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Lee S, Kim J, You JS, Hyun YM, Kim JY, Lee JE. Ischemic stroke outcome after promoting CD4+CD25+ Treg cell migration through CCR4 overexpression in a tMCAO animal model. Sci Rep 2024; 14:10201. [PMID: 38702399 PMCID: PMC11068779 DOI: 10.1038/s41598-024-60358-2] [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] [Received: 01/05/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
The importance of neuroinflammation during the ischemic stroke has been extensively studied. The role of CD4+CD25+ regulatory T (Treg) cells during the recovery phase have shown infarct size reduction and functional improvement, possibly through the mitigation of inflammatory immune responses. We aimed to investigate the molecular factors involved in microglia-Treg cell communication that result in Treg trafficking. First, we observed the migration patterns of CD8+ (cytotoxic) T cells and Treg cells and then searched for chemokines released by activated microglia in an oxygen-glucose deprivation (OGD) model. The transwell migration assay showed increased migration into OGD media for both cell types, in agreement with the increase in chemokines involved in immune cell trafficking from the mouse chemokine profiling array. MSCV retrovirus was transduced to overexpress CCR4 in Treg cells. CCR4-overexpressed Treg cells were injected into the mouse transient middle cerebral artery occlusion (tMCAO) model to evaluate the therapeutic potential via the tetrazolium chloride (TTC) assay and behavioral tests. A general improvement in the prognosis of animals after tMCAO was observed. Our results suggest the increased mobility of CCR4-overexpressed Treg cells in response to microglia-derived chemokines in vitro and the therapeutic potential of Treg cells with increased mobility in cellular therapy.
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Affiliation(s)
- Seowoo Lee
- Department of Anatomy, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jiwon Kim
- Department of Anatomy, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Je Sung You
- Department of Emergency Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-ro, Gangnam-gu, Seoul, 06273, Republic of Korea
| | - Young-Min Hyun
- Department of Anatomy, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Youl Kim
- Department of Anatomy, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Jong Eun Lee
- Department of Anatomy, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Brain Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
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2
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Georgiev P, Benamar M, Han S, Haigis MC, Sharpe AH, Chatila TA. Regulatory T cells in dominant immunologic tolerance. J Allergy Clin Immunol 2024; 153:28-41. [PMID: 37778472 PMCID: PMC10842646 DOI: 10.1016/j.jaci.2023.09.025] [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: 06/23/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/03/2023]
Abstract
Regulatory T cells expressing the transcription factor forkhead box protein 3 mediate peripheral immune tolerance both to self-antigens and to the commensal flora. Their defective function due to inborn errors of immunity or acquired insults is associated with a broad range of autoimmune and immune dysregulatory diseases. Although their function in suppressing autoimmunity and enforcing commensalism is established, a broader role for regulatory T cells in tissue repair and metabolic regulation has emerged, enabled by unique programs of tissue adaptability and specialization. In this review, we focus on the myriad roles played by regulatory T cells in immunologic tolerance and host homeostasis and the potential to harness these cells in novel therapeutic approaches to human diseases.
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Affiliation(s)
- Peter Georgiev
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, Mass; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, Mass
| | - Mehdi Benamar
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - SeongJun Han
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, Mass; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, Mass
| | - Marcia C Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, Mass
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, Mass
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Harvard Medical School, Boston, Mass.
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3
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Ma S, So M, Ghelani A, Srivas R, Sahoo A, Hall R, Liu W, Wu H, Yu S, Lu S, Song E, Cariaga T, Soto M, Zhou H, Li CM, Chaudhry A, Luo X, Sohn SJ. Attenuated IL-2 muteins leverage the TCR signal to enhance regulatory T cell homeostasis and response in vivo. Front Immunol 2023; 14:1257652. [PMID: 37809101 PMCID: PMC10556740 DOI: 10.3389/fimmu.2023.1257652] [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: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Interleukin-2 (IL-2), along with T-cell receptor (TCR) signaling, are required to control regulatory T cell (Treg) homeostasis and function in vivo. Due to the heightened sensitivity to IL-2, Tregs retain the ability to respond to low-dose or attenuated forms of IL-2, as currently being developed for clinical use to treat inflammatory diseases. While attenuated IL-2 increases Treg selectivity, the question remains as to whether a weakened IL-2 signal sufficiently enhances Treg suppressive function(s) toward disease modification. To understand this question, we characterized the in vivo activity and transcriptomic profiles of two different attenuated IL-2 muteins in comparison with wildtype (WT) IL-2. Our study showed that, in addition to favoring Tregs, the attenuated muteins induced disproportionately robust effects on Treg activation and conversion to effector Treg (eTreg) phenotype. Our data furthermore suggested that Tregs activated by attenuated IL-2 muteins showed reduced dependence on TCR signal, at least in part due to the enhanced ability of IL-2 muteins to amplify the TCR signal in vivo. These results point to a new paradigm wherein IL-2 influences Tregs' sensitivity to antigenic signal, and that the combination effect may be leveraged for therapeutic use of attenuated IL-2 muteins.
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Affiliation(s)
- Shining Ma
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Michelle So
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Aazam Ghelani
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Rohith Srivas
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Anupama Sahoo
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Robyn Hall
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Wenjun Liu
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Hao Wu
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Sherman Yu
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Shiping Lu
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Elly Song
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Taryn Cariaga
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Marcus Soto
- Amgen Research, Amgen Inc., Thousand Oaks, CA, United States
| | - Hong Zhou
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Chi-Ming Li
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | | | - Xin Luo
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
| | - Sue J. Sohn
- Amgen Research, Amgen Inc., South San Francisco, CA, United States
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4
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Ahmadi F, Junghus F, Ashworth C, Lappalainen A, Mörbe U, Kotarsky K, Agace WW. cDC1-derived IL-27 regulates small intestinal CD4+ T cell homeostasis in mice. J Exp Med 2023; 220:213747. [PMID: 36515659 PMCID: PMC9754766 DOI: 10.1084/jem.20221090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/20/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
The small intestinal lamina propria contains large numbers of IFNγ-producing T helper (Th1) cells that play important roles in intestinal homeostasis and host defense, but the mechanisms underlying their development remain poorly understood. Here, we demonstrate that Th1 cells accumulate in the SI-LP after weaning and are maintained there long term. While both Th17 and Th1 cell accumulation in the SI-LP was microbiota dependent, Th1 cell accumulation uniquely required IL-27 and MHCII expression by cDC1. This reflected a requirement for IL-27 signaling in the priming of Th1 cells rather than for their maintenance once in the mucosa. cDC1-derived IL-27 was essential for maintaining the Th1-Th17 balance within the SI-LP, and in its absence, remaining Th1 cells expressed enhanced levels of Th17 signature genes. In conclusion, we identify cDC1-derived IL-27 as a key regulator of SI-LP Th1-Th17 cell homeostasis.
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Affiliation(s)
- Fatemeh Ahmadi
- Immunology Section, Department of Experimental Medicine, Lund University, Lund, Sweden
| | - Fredrik Junghus
- Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Ashworth
- Immunology Section, Department of Experimental Medicine, Lund University, Lund, Sweden
| | - Amanda Lappalainen
- Immunology Section, Department of Experimental Medicine, Lund University, Lund, Sweden
| | - Urs Mörbe
- Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Knut Kotarsky
- Immunology Section, Department of Experimental Medicine, Lund University, Lund, Sweden
| | - William W Agace
- Immunology Section, Department of Experimental Medicine, Lund University, Lund, Sweden.,Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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5
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Kang X, Zhang K, Wang Y, Zhao Y, Lu Y. Single-cell RNA sequencing analysis of human chondrocytes reveals cell-cell communication alterations mediated by interactive signaling pathways in osteoarthritis. Front Cell Dev Biol 2023; 11:1099287. [PMID: 37082621 PMCID: PMC10112522 DOI: 10.3389/fcell.2023.1099287] [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: 11/15/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023] Open
Abstract
Objective: Osteoarthritis (OA) is a common joint disorder characterized by degenerative articular cartilage, subchondral bone remodeling, and inflammation. Increasing evidence suggests that the substantial crosstalk between cartilage and synovium is closely related to Osteoarthritis development, but the events that cause this degeneration remain unknown. This study aimed to explore the alterations in intercellular communication involved in the pathogenesis of Osteoarthritis using bioinformatics analysis. Methods: Single-cell transcriptome sequencing (scRNA-seq) profiles derived from articular cartilage tissue of patients with Osteoarthritis were downloaded from a public database. Chondrocyte heterogeneity was assessed using computational analysis, and cell type identification and clustering analysis were performed using the "FindClusters" function in the Seurat package. Intercellular communication networks, including major signaling inputs and outputs for cells, were predicted, and analyzed using CellChat. Results: Seven molecularly defined chondrocytes clusters (homeostatic chondrocytes, hypertrophic chondrocyte (HTC), pre-HTC, regulatory chondrocytes, fibro-chondrocytes (FC), pre-FC, and reparative chondrocyte) with different compositions were identified in the damaged cartilage. Compared to those in the intact cartilage, the overall cell-cell communication frequency and communication strength were remarkably increased in the damaged cartilage. The cellular communication among chondrocyte subtypes mediated by signaling pathways, such as PTN, VISFATIN, SPP1, and TGF-β, was selectively altered in Osteoarthritis. Moreover, we verified that SPP1 pathway enrichment scores increased, but VISFATIN pathway enrichment scores decreased based on the bulk rna-seq datasets in Osteoarthritis. Conclusion: Our results revealed alterations in cell-cell communication among OA-related chondrocyte subtypes that were mediated by specific signaling pathways, which might be a crucial underlying mechanism associated with Osteoarthritis progression.
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Affiliation(s)
- Xin Kang
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi'an, Shaanxi, China
| | - Kailiang Zhang
- Department of Orthopedics, The 960th Hospital of the PLA Joint Logistics Support Force, Jinan, Shandong, China
| | - Yakang Wang
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi'an, Shaanxi, China
| | - Yang Zhao
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi'an, Shaanxi, China
- *Correspondence: Yao Lu, ; Yang Zhao,
| | - Yao Lu
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi'an, Shaanxi, China
- *Correspondence: Yao Lu, ; Yang Zhao,
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6
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Selective activation and expansion of regulatory T cells using lipid encapsulated mRNA encoding a long-acting IL-2 mutein. Nat Commun 2022; 13:3866. [PMID: 35790728 PMCID: PMC9256694 DOI: 10.1038/s41467-022-31130-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 05/31/2022] [Indexed: 11/30/2022] Open
Abstract
Interleukin-2 (IL-2) is critical for regulatory T cell (Treg) function and homeostasis. At low doses, IL-2 can suppress immune pathologies by expanding Tregs that constitutively express the high affinity IL-2Rα subunit. However, even low dose IL-2, signaling through the IL2-Rβ/γ complex, may lead to the activation of proinflammatory, non-Treg T cells, so improving specificity toward Tregs may be desirable. Here we use messenger RNAs (mRNA) to encode a half-life-extended human IL-2 mutein (HSA-IL2m) with mutations promoting reliance on IL-2Rα. Our data show that IL-2 mutein subcutaneous delivery as lipid-encapsulated mRNA nanoparticles selectively activates and expands Tregs in mice and non-human primates, and also reduces disease severity in mouse models of acute graft versus host disease and experimental autoimmune encephalomyelitis. Single cell RNA-sequencing of mouse splenic CD4+ T cells identifies multiple Treg states with distinct response dynamics following IL-2 mutein treatment. Our results thus demonstrate the potential of mRNA-encoded HSA-IL2m immunotherapy to treat autoimmune diseases. IL-2 has been used to expand regulatory T (Treg) cells for treating inflammatory disorders. Here the authors test an engineered IL-2 mutein, delivered subcutaneously as mRNA, to show its increased specificity for activating and expanding Treg cells in both rodents and non-human primates, and to demonstrate its ability to suppress autoimmunity in mouse models.
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7
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Sjaastad LE, Owen DL, Tracy SI, Farrar MA. Phenotypic and Functional Diversity in Regulatory T Cells. Front Cell Dev Biol 2021; 9:715901. [PMID: 34631704 PMCID: PMC8495164 DOI: 10.3389/fcell.2021.715901] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/03/2021] [Indexed: 12/14/2022] Open
Abstract
The concept that a subset of T cells exists that specifically suppresses immune responses was originally proposed over 50 years ago. It then took the next 30 years to solidify the concept of regulatory T cells (Tregs) into the paradigm we understand today – namely a subset of CD4+ FOXP3+ T-cells that are critical for controlling immune responses to self and commensal or environmental antigens that also play key roles in promoting tissue homeostasis and repair. Expression of the transcription factor FOXP3 is a defining feature of Tregs, while the cytokine IL2 is necessary for robust Treg development and function. While our initial conception of Tregs was as a monomorphic lineage required to suppress all types of immune responses, recent work has demonstrated extensive phenotypic and functional diversity within the Treg population. In this review we address the ontogeny, phenotype, and function of the large number of distinct effector Treg subsets that have been defined over the last 15 years.
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Affiliation(s)
- Louisa E Sjaastad
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - David L Owen
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Sean I Tracy
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.,Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Michael A Farrar
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
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8
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Moorman CD, Sohn SJ, Phee H. Emerging Therapeutics for Immune Tolerance: Tolerogenic Vaccines, T cell Therapy, and IL-2 Therapy. Front Immunol 2021; 12:657768. [PMID: 33854514 PMCID: PMC8039385 DOI: 10.3389/fimmu.2021.657768] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/04/2021] [Indexed: 12/14/2022] Open
Abstract
Autoimmune diseases affect roughly 5-10% of the total population, with women affected more than men. The standard treatment for autoimmune or autoinflammatory diseases had long been immunosuppressive agents until the advent of immunomodulatory biologic drugs, which aimed at blocking inflammatory mediators, including proinflammatory cytokines. At the frontier of these biologic drugs are TNF-α blockers. These therapies inhibit the proinflammatory action of TNF-α in common autoimmune diseases such as rheumatoid arthritis, psoriasis, ulcerative colitis, and Crohn's disease. TNF-α blockade quickly became the "standard of care" for these autoimmune diseases due to their effectiveness in controlling disease and decreasing patient's adverse risk profiles compared to broad-spectrum immunosuppressive agents. However, anti-TNF-α therapies have limitations, including known adverse safety risk, loss of therapeutic efficacy due to drug resistance, and lack of efficacy in numerous autoimmune diseases, including multiple sclerosis. The next wave of truly transformative therapeutics should aspire to provide a cure by selectively suppressing pathogenic autoantigen-specific immune responses while leaving the rest of the immune system intact to control infectious diseases and malignancies. In this review, we will focus on three main areas of active research in immune tolerance. First, tolerogenic vaccines aiming at robust, lasting autoantigen-specific immune tolerance. Second, T cell therapies using Tregs (either polyclonal, antigen-specific, or genetically engineered to express chimeric antigen receptors) to establish active dominant immune tolerance or T cells (engineered to express chimeric antigen receptors) to delete pathogenic immune cells. Third, IL-2 therapies aiming at expanding immunosuppressive regulatory T cells in vivo.
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Affiliation(s)
| | | | - Hyewon Phee
- Department of Inflammation and Oncology, Amgen Research, Amgen Inc., South San Francisco, CA, United States
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9
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Huo Y, Sheng Z, Lu DR, Ellwanger DC, Li CM, Homann O, Wang S, Yin H, Ren R. Blinatumomab-induced T cell activation at single cell transcriptome resolution. BMC Genomics 2021; 22:145. [PMID: 33648458 PMCID: PMC7923532 DOI: 10.1186/s12864-021-07435-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/11/2021] [Indexed: 12/28/2022] Open
Abstract
Background Bi-specific T-cell engager (BiTE) antibody is a class of bispecific antibodies designed for cancer immunotherapy. Blinatumomab is the first approved BiTE to treat acute B cell lymphoblastic leukemia (B-ALL). It brings killer T and target B cells into close proximity, activating patient’s autologous T cells to kill malignant B cells via mechanisms such as cytolytic immune synapse formation and inflammatory cytokine production. However, the activated T-cell subtypes and the target cell-dependent T cell responses induced by blinatumomab, as well as the mechanisms of resistance to blinatumomab therapy are largely unknown. Results In this study, we performed single-cell sequencing analysis to identify transcriptional changes in T cells following blinatumomab-induced T cell activation using single cells from both, a human cell line model and a patient-derived model of blinatumomab-mediated cytotoxicity. In total, the transcriptome of 17,920 single T cells from the cell line model and 2271 single T cells from patient samples were analyzed. We found that CD8+ effector memory T cells, CD4+ central memory T cells, naïve T cells, and regulatory T cells were activated after blinatumomab treatment. Here, blinatumomab-induced transcriptional changes reflected the functional immune activity of the blinatumomab-activated T cells, including the upregulation of pathways such as the immune system, glycolysis, IFNA signaling, gap junctions, and IFNG signaling. Co-stimulatory (TNFRSF4 and TNFRSF18) and co-inhibitory (LAG3) receptors were similarly upregulated in blinatumomab-activated T cells, indicating ligand-dependent T cell functions. Particularly, B-ALL cell expression of TNFSF4, which encodes the ligand of T cell co-stimulatory receptor TNFRSF4, was found positively correlated with the response to blinatumomab treatment. Furthermore, recombinant human TNFSF4 protein enhanced the cytotoxic activity of blinatumomab against B-ALL cells. Conclusion These results reveal a target cell-dependent mechanism of T-cell activation by blinatumomab and suggest that TNFSF4 may be responsible for the resistant mechanism and a potential target for combination therapy with blinatumomab, to treat B-ALL or other B-cell malignancies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07435-2.
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Affiliation(s)
- Yi Huo
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine, Collaborative Innovation Center of Hematology, RuiJin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Building 11, No. 197, Ruijin No.2 Rd, Shanghai, 200025, P.R. China.,Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 13F, Building 2, No. 4560, Jinke Rd, Shanghai, 201210, P.R. China
| | - Zhen Sheng
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine, Collaborative Innovation Center of Hematology, RuiJin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Building 11, No. 197, Ruijin No.2 Rd, Shanghai, 200025, P.R. China.,Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 13F, Building 2, No. 4560, Jinke Rd, Shanghai, 201210, P.R. China
| | - Daniel R Lu
- Genome Analysis Unit, Amgen Research, Amgen Inc.,, South San Francisco, California, USA
| | - Daniel C Ellwanger
- Genome Analysis Unit, Amgen Research, Amgen Inc.,, South San Francisco, California, USA
| | - Chi-Ming Li
- Genome Analysis Unit, Amgen Research, Amgen Inc.,, South San Francisco, California, USA
| | - Oliver Homann
- Genome Analysis Unit, Amgen Research, Amgen Inc.,, South San Francisco, California, USA
| | - Songli Wang
- Genome Analysis Unit, Amgen Research, Amgen Inc.,, South San Francisco, California, USA
| | - Hong Yin
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 13F, Building 2, No. 4560, Jinke Rd, Shanghai, 201210, P.R. China.
| | - Ruibao Ren
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine, Collaborative Innovation Center of Hematology, RuiJin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Building 11, No. 197, Ruijin No.2 Rd, Shanghai, 200025, P.R. China.
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10
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Yamawaki TM, Lu DR, Ellwanger DC, Bhatt D, Manzanillo P, Arias V, Zhou H, Yoon OK, Homann O, Wang S, Li CM. Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling. BMC Genomics 2021; 22:66. [PMID: 33472597 PMCID: PMC7818754 DOI: 10.1186/s12864-020-07358-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/27/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Elucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. However, single-cell methods inherently suffer from limitations in the recovery of complete transcriptomes due to the prevalence of cellular and transcriptional dropout events. This issue is often compounded by limited sample availability and limited prior knowledge of heterogeneity, which can confound data interpretation. RESULTS Here, we systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes. We evaluated methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type. We observed higher mRNA detection sensitivity with the 10x Genomics 5' v1 and 3' v3 methods. We demonstrate that these methods have fewer dropout events, which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures. CONCLUSION Overall, our characterization of immune cell mixtures provides useful metrics, which can guide selection of a high-throughput single-cell RNA-seq method for profiling more complex immune-cell heterogeneity usually found in vivo.
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Affiliation(s)
- Tracy M Yamawaki
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Daniel R Lu
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Daniel C Ellwanger
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Dev Bhatt
- Oncology/Inflammation, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, United States
| | - Paolo Manzanillo
- Oncology/Inflammation, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, United States
| | - Vanessa Arias
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Hong Zhou
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Oh Kyu Yoon
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Oliver Homann
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Songli Wang
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Chi-Ming Li
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA.
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