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Huang Q, Li H, Zhang Y. A bibliometric and knowledge-map study on the treatment of hematological malignancies with CAR-T cells from 2012 to 2023. Hum Vaccin Immunother 2024; 20:2371664. [PMID: 38961667 PMCID: PMC11225924 DOI: 10.1080/21645515.2024.2371664] [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: 04/16/2024] [Accepted: 06/20/2024] [Indexed: 07/05/2024] Open
Abstract
Recently, CAR-T cell therapy in hematological malignancies has received extensive attention. The objective of this study is to gain a comprehensive understanding of the current research status, development trends, research hotspots, and emerging topics pertaining to CAR-T cells in the treatment of hematological malignancies. Articles pertaining to CAR-T cell therapy for hematological malignancies from the years 2012 to 2023 were obtained and assessed from the Web of Science Core Collection (WoSCC). A bibliometric approach was employed to conduct a scientific, comprehensive, and objective quantitative analysis, as well as a visual analysis, of this particular research domain. A comprehensive analysis was conducted on a corpus of 3643 articles, which were collaboratively authored by 72 countries and various research institutions. CAR-T cell research in treating hematological malignancies shows an increasing trend each year. Notably, the study identified the countries and institutions displaying the highest level of activity, the journals with the most citations and output, as well as the authors who garnered the highest frequency of citations and co-citations. Furthermore, the analysis successfully identified the research hotspots and highlighted six emerging topics within this domain. This study conducted a comprehensive exploration and analysis of the research status, development trends, research hotspots, and emerging topics about CAR-T cells in the treatment of hematological malignancies from 2012 to 2023. The findings of this study will serve as a valuable reference and guide for researchers seeking to delve deeper into this field and determine the future direction of their research.
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Affiliation(s)
- Qing Huang
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Huimin Li
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yuan Zhang
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, China
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2
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Wang B, Chen RQ, Li J, Roy K. Interfacing data science with cell therapy manufacturing: where we are and where we need to be. Cytotherapy 2024; 26:967-979. [PMID: 38842968 DOI: 10.1016/j.jcyt.2024.03.011] [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: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 08/25/2024]
Abstract
Although several cell-based therapies have received FDA approval, and others are showing promising results, scalable, and quality-driven reproducible manufacturing of therapeutic cells at a lower cost remains challenging. Challenges include starting material and patient variability, limited understanding of manufacturing process parameter effects on quality, complex supply chain logistics, and lack of predictive, well-understood product quality attributes. These issues can manifest as increased production costs, longer production times, greater batch-to-batch variability, and lower overall yield of viable, high-quality cells. The lack of data-driven insights and decision-making in cell manufacturing and delivery is an underlying commonality behind all these problems. Data collection and analytics from discovery, preclinical and clinical research, process development, and product manufacturing have not been sufficiently utilized to develop a "systems" understanding and identify actionable controls. Experience from other industries shows that data science and analytics can drive technological innovations and manufacturing optimization, leading to improved consistency, reduced risk, and lower cost. The cell therapy manufacturing industry will benefit from implementing data science tools, such as data-driven modeling, data management and mining, AI, and machine learning. The integration of data-driven predictive capabilities into cell therapy manufacturing, such as predicting product quality and clinical outcomes based on manufacturing data, or ensuring robustness and reliability using data-driven supply-chain modeling could enable more precise and efficient production processes and lead to better patient access and outcomes. In this review, we introduce some of the relevant computational and data science tools and how they are being or can be implemented in the cell therapy manufacturing workflow. We also identify areas where innovative approaches are required to address challenges and opportunities specific to the cell therapy industry. We conclude that interfacing data science throughout a cell therapy product lifecycle, developing data-driven manufacturing workflow, designing better data collection tools and algorithms, using data analytics and AI-based methods to better understand critical quality attributes and critical-process parameters, and training the appropriate workforce will be critical for overcoming current industry and regulatory barriers and accelerating clinical translation.
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Affiliation(s)
- Bryan Wang
- Marcus Center for Therapeutic Cell Characterization and Manufacturing, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA; NSF Engineering Research Center (ERC) for cell Manufacturing Technologies (CMaT), USA
| | - Rui Qi Chen
- H. Milton Stewart School of Industrial and Systems Engineering, Atlanta, GA, USA
| | - Jing Li
- H. Milton Stewart School of Industrial and Systems Engineering, Atlanta, GA, USA
| | - Krishnendu Roy
- NSF Engineering Research Center (ERC) for cell Manufacturing Technologies (CMaT), USA; Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Chemical and Biomolecular Engineering, School of Engineering, Vanderbilt University, Nashville, TN, USA.
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3
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Liu Z, Sun L, Zhu W, Zhu J, Wu C, Peng X, Tian H, Huang C, Zhu Z. Disulfidptosis signature predicts immune microenvironment and prognosis of gastric cancer. Biol Direct 2024; 19:65. [PMID: 39148138 PMCID: PMC11325698 DOI: 10.1186/s13062-024-00518-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 08/08/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Disulfidptosis is a newly identified mechanism of cell death triggered by disulfide stress. Thus, gaining a comprehensive understanding of the disulfidptosis signature present in gastric cancer (GC) could greatly enhance the development of personalized treatment strategies for this disease. METHODS We employed consensus clustering to identify various subtypes of disulfidptosis and examined the distinct tumor microenvironment (TME) associated with each subtype. The Disulfidptosis (Dis) score was used to quantify the subtype of disulfidptosis in each patient. Subsequently, we assessed the predictive value of Dis score in terms of GC prognosis and immune efficacy. Finally, we conducted in vitro experiments to explore the impact of Collagen X (COL10A1) on the progression of GC. RESULTS Two disulfidptosis-associated molecular subtypes (Discluster A and B) were identified, each with distinct prognosis, tumor microenvironment (TME), immune cell infiltration, and biological pathways. Discluster A, characterized by high expression of disulfidptosis genes, exhibited a high immune score but poor prognosis. Furthermore, the Dis score proved useful in predicting the prognosis and immune response in GC patients. Those in the low Dis score group showed better prognosis and increased sensitivity to immunotherapy. Finally, our experimental findings validated that downregulation of COL10A1 expression attenuates the proliferation and migration capabilities of GC cells while promoting apoptosis. CONCLUSIONS This study demonstrates that the disulfidptosis signature can assist in risk stratification and personalized treatment for patients with GC. The results offer valuable theoretical support for anti-tumor strategies.
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Affiliation(s)
- Zitao Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, MinDe Road, Nanchang, Jiangxi, P. R. China
| | - Liang Sun
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, MinDe Road, Nanchang, Jiangxi, P. R. China.
| | - Wenjie Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, MinDe Road, Nanchang, Jiangxi, P. R. China
| | - Jinfeng Zhu
- Hunan Provincial Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, Hunan, P. R. China
| | - Changlei Wu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, MinDe Road, Nanchang, Jiangxi, P. R. China
| | - Xingyu Peng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, MinDe Road, Nanchang, Jiangxi, P. R. China
| | - Huakai Tian
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P. R. China
| | - Chao Huang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, MinDe Road, Nanchang, Jiangxi, P. R. China
| | - Zhengming Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, MinDe Road, Nanchang, Jiangxi, P. R. China.
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4
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Wang L, Fang C, Kang Q, Huang W, Chen Z, Zhao W, Wang L, Wang Y, Tan K, Guo X, Xu Y, Wang S, Wang L, Qiao J, Tang Z, Yu C, Xu Y, Li Y, Yu L. Bispecific CAR-T cells targeting CD19/20 in patients with relapsed or refractory B cell non-Hodgkin lymphoma: a phase I/II trial. Blood Cancer J 2024; 14:130. [PMID: 39112452 PMCID: PMC11306243 DOI: 10.1038/s41408-024-01105-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 06/29/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024] Open
Abstract
Non-Hodgkin lymphoma (NHL) is a common malignancy in the hematologic system, and traditional therapy has limited efficacy for people with recurrent/refractory NHL (R/R NHL), especially for patients with diffuse large B cell lymphoma (DLBCL). Chimeric antigen receptor (CAR) T-cell therapy is a novel and effective immunotherapy strategy for R/R hematopoietic malignancies, but relapses can occur due to the loss of CAR-T cells in vivo or the loss of antigen. One strategy to avoid antigen loss after CAR-T cell therapy is to target one more antigen simultaneously. Tandem CAR targeting CD19 and CD22 has demonstrated the reliability of tandem CAR-T cell therapy for R/R B-ALL. This study explores the therapeutic potential of tandem CD19/20 CAR-T in the treatment of R/R B cell NHL. The efficacy and safety of autologous CD19/20 CAR-T cells in eleven R/R B cell NHL adult patients were evaluated in an open-label, single-arm trial. Most patients achieved complete response, exhibiting the efficacy and safety of tandem CD19/20 CAR-T cells. The TCR repertoire diversity of CAR-T cells decreased after infusion. The expanded TCR clones in vivo were mainly derived from TCR clones that had increased expression of genes associated with immune-related signaling pathways from the infusion product (IP). The kinetics of CAR-T cells in vivo were linked to an increase in the expression of genes related to immune response and cytolysis/cytotoxicity.
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Affiliation(s)
- Lixin Wang
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
- Shenzhen University-Haoshi Cell Therapy Institute, 155 Hong Tian Road, Bao An District, Shenzhen, 518125, China
| | - Chuling Fang
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Qingzheng Kang
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Wenfa Huang
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Ziren Chen
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Weiqiang Zhao
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Lei Wang
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Yiran Wang
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Kun Tan
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Xiao Guo
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Yuanyuan Xu
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Shuhong Wang
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Lijun Wang
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Jingqiao Qiao
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China
| | - Zhixiong Tang
- Shenzhen University-Haoshi Cell Therapy Institute, 155 Hong Tian Road, Bao An District, Shenzhen, 518125, China
- Shenzhen Haoshi Biotechnology Co, Ltd, 155 Hong Tian Road, Bao An District, Shenzhen, 518125, China
| | - Chuan Yu
- Shenzhen University-Haoshi Cell Therapy Institute, 155 Hong Tian Road, Bao An District, Shenzhen, 518125, China
- Shenzhen Haoshi Biotechnology Co, Ltd, 155 Hong Tian Road, Bao An District, Shenzhen, 518125, China
| | - Yang Xu
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yisheng Li
- Shenzhen University-Haoshi Cell Therapy Institute, 155 Hong Tian Road, Bao An District, Shenzhen, 518125, China.
- Shenzhen Haoshi Biotechnology Co, Ltd, 155 Hong Tian Road, Bao An District, Shenzhen, 518125, China.
| | - Li Yu
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen Clinical Research Center for Hematologic Disease, International Cancer Center, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Shenzhen, 518000, China.
- Shenzhen University-Haoshi Cell Therapy Institute, 155 Hong Tian Road, Bao An District, Shenzhen, 518125, China.
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5
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Gu X, Zhang Y, Zhou W, Wang F, Yan F, Gao H, Wang W. Infusion and delivery strategies to maximize the efficacy of CAR-T cell immunotherapy for cancers. Exp Hematol Oncol 2024; 13:70. [PMID: 39061100 PMCID: PMC11282638 DOI: 10.1186/s40164-024-00542-2] [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: 05/22/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has achieved substantial clinical outcomes for tumors, especially for hematological malignancies. However, extending the duration of remission, reduction of relapse for hematological malignancies and improvement of the anti-tumor efficacy for solid tumors are challenges for CAR-T cells immunotherapy. Besides the endeavors to enhance the functionality of CAR-T cell per se, optimization of the infusion and delivery strategies facilitates the breakthrough of the hurdles that limited the efficacy of this cancer immunotherapy. Here, we summarized the infusion and delivery strategies of CAR-T cell therapies under pre-clinical study, clinical trials and on-market status, through which the improvements of safety and efficacy for hematological and solid tumors were analyzed. Of note, novel infusion and delivery strategies, including local-regional infusion, biomaterials bearing the CAR-T cells and multiple infusion technique, overcome many limitations of CAR-T cell therapy. This review provides hints to determine infusion and delivery strategies of CAR-T cell cancer immunotherapy to maximize clinical benefits.
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Affiliation(s)
- Xinyu Gu
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, People's Republic of China
| | - Yalan Zhang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, People's Republic of China
| | - Weilin Zhou
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, People's Republic of China
| | - Fengling Wang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, People's Republic of China
| | - Feiyang Yan
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, People's Republic of China
| | - Haozhan Gao
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, People's Republic of China
| | - Wei Wang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, People's Republic of China.
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6
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Kaminski J, Fleming RA, Alvarez-Calderon F, Winschel MB, McGuckin C, Ho EE, Eng F, Rui X, Keskula P, Cagnin L, Charles J, Zavistaski J, Margossian SP, Kapadia MA, Rottman JB, Lane J, Baumeister SHC, Tkachev V, Shalek AK, Kean LS, Gerdemann U. B-cell-directed CAR T-cell therapy activates CD8+ cytotoxic CARneg bystander T cells in patients and nonhuman primates. Blood 2024; 144:46-60. [PMID: 38558106 DOI: 10.1182/blood.2023022717] [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: 10/19/2023] [Revised: 02/23/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024] Open
Abstract
ABSTRACT Chimeric antigen receptor (CAR) T cells hold promise as a therapy for B-cell-derived malignancies, and despite their impressive initial response rates, a significant proportion of patients ultimately experience relapse. Although recent studies have explored the mechanisms of in vivo CAR T-cell function, little is understood about the activation of surrounding CARneg bystander T cells and their potential to enhance tumor responses. We performed single-cell RNA sequencing on nonhuman primate (NHP) and patient-derived T cells to identify the phenotypic and transcriptomic hallmarks of bystander activation of CARneg T cells following B-cell-targeted CAR T-cell therapy. Using a highly translatable CD20 CAR NHP model, we observed a distinct population of activated CD8+ CARneg T cells emerging during CAR T-cell expansion. These bystander CD8+ CARneg T cells exhibited a unique transcriptional signature with upregulation of natural killer-cell markers (KIR3DL2, CD160, and KLRD1), chemokines, and chemokine receptors (CCL5, XCL1, and CCR9), and downregulation of naïve T-cell-associated genes (SELL and CD28). A transcriptionally similar population was identified in patients after a tisagenlecleucel infusion. Mechanistic studies revealed that interleukin-2 (IL-2) and IL-15 exposure induced bystander-like CD8+ T cells in a dose-dependent manner. In vitro activated and patient-derived T cells with a bystander phenotype efficiently killed leukemic cells through a T-cell receptor-independent mechanism. Collectively, to our knowledge, these data provide the first comprehensive identification and profiling of CARneg bystander CD8+ T cells following B-cell-targeting CAR T-cell therapy and suggest a novel mechanism through which CAR T-cell infusion might trigger enhanced antileukemic responses. Patient samples were obtained from the trial #NCT03369353, registered at www.ClinicalTrials.gov.
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Affiliation(s)
- James Kaminski
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ryan A Fleming
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
| | - Francesca Alvarez-Calderon
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Marlana B Winschel
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
| | - Connor McGuckin
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
| | | | | | - Xianliang Rui
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
| | - Paula Keskula
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
| | - Lorenzo Cagnin
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
| | - Joanne Charles
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
| | - Jillian Zavistaski
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
| | - Steven P Margossian
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Malika A Kapadia
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | | | - Jennifer Lane
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Susanne H C Baumeister
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Victor Tkachev
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, MA
| | - Leslie S Kean
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Ulrike Gerdemann
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
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7
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Yang GN, Sun YBY, Roberts PK, Moka H, Sung MK, Gardner-Russell J, El Wazan L, Toussaint B, Kumar S, Machin H, Dusting GJ, Parfitt GJ, Davidson K, Chong EW, Brown KD, Polo JM, Daniell M. Exploring single-cell RNA sequencing as a decision-making tool in the clinical management of Fuchs' endothelial corneal dystrophy. Prog Retin Eye Res 2024; 102:101286. [PMID: 38969166 DOI: 10.1016/j.preteyeres.2024.101286] [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: 01/17/2024] [Revised: 06/14/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has enabled the identification of novel gene signatures and cell heterogeneity in numerous tissues and diseases. Here we review the use of this technology for Fuchs' Endothelial Corneal Dystrophy (FECD). FECD is the most common indication for corneal endothelial transplantation worldwide. FECD is challenging to manage because it is genetically heterogenous, can be autosomal dominant or sporadic, and progress at different rates. Single-cell RNA sequencing has enabled the discovery of several FECD subtypes, each with associated gene signatures, and cell heterogeneity. Current FECD treatments are mainly surgical, with various Rho kinase (ROCK) inhibitors used to promote endothelial cell metabolism and proliferation following surgery. A range of emerging therapies for FECD including cell therapies, gene therapies, tissue engineered scaffolds, and pharmaceuticals are in preclinical and clinical trials. Unlike conventional disease management methods based on clinical presentations and family history, targeting FECD using scRNA-seq based precision-medicine has the potential to pinpoint the disease subtypes, mechanisms, stages, severities, and help clinicians in making the best decision for surgeries and the applications of therapeutics. In this review, we first discuss the feasibility and potential of using scRNA-seq in clinical diagnostics for FECD, highlight advances from the latest clinical treatments and emerging therapies for FECD, integrate scRNA-seq results and clinical notes from our FECD patients and discuss the potential of applying alternative therapies to manage these cases clinically.
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Affiliation(s)
- Gink N Yang
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Yu B Y Sun
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Philip Ke Roberts
- Department of Ophthalmology, Medical University Vienna, 18-20 Währinger Gürtel, Vienna, Austria
| | - Hothri Moka
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, UK
| | - Min K Sung
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, UK
| | - Jesse Gardner-Russell
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Layal El Wazan
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Bridget Toussaint
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Satheesh Kumar
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Heather Machin
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Lions Eye Donation Service, Level 7, Smorgon Family Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia
| | - Gregory J Dusting
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Geraint J Parfitt
- Mogrify Limited, 25 Cambridge Science Park Milton Road, Milton, Cambridge, UK
| | - Kathryn Davidson
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Elaine W Chong
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Department of Ophthalmology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Karl D Brown
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Jose M Polo
- Department of Anatomy and Development Biology, Monash University, Clayton, Australia
| | - Mark Daniell
- Centre for Eye Research Australia, Level 7, Peter Howson Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne and Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Lions Eye Donation Service, Level 7, Smorgon Family Wing, 32 Gisborne Street, East Melbourne, Victoria, Australia.
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8
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Shen L, Yan S, Xu A, Lan D, Jiang X, Peng Y, Wang S, Wang Z, Chen Y. Optimization of preparation method and specificity verification of cat CD19 monoclonal antibody for disease diagnosis and treatment. Heliyon 2024; 10:e33145. [PMID: 39022044 PMCID: PMC11253062 DOI: 10.1016/j.heliyon.2024.e33145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024] Open
Abstract
CD19 is a surface antigen on B cells that regulates B cell activation and proliferation, participating in B cell signaling. It is expressed in all B cell lineage tumor diseases, making CD19 a significant marker for detecting B cell tumor diseases and an important target for related immunotherapies. In recent years, with the deepening research on canine and feline diseases and the establishment of animal models, the demand for cat CD19 monoclonal antibodies (mAbs) has been steadily increasing. We successfully prepared cat CD19-specific monoclonal antibodies using a KLH-conjugated cat CD19 peptide as an antigen and optimized the antibody production method. The obtained monoclonal antibodies' molecular and cellular affinities were identified using CD19 peptides, eukaryotic overexpressed proteins, and peripheral blood mononuclear cells (PBMCs). The results indicate that the CD19-3H9 and CD19-8A7 monoclonal antibodies prepared in this study specifically bind to the CD19 molecule, demonstrating their suitability for use in ELISA, Western blot, and cell assays. This study successfully produced cat CD19 monoclonal antibodies with specificity and optimized the antibody preparation method, laying the foundation for the diagnosis and targeted drug combination therapy of B cell tumor diseases in both humans and pets.
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Affiliation(s)
- Liya Shen
- Nourse Science Centre for Pet Nutrition, Wuhu, 241200, China
- Shanghai Chowsing Pet Products Co., Ltd, Shanghai, 201702, China
- Wuhu Weishi Biotechnology Co., Ltd, Wuhu, 241204, China
| | - Shuqi Yan
- Nourse Science Centre for Pet Nutrition, Wuhu, 241200, China
- Shanghai Chowsing Pet Products Co., Ltd, Shanghai, 201702, China
- Wuhu Weishi Biotechnology Co., Ltd, Wuhu, 241204, China
| | - Aoyu Xu
- Joint Innovation Center, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Di Lan
- Nourse Science Centre for Pet Nutrition, Wuhu, 241200, China
- Shanghai Chowsing Pet Products Co., Ltd, Shanghai, 201702, China
- Wuhu Weishi Biotechnology Co., Ltd, Wuhu, 241204, China
| | - Xue Jiang
- Nourse Science Centre for Pet Nutrition, Wuhu, 241200, China
- Shanghai Chowsing Pet Products Co., Ltd, Shanghai, 201702, China
- Wuhu Weishi Biotechnology Co., Ltd, Wuhu, 241204, China
| | - Yuehan Peng
- Nourse Science Centre for Pet Nutrition, Wuhu, 241200, China
- Shanghai Chowsing Pet Products Co., Ltd, Shanghai, 201702, China
- Wuhu Weishi Biotechnology Co., Ltd, Wuhu, 241204, China
| | - Songjun Wang
- Nourse Science Centre for Pet Nutrition, Wuhu, 241200, China
- Shanghai Chowsing Pet Products Co., Ltd, Shanghai, 201702, China
- Wuhu Weishi Biotechnology Co., Ltd, Wuhu, 241204, China
| | - Zhanzhong Wang
- Nourse Science Centre for Pet Nutrition, Wuhu, 241200, China
- Shanghai Chowsing Pet Products Co., Ltd, Shanghai, 201702, China
- Wuhu Weishi Biotechnology Co., Ltd, Wuhu, 241204, China
| | - Yongyan Chen
- Joint Innovation Center, College of Life Sciences, Nankai University, Tianjin, 300071, China
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9
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Rathgeber AC, Ludwig LS, Penter L. Single-cell genomics-based immune and disease monitoring in blood malignancies. Clin Hematol Int 2024; 6:62-84. [PMID: 38884110 PMCID: PMC11180218 DOI: 10.46989/001c.117961] [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: 11/23/2023] [Accepted: 12/25/2023] [Indexed: 06/18/2024] Open
Abstract
Achieving long-term disease control using therapeutic immunomodulation is a long-standing concept with a strong tradition in blood malignancies. Besides allogeneic hematopoietic stem cell transplantation that continues to provide potentially curative treatment for otherwise challenging diagnoses, recent years have seen impressive progress in immunotherapies for leukemias and lymphomas with immune checkpoint blockade, bispecific monoclonal antibodies, and CAR T cell therapies. Despite their success, non-response, relapse, and immune toxicities remain frequent, thus prioritizing the elucidation of the underlying mechanisms and identifying predictive biomarkers. The increasing availability of single-cell genomic tools now provides a system's immunology view to resolve the molecular and cellular mechanisms of immunotherapies at unprecedented resolution. Here, we review recent studies that leverage these technological advancements for tracking immune responses, the emergence of immune resistance, and toxicities. As single-cell immune monitoring tools evolve and become more accessible, we expect their wide adoption for routine clinical applications to catalyze more precise therapeutic steering of personal immune responses.
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Affiliation(s)
- Anja C Rathgeber
- Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine
- Department of Hematology, Oncology, and Tumorimmunology Charité - Universitätsmedizin Berlin
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin
| | - Leif S Ludwig
- Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin
| | - Livius Penter
- Department of Hematology, Oncology, and Tumorimmunology Charité - Universitätsmedizin Berlin
- BIH Biomedical Innovation Academy Berlin Institute of Health at Charité - Universitätsmedizin Berlin
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10
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Dias J, Garcia J, Agliardi G, Roddie C. CAR-T cell manufacturing landscape-Lessons from the past decade and considerations for early clinical development. Mol Ther Methods Clin Dev 2024; 32:101250. [PMID: 38737799 PMCID: PMC11088187 DOI: 10.1016/j.omtm.2024.101250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
CAR-T cell therapies have consolidated their position over the last decade as an effective alternative to conventional chemotherapies for the treatment of a number of hematological malignancies. With an exponential increase in the number of commercial therapies and hundreds of phase 1 trials exploring CAR-T cell efficacy in different settings (including autoimmunity and solid tumors), demand for manufacturing capabilities in recent years has considerably increased. In this review, we explore the current landscape of CAR-T cell manufacturing and discuss some of the challenges limiting production capacity worldwide. We describe the latest technical developments in GMP production platform design to facilitate the delivery of a range of increasingly complex CAR-T cell products, and the challenges associated with translation of new scientific developments into clinical products for patients. We explore all aspects of the manufacturing process, namely early development, manufacturing technology, quality control, and the requirements for industrial scaling. Finally, we discuss the challenges faced as a small academic team, responsible for the delivery of a high number of innovative products to patients. We describe our experience in the setup of an effective bench-to-clinic pipeline, with a streamlined workflow, for implementation of a diverse portfolio of phase 1 trials.
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Affiliation(s)
- Juliana Dias
- Centre for Cell, Gene and Tissue Therapeutics, Royal Free Hospital NHS Foundation Trust, London NW3 2QG, UK
- Research Department of Haematology, Cancer Institute, University College London, London WC1E 6DD, UK
| | - John Garcia
- Centre for Cell, Gene and Tissue Therapeutics, Royal Free Hospital NHS Foundation Trust, London NW3 2QG, UK
- Research Department of Haematology, Cancer Institute, University College London, London WC1E 6DD, UK
| | - Giulia Agliardi
- Centre for Cell, Gene and Tissue Therapeutics, Royal Free Hospital NHS Foundation Trust, London NW3 2QG, UK
- Research Department of Haematology, Cancer Institute, University College London, London WC1E 6DD, UK
| | - Claire Roddie
- Research Department of Haematology, Cancer Institute, University College London, London WC1E 6DD, UK
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11
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Goto A, Moriya Y, Nakayama M, Iwasaki S, Yamamoto S. DMPK perspective on quantitative model analysis for chimeric antigen receptor cell therapy: Advances and challenges. Drug Metab Pharmacokinet 2024; 56:101003. [PMID: 38843652 DOI: 10.1016/j.dmpk.2024.101003] [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: 11/01/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 06/24/2024]
Abstract
Chimeric antigen receptor (CAR) cells are genetically engineered immune cells that specifically target tumor-associated antigens and have revolutionized cancer treatment, particularly in hematological malignancies, with ongoing investigations into their potential applications in solid tumors. This review provides a comprehensive overview of the current status and challenges in drug metabolism and pharmacokinetics (DMPK) for CAR cell therapy, specifically emphasizing on quantitative modeling and simulation (M&S). Furthermore, the recent advances in quantitative model analysis have been reviewed, ranging from clinical data characterization to mechanism-based modeling that connects in vitro and in vivo nonclinical and clinical study data. Additionally, the future perspectives and areas for improvement in CAR cell therapy translation have been reviewed. This includes using formulation quality considerations, characterization of appropriate animal models, refinement of in vitro models for bottom-up approaches, and enhancement of quantitative bioanalytical methodology. Addressing these challenges within a DMPK framework is pivotal in facilitating the translation of CAR cell therapy, ultimately enhancing the patients' lives through efficient CAR cell therapies.
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Affiliation(s)
- Akihiko Goto
- Center of Excellence for Drug Metabolism, Pharmacokinetics and Modeling, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Yuu Moriya
- Center of Excellence for Drug Metabolism, Pharmacokinetics and Modeling, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Miyu Nakayama
- Center of Excellence for Drug Metabolism, Pharmacokinetics and Modeling, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Shinji Iwasaki
- Center of Excellence for Drug Metabolism, Pharmacokinetics and Modeling, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Syunsuke Yamamoto
- Center of Excellence for Drug Metabolism, Pharmacokinetics and Modeling, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan.
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12
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Liu Z, Sun L, Peng X, Zhu J, Wu C, Zhu W, Huang C, Zhu Z. PANoptosis subtypes predict prognosis and immune efficacy in gastric cancer. Apoptosis 2024; 29:799-815. [PMID: 38347337 DOI: 10.1007/s10495-023-01931-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2023] [Indexed: 04/28/2024]
Abstract
PANoptosis is a form of inflammatory programmed cell death that is regulated by the PANoptosome. This PANoptosis possesses key characteristics of pyroptosis, apoptosis, and necroptosis, yet cannot be fully explained by any of these cell death modes. The unique nature of this cell death mechanism has garnered significant interest. However, the specific role of PANoptosis-associated features in gastric cancer (GC) is still uncertain. Patients were categorized into different PAN subtypes based on the expression of genes related to the PANoptosome. We conducted a systematic analysis to investigate the variations in prognosis and tumor microenvironment (TME) among these subtypes. Furthermore, we developed a risk score, called PANoptosis-related risk score (PANS), which is constructed from genes associated with the PANoptosis. We comprehensively analyzed the correlation between PANS and GC prognosis, TME, immunotherapy efficacy and chemotherapeutic drug sensitivity. Additionally, we performed in vitro experiments to validate the impact of Keratin 7 (KRT7) on GC. We identified two PAN subtypes (PANcluster A and B). PANoptosome genes were highly expressed in PANcluster A. PANcluster A has the characteristics of favorable prognosis, abundant infiltration of anti-tumor lymphocytes, and sensitivity to immunotherapy, thus it was categorized as an immune-inflammatory type. Meanwhile, our constructed PANS can effectively predict the prognosis and immune efficacy of GC. Patients with low PANS have a good prognosis, and have the characteristics of high tumor mutation load (TMB), high microsatellite instability (MSI), low tumor purity and sensitivity to immunotherapy. In addition, PANS can also identify suitable populations for different chemotherapy drugs. Finally, we confirmed that KRT7 is highly expressed in GC. Knocking down the expression of KRT7 significantly weakens the proliferation and migration abilities of GC cells. The models based on PANoptosis signature help to identify the TME features of GC and can effectively predict the prognosis and immune efficacy of GC. Furthermore, the experimental verification results of KRT7 provide theoretical support for anti-tumor treatment.
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Affiliation(s)
- Zitao Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Liang Sun
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Xingyu Peng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Jinfeng Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
- Hunan Provincial Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Changlei Wu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Wenjie Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Chao Huang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China.
| | - Zhengming Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 MinDe Road, Nanchang, 330006, Jiangxi, People's Republic of China.
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13
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Wang L, Jin G, Zhou Q, Liu Y, Zhao X, Li Z, Yin N, Peng M. Induction of immortal-like and functional CAR T cells by defined factors. J Exp Med 2024; 221:e20232368. [PMID: 38530240 DOI: 10.1084/jem.20232368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/10/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
Long-term antitumor efficacy of chimeric antigen receptor (CAR) T cells depends on their functional persistence in vivo. T cells with stem-like properties show better persistence, but factors conferring bona fide stemness to T cells remain to be determined. Here, we demonstrate the induction of CAR T cells into an immortal-like and functional state, termed TIF. The induction of CARTIF cells depends on the repression of two factors, BCOR and ZC3H12A, and requires antigen or CAR tonic signaling. Reprogrammed CARTIF cells possess almost infinite stemness, similar to induced pluripotent stem cells while retaining the functionality of mature T cells, resulting in superior antitumor effects. Following the elimination of target cells, CARTIF cells enter a metabolically dormant state, persisting in vivo with a saturable niche and providing memory protection. TIF represents a novel state of T cells with unprecedented stemness, which confers long-term functional persistence of CAR T cells in vivo and holds broad potential in T cell therapies.
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Affiliation(s)
- Lixia Wang
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Gang Jin
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Qiuping Zhou
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Yanyan Liu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Xiaocui Zhao
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Zhuoyang Li
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Na Yin
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Min Peng
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
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14
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Pfefferle A, Contet J, Wong K, Chen C, Verhoeyen E, Slichter CK, Schluns KS, Cursons J, Berry R, Nikolic I, Rautela J, Huntington ND. Optimisation of a primary human CAR-NK cell manufacturing pipeline. Clin Transl Immunology 2024; 13:e1507. [PMID: 38707997 PMCID: PMC11063921 DOI: 10.1002/cti2.1507] [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: 11/20/2023] [Revised: 03/20/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
Objectives Autologous chimeric antigen receptor (CAR) T-cell therapy of B-cell malignancies achieves long-term disease remission in a high fraction of patients and has triggered intense research into translating this successful approach into additional cancer types. However, the complex logistics involved in autologous CAR-T manufacturing, the compromised fitness of patient-derived T cells, the high rates of serious toxicities and the overall cost involved with product manufacturing and hospitalisation have driven innovation to overcome such hurdles. One alternative approach is the use of allogeneic natural killer (NK) cells as a source for CAR-NK cell therapy. However, this source has traditionally faced numerous manufacturing challenges. Methods To address this, we have developed an optimised expansion and transduction protocol for primary human NK cells primed for manufacturing scaling and clinical evaluation. We have performed an in-depth comparison of primary human NK cell sources as a starting material by characterising their phenotype, functionality, expansion potential and transduction efficiency at crucial timepoints of our CAR-NK manufacturing pipeline. Results We identified adult peripheral blood-derived NK cells to be the superior source for generating a CAR-NK cell product because of a higher maximum yield of CAR-expressing NK cells combined with potent natural, as well as CAR-mediated anti-tumor effector functions. Conclusions Our optimised manufacturing pipeline dramatically improves lentiviral transduction efficiency of primary human NK cells. We conclude that the exponential expansion pre- and post-transduction and high on-target cytotoxicity make peripheral blood-derived NK cells a feasible and attractive CAR-NK cell product for clinical utility.
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Affiliation(s)
- Aline Pfefferle
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
- oNKo‐Innate Pty LtdMoonee PondsVICAustralia
| | | | | | | | - Els Verhoeyen
- CIRI, Université de Lyon, INSERM U1111, ENS de LyonUniversité Lyon 1, CNRS, UMR 5308LyonFrance
- INSERM, C3MUniversité Côte d'AzurNiceFrance
| | | | | | | | | | | | - Jai Rautela
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
- oNKo‐Innate Pty LtdMoonee PondsVICAustralia
| | - Nicholas D Huntington
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
- oNKo‐Innate Pty LtdMoonee PondsVICAustralia
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15
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Rade M, Grieb N, Weiss R, Sia J, Fischer L, Born P, Boldt A, Fricke S, Franz P, Scolnick J, Venkatraman L, Xu S, Kloetzer C, Heyn S, Kubasch AS, Baber R, Wang SY, Bach E, Hoffmann S, Ussmann J, Schetschorke B, Hell S, Schwind S, Metzeler KH, Herling M, Jentzsch M, Franke GN, Sack U, Köhl U, Platzbecker U, Reiche K, Vucinic V, Merz M. Single-cell multiomic dissection of response and resistance to chimeric antigen receptor T cells against BCMA in relapsed multiple myeloma. NATURE CANCER 2024:10.1038/s43018-024-00763-8. [PMID: 38641734 DOI: 10.1038/s43018-024-00763-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/26/2024] [Indexed: 04/21/2024]
Abstract
Markers that predict response and resistance to chimeric antigen receptor (CAR) T cells in relapsed/refractory multiple myeloma are currently missing. We subjected mononuclear cells isolated from peripheral blood and bone marrow before and after the application of approved B cell maturation antigen-directed CAR T cells to single-cell multiomic analyses to identify markers associated with resistance and early relapse. Differences between responders and nonresponders were identified at the time of leukapheresis. Nonresponders showed an immunosuppressive microenvironment characterized by increased numbers of monocytes expressing the immune checkpoint molecule CD39 and suppressed CD8+ T cell and natural killer cell function. Analysis of CAR T cells showed cytotoxic and exhausted phenotypes in hyperexpanded clones compared to low/intermediate expanded clones. We identified potential immunotherapy targets on CAR T cells, like PD1, to improve their functionality and durability. Our work provides evidence that an immunosuppressive microenvironment causes resistance to CAR T cell therapies in multiple myeloma.
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Affiliation(s)
- Michael Rade
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Nora Grieb
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
- Innovation Center Computer Assisted Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Ronald Weiss
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | - Jaren Sia
- Singleron Biotechnologies, Cologne, Germany
| | - Luise Fischer
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Patrick Born
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Andreas Boldt
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | - Stephan Fricke
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | - Paul Franz
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | | | | | - Stacy Xu
- Singleron Biotechnologies, Cologne, Germany
| | - Christina Kloetzer
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Simone Heyn
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Anne Sophie Kubasch
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Ronny Baber
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- Leipzig Medical Biobank, University Leipzig, Leipzig, Germany
| | - Song Yau Wang
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Enrica Bach
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Sandra Hoffmann
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Jule Ussmann
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Birthe Schetschorke
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Saskia Hell
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Sebastian Schwind
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Klaus H Metzeler
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Marco Herling
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Madlen Jentzsch
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Georg-Nikolaus Franke
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Ulrich Sack
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | - Ulrike Köhl
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | - Uwe Platzbecker
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Kristin Reiche
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden, Leipzig, Germany
| | - Vladan Vucinic
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Maximilian Merz
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany.
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16
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Ito Y, Inoue S, Kagoya Y. Gene editing technology to improve antitumor T-cell functions in adoptive immunotherapy. Inflamm Regen 2024; 44:13. [PMID: 38468282 PMCID: PMC10926667 DOI: 10.1186/s41232-024-00324-7] [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: 01/05/2024] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Adoptive immunotherapy, in which tumor-reactive T cells are prepared in vitro for adoptive transfer to the patient, can induce an objective clinical response in specific types of cancer. In particular, chimeric antigen receptor (CAR)-redirected T-cell therapy has shown robust responses in hematologic malignancies. However, its efficacy against most of the other tumors is still insufficient, which remains an unmet medical need. Accumulating evidence suggests that modifying specific genes can enhance antitumor T-cell properties. Epigenetic factors have been particularly implicated in the remodeling of T-cell functions, including changes to dysfunctional states such as terminal differentiation and exhaustion. Genetic ablation of key epigenetic molecules prevents the dysfunctional reprogramming of T cells and preserves their functional properties.Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-based gene editing is a valuable tool to enable efficient and specific gene editing in cultured T cells. A number of studies have already identified promising targets to improve the therapeutic efficacy of CAR-T cells using genome-wide or focused CRISPR screening. In this review, we will present recent representative findings on molecular insights into T-cell dysfunction and how genetic modification contributes to overcoming it. We will also discuss several technical advances to achieve efficient gene modification using the CRISPR and other novel platforms.
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Affiliation(s)
- Yusuke Ito
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Satoshi Inoue
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yuki Kagoya
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, 160-8582, Japan.
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17
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Lin Y, Chen Y, Gan L, Li Z, Shen F. A prognostic model based on tumor microenvironment and immune cell in colorectal cancer. Scand J Gastroenterol 2024; 59:304-315. [PMID: 37978827 DOI: 10.1080/00365521.2023.2281252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is the second leading cause of cancer-related death. Immunotherapy is one of the new options for cancer treatment. This study aimed to develop an immune-related signature associated with CRC. METHODS We performed differential analysis to screen out the differentially expressed genes (DEGs) of The Cancer Genome Atlas-Colorectal Cancer (TCGA-CRC) datasets. Weighted gene co-expression network analysis (WGCNA) was performed to obtain the key module genes associated with differential immune cells. The candidate genes were obtained through overlapping key DEGs and key module genes. The univariate and multivariate Cox regression analyses were adopted to build a CRC prognostic signature. We further conducted immune feature estimation and chemotherapy analysis between two risk subgroups. Finally, we verified the expression of immune-related prognostic genes at the transcriptional level. RESULTS A total of 61 candidate genes were obtained by overlapping key DEGs and key module genes associated with differential immune cells. Then, an immune-related prognostic signature was built based on the three prognostic genes (HAMP, ADAM8, and CD1B). The independent prognostic analysis suggested that age, stage, and RiskScore could be used as independent prognostic factors. Further, we found significantly higher expression of three prognostic genes in the CRC group compared with the normal group. Finally, real-time polymerase chain reaction verified the expression of three genes in patients with CRC. CONCLUSION The prognostic signature comprising HAMP, ADAM8, and CD1B based on immune cells was established, providing a theoretical basis and reference value for the research of CRC.
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Affiliation(s)
- Yufu Lin
- Department of Oncology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Yabo Chen
- Department of General Practice, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Lu Gan
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhiyong Li
- Department of Oncology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Feng Shen
- Department of Oncology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
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18
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Ghaffari S, Saleh M, Akbari B, Ramezani F, Mirzaei HR. Applications of single-cell omics for chimeric antigen receptor T cell therapy. Immunology 2024; 171:339-364. [PMID: 38009707 DOI: 10.1111/imm.13720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy is a promising cancer treatment modality. The breakthroughs in CAR T cell therapy were, in part, possible with the help of cell analysis methods, such as single-cell analysis. Bulk analyses have provided invaluable information regarding the complex molecular dynamics of CAR T cells, but their results are an average of thousands of signals in CAR T or tumour cells. Since cancer is a heterogeneous disease where each minute detail of a subclone could change the outcome of the treatment, single-cell analysis could prove to be a powerful instrument in deciphering the secrets of tumour microenvironment for cancer immunotherapy. With the recent studies in all aspects of adoptive cell therapy making use of single-cell analysis, a comprehensive review of the recent preclinical and clinical findings in CAR T cell therapy was needed. Here, we categorized and summarized the key points of the studies in which single-cell analysis provided insights into the genomics, epigenomics, transcriptomics and proteomics as well as their respective multi-omics of CAR T cell therapy.
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Affiliation(s)
- Sasan Ghaffari
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Mahshid Saleh
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, Madison, Wisconsin, USA
| | - Behnia Akbari
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Faezeh Ramezani
- Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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19
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Haradhvala NJ, Maus MV. Understanding Mechanisms of Response to CAR T-cell Therapy through Single-Cell Sequencing: Insights and Challenges. Blood Cancer Discov 2024; 5:86-89. [PMID: 38324393 PMCID: PMC10905509 DOI: 10.1158/2643-3230.bcd-23-0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
SUMMARY Single-cell RNA sequencing has emerged as a powerful technique to understand the molecular features of chimeric antigen receptor (CAR) T cells that associate with clinical outcomes. Here we discuss the common themes that have emerged from across single-cell studies of CAR T-cell therapy, and summarize the challenges in interpreting this complex data type.
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Affiliation(s)
- Nicholas J. Haradhvala
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Marcela V. Maus
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, Massachusetts
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20
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Xia L, Lee C, Li JJ. Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nat Commun 2024; 15:1753. [PMID: 38409103 PMCID: PMC10897166 DOI: 10.1038/s41467-024-45891-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: 04/10/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) are commonly used for visualizing cell clusters; however, it is well known that t-SNE and UMAP's 2D embeddings might not reliably inform the similarities among cell clusters. Motivated by this challenge, we present a statistical method, scDEED, for detecting dubious cell embeddings output by a 2D-embedding method. By calculating a reliability score for every cell embedding based on the similarity between the cell's 2D-embedding neighbors and pre-embedding neighbors, scDEED identifies the cell embeddings with low reliability scores as dubious and those with high reliability scores as trustworthy. Moreover, by minimizing the number of dubious cell embeddings, scDEED provides intuitive guidance for optimizing the hyperparameters of an embedding method. We show the effectiveness of scDEED on multiple datasets for detecting dubious cell embeddings and optimizing the hyperparameters of t-SNE and UMAP.
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Affiliation(s)
- Lucy Xia
- Department of ISOM, School of Business and Management, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Christy Lee
- Department of Statistics and Data Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jingyi Jessica Li
- Department of Statistics and Data Science, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Radcliffe Institute of Advanced Study, Harvard University, Cambridge, MA, USA.
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21
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Liao YM, Hsu SH, Chiou SS. Harnessing the Transcriptional Signatures of CAR-T-Cells and Leukemia/Lymphoma Using Single-Cell Sequencing Technologies. Int J Mol Sci 2024; 25:2416. [PMID: 38397092 PMCID: PMC10889174 DOI: 10.3390/ijms25042416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Chimeric antigen receptor (CAR)-T-cell therapy has greatly improved outcomes for patients with relapsed or refractory hematological malignancies. However, challenges such as treatment resistance, relapse, and severe toxicity still hinder its widespread clinical application. Traditional transcriptome analysis has provided limited insights into the complex transcriptional landscape of both leukemia cells and engineered CAR-T-cells, as well as their interactions within the tumor microenvironment. However, with the advent of single-cell sequencing techniques, a paradigm shift has occurred, providing robust tools to unravel the complexities of these factors. These techniques enable an unbiased analysis of cellular heterogeneity and molecular patterns. These insights are invaluable for precise receptor design, guiding gene-based T-cell modification, and optimizing manufacturing conditions. Consequently, this review utilizes modern single-cell sequencing techniques to clarify the transcriptional intricacies of leukemia cells and CAR-Ts. The aim of this manuscript is to discuss the potential mechanisms that contribute to the clinical failures of CAR-T immunotherapy. We examine the biological characteristics of CAR-Ts, the mechanisms that govern clinical responses, and the intricacies of adverse events. By exploring these aspects, we hope to gain a deeper understanding of CAR-T therapy, which will ultimately lead to improved clinical outcomes and broader therapeutic applications.
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Affiliation(s)
- Yu-Mei Liao
- Division of Hematology-Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Shih-Hsien Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shyh-Shin Chiou
- Division of Hematology-Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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22
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Qin C, Dong MH, Zhou LQ, Wang W, Cai SB, You YF, Shang K, Xiao J, Wang D, Li CR, Zhang M, Bu BT, Tian DS, Wang W. Single-cell analysis of refractory anti-SRP necrotizing myopathy treated with anti-BCMA CAR-T cell therapy. Proc Natl Acad Sci U S A 2024; 121:e2315990121. [PMID: 38289960 PMCID: PMC10861907 DOI: 10.1073/pnas.2315990121] [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] [Accepted: 12/26/2023] [Indexed: 02/01/2024] Open
Abstract
Immune-mediated necrotizing myopathy (IMNM) is an autoimmune disorder associated with the presence of autoantibodies, characterized by severe clinical presentation with rapidly progressive muscular weakness and elevated levels of creatine kinase, while traditional pharmacological approaches possess varying and often limited effects. Considering the pathogenic role of autoantibodies, chimeric antigen receptor (CAR)-T cells targeting B cell maturation antigen (BCMA) have emerged as a promising therapeutic strategy. We reported here a patient with anti-signal recognition particle IMNM refractory to multiple available therapies, who was treated with BCMA-targeting CAR-T cells, exhibited favorable safety profiles, sustained reduction in pathogenic autoantibodies, and persistent clinical improvements over 18 mo. Longitudinal single-cell RNA, B cell receptor, T cell receptor sequencing analysis presented the normalization of immune microenvironment after CAR-T cell infusion, including reconstitution of B cell lineages, replacement of T cell subclusters, and suppression of overactivated immune cells. Analysis on characteristics of CAR-T cells in IMNM demonstrated a more active expansion of CD8+ CAR-T cells, with a dynamic phenotype shifting pattern similar in CD4+ and CD8+ CAR-T cells. A comparison of CD8+ CAR-T cells in patients with IMNM and those with malignancies collected at different timepoints revealed a more NK-like phenotype with enhanced tendency of cell death and neuroinflammation and inhibited proliferating ability of CD8+ CAR-T cells in IMNM while neuroinflammation might be the distinct characteristics. Further studies are warranted to define the molecular features of CAR-T cells in autoimmunity and to seek higher efficiency and longer persistence of CAR-T cells in treating autoimmune disorders.
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Affiliation(s)
- Chuan Qin
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan430030, China
| | - Ming-Hao Dong
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan430030, China
| | - Luo-Qi Zhou
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan430030, China
| | - Wen Wang
- Nanjing IASO Biotherapeutics Ltd., Nanjing210000, China
| | - Song-Bai Cai
- Nanjing IASO Biotherapeutics Ltd., Nanjing210000, China
| | - Yun-Fan You
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan430030, China
| | - Ke Shang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan430030, China
| | - Jun Xiao
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan430030, China
| | - Di Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Chun-Rui Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Min Zhang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan430030, China
| | - Bi-Tao Bu
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan430030, China
| | - Dai-Shi Tian
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan430030, China
| | - Wei Wang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan430030, China
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23
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Ligon JA, Ramakrishna S, Ceppi F, Calkoen FGJ, Diorio C, Davis KL, Jacoby E, Gottschalk S, Schultz LM, Capitini CM. INSPIRED Symposium Part 4B: Chimeric Antigen Receptor T Cell Correlative Studies-Established Findings and Future Priorities. Transplant Cell Ther 2024; 30:155-170. [PMID: 37863355 DOI: 10.1016/j.jtct.2023.10.012] [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: 10/03/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Chimeric antigen receptor (CAR) T cell therapy has revolutionized the treatment of B cell malignancies, with multiple CAR T cell products approved for numerous indications by regulatory agencies worldwide. However, significant work remains to be done to enhance these treatments. In March 2023, a group of experts in CAR T cell therapy assembled at the National Institutes of Health in Bethesda, Maryland at the Insights in Pediatric CAR T Cell Immunotherapy: Recent Advances and Future Directions (INSPIRED) Symposium to identify key areas for research for the coming years. In session 4B, correlative studies to be incorporated into future clinical trials and real-world settings were discussed. Active areas of research identified included (1) optimizing CAR T cell product manufacturing; (2) ensuring adequate lymphodepletion prior to CAR T cell administration; (3) overcoming immunoregulatory cells and tumor stroma present in the tumor microenvironment, particularly in solid tumors; (4) understanding tumor intrinsic properties that lead to CAR T cell immunotherapy resistance; and (5) uncovering biomarkers predictive of treatment resistance, treatment durability, or immune-related adverse events. Here we review the results of previously published clinical trials and real-world studies to summarize what is currently known about each of these topics. We then outline priorities for future research that we believe will be important for improving our understanding of CAR T cell therapy and ultimately leading to better outcomes for patients.
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Affiliation(s)
- John A Ligon
- Department of Pediatrics, Division of Hematology/Oncology, University of Florida, Gainesville, Florida; University of Florida Health Cancer Center, Gainesville, Florida.
| | - Sneha Ramakrishna
- Stanford Center for Cancer Cell Therapy, Stanford University School of Medicine, Stanford, California; Department of Pediatrics, Stanford University, Stanford, California
| | - Francesco Ceppi
- Division of Pediatrics, Department of Woman-Mother-Child, Pediatric Hematology-Oncology Unit, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Friso G J Calkoen
- Division of Pediatric Oncology, Princess Maxima Center, Utrecht, The Netherlands
| | - Caroline Diorio
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kara L Davis
- Stanford Center for Cancer Cell Therapy, Stanford University School of Medicine, Stanford, California; Department of Pediatrics, Stanford University, Stanford, California
| | - Elad Jacoby
- Pediatric Hemato-Oncology, Sheba Medical Center and Tel Aviv University, Tel Aviv, Israel
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liora M Schultz
- Stanford Center for Cancer Cell Therapy, Stanford University School of Medicine, Stanford, California; Department of Pediatrics, Stanford University, Stanford, California
| | - Christian M Capitini
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, Madison, Wisconsin
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24
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Zaninelli S, Meli C, Borleri G, Quaroni M, Pavoni C, Gaipa G, Biondi A, Introna M, Golay J, Rambaldi A, Rambaldi B. Optimization and validation of in vivo flow cytometry chimeric antigen receptor T cell detection method using CD19his indirect staining. Cytometry A 2024; 105:112-123. [PMID: 37707318 DOI: 10.1002/cyto.a.24796] [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: 06/27/2023] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/15/2023]
Abstract
CD19-targeted chimeric antigen receptor T (CAR-T) cell therapy has shown unprecedented results in patients with B cell relapsed/refractory acute lymphoblastic leukemia (R/R-ALL) and B cell non-Hodgkin lymphomas where no other curative options are available. In vivo monitoring of CAR-T cell kinetics is fundamental to understand the correlation between CAR-T cells expansion and persistence with treatment response and toxicity development. The aim of this study was to define a robust, sensitive, and universal method for CAR-T cell detection using flow cytometry. We set up and compared with each other three assays for CD19 CAR-T cell detection, all based on commercially available reagents. All methods used a recombinant human CD19 protein fragment recognized by the single-chain variable fragment of the CAR construct. The two indirect staining assays (CD19his + APC-conjugated antihistidine antibody and CD19bio + APC-conjugated antibiotin antibody) showed better sensitivity and specificity compared with the direct staining with CD19-FITC, and CD19his had a better cost-effective profile. We validated CAR detection with CD19his with parallel quantitative real-time polymerase chain reaction data and we could demonstrate a strong positive correlation. We also showed that CD19his staining can be easily included in a multicolor flow cytometry panel to achieve additional information about the cell phenotype of CAR-T cell positive subpopulations. Finally, this method can be used for different anti-CD19 CAR-T cell products and for different sample sources. These data demonstrate that detection of CAR-T cells by CD19his flow cytometry staining is a reliable, robust, and broadly applicable tool for in vivo monitoring of CAR-T cells.
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Affiliation(s)
- Silvia Zaninelli
- Division of Hematology, Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Cristian Meli
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
- Master of Science Programme in Biology Applied to Research in Biomedicine, Facoltà di Scienze e Tecnologie, Università degli Studi di Milano, Milan, Italy
| | - Gianmaria Borleri
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Michele Quaroni
- Laboratory of Cell and Gene Therapy Stefano Verri, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- M. Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Chiara Pavoni
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Giuseppe Gaipa
- Laboratory of Cell and Gene Therapy Stefano Verri, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- M. Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Andrea Biondi
- Laboratory of Cell and Gene Therapy Stefano Verri, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- M. Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Department of Pediatrics, University of Milano - Bicocca, Monza, Italy
| | - Martino Introna
- Division of Hematology, Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Josée Golay
- Division of Hematology, Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Alessandro Rambaldi
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
- Department of Oncology and Hematology, Università degli Studi di Milano, Milan, Italy
| | - Benedetta Rambaldi
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
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25
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Meng Z, Wang T, Hu Y, Ouyang H, Wang Q, Wu M, Zhou J, Lou X, Wang S, Dai J, Xia F. Macrophage Membrane-Camouflaged Aggregation-Induced Emission Nanoparticles Enhance Photodynamic-Immunotherapy to Delay Postoperative Tumor Recurrence. Adv Healthc Mater 2024; 13:e2302156. [PMID: 37838834 DOI: 10.1002/adhm.202302156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/07/2023] [Indexed: 10/16/2023]
Abstract
Surgery is a traditional tumor treatment, and immunotherapy can reduce the postoperative recurrence of tumors. However, the intrinsic limits of low responsive rate and non-tumor specificity of immunotherapy agents are still insufficient to address therapeutic demands. Herein, the macrophages membrane camouflaged nanoparticles (NPs), named M@PFC, consisting of the aggregation-induced emission photosensitizer (PF3-PPh3 ) and immune adjuvant (CpG), are reported. As the protein on the membrane interacts with the vascular cell adhesion molecule 1 (VCAM-1) of cancer cells, M@PFC efficiently transports CpG to the tumor. Meanwhile, M@PFC can evade clearance by the immune system and prolong the circulation time in vivo; thus, enhancing their accumulation in tumors. PF3-PPh3 promotes high production of reactive oxygen species (ROS) and triggers immune cell death (ICD) in tumor cells under light exposure. Importantly, CpG enrichment in tumors can stimulate tumor cells to produce immune factors to assist in enhancing ICD effects. The synergistic effect combining the PDT properties of the aggregation-induced emission (AIE)-active photosensitizer and immunotherapy properties of CpG significantly delays tumor recurrence after surgery. In conclusion, this strategy achieves the synergistic activation of the immune system for anti-tumor activity, providing a novel paradigm for the development of therapeutic nanodrugs to delay postoperative tumor recurrence.
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Affiliation(s)
- Zijuan Meng
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Tingting Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Yuxin Hu
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Hanzhi Ouyang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Quan Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Meng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430034, P. R. China
| | - Jian Zhou
- College of Material, Chemistry and Chemical Engineering, Hangzhou, Normal University, Hangzhou, 311121, P. R. China
| | - Xiaoding Lou
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
- Zhejiang Institute, China University of Geosciences, Hangzhou, 311305, P. R. China
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430034, P. R. China
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430034, P. R. China
| | - Fan Xia
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
- Zhejiang Institute, China University of Geosciences, Hangzhou, 311305, P. R. China
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26
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Chua ZM, Tajebe F, Abuwarwar M, Fletcher AL. Differential induction of T-cell tolerance by tumour fibroblast subsets. Curr Opin Immunol 2024; 86:102410. [PMID: 38237251 DOI: 10.1016/j.coi.2023.102410] [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: 08/21/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 04/22/2024]
Abstract
T-cell immunotherapy is now a first-line cancer treatment for metastatic melanoma and some lung cancer subtypes, which is a welcome clinical success. However, the response rates observed in these diseases are not yet replicated across other prominent solid tumour types, particularly stromal-rich subtypes with a complex microenvironment that suppresses infiltrating T cells. Cancer-associated fibroblasts (CAFs) are one of the most abundant and pro-pathogenic players in the tumour microenvironment, promoting tumour neogenesis, persistence and metastasis. Accumulating evidence is clear that CAFs subdue anti-tumour T-cell immunity and interfere with immunotherapy. CAFs can be grouped into different subtypes that operate synergistically to suppress T-cell function, including myofibroblastic CAFs, inflammatory CAFs and antigen-presenting CAFs, among other nomenclatures. Here, we review the mechanisms used by CAFs to induce T- cell tolerance and how these functions are likely to affect immunotherapy outcomes.
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Affiliation(s)
- Zoe Mx Chua
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Fitsumbhran Tajebe
- Department of Immunology and Molecular Biology, University of Gondar, Gondar 0000, Ethiopia
| | - Mohammed Abuwarwar
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Anne L Fletcher
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
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27
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Foley CR, Swan SL, Swartz MA. Engineering Challenges and Opportunities in Autologous Cellular Cancer Immunotherapy. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:188-198. [PMID: 38166251 PMCID: PMC11155266 DOI: 10.4049/jimmunol.2300642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 01/04/2024]
Abstract
The use of a patient's own immune or tumor cells, manipulated ex vivo, enables Ag- or patient-specific immunotherapy. Despite some clinical successes, there remain significant barriers to efficacy, broad patient population applicability, and safety. Immunotherapies that target specific tumor Ags, such as chimeric Ag receptor T cells and some dendritic cell vaccines, can mount robust immune responses against immunodominant Ags, but evolving tumor heterogeneity and antigenic downregulation can drive resistance. In contrast, whole tumor cell vaccines and tumor lysate-loaded dendritic cell vaccines target the patient's unique tumor antigenic repertoire without prior neoantigen selection; however, efficacy can be weak when lower-affinity clones dominate the T cell pool. Chimeric Ag receptor T cell and tumor-infiltrating lymphocyte therapies additionally face challenges related to genetic modification, T cell exhaustion, and immunotoxicity. In this review, we highlight some engineering approaches and opportunities to these challenges among four classes of autologous cell therapies.
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Affiliation(s)
- Colleen R. Foley
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Sheridan L. Swan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Melody A. Swartz
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
- Committee on Immunology, University of Chicago, Chicago, Illinois
- Ben May Department of Cancer Research, University of Chicago, Chicago, Illinois
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28
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Jin M, Huo D, Sun J, Hu J, Liu S, Zhan M, Zhang BZ, Huang JD. Enhancing immune responses of ESC-based TAA cancer vaccines with a novel OMV delivery system. J Nanobiotechnology 2024; 22:15. [PMID: 38166929 PMCID: PMC10763241 DOI: 10.1186/s12951-023-02273-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Embryonic stem cell (ESC)-derived epitopes can act as therapeutic tumor vaccines against different types of tumors Jin (Adv Healthc Mater 2023). However, these epitopes have poor immunogenicity and stimulate insufficient CD8+ T cell responses, which motivated us to develop a new method to deliver and enhance their effectiveness. Bacterial outer membrane vesicles (OMVs) can serve as immunoadjuvants and act as a delivery vector for tumor antigens. In the current study, we engineered a new OMV platform for the co-delivery of ESC-derived tumor antigens and immune checkpoint inhibitors (PD-L1 antibody). An engineered Staphylococcal Protein A (SpA) was created to non-specifically bind to anti-PD-L1 antibody. SpyCatcher (SpC) and SpA were fused into the cell outer membrane protein OmpA to capture SpyTag-attached peptides and PD-L1 antibody, respectively. The modified OMV was able to efficiently conjugate with ESC-derived TAAs and PD-L1 antibody (SpC-OMVs + SpT-peptides + anti-PD-L1), increasing the residence time of TAAs in the body. The results showed that the combination therapy of ESC-based TAAs and PD-L1 antibody delivered by OMV had significant inhibitory effects in mouse tumor model. Specifically, it was effective in reducing tumor growth by enhancing IFN-γ-CD8+ T cell responses and increasing the number of CD8+ memory cells and antigen-specific T cells. Overall, the new OMV delivery system is a versatile platform that can enhance the immune responses of ESC-based TAA cancer vaccines.
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Affiliation(s)
- Meiling Jin
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, China
| | - Da Huo
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, China
| | - Jingjing Sun
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, China
| | | | - Shuzhen Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, China
| | - Mingshuo Zhan
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, China
| | - Bao-Zhong Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, China
| | - Jian-Dong Huang
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, China.
- School of Biomedical Sciences, Faculty of Medicine, Li Ka Shing, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Department of Clinical Oncology, Shenzhen Key Laboratory for Cancer Metastasis and Personalized Therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
- Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen University, Guangzhou, 510120, China.
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29
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Penter L, Borji M, Nagler A, Lyu H, Lu WS, Cieri N, Maurer K, Oliveira G, Al'Khafaji AM, Garimella KV, Li S, Neuberg DS, Ritz J, Soiffer RJ, Garcia JS, Livak KJ, Wu CJ. Integrative genotyping of cancer and immune phenotypes by long-read sequencing. Nat Commun 2024; 15:32. [PMID: 38167262 PMCID: PMC10762175 DOI: 10.1038/s41467-023-44137-7] [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: 03/11/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to improve cell lineage identification. Due to constraints of short-read sequencing, current methods to detect natural genetic barcodes often require cumbersome primer panels and early commitment to targets. Here we devise a flexible long-read sequencing workflow and analysis pipeline, termed nanoranger, that starts from intermediate single-cell cDNA libraries to detect cell lineage-defining features, including single-nucleotide variants, fusion genes, isoforms, sequences of chimeric antigen and TCRs. Through systematic analysis of these classes of natural 'barcodes', we define the optimal targets for nanoranger, namely those loci close to the 5' end of highly expressed genes with transcript lengths shorter than 4 kB. As proof-of-concept, we apply nanoranger to longitudinal tracking of subclones of acute myeloid leukemia (AML) and describe the heterogeneous isoform landscape of thousands of marrow-infiltrating immune cells. We propose that enhanced cellular genotyping using nanoranger can improve the tracking of single-cell tumor and immune cell co-evolution.
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Grants
- P01 CA229092 NCI NIH HHS
- P50 CA101942 NCI NIH HHS
- UM1 CA186709 NCI NIH HHS
- U24 CA224316 NCI NIH HHS
- P01 CA066996 NCI NIH HHS
- U24 CA224331 NCI NIH HHS
- U24 CA224285 NCI NIH HHS
- R50 CA251956 NCI NIH HHS
- U24 CA224309 NCI NIH HHS
- U24 CA224319 NCI NIH HHS
- K08 CA245209 NCI NIH HHS
- This work was supported by National Institutes of Health, National Cancer Institute grant P01CA229092 (CJW), UM1CA186709 (Principal Investigator: Geoffrey Shapiro), National Cancer Institute Cancer Therapy Evaluation Program, Bristol-Myers Squibb, and LLS Therapy Accelerator Program. L.P. was supported by a research fellowship from the German Research Foundation (DFG, PE 3127/1-1) and is a Scholar of the American Society of Hematology, participant in the BIH Charité Digital Clinician Scientist Program funded by the DFG, the Charité – Universitätsmedizin Berlin, and the Berlin Institute of Health at Charité (BIH) and is supported by the Max-Eder program of the German Cancer Aid. A.A. is supported by the Broad Institute IGNITE award. K.M. is suppored by the ASCO YIA award. G.O. was supported by the Claudia Adams Barr Program for Innovative Cancer Research and by DF/HCC Kidney Cancer SPORE P50 CA101942. S.L. is supported by the National Institutes of Health, National Cancer Institute Research Specialist Award (R50CA251956). JSG is supported by the Conquer Cancer Foundation Career Development Award, Leukemia and Lymphoma Society Translational Research Program Award, and NIH K08CA245209. NCI CTEP provided study drug (Ipilimumab) support. This work was further supported by the CIMAC-CIDC Network. Scientific and financial support for the CIMAC-CIDC Network is provided through National Institutes of Health, National Cancer Institute Cooperative Agreements U24CA224319 (to the Icahn School of Medicine at Mount Sinai CIMAC), U24CA224331 (to the Dana-Farber Cancer Institute CIMAC), U24CA224285 (to the MD Anderson Cancer Center CIMAC), U24CA224309 (to the Stanford University CIMAC), and U24CA224316 (to the CIDC at Dana-Farber Cancer Institute). The CIMAC-CIDC website is found at https://cimac-network.org/.
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Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Mehdi Borji
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adi Nagler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Haoxiang Lyu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wesley S Lu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katie Maurer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aziz M Al'Khafaji
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Kiran V Garimella
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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30
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Li R, Wang J, Li X, Liang Y, Jiang Y, Zhang Y, Xu P, Deng L, Wang Z, Sun T, Wu J, Xie H, Wang Y. T-cell receptor sequencing reveals hepatocellular carcinoma immune characteristics according to Barcelona Clinic liver cancer stages within liver tissue and peripheral blood. Cancer Sci 2024; 115:94-108. [PMID: 37962061 PMCID: PMC10823291 DOI: 10.1111/cas.16013] [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: 07/02/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Analysis of T-cell receptor (TCR) repertoires in different stages of hepatocellular carcinoma (HCC) might help to elucidate its pathogenesis and progression. This study aimed to investigate TCR profiles in liver biopsies and peripheral blood mononuclear cells (PBMCs) in different Barcelona Clinic liver cancer (BCLC) stages of HCC. Ten patients in early stage (BCLC_A), 10 patients in middle stage (BCLC_B), and 10 patients in late stage (BCLC_C) cancer were prospectively enrolled. The liver tumor tissues, adjacent tissues, and PBMCs of each patient were collected and examined by TCR β sequencing. Based on the ImMunoGeneTics (IMGT) database, we aligned the V, D, J, and C gene segments and identified the frequency of CDR3 sequences and amino acids sequence. Diversity of TCR in PBMCs was higher than in both tumor tissues and adjacent tissues, regardless of BCLC stage and postoperative recurrence. TCR clonality was increased in T cells from peripheral blood in advanced HCC, compared with the early and middle stages. No statistical differences were observed between different BCLC stages, either in tumors or adjacent tissues. TCR clonality revealed no significant difference between recurrent tumor and non-recurrent tumor, therefore PBMCs was better to be representative of TCR characteristics in different stages of HCC compared to tumor tissues. Clonal expansion of T cells was associated with low risk of recurrence in HCC patients.
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Affiliation(s)
- Rui Li
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Junxiao Wang
- Interventional Radiology, The Fifth Medical CenterChinese PLA General HospitalBeijingChina
- Aerospace Medical Center, Aerospace Center HospitalPeking University Aerospace Clinical CollegeBeijingChina
| | - Xiubin Li
- Department of Urology, The Third Medical CenterChinese PLA General HospitalBeijingChina
| | - Yining Liang
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Yiyun Jiang
- Department of Pathology and Hepatology, The Fifth Medical CenterChinese PLA General HospitalBeijingChina
| | - Yuwei Zhang
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Pengfei Xu
- Hangzhou ImmuQuad BiotechnologiesHangzhouChina
| | - Ling Deng
- Hangzhou ImmuQuad BiotechnologiesHangzhouChina
| | - Zhe Wang
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Tao Sun
- Hangzhou ImmuQuad BiotechnologiesHangzhouChina
- Institute of Wenzhou, Zhejiang UniversityWenzhouChina
| | - Jian Wu
- Department of Laboratory MedicineThe Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Hui Xie
- Interventional Radiology, The Fifth Medical CenterChinese PLA General HospitalBeijingChina
| | - Yijin Wang
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
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31
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Chu GJ, Bailey CG, Nagarajah R, Sagnella SM, Adelstein S, Rasko JEJ. The 4-1BBζ costimulatory domain in chimeric antigen receptors enhances CD8+ T-cell functionality following T-cell receptor stimulation. Cancer Cell Int 2023; 23:327. [PMID: 38105188 PMCID: PMC10726568 DOI: 10.1186/s12935-023-03171-7] [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: 09/05/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Chimeric antigen receptor (CAR) T-cells have revolutionized the treatment of CD19- and B-cell maturation antigen-positive haematological malignancies. However, the effect of a CAR construct on the function of T-cells stimulated via their endogenous T-cell receptors (TCRs) has yet to be comprehensively investigated. METHODS Experiments were performed to systematically assess TCR signalling and function in CAR T-cells using anti-mesothelin human CAR T-cells as a model system. CAR T-cells expressing the CD28 or 4-1BB costimulatory endodomains were manufactured and compared to both untransduced T-cells and CAR T-cells with a non-functional endodomain. These cell products were treated with staphylococcal enterotoxin B to stimulate the TCR, and in vitro functional assays were performed by flow cytometry. RESULTS Increased proliferation, CD69 expression and IFNγ production were identified in CD8+ 4-1BBζ CAR T-cells compared to control untransduced CD8+ T-cells. These functional differences were associated with higher levels of phosphorylated ZAP70 after stimulation. In addition, these functional differences were associated with a differing immunophenotype, with a more than two-fold increase in central memory cells in CD8+ 4-1BBζ CAR T-cell products. CONCLUSION Our data indicate that the 4-1BBζ CAR enhances CD8+ TCR-mediated function. This could be beneficial if the TCR targets epitopes on malignant tissues or infectious agents, but detrimental if the TCR targets autoantigens.
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Affiliation(s)
- Gerard J Chu
- Gene and Stem Cell Therapy Program Centenary Institute, Camperdown, NSW, Australia
- Department of Clinical Immunology and Allergy, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program Centenary Institute, Camperdown, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, Camperdown, NSW, Australia
| | - Rajini Nagarajah
- Gene and Stem Cell Therapy Program Centenary Institute, Camperdown, NSW, Australia
| | - Sharon M Sagnella
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Stephen Adelstein
- Department of Clinical Immunology and Allergy, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, Camperdown, NSW, Australia.
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.
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32
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Liu Z, Sun L, Peng X, Liu S, Zhu Z, Huang C. An immunogenic cell death-related signature predicts prognosis and immunotherapy response in stomach adenocarcinoma. Apoptosis 2023; 28:1564-1583. [PMID: 37580435 DOI: 10.1007/s10495-023-01879-5] [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] [Accepted: 07/28/2023] [Indexed: 08/16/2023]
Abstract
The immunogenic cell death (ICD) is a specific type of regulatory cell death (RCD), which induces adaptive immunity against antigens of dead cells. ICDs have received increasing attention for their potential role in tumor microenvironment reprogramming and immunotherapy. However, the relationship between ICD-related features and stomach adenocarcinoma (STAD) prognosis, immune cell infiltration and immunotherapy remains unclear. Patients were divided into different ICD-related subtypes by consensus clustering. The differences in prognosis, Tumor microenvironment (TME), and immune checkpoint expression between different ICD-related subtypes were systematically assessed. Additionally, we constructed an ICD-related gene risk score (ICDRS). We systematically analyzed the correlation between ICDRS and prognosis, TME, immunotherapy response and drug sensitivity of gastric cancer. In addition, we explored the role of TGM2 in promoting gastric cancer progression through in vitro experiments. We identified three ICD-associated subtypes by consensus clustering. The ICD gene was highly expressed in Cluster B. Compared with the other two subtypes, Cluster B had better prognosis, higher immune response signaling activity, massive immune cell infiltration and lower tumor purity. Immune checkpoint (ICP) and human leukocyte antigen (HLA) related genes were also highly expressed in Cluster B. In addition, we found that ICDRS is an effective indicator for predicting the prognosis and immune efficacy of STAD. The low ICDRS group has the characteristics of good prognosis, high tumor mutation burden (TMB), high microsatellite instability (MSI), and sensitivity to immunotherapy, while the high ICDRS group is prone to immune escape and immunotherapy resistance. In addition, we found that down-regulating TGM2 gene can inhibit the proliferation and migration of gastric cancer cells through in vitro experiments. Our study found that the model based on ICD features is helpful to clarify the TME characteristics of STAD, and has important clinical significance for evaluating the prognosis and immunotherapy response of STAD patients. TGM2 plays an important role in the progression of STAD, suggesting that TGM2 can be used as a new target for the treatment of STAD.
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Affiliation(s)
- Zitao Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Liang Sun
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Xingyu Peng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Sicheng Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Zhengming Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China.
| | - Chao Huang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China.
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33
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Louie RHY, Cai C, Samir J, Singh M, Deveson IW, Ferguson JM, Amos TG, McGuire HM, Gowrishankar K, Adikari T, Balderas R, Bonomi M, Ruella M, Bishop D, Gottlieb D, Blyth E, Micklethwaite K, Luciani F. CAR + and CAR - T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies. Nat Commun 2023; 14:7767. [PMID: 38012187 PMCID: PMC10682404 DOI: 10.1038/s41467-023-43656-7] [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: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy is effective in treating B cell malignancies, but factors influencing the persistence of functional CAR+ T cells, such as product composition, patients' lymphodepletion, and immune reconstitution, are not well understood. To shed light on this issue, here we conduct a single-cell multi-omics analysis of transcriptional, clonal, and phenotypic profiles from pre- to 1-month post-infusion of CAR+ and CAR- T cells from patients from a CARTELL study (ACTRN12617001579381) who received a donor-derived 4-1BB CAR product targeting CD19. Following infusion, CAR+ T cells and CAR- T cells shows similar differentiation profiles with clonally expanded populations across heterogeneous phenotypes, demonstrating clonal lineages and phenotypic plasticity. We validate these findings in 31 patients with large B cell lymphoma treated with CD19 CAR T therapy. For these patients, we identify using longitudinal mass-cytometry data an association between NK-like subsets and clinical outcomes at 6 months with both CAR+ and CAR- T cells. These results suggest that non-CAR-derived signals can provide information about patients' immune recovery and be used as correlate of clinically relevant parameters.
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Affiliation(s)
- Raymond Hall Yip Louie
- School of Computer Science and Engineering, UNSW Sydney, Sydney, NSW, Australia
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Curtis Cai
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Jerome Samir
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | - Ira W Deveson
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | | | - Timothy G Amos
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | - Helen Marie McGuire
- Ramaciotti Facility for Human Systems Biology, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Infection, Immunity and Inflammation Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Kavitha Gowrishankar
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Thiruni Adikari
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | | | - Martina Bonomi
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- Department of Physics, University of Bologna, Bologna, Italy
| | - Marco Ruella
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - David Bishop
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - David Gottlieb
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Emily Blyth
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Kenneth Micklethwaite
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
- NSW Health Pathology Blood Transplant and Cell Therapies Laboratory - ICPMR Westmead, Sydney, NSW, Australia
| | - Fabio Luciani
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia.
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia.
- Garvan Institute for Medical Research, Sydney, NSW, Australia.
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Pu Z, Wang TB, Mou L. Revolutionizing cancer immunotherapy in solid tumor: CAR engineering and single-cell sequencing insights. Front Immunol 2023; 14:1310285. [PMID: 38090577 PMCID: PMC10712310 DOI: 10.3389/fimmu.2023.1310285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
The global increase in cancer incidence presents significant economic and societal challenges. While chimeric antigen receptor-modified T cell (CAR-T) therapy has demonstrated remarkable success in hematologic malignancies and has earned FDA approval, its translation to solid tumors encounters faces significant obstacles, primarily centered around identifying reliable tumor-associated antigens and navigating the complexities of the tumor microenvironment. Recent developments in single-cell RNA sequencing (scRNA-seq) have greatly enhanced our understanding of tumors by offering high-resolution, unbiased analysis of cellular heterogeneity and molecular patterns. These technologies have revolutionized our comprehension of tumor immunology and have led to notable progress in cancer immunotherapy. This mini-review explores the progress of chimeric antigen receptor (CAR) cell therapy in solid tumor treatment and the application of scRNA-seq at various stages following the administration of CAR cell products into the body. The advantages of scRNA-seq are poised to further advance the investigation of the biological characteristics of CAR cells in vivo, tumor immune evasion, the impact of different cellular components on clinical efficacy, the development of clinically relevant biomarkers, and the creation of new targeted drugs and combination therapy approaches. The integration of scRNA-seq with CAR therapy represents a promising avenue for future innovations in cancer immunotherapy. This synergy holds the potential to enhance the precision and efficacy of CAR cell therapies while expanding their applications to a broader range of malignancies.
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Affiliation(s)
- Zuhui Pu
- Imaging Department, Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, Guangdong, China
- MetaLife Lab, Shenzhen Institute of Translational Medicine, Shenzhen, Guangdong, China
| | - Tony Bowei Wang
- Biology Department, Skidmore College, Saratoga Springs, NY, United States
| | - Lisha Mou
- Imaging Department, Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, Guangdong, China
- MetaLife Lab, Shenzhen Institute of Translational Medicine, Shenzhen, Guangdong, China
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Liu J, Liu D, Hu G, Wang J, Chen D, Song C, Cai Y, Zhai C, Xu W. Circulating memory PD-1 +CD8 + T cells and PD-1 +CD8 +T/PD-1 +CD4 +T cell ratio predict response and outcome to immunotherapy in advanced gastric cancer patients. Cancer Cell Int 2023; 23:274. [PMID: 37974194 PMCID: PMC10655311 DOI: 10.1186/s12935-023-03137-9] [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: 06/15/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Limited benefit population of immunotherapy makes it urgent to select effective biomarkers for screening appropriate treatment population. Herein, we have investigated the predictive values of circulating CD8+ T cells and CD8+T/CD4+T cell ratio in advanced gastric cancer patients receiving immunotherapy. METHODS A retrospective cohort analysis of 187 advanced gastric cancer patients receiving sintilimab combined with oxaliplatin and capecitabine therapy in The Affiliated Xinghua People's Hospital, Medical School of Yangzhou University between December 2019 and February 2023 was conducted. The corresponding clinical outcomes of the variables were analyzed by receiver operating characteristic (ROC) curve, chi-square test, Kaplan-Meier methods and Cox proportional hazards regression models. RESULTS The optimal cutoff values for percentages of CD8+ T cells, naive CD8+ T cells (CD8+ Tn) and memory CD8+ T cells (CD8+ Tm) expressing programmed cell death -1(PD-1) as well as PD-1+CD8+T/PD-1+CD4+T cell ratio were 21.0, 21.5, 64.3 and 0.669, respectively. It was found that the mean percentages of CD8+ T and CD8+ Tm expressing PD-1 as well as PD-1+CD8+T/PD-1+CD4+T cell ratio were significantly higher in responder (R) than non-responder (NonR) advanced gastric cancer patients associated with a longer progression free survival (PFS) and overall survival (OS). We also observed this correlation in programmed cell death-ligand 1(PD-L1) combined positive score (CPS) ≥ 5 subgroups. Univariate and multivariate Cox regression analyses demonstrated that lower CD8+ T and CD8+ Tm expressing PD-1 as well as PD-1+CD8+T/PD-1+CD4+T cell ratio were independent risk factors in advanced gastric cancer patients receiving immunotherapy plus chemotherapy. CONCLUSION The circulating memory PD-1+CD8+ T cells and PD-1+CD8+T/PD-1+CD4+T cell ratio revealed high predictive values for response and prolonged survival outcomes in advanced gastric cancer patients receiving immunotherapy. Memory PD-1+CD8+ T cells and PD-1+CD8+T/PD-1+CD4+T cell ratio might be effective for screening benefit population of immunotherapy in advanced gastric cancer patients based on this preliminary evidence.
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Affiliation(s)
- Jiang Liu
- Department of Oncology, The Affiliated Xinghua People's Hospital, Medical School of Yangzhou University, 419 Ying Wu Nan Road, Xinghua, 225700, Jiangsu, People's Republic of China.
| | - Degan Liu
- Department of Oncology, The Affiliated Xinghua People's Hospital, Medical School of Yangzhou University, 419 Ying Wu Nan Road, Xinghua, 225700, Jiangsu, People's Republic of China
| | - Guangyin Hu
- Department of Oncology, The Affiliated Xinghua People's Hospital, Medical School of Yangzhou University, 419 Ying Wu Nan Road, Xinghua, 225700, Jiangsu, People's Republic of China
| | - Jingjing Wang
- Department of Oncology, The Affiliated Xinghua People's Hospital, Medical School of Yangzhou University, 419 Ying Wu Nan Road, Xinghua, 225700, Jiangsu, People's Republic of China
| | - Dadong Chen
- Department of Oncology, The Affiliated Xinghua People's Hospital, Medical School of Yangzhou University, 419 Ying Wu Nan Road, Xinghua, 225700, Jiangsu, People's Republic of China
| | - Chuanjun Song
- Department of Oncology, The Affiliated Xinghua People's Hospital, Medical School of Yangzhou University, 419 Ying Wu Nan Road, Xinghua, 225700, Jiangsu, People's Republic of China
| | - Yin Cai
- Department of Oncology, The Affiliated Xinghua People's Hospital, Medical School of Yangzhou University, 419 Ying Wu Nan Road, Xinghua, 225700, Jiangsu, People's Republic of China
| | - Chentong Zhai
- Department of Oncology, The Affiliated Xinghua People's Hospital, Medical School of Yangzhou University, 419 Ying Wu Nan Road, Xinghua, 225700, Jiangsu, People's Republic of China
| | - Wenjing Xu
- Department of Oncology, The Affiliated Xinghua People's Hospital, Medical School of Yangzhou University, 419 Ying Wu Nan Road, Xinghua, 225700, Jiangsu, People's Republic of China.
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Xia Y, Zhao Q, Shen X, Jin Y, Wang J, Zhu J, Chen L. Single-cell transcriptomic atlas throughout anti-BCMA CAR-T therapy in patients with multiple myeloma. Front Immunol 2023; 14:1278749. [PMID: 38035111 PMCID: PMC10682082 DOI: 10.3389/fimmu.2023.1278749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction The emergence of chimeric antigen receptor (CAR)-T therapy targeting B cell maturation antigen (BCMA) has improved the prognosis of patients with multiple myeloma (MM); however, the majority of patients eventually experience relapse. Methods In this study, employing the latest single-cell RNA sequencing technology, we examined 24 bone marrow or peripheral blood samples collected throughout the course of anti-BCMA CAR-T therapy, analyzing a total of 59,725 bone marrow cells and 72,479 peripheral blood cells. Results Our findings reveal that tumor cells in relapsed patient exhibit higher expression levels of HSP90B1 and HSPA5, and demonstrate significantly enriched pathways regarding endoplasmic reticulum stress and unfolded protein response. In the analysis of T cells, we observed that patient with impaired effector function and increased expression of immune checkpoints in endogenous T cell are more susceptible to relapse. Notably, T cells from both the bone marrow microenvironment and peripheral blood share highly similar biological characteristics. Discussion Overall, this study provides a comprehensive atlas of endogenous immune cells, particularly in the relatively long term, after CAR-T therapy. It offers clinical evidence for a deeper understanding of the internal environment post CAR-T treatment and for identifying mechanisms underlying relapse.
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Affiliation(s)
- Yuan Xia
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Department of Hematology, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, China
| | - Qian Zhao
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Xuxing Shen
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Yuanyuan Jin
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Jing Wang
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Jianfeng Zhu
- Department of Hematology, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, China
| | - Lijuan Chen
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
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Wu X, Zhou F, Cheng B, Tong G, Chen M, He L, Li Z, Yu S, Wang S, Lin L. Immune activity score to assess the prognosis, immunotherapy and chemotherapy response in gastric cancer and experimental validation. PeerJ 2023; 11:e16317. [PMID: 38025711 PMCID: PMC10655707 DOI: 10.7717/peerj.16317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/28/2023] [Indexed: 12/01/2023] Open
Abstract
Background Gastric cancer (GC) is an extremely heterogeneous malignancy with a complex tumor microenvironment (TME) that contributes to unsatisfactory prognosis. Methods The overall activity score for assessing the immune activity of GC patients was developed based on cancer immune cycle activity index in the Tracking Tumor Immunophenotype (TIP). Genes potentially affected by the overall activity score were screened using weighted gene co-expression network analysis (WGCNA). Based on the expression profile data of GC in The Cancer Genome Atlas (TCGA) database, COX analysis was applied to create an immune activity score (IAS). Differences in TME activity in the IAS groups were analyzed. We also evaluated the value of IAS in estimating immunotherapy and chemotherapy response based on immunotherapy cohort. Gene expression in IAS model and cell viability were determined by real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) and Cell Counting Kit-8 (CCK-8) assay, respectively. Results WGCAN analysis screened 629 overall activity score-related genes, which were mainly associated with T cell response and B cell response. COX analysis identified AKAP5, CTLA4, LRRC8C, AOAH-IT1, NPC2, RGS1 and SLC2A3 as critical genes affecting the prognosis of GC, based on which the IAS was developed. Further RT-qPCR analysis data showed that the expression of AKAP5 and CTLA4 was downregulated, while that of LRRC8C, AOAH-IT1, NPC2, RGS1 and SLC2A3 was significantly elevated in GC cell lines. Inhibition of AKAP5 increased cell viability but siAOAH-IT1 promoted viability of GC cells. IAS demonstrated excellent robustness in predicting immunotherapy outcome and GC prognosis, with low-IAS patients having better prognosis and immunotherapy. In addition, resistance to Erlotinib, Rapamycin, MG-132, Cyclopamine, AZ628, and Sorafenib was reduced in patients with low IAS. Conclusion IAS was a reliable prognostic indicator. For GC patients, IAS showed excellent robustness in predicting GC prognosis, immune activity status, immunotherapy response, and chemotherapeutic drug resistance. Our study provided novel insights into the prognostic assessment in GC.
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Affiliation(s)
- Xuan Wu
- Department of Medical Oncology, Peking University Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Shenzhen, China
- Cancer Institute of Shenzhen-PKU-HKUST Medical Center, Shenzhen, China
| | - Fengrui Zhou
- Department of Medical Oncology, Peking University Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Shenzhen, China
- Cancer Institute of Shenzhen-PKU-HKUST Medical Center, Shenzhen, China
| | - Boran Cheng
- Department of Medical Oncology, Peking University Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Shenzhen, China
- Cancer Institute of Shenzhen-PKU-HKUST Medical Center, Shenzhen, China
| | - Gangling Tong
- Department of Medical Oncology, Peking University Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Shenzhen, China
- Cancer Institute of Shenzhen-PKU-HKUST Medical Center, Shenzhen, China
| | - Minhua Chen
- Community Healthcare Center of Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Lirui He
- Department of Gastrointestinal Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zhu Li
- Department of Medical Oncology, Peking University Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Shenzhen, China
- Cancer Institute of Shenzhen-PKU-HKUST Medical Center, Shenzhen, China
| | - Shaokang Yu
- Department of Medical Oncology, Peking University Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Shenzhen, China
- Cancer Institute of Shenzhen-PKU-HKUST Medical Center, Shenzhen, China
| | - Shubin Wang
- Department of Medical Oncology, Peking University Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Shenzhen, China
- Cancer Institute of Shenzhen-PKU-HKUST Medical Center, Shenzhen, China
| | - Liping Lin
- Department of Oncology, Panyu Central Hospital, Cancer Institute of Panyu, Guangzhou, China
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Tang L, Huang ZP, Mei H, Hu Y. Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer. Mil Med Res 2023; 10:52. [PMID: 37941075 PMCID: PMC10631149 DOI: 10.1186/s40779-023-00486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023] Open
Abstract
Advances in chimeric antigen receptor (CAR)-T cell therapy have significantly improved clinical outcomes of patients with relapsed or refractory hematologic malignancies. However, progress is still hindered as clinical benefit is only available for a fraction of patients. A lack of understanding of CAR-T cell behaviors in vivo at the single-cell level impedes their more extensive application in clinical practice. Mounting evidence suggests that single-cell sequencing techniques can help perfect the receptor design, guide gene-based T cell modification, and optimize the CAR-T manufacturing conditions, and all of them are essential for long-term immunosurveillance and more favorable clinical outcomes. The information generated by employing these methods also potentially informs our understanding of the numerous complex factors that dictate therapeutic efficacy and toxicities. In this review, we discuss the reasons why CAR-T immunotherapy fails in clinical practice and what this field has learned since the milestone of single-cell sequencing technologies. We further outline recent advances in the application of single-cell analyses in CAR-T immunotherapy. Specifically, we provide an overview of single-cell studies focusing on target antigens, CAR-transgene integration, and preclinical research and clinical applications, and then discuss how it will affect the future of CAR-T cell therapy.
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Affiliation(s)
- Lu Tang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China
| | - Zhong-Pei Huang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China
| | - Heng Mei
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China.
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China.
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China.
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China.
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Li Z, Zhao L, Zhang Y, Zhu L, Mu W, Ge T, Jin J, Tan J, Cheng J, Wang J, Wang N, Zhou X, Chen L, Chang Z, Liu C, Bian Z, Liu B, Ye L, Lan Y, Huang L, Zhou J. Functional diversification and dynamics of CAR-T cells in patients with B-ALL. Cell Rep 2023; 42:113263. [PMID: 37851569 DOI: 10.1016/j.celrep.2023.113263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 08/03/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023] Open
Abstract
Understanding of cellular evolution and molecular programs of chimeric antigen receptor-engineered (CAR)-T cells post-infusion is pivotal for developing better treatment strategies. Here, we construct a longitudinal high-precision single-cell transcriptomic landscape of 7,578 CAR-T cells from 26 patients with B cell acute lymphoblastic leukemia (B-ALL) post-infusion. We molecularly identify eight CAR-T cell subtypes, including three cytotoxic subtypes with distinct kinetics and three dual-identity subtypes with non-T cell characteristics. Remarkably, long-term remission is coincident with the dominance of cytotoxic subtypes, while leukemia progression is correlated with the emergence of subtypes with B cell transcriptional profiles, which have dysfunctional features and might predict relapse. We further validate in vitro that the generation of B-featured CAR-T cells is induced by excessive tumor antigen stimulation or suppressed TCR signaling, while it is relieved by exogenous IL-12. Moreover, we define transcriptional hallmarks of CAR-T cell subtypes and reveal their molecular changes along computationally inferred cellular evolution in vivo. Collectively, these results decipher functional diversification and dynamics of peripheral CAR-T cells post-infusion.
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Affiliation(s)
- Zongcheng Li
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Senior Department of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China.
| | - Lei Zhao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Yuanyuan Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Li Zhu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Wei Mu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Tong Ge
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Jin Jin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Jiaqi Tan
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Jiali Cheng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Jue Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Na Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Xiaoxi Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Liting Chen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Zhilin Chang
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100850, China
| | - Chen Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100850, China
| | - Zhilei Bian
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Senior Department of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100850, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China.
| | - Lilin Ye
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China.
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China.
| | - Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China.
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan 432826, China; National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou 215006, China
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Bulliard Y, Andersson BS, Baysal MA, Damiano J, Tsimberidou AM. Reprogramming T cell differentiation and exhaustion in CAR-T cell therapy. J Hematol Oncol 2023; 16:108. [PMID: 37880715 PMCID: PMC10601191 DOI: 10.1186/s13045-023-01504-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
T cell differentiation is a highly regulated, multi-step process necessary for the progressive establishment of effector functions, immunological memory, and long-term control of pathogens. In response to strong stimulation, as seen in severe or chronic infections or cancer, T cells acquire a state of hypo-responsiveness known as exhaustion, limiting their effector function. Recent advances in autologous chimeric antigen receptor (CAR)-T cell therapies have revolutionized the treatment of hematologic malignancies by taking advantage of the basic principles of T cell biology to engineer products that promote long-lasting T cell response. However, many patients' malignancies remain unresponsive to treatment or are prone to recur. Discoveries in T cell biology, including the identification of key regulators of differentiation and exhaustion, offer novel opportunities to have a durable impact on the fate of CAR-T cells after infusion. Such next-generation CAR-T cell therapies and their clinical implementation may result in the next leap forward in cancer treatment for selected patients. In this context, this review summarizes the foundational principles of T cell differentiation and exhaustion and describes how they can be utilized and targeted to further improve the design and efficacy of CAR-T cell therapies.
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Affiliation(s)
| | - Borje S Andersson
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Mehmet A Baysal
- Unit 455, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Jason Damiano
- Appia Bio, 6160 Bristol Pkwy, Culver City, CA, 90230, USA
| | - Apostolia M Tsimberidou
- Unit 455, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.
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Yan KK, Condori J, Ma Z, Metais JY, Ju B, Ding L, Dhungana Y, Palmer LE, Langfitt DM, Ferrara F, Throm R, Shi H, Risch I, Bhatara S, Shaner B, Lockey TD, Talleur AC, Easton J, Meagher MM, Puck JM, Cowan MJ, Zhou S, Mamcarz E, Gottschalk S, Yu J. Integrome signatures of lentiviral gene therapy for SCID-X1 patients. SCIENCE ADVANCES 2023; 9:eadg9959. [PMID: 37801507 PMCID: PMC10558130 DOI: 10.1126/sciadv.adg9959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Lentiviral vector (LV)-based gene therapy holds promise for a broad range of diseases. Analyzing more than 280,000 vector integration sites (VISs) in 273 samples from 10 patients with X-linked severe combined immunodeficiency (SCID-X1), we discovered shared LV integrome signatures in 9 of 10 patients in relation to the genomics, epigenomics, and 3D structure of the human genome. VISs were enriched in the nuclear subcompartment A1 and integrated into super-enhancers close to nuclear pore complexes. These signatures were validated in T cells transduced with an LV encoding a CD19-specific chimeric antigen receptor. Intriguingly, the one patient whose VISs deviated from the identified integrome signatures had a distinct clinical course. Comparison of LV and gamma retrovirus integromes regarding their 3D genome signatures identified differences that might explain the lower risk of insertional mutagenesis in LV-based gene therapy. Our findings suggest that LV integrome signatures, shaped by common features such as genome organization, may affect the efficacy of LV-based cellular therapies.
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Affiliation(s)
- Koon-Kiu Yan
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jose Condori
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhijun Ma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jean-Yves Metais
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Bensheng Ju
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yogesh Dhungana
- Department of Computational Biology, 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
| | - Lance E. Palmer
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Deanna M. Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Francesca Ferrara
- Vector Development and Production Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert Throm
- Vector Development and Production Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hao Shi
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Isabel Risch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sheetal Bhatara
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Bridget Shaner
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Timothy D. Lockey
- Department of Therapeutics Production and Quality, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Aimee C. Talleur
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Michael M. Meagher
- Department of Therapeutics Production and Quality, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jennifer M. Puck
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA 94158, USA
| | - Morton J. Cowan
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA 94158, USA
| | - Sheng Zhou
- Experimental Cellular Therapeutics Laboratory, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ewelina Mamcarz
- Department of Bone Marrow Transplantation and Cellular Therapy, 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
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Calviño C, Ceballos C, Alfonso A, Jauregui P, Calleja-Cervantes ME, San Martin-Uriz P, Rodriguez-Marquez P, Martin-Mallo A, Iglesias E, Abizanda G, Rodriguez-Diaz S, Martinez-Turrillas R, Illarramendi J, Viguria MC, Redondo M, Rifon J, Villar S, Lasarte JJ, Inoges S, Lopez-Diaz de Cerio A, Hernaez M, Prosper F, Rodriguez-Madoz JR. Optimization of universal allogeneic CAR-T cells combining CRISPR and transposon-based technologies for treatment of acute myeloid leukemia. Front Immunol 2023; 14:1270843. [PMID: 37795087 PMCID: PMC10546312 DOI: 10.3389/fimmu.2023.1270843] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Despite the potential of CAR-T therapies for hematological malignancies, their efficacy in patients with relapse and refractory Acute Myeloid Leukemia has been limited. The aim of our study has been to develop and manufacture a CAR-T cell product that addresses some of the current limitations. We initially compared the phenotype of T cells from AML patients and healthy young and elderly controls. This analysis showed that T cells from AML patients displayed a predominantly effector phenotype, with increased expression of activation (CD69 and HLA-DR) and exhaustion markers (PD1 and LAG3), in contrast to the enriched memory phenotype observed in healthy donors. This differentiated and more exhausted phenotype was also observed, and corroborated by transcriptomic analyses, in CAR-T cells from AML patients engineered with an optimized CAR construct targeting CD33, resulting in a decreased in vivo antitumoral efficacy evaluated in xenograft AML models. To overcome some of these limitations we have combined CRISPR-based genome editing technologies with virus-free gene-transfer strategies using Sleeping Beauty transposons, to generate CAR-T cells depleted of HLA-I and TCR complexes (HLA-IKO/TCRKO CAR-T cells) for allogeneic approaches. Our optimized protocol allows one-step generation of edited CAR-T cells that show a similar phenotypic profile to non-edited CAR-T cells, with equivalent in vitro and in vivo antitumoral efficacy. Moreover, genomic analysis of edited CAR-T cells revealed a safe integration profile of the vector, with no preferences for specific genomic regions, with highly specific editing of the HLA-I and TCR, without significant off-target sites. Finally, the production of edited CAR-T cells at a larger scale allowed the generation and selection of enough HLA-IKO/TCRKO CAR-T cells that would be compatible with clinical applications. In summary, our results demonstrate that CAR-T cells from AML patients, although functional, present phenotypic and functional features that could compromise their antitumoral efficacy, compared to CAR-T cells from healthy donors. The combination of CRISPR technologies with transposon-based delivery strategies allows the generation of HLA-IKO/TCRKO CAR-T cells, compatible with allogeneic approaches, that would represent a promising option for AML treatment.
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MESH Headings
- Animals
- Humans
- Aged
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- T-Lymphocytes/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/metabolism
- Immunotherapy, Adoptive/methods
- Disease Models, Animal
- Hematopoietic Stem Cell Transplantation
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Affiliation(s)
- Cristina Calviño
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Candela Ceballos
- Hematology Department, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Ana Alfonso
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
| | - Patricia Jauregui
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Maria E. Calleja-Cervantes
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Computational Biology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | | | - Paula Rodriguez-Marquez
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Angel Martin-Mallo
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Elena Iglesias
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Gloria Abizanda
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | | | - Rebeca Martinez-Turrillas
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Jorge Illarramendi
- Hematology Department, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Maria C. Viguria
- Hematology Department, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Margarita Redondo
- Hematology Department, Hospital Universitario de Navarra, IdiSNA, Pamplona, Spain
| | - Jose Rifon
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
| | - Sara Villar
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Juan J. Lasarte
- Immunology and Immunotherapy Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Susana Inoges
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Immunology and Immunotherapy Department, Clinica Universidad de Navarra, Pamplona, Spain
| | - Ascension Lopez-Diaz de Cerio
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Immunology and Immunotherapy Department, Clinica Universidad de Navarra, Pamplona, Spain
| | - Mikel Hernaez
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Computational Biology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Data Science and Artificial Intelligence Institute (DATAI), Universidad de Navarra, Pamplona, Spain
| | - Felipe Prosper
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Juan R. Rodriguez-Madoz
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- Hemato-Oncology Program, Cima Universidad de Navarra, IdiSNA, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
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Xia L, Lee C, Li JJ. scDEED: a statistical method for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537839. [PMID: 37163087 PMCID: PMC10168265 DOI: 10.1101/2023.04.21.537839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-SNE and UMAP are commonly used for visualizing cell clusters; however, it is well known that t-SNE and UMAP's 2D embedding might not reliably inform the similarities among cell clusters. Motivated by this challenge, we developed a statistical method, scDEED, for detecting dubious cell embeddings output by any 2D-embedding method. By calculating a reliability score for every cell embedding, scDEED identifies the cell embeddings with low reliability scores as dubious and those with high reliability scores as trustworthy. Moreover, by minimizing the number of dubious cell embeddings, scDEED provides intuitive guidance for optimizing the hyperparameters of an embedding method. Applied to multiple scRNA-seq datasets, scDEED demonstrates its effectiveness for detecting dubious cell embeddings and optimizing the hyperparameters of t-SNE and UMAP.
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44
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Lan X, Zebley CC, Youngblood B. Cellular and molecular waypoints along the path of T cell exhaustion. Sci Immunol 2023; 8:eadg3868. [PMID: 37656775 PMCID: PMC10618911 DOI: 10.1126/sciimmunol.adg3868] [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: 12/20/2022] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
Thirty years of foundational research investigating molecular and cellular mechanisms promoting T cell exhaustion are now enabling rational design of T cell-based therapies for the treatment of chronic infections and cancer. Once described as a static cell fate, it is now well appreciated that the developmental path toward exhaustion is composed of a heterogeneous pool of cells with varying degrees of effector potential that ultimately converge on a terminally differentiated state. Recent description of the developmental stages along the differentiation trajectory of T cell exhaustion has provided insight into past immunotherapeutic success and future opportunities. Here, we discuss the hallmarks of distinct developmental stages occurring along the path to T cell dysfunction and the impact of these discrete CD8+ T cell fates on cancer immunotherapy.
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Affiliation(s)
- Xin Lan
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Caitlin C. Zebley
- Department of Immunology, 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
| | - Ben Youngblood
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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45
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Hur J, Kim H, Kim U, Kim GB, Kim J, Joo B, Cho D, Lee DS, Chung AJ. Genetically Stable and Scalable Nanoengineering of Human Primary T Cells via Cell Mechanoporation. NANO LETTERS 2023; 23:7341-7349. [PMID: 37506062 DOI: 10.1021/acs.nanolett.3c01720] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Effective tumor regression has been observed with chimeric antigen receptor (CAR) T cells; however, the development of an affordable, safe, and effective CAR-T cell treatment remains a challenge. One of the major obstacles is that the suboptimal genetic modification of T cells reduces their yield and antitumor activity, necessitating the development of a next-generation T cell engineering approach. In this study, we developed a nonviral T cell nanoengineering system that allows highly efficient delivery of diverse functional nanomaterials into primary human T cells in a genetically stable and scalable manner. Our platform leverages the unique cell deformation and restoration process induced by the intrinsic inertial flow in a microchannel to create nanopores in the cellular membrane for macromolecule internalization, leading to effective transfection with high scalability and viability. The proposed approach demonstrates considerable potential as a practical alternative technique for improving the current CAR-T cell manufacturing process.
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Affiliation(s)
- Jeongsoo Hur
- Department of Bioengineering, Korea University, Seoul 02841, Republic of Korea
| | - Hyelee Kim
- Department of Bioengineering, Korea University, Seoul 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health (PPH), Korea University, Seoul 02841, Republic of Korea
| | - Uijin Kim
- Department of Life Sciences, University of Seoul, Seoul 02504, Republic of Korea
| | - Gi-Beom Kim
- Department of Bioengineering, Korea University, Seoul 02841, Republic of Korea
- MxT Biotech, Seoul 04785, Republic of Korea
| | - Jinho Kim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06355, Republic of Korea
| | | | - Duck Cho
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06355, Republic of Korea
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 03063, Republic of Korea
| | - Dong-Sung Lee
- Department of Life Sciences, University of Seoul, Seoul 02504, Republic of Korea
| | - Aram J Chung
- Department of Bioengineering, Korea University, Seoul 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health (PPH), Korea University, Seoul 02841, Republic of Korea
- MxT Biotech, Seoul 04785, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
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46
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Strati P, Li X, Deng Q, Marques-Piubelli ML, Henderson J, Watson G, Deaton L, Cain T, Yang H, Ravanmehr V, Fayad LE, Iyer SP, Nastoupil LJ, Hagemeister FB, Parra ER, Saini N, Takahashi K, Fowler NH, Westin JR, Steiner RE, Nair R, Flowers CR, Wang L, Ahmed S, Al-Atrash G, Vega F, Neelapu SS, Green MR. Prolonged cytopenia following CD19 CAR T cell therapy is linked with bone marrow infiltration of clonally expanded IFNγ-expressing CD8 T cells. Cell Rep Med 2023; 4:101158. [PMID: 37586321 PMCID: PMC10439270 DOI: 10.1016/j.xcrm.2023.101158] [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: 10/18/2022] [Revised: 06/13/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
Autologous anti-CD19 chimeric antigen receptor T cell (CAR T) therapy is highly effective in relapsed/refractory large B cell lymphoma (rrLBCL) but is associated with toxicities that delay recovery. While the biological mechanisms of cytokine release syndrome and neurotoxicity have been investigated, the pathophysiology is poorly understood for prolonged cytopenia, defined as grade ≥3 cytopenia lasting beyond 30 days after CAR T infusion. We performed single-cell RNA sequencing of bone marrow samples from healthy donors and rrLBCL patients with or without prolonged cytopenia and identified significantly increased frequencies of clonally expanded CX3CR1hi cytotoxic T cells, expressing high interferon (IFN)-γ and cytokine signaling gene sets, associated with prolonged cytopenia. In line with this, we found that hematopoietic stem cells from these patients expressed IFN-γ response signatures. IFN-γ deregulates hematopoietic stem cell self-renewal and differentiation and can be targeted with thrombopoietin agonists or IFN-γ-neutralizing antibodies, highlighting a potential mechanism-based approach for the treatment of CAR T-associated prolonged cytopenia.
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Affiliation(s)
- Paolo Strati
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xubin Li
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qing Deng
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mario L Marques-Piubelli
- Department Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared Henderson
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Grace Watson
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Laurel Deaton
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Taylor Cain
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Haopeng Yang
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vida Ravanmehr
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luis E Fayad
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Swaminathan P Iyer
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loretta J Nastoupil
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Frederick B Hagemeister
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin R Parra
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neeraj Saini
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Koichi Takahashi
- Department Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nathan H Fowler
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason R Westin
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Raphael E Steiner
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ranjit Nair
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher R Flowers
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sairah Ahmed
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gheath Al-Atrash
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Hematopoietic Biology and Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francisco Vega
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sattva S Neelapu
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Michael R Green
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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47
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Dagar G, Gupta A, Masoodi T, Nisar S, Merhi M, Hashem S, Chauhan R, Dagar M, Mirza S, Bagga P, Kumar R, Akil ASAS, Macha MA, Haris M, Uddin S, Singh M, Bhat AA. Harnessing the potential of CAR-T cell therapy: progress, challenges, and future directions in hematological and solid tumor treatments. J Transl Med 2023; 21:449. [PMID: 37420216 PMCID: PMC10327392 DOI: 10.1186/s12967-023-04292-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023] Open
Abstract
Traditional cancer treatments use nonspecific drugs and monoclonal antibodies to target tumor cells. Chimeric antigen receptor (CAR)-T cell therapy, however, leverages the immune system's T-cells to recognize and attack tumor cells. T-cells are isolated from patients and modified to target tumor-associated antigens. CAR-T therapy has achieved FDA approval for treating blood cancers like B-cell acute lymphoblastic leukemia, large B-cell lymphoma, and multiple myeloma by targeting CD-19 and B-cell maturation antigens. Bi-specific chimeric antigen receptors may contribute to mitigating tumor antigen escape, but their efficacy could be limited in cases where certain tumor cells do not express the targeted antigens. Despite success in blood cancers, CAR-T technology faces challenges in solid tumors, including lack of reliable tumor-associated antigens, hypoxic cores, immunosuppressive tumor environments, enhanced reactive oxygen species, and decreased T-cell infiltration. To overcome these challenges, current research aims to identify reliable tumor-associated antigens and develop cost-effective, tumor microenvironment-specific CAR-T cells. This review covers the evolution of CAR-T therapy against various tumors, including hematological and solid tumors, highlights challenges faced by CAR-T cell therapy, and suggests strategies to overcome these obstacles, such as utilizing single-cell RNA sequencing and artificial intelligence to optimize clinical-grade CAR-T cells.
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Affiliation(s)
- Gunjan Dagar
- Department of Medical Oncology (Lab.), Dr. BRAIRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, Delhi, 110029, India
| | - Ashna Gupta
- Department of Medical Oncology (Lab.), Dr. BRAIRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, Delhi, 110029, India
| | - Tariq Masoodi
- Laboratory of Cancer Immunology and Genetics, Sidra Medicine, Doha, Qatar
| | - Sabah Nisar
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maysaloun Merhi
- National Center for Cancer Care and Research, Hamad Medical Corporation, 3050, Doha, Qatar
| | - Sheema Hashem
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Ravi Chauhan
- Department of Medical Oncology (Lab.), Dr. BRAIRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, Delhi, 110029, India
| | - Manisha Dagar
- Shiley Eye Institute, University of California San Diego, San Diego, CA, USA
| | - Sameer Mirza
- Department of Chemistry, College of Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Puneet Bagga
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Ammira S Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Pulwama, Jammu and Kashmir, India
| | - Mohammad Haris
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
- Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Shahab Uddin
- Laboratory Animal Research Center, Qatar University, Doha, Qatar.
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar.
| | - Mayank Singh
- Department of Medical Oncology (Lab.), Dr. BRAIRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, Delhi, 110029, India.
| | - Ajaz A Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar.
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48
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Barboy O, Katzenelenbogen Y, Shalita R, Amit I. In Synergy: Optimizing CAR T Development and Personalizing Patient Care Using Single-Cell Technologies. Cancer Discov 2023; 13:1546-1555. [PMID: 37219074 DOI: 10.1158/2159-8290.cd-23-0010] [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: 01/13/2023] [Revised: 04/02/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023]
Abstract
Chimeric antigen receptor (CAR) T therapies hold immense promise to revolutionize cancer treatment. Nevertheless, key challenges, primarily in solid tumor settings, continue to hinder the application of this technology. Understanding CAR T-cell mechanism of action, in vivo activity, and clinical implications is essential for harnessing its full therapeutic potential. Single-cell genomics and cell engineering tools are becoming increasingly effective for the comprehensive research of complex biological systems. The convergence of these two technologies can accelerate CAR T-cell development. Here, we examine the potential of applying single-cell multiomics for the development of next-generation CAR T-cell therapies. SIGNIFICANCE Although CAR T-cell therapies have demonstrated remarkable clinical results in treating cancer, their effectiveness in most patients and tumor types remains limited. Single-cell technologies, which are transforming our understanding of molecular biology, provide new opportunities to overcome the challenges of CAR T-cell therapies. Given the potential of CAR T-cell therapy to tip the balance in the fight against cancer, it is important to understand how single-cell multiomic approaches can be leveraged to develop the next generations of more effective and less toxic CAR T-cell products and to provide powerful decision-making tools for clinicians to optimize treatment and improve patient outcomes.
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Affiliation(s)
- Oren Barboy
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Rotem Shalita
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
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49
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Weng NP. Transcriptome-based measurement of CD8 + T cell age and its applications. Trends Immunol 2023; 44:542-550. [PMID: 37248098 PMCID: PMC10330598 DOI: 10.1016/j.it.2023.05.005] [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: 04/04/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/31/2023]
Abstract
The ability of T cells to undergo robust cell division in response to antigenic stimulation is essential for competent T cell function. However, this ability is reduced with aging and contributes to increased susceptibility to infectious diseases, cancers, and other diseases among older adults. To better understand T cell aging, improved measurements of age-related cellular changes in T cells are necessary. The recent development of machine learning (ML)-assisted transcriptome-based quantification of individual CD8+ T cell age represents a significant step forward in this regard. It reveals both prominent and subtle changes in gene expression and points to potential functional alterations of CD8+ T cells with aging. I argue that single-cell transcriptome-based age prediction in the immune system may have promising future applications.
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Affiliation(s)
- Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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50
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Anderson ND, Birch J, Accogli T, Criado I, Khabirova E, Parks C, Wood Y, Young MD, Porter T, Richardson R, Albon SJ, Popova B, Lopes A, Wynn R, Hough R, Gohil SH, Pule M, Amrolia PJ, Behjati S, Ghorashian S. Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia. Nat Med 2023; 29:1700-1709. [PMID: 37407840 PMCID: PMC10353931 DOI: 10.1038/s41591-023-02415-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/23/2023] [Indexed: 07/07/2023]
Abstract
In the context of relapsed and refractory childhood pre-B cell acute lymphoblastic leukemia (R/R B-ALL), CD19-targeting chimeric antigen receptor (CAR)-T cells often induce durable remissions, which requires the persistence of CAR-T cells. In this study, we systematically analyzed CD19 CAR-T cells of 10 children with R/R B-ALL enrolled in the CARPALL trial via high-throughput single-cell gene expression and T cell receptor sequencing of infusion products and serial blood and bone marrow samples up to 5 years after infusion. We show that long-lived CAR-T cells developed a CD4/CD8 double-negative phenotype with an exhausted-like memory state and distinct transcriptional signature. This persistence signature was dominant among circulating CAR-T cells in all children with a long-lived treatment response for which sequencing data were sufficient (4/4, 100%). The signature was also present across T cell subsets and clonotypes, indicating that persisting CAR-T cells converge transcriptionally. This persistence signature was also detected in two adult patients with chronic lymphocytic leukemia with decade-long remissions who received a different CD19 CAR-T cell product. Examination of single T cell transcriptomes from a wide range of healthy and diseased tissues across children and adults indicated that the persistence signature may be specific to long-lived CAR-T cells. These findings raise the possibility that a universal transcriptional signature of clinically effective, persistent CD19 CAR-T cells exists.
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Affiliation(s)
| | - Jack Birch
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Theo Accogli
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Ignacio Criado
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | | | | | | | | | | | - Rachel Richardson
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sarah J Albon
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Bilyana Popova
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Andre Lopes
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Robert Wynn
- Department of Bone Marrow Transplantation, Royal Manchester Children's Hospital, Manchester, UK
| | - Rachael Hough
- Children and Young People's Cancer Service, University College London Hospitals NHS Foundation Trust, London, UK
| | - Satyen H Gohil
- Department of Haematology, University College London Hospitals NHS Foundation Trust, London, UK
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Martin Pule
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Persis J Amrolia
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Bone Marrow Transplantation, Great Ormond Street Hospital for Children, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Sara Ghorashian
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK.
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK.
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