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Domingos IF, Carvalho LB, Lodeiro C, Gerivaz R, Prag G, Micaglio E, Muchtar E, Santos HM, Capelo JL. Dithiothreitol-based protein equalisation in the context of multiple myeloma: Enhancing proteomic analysis and therapeutic insights. Talanta 2024; 279:126589. [PMID: 39116730 DOI: 10.1016/j.talanta.2024.126589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Abstract
In this study, we employed the dithiothreitol-based protein equalisation technique and analytical proteomics to better understand myeloma diseases by comparing the proteomes of pellets and supernatants formed upon application of DTT on serum samples. The number of unique proteins found in pellets was 252 for healthy individuals and 223 for multiple myeloma patients. The comparison of these proteomes showed 97 dysregulated proteins. The unique proteins found for supernatants were 264 for healthy individuals and 235 for multiple myeloma patients. The comparison of these proteomes showed 87 dysregulated proteins. The analytical proteomic comparison of both groups of dysregulated proteins is translated into parallel dysregulated pathways, including chaperone-mediated autophagy and protein folding, addressing potential therapeutic interventions. Future research endeavours in personalised medicine should prioritize refining analytical proteomic methodologies using serum dithiothreitol-based protein equalisation to explore innovative therapeutic strategies. We highlight the advanced insights gained from this analytical strategy in studying multiple myeloma, emphasising its complex nature and the critical role of personalised, targeted analytical techniques in enhancing therapeutic efficacy in personalised medicine.
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Affiliation(s)
- Ines F Domingos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal
| | - Luis B Carvalho
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal
| | - Carlos Lodeiro
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal
| | - Rita Gerivaz
- Serviço de Hematologia, Hospital Garcia de Orta, Almada, Portugal
| | - Gali Prag
- School of Neurobiology, Biochemistry and Biophysics, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Israel
| | - Emanuele Micaglio
- Department of Arrhythmology, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097, Milan, Italy
| | - Eli Muchtar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Hugo M Santos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal; Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| | - Jose L Capelo
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal.
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2
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Perna F, Parekh S, Diorio C, Smith M, Subklewe M, Mehta R, Locke FL, Shah NN. CAR T-cell toxicities: from bedside to bench, how novel toxicities inform laboratory investigations. Blood Adv 2024; 8:4348-4358. [PMID: 38861351 DOI: 10.1182/bloodadvances.2024013044] [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: 02/28/2024] [Revised: 05/20/2024] [Accepted: 06/02/2024] [Indexed: 06/13/2024] Open
Abstract
ABSTRACT Multiple chimeric antigen receptor (CAR) T-cell therapies are US Food and Drug Administration-approved, and several are under development. Although effective for some cancers, toxicities remain a limitation. The most common toxicities, that is, cytokine release syndrome and immune effector cell-associated neurotoxicity syndrome, are well described. With increasing utilization, providers worldwide are reporting other emergent and often complicated toxicities. Given the evolving toxicity profiles and urgent need to catalog these emerging and emergent CAR T-cell toxicities and describe management approaches, the American Society of Hematology Subcommittee on Emerging Gene and Cell Therapies organized the first scientific workshop on CAR T-cell toxicities during the annual society meeting. The workshop functioned to (1) aggregate reports of CAR T-cell emergent toxicities, including movement disorders after B-cell maturation antigen CAR T cell, coagulation abnormalities, and prolonged cytopenia; (2) disseminate bedside-to-bench efforts elucidating pathophysiological mechanisms of CAR T-cell toxicities, including the intestinal microbiota and systemic immune dysregulation; and (3) highlight gaps in the availability of clinical tests, such as cytokine measurements, which could be used to expand our knowledge around the monitoring of toxicities. Key themes emerged. First, although clinical manifestations may develop before the pathophysiologic mechanisms are understood, they must be studied to aid in the detection and prevention of such toxicities. Second, systemic immune dysregulation appears to be central to these emergent toxicities, and research is needed to elucidate the links between tumors, CAR T cells, and microbiota. Finally, there was a consensus around the urgency to create a repository to capture emergent CAR T-cell toxicities and the real-world management.
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Affiliation(s)
- Fabiana Perna
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Moffitt Cancer Center, Tampa, FL
| | - Samir Parekh
- Division of Hematology and Medical Oncology, The Tish Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Caroline Diorio
- Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA
| | - Melody Smith
- Department of Medicine, Stanford University, Stanford, CA
| | - Marion Subklewe
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Rakesh Mehta
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Frederick L Locke
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Moffitt Cancer Center, Tampa, FL
| | - Nirali N Shah
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
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3
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Anderson GSF, Chapman MA. T cell-redirecting therapies in hematological malignancies: Current developments and novel strategies for improved targeting. Mol Ther 2024:S1525-0016(24)00482-9. [PMID: 39095991 DOI: 10.1016/j.ymthe.2024.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/17/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024] Open
Abstract
T cell-redirecting therapies (TCRTs), such as chimeric antigen receptor (CAR) or T cell receptor (TCR) T cells and T cell engagers, have emerged as a highly effective treatment modality, particularly in the B and plasma cell-malignancy setting. However, many patients fail to achieve deep and durable responses; while the lack of truly unique tumor antigens, and concurrent on-target/off-tumor toxicities, have hindered the development of TCRTs for many other cancers. In this review, we discuss the recent developments in TCRT targets for hematological malignancies, as well as novel targeting strategies that aim to address these, and other, challenges.
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Affiliation(s)
| | - Michael A Chapman
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QR, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK; Addenbrooke's Hospital, Cambridge Universities Foundation Trust, Cambridge CB2 0QQ, UK.
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4
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Walker IG, Roy JP, Anderson GSF, Guerrero Lopez J, Chapman MA. Targeting myeloma essential genes using NOT Gated CAR T-cells, a computational approach. Leukemia 2024; 38:1848-1852. [PMID: 38688994 PMCID: PMC11286523 DOI: 10.1038/s41375-024-02247-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Ieuan G Walker
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge Universities Foundation Trust, Cambridge, UK
| | - James P Roy
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | | | - Michael A Chapman
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Addenbrooke's Hospital, Cambridge Universities Foundation Trust, Cambridge, UK.
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5
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Ramberger E, Sapozhnikova V, Ng YLD, Dolnik A, Ziehm M, Popp O, Sträng E, Kull M, Grünschläger F, Krüger J, Benary M, Müller S, Gao X, Murgai A, Haji M, Schmidt A, Lutz R, Nogai A, Braune J, Laue D, Langer C, Khandanpour C, Bassermann F, Döhner H, Engelhardt M, Straka C, Hundemer M, Beule D, Haas S, Keller U, Einsele H, Bullinger L, Knop S, Mertins P, Krönke J. The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities. NATURE CANCER 2024; 5:1267-1284. [PMID: 38942927 PMCID: PMC11358022 DOI: 10.1038/s43018-024-00784-3] [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: 12/21/2022] [Accepted: 05/15/2024] [Indexed: 06/30/2024]
Abstract
Multiple myeloma (MM) is a plasma cell malignancy of the bone marrow. Despite therapeutic advances, MM remains incurable, and better risk stratification as well as new therapies are therefore highly needed. The proteome of MM has not been systematically assessed before and holds the potential to uncover insight into disease biology and improved prognostication in addition to genetic and transcriptomic studies. Here we provide a comprehensive multiomics analysis including deep tandem mass tag-based quantitative global (phospho)proteomics, RNA sequencing, and nanopore DNA sequencing of 138 primary patient-derived plasma cell malignancies encompassing treatment-naive MM, plasma cell leukemia and the premalignancy monoclonal gammopathy of undetermined significance, as well as healthy controls. We found that the (phospho)proteome of malignant plasma cells are highly deregulated as compared with healthy plasma cells and is both defined by chromosomal alterations as well as posttranscriptional regulation. A prognostic protein signature was identified that is associated with aggressive disease independent of established risk factors in MM. Integration with functional genetics and single-cell RNA sequencing revealed general and genetic subtype-specific deregulated proteins and pathways in plasma cell malignancies that include potential targets for (immuno)therapies. Our study demonstrates the potential of proteogenomics in cancer and provides an easily accessible resource for investigating protein regulation and new therapeutic approaches in MM.
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Affiliation(s)
- Evelyn Ramberger
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Valeriia Sapozhnikova
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Yuen Lam Dora Ng
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anna Dolnik
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Matthias Ziehm
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Eric Sträng
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Miriam Kull
- Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Florian Grünschläger
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Josefine Krüger
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Sina Müller
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Xiang Gao
- Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Arunima Murgai
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mohamed Haji
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Annika Schmidt
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Raphael Lutz
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Axel Nogai
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jan Braune
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik Laue
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
| | - Florian Bassermann
- Department of Medicine III, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Hartmut Döhner
- Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | | | | | - Michael Hundemer
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Simon Haas
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
| | - Ulrich Keller
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Lars Bullinger
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Knop
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany.
- Nuremberg General Hospital, Nuremberg, Germany.
- Paracelsus Medical School, Nuremberg, Germany.
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
| | - Jan Krönke
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany.
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6
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Di Meo F, Kale B, Koomen JM, Perna F. Mapping the cancer surface proteome in search of target antigens for immunotherapy. Mol Ther 2024:S1525-0016(24)00474-X. [PMID: 39068512 DOI: 10.1016/j.ymthe.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/26/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024] Open
Abstract
Immune-based therapeutic interventions recognizing proteins localized on the cell surface of cancer cells are emerging as a promising cancer treatment. Antibody-based therapies and engineered T cells are now approved by the Food and Drug Administration to treat some malignancies. These therapies utilize a few cell surface proteins highly expressed on cancer cells to release the negative regulation of immune activation that limits antitumor responses (e.g., PD-1, PD-L1, CTLA4) or to redirect the T cell specificity toward blood cancer cells (e.g., CD19 and B cell maturation antigen). One limitation preventing broader application of these novel therapeutic strategies to all cancer types is the lack of suitable target antigens for all indications owing in part to the challenges in identifying such targets. Ideal target antigens are cell surface proteins highly expressed on malignant cells and absent in healthy tissues. Technological advances in mass spectrometry, enrichment protocols, and computational tools for cell surface protein isolation and annotation have recently enabled comprehensive analyses of the cancer cell surface proteome, from which novel immunotherapeutic target antigens may emerge. Here, we review the most recent progress in this field.
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Affiliation(s)
- Francesco Di Meo
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA
| | - Brandon Kale
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Fabiana Perna
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA.
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7
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Hou T, Zhang P, Tian H, Luo Y, Li J, Zhang K, Li Y. Semaphorin 4A Maintains Trophoblastic Function via Activating the STAT3 Pathway. Biomolecules 2024; 14:826. [PMID: 39062540 PMCID: PMC11274653 DOI: 10.3390/biom14070826] [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: 05/29/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
The migration, proliferation, and apoptosis of trophoblastic cells play a crucial role in ensuring the effective preservation of pregnancy at the maternal-fetal interface. Any deviations in the structure and function of these cells might potentially result in the development of numerous pregnancy-related disorders, including missed abortion (MA). This study involved the examination of semaphorin 4A (SEMA4A) expression in missed abortion (n = 18) and normal early pregnancy (n = 18) villus. The findings of this study indicate a statistically significant decrease in the expression of SEMA4A in the villi of individuals diagnosed with missed abortion, as compared to the control group. The results of our vitro study showed that SEMA4A promoted the migration and proliferation of trophoblast cells and inhibited their apoptosis. Subsequent studies have shown that SEMA4A may be involved in regulating p-STAT3/STAT3, MMP9, bcl-2, and BAX levels. In summary, the findings of this study indicate a correlation between the decreased level of SEMA4A in chorionic villi and missed abortion. These results offer novel theoretical insights into the proper implantation and development of SEMA4A embryos at the maternal-fetal interface.
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Affiliation(s)
- Taotao Hou
- Graduate School of Hebei North University, Zhangjiakou 075000, China
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang 050051, China
- Department of Gynecology, Tianjin Beichen Hospital, Tianjin 300400, China
| | - Pingping Zhang
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang 050051, China
| | - Haishen Tian
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang 050051, China
| | - Yan Luo
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang 050051, China
| | - Juan Li
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang 050051, China
| | - Kuo Zhang
- Graduate School of University of Science and Technology Beijing, Beijing 100083, China
| | - Yali Li
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang 050051, China
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8
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da Silva Gonçalves CE, Fock RA. Semaphorins and the bone marrow microenvironment: New candidates that influence the hematopoietic system. Cytokine Growth Factor Rev 2024; 76:22-29. [PMID: 38472041 DOI: 10.1016/j.cytogfr.2024.02.002] [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: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
The bone marrow is a haven for hematopoietic and non-hematopoietic cells, creating complex micro-anatomical regions called niches. These distinct niches all participate in an intricate orchestra of cellular interactions that regulates the hematopoietic stem cell and its progenies. In this review, we provide a detailed description of the three most well-known bone marrow niches and their participation in hematopoiesis. We use pre-clinical data, including different in vitro and in vivo studies to discuss how a group of proteins called Semaphorins could potentially modulate both hematopoietic and non-hematopoietic cells, establishing links between the niches, semaphorins, and hematopoietic regulation. Thus, here we provide a deep dive into the inner functioning of the bone marrow and discuss the overarching implications that semaphorins might have on blood formation.
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Affiliation(s)
- Carlos E da Silva Gonçalves
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Ricardo A Fock
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
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9
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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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10
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Gou MJ, Charpentier J, Cobraiville G, Crommen J, Caers J, Fillet M. Improvement of untargeted proteomics workflow for surfaceome profiling and its evaluation through the implementation of quality controls: Application to multiple myeloma. Anal Chim Acta 2023; 1279:341764. [PMID: 37827665 DOI: 10.1016/j.aca.2023.341764] [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: 06/27/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Comprehensive surfaceome profiling of cancer cells using mass spectrometry (MS)-based technologies is a valuable approach to identify new antigens that could be targeted by immunotherapies. Multiple myeloma (MM) is an incurable hematological malignancy in which patients suffer from multiple relapses associated with drug resistance. Nevertheless, only three MM-specific antigens are currently targeted by approved immunotherapies which restrain the availability of efficient treatments for severe refractory patients affected by aggressive forms of the disease. Therefore, the discovery of new antigens in this context could open new perspectives for those patients. RESULTS In this study, the first objective was to improve a MS-based untargeted proteomics workflow in order to handle limited patient samples. For this purpose, a highly sensitive and robust miniaturized separation system (LC-Chip) coupled with drift tube ion mobility spectrometry and high-resolution MS was integrated in our workflow to maximize protein identification. As sample preparation can strongly influence the detectability of membrane-associated proteins, the critical steps in sample preparation were carefully optimized. As a result, 4.5 times more membrane-associated proteins were identified and experimental throughput was also drastically improved. In addition to workflow performance, particular attention was paid to assess the quality of the generated data. Indeed, several quality controls (QC) were implemented to assess data quality. Finally, the optimized workflow as well as selected QCs were evaluated in the analysis of samples containing limited number of cells. SIGNIFICANCE This work allowed the improvement of an untargeted proteomics workflow for surfaceome profiling in terms of performance. Besides, the reliability of the obtained data was evaluated through the introduction of QCs in the workflow. The applicability of the improved workflow as well as the implemented QCs for the analysis of MM primary cells obtained from patients was confirmed.
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Affiliation(s)
- Marie-Jia Gou
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hopital, Avenue Hippocrate 15, 4000, Liege, Belgium
| | - Julien Charpentier
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hopital, Avenue Hippocrate 15, 4000, Liege, Belgium
| | - Gaël Cobraiville
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hopital, Avenue Hippocrate 15, 4000, Liege, Belgium
| | - Jacques Crommen
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hopital, Avenue Hippocrate 15, 4000, Liege, Belgium
| | - Jo Caers
- Laboratory of Hematology, GIGA I3, University of Liège, Liège, Belgium; Department of Hematology, CHU de Liège, Liège, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hopital, Avenue Hippocrate 15, 4000, Liege, Belgium.
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11
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Colom Díaz PA, Mistry JJ, Trowbridge JJ. Hematopoietic stem cell aging and leukemia transformation. Blood 2023; 142:533-542. [PMID: 36800569 PMCID: PMC10447482 DOI: 10.1182/blood.2022017933] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/23/2023] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
With aging, hematopoietic stem cells (HSCs) have an impaired ability to regenerate, differentiate, and produce an entire repertoire of mature blood and immune cells. Owing to dysfunctional hematopoiesis, the incidence of hematologic malignancies increases among elderly individuals. Here, we provide an update on HSC-intrinsic and -extrinsic factors and processes that were recently discovered to contribute to the functional decline of HSCs during aging. In addition, we discuss the targets and timing of intervention approaches to maintain HSC function during aging and the extent to which these same targets may prevent or delay transformation to hematologic malignancies.
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12
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Lejeune M, Köse MC, Jassin M, Gou MJ, Herbet A, Duray E, Cobraiville G, Foguenne J, Boquet D, Gothot A, Beguin Y, Fillet M, Caers J. Integrative Analysis of Proteomics and Transcriptomics Reveals Endothelin Receptor B as Novel Single Target and Identifies New Combinatorial Targets for Multiple Myeloma. Hemasphere 2023; 7:e901. [PMID: 37359190 PMCID: PMC10289631 DOI: 10.1097/hs9.0000000000000901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/25/2023] [Indexed: 06/28/2023] Open
Abstract
Despite the recent introduction of next-generation immunotherapeutic agents, multiple myeloma (MM) remains incurable. New strategies targeting MM-specific antigens may result in a more effective therapy by preventing antigen escape, clonal evolution, and tumor resistance. In this work, we adapted an algorithm that integrates proteomic and transcriptomic results of myeloma cells to identify new antigens and possible antigen combinations. We performed cell surface proteomics on 6 myeloma cell lines based and combined these results with gene expression studies. Our algorithm identified 209 overexpressed surface proteins from which 23 proteins could be selected for combinatorial pairing. Flow cytometry analysis of 20 primary samples confirmed the expression of FCRL5, BCMA, and ICAM2 in all samples and IL6R, endothelin receptor B (ETB), and SLCO5A1 in >60% of myeloma cases. Analyzing possible combinations, we found 6 combinatorial pairs that can target myeloma cells and avoid toxicity on other organs. In addition, our studies identified ETB as a tumor-associated antigen that is overexpressed on myeloma cells. This antigen can be targeted with a new monoclonal antibody RB49 that recognizes an epitope located in a region that becomes highly accessible after activation of ETB by its ligand. In conclusion, our algorithm identified several candidate antigens that can be used for either single-antigen targeting approaches or for combinatorial targeting in new immunotherapeutic approaches in MM.
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Affiliation(s)
- Margaux Lejeune
- Laboratory of Hematology, GIGA I3, University of Liège, Belgium
| | - Murat Cem Köse
- Laboratory of Hematology, GIGA I3, University of Liège, Belgium
| | - Mégane Jassin
- Laboratory of Hematology, GIGA I3, University of Liège, Belgium
| | - Marie-Jia Gou
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Amaury Herbet
- Université Paris-Saclay, CEA, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Gif-sur-Yvette, France
| | - Elodie Duray
- Laboratory of Hematology, GIGA I3, University of Liège, Belgium
| | - Gaël Cobraiville
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Jacques Foguenne
- Department of Hematobiology and Immunohematology, CHU de Liège, Belgium
| | - Didier Boquet
- Université Paris-Saclay, CEA, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Gif-sur-Yvette, France
| | - André Gothot
- Department of Hematobiology and Immunohematology, CHU de Liège, Belgium
| | - Yves Beguin
- Laboratory of Hematology, GIGA I3, University of Liège, Belgium
- Department of Hematology, CHU de Liège, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Jo Caers
- Laboratory of Hematology, GIGA I3, University of Liège, Belgium
- Department of Hematology, CHU de Liège, Belgium
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13
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Chen M, Jiang J, Hou J. Single-cell technologies in multiple myeloma: new insights into disease pathogenesis and translational implications. Biomark Res 2023; 11:55. [PMID: 37259170 DOI: 10.1186/s40364-023-00502-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy characterized by clonal proliferation of plasma cells. Although therapeutic advances have been made to improve clinical outcomes and to prolong patients' survival in the past two decades, MM remains largely incurable. Single-cell sequencing (SCS) is a powerful method to dissect the cellular and molecular landscape at single-cell resolution, instead of providing averaged results. The application of single-cell technologies promises to address outstanding questions in myeloma biology and has revolutionized our understanding of the inter- and intra-tumor heterogeneity, tumor microenvironment, and mechanisms of therapeutic resistance in MM. In this review, we summarize the recently developed SCS methodologies and latest MM research progress achieved by single-cell profiling, including information regarding the cancer and immune cell landscapes, tumor heterogeneities, underlying mechanisms and biomarkers associated with therapeutic response and resistance. We also discuss future directions of applying transformative SCS approaches with contribution to clinical translation.
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Affiliation(s)
- Mengping Chen
- Department of Hematology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jinxing Jiang
- Department of Hematology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jian Hou
- Department of Hematology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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14
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Nojima S. Class IV semaphorins in disease pathogenesis. Pathol Int 2022; 72:471-487. [PMID: 36066011 DOI: 10.1111/pin.13270] [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: 05/16/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022]
Abstract
Semaphorins are a large family of secreted and/or transmembrane proteins, originally identified as proteins that function in axon guidance during neuronal development. However, semaphorins play crucial roles in other physiological and pathological processes, including immune responses, angiogenesis, maintenance of tissue homeostasis, and cancer progression. Class IV semaphorins may be present as transmembrane and soluble forms and are implicated in the pathogenesis of various diseases. This review discusses recent progress on the roles of class IV semaphorins determined by clinical and experimental pathology studies.
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Affiliation(s)
- Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.,Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
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15
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Parol W, Anderson GSF, Chapman MA. CAR-T cell therapies for cancer: what novel technologies are being developed for toxicity data? Expert Opin Drug Metab Toxicol 2022; 18:241-244. [PMID: 35686653 DOI: 10.1080/17425255.2022.2085551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/31/2022] [Indexed: 11/04/2022]
Affiliation(s)
- Wiktoria Parol
- University of Cambridge, MRC Toxicology Unit, Cambridge, UK
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