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Jha RM, Rajasundaram D, Sneiderman C, Schlegel BT, O'Brien C, Xiong Z, Janesko-Feldman K, Trivedi R, Vagni V, Zusman BE, Catapano JS, Eberle A, Desai SM, Jadhav AP, Mihaljevic S, Miller M, Raikwar S, Rani A, Rulney J, Shahjouie S, Raphael I, Kumar A, Phuah CL, Winkler EA, Simon DW, Kochanek PM, Kohanbash G. A single-cell atlas deconstructs heterogeneity across multiple models in murine traumatic brain injury and identifies novel cell-specific targets. Neuron 2024; 112:3069-3088.e4. [PMID: 39019041 DOI: 10.1016/j.neuron.2024.06.021] [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: 09/28/2023] [Revised: 05/07/2024] [Accepted: 06/20/2024] [Indexed: 07/19/2024]
Abstract
Traumatic brain injury (TBI) heterogeneity remains a critical barrier to translating therapies. Identifying final common pathways/molecular signatures that integrate this heterogeneity informs biomarker and therapeutic-target development. We present the first large-scale murine single-cell atlas of the transcriptomic response to TBI (334,376 cells) across clinically relevant models, sex, brain region, and time as a foundational step in molecularly deconstructing TBI heterogeneity. Results were unique to cell populations, injury models, sex, brain regions, and time, highlighting the importance of cell-level resolution. We identify cell-specific targets and previously unrecognized roles for microglial and ependymal subtypes. Ependymal-4 was a hub of neuroinflammatory signaling. A distinct microglial lineage shared features with disease-associated microglia at 24 h, with persistent gene-expression changes in microglia-4 even 6 months after contusional TBI, contrasting all other cell types that mostly returned to naive levels. Regional and sexual dimorphism were noted. CEREBRI, our searchable atlas (https://shiny.crc.pitt.edu/cerebri/), identifies previously unrecognized cell subtypes/molecular targets and is a leverageable platform for future efforts in TBI and other diseases with overlapping pathophysiology.
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Affiliation(s)
- Ruchira M Jha
- Department of Neurology, Barrow Neurological Institute, Phoenix, AZ 85013, USA; Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ 85013, USA; Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ 85013, USA; Safar Center for Resuscitation-Research, University of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Chaim Sneiderman
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Brent T Schlegel
- Department of Pediatrics, Division of Health Informatics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Casey O'Brien
- Department of Pediatrics, Division of Health Informatics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Zujian Xiong
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Keri Janesko-Feldman
- Safar Center for Resuscitation-Research, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Ria Trivedi
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vincent Vagni
- Safar Center for Resuscitation-Research, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Benjamin E Zusman
- Department of Neurology, Massachusetts General Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Joshua S Catapano
- Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Adam Eberle
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | | | - Ashutosh P Jadhav
- Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Sandra Mihaljevic
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Margaux Miller
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Sudhanshu Raikwar
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Anupama Rani
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Jarrod Rulney
- University of Arizona School of Medicine, Tucson, AZ 85724, USA
| | - Shima Shahjouie
- Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ 85013, USA; Department of Neurology, Pennsylvania State University, Hershey, PA 17033, USA
| | - Itay Raphael
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Aditya Kumar
- Department of Neurology, Barrow Neurological Institute, Phoenix, AZ 85013, USA; Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ 85013, USA; Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Chia-Ling Phuah
- Department of Neurology, Barrow Neurological Institute, Phoenix, AZ 85013, USA; Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, AZ 85013, USA; Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Ethan A Winkler
- Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dennis W Simon
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Patrick M Kochanek
- Safar Center for Resuscitation-Research, University of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Gary Kohanbash
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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2
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Beauregard MA, Bedford GC, Brenner DA, Sanchez Solis LD, Nishiguchi T, Abhimanyu, Longlax SC, Mahata B, Veiseh O, Wenzel PL, DiNardo AR, Hilton IB, Diehl MR. Persistent tailoring of MSC activation through genetic priming. Mol Ther Methods Clin Dev 2024; 32:101316. [PMID: 39282077 PMCID: PMC11396059 DOI: 10.1016/j.omtm.2024.101316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 08/05/2024] [Indexed: 09/18/2024]
Abstract
Mesenchymal stem/stromal cells (MSCs) are an attractive platform for cell therapy due to their safety profile and unique ability to secrete broad arrays of immunomodulatory and regenerative molecules. Yet, MSCs are well known to require preconditioning or priming to boost their therapeutic efficacy. Current priming methods offer limited control over MSC activation, yield transient effects, and often induce the expression of pro-inflammatory effectors that can potentiate immunogenicity. Here, we describe a genetic priming method that can both selectively and sustainably boost MSC potency via the controlled expression of the inflammatory-stimulus-responsive transcription factor interferon response factor 1 (IRF1). MSCs engineered to hyper-express IRF1 recapitulate many core responses that are accessed by biochemical priming using the proinflammatory cytokine interferon-γ (IFN-γ). This includes the upregulation of anti-inflammatory effector molecules and the potentiation of MSC capacities to suppress T cell activation. However, we show that IRF1-mediated genetic priming is much more persistent than biochemical priming and can circumvent IFN-γ-dependent expression of immunogenic MHC class II molecules. Together, the ability to sustainably activate and selectively tailor MSC priming responses creates the possibility of programming MSC activation more comprehensively for therapeutic applications.
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Affiliation(s)
| | - Guy C. Bedford
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Tomoki Nishiguchi
- The Global Tuberculosis Program, Texas Children’s Hospital, Immigrant and Global Health, WTS Center for Human Immunobiology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Abhimanyu
- The Global Tuberculosis Program, Texas Children’s Hospital, Immigrant and Global Health, WTS Center for Human Immunobiology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Santiago Carrero Longlax
- The Global Tuberculosis Program, Texas Children’s Hospital, Immigrant and Global Health, WTS Center for Human Immunobiology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Barun Mahata
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Omid Veiseh
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Pamela L. Wenzel
- Department of Integrative Biology & Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Immunology Program, The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Andrew R. DiNardo
- The Global Tuberculosis Program, Texas Children’s Hospital, Immigrant and Global Health, WTS Center for Human Immunobiology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Isaac B. Hilton
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Michael R. Diehl
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
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3
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Ortega-Prieto AM, Jimenez-Guardeño JM. Interferon-stimulated genes and their antiviral activity against SARS-CoV-2. mBio 2024; 15:e0210024. [PMID: 39171921 PMCID: PMC11389394 DOI: 10.1128/mbio.02100-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic remains an international health problem caused by the recent emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of May 2024, SARS-CoV-2 has caused more than 775 million cases and over 7 million deaths globally. Despite current vaccination programs, infections are still rapidly increasing, mainly due to the appearance and spread of new variants, variations in immunization rates, and limitations of current vaccines in preventing transmission. This underscores the need for pan-variant antivirals and treatments. The interferon (IFN) system is a critical element of the innate immune response and serves as a frontline defense against viruses. It induces a generalized antiviral state by transiently upregulating hundreds of IFN-stimulated genes (ISGs). To gain a deeper comprehension of the innate immune response to SARS-CoV-2, its connection to COVID-19 pathogenesis, and the potential therapeutic implications, this review provides a detailed overview of fundamental aspects of the diverse ISGs identified for their antiviral properties against SARS-CoV-2. It emphasizes the importance of these proteins in controlling viral replication and spread. Furthermore, we explore methodological approaches for the identification of ISGs and conduct a comparative analysis with other viruses. Deciphering the roles of ISGs and their interactions with viral pathogens can help identify novel targets for antiviral therapies and enhance our preparedness to confront current and future viral threats.
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Affiliation(s)
- Ana Maria Ortega-Prieto
- Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
| | - Jose M Jimenez-Guardeño
- Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
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4
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Mori S, Kohyama M, Yasumizu Y, Tada A, Tanzawa K, Shishido T, Kishida K, Jin H, Nishide M, Kawada S, Motooka D, Okuzaki D, Naito R, Nakai W, Kanda T, Murata T, Terao C, Ohmura K, Arase N, Kurosaki T, Fujimoto M, Suenaga T, Kumanogoh A, Sakaguchi S, Ogawa Y, Arase H. Neoself-antigens are the primary target for autoreactive T cells in human lupus. Cell 2024:S0092-8674(24)00913-9. [PMID: 39276775 DOI: 10.1016/j.cell.2024.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 05/06/2024] [Accepted: 08/12/2024] [Indexed: 09/17/2024]
Abstract
Major histocompatibility complex class II (MHC-II) is the most significant genetic risk factor for systemic lupus erythematosus (SLE), but the nature of the self-antigens that trigger autoimmunity remains unclear. Unusual self-antigens, termed neoself-antigens, are presented on MHC-II in the absence of the invariant chain essential for peptide presentation. Here, we demonstrate that neoself-antigens are the primary target for autoreactive T cells clonally expanded in SLE. When neoself-antigen presentation was induced by deleting the invariant chain in adult mice, neoself-reactive T cells were clonally expanded, leading to the development of lupus-like disease. Furthermore, we found that neoself-reactive CD4+ T cells were significantly expanded in SLE patients. A high frequency of Epstein-Barr virus reactivation is a risk factor for SLE. Neoself-reactive lupus T cells were activated by Epstein-Barr-virus-reactivated cells through downregulation of the invariant chain. Together, our findings imply that neoself-antigen presentation by MHC-II plays a crucial role in the pathogenesis of SLE.
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Affiliation(s)
- Shunsuke Mori
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan
| | - Masako Kohyama
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan; Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yoshiaki Yasumizu
- Department of Experimental Immunology, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
| | - Asa Tada
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan
| | - Kaito Tanzawa
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan; Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Tatsuya Shishido
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan; Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Kazuki Kishida
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Hui Jin
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Shoji Kawada
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan; Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan; Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Ryota Naito
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Wataru Nakai
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan; Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Teru Kanda
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi 981-8558, Japan
| | - Takayuki Murata
- Department of Virology, Graduate School of Medicine, Nagoya University, Nagoya 466-8550, Japan; Department of Virology, Fujita Health University School of Medicine, Nagoya 470-1192, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 351-0198, Japan; Clinical Research Center, Shizuoka General Hospital, Shizuoka 420-8527, Japan; The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; Department of Rheumatology, Kobe City Medical Center General Hospital, Kobe, Hyogo 650-0047, Japan
| | - Noriko Arase
- Department of Dermatology, Graduate school of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Manabu Fujimoto
- Department of Dermatology, Graduate school of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Tadahiro Suenaga
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan; Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Department of Immunology, Kitasato University School of Medicine, Sagamihara, Kanagawa 252-0374, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan; Center for advanced modalities and DDS, Osaka University, Osaka 565-0871, Japan
| | - Shimon Sakaguchi
- Department of Experimental Immunology, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan; Department of Experimental Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hisashi Arase
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan; Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Center for advanced modalities and DDS, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.
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5
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Jain KG, Liu Y, Zhao R, Muire PJ, Zhang J, Zang QS, Ji HL. Humanized L184Q Mutated Surfactant Protein C Gene Alters Alveolar Type 2 Epithelial Cell Fate. Int J Mol Sci 2024; 25:8723. [PMID: 39201410 PMCID: PMC11354303 DOI: 10.3390/ijms25168723] [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: 06/13/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 09/02/2024] Open
Abstract
Alveolar type 2 epithelial (AT2) cells synthesize surfactant protein C (SPC) and repair an injured alveolar epithelium. A mutated surfactant protein C gene (SftpcL184Q, Gene ID: 6440) in newborns has been associated with respiratory distress syndrome and pulmonary fibrosis. However, the underlying mechanisms causing Sftpc gene mutations to regulate AT2 lineage remain unclear. We utilized three-dimensional (3D) feeder-free AT2 organoids in vitro to simulate the alveolar epithelium and compared AT2 lineage characteristics between WT (C57BL/6) and SftpcL184Q mutant mice using colony formation assays, immunofluorescence, flow cytometry, qRT-PCR, and Western blot assays. The AT2 numbers were reduced significantly in SftpcL184Q mice. Organoid numbers and colony-forming efficiency were significantly attenuated in the 3D cultures of primary SftpcL184Q AT2 cells compared to those of WT mice. Podoplanin (PDPN, Alveolar type 1 cell (AT1) marker) expression and transient cell count was significantly increased in SftpcL184Q organoids compared to in the WT mice. The expression levels of CD74, heat shock protein 90 (HSP90), and ribosomal protein S3A1 (RPS3A1) were not significantly different between WT and SftpcL184Q AT2 cells. This study demonstrated that humanized SftpcL184Q mutation regulates AT2 lineage intrinsically. This regulation is independent of CD74, HSP90, and RPS3A1 pathways.
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Affiliation(s)
- Krishan G. Jain
- Department of Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA; (K.G.J.); (R.Z.); (Q.S.Z.)
| | - Yang Liu
- Department of Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA; (K.G.J.); (R.Z.); (Q.S.Z.)
| | - Runzhen Zhao
- Department of Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA; (K.G.J.); (R.Z.); (Q.S.Z.)
| | - Preeti J. Muire
- Burn and Shock Trauma Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
- Department of Orthopedics and Rehabilitation, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
- Infectious Diseases and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL 60153, USA;
- Departments of Pathology and Radiation Oncology, Loyola University Medical Center, Maywood, IL 60153, USA
| | - Qun Sophia Zang
- Department of Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA; (K.G.J.); (R.Z.); (Q.S.Z.)
- Burn and Shock Trauma Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
| | - Hong-Long Ji
- Department of Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA; (K.G.J.); (R.Z.); (Q.S.Z.)
- Burn and Shock Trauma Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
- Infectious Diseases and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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6
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Madzharova E, Sabino F, Kalogeropoulos K, Francavilla C, Auf dem Keller U. Substrate O-glycosylation actively regulates extracellular proteolysis. Protein Sci 2024; 33:e5128. [PMID: 39074261 DOI: 10.1002/pro.5128] [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: 03/23/2024] [Revised: 05/30/2024] [Accepted: 07/14/2024] [Indexed: 07/31/2024]
Abstract
Extracellular proteolysis critically regulates cellular and tissue responses and is often dysregulated in human diseases. The crosstalk between proteolytic processing and other major post-translational modifications (PTMs) is emerging as an important regulatory mechanism to modulate protease activity and maintain cellular and tissue homeostasis. Here, we focus on matrix metalloproteinase (MMP)-mediated cleavages and N-acetylgalactosamine (GalNAc)-type of O-glycosylation, two major PTMs of proteins in the extracellular space. We investigated the influence of truncated O-glycan trees, also referred to as Tn antigen, following the inactivation of C1GALT1-specific chaperone 1 (COSMC) on the general and MMP9-specific proteolytic processing in MDA-MB-231 breast cancer cells. Quantitative assessment of the proteome and N-terminome using terminal amine isotopic labelling of substrates (TAILS) technology revealed enhanced proteolysis by MMP9 within the extracellular proteomes of MDA-MB-231 cells expressing Tn antigen. In addition, we detected substantial modifications in the proteome and discovered novel ectodomain shedding events regulated by the truncation of O-glycans. These results highlight the critical role of mature O-glycosylation in fine-tuning proteolytic processing and proteome homeostasis by modulating protein susceptibility to proteolytic degradation. These data suggest a complex interplay between proteolysis and O-GalNAc glycosylation, possibly affecting cancer phenotypes.
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Affiliation(s)
- Elizabeta Madzharova
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fabio Sabino
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Chiara Francavilla
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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7
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Martínez-Hernández R, Sánchez de la Blanca N, Sacristán-Gómez P, Serrano-Somavilla A, Muñoz De Nova JL, Sánchez Cabo F, Heyn H, Sampedro-Núñez M, Marazuela M. Unraveling the molecular architecture of autoimmune thyroid diseases at spatial resolution. Nat Commun 2024; 15:5895. [PMID: 39003267 PMCID: PMC11246508 DOI: 10.1038/s41467-024-50192-5] [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: 11/08/2023] [Accepted: 06/25/2024] [Indexed: 07/15/2024] Open
Abstract
Autoimmune thyroid diseases (AITD) such as Graves' disease (GD) or Hashimoto's thyroiditis (HT) are organ-specific diseases that involve complex interactions between distinct components of thyroid tissue. Here, we use spatial transcriptomics to explore the molecular architecture, heterogeneity and location of different cells present in the thyroid tissue, including thyroid follicular cells (TFCs), stromal cells such as fibroblasts, endothelial cells, and thyroid infiltrating lymphocytes. We identify damaged antigen-presenting TFCs with upregulated CD74 and MIF expression in thyroid samples from AITD patients. Furthermore, we discern two main fibroblast subpopulations in the connective tissue including ADIRF+ myofibroblasts, mainly enriched in GD, and inflammatory fibroblasts, enriched in HT patients. We also demonstrate an increase of fenestrated PLVAP+ vessels in AITD, especially in GD. Our data unveil stromal and thyroid epithelial cell subpopulations that could play a role in the pathogenesis of AITD.
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Affiliation(s)
- Rebeca Martínez-Hernández
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain.
| | - Nuria Sánchez de la Blanca
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain
| | - Pablo Sacristán-Gómez
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain
| | - Ana Serrano-Somavilla
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain
| | - José Luis Muñoz De Nova
- Department of General and Digestive Surgery, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fátima Sánchez Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Miguel Sampedro-Núñez
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain
| | - Mónica Marazuela
- Department of Endocrinology and Nutrition Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER GCV14/ER/12), Madrid, Spain.
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8
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Zhang L, Woltering I, Holzner M, Brandhofer M, Schaefer CC, Bushati G, Ebert S, Yang B, Muenchhoff M, Hellmuth JC, Scherer C, Wichmann C, Effinger D, Hübner M, El Bounkari O, Scheiermann P, Bernhagen J, Hoffmann A. CD74 is a functional MIF receptor on activated CD4 + T cells. Cell Mol Life Sci 2024; 81:296. [PMID: 38992165 PMCID: PMC11335222 DOI: 10.1007/s00018-024-05338-5] [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: 03/26/2024] [Revised: 06/04/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024]
Abstract
Next to its classical role in MHC II-mediated antigen presentation, CD74 was identified as a high-affinity receptor for macrophage migration inhibitory factor (MIF), a pleiotropic cytokine and major determinant of various acute and chronic inflammatory conditions, cardiovascular diseases and cancer. Recent evidence suggests that CD74 is expressed in T cells, but the functional relevance of this observation is poorly understood. Here, we characterized the regulation of CD74 expression and that of the MIF chemokine receptors during activation of human CD4+ T cells and studied links to MIF-induced T-cell migration, function, and COVID-19 disease stage. MIF receptor profiling of resting primary human CD4+ T cells via flow cytometry revealed high surface expression of CXCR4, while CD74, CXCR2 and ACKR3/CXCR7 were not measurably expressed. However, CD4+ T cells constitutively expressed CD74 intracellularly, which upon T-cell activation was significantly upregulated, post-translationally modified by chondroitin sulfate and could be detected on the cell surface, as determined by flow cytometry, Western blot, immunohistochemistry, and re-analysis of available RNA-sequencing and proteomic data sets. Applying 3D-matrix-based live cell-imaging and receptor pathway-specific inhibitors, we determined a causal involvement of CD74 and CXCR4 in MIF-induced CD4+ T-cell migration. Mechanistically, proximity ligation assay visualized CD74/CXCR4 heterocomplexes on activated CD4+ T cells, which were significantly diminished after MIF treatment, pointing towards a MIF-mediated internalization process. Lastly, in a cohort of 30 COVID-19 patients, CD74 surface expression was found to be significantly upregulated on CD4+ and CD8+ T cells in patients with severe compared to patients with only mild disease course. Together, our study characterizes the MIF receptor network in the course of T-cell activation and reveals CD74 as a novel functional MIF receptor and MHC II-independent activation marker of primary human CD4+ T cells.
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Affiliation(s)
- Lin Zhang
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Iris Woltering
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Mathias Holzner
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Markus Brandhofer
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Carl-Christian Schaefer
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Genta Bushati
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Simon Ebert
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Bishan Yang
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Johannes C Hellmuth
- COVID-19 Registry of the LMU Munich (CORKUM), LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
- Department of Medicine III, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Clemens Scherer
- COVID-19 Registry of the LMU Munich (CORKUM), LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
- Department of Medicine I, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Christian Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - David Effinger
- Department of Anaesthesiology, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Marchioninistraße 15, 81377, Munich, Germany
- Walter Brendel Centre of Experimental Medicine, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Max Hübner
- Department of Anaesthesiology, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Marchioninistraße 15, 81377, Munich, Germany
- Walter Brendel Centre of Experimental Medicine, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Omar El Bounkari
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Patrick Scheiermann
- Department of Anaesthesiology, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Marchioninistraße 15, 81377, Munich, Germany
| | - Jürgen Bernhagen
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany.
- German Centre of Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.
| | - Adrian Hoffmann
- Division of Vascular Biology, Institute for Stroke and Dementia Research (ISD), LMU University Hospital (LMU Klinikum), Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Straße 17, 81377, Munich, Germany.
- Department of Anaesthesiology, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Marchioninistraße 15, 81377, Munich, Germany.
- German Centre of Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.
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9
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Iannucci J, Dominy R, Bandopadhyay S, Arthur EM, Noarbe B, Jullienne A, Krkasharyan M, Tobin RP, Pereverzev A, Beevers S, Venkatasamy L, Souza KA, Jupiter DC, Dabney A, Obenaus A, Newell-Rogers MK, Shapiro LA. Traumatic brain injury alters the effects of class II invariant peptide (CLIP) antagonism on chronic meningeal CLIP + B cells, neuropathology, and neurobehavioral impairment in 5xFAD mice. J Neuroinflammation 2024; 21:165. [PMID: 38937750 PMCID: PMC11212436 DOI: 10.1186/s12974-024-03146-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: 01/19/2024] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Traumatic brain injury (TBI) is a significant risk factor for Alzheimer's disease (AD), and accumulating evidence supports a role for adaptive immune B and T cells in both TBI and AD pathogenesis. We previously identified B cell and major histocompatibility complex class II (MHCII)-associated invariant chain peptide (CLIP)-positive B cell expansion after TBI. We also showed that antagonizing CLIP binding to the antigen presenting groove of MHCII after TBI acutely reduced CLIP + splenic B cells and was neuroprotective. The current study investigated the chronic effects of antagonizing CLIP in the 5xFAD Alzheimer's mouse model, with and without TBI. METHODS 12-week-old male wild type (WT) and 5xFAD mice were administered either CLIP antagonist peptide (CAP) or vehicle, once at 30 min after either sham or a lateral fluid percussion injury (FPI). Analyses included flow cytometric analysis of immune cells in dural meninges and spleen, histopathological analysis of the brain, magnetic resonance diffusion tensor imaging, cerebrovascular analysis, and assessment of motor and neurobehavioral function over the ensuing 6 months. RESULTS 9-month-old 5xFAD mice had significantly more CLIP + B cells in the meninges compared to age-matched WT mice. A one-time treatment with CAP significantly reduced this population in 5xFAD mice. Importantly, CAP also improved some of the immune, histopathological, and neurobehavioral impairments in 5xFAD mice over the ensuing six months. Although FPI did not further elevate meningeal CLIP + B cells, it did negate the ability of CAP to reduce meningeal CLIP + B cells in the 5xFAD mice. FPI at 3 months of age exacerbated some aspects of AD pathology in 5xFAD mice, including further reducing hippocampal neurogenesis, increasing plaque deposition in CA3, altering microgliosis, and disrupting the cerebrovascular structure. CAP treatment after injury ameliorated some but not all of these FPI effects.
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Affiliation(s)
- Jaclyn Iannucci
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Reagan Dominy
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Shreya Bandopadhyay
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - E Madison Arthur
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Brenda Noarbe
- Division of Biomedical Sciences, University of California Riverside, Riverside, CA, USA
| | - Amandine Jullienne
- Division of Biomedical Sciences, University of California Riverside, Riverside, CA, USA
| | - Margret Krkasharyan
- Division of Biomedical Sciences, University of California Riverside, Riverside, CA, USA
| | - Richard P Tobin
- Department of Surgery, Division of Surgical Oncology, University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - Aleksandr Pereverzev
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Samantha Beevers
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Lavanya Venkatasamy
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Karienn A Souza
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Daniel C Jupiter
- Department of Biostatistics and Data Science, Department of Orthopaedics and Rehabilitation, The University of Texas Medical Branch, Galveston, TX, USA
| | - Alan Dabney
- Department of Statistics, College of Arts & Sciences, Texas A&M University, College Station, TX, USA
| | - Andre Obenaus
- Division of Biomedical Sciences, University of California Riverside, Riverside, CA, USA
| | - M Karen Newell-Rogers
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA.
- Department of Medical Physiology, College of Medicine, Texas A&M University, Bryan, TX, USA.
| | - Lee A Shapiro
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA.
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10
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Li H, Cao Z, Liu Y, Xue Z, Li Y, Xing H, Xu Y, Gu R, Qiu S, Wei H, Wang M, Rao Q, Wang J. Slow-replicating leukemia cells represent a leukemia stem cell population with high cell-surface CD74 expression. Mol Oncol 2024. [PMID: 38922758 DOI: 10.1002/1878-0261.13690] [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: 12/07/2023] [Revised: 04/25/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Persistence of quiescent leukemia stem cells (LSCs) after treatment most likely contributes to chemotherapy resistance and poor prognosis of leukemia patients. Identification of this quiescent cell population would facilitate eradicating LSCs. Here, using a cell-tracing PKH26 (PKH) dye that can be equally distributed to daughter cells following cell division in vivo, we identify a label-retaining slow-cycling leukemia cell population from AML1-ETO9a (AE9a) leukemic mice. We find that, compared with cells not maintaining PKH-staining, a higher proportion of PKH-retaining cells are in G0 phase, and PKH-retaining cells exhibit increased colony formation ability and leukemia initiation potential. In addition, PKH-retaining cells possess high chemo-resistance and are more likely to be localized to the endosteal bone marrow region. Based on the transcriptional signature, HLA class II histocompatibility antigen gamma chain (Cd74) is highly expressed in PKH-retaining leukemia cells. Furthermore, cell surface CD74 was identified to be highly expressed in LSCs of AE9a mice and CD34+ human leukemia cells. Compared to Lin-CD74- leukemia cells, Lin-CD74+ leukemia cells of AE9a mice exhibit higher stemness properties. Collectively, our findings reveal that the identified slow-cycling leukemia cell population represents an LSC population, and CD74+ leukemia cells possess stemness properties, suggesting that CD74 is a candidate LSC surface marker.
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Affiliation(s)
- Huan Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zhijie Cao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yiming Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zhenya Xue
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yishuang Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Haiyan Xing
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yingxi Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Runxia Gu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Shaowei Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Hui Wei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Min Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Qing Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Cell Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
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11
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Cheong TC, Jang A, Wang Q, Leonardi GC, Ricciuti B, Alessi JV, Di Federico A, Awad MM, Lehtinen MK, Harris MH, Chiarle R. Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers. Nat Commun 2024; 15:5110. [PMID: 38877018 PMCID: PMC11178778 DOI: 10.1038/s41467-024-49499-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are followed typical recurrent patterns, but the underlying mechanisms and clinical implications of these patterns are poorly understood. By developing Functionally Active Chromosomal Translocation Sequencing (FACTS), we discover that typical TK fusions involving ALK, ROS1, RET and NTRK1 are selected from pools of chromosomal rearrangements by two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies. Our findings highlight the principles of oncogenic TK fusion formation and selection in cancers, with clinical implications for guiding targeted therapy.
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Affiliation(s)
- Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ahram Jang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Qi Wang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Giulia C Leonardi
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | | | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
- Division of Hematopathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy.
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12
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Liu Z, Chen M, Zheng W, Yuan S, Zhao W. Insights into the prognostic value and immunological role of CD74 in pan-cancer. Discov Oncol 2024; 15:222. [PMID: 38861249 PMCID: PMC11166624 DOI: 10.1007/s12672-024-01081-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND CD74 is a non-polymorphic type II transmembrane glycoprotein. It is involved in the regulation of T and B cell development, and dendritic cell (DC) motility. Numerous studies have found that CD74 exerts an essential role in tumor immunity, but the expression profile of CD74 is still not systematically reported, and its value in human pan-cancer analysis is unknown. In this study, we analyzed the expression pattern of CD74 in 33 cancers, and evaluated the significance of CD74 in prognosis prediction and cancer immunity. METHODS Pan-cancer dataset from UCSC Xena.We used the Sangerbox website combined with R software' Timer, CIBERSORT method and IOBR package to analyze and plot the data. Survival was assessed using the Kaplan-Meier method and log-rank test for 33 cancer types (p < 0.05). In addition, to explore the relationship between CD74 expression and immune checkpoints, immune cell infiltration, tumor mutational burden (TMB) and microsatellite instability (MSI), Spearman correlation analysis was performed. RESULTS This study comprehensively analyzed CD74 expression in 33 different tumor types, revealing that CD74 play an crucial role in cancer formation and development. CONCLUSIONS CD74 gene expression in different cancers is associated with immune cell infiltration and immunomodulators and may provide a promising target for survival and immunotherapy. Our study shows that CD74 has an essential role as a biomarker of prognosis during tumor development, which highlights the possibility of new targeted therapies.
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Affiliation(s)
- Zebiao Liu
- Pathology, Huizhou First Hospital, Huizhou, 516000, China
| | - Mingquan Chen
- Pathology, Huizhou First Hospital, Huizhou, 516000, China
| | - Wanhua Zheng
- Guangxi Universities Key Laboratory of Stem cell and Biopharmaceutical Technology, School of Life Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Shicheng Yuan
- Pathology, Huizhou First Hospital, Huizhou, 516000, China
| | - Wenli Zhao
- Pathology, Huizhou First Hospital, Huizhou, 516000, China.
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13
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Lovell JP, Duque C, Rousseau S, Bhalodia A, Bermea K, Cohen CD, Adamo L. B cell-mediated antigen presentation promotes adverse cardiac remodeling in chronic heart failure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593153. [PMID: 38766182 PMCID: PMC11100706 DOI: 10.1101/2024.05.08.593153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Cardiovascular disease remains the leading cause of death worldwide. A primary driver of cardiovascular mortality is ischemic heart failure, a form of cardiac dysfunction that can develop in patients who survive myocardial infarction. Acute cardiac damage triggers robust changes in the spleen with rapid migration of immune cells from the spleen to the heart. Activating this "cardio-splenic" axis contributes to progressive cardiac dysfunction. The cardio-splenic axis has, therefore, been identified as a promising therapeutic target to prevent or treat heart failure. However, our understanding of the precise mechanisms by which specific immune cells contribute to adverse cardiac remodeling within the cardio-splenic axis remains limited. Here, we show that splenic B cells contribute to the development of heart failure via MHC II-mediated antigen presentation. We found that the adoptive transfer of splenic B cells from mice with ischemic heart failure promoted adverse cardiac remodeling and splenic inflammatory changes in naïve recipient mice. Based on single-cell RNA sequencing analysis of splenic B cells from mice with ischemic heart failure, we hypothesized that B cells contributed to adverse cardiac remodeling through antigen presentation by MHC II molecules. This mechanism was confirmed using transgenic mice with B cell-specific MHC II deletion, and by analyzing circulating B cells from humans who experienced myocardial infarction. Our results broaden our understanding of B lymphocyte biology, reshape current models of immune activation in response to myocardial injury, and point towards MHC II-mediated signaling in B cells as a novel and specific therapeutic target in chronic heart failure.
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14
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Tanese K, Ogata D. The role of macrophage migration inhibitory factor family and CD74 in the pathogenesis of melanoma. Exp Dermatol 2024; 33:e15122. [PMID: 38884501 DOI: 10.1111/exd.15122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
Melanoma is an aggressive tumour with poor prognosis that arises from the malignant transformation of melanocytes. Over the past few decades, intense research into the pathogenesis of melanoma has led to the development of BRAF and immune checkpoint inhibitors, including antibodies against programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4), which have shown clinically significant efficacy. However, some tumours do not respond to these therapies initially or become treatment resistant. Most melanoma tissues appear to possess biological characteristics that allow them to evade these treatments, and identifying these characteristics is one of the major challenges facing cancer researchers. One such characteristic that has recently gained attention is the role of macrophage migration inhibitory factor (MIF) and its receptor CD74. This review outlines the cellular and molecular functions of CD74, MIF and their family of proteins. We then review their roles in tumours based on previous reports, highlight their pathological significance in melanoma and discuss their potential as therapeutic targets.
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Affiliation(s)
- Keiji Tanese
- Department of Dermatology, Toho University School of Medicine, Tokyo, Japan
| | - Dai Ogata
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
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15
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Langguth M, Maranou E, Koskela SA, Elenius O, Kallionpää RE, Birkman EM, Pulkkinen OI, Sundvall M, Salmi M, Figueiredo CR. TIMP-1 is an activator of MHC-I expression in myeloid dendritic cells with implications for tumor immunogenicity. Genes Immun 2024; 25:188-200. [PMID: 38777826 PMCID: PMC11178497 DOI: 10.1038/s41435-024-00274-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Immune checkpoint therapies (ICT) for advanced solid tumors mark a new milestone in cancer therapy. Yet their efficacy is often limited by poor immunogenicity, attributed to inadequate priming and generation of antitumor T cells by dendritic cells (DCs). Identifying biomarkers to enhance DC functions in such tumors is thus crucial. Tissue Inhibitor of Metalloproteinases-1 (TIMP-1), recognized for its influence on immune cells, has an underexplored relationship with DCs. Our research reveals a correlation between high TIMP1 levels in metastatic melanoma and increased CD8 + T cell infiltration and survival. Network studies indicate a functional connection with HLA genes. Spatial transcriptomic analysis of a national melanoma cohort revealed that TIMP1 expression in immune compartments associates with an HLA-A/MHC-I peptide loading signature in lymph nodes. Primary human and bone-marrow-derived DCs secrete TIMP-1, which notably increases MHC-I expression in classical type 1 dendritic cells (cDC1), especially under melanoma antigen exposure. TIMP-1 affects the immunoproteasome/TAP complex, as seen by upregulated PSMB8 and TAP-1 levels of myeloid DCs. This study uncovers the role of TIMP-1 in DC-mediated immunogenicity with insights into CD8 + T cell activation, providing a foundation for mechanistic exploration and highlighting its potential as a new target for combinatorial immunotherapy to enhance ICT effectiveness.
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Affiliation(s)
- Miriam Langguth
- Medical Immune Oncology Research Group (MIORG), Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Eleftheria Maranou
- Medical Immune Oncology Research Group (MIORG), Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Saara A Koskela
- Medical Immune Oncology Research Group (MIORG), Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Oskar Elenius
- Medical Immune Oncology Research Group (MIORG), Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Roosa E Kallionpää
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Eva-Maria Birkman
- Department of Pathology, Laboratory Division, Turku University Hospital and University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Otto I Pulkkinen
- Medical Immune Oncology Research Group (MIORG), Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Maria Sundvall
- Cancer Research Unit, Institute of Biomedicine, and FICAN West Cancer Center Laboratory, University of Turku, and Turku University Hospital, Kiinamyllynkatu 10, 20520, Turku, Finland
- Department of Oncology, Turku University Hospital, Turku, Finland
| | - Marko Salmi
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
- MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Carlos R Figueiredo
- Medical Immune Oncology Research Group (MIORG), Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland.
- Cancer Research Unit, Institute of Biomedicine, and FICAN West Cancer Center Laboratory, University of Turku, and Turku University Hospital, Kiinamyllynkatu 10, 20520, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland.
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16
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Pekayvaz K, Losert C, Knottenberg V, Gold C, van Blokland IV, Oelen R, Groot HE, Benjamins JW, Brambs S, Kaiser R, Gottschlich A, Hoffmann GV, Eivers L, Martinez-Navarro A, Bruns N, Stiller S, Akgöl S, Yue K, Polewka V, Escaig R, Joppich M, Janjic A, Popp O, Kobold S, Petzold T, Zimmer R, Enard W, Saar K, Mertins P, Huebner N, van der Harst P, Franke LH, van der Wijst MGP, Massberg S, Heinig M, Nicolai L, Stark K. Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes. Nat Med 2024; 30:1696-1710. [PMID: 38773340 PMCID: PMC11186793 DOI: 10.1038/s41591-024-02953-4] [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: 05/02/2023] [Accepted: 03/26/2024] [Indexed: 05/23/2024]
Abstract
Acute and chronic coronary syndromes (ACS and CCS) are leading causes of mortality. Inflammation is considered a key pathogenic driver of these diseases, but the underlying immune states and their clinical implications remain poorly understood. Multiomic factor analysis (MOFA) allows unsupervised data exploration across multiple data types, identifying major axes of variation and associating these with underlying molecular processes. We hypothesized that applying MOFA to multiomic data obtained from blood might uncover hidden sources of variance and provide pathophysiological insights linked to clinical needs. Here we compile a longitudinal multiomic dataset of the systemic immune landscape in both ACS and CCS (n = 62 patients in total, n = 15 women and n = 47 men) and validate this in an external cohort (n = 55 patients in total, n = 11 women and n = 44 men). MOFA reveals multicellular immune signatures characterized by distinct monocyte, natural killer and T cell substates and immune-communication pathways that explain a large proportion of inter-patient variance. We also identify specific factors that reflect disease state or associate with treatment outcome in ACS as measured using left ventricular ejection fraction. Hence, this study provides proof-of-concept evidence for the ability of MOFA to uncover multicellular immune programs in cardiovascular disease, opening new directions for mechanistic, biomarker and therapeutic studies.
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Grants
- Deutsche Forschungsgemeinschaft (German Research Foundation)
- Deutsches Zentrum fr Herz-Kreislaufforschung (Deutsches Zentrum fr Herz-Kreislaufforschung e.V.)
- Deutsche Herzstiftung e.V., Frankfurt a.M. Institutional Strategy LMUexcellent of LMU Munich Else-Krner-Fresenius Stiftung DFG Clinician Scientist Programme PRIME DZHK Sule B Antrag DZHK B 21-014 SE
- Was supported by the Helmholtz Association under the joint research school ;Munich School for Data Science MUDS
- DFG GO 3823/1-1, grant number: 510821390 Frderprogramm fr Forschung und Lehre der Medizinischen Fakultt der LMU the Bavarian Cancer Research Center (BZKF) Else Kroner-Fresenius-Stiftung
- Was supported by a grant from the Frderprogramm fur Forschung und Lehre (FFoLe) of the Ludwig Maximilian University (LMU) of Munich.
- DFG SFB 1123, Z02
- DFG EN 1093/2-1
- DFG KO5055-2-1 and KO5055/3-1 the Bavarian Cancer Research Center (BZKF) the international doctoral program i-Target: immunotargeting of cancer the Melanoma Research Alliance (grant number 409510), Marie Sklodowska-Curie Training Network for Optimizing Adoptive T Cell Therapy of Cancer (funded by the Horizon 2020 programme of the European Union; grant 955575), Else Kroner-Fresenius-Stiftung (IOLIN), German Cancer Aid (AvantCAR.de), the Wilhelm-Sander-Stiftung, Ernst Jung Stiftung, Institutional Strategy LMUexcellent of LMU Munich (within the framework of the German Excellence Initiative), the Go-Bio-Initiative, the m4-Award of the Bavarian Ministry for Economical Affairs, Bundesministerium fur Bildung und Forschung, European Research Council (Starting Grant 756017 and PoC Grant 101100460, by the SFB-TRR 338/1 2021452881907, Fritz-Bender Foundation, Deutsche Jose#x0301; Carreras Leuk#x00E4;mie Stiftung, Hector Foundation, the Bavarian Research Foundation, the Bruno and Helene J#x00F6;ster Foundation (360#x00B0; CAR)
- T.P. from the DFG (PE 2704/3-1)
- DFG SFB1243, A14 DFG EN 1093/2-1,
- DZHK Säule B Antrag DZHK B 21-014 SE
- DZHK Säule B Antrag DZHK B 21-014 SE DFG SFB-1470-B03 the Chan Zuckerberg Foundation ERC Advanced Grant under the European Union Horizon 2020 Research and Innovation Program (AdG788970)
- Deutsche Forschungsgemeinschaft (DFG) SFB 914, B02 and Z01 DFG SFB 1123, B06 DFG SFB1321, P10 DFG FOR 2033 ERC-2018-ADG German Centre for Cardiovascular Research (DZHK) MHA 1.4VD
- DZHK project 81Z0600106 Supported by the Chan Zuckerberg Foundation
- DZHK S#x00E4;ule B Antrag DZHK B 21-014 SE Deutsche Herzstiftung e.V., Frankfurt a.M. DFG SFB 1123, B06 DFG NI 2219/2-1 Corona Foundation German Centre for Cardiovascular Research (DZHK) Clinician Scientist Programme the Ernst und Berta Grimmke Stiftung the GTH Junior research grant
- DZHK partner site project Deutsche Forschungsgemeinschaft (DFG) SFB 914, B02 DFG SFB 1123, A07 DFG SFB 359, A03 ERC grant 947611
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Affiliation(s)
- Kami Pekayvaz
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
| | - Corinna Losert
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | | | - Christoph Gold
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Irene V van Blokland
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Roy Oelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hilde E Groot
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jan Walter Benjamins
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sophia Brambs
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Rainer Kaiser
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Adrian Gottschlich
- Department of Medicine III, LMU University Hospital, Munich, Germany
- Division of Clinical Pharmacology, LMU University Hospital, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Gordon Victor Hoffmann
- Division of Clinical Pharmacology, LMU University Hospital, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Luke Eivers
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | | | - Nils Bruns
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Susanne Stiller
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Sezer Akgöl
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Keyang Yue
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Vivien Polewka
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Raphael Escaig
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Markus Joppich
- Department of Informatics, Ludwig-Maximilian University, Munich, Germany
| | - Aleksandar Janjic
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilian University, Munich, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Sebastian Kobold
- Division of Clinical Pharmacology, LMU University Hospital, Member of the German Center for Lung Research (DZL), Munich, Germany
- German Cancer Consortium (DKTK), a partnership between DKFZ and LMU University Hospital, Partner Site Munich, Munich, Germany
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Petzold
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Ralf Zimmer
- Department of Informatics, Ludwig-Maximilian University, Munich, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilian University, Munich, Germany
| | - Kathrin Saar
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Norbert Huebner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lude H Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Monique G P van der Wijst
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Steffen Massberg
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Matthias Heinig
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany.
- Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
| | - Leo Nicolai
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
| | - Konstantin Stark
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
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17
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Díaz-Rivera J, Rodríguez-Rivera MA, Meléndez-Vázquez NM, Godoy-Vitorino F, Dorta-Estremera SM. Immune and Microbial Signatures Associated with PD-1 Blockade Sensitivity in a Preclinical Model for HPV+ Oropharyngeal Cancer. Cancers (Basel) 2024; 16:2065. [PMID: 38893183 PMCID: PMC11171047 DOI: 10.3390/cancers16112065] [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: 04/17/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
The United States is suffering from an epidemic associated with high-risk strains of the Human Papillomavirus (HPV) predominantly responsible for the development of head and neck squamous cell carcinoma (HNSCC). Treatment with immune checkpoint inhibitors targeting programmed death 1 (PD-1) or its ligand PD-L1 has shown poor efficacy in HNSCC patients, observing only a 20-30% response. Therefore, biological marker identification associated with PD-1 blockade response is important to improve prognosis and define novel therapeutics for HNSCC patients. Therapy response was associated with increased frequencies of activated CD27+T cells, activated CD79a+ B cells, antigen-presenting CD74+ dendritic and B cells, and PD-L1+ and PD-L2+ myeloid-derived suppressor cells (MDSCs). The oral microbiota composition differed significantly in mice bearing tongue tumors and treated with anti-PD-1. A higher abundance of Allobaculum, Blautia, Faecalibacterium, Dorea, or Roseburia was associated with response to the therapy. However, an increase in Enterococcus was attributed to tongue tumor-bearing non-responding mice. Our findings indicate that differences in immune phenotypes, protein expression, and bacterial abundance occur as mice develop tongue tumors and are treated with anti-PD-1. These results may have a clinical impact as specific bacteria and immune phenotype could serve as biomarkers for treatment response in HNSCC.
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Affiliation(s)
- Jennifer Díaz-Rivera
- Cancer Biology Division, Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR 00936, USA; (J.D.-R.); (M.A.R.-R.)
- Microbiology and Medical Zoology Department, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA; (N.M.M.-V.); (F.G.-V.)
| | - Michael A. Rodríguez-Rivera
- Cancer Biology Division, Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR 00936, USA; (J.D.-R.); (M.A.R.-R.)
- Microbiology and Medical Zoology Department, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA; (N.M.M.-V.); (F.G.-V.)
| | - Natalie M. Meléndez-Vázquez
- Microbiology and Medical Zoology Department, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA; (N.M.M.-V.); (F.G.-V.)
| | - Filipa Godoy-Vitorino
- Microbiology and Medical Zoology Department, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA; (N.M.M.-V.); (F.G.-V.)
| | - Stephanie M. Dorta-Estremera
- Cancer Biology Division, Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR 00936, USA; (J.D.-R.); (M.A.R.-R.)
- Microbiology and Medical Zoology Department, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA; (N.M.M.-V.); (F.G.-V.)
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18
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Weisbrod L, Capriotti L, Hofmann M, Spieler V, Dersch H, Voedisch B, Schmidt P, Knake S. FASTMAP-a flexible and scalable immunopeptidomics pipeline for HLA- and antigen-specific T-cell epitope mapping based on artificial antigen-presenting cells. Front Immunol 2024; 15:1386160. [PMID: 38779658 PMCID: PMC11109385 DOI: 10.3389/fimmu.2024.1386160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
The study of peptide repertoires presented by major histocompatibility complex (MHC) molecules and the identification of potential T-cell epitopes contribute to a multitude of immunopeptidome-based treatment approaches. Epitope mapping is essential for the development of promising epitope-based approaches in vaccination as well as for innovative therapeutics for autoimmune diseases, infectious diseases, and cancer. It also plays a critical role in the immunogenicity assessment of protein therapeutics with regard to safety and efficacy concerns. The main challenge emerges from the highly polymorphic nature of the human leukocyte antigen (HLA) molecules leading to the requirement of a peptide mapping strategy for a single HLA allele. As many autoimmune diseases are linked to at least one specific antigen, we established FASTMAP, an innovative strategy to transiently co-transfect a single HLA allele combined with a disease-specific antigen into a human cell line. This approach allows the specific identification of HLA-bound peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Using FASTMAP, we found a comparable spectrum of endogenous peptides presented by the most frequently expressed HLA alleles in the world's population compared to what has been described in literature. To ensure a reliable peptide mapping workflow, we combined the HLA alleles with well-known human model antigens like coagulation factor VIII, acetylcholine receptor subunit alpha, protein structures of the SARS-CoV-2 virus, and myelin basic protein. Using these model antigens, we have been able to identify a broad range of peptides that are in line with already published and in silico predicted T-cell epitopes of the specific HLA/model antigen combination. The transient co-expression of a single affinity-tagged MHC molecule combined with a disease-specific antigen in a human cell line in our FASTMAP pipeline provides the opportunity to identify potential T-cell epitopes/endogenously processed MHC-bound peptides in a very cost-effective, fast, and customizable system with high-throughput potential.
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Affiliation(s)
- Luisa Weisbrod
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Luigi Capriotti
- Analytical Biochemistry, Research and Development, CSL Behring AG, Bern, Switzerland
| | - Marco Hofmann
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Valerie Spieler
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Herbert Dersch
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Bernd Voedisch
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Peter Schmidt
- Protein Biochemistry, Bio21 Institute, CSL Limited, Parkville, VIC, Australia
| | - Susanne Knake
- Department of Neurology, Epilepsy Center Hessen, Philipps University Marburg, Marburg, Germany
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19
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Wang N, Waghray D, Caveney NA, Jude KM, Garcia KC. Structural insights into human MHC-II association with invariant chain. Proc Natl Acad Sci U S A 2024; 121:e2403031121. [PMID: 38687785 PMCID: PMC11087810 DOI: 10.1073/pnas.2403031121] [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: 02/13/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Abstract
The loading of processed peptides on to major histocompatibility complex II (MHC-II) molecules for recognition by T cells is vital to cell-mediated adaptive immunity. As part of this process, MHC-II associates with the invariant chain (Ii) during biosynthesis in the endoplasmic reticulum to prevent premature peptide loading and to serve as a scaffold for subsequent proteolytic processing into MHC-II-CLIP. Cryo-electron microscopy structures of full-length Human Leukocyte Antigen-DR (HLA-DR) and HLA-DQ complexes associated with Ii, resolved at 3.0 to 3.1 Å, elucidate the trimeric assembly of the HLA/Ii complex and define atomic-level interactions between HLA, Ii transmembrane domains, loop domains, and class II-associated invariant chain peptides (CLIP). Together with previous structures of MHC-II peptide loading intermediates DO and DM, our findings complete the structural path governing class II antigen presentation.
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Affiliation(s)
- Nan Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- HHMI, Stanford University School of Medicine, Stanford, CA94305
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
| | - Nathanael A. Caveney
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
| | - Kevin M. Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- HHMI, Stanford University School of Medicine, Stanford, CA94305
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- HHMI, Stanford University School of Medicine, Stanford, CA94305
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
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20
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Fey RM, Nichols RA, Tran TT, Vandenbark AA, Kulkarni RP. MIF and CD74 as Emerging Biomarkers for Immune Checkpoint Blockade Therapy. Cancers (Basel) 2024; 16:1773. [PMID: 38730725 PMCID: PMC11082995 DOI: 10.3390/cancers16091773] [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: 03/14/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Immune checkpoint blockade (ICB) therapy is used to treat a wide range of cancers; however, some patients are at risk of developing treatment resistance and/or immune-related adverse events (irAEs). Thus, there is a great need for the identification of reliable predictive biomarkers for response and toxicity. The cytokine MIF (macrophage migration inhibitory factor) and its cognate receptor CD74 are intimately connected with cancer progression and have previously been proposed as prognostic biomarkers for patient outcome in various cancers, including solid tumors such as malignant melanoma. Here, we assess their potential as predictive biomarkers for response to ICB therapy and irAE development. We provide a brief overview of their function and roles in the context of cancer and autoimmune disease. We also review the evidence showing that MIF and CD74 may be of use as predictive biomarkers of patient response to ICB therapy and irAE development. We also highlight that careful consideration is required when assessing the potential of serum MIF levels as a biomarker due to its reported circadian expression in human plasma. Finally, we suggest future directions for the establishment of MIF and CD74 as predictive biomarkers for ICB therapy and irAE development to guide further research in this field.
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Affiliation(s)
- Rosalyn M. Fey
- Department of Dermatology, Oregon Health & Science University, Portland, OR 97239, USA (R.A.N.)
| | - Rebecca A. Nichols
- Department of Dermatology, Oregon Health & Science University, Portland, OR 97239, USA (R.A.N.)
| | - Thuy T. Tran
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Arthur A. Vandenbark
- Neuroimmunology Research, R&D-31, VA Portland Health Care System, Portland, OR 97239, USA
- Department of Neurology, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rajan P. Kulkarni
- Department of Dermatology, Oregon Health & Science University, Portland, OR 97239, USA (R.A.N.)
- Cancer Early Detection Advanced Research Center (CEDAR), Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
- Operative Care Division, U.S. Department of Veterans Affairs Portland Health Care System, Portland, OR 97239, USA
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21
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Cardeira-da-Silva J, Wang Q, Sagvekar P, Mintcheva J, Latting S, Günther S, Ramadass R, Yekelchyk M, Preussner J, Looso M, Junker JP, Stainier DYR. Antigen presentation plays positive roles in the regenerative response to cardiac injury in zebrafish. Nat Commun 2024; 15:3637. [PMID: 38684665 PMCID: PMC11058276 DOI: 10.1038/s41467-024-47430-1] [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: 04/25/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
In contrast to adult mammals, adult zebrafish can fully regenerate injured cardiac tissue, and this regeneration process requires an adequate and tightly controlled immune response. However, which components of the immune response are required during regeneration is unclear. Here, we report positive roles for the antigen presentation-adaptive immunity axis during zebrafish cardiac regeneration. We find that following the initial innate immune response, activated endocardial cells (EdCs), as well as immune cells, start expressing antigen presentation genes. We also observe that T helper cells, a.k.a. Cd4+ T cells, lie in close physical proximity to these antigen-presenting EdCs. We targeted Major Histocompatibility Complex (MHC) class II antigen presentation by generating cd74a; cd74b mutants, which display a defective immune response. In these mutants, Cd4+ T cells and activated EdCs fail to efficiently populate the injured tissue and EdC proliferation is significantly decreased. cd74a; cd74b mutants exhibit additional defects in cardiac regeneration including reduced cardiomyocyte dedifferentiation and proliferation. Notably, Cd74 also becomes activated in neonatal mouse EdCs following cardiac injury. Altogether, these findings point to positive roles for antigen presentation during cardiac regeneration, potentially involving interactions between activated EdCs, classical antigen-presenting cells, and Cd4+ T cells.
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Affiliation(s)
- João Cardeira-da-Silva
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
| | - Qianchen Wang
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Pooja Sagvekar
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Janita Mintcheva
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Humboldt University of Berlin, Berlin, Germany
| | - Stephan Latting
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Radhan Ramadass
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Michail Yekelchyk
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jens Preussner
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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22
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Pang L, Xiang F, Yang H, Shen X, Fang M, Li R, Long Y, Li J, Yu Y, Pang B. Single-cell integrative analysis reveals consensus cancer cell states and clinical relevance in breast cancer. Sci Data 2024; 11:289. [PMID: 38472225 DOI: 10.1038/s41597-024-03127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024] Open
Abstract
High heterogeneity and complex interactions of malignant cells in breast cancer has been recognized as a driver of cancer progression and therapeutic failure. However, complete understanding of common cancer cell states and their underlying driver factors remain scarce and challenging. Here, we revealed seven consensus cancer cell states recurring cross patients by integrative analysis of single-cell RNA sequencing data of breast cancer. The distinct biological functions, the subtype-specific distribution, the potential cells of origin and the interrelation of consensus cancer cell states were systematically elucidated and validated in multiple independent datasets. We further uncovered the internal regulons and external cell components in tumor microenvironments, which contribute to the consensus cancer cell states. Using the state-specific signature, we also inferred the abundance of cells with each consensus cancer cell state by deconvolution of large breast cancer RNA-seq cohorts, revealing the association of immune-related state with better survival. Our study provides new insights for the cancer cell state composition and potential therapeutic strategies of breast cancer.
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Affiliation(s)
- Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Fengyu Xiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Huan Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xinyue Shen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Ming Fang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Ran Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yongjin Long
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jiali Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yonghuan Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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23
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Stoll AC, Kemp CJ, Patterson JR, Howe JW, Steece-Collier K, Luk KC, Sortwell CE, Benskey MJ. Neuroinflammatory gene expression profiles of reactive glia in the substantia nigra suggest a multidimensional immune response to alpha synuclein inclusions. Neurobiol Dis 2024; 191:106411. [PMID: 38228253 PMCID: PMC10869642 DOI: 10.1016/j.nbd.2024.106411] [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: 08/30/2023] [Revised: 11/09/2023] [Accepted: 01/12/2024] [Indexed: 01/18/2024] Open
Abstract
Parkinson's disease (PD) pathology is characterized by alpha-synuclein (α-syn) aggregates, degeneration of dopamine neurons in the substantia nigra pars compacta (SNpc), and neuroinflammation. The presence of reactive glia correlates with deposition of pathological α-syn in early-stage PD. Thus, understanding the neuroinflammatory response of microglia and astrocytes to synucleinopathy may identify therapeutic targets. Here we characterized the neuroinflammatory gene expression profile of reactive microglia and astrocytes in the SNpc during early synucleinopathy in the rat α-syn pre-formed fibril (PFF) model. Rats received intrastriatal injection of α-syn PFFs and expression of immune genes was quantified with droplet digital PCR (ddPCR), after which fluorescent in situ hybridization (FISH) was used to localize gene expression to microglia or astrocytes in the SNpc. Genes previously associated with reactive microglia (Cd74, C1qa, Stat1, Axl, Casp1, Il18, Lyz2) and reactive astrocytes (C3, Gbp2, Serping1) were significantly upregulated in the SN of PFF injected rats. Localization of gene expression to SNpc microglia near α-syn aggregates identified a unique α-syn aggregate microglial gene expression profile characterized by upregulation of Cd74, Cxcl10, Rt-1a2, Grn, Csf1r, Tyrobp, C3, C1qa, Serping1 and Fcer1g. Importantly, significant microglial upregulation of Cd74 and C3 were only observed following injection of α-syn PFFs, not α-syn monomer, confirming specificity to α-syn aggregation. Serping1 expression also localized to astrocytes in the SNpc. Interestingly, C3 expression in the SNpc localized to microglia at 2- and 4-months post-PFF, but to astrocytes at 6-months post-PFF. We also observed expression of Rt1-a2 and Cxcl10 in SNpc dopamine neurons. Cumulatively our results identify a dynamic, yet reproducible gene expression profile of reactive microglia and astrocytes associated with early synucleinopathy in the rat SNpc.
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Affiliation(s)
- Anna C Stoll
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI, USA; Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
| | - Christopher J Kemp
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI, USA
| | - Joseph R Patterson
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI, USA
| | - Jacob W Howe
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI, USA
| | - Kathy Steece-Collier
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI, USA
| | - Kelvin C Luk
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Caryl E Sortwell
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI, USA
| | - Matthew J Benskey
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI, USA.
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24
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Song Y, Zhang X, Desmarais JA, Nagano M. Postnatal development of mouse spermatogonial stem cells as determined by immunophenotype, regenerative capacity, and long-term culture-initiating ability: a model for practical applications. Sci Rep 2024; 14:2299. [PMID: 38280889 PMCID: PMC10821885 DOI: 10.1038/s41598-024-52824-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/24/2024] [Indexed: 01/29/2024] Open
Abstract
Spermatogonial stem cells (SSCs) are the foundation of life-long spermatogenesis. While SSC research has advanced greatly over the past two decades, characterization of SSCs during postnatal development has not been well documented. Using the mouse as a model, in this study, we defined the immunophenotypic profiles of testis cells during the course of postnatal development using multi-parameter flow cytometry with up to five cell-surface antigens. We found that the profiles progress over time in a manner specific to developmental stages. We then isolated multiple cell fractions at different developmental stages using fluorescent-activated cell sorting (FACS) and identified specific cell populations with prominent capacities to regenerate spermatogenesis upon transplantation and to initiate long-term SSC culture. The data indicated that the cell fraction with the highest level of regeneration capacity exhibited the most prominent potential to initiate SSC culture, regardless of age. Interestingly, refinement of cell fractionation using GFRA1 and KIT did not lead to further enrichment of regenerative and culture-initiating stem cells, suggesting that when a high degree of SSC enrichment is achieved, standard markers of SSC self-renewal or commitment may lose their effectiveness to distinguish cells at the stem cell state from committed progenitors. This study provides a significant information resource for future studies and practical applications of mammalian SSCs.
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Affiliation(s)
- Youngmin Song
- Department of Obstetrics and Gynecology, McGill University, and the Child Health and Human Development Program, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Rm# EM0.2212, Montreal, QC, H4A 3J1, Canada
| | - Xiangfan Zhang
- Department of Obstetrics and Gynecology, McGill University, and the Child Health and Human Development Program, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Rm# EM0.2212, Montreal, QC, H4A 3J1, Canada
| | - Joëlle A Desmarais
- Department of Obstetrics and Gynecology, McGill University, and the Child Health and Human Development Program, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Rm# EM0.2212, Montreal, QC, H4A 3J1, Canada
- JEFO Nutrition Inc, 5020 Avenue Jefo, Saint-Hyachinthe, Quebec, J2R 2E7, Canada
| | - Makoto Nagano
- Department of Obstetrics and Gynecology, McGill University, and the Child Health and Human Development Program, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Rm# EM0.2212, Montreal, QC, H4A 3J1, Canada.
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25
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Wang J, Li X, Xiao G, Desai J, Frentzas S, Wang ZM, Xia Y, Li B. CD74 is associated with inflamed tumor immune microenvironment and predicts responsiveness to PD-1/CTLA-4 bispecific antibody in patients with solid tumors. Cancer Immunol Immunother 2024; 73:36. [PMID: 38280003 PMCID: PMC10822011 DOI: 10.1007/s00262-023-03604-2] [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: 10/27/2023] [Accepted: 12/03/2023] [Indexed: 01/29/2024]
Abstract
INTRODUCTION Cadonilimab (AK104) is a first-in-class tetravalent bispecific antibody that targets both PD-1 and CTLA-4, showing a manageable safety profile and favorable clinical benefits. This study aimed to identify the biomarkers of clinical response and explore the immune response within the tumor microenvironment upon the AK104 therapy in advanced solid tumors. MATERIAL AND METHODS Gene expression profiles of paired pre- and post-treatment tumor tissues from twenty-one patients were analyzed. The association of gene expression levels with either clinical efficacy or prognosis was evaluated and subsequently validated with published datasets using log-rank for Kaplan-Meier estimates. Comparative immune profile analyses of tumor microenvironment before and after AK104 treatment were conducted. The visualization of tumor-infiltrating lymphocytes was performed using multiplex immunohistochemistry. The predictive value of CD74 was further validated with protein expression by immunohistochemistry. RESULTS Baseline CD74 gene expression was associated with favorable patient outcomes (overall survival [OS], HR = 0.33, 95% CI 0.11-1.03, p = 0.0463), which was further confirmed with the published datasets. Tumors with high CD74 gene expression at baseline were more likely to exhibit an immune-inflamed microenvironment. AK104 efficiently enhanced the infiltration of immune cells in the tumor microenvironment. Additionally, high CD74 protein expression (≥ 10% of the tumor area occupied by CD74 stained immune cells) at baseline was associated with better progressive-free survival (HR = 0.21, 95% CI 0.06-0.68, p = 0.0065) and OS (HR = 0.35, 95% CI 0.12-1.08, p = 0.0615). CONCLUSIONS Our findings demonstrate that CD74 is a promising predictive biomarker for AK104 therapeutic response in advanced solid tumors. Trial registration number NCT03261011.
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Affiliation(s)
- Jianghua Wang
- Research and Development Department, Akeso Biopharma Inc, Zhongshan, Guangdong, China
| | - Xiaoting Li
- Research and Development Department, Akeso Biopharma Inc, Zhongshan, Guangdong, China
| | - Guanxi Xiao
- Research and Development Department, Akeso Biopharma Inc, Zhongshan, Guangdong, China
| | - Jayesh Desai
- Department of Oncology, Sir Peter MacCallum, The University of Melbourne, Parkville, VIC, Australia
| | - Sophia Frentzas
- Department of Medical Oncology, Monash Health, Melbourne, VIC, Australia
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Zhongmin Maxwell Wang
- Procurement and Sourcing Department and Clinical Operation Department, Akeso Biopharma Inc, Zhongshan, Guangdong, China
| | - Yu Xia
- President Office, Akeso Biopharma Inc, Zhongshan, Guangdong, China
| | - Baiyong Li
- Research and Development Department, Akeso Biopharma Inc, Zhongshan, Guangdong, China.
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26
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Chiarle R, Cheong TC, Jang A, Wang Q, Leonardi G, Ricciuti B, Alessi J, Federico AD, Awad M, Lehtinen M, Harris M. Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers. RESEARCH SQUARE 2024:rs.3.rs-3782958. [PMID: 38313284 PMCID: PMC10836111 DOI: 10.21203/rs.3.rs-3782958/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are typical and recurrent, but the underlying mechanisms and clinical implications of these patterns are poorly understood. Here, we investigated structures of > 8,000 kinase fusions and explore their generative mechanisms by applying newly developed experimental framework integrating high-throughput genome-wide gene fusion sequencing and clonal selection called Functionally Active Chromosomal Translocation Sequencing (FACTS). We discovered that typical oncogenic TK fusions recurrently seen in patients are selected from large pools of chromosomal rearrangements spontaneously occurring in cells based on two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies, as well as a shorter progression-free survival (PFS) and overall survival (OS) compared to patients with typical TK fusions. These findings highlight the principles of oncogenic TK fusion formation and their selection in cancers, with clinical implications for guiding targeted therapy.
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Affiliation(s)
| | | | - Ahram Jang
- Boston Children's Hospital and Harvard Medical School
| | - Qi Wang
- Boston Children's Hospital and Harvard Medical School
| | | | | | | | | | | | | | - Marian Harris
- Boston Children's Hospital and Harvard Medical School
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27
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Soltani S, Jamshidi A, Mahmoudi M, Farhadi E. Potential Roles for B cells and Autoantibodies in Ankylosing Spondylitis. Curr Rheumatol Rev 2024; 20:157-164. [PMID: 37870058 DOI: 10.2174/0115733971243468231012044909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 08/26/2023] [Accepted: 09/15/2023] [Indexed: 10/24/2023]
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory rheumatic disease that predominantly affects young males. AS is a condition in which the spine and sacroiliac joints become inflamed. More specifically, most AS patients experience spine malformations over time, resulting in functional incapability. The etiopathogenesis of AS is a complex combination of genetic predisposition and environmental factors. Extensive studies on AS have revealed the central role of genetics and immune reactions in its etiology. However, an utmost agreement has yet to be created. The available evidence suggests that both autoinflammation and T-cell-mediated autoimmune processes have significant roles in the disease process of AS. So far, B cells have obtained moderately little attention in AS pathogenesis, primarily because of the absence of disease-defining autoantibodies. However, against general dogma, evidence is mounting showing B cell involvement. Disruptions depict this in circulating B cell populations, the increased expression of immunoglobulin (Ig)G, IgA, and IgM, and B cell infiltration within the axial skeleton of AS patients. Meanwhile, compared to many other inflammatory autoimmune disorders, AS has no disease-specific autoantibodies that help disease diagnosis. This study has provided an overview of the B lymphocytes and antibodies' role in AS pathogenesis. It also introduces autoantibodies that can be the prognosis and diagnosis biomarkers of AS.
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Affiliation(s)
- Samaneh Soltani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Chronic Inflammatory Diseases, Tehran University of Medical Sciences, Tehran, Iran
| | - Elham Farhadi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Chronic Inflammatory Diseases, Tehran University of Medical Sciences, Tehran, Iran
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28
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Suzuki A, Nojima S, Tahara S, Motooka D, Kohara M, Okuzaki D, Hirokawa M, Morii E. Identification of invasive subpopulations using spatial transcriptome analysis in thyroid follicular tumors. J Pathol Transl Med 2024; 58:22-28. [PMID: 38229431 DOI: 10.4132/jptm.2023.11.21] [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: 10/27/2023] [Accepted: 11/21/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Follicular tumors include follicular thyroid adenomas and carcinomas; however, it is difficult to distinguish between the two when the cytology or biopsy material is obtained from a portion of the tumor. The presence or absence of invasion in the resected material is used to differentiate between adenomas and carcinomas, which often results in the unnecessary removal of the adenomas. If nodules that may be follicular thyroid carcinomas are identified preoperatively, active surveillance of other nodules as adenomas is possible, which reduces the risk of surgical complications and the expenses incurred during medical treatment. Therefore, we aimed to identify biomarkers in the invasive subpopulation of follicular tumor cells. METHODS We performed a spatial transcriptome analysis of a case of follicular thyroid carcinoma and examined the dynamics of CD74 expression in 36 cases. RESULTS We identified a subpopulation in a region close to the invasive area, and this subpopulation expressed high levels of CD74. Immunohistochemically, CD74 was highly expressed in the invasive and peripheral areas of the tumor. CONCLUSIONS Although high CD74 expression has been reported in papillary and anaplastic thyroid carcinomas, it has not been analyzed in follicular thyroid carcinomas. Furthermore, the heterogeneity of CD74 expression in thyroid tumors has not yet been reported. The CD74-positive subpopulation identified in this study may be useful in predicting invasion of follicular thyroid carcinomas.
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Affiliation(s)
- Ayana Suzuki
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Diagnostic Pathology and Cytology, Kuma Hospital, Kobe, Hyogo, Japan
| | - Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Shinichiro Tahara
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Masaharu Kohara
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Mitsuyoshi Hirokawa
- Department of Diagnostic Pathology and Cytology, Kuma Hospital, Kobe, Hyogo, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
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29
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Krause GJ, Kirchner P, Stiller B, Morozova K, Diaz A, Chen KH, Krogan NJ, Agullo-Pascual E, Clement CC, Lindenau K, Swaney DL, Dilipkumar S, Bravo-Cordero JJ, Santambrogio L, Cuervo AM. Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy. Cell Rep 2023; 42:113529. [PMID: 38060380 PMCID: PMC10807933 DOI: 10.1016/j.celrep.2023.113529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/12/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023] Open
Abstract
Chaperone-mediated autophagy (CMA) and endosomal microautophagy (eMI) are pathways for selective degradation of cytosolic proteins in lysosomes and late endosomes, respectively. These autophagic processes share as a first step the recognition of the same five-amino-acid motif in substrate proteins by the Hsc70 chaperone, raising the possibility of coordinated activity of both pathways. In this work, we show the existence of a compensatory relationship between CMA and eMI and identify a role for the chaperone protein Bag6 in triage and internalization of eMI substrates into late endosomes. Association and dynamics of Bag6 at the late endosome membrane change during starvation, a stressor that, contrary to other autophagic pathways, causes a decline in eMI activity. Collectively, these results show a coordinated function of eMI with CMA, identify the interchangeable subproteome degraded by these pathways, and start to elucidate the molecular mechanisms that facilitate the switch between them.
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Affiliation(s)
- Gregory J Krause
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Philipp Kirchner
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Barbara Stiller
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kateryna Morozova
- Department of Radiation Oncology, Weill Cornell School of Medicine, New York, NY 10021, USA
| | - Antonio Diaz
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kuei-Ho Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; The J. David Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; The J. David Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Cristina C Clement
- Department of Radiation Oncology, Weill Cornell School of Medicine, New York, NY 10021, USA
| | - Kristen Lindenau
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; The J. David Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shilpa Dilipkumar
- Microscopy CoRE, Dean's CoREs, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jose Javier Bravo-Cordero
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Santambrogio
- Department of Radiation Oncology, Weill Cornell School of Medicine, New York, NY 10021, USA.
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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30
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Dezfulian MH, Kula T, Pranzatelli T, Kamitaki N, Meng Q, Khatri B, Perez P, Xu Q, Chang A, Kohlgruber AC, Leng Y, Jupudi AA, Joachims ML, Chiorini JA, Lessard CJ, Farris AD, Muthuswamy SK, Warner BM, Elledge SJ. TScan-II: A genome-scale platform for the de novo identification of CD4 + T cell epitopes. Cell 2023; 186:5569-5586.e21. [PMID: 38016469 PMCID: PMC10841602 DOI: 10.1016/j.cell.2023.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/12/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023]
Abstract
CD4+ T cells play fundamental roles in orchestrating immune responses and tissue homeostasis. However, our inability to associate peptide human leukocyte antigen class-II (HLA-II) complexes with their cognate T cell receptors (TCRs) in an unbiased manner has hampered our understanding of CD4+ T cell function and role in pathologies. Here, we introduce TScan-II, a highly sensitive genome-scale CD4+ antigen discovery platform. This platform seamlessly integrates the endogenous HLA-II antigen-processing machinery in synthetic antigen-presenting cells and TCR signaling in T cells, enabling the simultaneous screening of multiple HLAs and TCRs. Leveraging genome-scale human, virome, and epitope mutagenesis libraries, TScan-II facilitates de novo antigen discovery and deep exploration of TCR specificity. We demonstrate TScan-II's potential for basic and translational research by identifying a non-canonical antigen for a cancer-reactive CD4+ T cell clone. Additionally, we identified two antigens for clonally expanded CD4+ T cells in Sjögren's disease, which bind distinct HLAs and are expressed in HLA-II-positive ductal cells within affected salivary glands.
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Affiliation(s)
- Mohammad H Dezfulian
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Tomasz Kula
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Thomas Pranzatelli
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Qingda Meng
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Bhuwan Khatri
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Paola Perez
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Qikai Xu
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Aiquan Chang
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ayano C Kohlgruber
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yumei Leng
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ananth Aditya Jupudi
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Departmentment of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michelle L Joachims
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - John A Chiorini
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Christopher J Lessard
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - A Darise Farris
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Departmentment of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Senthil K Muthuswamy
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Blake M Warner
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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31
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Evans KT, Blake K, Longworth A, Coburn MA, Insua-Rodríguez J, McMullen TP, Nguyen QH, Ma D, Lev T, Hernandez GA, Oganyan AK, Orujyan D, Edwards RA, Pridans C, Green KN, Villalta SA, Blurton-Jones M, Lawson DA. Microglia promote anti-tumour immunity and suppress breast cancer brain metastasis. Nat Cell Biol 2023; 25:1848-1859. [PMID: 37957324 PMCID: PMC11414741 DOI: 10.1038/s41556-023-01273-y] [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: 04/08/2021] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Breast cancer brain metastasis (BCBM) is a lethal disease with no effective treatments. Prior work has shown that brain cancers and metastases are densely infiltrated with anti-inflammatory, protumourigenic tumour-associated macrophages, but the role of brain-resident microglia remains controversial because they are challenging to discriminate from other tumour-associated macrophages. Using single-cell RNA sequencing, genetic and humanized mouse models, we specifically identify microglia and find that they play a distinct pro-inflammatory and tumour-suppressive role in BCBM. Animals lacking microglia show increased metastasis, decreased survival and reduced natural killer and T cell responses, showing that microglia are critical to promote anti-tumour immunity to suppress BCBM. We find that the pro-inflammatory response is conserved in human microglia, and markers of their response are associated with better prognosis in patients with BCBM. These findings establish an important role for microglia in anti-tumour immunity and highlight them as a potential immunotherapy target for brain metastasis.
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Affiliation(s)
- Katrina T Evans
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Kerrigan Blake
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Aaron Longworth
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Morgan A Coburn
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | - Jacob Insua-Rodríguez
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Timothy P McMullen
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Quy H Nguyen
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Dennis Ma
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Tatyana Lev
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Grace A Hernandez
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Armani K Oganyan
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Davit Orujyan
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Robert A Edwards
- Department of Pathology, University of California, Irvine, Irvine, CA, USA
| | - Clare Pridans
- University of Edinburgh Centre for Inflammation Research, Edinburgh, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Kim N Green
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | - S Armando Villalta
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | - Devon A Lawson
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA.
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA.
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32
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Avşar G, Pir P. An integrated study to decipher immunosuppressive cellular communication in the PDAC environment. NPJ Syst Biol Appl 2023; 9:56. [PMID: 37945567 PMCID: PMC10636193 DOI: 10.1038/s41540-023-00320-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one the most aggressive cancers and characterized by a highly rigid and immunosuppressive tumor microenvironment (TME). The extensive cellular interactions are known to play key roles in the immune evasion, chemoresistance, and poor prognosis. Here, we used the spatial transcriptomics, scRNA-seq, and bulk RNA-seq datasets to enhance the insights obtained from each to decipher the cellular communication in the TME. The complex crosstalk in PDAC samples was revealed by the single-cell and spatial transcriptomics profiles of the samples. We show that tumor-associated macrophages (TAMs) are the central cell types in the regulation of microenvironment in PDAC. They colocalize with the cancer cells and tumor-suppressor immune cells and take roles to provide an immunosuppressive environment. LGALS9 gene which is upregulated in PDAC tumor samples in comparison to healthy samples was also found to be upregulated in TAMs compared to tumor-suppressor immune cells in cancer samples. Additionally, LGALS9 was found to be the primary component in the crosstalk between TAMs and the other cells. The widespread expression of P4HB gene and its interaction with LGALS9 was also notable. Our findings point to a profound role of TAMs via LGALS9 and its interaction with P4HB that should be considered for further elucidation as target in the combinatory immunotherapies for PDAC.
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Affiliation(s)
- Gülben Avşar
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey.
- Turkish Academy of Sciences, Ankara, Turkey.
| | - Pınar Pir
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
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33
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Balasubramanian I, Bandyopadhyay S, Flores J, Bianchi‐Smak J, Lin X, Liu H, Sun S, Golovchenko NB, Liu Y, Wang D, Patel R, Joseph I, Suntornsaratoon P, Vargas J, Green PHR, Bhagat G, Lagana SM, Ying W, Zhang Y, Wang Z, Li WV, Singh S, Zhou Z, Kollias G, Farr LA, Moonah SN, Yu S, Wei Z, Bonder EM, Zhang L, Kiela PR, Edelblum KL, Ferraris R, Liu T, Gao N. Infection and inflammation stimulate expansion of a CD74 + Paneth cell subset to regulate disease progression. EMBO J 2023; 42:e113975. [PMID: 37718683 PMCID: PMC10620768 DOI: 10.15252/embj.2023113975] [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: 03/08/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Paneth cells (PCs), a specialized secretory cell type in the small intestine, are increasingly recognized as having an essential role in host responses to microbiome and environmental stresses. Whether and how commensal and pathogenic microbes modify PC composition to modulate inflammation remain unclear. Using newly developed PC-reporter mice under conventional and gnotobiotic conditions, we determined PC transcriptomic heterogeneity in response to commensal and invasive microbes at single cell level. Infection expands the pool of CD74+ PCs, whose number correlates with auto or allogeneic inflammatory disease progressions in mice. Similar correlation was found in human inflammatory disease tissues. Infection-stimulated cytokines increase production of reactive oxygen species (ROS) and expression of a PC-specific mucosal pentraxin (Mptx2) in activated PCs. A PC-specific ablation of MyD88 reduced CD74+ PC population, thus ameliorating pathogen-induced systemic disease. A similar phenotype was also observed in mice lacking Mptx2. Thus, infection stimulates expansion of a PC subset that influences disease progression.
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Affiliation(s)
| | | | - Juan Flores
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | | | - Xiang Lin
- Department of Computer ScienceNew Jersey Institute of TechnologyNewarkNJUSA
| | - Haoran Liu
- Department of Computer ScienceNew Jersey Institute of TechnologyNewarkNJUSA
| | - Shengxiang Sun
- Department of Pathology and ImmunologyWashington University School of MedicineSaint LouisMOUSA
| | | | - Yue Liu
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Dahui Wang
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Radha Patel
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Ivor Joseph
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Panan Suntornsaratoon
- Department of Pharmacology, Physiology & NeuroscienceRutgers New Jersey Medical SchoolNewarkNJUSA
| | - Justin Vargas
- Department of Medicine, Celiac Disease CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Peter HR Green
- Department of Medicine, Celiac Disease CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Govind Bhagat
- Department of Medicine, Celiac Disease CenterColumbia University Irving Medical CenterNew YorkNYUSA
- Department of Pathology and Cell BiologyColumbia University Irving Medical CenterNew YorkNYUSA
| | - Stephen M Lagana
- Department of Pathology and Cell BiologyColumbia University Irving Medical CenterNew YorkNYUSA
| | - Wang Ying
- Hackensack Meridian Health Center for Discovery and InnovationNutleyNJUSA
| | - Yi Zhang
- Hackensack Meridian Health Center for Discovery and InnovationNutleyNJUSA
| | - Zhihan Wang
- Department of StatisticsRutgers UniversityNew BrunswickNJUSA
| | - Wei Vivian Li
- Department of Biostatistics and EpidemiologyRutgers UniversityNew BrunswickNJUSA
| | - Sukhwinder Singh
- Department of PathologyRutgers New Jersey Medical SchoolNewarkNJUSA
| | - Zhongren Zhou
- Department of Pathology & Laboratory Medicine, Robert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNJUSA
| | - George Kollias
- Biomedical Sciences Research Centre, “Alexander Fleming”VariGreece
| | - Laura A Farr
- Division of Infectious Diseases and International HealthUniversity of VirginiaCharlottesvilleVAUSA
| | - Shannon N Moonah
- Division of Infectious Diseases and International HealthUniversity of VirginiaCharlottesvilleVAUSA
| | - Shiyan Yu
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Zhi Wei
- Department of Computer ScienceNew Jersey Institute of TechnologyNewarkNJUSA
| | - Edward M Bonder
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
| | - Lanjing Zhang
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
- Department of PathologyPenn Medicine Princeton Medical CenterPlainsboroNJUSA
| | - Pawel R Kiela
- Departments of Pediatrics and Immunology, and Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children's Research CenterThe University of Arizona Health SciencesTucsonAZUSA
| | - Karen L Edelblum
- Center for Immunity and InflammationRutgers New Jersey Medical SchoolNewarkNJUSA
| | - Ronaldo Ferraris
- Department of Pharmacology, Physiology & NeuroscienceRutgers New Jersey Medical SchoolNewarkNJUSA
| | - Ta‐Chiang Liu
- Department of Pathology and ImmunologyWashington University School of MedicineSaint LouisMOUSA
| | - Nan Gao
- Department of Biological SciencesRutgers UniversityNewarkNJUSA
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Zhang Z, Sun S. Linking ALS mutations to the disruption of the MHC-II pathway. Proc Natl Acad Sci U S A 2023; 120:e2315240120. [PMID: 37819987 PMCID: PMC10614208 DOI: 10.1073/pnas.2315240120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Affiliation(s)
- Zhe Zhang
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Shuying Sun
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD21205
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD21205
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35
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Leinung N, Mentrup T, Patel M, Gallagher T, Schröder B. Dynamic association of the intramembrane proteases SPPL2a/b and their substrates with tetraspanin-enriched microdomains. iScience 2023; 26:107819. [PMID: 37736044 PMCID: PMC10509304 DOI: 10.1016/j.isci.2023.107819] [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: 02/04/2023] [Revised: 07/21/2023] [Accepted: 08/31/2023] [Indexed: 09/23/2023] Open
Abstract
Signal peptide peptidase-like 2a and b (SPPL2a/b) are aspartyl intramembrane proteases and cleave tail-anchored proteins as well as N-terminal fragments (NTFs) derived from type II-oriented transmembrane proteins. How these proteases recruit substrates and cleavage is regulated, is still incompletely understood. We found that SPPL2a/b localize to detergent-resistant membrane (DRM) domains with the characteristics of tetraspanin-enriched microdomains (TEMs). Based on this, association with several tetraspanins was evaluated. We demonstrate that not only SPPL2a/b but also their substrates tumor necrosis factor (TNF) and CD74 associate with tetraspanins like CD9, CD81, and CD82 and/or TEMs and analyze the stability of these complexes in different detergents. CD9 and CD81 deficiency has protease- and substrate-selective effects on SPPL2a/b function. Our findings suggest that reciprocal interactions with tetraspanins may assist protease-substrate encounters of SPPL2a/b within the membrane. Beyond SPP/SPPL proteases, this supports previous concepts that tetraspanins facilitate membrane-embedded proteolytic processes.
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Affiliation(s)
- Nadja Leinung
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Torben Mentrup
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Mehul Patel
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Bernd Schröder
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
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36
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Chi B, Öztürk MM, Paraggio CL, Leonard CE, Sanita ME, Dastpak M, O’Connell JD, Coady JA, Zhang J, Gygi SP, Lopez-Gonzalez R, Yin S, Reed R. Causal ALS genes impact the MHC class II antigen presentation pathway. Proc Natl Acad Sci U S A 2023; 120:e2305756120. [PMID: 37722062 PMCID: PMC10523463 DOI: 10.1073/pnas.2305756120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/18/2023] [Indexed: 09/20/2023] Open
Abstract
Mutations in RNA/DNA-binding proteins cause amyotrophic lateral sclerosis (ALS), but the underlying disease mechanisms remain unclear. Here, we report that a set of ALS-associated proteins, namely FUS, EWSR1, TAF15, and MATR3, impact the expression of genes encoding the major histocompatibility complex II (MHC II) antigen presentation pathway. Both subunits of the MHC II heterodimer, HLA-DR, are down-regulated in ALS gene knockouts/knockdown in HeLa and human microglial cells, due to loss of the MHC II transcription factor CIITA. Importantly, hematopoietic progenitor cells (HPCs) derived from human embryonic stem cells bearing the FUSR495X mutation and HPCs derived from C9ORF72 ALS patient induced pluripotent stem cells also exhibit disrupted MHC II expression. Given that HPCs give rise to numerous immune cells, our data raise the possibility that loss of the MHC II pathway results in global failure of the immune system to protect motor neurons from damage that leads to ALS.
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Affiliation(s)
- Binkai Chi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Muhammet M. Öztürk
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Christina L. Paraggio
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Claudia E. Leonard
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Maria E. Sanita
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Mahtab Dastpak
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Jeremy D. O’Connell
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Jordan A. Coady
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Jiuchun Zhang
- Harvard Medical School Cell Biology Initiative for Genome Editing and Neurodegeneration, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Steven P. Gygi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Rodrigo Lopez-Gonzalez
- Department of Neurosciences Lerner Research Institute, Cleveland Clinic, Cleveland, OH44196
| | - Shanye Yin
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY10461
| | - Robin Reed
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
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37
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Chan WK, Williams J, Sorathia K, Pray B, Abusaleh K, Bian Z, Sharma A, Hout I, Nishat S, Hanel W, Sloan SL, Yasin A, Denlinger N, Zhang X, Muthusamy N, Vasu S, de Lima M, Yang Y, Baiocchi R, Alinari L. A novel CAR-T cell product targeting CD74 is an effective therapeutic approach in preclinical mantle cell lymphoma models. Exp Hematol Oncol 2023; 12:79. [PMID: 37740214 PMCID: PMC10517521 DOI: 10.1186/s40164-023-00437-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a rare B-cell non-Hodgkin lymphoma subtype which remains incurable despite multimodal approach including chemoimmunotherapy followed by stem cell transplant, targeted approaches such as the BTK inhibitor ibrutinib, and CD19 chimeric antigen receptor (CAR) T cells. CD74 is a nonpolymorphic type II integral membrane glycoprotein identified as an MHC class II chaperone and a receptor for macrophage migration inhibitory factor. Our group previously reported on CD74's abundant expression in MCL and its ability to increase via pharmacological inhibition of autophagosomal degradation. Milatuzumab, a fully humanized anti-CD74 monoclonal antibody, demonstrated significant activity in preclinical lymphoma models but failed to provide meaningful benefits in clinical trials mainly due to its short half-life. We hypothesized that targeting CD74 using a CAR-T cell would provide potent and durable anti-MCL activity. METHODS We engineered a second generation anti-CD74 CAR with 4-1BB and CD3ζ signaling domains (74bbz). Through in silico and rational mutagenesis on the scFV domain, the 74bbz CAR was functionally optimized for superior antigen binding affinity, proliferative signaling, and cytotoxic activity against MCL cells in vitro and in vivo. RESULTS Functionally optimized 74bbz CAR-T cells (clone 42105) induced significant killing of MCL cell lines, and primary MCL patient samples including one relapse after commercial CD19 CAR-T cell therapy with direct correlation between antigen density and cytotoxicity. It significantly prolonged the survival of an animal model established in NOD-SCIDγc-/- (NSG) mice engrafted with a human MCL cell line Mino subcutaneously compared to controls. Finally, while CD74 is also expressed on normal immune cell subsets, treatment with 74bbz CAR-T cells resulted in minimal cytotoxicity against these cells both in vitro and in vivo. CONCLUSIONS Targeting CD74 with 74bbz CAR-T cells represents a new cell therapy to provide a potent and durable and anti-MCL activity.
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Affiliation(s)
- Wing Keung Chan
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Jessica Williams
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Kinnari Sorathia
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Betsy Pray
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Kaled Abusaleh
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Zehua Bian
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Archisha Sharma
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Ian Hout
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Shamama Nishat
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Walter Hanel
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Shelby L Sloan
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Aneeq Yasin
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Nathan Denlinger
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Xiaoli Zhang
- Department of Biomedical Informatics/Center for Biostatistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Natarajan Muthusamy
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Sumithira Vasu
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Marcos de Lima
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Yiping Yang
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Robert Baiocchi
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA
| | - Lapo Alinari
- Department of Internal Medicine, Division of Hematology, College of Medicine, The Ohio State University, 400 W. 12th Ave, 481D Wiseman Hall, Columbus, OH, 43210, USA.
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38
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Xiang Z, Tian Z, Wang G, Liu L, Li K, Wang W, Lei X, Ren L, Wang J. CD74 Interacts with Proteins of Enterovirus D68 To Inhibit Virus Replication. Microbiol Spectr 2023; 11:e0080123. [PMID: 37409968 PMCID: PMC10434063 DOI: 10.1128/spectrum.00801-23] [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: 02/22/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
Enterovirus D68 (EV-D68) is a member of the species Enterovirus D in the genus Enterovirus of the family Picornaviridae. As an emerging non-polio enterovirus, EV-D68 is widely spread all over the world and causes severe neurological and respiratory illnesses. Although the intrinsic restriction factors in the cell provide a frontline defense, the molecular nature of virus-host interactions remains elusive. Here, we provide evidence that the major histocompatibility complex class II chaperone, CD74, inhibits EV-D68 replication in infected cells by interacting with the second hydrophobic region of 2B protein, while EV-D68 attenuates the antiviral role of CD74 through 3Cpro cleavage. 3Cpro cleaves CD74 at Gln-125. The equilibrium between CD74 and EV-D68 3Cpro determines the outcome of viral infection. IMPORTANCE As an emerging non-polio enterovirus, EV-D68 is widely spread all over the world and causes severe neurological and respiratory illnesses. Here, we report that CD74 inhibits viral replication in infected cells by targeting 2B protein of EV-D68, while EV-D68 attenuates the antiviral role of CD74 through 3Cpro cleavage. The equilibrium between CD74 and EV-D68 3Cpro determines the outcome of viral infection.
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Affiliation(s)
- Zichun Xiang
- NHC Key Laboratory of System Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Zhongqin Tian
- NHC Key Laboratory of System Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Guanying Wang
- NHC Key Laboratory of System Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Lulu Liu
- NHC Key Laboratory of System Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Kailin Li
- NHC Key Laboratory of System Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Wenjing Wang
- NHC Key Laboratory of System Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Xiaobo Lei
- NHC Key Laboratory of System Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Lili Ren
- NHC Key Laboratory of System Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Jianwei Wang
- NHC Key Laboratory of System Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
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Choi J, Zhang X, Li W, Houston M, Peregrina K, Dubin R, Ye K, Augenlicht L. Dynamic Intestinal Stem Cell Plasticity and Lineage Remodeling by a Nutritional Environment Relevant to Human Risk for Tumorigenesis. Mol Cancer Res 2023; 21:808-824. [PMID: 37097719 PMCID: PMC10390890 DOI: 10.1158/1541-7786.mcr-22-1000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/27/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
New Western-style diet 1 (NWD1), a purified diet establishing mouse exposure to key nutrients recapitulating levels that increase human risk for intestinal cancer, reproducibly causes mouse sporadic intestinal and colonic tumors reflecting human etiology, incidence, frequency, and lag with developmental age. Complex NWD1 stem cell and lineage reprogramming was deconvolved by bulk and single-cell RNA sequencing, single-cell Assay for Transposase-Accessible Chromatin using sequencing, functional genomics, and imaging. NWD1 extensively, rapidly, and reversibly, reprogrammed Lgr5hi stem cells, epigenetically downregulating Ppargc1a expression, altering mitochondrial structure and function. This suppressed Lgr5hi stem cell functions and developmental maturation of Lgr5hi cell progeny as cells progressed through progenitor cell compartments, recapitulated by Ppargc1a genetic inactivation in Lgr5hi cells in vivo. Mobilized Bmi1+, Ascl2hi cells adapted lineages to the nutritional environment and elevated antigen processing and presentation pathways, especially in mature enterocytes, causing chronic, protumorigenic low-level inflammation. There were multiple parallels between NWD1 remodeling of stem cells and lineages with pathogenic mechanisms in human inflammatory bowel disease, also protumorigenic. Moreover, the shift to alternate stem cells reflects that the balance between Lgr5-positive and -negative stem cells in supporting human colon tumors is determined by environmental influences. Stem cell and lineage plasticity in response to nutrients supports historic concepts of homeostasis as a continual adaptation to environment, with the human mucosa likely in constant flux in response to changing nutrient exposures. IMPLICATIONS Although oncogenic mutations provide a competitive advantage to intestinal epithelial cells in clonal expansion, the competition is on a playing field dynamically sculpted by the nutritional environment, influencing which cells dominate in mucosal maintenance and tumorigenesis.
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Affiliation(s)
- Jiahn Choi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Xusheng Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Wenge Li
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Michele Houston
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Karina Peregrina
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Robert Dubin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Leonard Augenlicht
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
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Lobos Patorniti N, Zulkefli KL, McAdam ME, Vargas P, Bakke O, Progida C. Rai14 is a novel interactor of Invariant chain that regulates macropinocytosis. Front Immunol 2023; 14:1182180. [PMID: 37545539 PMCID: PMC10401043 DOI: 10.3389/fimmu.2023.1182180] [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: 03/08/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023] Open
Abstract
Invariant chain (Ii, CD74) is a type II transmembrane glycoprotein that acts as a chaperone and facilitates the folding and transport of MHC II chains. By assisting the assembly and subcellular targeting of MHC II complexes, Ii has a wide impact on the functions of antigen-presenting cells such as antigen processing, endocytic maturation, signal transduction, cell migration, and macropinocytosis. Ii is a multifunctional molecule that can alter endocytic traffic and has several interacting molecules. To understand more about Ii's function and to identify further Ii interactors, a yeast two-hybrid screening was performed. Retinoic Acid-Induced 14 (Rai14) was detected as a putative interaction partner, and the interaction was confirmed by co-immunoprecipitation. Rai14 is a poorly characterized protein, which is believed to have a role in actin cytoskeleton and membrane remodeling. In line with this, we found that Rai14 localizes to membrane ruffles, where it forms macropinosomes. Depletion of Rai14 in antigen-presenting cells delays MHC II internalization, affecting macropinocytic activity. Intriguingly, we demonstrated that, similar to Ii, Rai14 is a positive regulator of macropinocytosis and a negative regulator of cell migration, two antagonistic processes in antigen-presenting cells. This antagonism is known to depend on the interaction between myosin II and Ii. Here, we show that Rai14 also binds to myosin II, suggesting that Ii, myosin II, and Rai14 work together to coordinate macropinocytosis and cell motility.
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Affiliation(s)
| | | | | | - Pablo Vargas
- Inserm U1151, Institut Necker Enfants Malades, Paris, France
| | - Oddmund Bakke
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Cinzia Progida
- Department of Biosciences, University of Oslo, Oslo, Norway
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Wong-Benito V, de Rijke J, Dixon B. Antigen presentation in vertebrates: Structural and functional aspects. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 144:104702. [PMID: 37116963 DOI: 10.1016/j.dci.2023.104702] [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: 02/11/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 06/05/2023]
Abstract
Antigen presentation is a key process of the immune system and is responsible for the activation of T cells. The main characters are the major histocompatibility complex class I (MHC-I) and class II (MHC-II) molecules, and accessory proteins that act as chaperones for these glycoproteins. Current knowledge of this process and also the elucidation of the structural features of these proteins, has been extensively reviewed in humans. Unfortunately, this is not the case for non-human species, wherein the function and structural characteristic of the antigen presentation proteins is far from being understood. The majority of previous studies in non-human species, especially in teleost fish and lower vertebrates, are limited to the transcriptomic level, which leads to gaps in the knowledge about the functional process of antigen presentation in these species. This review summarizes what is known so far about antigen presentation pathways in vertebrates from a structural and functional perspective. The focus is not only on the MHC receptors, but also, on the forgotten characters of these pathways such as the proteins of the peptide loading complex, and the MHC-II chaperone invariant chain.
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Affiliation(s)
| | - Jill de Rijke
- Department of Biology, University of Waterloo, Canada
| | - Brian Dixon
- Department of Biology, University of Waterloo, Canada.
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Yang J, Liu K, Yang L, Ji J, Qin J, Deng H, Wang Z. Identification and validation of a novel cuproptosis-related stemness signature to predict prognosis and immune landscape in lung adenocarcinoma by integrating single-cell and bulk RNA-sequencing. Front Immunol 2023; 14:1174762. [PMID: 37287976 PMCID: PMC10242006 DOI: 10.3389/fimmu.2023.1174762] [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: 02/27/2023] [Accepted: 05/11/2023] [Indexed: 06/09/2023] Open
Abstract
Background Cancer stem cells (CSCs) play vital roles in lung adenocarcinoma (LUAD) recurrence, metastasis, and drug resistance. Cuproptosis has provided a novel insight into the treatment of lung CSCs. However, there is a lack of knowledge regarding the cuproptosis-related genes combined with the stemness signature and their roles in the prognosis and immune landscape of LUAD. Methods Cuproptosis-related stemness genes (CRSGs) were identified by integrating single-cell and bulk RNA-sequencing data in LUAD patients. Subsequently, cuproptosis-related stemness subtypes were classified using consensus clustering analysis, and a prognostic signature was constructed by univariate and least absolute shrinkage operator (LASSO) Cox regression. The association between signature with immune infiltration, immunotherapy, and stemness features was also investigated. Finally, the expression of CRSGs and the functional roles of target gene were validated in vitro. Results We identified six CRSGs that were mainly expressed in epithelial and myeloid cells. Three distinct cuproptosis-related stemness subtypes were identified and associated with the immune infiltration and immunotherapy response. Furthermore, a prognostic signature was constructed to predict the overall survival (OS) of LUAD patients based on eight differently expressed genes (DEGs) with cuproptosis-related stemness signature (KLF4, SCGB3A1, COL1A1, SPP1, C4BPA, TSPAN7, CAV2, and CTHRC1) and confirmed in validation cohorts. We also developed an accurate nomogram to improve clinical applicability. Patients in the high-risk group showed worse OS with lower levels of immune cell infiltration and higher stemness features. Ultimately, further cellular experiments were performed to verify the expression of CRSGs and prognostic DEGs and demonstrate that SPP1 could affect the proliferation, migration, and stemness of LUAD cells. Conclusion This study developed a novel cuproptosis-related stemness signature that can be used to predict the prognosis and immune landscape of LUAD patients, and provided potential therapeutic targets for lung CSCs in the future.
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Affiliation(s)
- Jia Yang
- *Correspondence: Zhongqi Wang, ; Jia Yang,
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Urbiola-Salvador V, Lima de Souza S, Grešner P, Qureshi T, Chen Z. Plasma Proteomics Unveil Novel Immune Signatures and Biomarkers upon SARS-CoV-2 Infection. Int J Mol Sci 2023; 24:ijms24076276. [PMID: 37047248 PMCID: PMC10093853 DOI: 10.3390/ijms24076276] [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: 01/29/2023] [Revised: 03/07/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Several elements have an impact on COVID-19, including comorbidities, age and sex. To determine the protein profile changes in peripheral blood caused by a SARS-CoV-2 infection, a proximity extension assay was used to quantify 1387 proteins in plasma samples among 28 Finnish patients with COVID-19 with and without comorbidities and their controls. Key immune signatures, including CD4 and CD28, were changed in patients with comorbidities. Importantly, several unreported elevated proteins in patients with COVID-19, such as RBP2 and BST2, which show anti-microbial activity, along with proteins involved in extracellular matrix remodeling, including MATN2 and COL6A3, were identified. RNF41 was downregulated in patients compared to healthy controls. Our study demonstrates that SARS-CoV-2 infection causes distinct plasma protein changes in the presence of comorbidities despite the interpatient heterogeneity, and several novel potential biomarkers associated with a SARS-CoV-2 infection alone and in the presence of comorbidities were identified. Protein changes linked to the generation of SARS-CoV-2-specific antibodies, long-term effects and potential association with post-COVID-19 condition were revealed. Further study to characterize the identified plasma protein changes from larger cohorts with more diverse ethnicities of patients with COVID-19 combined with functional studies will facilitate the identification of novel diagnostic, prognostic biomarkers and potential therapeutic targets for patients with COVID-19.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, 80-307 Gdańsk, Pomerania, Poland
| | - Suiane Lima de Souza
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, North Ostrobothnia, Finland
| | - Peter Grešner
- Department of Translational Oncology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Medical University of Gdańsk, 80-211 Gdańsk, Pomerania, Poland
| | - Talha Qureshi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, North Ostrobothnia, Finland
| | - Zhi Chen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, North Ostrobothnia, Finland
- Correspondence:
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da Rosa NN, Appel JM, Irioda AC, Mogharbel BF, de Oliveira NB, Perussolo MC, Stricker PEF, Rosa-Fernandes L, Marinho CRF, de Carvalho KAT. Three-Dimensional Bioprinting of an In Vitro Lung Model. Int J Mol Sci 2023; 24:5852. [PMID: 36982923 PMCID: PMC10059924 DOI: 10.3390/ijms24065852] [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: 02/06/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
In December 2019, COVID-19 emerged in China, and in January 2020, the World Health Organization declared a state of international emergency. Within this context, there is a significant search for new drugs to fight the disease and a need for in vitro models for preclinical drug tests. This study aims to develop a 3D lung model. For the execution, Wharton's jelly mesenchymal stem cells (WJ-MSC) were isolated and characterized through flow cytometry and trilineage differentiation. For pulmonary differentiation, the cells were seeded in plates coated with natural functional biopolymer matrix as membrane until spheroid formation, and then the spheroids were cultured with differentiation inductors. The differentiated cells were characterized using immunocytochemistry and RT-PCR, confirming the presence of alveolar type I and II, ciliated, and goblet cells. Then, 3D bioprinting was performed with a sodium alginate and gelatin bioink in an extrusion-based 3D printer. The 3D structure was analyzed, confirming cell viability with a live/dead assay and the expression of lung markers with immunocytochemistry. The results showed that the differentiation of WJ-MSC into lung cells was successful, as well as the bioprinting of these cells in a 3D structure, a promising alternative for in vitro drug testing.
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Affiliation(s)
- Nádia Nascimento da Rosa
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Julia Maurer Appel
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Ana Carolina Irioda
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Bassam Felipe Mogharbel
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Nathalia Barth de Oliveira
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Maiara Carolina Perussolo
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Priscila Elias Ferreira Stricker
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
| | - Lívia Rosa-Fernandes
- Experimental Immunoparasitology Laboratory, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (L.R.-F.); (C.R.F.M.)
| | - Cláudio Romero Farias Marinho
- Experimental Immunoparasitology Laboratory, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (L.R.-F.); (C.R.F.M.)
| | - Katherine Athayde Teixeira de Carvalho
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, Pelé Pequeno Príncipe Research Institute & Pequeno Príncipe Faculties, Curitiba 80240-020, Brazil; (N.N.d.R.); (J.M.A.); (A.C.I.); (B.F.M.); (N.B.d.O.); (M.C.P.); (P.E.F.S.)
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Zhang J, Li W, Xiong Z, Zhu J, Ren X, Wang S, Kuang H, Lin X, Mora A, Li X. PDGF-D-induced immunoproteasome activation and cell-cell interactions. Comput Struct Biotechnol J 2023; 21:2405-2418. [PMID: 37066124 PMCID: PMC10090480 DOI: 10.1016/j.csbj.2023.03.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
Platelet-derived growth factor-D (PDGF-D) is abundantly expressed in ocular diseases. Yet, it remains unknown whether and how PDGF-D affects ocular cells or cell-cell interactions in the eye. In this study, using single-cell RNA sequencing (scRNA-seq) and a mouse model of PDGF-D overexpression in retinal pigment epithelial (RPE) cells, we found that PDGF-D overexpression markedly upregulated the key immunoproteasome genes, leading to increased antigen processing/presentation capacity of RPE cells. Also, more than 6.5-fold ligand-receptor pairs were found in the PDGF-D overexpressing RPE-choroid tissues, suggesting markedly increased cell-cell interactions. Moreover, in the PDGF-D-overexpressing tissues, a unique cell population with a transcriptomic profile of both stromal cells and antigen-presenting RPE cells was detected, suggesting PDGF-D-induced epithelial-mesenchymal transition of RPE cells. Importantly, administration of ONX-0914, an immunoproteasome inhibitor, suppressed choroidal neovascularization (CNV) in a mouse CNV model in vivo. Together, we show that overexpression of PDGF-D increased pro-angiogenic immunoproteasome activities, and inhibiting immunoproteasome pathway may have therapeutic value for the treatment of neovascular diseases.
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Maddipatla SC, Kolachala VL, Venkateswaran S, Dodd AF, Pelia RS, Geem D, Yin H, Sun Y, Xu C, Mo A, Kosters A, Yang J, Matthews JD, Ghosn E, Kugathasan S, Qiu P. Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Naïve and Treated Crohn's Disease. Inflamm Bowel Dis 2023; 29:274-285. [PMID: 36206201 PMCID: PMC9890215 DOI: 10.1093/ibd/izac201] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Crohn's disease is a lifelong disease characterized by chronic inflammation of the gastrointestinal tract. Defining the cellular and transcriptional composition of the mucosa at different stages of disease progression is needed for personalized therapy in Crohn's. METHODS Ileal biopsies were obtained from (1) control subjects (n = 6), (2) treatment-naïve patients (n = 7), and (3) established (n = 14) Crohn's patients along with remission (n = 3) and refractory (n = 11) treatment groups. The biopsies processed using 10x Genomics single cell 5' yielded 139 906 cells. Gene expression count matrices of all samples were analyzed by reciprocal principal component integration, followed by clustering analysis. Manual annotations of the clusters were performed using canonical gene markers. Cell type proportions, differential expression analysis, and gene ontology enrichment were carried out for each cell type. RESULTS We identified 3 cellular compartments with 9 epithelial, 1 stromal, and 5 immune cell subtypes. We observed differences in the cellular composition between control, treatment-naïve, and established groups, with the significant changes in the epithelial subtypes of the treatment-naïve patients, including microfold, tuft, goblet, enterocyte,s and BEST4+ cells. Surprisingly, fewer changes in the composition of the immune compartment were observed; however, gene expression in the epithelial and immune compartment was different between Crohn's phenotypes, indicating changes in cellular activity. CONCLUSIONS Our study identified cellular and transcriptional signatures associated with treatment-naïve Crohn's disease that collectively point to dysfunction of the intestinal barrier with an increase in inflammatory cellular activity. Our analysis also highlights the heterogeneity among patients within the same disease phenotype, shining a new light on personalized treatment responses and strategies.
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Affiliation(s)
- Sushma Chowdary Maddipatla
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Vasantha L Kolachala
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Anne F Dodd
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Ranjit Singh Pelia
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Duke Geem
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Hong Yin
- Department of Pathology, Children’s Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | - Yutong Sun
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Congmin Xu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Angela Mo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Astrid Kosters
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Junkai Yang
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jason D Matthews
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Eliver Ghosn
- Emory Vaccine Center, Lowance Center for Human Immunology, Departments of Medicine and Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
- Genetics and Molecular Biology Program, Emory University School of Medicine, Atlanta, GA, USAand
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
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Wood-Trageser MA, Lesniak D, Gambella A, Golnoski K, Feng S, Bucuvalas J, Sanchez-Fueyo A, Demetris AJ. Next-generation pathology detection of T cell-antigen-presenting cell immune synapses in human liver allografts. Hepatology 2023; 77:355-366. [PMID: 35819312 PMCID: PMC9834436 DOI: 10.1002/hep.32666] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND AND AIMS In otherwise near-normal appearing biopsies by routine light microscopy, next-generation pathology (NGP) detected close pairings (immune pairs; iPAIRs) between lymphocytes and antigen-presenting cells (APCs) that predicted immunosuppression weaning failure in pediatric liver transplant (LTx) recipients (Immunosuppression Withdrawal for Stable Pediatric Liver Transplant Recipients [iWITH], NCT01638559). We hypothesized that NGP-detected iPAIRs enrich for true immune synapses, as determined by nuclear shape metrics, intercellular distances, and supramolecular activation complex (SMAC) formation. APPROACH AND RESULTS Intralobular iPAIRs (CD45 high lymphocyte-major histocompatibility complex II + APC pairs; n = 1167, training set) were identified at low resolution from multiplex immunohistochemistry-stained liver biopsy slides from several multicenter LTx immunosuppression titration clinical trials (iWITH; NCT02474199 (Donor Alloantigen Reactive Tregs (darTregs) for Calcineurin Inhibitor (CNI) Reduction (ARTEMIS); Prospective Longitudinal Study of iWITH Screen Failures Secondary to Histopathology). After excluding complex multicellular aggregates, high-resolution imaging was used to examine immune synapse formation ( n = 998). By enriching for close intranuclear lymphocyte-APC distance (mean: 0.713 μm) and lymphocyte nuclear flattening (mean ferret diameter: 2.1), SMAC formation was detected in 29% of iPAIR-engaged versus 9.5% of unpaired lymphocytes. Integration of these morphometrics enhanced NGP detection of immune synapses (ai-iSYN). Using iWITH preweaning biopsies from eligible patients ( n = 53; 18 tolerant, 35 nontolerant; testing set), ai-iSYN accurately predicted (87.3% accuracy vs. 81.4% for iPAIRs; 100% sensitivity, 75% specificity) immunosuppression weaning failure. This confirmed the presence and importance of intralobular immune synapse formation in liver allografts. Stratification of biopsy mRNA expression data by immune synapse quantity yielded the top 20 genes involved in T cell activation and immune synapse formation and stability. CONCLUSIONS NGP-detected immune synapses (subpathological rejection) in LTx patients prior to immunosuppression reduction suggests that NGP-detected (allo)immune activity usefulness for titration of immunosuppressive therapy in various settings.
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Affiliation(s)
- Michelle A Wood-Trageser
- Division of Liver and Transplant Pathology , University of Pittsburgh , Pittsburgh , Pennsylvania , USA
| | - Drew Lesniak
- Division of Liver and Transplant Pathology , University of Pittsburgh , Pittsburgh , Pennsylvania , USA
| | - Alessandro Gambella
- Division of Liver and Transplant Pathology , University of Pittsburgh , Pittsburgh , Pennsylvania , USA
- Pathology Unit, Department of Medical Sciences , University of Turin , Torino , Italy
| | - Kayla Golnoski
- Division of Liver and Transplant Pathology , University of Pittsburgh , Pittsburgh , Pennsylvania , USA
| | - Sandy Feng
- Division of Transplantation, Department of Surgery , University of California San Francisco , San Francisco , California , USA
| | - John Bucuvalas
- Mount Sinai Kravis Children's Hospital and Recanati/Miller Transplantation Institute , Mount Sinai Health System , New York , New York , USA
| | | | - A Jake Demetris
- Division of Liver and Transplant Pathology , University of Pittsburgh , Pittsburgh , Pennsylvania , USA
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Localization of Chicken Rab22a in Cells and Its Relationship to BF or Ii Molecules and Genes. Animals (Basel) 2023; 13:ani13030387. [PMID: 36766276 PMCID: PMC9913282 DOI: 10.3390/ani13030387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Rab22a is an important small GTPase protein the molecule that is involved in intracellular transportation and regulation of proteins. It also plays an important role in antigens uptake, transportation, regulation of endosome morphology, and also regulates the transport of antigens to MHC (Major Histocompatibility Complex) molecules. To investigate the role of Rab22a, the intracellular co-localization of chicken Rab22a (cRab22a) molecule and its relationship to BF and chicken invariant chain (cIi) molecules was studied. A 3D protein structure of Rab22a was constructed by using informatics tools (DNASTAR 4.0 and DNAMAN). Based on the model, the corresponding recombinant eukaryotic plasmids were constructed by point mutations in the protein's structural domains. HEK 293T cells were co-transfected with plasmids pEGFP-C1-cIi to observe the intracellular co-localization. Secondly, the DC2.4 Mouse Dendritic Cell and Murine RAW 264.7 cells were transfected with recombinant plasmids of pmCherry-cRab22a and pmCherry-mRab22a respectively. Subsequently, the intracellular localization of cRab22a in early and late endosomes was observed with specific antibodies against EEA1 and LAMP1 respectively. For gene expression-based studies, the cRab22a gene was down-regulated and up-regulated in HD11 cells, following the detection of transcription levels of the BFa (MHCIa) and cIi genes by real-time quantitative PCR (RT-qPCR). The interactions of the cRab22a gene with BFa and cIi were detected by co-immunoprecipitation (Co-IP) and Western blot. The results showed that the protein structures of chicken and mouse Rab22a were highly homologous (95.4%), and both localize to the early and late endosomes. Ser41 and Tyr74 are key amino acids in the Switch regions of Rab22a which maintain its intracellular localization. The down-regulation of cRab22a gene expression significantly reduced (p < 0.01) the transcription of BFa (MHCIa) and cIi in HD11 cells. However, when the expression of the cRab22a gene was increased 55 times as compared to control cells, the expression of the BFa (MHCIa) gene was increased 1.7 times compared to the control cells (p < 0.01), while the expression of the cIi gene did not significantly differ from control (p > 0.05). Western blot results showed that cRab22a could not directly bind to BFa and cIi. So, cRab22a can regulate BFa and cIi protein molecules indirectly. It is concluded that cRab22a was localized with cIi in the endosome. The Switch regions of cRab22a are the key domains that affect intracellular localization and colocalization of the cIi molecule.
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Li QL, Tang J, Zhao L, Ruze A, Shan XF, Gao XM. The role of CD74 in cardiovascular disease. Front Cardiovasc Med 2023; 9:1049143. [PMID: 36712241 PMCID: PMC9877307 DOI: 10.3389/fcvm.2022.1049143] [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: 09/20/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Leukocyte differentiation antigen 74 (CD74), also known as invariant chain, is a molecular chaperone of major histocompatibility complex class II (MHC II) molecules involved in antigen presentation. CD74 has recently been shown to be a receptor for the macrophage migration inhibitory factor family proteins (MIF/MIF2). Many studies have revealed that CD74 plays an important role in cardiovascular disease. In this review, we summarize the structure and main functions of CD74 and then focus on the recent research progress on the role of CD74 in cardiovascular diseases. In addition, we also discuss potential treatment strategies that target CD74. Our systematic review of the role of CD74 in cardiovascular disease will fill some knowledge gaps in the field.
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Affiliation(s)
- Qiu-Lin Li
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asian, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China,Xinjiang Key Laboratory of Medical Animal Model Research, Ürümqi, China
| | - Jing Tang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asian, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China,Xinjiang Key Laboratory of Medical Animal Model Research, Ürümqi, China,Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Ling Zhao
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asian, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China,Xinjiang Key Laboratory of Medical Animal Model Research, Ürümqi, China
| | - Amanguli Ruze
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asian, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China,Xinjiang Key Laboratory of Medical Animal Model Research, Ürümqi, China
| | - Xue-Feng Shan
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asian, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China,Xinjiang Key Laboratory of Medical Animal Model Research, Ürümqi, China
| | - Xiao-Ming Gao
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asian, Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China,Xinjiang Key Laboratory of Medical Animal Model Research, Ürümqi, China,Clinical Medical Research Institute of Xinjiang Medical University, Ürümqi, China,*Correspondence: Xiao-Ming Gao,
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50
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Dixon S, Karrow NA, Borkowski E, Suarez-Vega A, Menzies PI, Kennedy D, Peregrine AS, Mallard BA, Cánovas Á. Identifying hepatic genes regulating the ovine response to gastrointestinal nematodes using RNA-Sequencing. Front Genet 2023; 14:1111426. [PMID: 36873933 PMCID: PMC9981634 DOI: 10.3389/fgene.2023.1111426] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/17/2023] [Indexed: 02/19/2023] Open
Abstract
Gastrointestinal nematode (GIN) infections are considered the most important disease of grazing sheep and due to increasing anthelmintic resistance, chemical control alone is inadequate. Resistance to Gastrointestinal nematode infection is a heritable trait, and through natural selection many sheep breeds have higher resistance. Studying the transcriptome from GIN-exposed and GIN-unexposed sheep using RNA-Sequencing technology can provide measurements of transcript levels associated with the host response to Gastrointestinal nematode infection, and these transcripts may harbor genetic markers that can be used in selective breeding programs to enhance disease resistance. The objective of this study was to compare liver transcriptomes of sheep naturally exposed to Gastrointestinal nematode s, with either high or low parasite burdens, to GIN-unexposed control sheep in order to identify key regulator genes and biological processes associated with Gastrointestinal nematode infection. Differential gene expression analysis revealed no significant differentially expressed genes (DEG) between sheep with a high or low parasite burden (p-value ≤0.01; False Discovery Rate (FDR) ≤ 0.05; and Fold-Change (FC) of > ±2). However, when compared to the control group, low parasite burden sheep showed 146 differentially expressed genes (64 upregulated and 82 downregulated in the low parasite burden group relative to the control), and high parasite burden sheep showed 159 differentially expressed genes (57 upregulated and 102 downregulated in the low parasite burden group relative to the control) (p-value ≤0.01; FDR ≤0.05; and FC of > ±2). Among these two lists of significant differentially expressed genes, 86 differentially expressed genes (34 upregulated, 52 downregulated in the parasited group relative to the control) were found in common between the two parasite burden groups compared to the control (GIN-unexposed sheep). Functional analysis of these significant 86 differentially expressed genes found upregulated genes involved in immune response and downregulated genes involved in lipid metabolism. Results of this study offer insight into the liver transcriptome during natural Gastrointestinal nematode exposure that helps provide a better understanding of the key regulator genes involved in Gastrointestinal nematode infection in sheep.
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Affiliation(s)
- Samantha Dixon
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Niel A Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Emma Borkowski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Aroa Suarez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Paula I Menzies
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Delma Kennedy
- Ontario Ministry of Agriculture, Food and Rural Affairs, Guelph, ON, Canada
| | - Andrew S Peregrine
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Bonnie A Mallard
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Ángela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
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