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Seiler S, Rudolf F, Gomes FR, Pavlovic A, Nebel J, Seidenbecher CI, Foo LC. Astrocyte-derived factors regulate CNS myelination. Glia 2024. [PMID: 39092473 DOI: 10.1002/glia.24596] [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: 10/03/2023] [Revised: 06/20/2024] [Accepted: 07/10/2024] [Indexed: 08/04/2024]
Abstract
The role that astrocytes play in central nervous system (CNS) myelination is poorly understood. We investigated the contribution of astrocyte-derived factors to myelination and revealed a substantial overlap in the secretomes of human and rat astrocytes. Using in vitro myelinating co-cultures of primary retinal ganglion cells and cortical oligodendrocyte precursor cells, we discovered that factors secreted by resting astrocytes, but not reactive astrocytes, facilitated myelination. Soluble brevican emerged as a new enhancer of developmental myelination in vivo, CNS and its absence was linked to remyelination deficits following an immune-mediated damage in an EAE mouse model. The observed reduction of brevican expression in reactive astrocytes and human MS lesions suggested a potential link to the compromised remyelination characteristic of neurodegenerative diseases. Our findings suggested brevican's role in myelination may be mediated through interactions with binding partners such as contactin-1 and tenascin-R. Proteomic analysis of resting versus reactive astrocytes highlighted a shift in protein expression profiles, pinpointing candidates that either facilitate or impede CNS repair, suggesting that depending on their reactivity state, astrocytes play a dual role during myelination.
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Affiliation(s)
- Sybille Seiler
- F. Hoffmann-La Roche, pRED, Neuroscience, Discovery & Translational Area (NRD), Basel, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
| | - Franziska Rudolf
- F. Hoffmann-La Roche, pRED, Neuroscience, Discovery & Translational Area (NRD), Basel, Switzerland
| | - Filipa Ramilo Gomes
- F. Hoffmann-La Roche, pRED, Neuroscience, Discovery & Translational Area (NRD), Basel, Switzerland
| | - Anto Pavlovic
- F. Hoffmann-La Roche, pRED, Neuroscience, Discovery & Translational Area (NRD), Basel, Switzerland
| | - Jana Nebel
- Department Neurochemistry & Molecular Biology, Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany
| | - Constanze I Seidenbecher
- Department Neurochemistry & Molecular Biology, Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Lynette C Foo
- F. Hoffmann-La Roche, pRED, Neuroscience, Discovery & Translational Area (NRD), Basel, Switzerland
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2
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Wichmann CW, Morgan KA, Cao Z, Osellame LD, Guo N, Gan H, Reilly E, Burvenich IJG, O'Keefe GJ, Donnelly PS, Scott AM. Radiolabeling and Preclinical Evaluation of Therapeutic Efficacy of 225Ac-ch806 in Glioblastoma and Colorectal Cancer Xenograft Models. J Nucl Med 2024:jnumed.123.266894. [PMID: 39054282 DOI: 10.2967/jnumed.123.266894] [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: 10/29/2023] [Accepted: 06/05/2024] [Indexed: 07/27/2024] Open
Abstract
The epidermal growth factor receptor (EGFR) protein is highly expressed in a range of malignancies. Although therapeutic interventions directed toward EGFR have yielded therapeutic responses in cancer patients, side effects are common because of normal-tissue expression of wild-type EGFR. We developed a novel tumor-specific anti-EGFR chimeric antibody ch806 labeled with 225Ac and evaluated its in vitro properties and therapeutic efficacy in murine models of glioblastoma and colorectal cancer. Methods: 225Ac-ch806 was prepared using different chelators, yielding [225Ac]Ac-macropa-tzPEG3Sq-ch806 and [225Ac]Ac-DOTA-dhPzPEG4-ch806. Radiochemical yield, purity, apparent specific activity, and serum stability of 225Ac-ch806 were quantified. In vitro cell killing effect was examined. The biodistribution and therapeutic efficacy of 225Ac-ch806 were investigated in mice with U87MG.de2-7 and DiFi tumors. Pharmacodynamic analysis of tumors after therapy was performed, including DNA double-strand break immunofluorescence of γH2AX, as well as immunohistochemistry for proliferation, cell cycle arrest, and apoptosis. Results: [225Ac]Ac-macropa-tzPEG3Sq-ch806 surpassed [225Ac]Ac-DOTA-dhPzPEG4-ch806 in radiochemical yield, purity, apparent specific activity, and serum stability. [225Ac]Ac-macropa-tzPEG3Sq-ch806 was therefore used for both in vitro and in vivo studies. It displayed a significant, specific, and dose-dependent in vitro cell-killing effect in U87MG.de2-7 cells. 225Ac-ch806 also displayed high tumor uptake and minimal uptake in normal tissues. 225Ac-ch806 significantly inhibited tumor growth and prolonged survival in both U87MG.de2-7 and DiFi models. Enhanced γH2AX staining was observed in 225Ac-ch806-treated tumors compared with controls. Reduced Ki-67 expression was evident in all 225Ac-ch806-treated tumors. Increased expression of p21 and cleaved caspase 3 was shown in U87MG.de2-7 and DiFi tumors treated with 225Ac-ch806. Conclusion: In glioblastoma and colorectal tumor models, 225Ac-ch806 significantly inhibited tumor growth via induction of double-strand breaks, thereby constraining cancer cell proliferation while inducing cell cycle arrest and apoptosis. These findings underscore the potential clinical applicability of 225Ac-ch806 as a potential therapy for EGFR-expressing solid tumors.
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Affiliation(s)
- Christian W Wichmann
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia;
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria, Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Katherine A Morgan
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Zhipeng Cao
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria, Australia
| | - Laura D Osellame
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Nancy Guo
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Hui Gan
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Edward Reilly
- AbbVie-Oncology Discovery, North Chicago, Illinois; and
| | - Ingrid J G Burvenich
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Graeme J O'Keefe
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria, Australia
| | - Paul S Donnelly
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew M Scott
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
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3
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Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Science 2024; 385:eadl5763. [PMID: 39024454 DOI: 10.1126/science.adl5763] [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: 10/29/2023] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
Proximity labeling proteomics (PLP) strategies are powerful approaches to yield snapshots of protein neighborhoods. Here, we describe a multiscale PLP method with adjustable resolution that uses a commercially available photocatalyst, Eosin Y, which upon visible light illumination activates different photo-probes with a range of labeling radii. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor and orthogonally validated more than 20 neighbors using immunoassays and AlphaFold-Multimer prediction. We further profiled the protein neighborhoods of cell-cell synapses induced by bispecific T cell engagers and chimeric antigen receptor T cells. This integrated multiscale PLP platform maps local and distal protein networks on and between cell surfaces, which will aid in the systematic construction of the cell surface interactome, revealing horizontal signaling partners and reveal new immunotherapeutic opportunities.
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Affiliation(s)
- Zhi Lin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kaitlin Schaefer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zi Yao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrea Fossati
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ajikarunia Palar
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
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4
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Peng L, Renauer PA, Sferruzza G, Yang L, Zou Y, Fang Z, Park JJ, Chow RD, Zhang Y, Lin Q, Bai M, Sanchez A, Zhang Y, Lam SZ, Ye L, Chen S. In vivo AAV-SB-CRISPR screens of tumor-infiltrating primary NK cells identify genetic checkpoints of CAR-NK therapy. Nat Biotechnol 2024:10.1038/s41587-024-02282-4. [PMID: 38918616 DOI: 10.1038/s41587-024-02282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 05/10/2024] [Indexed: 06/27/2024]
Abstract
Natural killer (NK) cells have clinical potential against cancer; however, multiple limitations hinder the success of NK cell therapy. Here, we performed unbiased functional mapping of tumor-infiltrating NK (TINK) cells using in vivo adeno-associated virus (AAV)-SB (Sleeping Beauty)-CRISPR (clustered regularly interspaced short palindromic repeats) screens in four solid tumor mouse models. In parallel, we characterized single-cell transcriptomic landscapes of TINK cells, which identified previously unexplored subpopulations of NK cells and differentially expressed TINK genes. As a convergent hit, CALHM2-knockout (KO) NK cells showed enhanced cytotoxicity and tumor infiltration in mouse primary NK cells and human chimeric antigen receptor (CAR)-NK cells. CALHM2 mRNA reversed the CALHM2-KO phenotype. CALHM2 KO in human primary NK cells enhanced their cytotoxicity, degranulation and cytokine production. Transcriptomics profiling revealed CALHM2-KO-altered genes and pathways in both baseline and stimulated conditions. In a solid tumor model resistant to unmodified CAR-NK cells, CALHM2-KO CAR-NK cells showed potent in vivo antitumor efficacy. These data identify endogenous genetic checkpoints that naturally limit NK cell function and demonstrate the use of CALHM2 KO for engineering enhanced NK cell-based immunotherapies.
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Affiliation(s)
- Lei Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Paul A Renauer
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Giacomo Sferruzza
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Luojia Yang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Yongji Zou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Zhenghao Fang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Jonathan J Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
- M.D.-Ph.D. Program, Yale University, West Haven, CT, USA
| | - Ryan D Chow
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
- M.D.-Ph.D. Program, Yale University, West Haven, CT, USA
| | - Yueqi Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Qianqian Lin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Meizhu Bai
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Angelica Sanchez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Yale College, Yale University, New Haven, CT, USA
| | - Yongzhan Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Stanley Z Lam
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Lupeng Ye
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- System Biology Institute, Yale University, West Haven, CT, USA.
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA.
- Nanjing University, Nanjing, China.
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- System Biology Institute, Yale University, West Haven, CT, USA.
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA.
- Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA.
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA.
- M.D.-Ph.D. Program, Yale University, West Haven, CT, USA.
- Immunobiology Program, Yale University, New Haven, CT, USA.
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA.
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Liver Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA.
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5
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Bordeleau ME, Audemard É, Métois A, Theret L, Lisi V, Farah A, Spinella JF, Chagraoui J, Moujaber O, Aubert L, Khakipoor B, Mallinger L, Boivin I, Mayotte N, Hajmirza A, Bonneil É, Béliveau F, Pfammatter S, Feghaly A, Boucher G, Gendron P, Thibault P, Barabé F, Lemieux S, Richard-Carpentier G, Hébert J, Lavallée VP, Roux PP, Sauvageau G. Immunotherapeutic targeting of surfaceome heterogeneity in AML. Cell Rep 2024; 43:114260. [PMID: 38838225 DOI: 10.1016/j.celrep.2024.114260] [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: 10/05/2023] [Revised: 01/29/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
Immunotherapy remains underexploited in acute myeloid leukemia (AML) compared to other hematological malignancies. Currently, gemtuzumab ozogamicin is the only therapeutic antibody approved for this disease. Here, to identify potential targets for immunotherapeutic intervention, we analyze the surface proteome of 100 genetically diverse primary human AML specimens for the identification of cell surface proteins and conduct single-cell transcriptome analyses on a subset of these specimens to assess antigen expression at the sub-population level. Through this comprehensive effort, we successfully identify numerous antigens and markers preferentially expressed by primitive AML cells. Many identified antigens are targeted by therapeutic antibodies currently under clinical evaluation for various cancer types, highlighting the potential therapeutic value of the approach. Importantly, this initiative uncovers AML heterogeneity at the surfaceome level, identifies several antigens and potential primitive cell markers characterizing AML subgroups, and positions immunotherapy as a promising approach to target AML subgroup specificities.
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Affiliation(s)
- Marie-Eve Bordeleau
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Éric Audemard
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Arnaud Métois
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Louis Theret
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Véronique Lisi
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada
| | - Azer Farah
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada
| | - Jean-François Spinella
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Jalila Chagraoui
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Ossama Moujaber
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Léo Aubert
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Banafsheh Khakipoor
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada
| | - Laure Mallinger
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Isabel Boivin
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Nadine Mayotte
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Azadeh Hajmirza
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Éric Bonneil
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - François Béliveau
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada
| | - Sybille Pfammatter
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Albert Feghaly
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Geneviève Boucher
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Patrick Gendron
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Pierre Thibault
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Department of Chemistry, Faculty of Arts and Science, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Frédéric Barabé
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Centre de Recherche du Centre Hospitalier Universitaire de Québec, Université Laval, Québec, QC G1V 4G2, Canada
| | - Sébastien Lemieux
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Guillaume Richard-Carpentier
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Medicine, Division of Medical Oncology and Hematology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Josée Hébert
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada; Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada.
| | - Vincent-Philippe Lavallée
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Hematology and Oncology Division, Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC H3T 1C5, Canada.
| | - Philippe P Roux
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Guy Sauvageau
- The Leucegene project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada; Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montréal, QC H1T 2M4, Canada.
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6
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Kageler L, Perr J, Flynn RA. Tools to investigate the cell surface: Proximity as a central concept in glycoRNA biology. Cell Chem Biol 2024; 31:1132-1144. [PMID: 38772372 PMCID: PMC11193615 DOI: 10.1016/j.chembiol.2024.04.015] [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: 01/17/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Proximity is a fundamental concept in chemistry and biology, referring to the convergence of molecules to facilitate new molecular interactions or reactions. Hybrid biopolymers like glycosylphosphatidylinositol (GPI)-anchored proteins, ubiquitinated proteins, glycosylated RNAs (glycoRNAs), and RNAylated proteins exemplify this by covalent bonding of moieties that are often orthogonally active. Hybrid molecules like glycoRNAs are localized to new physical spaces, generating new interfaces for biological functions. To fully investigate the compositional and spatial features of molecules like glycoRNAs, flexible genetic and chemical tools that encompass different encoding and targeting biopolymers are required. Here we discuss concepts of molecular proximity and explore newer proximity labeling technologies that facilitate applications in RNA biology, cell surface biology, and the interface therein with a particular focus on glycoRNA biology. We review the advantages and disadvantages of methods pertaining to cell surface RNA identification and provide insights into the vast opportunities for method development in this area.
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Affiliation(s)
- Lauren Kageler
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan Perr
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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7
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Savage SR, Yi X, Lei JT, Wen B, Zhao H, Liao Y, Jaehnig EJ, Somes LK, Shafer PW, Lee TD, Fu Z, Dou Y, Shi Z, Gao D, Hoyos V, Gao Q, Zhang B. Pan-cancer proteogenomics expands the landscape of therapeutic targets. Cell 2024:S0092-8674(24)00583-X. [PMID: 38917788 DOI: 10.1016/j.cell.2024.05.039] [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: 02/16/2023] [Revised: 04/03/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
Fewer than 200 proteins are targeted by cancer drugs approved by the Food and Drug Administration (FDA). We integrate Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteogenomics data from 1,043 patients across 10 cancer types with additional public datasets to identify potential therapeutic targets. Pan-cancer analysis of 2,863 druggable proteins reveals a wide abundance range and identifies biological factors that affect mRNA-protein correlation. Integration of proteomic data from tumors and genetic screen data from cell lines identifies protein overexpression- or hyperactivation-driven druggable dependencies, enabling accurate predictions of effective drug targets. Proteogenomic identification of synthetic lethality provides a strategy to target tumor suppressor gene loss. Combining proteogenomic analysis and MHC binding prediction prioritizes mutant KRAS peptides as promising public neoantigens. Computational identification of shared tumor-associated antigens followed by experimental confirmation nominates peptides as immunotherapy targets. These analyses, summarized at https://targets.linkedomics.org, form a comprehensive landscape of protein and peptide targets for companion diagnostics, drug repurposing, and therapy development.
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Affiliation(s)
- Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongwei Zhao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of the Ministry of China, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lauren K Somes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Paul W Shafer
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tobie D Lee
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zile Fu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of the Ministry of China, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daming Gao
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Valentina Hoyos
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of the Ministry of China, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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8
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Lau R, Yu L, Roumeliotis TI, Stewart A, Pickard L, Choudhary JS, Banerji U. Secretome of Cancer-Associated Fibroblasts (CAFs) Influences Drug Sensitivity in Cancer Cells. J Proteome Res 2024; 23:2160-2168. [PMID: 38767394 PMCID: PMC11165579 DOI: 10.1021/acs.jproteome.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/20/2024] [Accepted: 05/04/2024] [Indexed: 05/22/2024]
Abstract
Resistance is a major problem with effective cancer treatment and the stroma forms a significant portion of the tumor mass but traditional drug screens involve cancer cells alone. Cancer-associated fibroblasts (CAFs) are a major tumor stroma component and its secreted proteins may influence the function of cancer cells. The majority of secretome studies compare different cancer or CAF cell lines exclusively. Here, we present the direct characterization of the secreted protein profiles between CAFs and KRAS mutant-cancer cell lines from colorectal, lung, and pancreatic tissues using multiplexed mass spectrometry. 2573 secreted proteins were annotated, and differential analysis highlighted understudied CAF-enriched secreted proteins, including Wnt family member 5B (WNT5B), in addition to established CAF markers, such as collagens. The functional role of CAF secreted proteins was explored by assessing its effect on the response to 97 anticancer drugs since stromal cells may cause a differing cancer drug response, which may be missed on routine drug screening using cancer cells alone. CAF secreted proteins caused specific effects on each of the cancer cell lines, which highlights the complexity and challenges in cancer treatment and so the importance to consider stromal elements.
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Affiliation(s)
- Rachel Lau
- Clinical
Pharmacology and Adaptive Therapy Group, The Institute of Cancer Research and The Royal Marsden NHS Foundation
Trust, London SM2 5PT, United
Kingdom
| | - Lu Yu
- Functional
Proteomics Group, Chester Beatty Laboratories,
The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Theodoros I. Roumeliotis
- Functional
Proteomics Group, Chester Beatty Laboratories,
The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Adam Stewart
- Clinical
Pharmacology and Adaptive Therapy Group, The Institute of Cancer Research and The Royal Marsden NHS Foundation
Trust, London SM2 5PT, United
Kingdom
| | - Lisa Pickard
- Clinical
Pharmacology and Adaptive Therapy Group, The Institute of Cancer Research and The Royal Marsden NHS Foundation
Trust, London SM2 5PT, United
Kingdom
| | - Jyoti S. Choudhary
- Functional
Proteomics Group, Chester Beatty Laboratories,
The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Udai Banerji
- Clinical
Pharmacology and Adaptive Therapy Group, The Institute of Cancer Research and The Royal Marsden NHS Foundation
Trust, London SM2 5PT, United
Kingdom
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9
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Shaw TI, Wagner J, Tian L, Wickman E, Poudel S, Wang J, Paul R, Koo SC, Lu M, Sheppard H, Fan Y, O'Neill FH, Lau CC, Zhou X, Zhang J, Gottschalk S. Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression. Nat Commun 2024; 15:3732. [PMID: 38702309 PMCID: PMC11068777 DOI: 10.1038/s41467-024-47649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/09/2024] [Indexed: 05/06/2024] Open
Abstract
Immunotherapy with chimeric antigen receptor T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific exons present a promising reservoir of targets; however, these have not been explored and validated systematically in a pan-cancer fashion. To identify cancer specific exon targets, here we analyze 1532 RNA-seq datasets from 16 types of pediatric solid and brain tumors for comparison with normal tissues using a newly developed workflow. We find 2933 exons in 157 genes encoding proteins of the surfaceome or matrisome with high cancer specificity either at the gene (n = 148) or the alternatively spliced isoform (n = 9) level. Expression of selected alternatively spliced targets, including the EDB domain of fibronectin 1, and gene targets, such as COL11A1, are validated in pediatric patient derived xenograft tumors. We generate T cells expressing chimeric antigen receptors specific for the EDB domain or COL11A1 and demonstrate that these have antitumor activity. The full target list, explorable via an interactive web portal ( https://cseminer.stjude.org/ ), provides a rich resource for developing immunotherapy of pediatric solid and brain tumors using gene or AS targets with high expression specificity in cancer.
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Affiliation(s)
- Timothy I Shaw
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jessica Wagner
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Elizabeth Wickman
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Robin Paul
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Selene C Koo
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Meifen Lu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Heather Sheppard
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Francis H O'Neill
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Ching C Lau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Connecticut Children's Medical Center, Hartford, CT, 06106, USA
- University of Connecticut School of Medicine, Farmington, CT, 06032, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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10
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Sychev ZE, Day A, Bergom HE, Larson G, Ali A, Ludwig M, Boytim E, Coleman I, Corey E, Plymate SR, Nelson PS, Hwang JH, Drake JM. Unraveling the Global Proteome and Phosphoproteome of Prostate Cancer Patient-Derived Xenografts. Mol Cancer Res 2024; 22:452-464. [PMID: 38345532 PMCID: PMC11063764 DOI: 10.1158/1541-7786.mcr-23-0976] [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: 11/21/2023] [Revised: 01/26/2024] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
Resistance to androgen-deprivation therapies leads to metastatic castration-resistant prostate cancer (mCRPC) of adenocarcinoma (AdCa) origin that can transform into emergent aggressive variant prostate cancer (AVPC), which has neuroendocrine (NE)-like features. In this work, we used LuCaP patient-derived xenograft (PDX) tumors, clinically relevant models that reflect and retain key features of the tumor from advanced prostate cancer patients. Here we performed proteome and phosphoproteome characterization of 48 LuCaP PDX tumors and identified over 94,000 peptides and 9,700 phosphopeptides corresponding to 7,738 proteins. We compared 15 NE versus 33 AdCa samples, which included six different PDX tumors for each group in biological replicates, and identified 309 unique proteins and 476 unique phosphopeptides that were significantly altered and corresponded to proteins that are known to distinguish these two phenotypes. Assessment of concordance from PDX tumor-matched protein and mRNA revealed increased dissonance in transcriptionally regulated proteins in NE and metabolite interconversion enzymes in AdCa. IMPLICATIONS Overall, our study highlights the importance of protein-based identification when compared with RNA and provides a rich resource of new and feasible targets for clinical assay development and in understanding the underlying biology of these tumors.
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Affiliation(s)
- Zoi E. Sychev
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota
| | - Abderrahman Day
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota
| | - Hannah E. Bergom
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota
| | - Gabrianne Larson
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota
| | - Atef Ali
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota
| | - Megan Ludwig
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota
| | - Ella Boytim
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota
| | - Ilsa Coleman
- Fred Hutchinson Cancer Center, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Stephen R. Plymate
- Department of Urology, University of Washington, Seattle, Washington
- Division of Gerontology and Geriatrics Medicine, University of Washington, Seattle, Washington
- Geriatric Research Education and Clinical Center, Seattle Veterans Affairs Medical Center, Seattle Washington
| | | | - Justin H. Hwang
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota
- Department of Medicine, University of Minnesota Masonic Cancer Center, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Justin M. Drake
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Department of Urology, University of Minnesota, Minneapolis, Minnesota
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11
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Scarfò R, Randolph LN, Abou Alezz M, El Khoury M, Gersch A, Li ZY, Luff SA, Tavosanis A, Ferrari Ramondo G, Valsoni S, Cascione S, Didelon E, Passerini L, Amodio G, Brandas C, Villa A, Gregori S, Merelli I, Freund JN, Sturgeon CM, Tavian M, Ditadi A. CD32 captures committed haemogenic endothelial cells during human embryonic development. Nat Cell Biol 2024; 26:719-730. [PMID: 38594587 PMCID: PMC11098737 DOI: 10.1038/s41556-024-01403-0] [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: 04/06/2023] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
During embryonic development, blood cells emerge from specialized endothelial cells, named haemogenic endothelial cells (HECs). As HECs are rare and only transiently found in early developing embryos, it remains difficult to distinguish them from endothelial cells. Here we performed transcriptomic analysis of 28- to 32-day human embryos and observed that the expression of Fc receptor CD32 (FCGR2B) is highly enriched in the endothelial cell population that contains HECs. Functional analyses using human embryonic and human pluripotent stem cell-derived endothelial cells revealed that robust multilineage haematopoietic potential is harboured within CD32+ endothelial cells and showed that 90% of CD32+ endothelial cells are bona fide HECs. Remarkably, these analyses indicated that HECs progress through different states, culminating in FCGR2B expression, at which point cells are irreversibly committed to a haematopoietic fate. These findings provide a precise method for isolating HECs from human embryos and human pluripotent stem cell cultures, thus allowing the efficient generation of haematopoietic cells in vitro.
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Affiliation(s)
- Rebecca Scarfò
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lauren N Randolph
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Monah Abou Alezz
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mahassen El Khoury
- Université de Strasbourg, Inserm, IRFAC/UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France
| | - Amélie Gersch
- Université de Strasbourg, Inserm, IRFAC/UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France
| | - Zhong-Yin Li
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephanie A Luff
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrea Tavosanis
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Ferrari Ramondo
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Valsoni
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Cascione
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Emma Didelon
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Passerini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giada Amodio
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Brandas
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anna Villa
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Institute of Genetic and Biomedical Research, Milan Unit, National Research Council, Milan, Italy
| | - Silvia Gregori
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Institute for Biomedical Technologies, National Research Council, Milan, Italy
| | - Jean-Noël Freund
- Université de Strasbourg, Inserm, IRFAC/UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France
- INSERM U1256-NGERE, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Christopher M Sturgeon
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manuela Tavian
- Université de Strasbourg, Inserm, IRFAC/UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France.
| | - Andrea Ditadi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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12
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Sirén H. Research of saccharides and related biocomplexes: A review with recent techniques and applications. J Sep Sci 2024; 47:e2300668. [PMID: 38699940 DOI: 10.1002/jssc.202300668] [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: 09/12/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 05/05/2024]
Abstract
Saccharides and biocompounds as saccharide (sugar) complexes have various roles and biological functions in living organisms due to modifications via nucleophilic substitution, polymerization, and complex formation reactions. Mostly, mono-, di-, oligo-, and polysaccharides are stabilized to inactive glycosides, which are formed in metabolic pathways. Natural saccharides are important in food and environmental monitoring. Glycosides with various functionalities are significant in clinical and medical research. Saccharides are often studied with the chromatographic methods of hydrophilic interaction liquid chromatography and anion exchange chromatograpy, but also with capillary electrophoresis and mass spectrometry with their on-line coupling systems. Sample preparation is important in the identification of saccharide compounds. The cases discussed here focus on bioscience, clinical, and food applications.
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Affiliation(s)
- Heli Sirén
- Chemicum Building, University of Helsinki, Helsinki, Finland
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13
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Xu X, Yin K, Wu R. Systematic Investigation of the Trafficking of Glycoproteins on the Cell Surface. Mol Cell Proteomics 2024; 23:100761. [PMID: 38593903 PMCID: PMC11087972 DOI: 10.1016/j.mcpro.2024.100761] [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: 02/22/2024] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024] Open
Abstract
Glycoproteins located on the cell surface play a pivotal role in nearly every extracellular activity. N-glycosylation is one of the most common and important protein modifications in eukaryotic cells, and it often regulates protein folding and trafficking. Glycosylation of cell-surface proteins undergoes meticulous regulation by various enzymes in the endoplasmic reticulum (ER) and the Golgi, ensuring their proper folding and trafficking to the cell surface. However, the impacts of protein N-glycosylation, N-glycan maturity, and protein folding status on the trafficking of cell-surface glycoproteins remain to be explored. In this work, we comprehensively and site-specifically studied the trafficking of cell-surface glycoproteins in human cells. Integrating metabolic labeling, bioorthogonal chemistry, and multiplexed proteomics, we investigated 706 N-glycosylation sites on 396 cell-surface glycoproteins in monocytes, either by inhibiting protein N-glycosylation, disturbing N-glycan maturation, or perturbing protein folding in the ER. The current results reveal their distinct impacts on the trafficking of surface glycoproteins. The inhibition of protein N-glycosylation dramatically suppresses the trafficking of many cell-surface glycoproteins. The N-glycan immaturity has more substantial effects on proteins with high N-glycosylation site densities, while the perturbation of protein folding in the ER exerts a more pronounced impact on surface glycoproteins with larger sizes. Furthermore, for N-glycosylated proteins, their trafficking to the cell surface is related to the secondary structures and adjacent amino acid residues of glycosylation sites. Systematic analysis of surface glycoprotein trafficking advances our understanding of the mechanisms underlying protein secretion and surface presentation.
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Affiliation(s)
- Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA.
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14
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Ammons DT, Hopkins LS, Cronise KE, Kurihara J, Regan DP, Dow S. Single-cell RNA sequencing reveals the cellular and molecular heterogeneity of treatment-naïve primary osteosarcoma in dogs. Commun Biol 2024; 7:496. [PMID: 38658617 PMCID: PMC11043452 DOI: 10.1038/s42003-024-06182-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Osteosarcoma (OS) is a heterogeneous, aggressive malignancy of the bone that disproportionally affects children and adolescents. Therapeutic interventions for OS are limited, which is in part due to the complex tumor microenvironment (TME). As such, we used single-cell RNA sequencing (scRNA-seq) to describe the cellular and molecular composition of the TME in 6 treatment-naïve dogs with spontaneously occurring primary OS. Through analysis of 35,310 cells, we identified 41 transcriptomically distinct cell types including the characterization of follicular helper T cells, mature regulatory dendritic cells (mregDCs), and 8 tumor-associated macrophage (TAM) populations. Cell-cell interaction analysis predicted that mregDCs and TAMs play key roles in modulating T cell mediated immunity. Furthermore, we completed cross-species cell type gene signature homology analysis and found a high degree of similarity between human and canine OS. The data presented here act as a roadmap of canine OS which can be applied to advance translational immuno-oncology research.
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Affiliation(s)
- Dylan T Ammons
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Leone S Hopkins
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kathryn E Cronise
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jade Kurihara
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Daniel P Regan
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Steven Dow
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
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15
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Wang T, Ma S, Ji G, Wang G, Liu Y, Zhang L, Zhang Y, Lu H. A chemical proteomics approach for global mapping of functional lysines on cell surface of living cell. Nat Commun 2024; 15:2997. [PMID: 38589397 PMCID: PMC11001985 DOI: 10.1038/s41467-024-47033-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Cell surface proteins are responsible for many crucial physiological roles, and they are also the major category of drug targets as the majority of therapeutics target membrane proteins on the surface of cells to alter cellular signaling. Despite its great significance, ligand discovery against membrane proteins has posed a great challenge mainly due to the special property of their natural habitat. Here, we design a new chemical proteomic probe OPA-S-S-alkyne that can efficiently and selectively target the lysines exposed on the cell surface and develop a chemical proteomics strategy for global analysis of surface functionality (GASF) in living cells. In total, we quantified 2639 cell surface lysines in Hela cell and several hundred residues with high reactivity were discovered, which represents the largest dataset of surface functional lysine sites to date. We discovered and validated that hyper-reactive lysine residues K382 on tyrosine kinase-like orphan receptor 2 (ROR2) and K285 on Endoglin (ENG/CD105) are at the protein interaction interface in co-crystal structures of protein complexes, emphasizing the broad potential functional consequences of cell surface lysines and GASF strategy is highly desirable for discovering new active and ligandable sites that can be functionally interrogated for drug discovery.
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Affiliation(s)
- Ting Wang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Shiyun Ma
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Guanghui Ji
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Guoli Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Yang Liu
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Ying Zhang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China.
| | - Haojie Lu
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China.
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16
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Kamiya T, Masuko T, Borroto-Escuela DO, Okado H, Nakata H. In Silico Analyses of Vertebrate G-Protein-Coupled Receptor Fusions United With or Without an Additional Transmembrane Sequence Indicate Classification into Three Groups of Linkers. Protein J 2024; 43:225-242. [PMID: 38616227 DOI: 10.1007/s10930-024-10184-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 04/16/2024]
Abstract
Natural G-protein-coupled receptors (GPCRs) rarely have an additional transmembrane (TM) helix, such as an artificial TM-linker that can unite two class A GPCRs in tandem as a single-polypeptide chain (sc). Here, we report that three groups of TM-linkers exist in the intervening regions of natural GPCR fusions from vertebrates: (1) the original consensus (i.e., consensus 1) and consensus 2~4 (related to GPCR itself or its receptor-interacting proteins); (2) the consensus but GPCR-unrelated ones, 1~7; and (3) the inability to apply 1/2 that show no similarity to any other proteins. In silico analyses indicated that all natural GPCR fusions from Amphibia lack a TM-linker, and reptiles have no GPCR fusions; moreover, in either the GPCR-GPCR fusion or fusion protein of (GPCR monomer) and non-GPCR proteins from vertebrates, excluding tetrapods, i.e., so-called fishes, TM-linkers differ from previously reported mammalian and are avian sequences and are classified as Groups 2 and 3. Thus, previously reported TM-linkers were arranged: Consensus 1 is [T(I/A/P)(A/S)-(L/N)(I/W/L)(I/A/V)GL(L/G)(A/T)(S/L/G)(I/L)] first identified in invertebrate sea anemone Exaiptasia diaphana (LOC110241027) and (330-SPSFLCI-L-SLL-340) identified in a tropical bird Opisthocomus hoazin protein LOC104327099 (XP_009930279.1); GPCR-related consensus 2~4 are, respectively, (371-prlilyavfc fgtatg-386) in the desert woodrat Neotoma lepida A6R68_19462 (OBS78147.1), (363-lsipfcll yiaallgnfi llfvi-385) in Gavia stellate (red-throated loon) LOC104264164 (XP_009819412.1), and (479-ti vvvymivcvi glvgnflvmy viir-504) in a snailfish GPCR (TNN80062.1); In Mammals Neotoma lepida, Aves Erythrura gouldiae, and fishes protein (respectively, OBS83645.1, RLW13346.1 and KPP79779.1), the TM-linkers are Group 2. Here, we categorized, for the first time, natural TM-linkers as rare evolutionary events among all vertebrates.
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Affiliation(s)
- Toshio Kamiya
- Department of Molecular Cell Signaling, Tokyo Metropolitan Institute for Neuroscience, 2-6 Musashidai, Fuchu, Tokyo, 183-8526, Japan.
- Department of Neurology, Tokyo Metropolitan Institute for Neuroscience, 2-6 Musashidai, Fuchu, Tokyo, 183-8526, Japan.
- Cell Biology Laboratory, School of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan.
- Division of Gene Regulation, Institute for Advanced Medical Research, Keio University School of Medicine, 35 Shinano-Machi, Shinjuku-Ku, Tokyo, 160-8582, Japan.
- Neural Development Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-Ku, Tokyo, 156-8506, Japan.
- Learning and Memory Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa Setagaya-Ku, Tokyo, 156-8506, Japan.
| | - Takashi Masuko
- Cell Biology Laboratory, School of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan
| | | | - Haruo Okado
- Neural Development Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-Ku, Tokyo, 156-8506, Japan
| | - Hiroyasu Nakata
- Department of Molecular Cell Signaling, Tokyo Metropolitan Institute for Neuroscience, 2-6 Musashidai, Fuchu, Tokyo, 183-8526, Japan
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17
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Nejo T, Wang L, Leung KK, Wang A, Lakshmanachetty S, Gallus M, Kwok DW, Hong C, Chen LH, Carrera DA, Zhang MY, Stevers NO, Maldonado GC, Yamamichi A, Watchmaker PB, Naik A, Shai A, Phillips JJ, Chang SM, Wiita AP, Wells JA, Costello JF, Diaz AA, Okada H. Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma. Sci Rep 2024; 14:6362. [PMID: 38493204 PMCID: PMC10944514 DOI: 10.1038/s41598-024-56684-0] [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: 11/29/2023] [Accepted: 03/09/2024] [Indexed: 03/18/2024] Open
Abstract
Despite advancements in cancer immunotherapy, solid tumors remain formidable challenges. In glioma, profound inter- and intra-tumoral heterogeneity of antigen landscape hampers therapeutic development. Therefore, it is critical to consider alternative sources to expand the repertoire of targetable (neo-)antigens and improve therapeutic outcomes. Accumulating evidence suggests that tumor-specific alternative splicing (AS) could be an untapped reservoir of antigens. In this study, we investigated tumor-specific AS events in glioma, focusing on those predicted to generate major histocompatibility complex (MHC)-presentation-independent, cell-surface antigens that could be targeted by antibodies and chimeric antigen receptor-T cells. We systematically analyzed bulk RNA-sequencing datasets comparing 429 tumor samples (from The Cancer Genome Atlas) and 9166 normal tissue samples (from the Genotype-Tissue Expression project), and identified 13 AS events in 7 genes predicted to be expressed in more than 10% of the patients, including PTPRZ1 and BCAN, which were corroborated by an external RNA-sequencing dataset. Subsequently, we validated our predictions and elucidated the complexity of the isoforms using full-length transcript amplicon sequencing on patient-derived glioblastoma cells. However, analyses of the RNA-sequencing datasets of spatially mapped and longitudinally collected clinical tumor samples unveiled remarkable spatiotemporal heterogeneity of the candidate AS events. Furthermore, proteomics analysis did not reveal any peptide spectra matching the putative antigens. Our investigation illustrated the diverse characteristics of the tumor-specific AS events and the challenges of antigen exploration due to their notable spatiotemporal heterogeneity and elusive nature at the protein levels. Redirecting future efforts toward intracellular, MHC-presented antigens could offer a more viable avenue.
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Affiliation(s)
- Takahide Nejo
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Lin Wang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Albert Wang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Senthilnath Lakshmanachetty
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Marco Gallus
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Darwin W Kwok
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Lee H Chen
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Diego A Carrera
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Michael Y Zhang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Gabriella C Maldonado
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Akane Yamamichi
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Payal B Watchmaker
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Akul Naik
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- The Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Aaron A Diaz
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Hideho Okada
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- The Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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18
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Driscoll CL, Keeble AH, Howarth MR. SpyMask enables combinatorial assembly of bispecific binders. Nat Commun 2024; 15:2403. [PMID: 38493197 PMCID: PMC10944524 DOI: 10.1038/s41467-024-46599-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Bispecific antibodies are a successful and expanding therapeutic class. Standard approaches to generate bispecifics are complicated by the need for disulfide reduction/oxidation or specialized formats. Here we present SpyMask, a modular approach to bispecifics using SpyTag/SpyCatcher spontaneous amidation. Two SpyTag-fused antigen-binding modules can be precisely conjugated onto DoubleCatcher, a tandem SpyCatcher where the second SpyCatcher is protease-activatable. We engineer a panel of structurally-distinct DoubleCatchers, from which binders project in different directions. We establish a generalized methodology for one-pot assembly and purification of bispecifics in 96-well plates. A panel of binders recognizing different HER2 epitopes were coupled to DoubleCatcher, revealing unexpected combinations with anti-proliferative or pro-proliferative activity on HER2-addicted cancer cells. Bispecific activity depended sensitively on both binder orientation and DoubleCatcher scaffold geometry. These findings support the need for straightforward assembly in different formats. SpyMask provides a scalable tool to discover synergy in bispecific activity, through modulating receptor organization and geometry.
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Affiliation(s)
- Claudia L Driscoll
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Anthony H Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Mark R Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
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19
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Khan S, Zuccato JA, Ignatchenko V, Singh O, Govindarajan M, Waas M, Mejia-Guerrero S, Gao A, Zadeh G, Kislinger T. Organelle resolved proteomics uncovers PLA2R1 as a novel cell surface marker required for chordoma growth. Acta Neuropathol Commun 2024; 12:39. [PMID: 38454495 PMCID: PMC10921702 DOI: 10.1186/s40478-024-01751-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 02/25/2024] [Indexed: 03/09/2024] Open
Abstract
Chordomas are clinically aggressive tumors with a high rate of disease progression despite maximal therapy. Given the limited therapeutic options available, there remains an urgent need for the development of novel therapies to improve clinical outcomes. Cell surface proteins are attractive therapeutic targets yet are challenging to profile with common methods. Four chordoma cell lines were analyzed by quantitative proteomics using a differential ultracentrifugation organellar fractionation approach. A subtractive proteomics strategy was applied to select proteins that are plasma membrane enriched. Systematic data integration prioritized PLA2R1 (secretory phospholipase A2 receptor-PLA2R1) as a chordoma-enriched surface protein. The expression profile of PLA2R1 was validated across chordoma cell lines, patient surgical tissue samples, and normal tissue lysates via immunoblotting. PLA2R1 expression was further validated by immunohistochemical analysis in a richly annotated cohort of 25-patient tissues. Immunohistochemistry analysis revealed that elevated expression of PLA2R1 is correlated with poor prognosis. Using siRNA- and CRISPR/Cas9-mediated knockdown of PLA2R1, we demonstrated significant inhibition of 2D, 3D and in vivo chordoma growth. PLA2R1 depletion resulted in cell cycle defects and metabolic rewiring via the MAPK signaling pathway, suggesting that PLA2R1 plays an essential role in chordoma biology. We have characterized the proteome of four chordoma cell lines and uncovered PLA2R1 as a novel cell-surface protein required for chordoma cell survival and association with patient outcome.
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Affiliation(s)
- Shahbaz Khan
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
| | - Jeffrey A Zuccato
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Canada
| | - Vladimir Ignatchenko
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
| | - Olivia Singh
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
| | - Meinusha Govindarajan
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Matthew Waas
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
| | - Salvador Mejia-Guerrero
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
| | - Andrew Gao
- Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
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20
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Müller GA, Müller TD. Transfer of membrane(s) matter(s)-non-genetic inheritance of (metabolic) phenotypes? Front Mol Biosci 2024; 11:1347397. [PMID: 38516184 PMCID: PMC10955475 DOI: 10.3389/fmolb.2024.1347397] [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: 11/30/2023] [Accepted: 01/26/2024] [Indexed: 03/23/2024] Open
Abstract
Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are anchored at the outer phospholipid layer of eukaryotic plasma membranes exclusively by a glycolipid. GPI-APs are not only released into extracellular compartments by lipolytic cleavage. In addition, certain GPI-APs with the glycosylphosphatidylinositol anchor including their fatty acids remaining coupled to the carboxy-terminus of their protein components are also detectable in body fluids, in response to certain stimuli, such as oxidative stress, radicals or high-fat diet. As a consequence, the fatty acid moieties of GPI-APs must be shielded from access of the aqueous environment by incorporation into membranes of extracellular vesicles or into micelle-like complexes together with (lyso)phospholipids and cholesterol. The GPI-APs released from somatic cells and tissues are transferred via those complexes or EVs to somatic as well as pluripotent stem cells with metabolic consequences, such as upregulation of glycogen and lipid synthesis. From these and additional findings, the following hypotheses are developed: i) Transfer of GPI-APs via EVs or micelle-like complexes leads to the induction of new phenotypes in the daughter cells or zygotes, which are presumably not restricted to metabolism. ii) The membrane topographies transferred by the concerted action of GPI-APs and interacting components are replicated by self-organization and self-templation and remain accessible to structural changes by environmental factors. iii) Transfer from mother cells and gametes to their daughter cells and zygotes, respectively, is not restricted to DNA and genes, but also encompasses non-genetic matter, such as GPI-APs and specific membrane constituents. iv) The intergenerational transfer of membrane matter between mammalian organisms is understood as an epigenetic mechanism for phenotypic plasticity, which does not rely on modifications of DNA and histones, but is regarded as molecular mechanism for the inheritance of acquired traits, such as complex metabolic diseases. v) The missing interest in research of non-genetic matter of inheritance, which may be interpreted in the sense of Darwin's "Gemmules" or Galton's "Stirps", should be addressed in future investigations of the philosophy of science and sociology of media.
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Affiliation(s)
- Günter A. Müller
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), Oberschleissheim, Germany
- Department of Media Studies, Media, Culture and Society, Faculty of Arts and Humanities, University Paderborn, Paderborn, Germany
| | - Timo D. Müller
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC) at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Oberschleissheim, Germany
- German Center for Diabetes Research (DZD), Oberschleissheim, Germany
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21
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Udani S, Langerman J, Koo D, Baghdasarian S, Cheng B, Kang S, Soemardy C, de Rutte J, Plath K, Di Carlo D. Associating growth factor secretions and transcriptomes of single cells in nanovials using SEC-seq. NATURE NANOTECHNOLOGY 2024; 19:354-363. [PMID: 38082117 DOI: 10.1038/s41565-023-01560-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/31/2023] [Indexed: 01/23/2024]
Abstract
Cells secrete numerous bioactive molecules that are essential for the function of healthy organisms. However, scalable methods are needed to link individual cell secretions to their transcriptional state over time. Here, by developing and using secretion-encoded single-cell sequencing (SEC-seq), which exploits hydrogel particles with subnanolitre cavities (nanovials) to capture individual cells and their secretions, we simultaneously measured the secretion of vascular endothelial growth factor A (VEGF-A) and the transcriptome for thousands of individual mesenchymal stromal cells. Our data indicate that VEGF-A secretion is heterogeneous across the cell population and is poorly correlated with the VEGFA transcript level. The highest VEGF-A secretion occurs in a subpopulation of mesenchymal stromal cells characterized by a unique gene expression signature comprising a surface marker, interleukin-13 receptor subunit alpha 2 (IL13RA2), which allowed the enrichment of this subpopulation. SEC-seq enables the identification of gene signatures linked to specific secretory states, facilitating mechanistic studies, the isolation of secretory subpopulations and the development of means to modulate cellular secretion.
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Affiliation(s)
- Shreya Udani
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Justin Langerman
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Doyeon Koo
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Sevana Baghdasarian
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Brian Cheng
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Simran Kang
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Citradewi Soemardy
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
- Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, CA, USA.
| | - Dino Di Carlo
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA.
- Partillion Bioscience, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Mechanical and Aerospace Engineering, University of California Los Angeles, Los Angeles, CA, USA.
- California NanoSystems Institute (CNSI), University of California Los Angeles, Los Angeles, CA, USA.
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22
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Mattson NM, Chan AKN, Miyashita K, Mukhaleva E, Chang WH, Yang L, Ma N, Wang Y, Pokharel SP, Li M, Liu Q, Xu X, Chen R, Singh P, Zhang L, Elsayed Z, Chen B, Keen D, Pirrotte P, Rosen ST, Chen J, LaBarge MA, Shively JE, Vaidehi N, Rockne RC, Feng M, Chen CW. A novel class of inhibitors that disrupts the stability of integrin heterodimers identified by CRISPR-tiling-instructed genetic screens. Nat Struct Mol Biol 2024; 31:465-475. [PMID: 38316881 PMCID: PMC10948361 DOI: 10.1038/s41594-024-01211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024]
Abstract
The plasma membrane is enriched for receptors and signaling proteins that are accessible from the extracellular space for pharmacological intervention. Here we conducted a series of CRISPR screens using human cell surface proteome and integrin family libraries in multiple cancer models. Our results identified ITGAV (integrin αV) and its heterodimer partner ITGB5 (integrin β5) as the essential integrin α/β pair for cancer cell expansion. High-density CRISPR gene tiling further pinpointed the integral pocket within the β-propeller domain of ITGAV for integrin αVβ5 dimerization. Combined with in silico compound docking, we developed a CRISPR-Tiling-Instructed Computer-Aided (CRISPR-TICA) pipeline for drug discovery and identified Cpd_AV2 as a lead inhibitor targeting the β-propeller central pocket of ITGAV. Cpd_AV2 treatment led to rapid uncoupling of integrin αVβ5 and cellular apoptosis, providing a unique class of therapeutic action that eliminates the integrin signaling via heterodimer dissociation. We also foresee the CRISPR-TICA approach to be an accessible method for future drug discovery studies.
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Affiliation(s)
- Nicole M Mattson
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Anthony K N Chan
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Kazuya Miyashita
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Wen-Han Chang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Yingyu Wang
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sheela Pangeni Pokharel
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Mingli Li
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Qiao Liu
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Xiaobao Xu
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Renee Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Priyanka Singh
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Leisi Zhang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Zeinab Elsayed
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Bryan Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Denise Keen
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Patrick Pirrotte
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Steven T Rosen
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mark A LaBarge
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - John E Shively
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Immunology and Theranostics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Russell C Rockne
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mingye Feng
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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23
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Milione RR, Schell BB, Douglas CJ, Seath CP. Creative approaches using proximity labeling to gain new biological insights. Trends Biochem Sci 2024; 49:224-235. [PMID: 38160064 PMCID: PMC10939868 DOI: 10.1016/j.tibs.2023.12.005] [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: 09/19/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
At its most fundamental level, life is a collection of synchronized cellular processes driven by interactions among biomolecules. Proximity labeling has emerged as a powerful technique to capture these interactions in native settings, revealing previously unexplored elements of biology. This review highlights recent developments in proximity labeling, focusing on methods that push the fundamental technologies beyond the classic bait-prey paradigm, such as RNA-protein interactions, ligand/small-molecule-protein interactions, cell surface protein interactions, and subcellular protein trafficking. The advancement of proximity labeling methods to address different biological problems will accelerate our understanding of the complex biological systems that make up life.
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Affiliation(s)
- Ryan R Milione
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Bin-Bin Schell
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Cameron J Douglas
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Ciaran P Seath
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA.
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24
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Kasap C, Izgutdina A, Patiño-Escobar B, Kang A, Chilakapati N, Akagi N, Johnson H, Rashid T, Werner J, Barpanda A, Geng H, Lin YHT, Rampersaud S, Gil-Alós D, Sobh A, Dupéré-Richer D, Wicaksono G, Kawehi Kelii K, Dalal R, Ramos E, Vijayanarayanan A, Salangsang F, Phojanakong P, Serrano JAC, Zakraoui O, Tariq I, Steri V, Shanmugam M, Boise LH, Kortemme T, Stieglitz E, Licht JD, Karlon WJ, Barwick BG, Wiita AP. Targeting high-risk multiple myeloma genotypes with optimized anti-CD70 CAR-T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581875. [PMID: 38463958 PMCID: PMC10925123 DOI: 10.1101/2024.02.24.581875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Despite the success of BCMA-targeting CAR-Ts in multiple myeloma, patients with high-risk cytogenetic features still relapse most quickly and are in urgent need of additional therapeutic options. Here, we identify CD70, widely recognized as a favorable immunotherapy target in other cancers, as a specifically upregulated cell surface antigen in high risk myeloma tumors. We use a structure-guided design to define a CD27-based anti-CD70 CAR-T design that outperforms all tested scFv-based CARs, leading to >80-fold improved CAR-T expansion in vivo. Epigenetic analysis via machine learning predicts key transcription factors and transcriptional networks driving CD70 upregulation in high risk myeloma. Dual-targeting CAR-Ts against either CD70 or BCMA demonstrate a potential strategy to avoid antigen escape-mediated resistance. Together, these findings support the promise of targeting CD70 with optimized CAR-Ts in myeloma as well as future clinical translation of this approach.
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Affiliation(s)
- Corynn Kasap
- Dept. of Medicine, Division of Hematology/Oncology, University of California, San Francisco, CA
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Adila Izgutdina
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | | | - Amrik Kang
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
- Medical Scientist Training Program, University of California, San Francisco, CA
| | - Nikhil Chilakapati
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Naomi Akagi
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Haley Johnson
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Tasfia Rashid
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Juwita Werner
- Dept. of Pediatrics, Division of Oncology, University of California, San Francisco, CA
| | - Abhilash Barpanda
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Huimin Geng
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Yu-Hsiu T. Lin
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Sham Rampersaud
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Daniel Gil-Alós
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
- Dept of Hematology, Hospital 12 de Octubre, Madrid, Spain
| | - Amin Sobh
- University of Florida Health Cancer Center, The University of Florida Cancer and Genetics Research Complex, Gainesville, Florida
- Division of Hematology/Oncology, The University of Florida College of Medicine, Gainesville, Florida
| | - Daphné Dupéré-Richer
- University of Florida Health Cancer Center, The University of Florida Cancer and Genetics Research Complex, Gainesville, Florida
- Division of Hematology/Oncology, The University of Florida College of Medicine, Gainesville, Florida
| | - Gianina Wicaksono
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - K.M. Kawehi Kelii
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Radhika Dalal
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
| | - Emilio Ramos
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | | | - Fernando Salangsang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Paul Phojanakong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | | | - Ons Zakraoui
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Isa Tariq
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Mala Shanmugam
- Department of Hematology and Medical Oncology, Winship Cancer Institute, School of Medicine, Emory University, Atlanta, GA
| | - Lawrence H. Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, School of Medicine, Emory University, Atlanta, GA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA
| | - Elliot Stieglitz
- Dept. of Pediatrics, Division of Oncology, University of California, San Francisco, CA
| | - Jonathan D. Licht
- University of Florida Health Cancer Center, The University of Florida Cancer and Genetics Research Complex, Gainesville, Florida
- Division of Hematology/Oncology, The University of Florida College of Medicine, Gainesville, Florida
| | - William J. Karlon
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
| | - Benjamin G. Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, School of Medicine, Emory University, Atlanta, GA
| | - Arun P. Wiita
- Dept. of Laboratory Medicine, University of California, San Francisco, CA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA
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25
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de Oliveira KG, Bång-Rudenstam A, Beyer S, Boukredine A, Talbot H, Governa V, Johansson MC, Månsson AS, Forsberg-Nilsson K, Bengzon J, Malmström J, Welinder C, Belting M. Decoding of the surfaceome and endocytome in primary glioblastoma cells identifies potential target antigens in the hypoxic tumor niche. Acta Neuropathol Commun 2024; 12:35. [PMID: 38414005 PMCID: PMC10898066 DOI: 10.1186/s40478-024-01740-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: 12/13/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
Immunotherapies with antibody-drug-conjugates (ADC) and CAR-T cells, targeted at tumor surface antigens (surfaceome), currently revolutionize clinical oncology. However, target identification warrants a better understanding of the surfaceome and how it is modulated by the tumor microenvironment. Here, we decode the surfaceome and endocytome and its remodeling by hypoxic stress in glioblastoma (GBM), the most common and aggressive brain tumor in adults. We employed a comprehensive approach for global and dynamic profiling of the surfaceome and endocytosed (endocytome) proteins and their regulation by hypoxia in patient-derived GBM cultures. We found a heterogeneous surface-endocytome profile and a divergent response to hypoxia across GBM cultures. We provide a quantitative ranking of more than 600 surface resident and endocytosed proteins, and their regulation by hypoxia, serving as a resource to the cancer research community. As proof-of-concept, the established target antigen CD44 was identified as a commonly and abundantly expressed surface protein with high endocytic activity. Among hypoxia induced proteins, we reveal CXADR, CD47, CD81, BSG, and FXYD6 as potential targets of the stressed GBM niche. We could validate these findings by immunofluorescence analyses in patient tumors and by increased expression in the hypoxic core of GBM spheroids. Selected candidates were finally confronted by treatment studies, showing their high capacity for internalization and ADC delivery. Importantly, we highlight the limited correlation between transcriptomics and proteomics, emphasizing the critical role of membrane protein enrichment strategies and quantitative mass spectrometry. Our findings provide a comprehensive understanding of the surface-endocytome and its remodeling by hypoxia in GBM as a resource for exploration of targets for immunotherapeutic approaches in GBM.
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Affiliation(s)
- Kelin Gonçalves de Oliveira
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Anna Bång-Rudenstam
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Sarah Beyer
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Axel Boukredine
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Hugo Talbot
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Valeria Governa
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Maria C Johansson
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Ann-Sofie Månsson
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Division of Cancer and Stem Cells, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Johan Bengzon
- Department of Clinical Sciences, Section of Neurosurgery, Lund University, Lund, Sweden
| | - Johan Malmström
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Mattias Belting
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden.
- Department of Hematology, Oncology and Radiophysics, Skåne University Hospital, Lund, Sweden.
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26
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Zhang X, Wang H. Unlocking CAR T cell potential: Inosine-induced stemness and enhanced potency. Cancer Cell 2024; 42:175-177. [PMID: 38278148 DOI: 10.1016/j.ccell.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
Adenosine (Ado) drives immune suppression in the tumor microenvironment. In this issue of Cancer Cell, Klysz et al. investigate Ado-mediated immunosuppression. Overexpression of Ado deaminase (ADA-OE), metabolizing Ado to inosine (INO), induces stemness and improves CAR T cell functionality. Likewise, exposure to INO enhances CAR T cells' function and induces stemness features.
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Affiliation(s)
- Xingying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
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27
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Klysz DD, Fowler C, Malipatlolla M, Stuani L, Freitas KA, Chen Y, Meier S, Daniel B, Sandor K, Xu P, Huang J, Labanieh L, Keerthi V, Leruste A, Bashti M, Mata-Alcazar J, Gkitsas N, Guerrero JA, Fisher C, Patel S, Asano K, Patel S, Davis KL, Satpathy AT, Feldman SA, Sotillo E, Mackall CL. Inosine induces stemness features in CAR-T cells and enhances potency. Cancer Cell 2024; 42:266-282.e8. [PMID: 38278150 PMCID: PMC10923096 DOI: 10.1016/j.ccell.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/31/2023] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
Adenosine (Ado) mediates immune suppression in the tumor microenvironment and exhausted CD8+ CAR-T cells express CD39 and CD73, which mediate proximal steps in Ado generation. Here, we sought to enhance CAR-T cell potency by knocking out CD39, CD73, or adenosine receptor 2a (A2aR) but observed only modest effects. In contrast, overexpression of Ado deaminase (ADA-OE), which metabolizes Ado to inosine (INO), induced stemness and enhanced CAR-T functionality. Similarly, CAR-T cell exposure to INO augmented function and induced features of stemness. INO induced profound metabolic reprogramming, diminishing glycolysis, increasing mitochondrial and glycolytic capacity, glutaminolysis and polyamine synthesis, and reprogrammed the epigenome toward greater stemness. Clinical scale manufacturing using INO generated enhanced potency CAR-T cell products meeting criteria for clinical dosing. These results identify INO as a potent modulator of CAR-T cell metabolism and epigenetic stemness programming and deliver an enhanced potency platform for cell manufacturing.
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Affiliation(s)
- Dorota D Klysz
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Carley Fowler
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Meena Malipatlolla
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lucille Stuani
- Department of Pediatrics, Division of Pediatric Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine A Freitas
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Yiyun Chen
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Stefanie Meier
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Bence Daniel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Katalin Sandor
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peng Xu
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jing Huang
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Louai Labanieh
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Vimal Keerthi
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Amaury Leruste
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Malek Bashti
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Janette Mata-Alcazar
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nikolaos Gkitsas
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin A Guerrero
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Chris Fisher
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sunny Patel
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyle Asano
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Shabnum Patel
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kara L Davis
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Division of Pediatric Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven A Feldman
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pediatrics, Division of Pediatric Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Division of Bone Marrow Transplantation and Cell Therapy, Stanford University School of Medicine, Stanford, CA, USA.
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28
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Taherian Fard A, Leeson HC, Aguado J, Pietrogrande G, Power D, Gómez-Inclán C, Zheng H, Nelson CB, Soheilmoghaddam F, Glass N, Dharmaratne M, Watson ER, Lu J, Martin S, Pickett HA, Cooper-White J, Wolvetang EJ, Mar JC. Deconstructing heterogeneity of replicative senescence in human mesenchymal stem cells at single cell resolution. GeroScience 2024; 46:999-1015. [PMID: 37314668 PMCID: PMC10828319 DOI: 10.1007/s11357-023-00829-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 05/15/2023] [Indexed: 06/15/2023] Open
Abstract
Following prolonged cell division, mesenchymal stem cells enter replicative senescence, a state of permanent cell cycle arrest that constrains the use of this cell type in regenerative medicine applications and that in vivo substantially contributes to organismal ageing. Multiple cellular processes such as telomere dysfunction, DNA damage and oncogene activation are implicated in promoting replicative senescence, but whether mesenchymal stem cells enter different pre-senescent and senescent states has remained unclear. To address this knowledge gap, we subjected serially passaged human ESC-derived mesenchymal stem cells (esMSCs) to single cell profiling and single cell RNA-sequencing during their progressive entry into replicative senescence. We found that esMSC transitioned through newly identified pre-senescent cell states before entering into three different senescent cell states. By deconstructing this heterogeneity and temporally ordering these pre-senescent and senescent esMSC subpopulations into developmental trajectories, we identified markers and predicted drivers of these cell states. Regulatory networks that capture connections between genes at each timepoint demonstrated a loss of connectivity, and specific genes altered their gene expression distributions as cells entered senescence. Collectively, this data reconciles previous observations that identified different senescence programs within an individual cell type and should enable the design of novel senotherapeutic regimes that can overcome in vitro MSC expansion constraints or that can perhaps slow organismal ageing.
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Affiliation(s)
- Atefeh Taherian Fard
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Hannah C Leeson
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Julio Aguado
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Giovanni Pietrogrande
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Dominique Power
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Cecilia Gómez-Inclán
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Huiwen Zheng
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Christopher B Nelson
- Children's Medical Research Institute, University of Sydney, Westmead, Sydney, NSW, Australia
| | - Farhad Soheilmoghaddam
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
- School of Chemical Engineering, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Australia
| | - Nick Glass
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Malindrie Dharmaratne
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Ebony R Watson
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Jennifer Lu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Sally Martin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, University of Sydney, Westmead, Sydney, NSW, Australia
| | - Justin Cooper-White
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
- School of Chemical Engineering, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Australia
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia.
| | - Jessica C Mar
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia.
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29
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Dabiri H, Habibi-Anbouhi M, Ziaei V, Moghadasi Z, Sadeghizadeh M, Hajizadeh-Saffar E. Candidate Biomarkers for Targeting in Type 1 Diabetes; A Bioinformatic Analysis of Pancreatic Cell Surface Antigens. CELL JOURNAL 2024; 26:51-61. [PMID: 38351729 PMCID: PMC10864774 DOI: 10.22074/cellj.2023.1996297.1262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/27/2023] [Accepted: 10/24/2023] [Indexed: 02/18/2024]
Abstract
OBJECTIVE Type 1 diabetes (T1Ds) is an autoimmune disease in which the immune system invades and destroys insulin-producing cells. Nevertheless, at the time of diagnosis, about 30-40% of pancreatic beta cells are healthy and capable of producing insulin. Bi-specific antibodies, chimeric antigen receptor regulatory T cells (CAR-Treg cells), and labeled antibodies could be a new emerging option for the treatment or diagnosis of type I diabetic patients. The aim of the study is to choose appropriate cell surface antigens in the pancreas tissue for generating an antibody for type I diabetic patients. MATERIALS AND METHODS In this bioinformatics study, we extracted pancreas-specific proteins from two large databases; the Human Protein Atlas (HPA) and Genotype-Tissue Expression (GTEx) Portal. Pancreatic-enriched genes were chosen and narrowed down by Protter software for the investigation of accessible extracellular domains. The immunohistochemistry (IHC) data of the protein atlas database were used to evaluate the protein expression of selected antigens. We explored the function of candidate antigens by using the GeneCards database to evaluate the potential dysfunction or activation/hyperactivation of antigens after antibody binding. RESULTS The results showed 429 genes are highly expressed in the pancreas tissue. Also, eighteen genes encoded plasma membrane proteins that have high expression in the microarray (GEO) dataset. Our results introduced four structural proteins, including NPHS1, KIRREL2, GP2, and CUZD1, among all seventeen candidate proteins. CONCLUSION The presented antigens can potentially be used to produce specific pancreatic antibodies that guide CARTreg, bi-specific, or labeling molecules to the pancreas for treatment, detection, or other molecular targeted therapy scopes for type I diabetes.
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Affiliation(s)
- Hamed Dabiri
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Vahab Ziaei
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Moghadasi
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ensiyeh Hajizadeh-Saffar
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Advanced Therapy Medicinal Product Technology Development Center (ATMP-TDC), Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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30
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Bartholow T, Burroughs PW, Elledge SK, Byrnes JR, Kirkemo LL, Garda V, Leung KK, Wells JA. Photoproximity Labeling from Single Catalyst Sites Allows Calibration and Increased Resolution for Carbene Labeling of Protein Partners In Vitro and on Cells. ACS CENTRAL SCIENCE 2024; 10:199-208. [PMID: 38292613 PMCID: PMC10823516 DOI: 10.1021/acscentsci.3c01473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 02/01/2024]
Abstract
The cell surface proteome (surfaceome) plays a pivotal role in virtually all extracellular biology, and yet we are only beginning to understand the protein complexes formed in this crowded environment. Recently, a high-resolution approach (μMap) was described that utilizes multiple iridium-photocatalysts attached to a secondary antibody, directed to a primary antibody of a protein of interest, to identify proximal neighbors by light-activated conversion of a biotin-diazirine to a highly reactive carbene followed by LC/MS (Geri, J. B.; Oakley, J. V.; Reyes-Robles, T.; Wang, T.; McCarver, S. J.; White, C. H.; Rodriguez-Rivera, F. P.; Parker, D. L.; Hett, E. C.; Fadeyi, O. O.; Oslund, R. C.; MacMillan, D. W. C. Science2020, 367, 1091-1097). Here we calibrated the spatial resolution for carbene labeling using site-specific conjugation of a single photocatalyst to a primary antibody drug, trastuzumab (Traz), in complex with its structurally well-characterized oncogene target, HER2. We observed relatively uniform carbene labeling across all amino acids, and a maximum distance of ∼110 Å from the fixed photocatalyst. When targeting HER2 overexpression cells, we identified 20 highly enriched HER2 neighbors, compared to a nonspecific membrane tethered catalyst. These studies identify new HER2 interactors and calibrate the radius of carbene photoprobe labeling for the surfaceome.
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Affiliation(s)
- Thomas
G. Bartholow
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Paul W.W. Burroughs
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Susanna K. Elledge
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James R. Byrnes
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Lisa L. Kirkemo
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Virginia Garda
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Kevin K. Leung
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James A. Wells
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
- Department
of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
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31
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Yin Y, Zhao SL, Rane D, Lin Z, Wu M, Peterson BR. Quantification of Binding of Small Molecules to Native Proteins Overexpressed in Living Cells. J Am Chem Soc 2024; 146:187-200. [PMID: 38118119 PMCID: PMC10910633 DOI: 10.1021/jacs.3c07488] [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] [Indexed: 12/22/2023]
Abstract
The affinity and selectivity of small molecules for proteins drive drug discovery and development. We report a fluorescent probe cellular binding assay (FPCBA) for determination of these values for native (untagged) proteins overexpressed in living cells. This method uses fluorophores such as Pacific Blue (PB) linked to cell-permeable protein ligands to generate probes that rapidly and reversibly equilibrate with intracellular targets, as established by kinetic assays of cellular uptake and efflux. To analyze binding to untagged proteins, an internal ribosomal entry site (IRES) vector was employed that allows a single mRNA to encode both the protein target and a separate orthogonal fluorescent protein (mVenus). This enabled cellular uptake of the probe to be correlated with protein expression by flow cytometry, allowing measurement of cellular dissociation constants (Kd) of the probe. This approach was validated by studies of the binding of allosteric activators to eight different Protein Kinase C (PKC) isozymes. Full-length PKCs expressed in transiently transfected HEK293T cells were used to measure cellular Kd values of a probe comprising PB linked to the natural product phorbol via a carbamate. These values were further used to determine competitive binding constants (cellular Ki values) of the nonfluorescent phorbol ester PDBu and the anticancer agent bryostatin 1 for each isozyme. For some PKC-small molecule pairs, these cellular Ki values matched known biochemical Ki values, but for others, altered selectivity was observed in cells. This approach can facilitate quantification of interactions of small molecules with physiologically relevant native proteins.
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Affiliation(s)
- Yuwen Yin
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
| | - Serena Li Zhao
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
| | - Digamber Rane
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
| | - Zhihong Lin
- The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, 460 W. 10 Ave., Columbus, OH 43210, USA
| | - Meng Wu
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, 460 W. 10 Ave., Columbus, OH 43210, USA
| | - Blake R. Peterson
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, 460 W. 10 Ave., Columbus, OH 43210, USA
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32
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Shaw TI, Wagner J, Tian L, Wickman E, Poudel S, Wang J, Paul R, Koo SC, Lu M, Sheppard H, Fan Y, O’Neil F, Lau CC, Zhou X, Zhang J, Gottschalk S. Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression. RESEARCH SQUARE 2024:rs.3.rs-3821632. [PMID: 38260279 PMCID: PMC10802740 DOI: 10.21203/rs.3.rs-3821632/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Immunotherapy with CAR T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific exons (CSE) present a promising reservoir of targets; however, these have not been explored and validated systematically in a pan-cancer fashion. To identify CSE targets, we analyzed 1,532 RNA-seq datasets from 16 types of pediatric solid and brain tumors for comparison with normal tissues using a newly developed workflow. We found 2,933 exons in 157 genes encoding proteins of the surfaceome or matrisome with high cancer specificity either at the gene (n=148) or the alternatively spliced (AS) isoform (n=9) level. Expression of selected AS targets, including the EDB domain of FN1 (EDB), and gene targets, such as COL11A1, were validated in pediatric PDX tumors. We generated CAR T cells specific to EDB or COL11A1 and demonstrated that COL11A1-CAR T-cells have potent antitumor activity. The full target list, explorable via an interactive web portal (https://cseminer.stjude.org/), provides a rich resource for developing immunotherapy of pediatric solid and brain tumors using gene or AS targets with high expression specificity in cancer.
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Affiliation(s)
- Timothy I Shaw
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jessica Wagner
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Wickman
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robin Paul
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Selene C. Koo
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Meifen Lu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Heather Sheppard
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Francis O’Neil
- The Jackson Laboratory Cancer Center, Farmington, CT, USA
| | - Ching C. Lau
- The Jackson Laboratory Cancer Center, Farmington, CT, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Ye X. Quantitative Membrane Proteomics for Discovery of Actionable Drug Targets at the Surface of RAS-Driven Human Cancer Cells. Methods Mol Biol 2024; 2823:27-46. [PMID: 39052212 DOI: 10.1007/978-1-0716-3922-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
With the advent of promising lung cancer immunotherapies targeting proteins at the cell surface of RAS-driven human cancers, the mass spectrometry (MS)-based surfaceomics remains a feasible strategy for therapeutic target discovery. This chapter describes a protocol for discovery of druggable protein targets at the surface of RAS-driven human cancer cells. This method relies on bottom-up MS-based quantitative surfaceomics that employs in parallel, targeted hydrazide-based cell-surface glycoproteomics and global shotgun membrane proteomics to enable unbiased quantitative profiling of thousands of cell surface membrane proteins. A large-scale molecular map of the KRASG12V surface was attained, resulting in confident detection and quantitation of more than 500 cell surface membrane proteins that were found to be unique or upregulated at the surface of cells harboring the KRASG12V mutant. A multistep bioinformatic progression revealed a subset of unique and/or significantly upregulated proteins as priority drug targets selected for orthogonal cross-validation using immunofluorescence, structured illumination microscopy, and western blotting. Among cross-validated targets, CUB domain containing protein 1 (CDCP1) and basigin (BSG-CD147) were selected as leading targets due to their involvement in cell adhesion and migration, consistent with the KRASG12V malignant phenotype as revealed by scanning electron microscopy and phenotypic cancer cell assays. Follow-up studies confirmed CDCP1 as an actionable therapeutic target, resulting in development of recombinant antibodies capable of killing KRAS-transformed cancer cells in preclinical setting. The present MS-based surfaceomics workflow represents a powerful drug target discovery platform that enables development of innovative immunotherapeutics (e.g., antibody drug conjugate against CDCP1) for attacking oncogenic RAS-driven cancers at the cell surface.
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Affiliation(s)
- Xiaoying Ye
- Analytical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA.
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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Xu X, Yin K, Xu S, Wang Z, Wu R. Mass spectrometry-based methods for investigating the dynamics and organization of the surfaceome: exploring potential clinical implications. Expert Rev Proteomics 2024; 21:99-113. [PMID: 38300624 PMCID: PMC10928381 DOI: 10.1080/14789450.2024.2314148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Cell-surface proteins are extremely important for many cellular events, such as regulating cell-cell communication and cell-matrix interactions. Aberrant alterations in surface protein expression, modification (especially glycosylation), and interactions are directly related to human diseases. Systematic investigation of surface proteins advances our understanding of protein functions, cellular activities, and disease mechanisms, which will lead to identifying surface proteins as disease biomarkers and drug targets. AREAS COVERED In this review, we summarize mass spectrometry (MS)-based proteomics methods for global analysis of cell-surface proteins. Then, investigations of the dynamics of surface proteins are discussed. Furthermore, we summarize the studies for the surfaceome interaction networks. Additionally, biological applications of MS-based surfaceome analysis are included, particularly highlighting the significance in biomarker identification, drug development, and immunotherapies. EXPERT OPINION Modern MS-based proteomics provides an opportunity to systematically characterize proteins. However, due to the complexity of cell-surface proteins, the labor-intensive workflow, and the limit of clinical samples, comprehensive characterization of the surfaceome remains extraordinarily challenging, especially in clinical studies. Developing and optimizing surfaceome enrichment methods and utilizing automated sample preparation workflow can expand the applications of surfaceome analysis and deepen our understanding of the functions of cell-surface proteins.
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Affiliation(s)
- Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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35
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Kofoed C, Tay NES, Ye X, Erkalo G, Muir TW. Cell surface sculpting using logic-gated protein actuators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572113. [PMID: 38187604 PMCID: PMC10769198 DOI: 10.1101/2023.12.18.572113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Cell differentiation and tissue specialization lead to unique cellular surface landscapes and exacerbated or loss of expression patterns can result in further heterogenicity distinctive of pathological phenotypes1-3. Immunotherapies and emerging protein therapeutics seek to exploit such differences by engaging cell populations selectively based on their surface markers. Since a single surface antigen rarely defines a specific cell type4,5, the development of programmable molecular systems that integrate multiple cell surface features to convert on-target inputs to user-defined outputs is highly desirable. Here, we describe an autonomous decision-making protein device driven by proximity-gated protein trans-splicing that allows local generation of an active protein from two otherwise inactive fragments. We show that this protein actuator platform can perform various Boolean logic operations on cell surfaces, allowing highly selective recruitment of enzymatic and cytotoxic activities to specific cells within mixed populations. Due to its intrinsic modularity and tunability, this technology is expected to be compatible with different types of inputs, targeting modalities and functional outputs, and as such will have broad application in the synthetic biology and biotechnology areas.
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Affiliation(s)
- Christian Kofoed
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | | | - Xuanjia Ye
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Girum Erkalo
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA
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Yamada K, Shioya R, Nishino K, Furihata H, Hijikata A, Kaneko MK, Kato Y, Shirai T, Kosako H, Sawasaki T. Proximity extracellular protein-protein interaction analysis of EGFR using AirID-conjugated fragment of antigen binding. Nat Commun 2023; 14:8301. [PMID: 38097606 PMCID: PMC10721602 DOI: 10.1038/s41467-023-43931-7] [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: 01/27/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
Receptor proteins, such as epidermal growth factor receptor (EGFR), interact with other proteins in the extracellular region of the cell membrane to drive intracellular signalling. Therefore, analysis of extracellular protein-protein interactions (exPPIs) is important for understanding the biological function of receptor proteins. Here, we present an approach using a proximity biotinylation enzyme (AirID) fusion fragment of antigen binding (FabID) to analyse the proximity exPPIs of EGFR. AirID was C-terminally fused to the Fab fragment against EGFR (EGFR-FabID), which could then biotinylate the extracellular region of EGFR in several cell lines. Liquid Chromatography-Mass Spectrometry (LC-MS/MS) analysis indicated that many known EGFR interactors were identified as proximity exPPIs, along with many unknown candidate interactors, using EGFR-FabID. Interestingly, these proximity exPPIs were influenced by treatment with EGF ligand and its specific kinase inhibitor, gefitinib. These results indicate that FabID provides accurate proximity exPPI analysis of target receptor proteins on cell membranes with ligand and drug responses.
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Affiliation(s)
- Kohdai Yamada
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Ryouhei Shioya
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hirotake Furihata
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Atsushi Hijikata
- Laboratory of Computational Genomics, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, 192-0392, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of BioScience and Technology, 1266 Tamura, Nagahama, 526-0829, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan.
| | - Tatsuya Sawasaki
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
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Hackert NS, Radtke FA, Exner T, Lorenz HM, Müller-Tidow C, Nigrovic PA, Wabnitz G, Grieshaber-Bouyer R. Human and mouse neutrophils share core transcriptional programs in both homeostatic and inflamed contexts. Nat Commun 2023; 14:8133. [PMID: 38065997 PMCID: PMC10709367 DOI: 10.1038/s41467-023-43573-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Neutrophils are frequently studied in mouse models, but the extent to which findings translate to humans remains poorly defined. In an integrative analysis of 11 mouse and 13 human datasets, we find a strong correlation of neutrophil gene expression across species. In inflammation, neutrophils display substantial transcriptional diversity but share a core inflammation program. This program includes genes encoding IL-1 family members, CD14, IL-4R, CD69, and PD-L1. Chromatin accessibility of core inflammation genes increases in blood compared to bone marrow and further in tissue. Transcription factor enrichment analysis implicates members of the NF-κB family and AP-1 complex as important drivers, and HoxB8 neutrophils with JunB knockout show a reduced expression of core inflammation genes in resting and activated cells. In independent single-cell validation data, neutrophil activation by type I or type II interferon, G-CSF, and E. coli leads to upregulation in core inflammation genes. In COVID-19 patients, higher expression of core inflammation genes in neutrophils is associated with more severe disease. In vitro treatment with GM-CSF, LPS, and type II interferon induces surface protein upregulation of core inflammation members. Together, we demonstrate transcriptional conservation in neutrophils in homeostasis and identify a core inflammation program shared across heterogeneous inflammatory conditions.
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Affiliation(s)
- Nicolaj S Hackert
- Division of Rheumatology, Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Felix A Radtke
- Division of Rheumatology, Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tarik Exner
- Division of Rheumatology, Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hanns-Martin Lorenz
- Division of Rheumatology, Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Peter A Nigrovic
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Guido Wabnitz
- Institute for Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ricardo Grieshaber-Bouyer
- Division of Rheumatology, Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.
- Institute for Immunology, Heidelberg University Hospital, Heidelberg, Germany.
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich Alexander Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich Alexander Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.
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Garapati K, Ding H, Charlesworth MC, Kim Y, Zenka R, Saraswat M, Mun DG, Chavan S, Shingade A, Lucien F, Zhong J, Kandasamy RK, Pandey A. sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides. Clin Proteomics 2023; 20:56. [PMID: 38053024 PMCID: PMC10696767 DOI: 10.1186/s12014-023-09445-6] [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: 08/21/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Cell surface proteins perform critical functions related to immune response, signal transduction, cell-cell interactions, and cell migration. Expression of specific cell surface proteins can determine cell-type identity, and can be altered in diseases including infections, cancer and genetic disorders. Identification of the cell surface proteome remains a challenge despite several enrichment methods exploiting their biochemical and biophysical properties. METHODS Here, we report a novel method for enrichment of proteins localized to cell surface. We developed this new approach designated surface Biotinylation Site Identification Technology (sBioSITe) by adapting our previously published method for direct identification of biotinylated peptides. In this strategy, the primary amine groups of lysines on proteins on the surface of live cells are first labeled with biotin, and subsequently, biotinylated peptides are enriched by anti-biotin antibodies and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS By direct detection of biotinylated lysines from PC-3, a prostate cancer cell line, using sBioSITe, we identified 5851 peptides biotinylated on the cell surface that were derived from 1409 proteins. Of these proteins, 533 were previously shown or predicted to be localized to the cell surface or secreted extracellularly. Several of the identified cell surface markers have known associations with prostate cancer and metastasis including CD59, 4F2 cell-surface antigen heavy chain (SLC3A2) and adhesion G protein-coupled receptor E5 (CD97). Importantly, we identified several biotinylated peptides derived from plectin and nucleolin, both of which are not annotated in surface proteome databases but have been shown to have aberrant surface localization in certain cancers highlighting the utility of this method. CONCLUSIONS Detection of biotinylation sites on cell surface proteins using sBioSITe provides a reliable method for identifying cell surface proteins. This strategy complements existing methods for detection of cell surface expressed proteins especially in discovery-based proteomics approaches.
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Affiliation(s)
- Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Husheng Ding
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Yohan Kim
- Department of Urology, Mayo Clinic, Rochester, MN, USA
| | - Roman Zenka
- Proteomics Core, Mayo Clinic, Rochester, MN, USA
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Sandip Chavan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ashish Shingade
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Fabrice Lucien
- Department of Urology, Mayo Clinic, Rochester, MN, USA
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Jun Zhong
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Richard K Kandasamy
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
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39
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Tremblay TL, Fauteux F, Callaghan D, Hill JJ. Cell surface profiling of cultured cells by direct hydrazide capture of oxidized glycoproteins. MethodsX 2023; 11:102349. [PMID: 37680365 PMCID: PMC10480300 DOI: 10.1016/j.mex.2023.102349] [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: 06/08/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Glycoproteins are a particularly interesting subset of the cellular proteome as a high proportion of proteins present on the extracellular cell surface are glycosylated. These cell surface proteins are ideal targets for biologic drug therapies or for diagnostics tests. Here, we describe a modification of the well-described Cell Surface Capture (CSC) method for the selective isolation and identification of cell surface glycoproteins that contain N-linked carbohydrates. This modification, which we refer to as Direct Cell Surface Capture (D-CSC), is based on oxidation of cell surface glycans on intact cells, followed by direct conjugation of the oxidized oligosaccharides to a solid support using hydrazide chemistry, with no biotinylation step. As a proof-of-principle, we applied D-CSC to the analysis of cell surface membrane proteins of three adherent cancer cell lines (A549, OVCAR3, and U87MG) and compared our results to those published using the well-established Cell Surface Capture (CSC) method, demonstrating comparable selectivity for cell surface proteins. •A method enabling the identification of cell surface proteins from cells in culture is described.•Application of this method to profile the cell surface on three different cancer cell lines is included.
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Affiliation(s)
- Tammy-Lynn Tremblay
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A0R6, Canada
| | - François Fauteux
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A0R6, Canada
| | - Deborah Callaghan
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A0R6, Canada
| | - Jennifer J. Hill
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A0R6, Canada
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40
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Ignatieva EV, Lashin SA, Mustafin ZS, Kolchanov NA. Evolution of human genes encoding cell surface receptors involved in the regulation of appetite: an analysis based on the phylostratigraphic age and divergence indexes. Vavilovskii Zhurnal Genet Selektsii 2023; 27:829-838. [PMID: 38213702 PMCID: PMC10777300 DOI: 10.18699/vjgb-23-96] [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: 08/11/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 01/13/2024] Open
Abstract
Genes encoding cell surface receptors make up a significant portion of the human genome (more than a thousand genes) and play an important role in gene networks. Cell surface receptors are transmembrane proteins that interact with molecules (ligands) located outside the cell. This interaction activates signal transduction pathways in the cell. A large number of exogenous ligands of various origins, including drugs, are known for cell surface receptors, which accounts for interest in them from biomedical researchers. Appetite (the desire of the animal organism to consume food) is one of the most primitive instincts that contribute to survival. However, when the supply of nutrients is stable, the mechanism of adaptation to adverse factors acquired in the course of evolution turned out to be excessive, and therefore obesity has become one of the most serious public health problems of the twenty-first century. Pathological human conditions characterized by appetite violations include both hyperphagia, which inevitably leads to obesity, and anorexia nervosa induced by psychosocial stimuli, as well as decreased appetite caused by neurodegeneration, inflammation or cancer. Understanding the evolutionary mechanisms of human diseases, especially those related to lifestyle changes that have occurred over the past 100-200 years, is of fundamental and applied importance. It is also very important to identify relationships between the evolutionary characteristics of genes in gene networks and the resistance of these networks to changes caused by mutations. The aim of the current study is to identify the distinctive features of human genes encoding cell surface receptors involved in appetite regulation using the phylostratigraphic age index (PAI) and divergence index (DI). The values of PAI and DI were analyzed for 64 human genes encoding cell surface receptors, the orthologs of which were involved in the regulation of appetite in model animal species. It turned out that the set of genes under consideration contains an increased number of genes with the same phylostratigraphic age (PAI = 5, the stage of vertebrate divergence), and almost all of these genes (28 out of 31) belong to the superfamily of G-protein coupled receptors. Apparently, the synchronized evolution of such a large group of genes (31 genes out of 64) is associated with the development of the brain as a separate organ in the first vertebrates. When studying the distribution of genes from the same set by DI values, a significant enrichment with genes having a low DIs was revealed: eight genes (GPR26, NPY1R, GHSR, ADIPOR1, DRD1, NPY2R, GPR171, NPBWR1) had extremely low DIs (less than 0.05). Such low DI values indicate that most likely these genes are subjected to stabilizing selection. It was also found that the group of genes with low DIs was enriched with genes that had brain-specific patterns of expression. In particular, GPR26, which had the lowest DI, is in the group of brain-specific genes. Because the endogenous ligand for the GPR26 receptor has not yet been identified, this gene seems to be an extremely interesting object for further theoretical and experimental research. We believe that the features of the genes encoding cell surface receptors we have identified using the evolutionary metrics PAI and DI can be a starting point for further evolutionary analysis of the gene network regulating appetite.
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Affiliation(s)
- E V Ignatieva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S A Lashin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Z S Mustafin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Kolchanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Nejo T, Wang L, Leung KK, Wang A, Lakshmanachetty S, Gallus M, Kwok DW, Hong C, Chen LH, Carrera DA, Zhang MY, Stevers NO, Maldonado GC, Yamamichi A, Watchmaker P, Naik A, Shai A, Phillips JJ, Chang SM, Wiita AP, Wells JA, Costello JF, Diaz AA, Okada H. Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564156. [PMID: 37961484 PMCID: PMC10634890 DOI: 10.1101/2023.10.26.564156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background Despite advancements in cancer immunotherapy, solid tumors remain formidable challenges. In glioma, profound inter-and intra-tumoral heterogeneity of antigen landscape hampers therapeutic development. Therefore, it is critical to consider alternative sources to expand the repertoire of targetable (neo-)antigens and improve therapeutic outcomes. Accumulating evidence suggests that tumor-specific alternative splicing (AS) could be an untapped reservoir of neoantigens. Results In this study, we investigated tumor-specific AS events in glioma, focusing on those predicted to generate major histocompatibility complex (MHC)-presentation-independent, cell-surface neoantigens that could be targeted by antibodies and chimeric antigen receptor (CAR)-T cells. We systematically analyzed bulk RNA-sequencing datasets comparing 429 tumor samples (from The Cancer Genome Atlas [TCGA]) and 9,166 normal tissue samples (from the Genotype-Tissue Expression project [GTEx]), and identified 13 AS events in 7 genes predicted to be expressed in more than 10% of the patients, including PTPRZ1 and BCAN , which were corroborated by an external RNA-sequencing dataset. Subsequently, we validated our predictions and elucidated the complexity of the isoforms using full-length transcript amplicon sequencing on patient-derived glioblastoma cells. However, analyses of the RNA-sequencing datasets of spatially mapped and longitudinally collected clinical tumor samples unveiled remarkable spatiotemporal heterogeneity of the candidate AS events. Furthermore, proteomics analysis did not reveal any peptide spectra matching the putative neoantigens. Conclusions Our investigation illustrated the diverse characteristics of the tumor-specific AS events and the challenges of antigen exploration due to their notable spatiotemporal heterogeneity and elusive nature at the protein levels. Redirecting future efforts toward intracellular, MHC-presented antigens could offer a more viable avenue.
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42
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Bi W, Kraft A, Engelskircher S, Mischke J, Witte M, Klawonn F, van Ham M, Cornberg M, Wedemeyer H, Hengst J, Jänsch L. Proteomics reveals a global phenotypic shift of NK cells in HCV patients treated with direct-acting antivirals. Eur J Immunol 2023; 53:e2250291. [PMID: 37515498 DOI: 10.1002/eji.202250291] [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: 11/28/2022] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 07/31/2023]
Abstract
Chronic hepatitis C virus (HCV) infections compromise natural killer (NK)-cell immunity. Direct-acting antivirals (DAA) effectively eliminate HCV, but the long-term effects on NK cells in cured patients are debated. We conducted a proteomic study on CD56+ NK cells of chronic HCV-infected patients before and 1 year after DAA therapy. Donor-variation was observed in NK-cell proteomes of HCV-infected patients, with 46 dysregulated proteins restored after DAA therapy. However, 30% of the CD56+ NK-cell proteome remained altered 1 year post-therapy, indicating a phenotypic shift with low donor-variation. NK cells from virus-negative cured patients exhibited global regulation of RNA-processing and pathways related to "stimuli response", "chemokine signaling", and "cytotoxicity regulation". Proteomics identified downregulation of vesicle transport components (CD107a, COPI/II complexes) and altered receptor expression profiles, indicating an inhibited NK-cell phenotype. Yet, activated NK cells from HCV patients before and after therapy effectively upregulated IFN-γ and recruited CD107a. Conversely, reduced surface expression levels of Tim-3 and 2B4 were observed before and after therapy. In conclusion, this study reveals long-term effects on the CD56+ NK-cell compartment in convalescent HCV patients 1 year after therapy, with limited abundance of vesicle transport complexes and surface receptors, associated with a responsive NK-cell phenotype.
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Affiliation(s)
- Wenjie Bi
- Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, P. R. China
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Anke Kraft
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School (MHH), Hannover, Germany
- Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany
- German Centre for Infection Research (DZIF), Partner site Hannover-Braunschweig, Hannover, Germany
- TWINCORE, A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Sophie Engelskircher
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School (MHH), Hannover, Germany
- Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany
| | - Jasmin Mischke
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School (MHH), Hannover, Germany
- Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany
- German Centre for Infection Research (DZIF), Partner site Hannover-Braunschweig, Hannover, Germany
- TWINCORE, A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Moana Witte
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School (MHH), Hannover, Germany
- Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany
| | - Frank Klawonn
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Department of Computer Science, Ostfalia University, Wolfenbüttel, Germany
| | - Marco van Ham
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Markus Cornberg
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School (MHH), Hannover, Germany
- Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany
- German Centre for Infection Research (DZIF), Partner site Hannover-Braunschweig, Hannover, Germany
- TWINCORE, A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Heiner Wedemeyer
- Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany
- German Centre for Infection Research (DZIF), Partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence Resolving Infection Susceptibility (RESIST; EXC 2155), Hannover Medical School, Hannover, Germany
| | - Julia Hengst
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School (MHH), Hannover, Germany
| | - Lothar Jänsch
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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43
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Mahoney SA, Dey AK, Basisty N, Herman AB. Identification and functional analysis of senescent cells in the cardiovascular system using omics approaches. Am J Physiol Heart Circ Physiol 2023; 325:H1039-H1058. [PMID: 37656130 PMCID: PMC10908411 DOI: 10.1152/ajpheart.00352.2023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide, and senescent cells have emerged as key contributors to its pathogenesis. Senescent cells exhibit cell cycle arrest and secrete a range of proinflammatory factors, termed the senescence-associated secretory phenotype (SASP), which promotes tissue dysfunction and exacerbates CVD progression. Omics technologies, specifically transcriptomics and proteomics, offer powerful tools to uncover and define the molecular signatures of senescent cells in cardiovascular tissue. By analyzing the comprehensive molecular profiles of senescent cells, omics approaches can identify specific genetic alterations, gene expression patterns, protein abundances, and metabolite levels associated with senescence in CVD. These omics-based discoveries provide insights into the mechanisms underlying senescence-induced cardiovascular damage, facilitating the development of novel diagnostic biomarkers and therapeutic targets. Furthermore, integration of multiple omics data sets enables a systems-level understanding of senescence in CVD, paving the way for precision medicine approaches to prevent or treat cardiovascular aging and its associated complications.
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Affiliation(s)
- Sophia A Mahoney
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, Colorado, United States
| | - Amit K Dey
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States
| | - Nathan Basisty
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States
| | - Allison B Herman
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States
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44
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Gottschlich A, Thomas M, Grünmeier R, Lesch S, Rohrbacher L, Igl V, Briukhovetska D, Benmebarek MR, Vick B, Dede S, Müller K, Xu T, Dhoqina D, Märkl F, Robinson S, Sendelhofert A, Schulz H, Umut Ö, Kavaka V, Tsiverioti CA, Carlini E, Nandi S, Strzalkowski T, Lorenzini T, Stock S, Müller PJ, Dörr J, Seifert M, Cadilha BL, Brabenec R, Röder N, Rataj F, Nüesch M, Modemann F, Wellbrock J, Fiedler W, Kellner C, Beltrán E, Herold T, Paquet D, Jeremias I, von Baumgarten L, Endres S, Subklewe M, Marr C, Kobold S. Single-cell transcriptomic atlas-guided development of CAR-T cells for the treatment of acute myeloid leukemia. Nat Biotechnol 2023; 41:1618-1632. [PMID: 36914885 PMCID: PMC7615296 DOI: 10.1038/s41587-023-01684-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Chimeric antigen receptor T cells (CAR-T cells) have emerged as a powerful treatment option for individuals with B cell malignancies but have yet to achieve success in treating acute myeloid leukemia (AML) due to a lack of safe targets. Here we leveraged an atlas of publicly available RNA-sequencing data of over 500,000 single cells from 15 individuals with AML and tissue from 9 healthy individuals for prediction of target antigens that are expressed on malignant cells but lacking on healthy cells, including T cells. Aided by this high-resolution, single-cell expression approach, we computationally identify colony-stimulating factor 1 receptor and cluster of differentiation 86 as targets for CAR-T cell therapy in AML. Functional validation of these established CAR-T cells shows robust in vitro and in vivo efficacy in cell line- and human-derived AML models with minimal off-target toxicity toward relevant healthy human tissues. This provides a strong rationale for further clinical development.
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Affiliation(s)
- Adrian Gottschlich
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Moritz Thomas
- Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Ruth Grünmeier
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Stefanie Lesch
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Lisa Rohrbacher
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Laboratory for Translational Cancer Immunology, Gene Center, LMU Munich, Munich, Germany
| | - Veronika Igl
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Daria Briukhovetska
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Mohamed-Reda Benmebarek
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Munich, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
| | - Sertac Dede
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Katharina Müller
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Tao Xu
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Dario Dhoqina
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Florian Märkl
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sophie Robinson
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | - Heiko Schulz
- Institute of Pathology, LMU Munich, Munich, Germany
| | - Öykü Umut
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Vladyslav Kavaka
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Christina Angeliki Tsiverioti
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Emanuele Carlini
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sayantan Nandi
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Thaddäus Strzalkowski
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Theo Lorenzini
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sophia Stock
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Philipp Jie Müller
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Janina Dörr
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Matthias Seifert
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Bruno L Cadilha
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Ruben Brabenec
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany
| | - Natalie Röder
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Felicitas Rataj
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Manuel Nüesch
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Franziska Modemann
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf Hamburg, Hamburg, Germany
| | - Jasmin Wellbrock
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Walter Fiedler
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kellner
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, LMU Munich, Munich, Germany
| | - Eduardo Beltrán
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Munich, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Louisa von Baumgarten
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Department of Neurosurgery, LMU Munich, Munich, Germany
| | - Stefan Endres
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Munich, Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Laboratory for Translational Cancer Immunology, Gene Center, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany
| | - Sebastian Kobold
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Munich, Research Center for Environmental Health (HMGU), Neuherberg, Germany.
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Kwon J, Kang J, Jo A, Seo K, An D, Baykan MY, Lee JH, Kim N, Eum HH, Hwang S, Lee JM, Park WY, An HJ, Lee HO, Park JE, Choi JK. Single-cell mapping of combinatorial target antigens for CAR switches using logic gates. Nat Biotechnol 2023; 41:1593-1605. [PMID: 36797491 DOI: 10.1038/s41587-023-01686-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/20/2023] [Indexed: 02/18/2023]
Abstract
Identification of optimal target antigens that distinguish cancer cells from normal surrounding tissue cells remains a key challenge in chimeric antigen receptor (CAR) cell therapy for tumors with intratumoral heterogeneity. In this study, we dissected tissue complexity to the level of individual cells through the construction of a single-cell expression atlas that integrates ~1.4 million tumor, tumor-infiltrating normal and reference normal cells from 412 tumors and 12 normal organs. We used a two-step screening method using random forest and convolutional neural networks to select gene pairs that contribute most to discrimination between individual malignant and normal cells. Tumor coverage and specificity are evaluated for the AND, OR and NOT logic gates based on the combinatorial expression pattern of the pairing genes across individual single cells. Single-cell transcriptome-coupled epitope profiling validates the AND, OR and NOT switch targets identified in ovarian cancer and colorectal cancer.
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Affiliation(s)
- Joonha Kwon
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Junho Kang
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Areum Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kayoung Seo
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Dohyeon An
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Mert Yakup Baykan
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Jun Hyeong Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Nayoung Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hye Hyeon Eum
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sohyun Hwang
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si, Republic of Korea
- Department of Biomedical Science, CHA University, Pocheon-si, Republic of Korea
| | - Ji Min Lee
- CHA Advanced Research Institute, CHA Bundang Medical Center, Seongnam-si, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Hee Jung An
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si, Republic of Korea.
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Jong-Eun Park
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
- Penta Medix Co., Ltd., Seongnam-si, Republic of Korea.
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46
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Oates TCL, Moura PL, Cross S, Roberts K, Baum HE, Haydn‐Smith KL, Wilson MC, Heesom KJ, Severn CE, Toye AM. Defining the proteomic landscape of cultured macrophages and their polarization continuum. Immunol Cell Biol 2023; 101:947-963. [PMID: 37694300 PMCID: PMC10953363 DOI: 10.1111/imcb.12687] [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: 05/10/2023] [Revised: 07/28/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023]
Abstract
Macrophages have previously been characterized based on phenotypical and functional differences into suggested simplified subtypes of MØ, M1, M2a and M2c. These macrophage subtypes can be generated in a well-established primary monocyte culture model that produces cells expressing accepted subtype surface markers. To determine how these subtypes retain functional similarities and better understand their formation, we generated all four subtypes from the same donors. Comparative whole-cell proteomics confirmed that four distinct macrophage subtypes could be induced from the same donor material, with > 50% of 5435 identified proteins being significantly altered in abundance between subtypes. Functional assessment highlighted that these distinct protein expression profiles are primed to enable specific cell functions, indicating that this shifting proteome is predictive of meaningful changes in cell characteristics. Importantly, the 2552 proteins remained consistent in abundance across all macrophage subtypes examined, demonstrating maintenance of a stable core proteome that likely enables swift polarity changes. We next explored the cross-polarization capabilities of preactivated M1 macrophages treated with dexamethasone. Importantly, these treated cells undergo a partial repolarization toward the M2c surface markers but still retain the M1 functional phenotype. Our investigation of polarized macrophage subtypes therefore provides evidence of a sliding scale of macrophage functionality, with these data sets providing a valuable benchmark resource for further studies of macrophage polarity, with relevance for cell therapy development and drug discovery.
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Affiliation(s)
- Tiah CL Oates
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUK
- National Institute for Health Research Blood and Transplant Research Unit (NIHR BTRU) in Red Blood Cell ProductsUniversity of BristolBristolUK
| | - Pedro L Moura
- Center for Haematology and Regenerative Medicine, Department of Medicine (MedH)Karolinska InstitutetHuddingeSweden
| | | | - Kiren Roberts
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUK
| | - Holly E Baum
- Max Planck Bristol Centre for Minimal Biology, School of ChemistryUniversity of BristolBristolUK
| | - Katy L Haydn‐Smith
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUK
| | | | - Kate J Heesom
- Proteomics Facility, Biomedical Sciences BuildingUniversity of BristolBristolUK
| | - Charlotte E Severn
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUK
- National Institute for Health Research Blood and Transplant Research Unit (NIHR BTRU) in Red Blood Cell ProductsUniversity of BristolBristolUK
| | - Ashley M Toye
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUK
- National Institute for Health Research Blood and Transplant Research Unit (NIHR BTRU) in Red Blood Cell ProductsUniversity of BristolBristolUK
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47
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Tusnády GE, Zeke A, Kálmán ZE, Fatoux M, Ricard-Blum S, Gibson TJ, Dobson L. LeishMANIAdb: a comparative resource for Leishmania proteins. Database (Oxford) 2023; 2023:baad074. [PMID: 37935582 PMCID: PMC10627299 DOI: 10.1093/database/baad074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/09/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023]
Abstract
Leishmaniasis is a detrimental disease causing serious changes in quality of life and some forms can lead to death. The disease is spread by the parasite Leishmania transmitted by sandfly vectors and their primary hosts are vertebrates including humans. The pathogen penetrates host cells and secretes proteins (the secretome) to repurpose cells for pathogen growth and to alter cell signaling via host-pathogen protein-protein interactions). Here, we present LeishMANIAdb, a database specifically designed to investigate how Leishmania virulence factors may interfere with host proteins. Since the secretomes of different Leishmania species are only partially characterized, we collated various experimental evidence and used computational predictions to identify Leishmania secreted proteins to generate a user-friendly unified web resource allowing users to access all information available on experimental and predicted secretomes. In addition, we manually annotated host-pathogen interactions of 211 proteins and the localization/function of 3764 transmembrane (TM) proteins of different Leishmania species. We also enriched all proteins with automatic structural and functional predictions that can provide new insights in the molecular mechanisms of infection. Our database may provide novel insights into Leishmania host-pathogen interactions and help to identify new therapeutic targets for this neglected disease. Database URL https://leishmaniadb.ttk.hu/.
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Affiliation(s)
- Gábor E Tusnády
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest 1117, Hungary
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7, Budapest 1094, Hungary
| | - András Zeke
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest 1117, Hungary
| | - Zsófia E Kálmán
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Marie Fatoux
- ICBMS UMR CNRS 5246, University Lyon 1, Rue Victor Grignard, Villeurbanne 69622, France
- UMR CNRS 5086, University Lyon 1, 7 Passage du Vercors, Lyon 69367, France
| | - Sylvie Ricard-Blum
- ICBMS UMR CNRS 5246, University Lyon 1, Rue Victor Grignard, Villeurbanne 69622, France
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Laszlo Dobson
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest 1117, Hungary
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
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48
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Zhang X, Tang L, Yang J, Meng L, Chen J, Zhou L, Wang J, Xiong M, Zhang Z. Soluble TREM2 ameliorates tau phosphorylation and cognitive deficits through activating transgelin-2 in Alzheimer's disease. Nat Commun 2023; 14:6670. [PMID: 37865646 PMCID: PMC10590452 DOI: 10.1038/s41467-023-42505-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 10/12/2023] [Indexed: 10/23/2023] Open
Abstract
Triggering receptor expressed on myeloid cells 2 (TREM2) is a transmembrane protein that is predominantly expressed by microglia in the brain. The proteolytic shedding of TREM2 results in the release of soluble TREM2 (sTREM2), which is increased in the cerebrospinal fluid of patients with Alzheimer's disease (AD). It remains unknown whether sTREM2 regulates the pathogenesis of AD. Here we identified transgelin-2 (TG2) expressed on neurons as the receptor for sTREM2. The microglia-derived sTREM2 binds to TG2, induces RhoA phosphorylation at S188, and deactivates the RhoA-ROCK-GSK3β pathway, ameliorating tau phosphorylation. The sTREM2 (77-89) fragment, which is the minimal active sequence of sTREM2 to activate TG2, mimics the inhibitory effect of sTREM2 on tau phosphorylation. Overexpression of sTREM2 or administration of the active peptide rescues tau pathology and behavioral defects in the tau P301S transgenic mice. Together, these findings demonstrate that the sTREM2-TG2 interaction mediates the cross-talk between microglia and neurons. sTREM2 and its active peptide may be a potential therapeutic intervention for tauopathies including AD.
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Affiliation(s)
- Xingyu Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Li Tang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jiaolong Yang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Lanxia Meng
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jiehui Chen
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Lingyan Zhou
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jiangyu Wang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Min Xiong
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Zhentao Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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49
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Datta S, Chen DY, Tavares AH, Reyes-Robles T, Ryu KA, Khan N, Bechtel TJ, Bertoch JM, White CH, Hazuda DJ, Vora KA, Hett EC, Fadeyi OO, Oslund RC, Emili A, Saeed M. High-resolution photocatalytic mapping of SARS-CoV-2 spike interactions on the cell surface. Cell Chem Biol 2023; 30:1313-1322.e7. [PMID: 37499664 DOI: 10.1016/j.chembiol.2023.06.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/03/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023]
Abstract
Identifying virus-host interactions on the cell surface can improve our understanding of viral entry and pathogenesis. SARS-CoV-2, the causative agent of the COVID-19 disease, uses ACE2 as a receptor to enter cells. Yet the full repertoire of cell surface proteins that contribute to viral entry is unknown. We developed a photocatalyst-based viral-host protein microenvironment mapping platform (ViraMap) to probe the molecular neighborhood of the SARS-CoV-2 spike protein on the human cell surface. Application of ViraMap to ACE2-expressing cells captured ACE2, the established co-receptor NRP1, and several novel cell surface proteins. We systematically analyzed the relevance of these candidate proteins to SARS-CoV-2 entry by knockdown and overexpression approaches in pseudovirus and authentic infection models and identified PTGFRN and EFNB1 as bona fide viral entry factors. Our results highlight additional host targets that participate in SARS-CoV-2 infection and showcase ViraMap as a powerful platform for defining viral interactions on the cell surface.
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Affiliation(s)
- Suprama Datta
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA; Center for Network Systems Biology, Boston University, Boston, MA 02118, USA
| | - Da-Yuan Chen
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Alexander H Tavares
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Tamara Reyes-Robles
- Merck Exploratory Science Center, Merck & Co., Inc, Cambridge, MA 02141, USA
| | - Keun Ah Ryu
- Merck Exploratory Science Center, Merck & Co., Inc, Cambridge, MA 02141, USA
| | - Nazimuddin Khan
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Tyler J Bechtel
- Merck Exploratory Science Center, Merck & Co., Inc, Cambridge, MA 02141, USA
| | - Jayde M Bertoch
- Merck Exploratory Science Center, Merck & Co., Inc, Cambridge, MA 02141, USA
| | - Cory H White
- Merck Exploratory Science Center, Merck & Co., Inc, Cambridge, MA 02141, USA
| | - Daria J Hazuda
- Merck Exploratory Science Center, Merck & Co., Inc, Cambridge, MA 02141, USA; Department of Infectious Diseases and Vaccines Research, Merck & Co., Inc, West Point, PA 19486, USA
| | - Kalpit A Vora
- Department of Infectious Diseases and Vaccines Research, Merck & Co., Inc, West Point, PA 19486, USA
| | - Erik C Hett
- Merck Exploratory Science Center, Merck & Co., Inc, Cambridge, MA 02141, USA
| | | | - Rob C Oslund
- Merck Exploratory Science Center, Merck & Co., Inc, Cambridge, MA 02141, USA.
| | - Andrew Emili
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; Center for Network Systems Biology, Boston University, Boston, MA 02118, USA.
| | - Mohsan Saeed
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA.
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50
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Wu T, Tan JHL, Sin W, Luah YH, Tan SY, Goh M, Birnbaum ME, Chen Q, Cheow LF. Cell Granularity Reflects Immune Cell Function and Enables Selection of Lymphocytes with Superior Attributes for Immunotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302175. [PMID: 37544893 PMCID: PMC10558660 DOI: 10.1002/advs.202302175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/20/2023] [Indexed: 08/08/2023]
Abstract
In keeping with the rule of "form follows function", morphological aspects of a cell can reflect its role. Here, it is shown that the cellular granularity of a lymphocyte, represented by its intrinsic side scatter (SSC), is a potent indicator of its cell state and function. The granularity of a lymphocyte increases from naïve to terminal effector state. High-throughput cell-sorting yields a SSChigh population that can mediate immediate effector functions, and a highly prolific SSClow population that can give rise to the replenishment of the memory pool. CAR-T cells derived from the younger SSClow population possess desirable attributes for immunotherapy, manifested by increased naïve-like cells and stem cell memory (TSCM )-like cells together with a balanced CD4/CD8 ratio, as well as enhanced target-killing in vitro and in vivo. Altogether, lymphocyte segregation based on biophysical properties is an effective approach for label-free selection of cells that share collective functions and can have important applications for cell-based immunotherapies.
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Affiliation(s)
- Tongjin Wu
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
| | - Joel Heng Loong Tan
- Institute of Molecular and Cell Biology (IMCB)Agency for ScienceTechnology and Research (A*STAR)Singapore138673Singapore
| | - Wei‐Xiang Sin
- Critical Analytics for Manufacturing of Personalized MedicineSingapore‐MIT Alliance for Research and TechnologySingapore138602Singapore
| | - Yen Hoon Luah
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
- Critical Analytics for Manufacturing of Personalized MedicineSingapore‐MIT Alliance for Research and TechnologySingapore138602Singapore
| | - Sue Yee Tan
- Institute of Molecular and Cell Biology (IMCB)Agency for ScienceTechnology and Research (A*STAR)Singapore138673Singapore
| | - Myra Goh
- Institute of Molecular and Cell Biology (IMCB)Agency for ScienceTechnology and Research (A*STAR)Singapore138673Singapore
| | - Michael E. Birnbaum
- Critical Analytics for Manufacturing of Personalized MedicineSingapore‐MIT Alliance for Research and TechnologySingapore138602Singapore
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Qingfeng Chen
- Institute of Molecular and Cell Biology (IMCB)Agency for ScienceTechnology and Research (A*STAR)Singapore138673Singapore
| | - Lih Feng Cheow
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
- Critical Analytics for Manufacturing of Personalized MedicineSingapore‐MIT Alliance for Research and TechnologySingapore138602Singapore
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