boone F, Vandendriessche C, Paesmans I, Maurin H, Vandenbroucke RE, Hoste E, Voet S, Scheyltjens I, Pavie B, Lippens S, Schwabenland M, Prinz M, Saido T, Bottelbergs A, Movahedi K, Lamkanfi M, van Loo G. Inflammasome signaling is dispensable for ß-amyloid-induced neuropathology in preclinical models of Alzheimer's disease. Front Immunol 2024; 15:1323409. [PMID: 38352874 PMCID: PMC10863058 DOI: 10.3389/fimmu.2024.1323409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Background Alzheimer's disease (AD) is the most common neurodegenerative disorder affecting memory and cognition. The disease is accompanied by an abnormal deposition of ß-amyloid plaques in the brain that contributes to neurodegeneration and is known to induce glial inflammation. Studies in the APP/PS1 mouse model of ß-amyloid-induced neuropathology have suggested a role for inflammasome activation in ß-amyloid-induced neuroinflammation and neuropathology. Methods Here, we evaluated the in vivo role of microglia-selective and full body inflammasome signalling in several mouse models of ß-amyloid-induced AD neuropathology. Results Microglia-specific deletion of the inflammasome regulator A20 and inflammasome effector protease caspase-1 in the AppNL-G-F and APP/PS1 models failed to identify a prominent role for microglial inflammasome signalling in ß-amyloid-induced neuropathology. Moreover, global inflammasome inactivation through respectively full body deletion of caspases 1 and 11 in AppNL-G-F mice and Nlrp3 deletion in APP/PS1 mice also failed to modulate amyloid pathology and disease progression. In agreement, single-cell RNA sequencing did not reveal an important role for Nlrp3 signalling in driving microglial activation and the transition into disease-associated states, both during homeostasis and upon amyloid pathology. Conclusion Collectively, these results question a generalizable role for inflammasome activation in preclinical amyloid-only models of neuroinflammation.
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Affiliation(s)
- Sahana Srinivasan
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Daliya Kancheva
- Brain and Systems Immunology Lab, Brussels Center for Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sofie De Ren
- Neuroscience Therapeutic Area, Janssen Research and Development, Beerse, Belgium
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Saitama, Japan
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Maude Jans
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Fleur Boone
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Charysse Vandendriessche
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Ine Paesmans
- Neuroscience Therapeutic Area, Janssen Research and Development, Beerse, Belgium
| | - Hervé Maurin
- Neuroscience Therapeutic Area, Janssen Research and Development, Beerse, Belgium
| | - Roosmarijn E. Vandenbroucke
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Esther Hoste
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Sofie Voet
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Isabelle Scheyltjens
- Brain and Systems Immunology Lab, Brussels Center for Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Benjamin Pavie
- VIB Center for Inflammation Research, Ghent, Belgium
- VIB Bioimaging Core, Ghent, Belgium
| | - Saskia Lippens
- VIB Center for Inflammation Research, Ghent, Belgium
- VIB Bioimaging Core, Ghent, Belgium
| | - Marius Schwabenland
- Institute of Neuropathology Medical Center, University of Freiburg, Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology Medical Center, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Takaomi Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Saitama, Japan
| | - Astrid Bottelbergs
- Neuroscience Therapeutic Area, Janssen Research and Development, Beerse, Belgium
| | - Kiavash Movahedi
- Brain and Systems Immunology Lab, Brussels Center for Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mohamed Lamkanfi
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Geert van Loo
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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7
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Shi X, Baracho GV, Lomas WE, Song HW, Widmann SJ, Tyznik AJ. Co-staining with Fluorescent Antibodies and Antibody-Derived Tags for Cell Sorting Prior to CITE-Seq. Methods Mol Biol 2024; 2779:287-303. [PMID: 38526791 DOI: 10.1007/978-1-0716-3738-8_13] [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: 03/27/2024]
Abstract
The paired detection of the transcriptome and proteome at single-cell resolution provides exquisite insight to immune mechanisms in health and disease. Here, we describe a detailed protocol wherein we combine cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq), a technique utilizing antibody-derived tags (ADTs) to profile mRNA and proteins simultaneously via sequencing, with fluorescence-activated cell sorting to enrich cell populations. Our protocol provides step-by-step guidance on co-staining cells with both fluorescent antibodies and ADTs simultaneously, instructions on cell sorting and an overview of the single-cell capture workflow using the BD Rhapsody™ system. This method is useful for in-depth single-cell characterization on sorted rare cell populations.
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8
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Santorella E, Balsbaugh JL, Ge S, Saboori P, Baker D, Pachter JS. Proteomic interrogation of the meninges reveals the molecular identities of structural components and regional distinctions along the CNS axis. Fluids Barriers CNS 2023; 20:74. [PMID: 37858244 PMCID: PMC10588166 DOI: 10.1186/s12987-023-00473-w] [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] [Received: 07/24/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
The meninges surround the brain and spinal cord, affording physical protection while also serving as a niche of neuroimmune activity. Though possessing stromal qualities, its complex cellular and extracellular makeup has yet to be elaborated, and it remains unclear whether the meninges vary along the neuroaxis. Hence, studies were carried-out to elucidate the protein composition and structural organization of brain and spinal cord meninges in normal, adult Biozzi ABH mice. First, shotgun, bottom-up proteomics was carried-out. Prominent proteins at both brain and spinal levels included Type II collagen and Type II keratins, representing extracellular matrix (ECM) and cytoskeletal categories, respectively. While the vast majority of total proteins detected was shared between both meningeal locales, more were uniquely detected in brain than in spine. This pattern was also seen when total proteins were subdivided by cellular compartment, except in the case of the ECM category where brain and spinal meninges each had near equal number of unique proteins, and Type V and type III collagen registered exclusively in the spine. Quantitative analysis revealed differential expression of several collagens and cytoskeletal proteins between brain and spinal meninges. High-resolution immunofluorescence and immunogold-scanning electronmicroscopy on sections from whole brain and spinal cord - still encased within bone -identified major proteins detected by proteomics, and highlighted their association with cellular and extracellular elements of variously shaped arachnoid trabeculae. Western blotting aligned with the proteomic and immunohistological analyses, reinforcing differential appearance of proteins in brain vs spinal meninges. Results could reflect regional distinctions in meninges that govern protective and/or neuroimmune functions.
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Affiliation(s)
- Elise Santorella
- Department of Immunology, UConn Health, 263 Farmington Ave, Farmington, CT, 06030, USA
| | - Jeremy L Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT, 06269, USA
| | - Shujun Ge
- Department of Immunology, UConn Health, 263 Farmington Ave, Farmington, CT, 06030, USA
| | - Parisa Saboori
- Department of Mechanical Engineering, Manhattan College, Bronx, NY, 10071, USA
| | - David Baker
- Blizard Institute, Queen Mary University of London, London, England
| | - Joel S Pachter
- Department of Immunology, UConn Health, 263 Farmington Ave, Farmington, CT, 06030, USA.
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Hwang S, Jang J, Park K, Yim YS. Unveiling the enigma of Brain-resident immune cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559602. [PMID: 37808712 PMCID: PMC10557645 DOI: 10.1101/2023.09.26.559602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The immune system has been extensively studied in traditional immune hubs like the spleen and lymph nodes. However, recent advances in immunology highlight unique immune cell characteristics across anatomical compartments. In this study, we challenged conventional thinking by uncovering distinct immune cell populations within the brain parenchyma, separate from those in the blood, meninges, and choroid plexus, with unique transcriptional profiles. Brain-resident immune cells are not derived from maternal immune cells, and age-related changes, with an increase in CD8 + T cells in aged mice, are noted. Alzheimer's disease (AD) alters microglia's interaction with brain-resident immune cells, emphasizing immune-brain dynamics. Furthermore, we reveal dynamic immune cell interactions and essential cytokine roles in brain homeostasis, with stable cytokine expression but emerging signaling pathways in AD. In summary, this study advances our understanding of brain-resident immune cells in both normal and pathological conditions.
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10
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Han X, Xu X, Yang C, Liu G. Microfluidic design in single-cell sequencing and application to cancer precision medicine. CELL REPORTS METHODS 2023; 3:100591. [PMID: 37725985 PMCID: PMC10545941 DOI: 10.1016/j.crmeth.2023.100591] [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: 03/31/2023] [Revised: 07/01/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023]
Abstract
Single-cell sequencing (SCS) is a crucial tool to reveal the genetic and functional heterogeneity of tumors, providing unique insights into the clonal evolution, microenvironment, drug resistance, and metastatic progression of cancers. Microfluidics is a critical component of many SCS technologies and workflows, conferring advantages in throughput, economy, and automation. Here, we review the current landscape of microfluidic architectures and sequencing techniques for single-cell omics analysis and highlight how these have enabled recent applications in oncology research. We also discuss the challenges and the promise of microfluidics-based single-cell analysis in the future of precision oncology.
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Affiliation(s)
- Xin Han
- CUHK(SZ)-Boyalife Joint Laboratory of Regenerative Medicine Engineering, Biomedical Engineering Programme, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Xing Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China; Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related 12 Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Chaoyang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China; Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related 12 Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.
| | - Guozhen Liu
- CUHK(SZ)-Boyalife Joint Laboratory of Regenerative Medicine Engineering, Biomedical Engineering Programme, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China.
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11
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Clappaert EJ, Kancheva D, Brughmans J, Debraekeleer A, Bardet PMR, Elkrim Y, Lacroix D, Živalj M, Hamouda AE, Van Ginderachter JA, Deschoemaeker S, Laoui D. Flt3L therapy increases the abundance of Treg-promoting CCR7 + cDCs in preclinical cancer models. Front Immunol 2023; 14:1166180. [PMID: 37622122 PMCID: PMC10445485 DOI: 10.3389/fimmu.2023.1166180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Conventional dendritic cells (cDCs) are at the forefront of activating the immune system to mount an anti-tumor immune response. Flt3L is a cytokine required for DC development that can increase DC abundance in the tumor when administered therapeutically. However, the impact of Flt3L on the phenotype of distinct cDC subsets in the tumor microenvironment is still largely undetermined. Here, using multi-omic single-cell analysis, we show that Flt3L therapy increases all cDC subsets in orthotopic E0771 and TS/A breast cancer and LLC lung cancer models, but this did not result in a reduction of tumor growth in any of the models. Interestingly, a CD81+migcDC1 population, likely developing from cDC1, was induced upon Flt3L treatment in E0771 tumors as well as in TS/A breast and LLC lung tumors. This CD81+migcDC1 subset is characterized by the expression of both canonical cDC1 markers as well as migratory cDC activation and regulatory markers and displayed a Treg-inducing potential. To shift the cDC phenotype towards a T-cell stimulatory phenotype, CD40 agonist therapy was administered to E0771 tumor-bearing mice in combination with Flt3L. However, while αCD40 reduced tumor growth, Flt3L failed to improve the therapeutic response to αCD40 therapy. Interestingly, Flt3L+αCD40 combination therapy increased the abundance of Treg-promoting CD81+migcDC1. Nonetheless, while Treg-depletion and αCD40 therapy were synergistic, the addition of Flt3L to this combination did not result in any added benefit. Overall, these results indicate that merely increasing cDCs in the tumor by Flt3L treatment cannot improve anti-tumor responses and therefore might not be beneficial for the treatment of cancer, though could still be of use to increase cDC numbers for autologous DC-therapy.
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Affiliation(s)
- Emile J. Clappaert
- Laboratory of Dendritic Cell Biology and Cancer Immunotherapy, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium
| | - Daliya Kancheva
- Laboratory of Dendritic Cell Biology and Cancer Immunotherapy, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium
| | - Jan Brughmans
- Laboratory of Dendritic Cell Biology and Cancer Immunotherapy, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ayla Debraekeleer
- Laboratory of Dendritic Cell Biology and Cancer Immunotherapy, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Pauline M. R. Bardet
- Laboratory of Dendritic Cell Biology and Cancer Immunotherapy, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yvon Elkrim
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium
| | - Dagmar Lacroix
- Laboratory of Dendritic Cell Biology and Cancer Immunotherapy, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Maida Živalj
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium
| | - Ahmed E.I. Hamouda
- Laboratory of Dendritic Cell Biology and Cancer Immunotherapy, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jo A. Van Ginderachter
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium
| | - Sofie Deschoemaeker
- Laboratory of Dendritic Cell Biology and Cancer Immunotherapy, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Damya Laoui
- Laboratory of Dendritic Cell Biology and Cancer Immunotherapy, VIB Center for Inflammation Research, Brussels, Belgium
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
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12
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Claeys W, Van Hoecke L, Lernout H, De Nolf C, Van Imschoot G, Van Wonterghem E, Verhaege D, Castelein J, Geerts A, Van Steenkiste C, Vandenbroucke RE. Experimental hepatic encephalopathy causes early but sustained glial transcriptional changes. J Neuroinflammation 2023; 20:130. [PMID: 37248507 DOI: 10.1186/s12974-023-02814-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/21/2023] [Indexed: 05/31/2023] Open
Abstract
Hepatic encephalopathy (HE) is a common complication of liver cirrhosis, associated with high morbidity and mortality, for which no brain-targeted therapies exist at present. The interplay between hyperammonemia and inflammation is thought to drive HE development. As such, astrocytes, the most important ammonia-metabolizing cells in the brain, and microglia, the main immunomodulatory cells in the brain, have been heavily implicated in HE development. As insight into cellular perturbations driving brain pathology remains largely elusive, we aimed to investigate cell-type specific transcriptomic changes in the HE brain. In the recently established mouse bile duct ligation (BDL) model of HE, we performed RNA-Seq of sorted astrocytes and microglia at 14 and 28 days after induction. This revealed a marked transcriptional response in both cell types which was most pronounced in microglia. In both cell types, pathways related to inflammation and hypoxia, mechanisms commonly implicated in HE, were enriched. Additionally, astrocytes exhibited increased corticoid receptor and oxidative stress signaling, whereas microglial transcriptome changes were linked to immune cell attraction. Accordingly, both monocytes and neutrophils accumulated in the BDL mouse brain. Time-dependent changes were limited in both cell types, suggesting early establishment of a pathological phenotype. While HE is often considered a unique form of encephalopathy, astrocytic and microglial transcriptomes showed significant overlap with previously established gene expression signatures in other neuroinflammatory diseases like septic encephalopathy and stroke, suggesting common pathophysiological mechanisms. Our dataset identifies key molecular mechanisms involved in preclinical HE and provides a valuable resource for development of novel glial-directed therapeutic strategies.
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Affiliation(s)
- Wouter Claeys
- Hepatology Research Unit, Department of Internal Medicine and Paediatrics, Ghent University, 9000, Ghent, Belgium
- Liver Research Center Ghent, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
- Barriers in Inflammation, VIB Center for Inflammation Research, VIB, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
| | - Lien Van Hoecke
- Barriers in Inflammation, VIB Center for Inflammation Research, VIB, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
| | - Hannah Lernout
- Barriers in Inflammation, VIB Center for Inflammation Research, VIB, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- IBD Research Unit, Department of Internal Medicine and Paediatrics, Ghent University, 9000, Ghent, Belgium
| | - Clint De Nolf
- Barriers in Inflammation, VIB Center for Inflammation Research, VIB, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
- Department of Internal Medicine and Paediatrics, Ghent University, 9000, Ghent, Belgium
| | - Griet Van Imschoot
- Barriers in Inflammation, VIB Center for Inflammation Research, VIB, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
| | - Elien Van Wonterghem
- Barriers in Inflammation, VIB Center for Inflammation Research, VIB, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
| | - Daan Verhaege
- Barriers in Inflammation, VIB Center for Inflammation Research, VIB, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
| | - Jonas Castelein
- Barriers in Inflammation, VIB Center for Inflammation Research, VIB, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
| | - Anja Geerts
- Hepatology Research Unit, Department of Internal Medicine and Paediatrics, Ghent University, 9000, Ghent, Belgium
- Liver Research Center Ghent, Ghent University Hospital, Ghent University, 9000, Ghent, Belgium
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
| | - Christophe Van Steenkiste
- Department of Gastroenterology and Hepatology, Antwerp University, Antwerp, Belgium
- Department of Gastroenterology and Hepatology, Maria Middelares Hospital, Ghent, Belgium
| | - Roosmarijn E Vandenbroucke
- Barriers in Inflammation, VIB Center for Inflammation Research, VIB, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium.
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13
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Su Y, Zheng H, Shi C, Li X, Zhang S, Guo G, Yu W, Zhang S, Hu Z, Yang J, Xia Z, Mao C, Xu Y. Meningeal immunity and neurological diseases: new approaches, new insights. J Neuroinflammation 2023; 20:125. [PMID: 37231449 DOI: 10.1186/s12974-023-02803-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
The meninges, membranes surrounding the central nervous system (CNS) boundary, harbor a diverse array of immunocompetent immune cells, and therefore, serve as an immunologically active site. Meningeal immunity has emerged as a key factor in modulating proper brain function and social behavior, performing constant immune surveillance of the CNS, and participating in several neurological diseases. However, it remains to be determined how meningeal immunity contributes to CNS physiology and pathophysiology. With the advances in single-cell omics, new approaches, such as single-cell technologies, unveiled the details of cellular and molecular mechanisms underlying meningeal immunity in CNS homeostasis and dysfunction. These new findings contradict some previous dogmas and shed new light on new possible therapeutic targets. In this review, we focus on the complicated multi-components, powerful meningeal immunosurveillance capability, and its crucial involvement in physiological and neuropathological conditions, as recently revealed by single-cell technologies.
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Affiliation(s)
- Yun Su
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China
- The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Huimin Zheng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China
- The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Changhe Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Xinwei Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China
- The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shuyu Zhang
- Neuro-Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Guangyu Guo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China
| | - Wenkai Yu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shuo Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China
- The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhengwei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China
- The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jing Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zongping Xia
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China
| | - Chengyuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China.
- The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Sino-British Research Centre for Molecular Oncology, National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No.1 Eastern Jian-She Road, Zhengzhou, 450052, Henan, China.
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, Zhengzhou, 450052, Henan, China.
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14
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Colpitts SJ, Budd MA, Monajemi M, Reid KT, Murphy JM, Ivison S, Verchere CB, Levings MK, Crome SQ. Strategies for optimizing CITE-seq for human islets and other tissues. Front Immunol 2023; 14:1107582. [PMID: 36936943 PMCID: PMC10014726 DOI: 10.3389/fimmu.2023.1107582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/30/2023] [Indexed: 03/05/2023] Open
Abstract
Defining the immunological landscape of human tissue is an important area of research, but challenges include the impact of tissue disaggregation on cell phenotypes and the low abundance of immune cells in many tissues. Here, we describe methods to troubleshoot and standardize Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) for studies involving enzymatic digestion of human tissue. We tested epitope susceptibility of 92 antibodies commonly used to differentiate immune lineages and cell states on human peripheral blood mononuclear cells following treatment with an enzymatic digestion cocktail used to isolate islets. We observed CD4, CD8a, CD25, CD27, CD120b, CCR4, CCR6, and PD1 display significant sensitivity to enzymatic treatment, effects that often could not be overcome with alternate antibodies. Comparison of flow cytometry-based CITE-seq antibody titrations and sequencing data supports that for the majority of antibodies, flow cytometry accurately predicts optimal antibody concentrations for CITE-seq. Comparison by CITE-seq of immune cells in enzymatically digested islet tissue and donor-matched spleen not treated with enzymes revealed little digestion-induced epitope cleavage, suggesting increased sensitivity of CITE-seq and/or that the islet structure may protect resident immune cells from enzymes. Within islets, CITE-seq identified immune cells difficult to identify by transcriptional signatures alone, such as distinct tissue-resident T cell subsets, mast cells, and innate lymphoid cells (ILCs). Collectively this study identifies strategies for the rational design and testing of CITE-seq antibodies for single-cell studies of immune cells within islets and other tissues.
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Affiliation(s)
- Sarah J. Colpitts
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Matthew A. Budd
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mahdis Monajemi
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Kyle T. Reid
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Julia M. Murphy
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Sabine Ivison
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - C. Bruce Verchere
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Canada and Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Megan K. Levings, ; Sarah Q. Crome, ; C. Bruce Verchere,
| | - Megan K. Levings
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Megan K. Levings, ; Sarah Q. Crome, ; C. Bruce Verchere,
| | - Sarah Q. Crome
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
- *Correspondence: Megan K. Levings, ; Sarah Q. Crome, ; C. Bruce Verchere,
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15
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De Vlaminck K, Van Hove H, Kancheva D, Scheyltjens I, Pombo Antunes AR, Bastos J, Vara-Perez M, Ali L, Mampay M, Deneyer L, Miranda JF, Cai R, Bouwens L, De Bundel D, Caljon G, Stijlemans B, Massie A, Van Ginderachter JA, Vandenbroucke RE, Movahedi K. Differential plasticity and fate of brain-resident and recruited macrophages during the onset and resolution of neuroinflammation. Immunity 2022; 55:2085-2102.e9. [PMID: 36228615 DOI: 10.1016/j.immuni.2022.09.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 07/11/2022] [Accepted: 09/07/2022] [Indexed: 11/05/2022]
Abstract
Microglia and border-associated macrophages (BAMs) are brain-resident self-renewing cells. Here, we examined the fate of microglia, BAMs, and recruited macrophages upon neuroinflammation and through resolution. Upon infection, Trypanosoma brucei parasites invaded the brain via its border regions, triggering brain barrier disruption and monocyte infiltration. Fate mapping combined with single-cell sequencing revealed microglia accumulation around the ventricles and expansion of epiplexus cells. Depletion experiments using genetic targeting revealed that resident macrophages promoted initial parasite defense and subsequently facilitated monocyte infiltration across brain barriers. These recruited monocyte-derived macrophages outnumbered resident macrophages and exhibited more transcriptional plasticity, adopting antimicrobial gene expression profiles. Recruited macrophages were rapidly removed upon disease resolution, leaving no engrafted monocyte-derived cells in the parenchyma, while resident macrophages progressively reverted toward a homeostatic state. Long-term transcriptional alterations were limited for microglia but more pronounced in BAMs. Thus, brain-resident and recruited macrophages exhibit diverging responses and dynamics during infection and resolution.
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Affiliation(s)
- Karen De Vlaminck
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hannah Van Hove
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daliya Kancheva
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Isabelle Scheyltjens
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ana Rita Pombo Antunes
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jonathan Bastos
- Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Monica Vara-Perez
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Leen Ali
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Myrthe Mampay
- Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lauren Deneyer
- Laboratory of Neuro-Aging & Viro-Immunotherapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Juliana Fabiani Miranda
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ruiyao Cai
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, Germany
| | - Luc Bouwens
- Cell Differentiation Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Dimitri De Bundel
- Department of Pharmaceutical Chemistry, Drug Analysis and Drug Information, Research Group Experimental Pharmacology, Center for Neurosciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Benoît Stijlemans
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ann Massie
- Laboratory of Neuro-Aging & Viro-Immunotherapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jo A Van Ginderachter
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Roosmarijn E Vandenbroucke
- Barriers in Inflammation Laboratory, VIB Center for Inflammation Research, Ghent, Belgium; Ghent Gut Inflammation Group, Ghent University, Ghent, Belgium
| | - Kiavash Movahedi
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium.
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