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Yuan J, Zhang J, Zhao B, Liu F, Liu T, Duan Y, Chen Y, Chen X, Zou Y, Zhang L, Guo Y, Yang W, Yang Y, Wei J, Zhu X, Zhang Y. Single-cell transcriptomic analysis of the immune microenvironment in pediatric acute leukemia. Cancer Lett 2024; 596:217018. [PMID: 38844062 DOI: 10.1016/j.canlet.2024.217018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/25/2024] [Accepted: 06/02/2024] [Indexed: 06/11/2024]
Abstract
Relapse and treatment resistance pose significant challenges in the management of pediatric B cell acute lymphoblastic leukemia (B-ALL) and acute myeloid leukemia (AML). The efficacy of immunotherapy in leukemia remains limited due to factors such as the immunosuppressive tumor microenvironment (TME) and lack of suitable immunotherapeutic targets. Thus, an in-depth characterization of the TME in pediatric leukemia is warranted to improve the efficacy of immunotherapy. Here, we used single-cell RNA sequencing (scRNA-seq) to characterize the TME of pediatric B-ALL and AML, focusing specifically on bone-marrow-derived T cells. Moreover, we investigated the transcriptome changes during the initiation, remission, and relapse stages of pediatric AML. Our findings revealed that specific functional expression programs correlated with fluctuations in various T cell subsets, which may be associated with AML progression and relapse. Furthermore, our analysis of cellular communication networks led to the identification of VISTA, CD244, and TIM3 as potential immunotherapeutic targets in pediatric AML. Finally, we detected elevated proportions of γδ T cells and associated functional genes in samples from pediatric patients diagnosed with B-ALL and AML, which could inform the development of novel therapeutic approaches, potentially focusing on γδ T cells.
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Affiliation(s)
- Jiapei Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China.
| | - Jingliao Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Beibei Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Fang Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Tianfeng Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Yongjuan Duan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Yumei Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Xiaojuan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Yao Zou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Li Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Ye Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Wenyu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China
| | - Yang Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China; Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Family Planning, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jun Wei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China.
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China.
| | - Yingchi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College., Tianjin, China.
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2
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Lenk L, Baccelli I, Laqua A, Heymann J, Reimer C, Dietterle A, Winterberg D, Mary C, Corallo F, Taurelle J, Narbeburu E, Neyton S, Déramé M, Pengam S, Vogiatzi F, Bornhauser B, Bourquin JP, Raffel S, Dovhan V, Schüler T, Escherich G, den Boer ML, Boer JM, Wessels W, Peipp M, Alten J, Antić Ž, Bergmann AK, Schrappe M, Cario G, Brüggemann M, Poirier N, Schewe DM. The IL-7R antagonist lusvertikimab reduces leukemic burden in xenograft ALL via antibody-dependent cellular phagocytosis. Blood 2024; 143:2735-2748. [PMID: 38518105 DOI: 10.1182/blood.2023021088] [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: 05/08/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 03/24/2024] Open
Abstract
ABSTRACT Acute lymphoblastic leukemia (ALL) arises from the uncontrolled proliferation of B-cell precursors (BCP-ALL) or T cells (T-ALL). Current treatment protocols obtain high cure rates in children but are based on toxic polychemotherapy. Novel therapies are urgently needed, especially in relapsed/refractory (R/R) disease, high-risk (HR) leukemias and T-ALL, in which immunotherapy approaches remain scarce. Although the interleukin-7 receptor (IL-7R) plays a pivotal role in ALL development, no IL-7R-targeting immunotherapy has yet reached clinical application in ALL. The IL-7Rα chain (CD127)-targeting IgG4 antibody lusvertikimab (LUSV; formerly OSE-127) is a full antagonist of the IL-7R pathway, showing a good safety profile in healthy volunteers. Here, we show that ∼85% of ALL cases express surface CD127. We demonstrate significant in vivo efficacy of LUSV immunotherapy in a heterogeneous cohort of BCP- and T-ALL patient-derived xenografts (PDX) in minimal residual disease (MRD) and overt leukemia models, including R/R and HR leukemias. Importantly, LUSV was particularly effective when combined with polychemotherapy in a phase 2-like PDX study with CD127high samples leading to MRD-negativity in >50% of mice treated with combination therapy. Mechanistically, LUSV targeted ALL cells via a dual mode of action comprising direct IL-7R antagonistic activity and induction of macrophage-mediated antibody-dependent cellular phagocytosis (ADCP). LUSV-mediated in vitro ADCP levels significantly correlated with CD127 expression levels and the reduction of leukemia burden upon treatment of PDX animals in vivo. Altogether, through its dual mode of action and good safety profile, LUSV may represent a novel immunotherapy option for any CD127+ ALL, particularly in combination with standard-of-care polychemotherapy.
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MESH Headings
- Animals
- Humans
- Mice
- Xenograft Model Antitumor Assays
- Receptors, Interleukin-7/antagonists & inhibitors
- Mice, SCID
- Phagocytosis/drug effects
- Interleukin-7 Receptor alpha Subunit
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Female
- Mice, Inbred NOD
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Monoclonal, Humanized/pharmacology
- Cell Line, Tumor
- Antineoplastic Agents, Immunological/pharmacology
- Antineoplastic Agents, Immunological/therapeutic use
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Affiliation(s)
- Lennart Lenk
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | - Anna Laqua
- Department of Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Julia Heymann
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Claas Reimer
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Anna Dietterle
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Dorothee Winterberg
- Division of Antibody-Based Immunotherapy, Department of Medicine II, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | | | | | | | | | | | | | - Fotini Vogiatzi
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Beat Bornhauser
- Department of Pediatric Hematology/Oncology, University Children's Hospital, Zurich, Switzerland
| | - Jean-Pierre Bourquin
- Department of Pediatric Hematology/Oncology, University Children's Hospital, Zurich, Switzerland
| | - Simon Raffel
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vladyslava Dovhan
- Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Gabriele Escherich
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Wiebke Wessels
- Department of Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Matthias Peipp
- Division of Antibody-Based Immunotherapy, Department of Medicine II, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Julia Alten
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Željko Antić
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Anke K Bergmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Martin Schrappe
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Gunnar Cario
- Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Monika Brüggemann
- Department of Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Denis M Schewe
- Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
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3
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Hu Z, Jia Z, Liu J, Mao A, Han H, Gu Z. MD-ALL: an integrative platform for molecular diagnosis of B-acute lymphoblastic leukemia. Haematologica 2024; 109:1741-1754. [PMID: 37981856 PMCID: PMC11141650 DOI: 10.3324/haematol.2023.283706] [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: 06/07/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023] Open
Abstract
B-acute lymphoblastic leukemia (B-ALL) consists of dozens of subtypes defined by distinct gene expression profiles (GEP) and various genetic lesions. With the application of transcriptome sequencing (RNA sequencing [RNA-seq]), multiple novel subtypes have been identified, which lead to an advanced B-ALL classification and risk-stratification system. However, the complexity of analyzing RNA-seq data for B-ALL classification hinders the implementation of the new B-ALL taxonomy. Here, we introduce Molecular Diagnosis of Acute Lymphoblastic Leukemia (MD-ALL), an integrative platform featuring sensitive and accurate B-ALL classification based on GEP and sentinel genetic alterations from RNA-seq data. In this study, we systematically analyzed 2,955 B-ALL RNA-seq samples and generated a reference dataset representing all the reported B-ALL subtypes. Using multiple machine learning algorithms, we identified the feature genes and then established highly sensitive and accurate models for B-ALL classification using either bulk or single-cell RNA-seq data. Importantly, this platform integrates multiple aspects of key genetic lesions acquired from RNA-seq data, which include sequence mutations, large-scale copy number variations, and gene rearrangements, to perform comprehensive and definitive B-ALL classification. Through validation in a hold-out cohort of 974 samples, our models demonstrated superior performance for B-ALL classification compared with alternative tools. Moreover, to ensure accessibility and user-friendly navigation even for users with limited or no programming background, we developed an interactive graphical user interface for this MD-ALL platform, using the R Shiny package. In summary, MD-ALL is a user-friendly B-ALL classification platform designed to enable integrative, accurate, and comprehensive B-ALL subtype classification. MD-ALL is available from https://github.com/gu-lab20/MD-ALL.
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Affiliation(s)
- Zunsong Hu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | - Zhilian Jia
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | - Jiangyue Liu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, CA, USA; Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA
| | - Allen Mao
- Research Informatics, City of Hope National Medical Center, Duarte, CA
| | - Helen Han
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA.
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4
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Shi S, Xing H, Xu X, Chai J, Lu Z, Wang J, Wang B. CXCR6 defines therapeutic subtypes of CD4 + cytotoxic T cell lineage for adoptive cell transfer therapy in pediatric B cell acute lymphoblastic leukemia. Int Immunopharmacol 2024; 132:111972. [PMID: 38569429 DOI: 10.1016/j.intimp.2024.111972] [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: 01/16/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
The potential of cytotoxic CD4+ T cells and tissue resident memory T cells (Trm) in achieving adult leukemia remission have been highlighted [1,2]. We hypothesized that CXCR6 could serve as a marker for cytotoxic CD4+ Trm cells in the bone marrow (BM) of pediatric B-ALL patients. Flow cytometry (FCM) and published single cell RNA sequencing (scRNA-seq) datasets were employed to characterize CXCR6+CD4+ T cells in the BM and peripheral blood (PB) of pediatric B-ALL patients and healthy donors. FCM, scRNA-seq and co-culture were utilized to explore the cytotoxicity of CXCR6+CD4+ T cells in vitro based on in vitro induction of CXCR6+CD4+ T cells using tumor antigens and peripheral blood mononuclear cells (PBMCs). The ssGSEA based on the cell markers identified according to the in vivo scRNA-seq data, the TARGET-ALL-P2 datasets, and integrated machine learning algorithm were employed to figure out the key cells with prognostic values, followed by simulation of adoptive cell transfer therapy (ACT). Integrated machine learning identified the high-risk cells for disease free survival, and overall survival, while simulation of ACT therapy using CXCR6+CD4+T cells indicated that CXCR6+CD4+ T cells could remodel the bone marrow microenvironments towards anti-tumor. Based on the expression of genes involved in formation of resident memory T cells, CXCR6 is not a marker of resident memory CD4+T cells but defines therapeutic subtypes of CD4+ cytotoxic T cell lineage for pediatric B-ALL.
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Affiliation(s)
- Shaojie Shi
- Department of Immunology, Binzhou Medical University, Yantai, China
| | - Haiyan Xing
- Department of Allergy, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, China
| | - Xiangping Xu
- Department of Immunology, Binzhou Medical University, Yantai, China
| | - Jinquan Chai
- Department of Immunology, Binzhou Medical University, Yantai, China
| | - Zixuan Lu
- Department of Immunology, Binzhou Medical University, Yantai, China
| | - Jianyong Wang
- Department of Pediatrics, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, China.
| | - Bin Wang
- Department of Immunology, Binzhou Medical University, Yantai, China.
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5
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Ma L, Ramasubramanian R, Mehta N, Cossette B, Morgan D, Sukaj I, Bergaggio E, Kadauke S, Myers R, Paruzzo L, Ghilardi G, Grzywa T, Cozzone A, Schuster S, Frey N, Zhang L, Yousefpour P, Abraham W, Suh H, Ruella M, Grupp S, Chiarle R, Wittrup KD, Irvine DJ. Directed evolution-based discovery of ligands for in vivo restimulation of CAR-T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589780. [PMID: 38659938 PMCID: PMC11042270 DOI: 10.1101/2024.04.16.589780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Chimeric antigen receptor (CAR) T cell therapy targeting CD19 elicits remarkable clinical efficacy in B-cell malignancies, but many patients relapse due to failed expansion and/or progressive loss of CAR-T cells. We recently reported a strategy to potently restimulate CAR-T cells in vivo, enhancing their functionality by administration of a vaccine-like stimulus comprised of surrogate peptide ligands for a CAR linked to a lymph node-targeting amphiphilic PEG-lipid (termed CAR-T-vax). Here, we demonstrate a general strategy to generate and optimize peptide mimotopes enabling CAR-T-vax generation for any CAR. Using the clinical CD19 CAR FMC63 as a test case, we employed yeast surface display to identify peptide binders to soluble IgG versions of FMC63, which were subsequently affinity matured by directed evolution. CAR-T vaccines using these optimized mimotopes triggered marked expansion of both murine CD19 CAR-T cells in a syngeneic model and human CAR-T cells in a humanized mouse model of B cell acute lymphoblastic leukemia (B-ALL), and enhanced control of leukemia progression. This approach thus enables vaccine boosting to be applied to any clinically-relevant CAR-T cell product.
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6
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Wu CH, Weng TF, Li JP, Wu KH. Biology and Therapeutic Properties of Mesenchymal Stem Cells in Leukemia. Int J Mol Sci 2024; 25:2527. [PMID: 38473775 DOI: 10.3390/ijms25052527] [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: 01/07/2024] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
This comprehensive review delves into the multifaceted roles of mesenchymal stem cells (MSCs) in leukemia, focusing on their interactions within the bone marrow microenvironment and their impact on leukemia pathogenesis, progression, and treatment resistance. MSCs, characterized by their ability to differentiate into various cell types and modulate the immune system, are integral to the BM niche, influencing hematopoietic stem cell maintenance and functionality. This review extensively explores the intricate relationship between MSCs and leukemic cells in acute myeloid leukemia, acute lymphoblastic leukemia, chronic myeloid leukemia, and chronic lymphocytic leukemia. This review also addresses the potential clinical applications of MSCs in leukemia treatment. MSCs' role in hematopoietic stem cell transplantation, their antitumor effects, and strategies to disrupt chemo-resistance are discussed. Despite their therapeutic potential, the dual nature of MSCs in promoting and inhibiting tumor growth poses significant challenges. Further research is needed to understand MSCs' biological mechanisms in hematologic malignancies and develop targeted therapeutic strategies. This in-depth exploration of MSCs in leukemia provides crucial insights for advancing treatment modalities and improving patient outcomes in hematologic malignancies.
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Affiliation(s)
- Cheng-Hsien Wu
- School of Medicine, National Defense Medical Center, Taipei 114, Taiwan
| | - Te-Fu Weng
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung 402, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan
| | - Ju-Pi Li
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung 402, Taiwan
- Department of Pathology, School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan
| | - Kang-Hsi Wu
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung 402, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan
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7
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Jin W, Dai Y, Chen L, Zhu H, Dong F, Zhu H, Meng G, Li J, Chen S, Chen Z, Fang H, Wang K. Cellular hierarchy insights reveal leukemic stem-like cells and early death risk in acute promyelocytic leukemia. Nat Commun 2024; 15:1423. [PMID: 38365836 PMCID: PMC10873341 DOI: 10.1038/s41467-024-45737-7] [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: 04/20/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
Acute promyelocytic leukemia (APL) represents a paradigm for targeted differentiation therapy, with a minority of patients experiencing treatment failure and even early death. We here report a comprehensive single-cell analysis of 16 APL patients, uncovering cellular compositions and their impact on all-trans retinoic acid (ATRA) response in vivo and early death. We unveil a cellular differentiation hierarchy within APL blasts, rooted in leukemic stem-like cells. The oncogenic PML/RARα fusion protein exerts branch-specific regulation in the APL trajectory, including stem-like cells. APL cohort analysis establishes an association of leukemic stemness with elevated white blood cell counts and FLT3-ITD mutations. Furthermore, we construct an APL-specific stemness score, which proves effective in assessing early death risk. Finally, we show that ATRA induces differentiation of primitive blasts and patients with early death exhibit distinct stemness-associated transcriptional programs. Our work provides a thorough survey of APL cellular hierarchies, offering insights into cellular dynamics during targeted therapy.
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Affiliation(s)
- Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Honghu Zhu
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Fangyi Dong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hongming Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guoyu Meng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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8
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Liu J, Jiang P, Lu Z, Yu Z, Qian P. Decoding leukemia at the single-cell level: clonal architecture, classification, microenvironment, and drug resistance. Exp Hematol Oncol 2024; 13:12. [PMID: 38291542 PMCID: PMC10826069 DOI: 10.1186/s40164-024-00479-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024] Open
Abstract
Leukemias are refractory hematological malignancies, characterized by marked intrinsic heterogeneity which poses significant obstacles to effective treatment. However, traditional bulk sequencing techniques have not been able to effectively unravel the heterogeneity among individual tumor cells. With the emergence of single-cell sequencing technology, it has bestowed upon us an unprecedented resolution to comprehend the mechanisms underlying leukemogenesis and drug resistance across various levels, including the genome, epigenome, transcriptome and proteome. Here, we provide an overview of the currently prevalent single-cell sequencing technologies and a detailed summary of single-cell studies conducted on leukemia, with a specific focus on four key aspects: (1) leukemia's clonal architecture, (2) frameworks to determine leukemia subtypes, (3) tumor microenvironment (TME) and (4) the drug-resistant mechanisms of leukemia. This review provides a comprehensive summary of current single-cell studies on leukemia and highlights the markers and mechanisms that show promising clinical implications for the diagnosis and treatment of leukemia.
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Affiliation(s)
- Jianche Liu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- International Campus, Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Penglei Jiang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Zhejiang University, Hangzhou, 310058, China
| | - Zezhen Lu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- International Campus, Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Zebin Yu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- Institute of Hematology, Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Zhejiang University, Hangzhou, 310058, China
| | - Pengxu Qian
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China.
- Institute of Hematology, Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Zhejiang University, Hangzhou, 310058, China.
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9
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Zhang J, Duan Y, Wu P, Chang Y, Wang Y, Hu T, Liu C, Chen X, Zong S, Chen X, Wu Y, Jin L, Lan Y, Liu X, Cheng X, Ding F, Li T, Chen X, Guo Y, Chen Y, Yang W, Zhang L, Zou Y, Cheng T, Zhu X, Zhang Y. Clonal evolution dissection reveals that a high MSI2 level promotes chemoresistance in T-cell acute lymphoblastic leukemia. Blood 2024; 143:320-335. [PMID: 37801708 DOI: 10.1182/blood.2023020490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 10/08/2023] Open
Abstract
ABSTRACT T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive cancer with resistant clonal propagation in recurrence. We performed high-throughput droplet-based 5' single-cell RNA with paired T-cell receptor (TCR) sequencing of paired diagnosis-relapse (Dx_Rel) T-ALL samples to dissect the clonal diversities. Two leukemic evolutionary patterns, "clonal shift" and "clonal drift" were unveiled. Targeted single-cell DNA sequencing of paired Dx_Rel T-ALL samples further corroborated the existence of the 2 contrasting clonal evolution patterns, revealing that dynamic transcriptional variation might cause the mutationally static clones to evolve chemotherapy resistance. Analysis of commonly enriched drifted gene signatures showed expression of the RNA-binding protein MSI2 was significantly upregulated in the persistent TCR clonotypes at relapse. Integrated in vitro and in vivo functional studies suggested that MSI2 contributed to the proliferation of T-ALL and promoted chemotherapy resistance through the posttranscriptional regulation of MYC, pinpointing MSI2 as an informative biomarker and novel therapeutic target in T-ALL.
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Affiliation(s)
- Jingliao Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yongjuan Duan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Peng Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | | | - Yue Wang
- Novogene Co, Ltd, Beijing, China
| | - Tianyuan Hu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Chao Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaoyan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Suyu Zong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaoli Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yangping Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Linlin Jin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yang Lan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaoming Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xuelian Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | | | - Tianyu Li
- Wuxi Children's Hospital, Jiangsu, China
| | - Xiaojuan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Ye Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yumei Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Wenyu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Li Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yao Zou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yingchi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
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10
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Poveda-Garavito N, Combita AL. Contribution of the TIME in BCP-ALL: the basis for novel approaches therapeutics. Front Immunol 2024; 14:1325255. [PMID: 38299154 PMCID: PMC10827891 DOI: 10.3389/fimmu.2023.1325255] [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: 10/20/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024] Open
Abstract
The bone marrow (BM) niche is a microenvironment where both immune and non-immune cells functionally interact with hematopoietic stem cells (HSC) and more differentiated progenitors, contributing to the regulation of hematopoiesis. It is regulated by various signaling molecules such as cytokines, chemokines, and adhesion molecules in its microenvironment. However, despite the strict regulation of BM signals to maintain their steady state, accumulating evidence in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) indicates that leukemic cells can disrupt the physiological hematopoietic niche in the BM, creating a new leukemia-supportive microenvironment. This environment favors immunological evasion mechanisms and the interaction of these cells with the development and progression of BCP-ALL. With a growing understanding of the tumor immune microenvironment (TIME) in the development and progression of BCP-ALL, current strategies focused on "re-editing" TIME to promote antitumor immunity have been developed. In this review, we summarize how TIME cells are disrupted by the presence of leukemic cells, evading immunosurveillance mechanisms in the BCP-ALL model. We also explore the crosstalk between TIME and leukemic cells that leads to treatment resistance, along with the most promising immuno-therapy strategies. Understanding and further research into the role of the BM microenvironment in leukemia progression and relapse are crucial for developing more effective treatments and reducing patient mortality.
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Affiliation(s)
- Nathaly Poveda-Garavito
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología (INC), Bogotá, Colombia
- Grupo de Investigación Traslacional en Oncología, Instituto Nacional de Cancerología (INC), Bogotá, Colombia
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Alba Lucía Combita
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología (INC), Bogotá, Colombia
- Grupo de Investigación Traslacional en Oncología, Instituto Nacional de Cancerología (INC), Bogotá, Colombia
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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11
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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
- 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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12
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Calderon A, Han C, Karma S, Wang E. Non-genetic mechanisms of drug resistance in acute leukemias. Trends Cancer 2024; 10:38-51. [PMID: 37839973 DOI: 10.1016/j.trecan.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
Acute leukemia is characterized by clonal heterogeneity that contributes to poor drug responses in patients. Despite treatment advances, the occurrence of relapse remains a major barrier to achieving cures as current therapeutic approaches are inadequate to effectively prevent or overcome resistance. Given that only a few genetic mutations are associated with relapse in acute leukemia patients, there is a growing focus on 'non-genetic' mechanisms that affect the hallmarks of cancer to allow leukemic cells to survive post therapy. In this review, we provide an overview of the therapeutic landscape in acute leukemias. Importantly, we discuss non-genetic mechanisms exploited by leukemic cells to promote their survival after treatment. Last, we present current strategies to prevent or overcome drug resistance in this disease.
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Affiliation(s)
| | - Cuijuan Han
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Sadik Karma
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | - Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
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13
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Iacobucci I, Zeng AGX, Gao Q, Garcia-Prat L, Baviskar P, Shah S, Murison A, Voisin V, Chan-Seng-Yue M, Cheng C, Qu C, Bailey C, Lear M, Witkowski MT, Zhou X, Peraza AZ, Gangwani K, Advani AS, Luger SM, Litzow MR, Rowe JM, Paietta EM, Stock W, Dick JE, Mullighan CG. SINGLE CELL DISSECTION OF DEVELOPMENTAL ORIGINS AND TRANSCRIPTIONAL HETEROGENEITY IN B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569954. [PMID: 38106088 PMCID: PMC10723356 DOI: 10.1101/2023.12.04.569954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Sequencing of bulk tumor populations has improved genetic classification and risk assessment of B-ALL, but does not directly examine intratumor heterogeneity or infer leukemia cellular origins. We profiled 89 B-ALL samples by single-cell RNA-seq (scRNA-seq) and compared them to a reference map of normal human B-cell development established using both functional and molecular assays. Intra-sample heterogeneity was driven by cell cycle, metabolism, differentiation, and inflammation transcriptional programs. By inference of B lineage developmental state composition, nearly all samples possessed a high abundance of pro-B cells, with variation between samples mainly driven by sub-populations. However, ZNF384- r and DUX4- r B-ALL showed composition enrichment of hematopoietic stem cells, BCR::ABL1 and KMT2A -r ALL of Early Lymphoid progenitors, MEF2D -r and TCF3::PBX1 of Pre-B cells. Enrichment of Early Lymphoid progenitors correlated with high-risk clinical features. Understanding variation in transcriptional programs and developmental states of B-ALL by scRNA-seq refines existing clinical and genomic classifications and improves prediction of treatment outcome.
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14
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Silva FS, Barros-Lima A, Souza-Barros M, Crespo-Neto JA, Santos VGR, Pereira DS, Alves-Hanna FS, Magalhães-Gama F, Faria JAQA, Costa AG. A dual-role for IL-10: From leukemogenesis to the tumor progression in acute lymphoblastic leukemia. Cytokine 2023; 171:156371. [PMID: 37725872 DOI: 10.1016/j.cyto.2023.156371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer in the world, and accounts for 25% of all childhood cancers among children under 15 years of age. Longitudinal studies have shown that children with ALL are born with a deregulated immune response that, together with postnatal environmental exposures, favor the onset of the disease. In this context, IL-10, a key cytokine in the regulation of the immune response, presents itself as a paradoxical mediator, initially influencing the development of ALL through the regulation of inflammatory processes and later on the progression of malignancy, with the increase of this molecule in the leukemia microenvironment. According to the literature, this cytokine plays a critical role in the natural history of the disease and plays an important role in two different though complex scenarios. Thus, in this review, we explore the dual role of IL-10 in ALL, and describe its biological characteristics, immunological mechanisms and genetics, as well as its impact on the leukemia microenvironment and its clinical implications.
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Affiliation(s)
- Flavio Souza Silva
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil; Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | - Amanda Barros-Lima
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil; Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | - Mateus Souza-Barros
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil; Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | - Juniel Assis Crespo-Neto
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | | | - Daniele Sá Pereira
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil; Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil; Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
| | - Fabíola Silva Alves-Hanna
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil; Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | - Fábio Magalhães-Gama
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Instituto René Rachou - Fundação Oswaldo Cruz (FIOCRUZ) Minas, Belo Horizonte, Brazil
| | - Jerusa Araújo Quintão Arantes Faria
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil
| | - Allyson Guimarães Costa
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil; Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil; Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil; Escola de Enfermagem de Manaus, UFAM, Manaus, Brazil.
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15
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Jensen CT, Åhsberg J, Tingvall-Gustafsson J, Somasundaram R, Lang S, Ungerbäck J, Porwit A, Soneji S, Sigvardsson M. B-lineage acute lymphoblastic leukemia causes cellautonomous defects in long-term hematopoietic stem cell function. Haematologica 2023; 108:3175-3180. [PMID: 36861396 PMCID: PMC10620591 DOI: 10.3324/haematol.2022.282430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Affiliation(s)
| | - Josefine Åhsberg
- Department of Clinical and Experimental Medicine, Linköping University
| | | | | | - Stefan Lang
- Division of Molecular Hematology, Lund University, Lund
| | | | - Anna Porwit
- Division of Pathology, Lund University, Lund
| | - Shamit Soneji
- Division of Molecular Hematology, Lund University, Lund
| | - Mikael Sigvardsson
- Division of Molecular Hematology, Lund University, Lund, Sweden; Department of Clinical and Experimental Medicine, Linköping University.
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16
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Chaudagar K, Rameshbabu S, Mei S, Hirz T, Hu YM, Argulian A, Labadie B, Desai K, Grimaldo S, Kahramangil D, Nair R, DSouza S, Zhou D, Li M, Doughan F, Chen R, Shafran J, Loyd M, Xia Z, Sykes DB, Moran A, Patnaik A. Androgen blockade primes NLRP3 in macrophages to induce tumor phagocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.557996. [PMID: 37904975 PMCID: PMC10614738 DOI: 10.1101/2023.09.15.557996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Immune-based therapies induce durable remissions in subsets of patients across multiple malignancies. However, there is limited efficacy of immunotherapy in metastatic castrate-resistant prostate cancer (mCRPC), manifested by an enrichment of immunosuppressive (M2) tumor- associated macrophages (TAM) in the tumor immune microenvironment (TME). Therefore, therapeutic strategies to overcome TAM-mediated immunosuppression are critically needed in mCRPC. Here we discovered that NLR family pyrin domain containing 3 (NLRP3), an innate immune sensing protein, is highly expressed in TAM from metastatic PC patients treated with standard-of-care androgen deprivation therapy (ADT). Importantly, ex vivo studies revealed that androgen receptor (AR) blockade in TAM upregulates NLRP3 expression, but not inflammasome activity, and concurrent AR blockade/NLRP3 agonist (NLRP3a) treatment promotes cancer cell phagocytosis by immunosuppressive M2 TAM. In contrast, NLRP3a monotherapy was sufficient to enhance phagocytosis of cancer cells in anti-tumor (M1) TAM, which exhibit high de novo NLRP3 expression. Critically, combinatorial treatment with ADT/NLRP3a in a murine model of advanced PC resulted in significant tumor control, with tumor clearance in 55% of mice via TAM phagocytosis. Collectively, our results demonstrate NLRP3 as an AR-regulated "macrophage phagocytic checkpoint", inducibly expressed in TAM by ADT and activated by NLRP3a treatment, the combination resulting in TAM-mediated phagocytosis and tumor control.
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17
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Chen S, Jiang W, Du Y, Yang M, Pan Y, Li H, Cui M. Single-cell analysis technologies for cancer research: from tumor-specific single cell discovery to cancer therapy. Front Genet 2023; 14:1276959. [PMID: 37900181 PMCID: PMC10602688 DOI: 10.3389/fgene.2023.1276959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Single-cell sequencing (SCS) technology is changing our understanding of cellular components, functions, and interactions across organisms, because of its inherent advantage of avoiding noise resulting from genotypic and phenotypic heterogeneity across numerous samples. By directly and individually measuring multiple molecular characteristics of thousands to millions of single cells, SCS technology can characterize multiple cell types and uncover the mechanisms of gene regulatory networks, the dynamics of transcription, and the functional state of proteomic profiling. In this context, we conducted systematic research on SCS techniques, including the fundamental concepts, procedural steps, and applications of scDNA, scRNA, scATAC, scCITE, and scSNARE methods, focusing on the unique clinical advantages of SCS, particularly in cancer therapy. We have explored challenging but critical areas such as circulating tumor cells (CTCs), lineage tracing, tumor heterogeneity, drug resistance, and tumor immunotherapy. Despite challenges in managing and analyzing the large amounts of data that result from SCS, this technique is expected to reveal new horizons in cancer research. This review aims to emphasize the key role of SCS in cancer research and promote the application of single-cell technologies to cancer therapy.
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Affiliation(s)
- Siyuan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Weibo Jiang
- Department of Orthopaedic, The Second Hospital of Jilin University, Changchun, China
| | - Yanhui Du
- Department of Orthopaedics, Jilin Province People’s Hospital, Changchun, China
| | - Manshi Yang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yihan Pan
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Huan Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Mengying Cui
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
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18
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Peroni E, Randi ML, Rosato A, Cagnin S. Acute myeloid leukemia: from NGS, through scRNA-seq, to CAR-T. dissect cancer heterogeneity and tailor the treatment. J Exp Clin Cancer Res 2023; 42:259. [PMID: 37803464 PMCID: PMC10557350 DOI: 10.1186/s13046-023-02841-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
Acute myeloid leukemia (AML) is a malignant blood cancer with marked cellular heterogeneity due to altered maturation and differentiation of myeloid blasts, the possible causes of which are transcriptional or epigenetic alterations, impaired apoptosis, and excessive cell proliferation. This neoplasm has a high rate of resistance to anticancer therapies and thus a high risk of relapse and mortality because of both the biological diversity of the patient and intratumoral heterogeneity due to the acquisition of new somatic changes. For more than 40 years, the old gold standard "one size fits all" treatment approach included intensive chemotherapy treatment with anthracyclines and cytarabine.The manuscript first traces the evolution of the understanding of the pathology from the 1970s to the present. The enormous strides made in its categorization prove to be crucial for risk stratification, enabling an increasingly personalized diagnosis and treatment approach.Subsequently, we highlight how, over the past 15 years, technological advances enabling single cell RNA sequencing and T-cell modification based on the genomic tools are affecting the classification and treatment of AML. At the dawn of the new millennium, the advent of high-throughput next-generation sequencing technologies has enabled the profiling of patients evidencing different facets of the same disease, stratifying risk, and identifying new possible therapeutic targets that have subsequently been validated. Currently, the possibility of investigating tumor heterogeneity at the single cell level, profiling the tumor at the time of diagnosis or after treatments exist. This would allow the identification of underrepresented cellular subclones or clones resistant to therapeutic approaches and thus responsible for post-treatment relapse that would otherwise be difficult to detect with bulk investigations on the tumor biopsy. Single-cell investigation will then allow even greater personalization of therapy to the genetic and transcriptional profile of the tumor, saving valuable time and dangerous side effects. The era of personalized medicine will take a huge step forward through the disclosure of each individual piece of the complex puzzle that is cancer pathology, to implement a "tailored" therapeutic approach based also on engineered CAR-T cells.
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Affiliation(s)
- Edoardo Peroni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padova, 35128, Italy.
| | - Maria Luigia Randi
- First Medical Clinic, Department of Medicine-DIMED, University of Padua, Padua, Italy
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padova, 35128, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, 35131, Italy
- CIR-Myo Myology Center, University of Padova, Padova, 35131, Italy
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19
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Amani V, Riemondy KA, Fu R, Griesinger AM, Grimaldo E, De Sousa GR, Gilani A, Hemenway M, Foreman NK, Donson AM, Willard N. Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas. Acta Neuropathol Commun 2023; 11:158. [PMID: 37770931 PMCID: PMC10537467 DOI: 10.1186/s40478-023-01639-1] [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: 06/13/2023] [Accepted: 08/17/2023] [Indexed: 09/30/2023] Open
Abstract
Plexiform neurofibroma (PN) is a leading cause of morbidity in children with the genetic condition Neurofibromatosis Type 1 (NF1), often disfiguring or threatening vital structures. During formation of PN, a complex tumor microenvironment (TME) develops, with recruitment of neoplastic and non-neoplastic cell types being critical for growth and progression. Due to the cohesive cellularity of PN, single-cell RNA-sequencing is difficult and may result in a loss of detection of critical cellular subpopulations. To bypass this barrier, we performed single-nuclei RNA-sequencing (snRNA-seq) on 8 frozen PN samples, and integrated this with spatial transcriptomics (ST) in 4 PN samples and immunohistochemistry to provide morphological context to transcriptomic data. SnRNA-seq analysis definitively charted the heterogeneous cellular subpopulations in the PN TME, with the predominant fraction being fibroblast subtypes. PN showed a remarkable amount of inter-sample homogeneity regarding cellular subpopulation proportions despite being resected from a variety of anatomical locations. ST analysis identified distinct cellular subpopulations which were annotated using snRNA-seq data and correlated with histological features. Schwann cell/fibroblast interactions were identified by receptor/ligand interaction analysis demonstrating a high probability of Neurexin 1/Neuroligin 1 (NRXN1/NLGN1) receptor-ligand cross-talk predicted between fibroblasts and non-myelinated Schwann cells (NM-SC) and subtypes, respectively. We observed aberrant expression of NRXN1 and NLGN1 in our PN snRNA-seq data compared to a normal mouse sciatic nerve single-cell RNA-seq dataset. This pathway has never been described in PN and may indicate a clear and direct communication pathway between putative NM-SC cells of origin and surrounding fibroblasts, potentially driving disease progression. SnRNA-seq integrated with spatial transcriptomics advances our understanding of the complex cellular heterogeneity of PN TME and identify potential novel communication pathways that may drive disease progression, a finding that could provide translational therapy options for patients with these devastating tumors of childhood and early adulthood.
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Affiliation(s)
- Vladimir Amani
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA.
| | - Kent A Riemondy
- RNA Biosciences Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rui Fu
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Andrea M Griesinger
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Enrique Grimaldo
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Graziella Ribeiro De Sousa
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Ahmed Gilani
- Department of Pathology, University of Colorado Denver, Aurora, CO, USA
| | - Molly Hemenway
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Denver, Aurora, CO, USA
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20
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Van Morckhoven D, Dubois N, Bron D, Meuleman N, Lagneaux L, Stamatopoulos B. Extracellular vesicles in hematological malignancies: EV-dence for reshaping the tumoral microenvironment. Front Immunol 2023; 14:1265969. [PMID: 37822925 PMCID: PMC10562589 DOI: 10.3389/fimmu.2023.1265969] [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: 07/24/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
Following their discovery at the end of the 20th century, extracellular vesicles (EVs) ranging from 50-1,000 nm have proven to be paramount in the progression of many cancers, including hematological malignancies. EVs are a heterogeneous group of cell-derived membranous structures that include small EVs (commonly called exosomes) and large EVs (microparticles). They have been demonstrated to participate in multiple physiological and pathological processes by allowing exchange of biological material (including among others proteins, DNA and RNA) between cells. They are therefore a crucial way of intercellular communication. In this context, malignant cells can release these extracellular vesicles that can influence their microenvironment, induce the formation of a tumorigenic niche, and prepare and establish distant niches facilitating metastasis by significantly impacting the phenotypes of surrounding cells and turning them toward supportive roles. In addition, EVs are also able to manipulate the immune response and to establish an immunosuppressive microenvironment. This in turn allows for ideal conditions for heightened chemoresistance and increased disease burden. Here, we review the latest findings and reports studying the effects and therapeutic potential of extracellular vesicles in various hematological malignancies. The study of extracellular vesicles remains in its infancy; however, rapid advances in the analysis of these vesicles in the context of disease allow us to envision prospects to improve the detection and treatment of hematological malignancies.
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Affiliation(s)
- David Van Morckhoven
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Nathan Dubois
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Dominique Bron
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Departement of Hematology, Jules Bordet Institute, Brussels, Belgium
| | - Nathalie Meuleman
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Departement of Hematology, Jules Bordet Institute, Brussels, Belgium
| | - Laurence Lagneaux
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Basile Stamatopoulos
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
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21
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Wong H, Sugimura R. Immune-epigenetic crosstalk in haematological malignancies. Front Cell Dev Biol 2023; 11:1233383. [PMID: 37808081 PMCID: PMC10551137 DOI: 10.3389/fcell.2023.1233383] [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: 06/02/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Haematological malignancies comprise a diverse set of lymphoid and myeloid neoplasms which can arise during any stage of haematopoiesis in the bone marrow. Accumulating evidence suggests that chronic inflammation generated by inflammatory cytokines secreted by tumour and the tumour-associated cells within the bone marrow microenvironment initiates signalling pathways in malignant cells, resulting in activation of master transcription factors including Smads, STAT3, and NF-κB which confer cancer stem cell phenotypes and drive disease progression. Deciphering the molecular mechanisms for how immune cells interact with malignant cells to induce such epigenetic modifications, specifically DNA methylation, histone modification, expression of miRNAs and lnRNAs to perturbate haematopoiesis could provide new avenues for developing novel targeted therapies for haematological malignancies. Here, the complex positive and negative feedback loops involved in inflammatory cytokine-induced cancer stem cell generation and drug resistance are reviewed to highlight the clinical importance of immune-epigenetic crosstalk in haematological malignancies.
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Affiliation(s)
| | - Ryohichi Sugimura
- School of Biomedical Sciences, Lee Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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22
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Feng Y, Wang S, Xie J, Ding B, Wang M, Zhang P, Mi P, Wang C, Liu R, Zhang T, Yu X, Yuan D, Zhang C. Spatial transcriptomics reveals heterogeneity of macrophages in the tumor microenvironment of granulomatous slack skin. J Pathol 2023; 261:105-119. [PMID: 37550813 DOI: 10.1002/path.6151] [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: 11/30/2022] [Revised: 04/30/2023] [Accepted: 06/01/2023] [Indexed: 08/09/2023]
Abstract
Granulomatous slack skin (GSS) is an extremely rare subtype of cutaneous T-cell lymphoma accompanied by an abundant number of macrophages and is clinically characterized by the development of pendulous skin folds. However, the characteristics of these macrophages in GSS remain unclear. Here, we conducted a spatial transcriptomic study on one frozen GSS sample and drew transcriptomic maps of GSS for the first time. Gene expression analysis revealed the enrichment of three clusters with macrophage transcripts, each exhibiting distinct characteristics suggesting that their primary composition consists of different subpopulations of macrophages. The CD163+ /CD206+ cluster showed a tumor-associated macrophage (TAM) M2-like phenotype and highly expressed ZFP36, CCL2, TNFAIP6, and KLF2, which are known to be involved in T-cell interaction and tumor progression. The APOC1+ /APOE+ cluster presented a non-M1 or -M2 phenotype and may be related to lipid metabolism. The CD11c+ /LYZ+ cluster exhibited an M1-like phenotype. Notably, these cells strongly expressed MMP9, MMP12, CHI3L1, CHIT1, COL1A1, TIMP1, and SPP1, which are responsible for extracellular matrix (ECM) degradation and tissue remodeling. This may partially explain the symptoms of cutaneous relaxation in GSS. Further immunohistochemistry on four GSS cases demonstrated that CD11c predominantly marked granulomas and multinucleated giant cells, whereas CD163 was mainly expressed on scattered macrophages, appearing as a mutually exclusive pattern. The expression pattern of MMP9 overlapped with that of CD11c, implying that CD11c+ macrophages may be a source of MMP9. Our data shed light on the characteristics of macrophages in the GSS microenvironment and provide a theoretical basis for the application of MMP9 inhibitors to prevent cutaneous relaxation of GSS. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Yawei Feng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Shiguan Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Jianjun Xie
- Department of Pathology, Qingdao Chengyang People's Hospital, Qingdao, PR China
| | - Bin Ding
- Department of Pathology, Affiliated Qingdao Central Hospital, Qingdao University, Qingdao, PR China
| | - Min Wang
- Department of Pathology, The Second People's Hospital of Liaocheng, Linqing, PR China
| | - Peng Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Ping Mi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Chunxue Wang
- Institute of Pathology and Pathophysiology, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Ruirui Liu
- Institute of Pathology and Pathophysiology, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Tingguo Zhang
- Institute of Pathology and Pathophysiology, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, PR China
| | - Xiaojing Yu
- Department of Dermatology, Qilu Hospital of Shandong University, Jinan, PR China
| | - Detian Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, PR China
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23
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Huang D, Ma N, Li X, Gou Y, Duan Y, Liu B, Xia J, Zhao X, Wang X, Li Q, Rao J, Zhang X. Advances in single-cell RNA sequencing and its applications in cancer research. J Hematol Oncol 2023; 16:98. [PMID: 37612741 PMCID: PMC10463514 DOI: 10.1186/s13045-023-01494-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Cancers are a group of heterogeneous diseases characterized by the acquisition of functional capabilities during the transition from a normal to a neoplastic state. Powerful experimental and computational tools can be applied to elucidate the mechanisms of occurrence, progression, metastasis, and drug resistance; however, challenges remain. Bulk RNA sequencing techniques only reflect the average gene expression in a sample, making it difficult to understand tumor heterogeneity and the tumor microenvironment. The emergence and development of single-cell RNA sequencing (scRNA-seq) technologies have provided opportunities to understand subtle changes in tumor biology by identifying distinct cell subpopulations, dissecting the tumor microenvironment, and characterizing cellular genomic mutations. Recently, scRNA-seq technology has been increasingly used in cancer studies to explore tumor heterogeneity and the tumor microenvironment, which has increased the understanding of tumorigenesis and evolution. This review summarizes the basic processes and development of scRNA-seq technologies and their increasing applications in cancer research and clinical practice.
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Affiliation(s)
- Dezhi Huang
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Naya Ma
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Xinlei Li
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Yang Gou
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Yishuo Duan
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Bangdong Liu
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Jing Xia
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Xianlan Zhao
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Xiaoqi Wang
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Qiong Li
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
| | - Jun Rao
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
| | - Xi Zhang
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
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24
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Contreras Yametti GP, Evensen NA, Schloss JM, Aldebert C, Duan E, Zhang Y, Hu J, Chambers TM, Scheurer ME, Teachey DT, Rabin KR, Raetz EA, Aifantis I, Carroll WL, Witkowski MT. Flow cytometric assessment of leukemia-associated monocytes in childhood B-cell acute lymphoblastic leukemia outcome. Blood Adv 2023; 7:3928-3931. [PMID: 37196626 PMCID: PMC10405191 DOI: 10.1182/bloodadvances.2023010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023] Open
Affiliation(s)
| | - Nikki A. Evensen
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | - Jennifer M. Schloss
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | - Clemence Aldebert
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | - Emily Duan
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | - Yan Zhang
- Division of Biostatistics, Department of Population Health, NYU Langone Health, New York, NY
| | - Jiyuan Hu
- Division of Biostatistics, Department of Population Health, NYU Langone Health, New York, NY
| | - Tiffany M. Chambers
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Michael E. Scheurer
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - David T. Teachey
- Department of Pediatrics and the Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Karen R. Rabin
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Elizabeth A. Raetz
- Division of Pediatric Hematology Oncology, Department of Pediatrics, NYU Langone Health, New York, NY
| | | | - William L. Carroll
- Division of Pediatric Hematology Oncology, Department of Pediatrics, NYU Langone Health, New York, NY
- Department of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | - Matthew T. Witkowski
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
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25
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Wang H, Qiu Y, Zhang H, Chang N, Hu Y, Chen J, Hu R, Liao P, Li Z, Yang Y, Cen Q, Ding X, Li M, Xie X, Li Y. Histone acetylation by HBO1 (KAT7) activates Wnt/β-catenin signaling to promote leukemogenesis in B-cell acute lymphoblastic leukemia. Cell Death Dis 2023; 14:498. [PMID: 37542030 PMCID: PMC10403501 DOI: 10.1038/s41419-023-06019-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023]
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) is an aggressive hematological disorder with a dismal prognosis. The dysregulation of histone acetylation is of great significance in the pathogenesis and progression of B-ALL. Regarded as a fundamental acetyltransferase gene, the role of HBO1 (lysine acetyltransferase 7/KAT7) in B-ALL has not been investigated. Herein, we found that HBO1 expression was elevated in human B-ALL cells and associated with poor disease-free survival. Strikingly, HBO1 knockdown inhibited viability, proliferation, and G1-S cycle progression in B-ALL cells, while provoking apoptosis. In contrast, ectopic overexpression of HBO1 enhanced cell viability and proliferation but inhibited apoptotic activation. The results of in vivo experiments also certificated the inhibitory effect of HBO1 knockdown on tumor growth. Mechanistically, HBO1 acetylated histone H3K14, H4K8, and H4K12, followed by upregulating CTNNB1 expression, resulting in activation of the Wnt/β-catenin signaling pathway. Moreover, a novel small molecule inhibitor of HBO1, WM-3835, potently inhibited the progression of B-ALL. Our data identified HBO1 as an efficacious regulator of CTNNB1 with therapeutic potential in B-ALL.
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Affiliation(s)
- Hao Wang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Yingqi Qiu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Honghao Zhang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China.
| | - Ning Chang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Yuxing Hu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Jianyu Chen
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Rong Hu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Peiyun Liao
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Zhongwei Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Yulu Yang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Qingyan Cen
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Xiangyang Ding
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Meifang Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Xiaoling Xie
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China.
| | - Yuhua Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510005, P. R. China.
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26
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Park CS, Yoshihara H, Gao Q, Qu C, Iacobucci I, Ghate PS, Connelly JP, Pruett-Miller SM, Wagner B, Robinson CG, Mishra A, Peng J, Yang L, Rankovic Z, Finkelstein D, Luger S, Litzow M, Paietta EM, Hebbar N, Velasquez MP, Mullighan CG. Stromal-induced epithelial-mesenchymal transition induces targetable drug resistance in acute lymphoblastic leukemia. Cell Rep 2023; 42:112804. [PMID: 37453060 PMCID: PMC10529385 DOI: 10.1016/j.celrep.2023.112804] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 04/05/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
The bone marrow microenvironment (BME) drives drug resistance in acute lymphoblastic leukemia (ALL) through leukemic cell interactions with bone marrow (BM) niches, but the underlying mechanisms remain unclear. Here, we show that the interaction between ALL and mesenchymal stem cells (MSCs) through integrin β1 induces an epithelial-mesenchymal transition (EMT)-like program in MSC-adherent ALL cells, resulting in drug resistance and enhanced survival. Moreover, single-cell RNA sequencing analysis of ALL-MSC co-culture identifies a hybrid cluster of MSC-adherent ALL cells expressing both B-ALL and MSC signature genes, orchestrated by a WNT/β-catenin-mediated EMT-like program. Blockade of interaction between β-catenin and CREB binding protein impairs the survival and drug resistance of MSC-adherent ALL cells in vitro and results in a reduction in leukemic burden in vivo. Targeting of this WNT/β-catenin-mediated EMT-like program is a potential therapeutic approach to overcome cell extrinsically acquired drug resistance in ALL.
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Affiliation(s)
- Chun Shik Park
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hiroki Yoshihara
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Pankaj S Ghate
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ben Wagner
- Cell and Tissue Imaging Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Camenzind G Robinson
- Cell and Tissue Imaging Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Selina Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19106, USA
| | - Mark Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Nikhil Hebbar
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - M Paulina Velasquez
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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27
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Hockney S, Parker J, Turner JE, Todd X, Todryk S, Gieling RG, Hilgen G, Simoes DCM, Pal D. Next generation organoid engineering to replace animals in cancer drug testing. Biochem Pharmacol 2023; 213:115586. [PMID: 37164297 DOI: 10.1016/j.bcp.2023.115586] [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: 01/31/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/12/2023]
Abstract
Cancer therapies have several clinical challenges associated with them, namely treatment toxicity, treatment resistance and relapse. Due to factors ranging from patient profiles to the tumour microenvironment (TME), there are several hurdles to overcome in developing effective treatments that have low toxicity that can mitigate emergence of resistance and occurrence of relapse. De novo cancer development has the highest drug attrition rates with only 1 in 10,000 preclinical candidates reaching the market. To alleviate this high attrition rate, more mimetic and sustainable preclinical models that can capture the disease biology as in the patient, are required. Organoids and next generation 3D tissue engineering is an emerging area that aims to address this problem. Advancement of three-dimensional (3D) in vitro cultures into complex organoid models incorporating multiple cell types alongside acellular aspects of tissue microenvironments can provide a system for therapeutic testing. Development of microfluidic technologies have furthermore increased the biomimetic nature of these models. Additionally, 3D bio-printing facilitates generation of tractable ex vivo models in a controlled, scalable and reproducible manner. In this review we highlight some of the traditional preclinical models used in cancer drug testing and debate how next generation organoids are being used to replace not only animal models, but also some of the more elementary in vitro approaches, such as cell lines. Examples of applications of the various models will be appraised alongside the future challenges that still need to be overcome.
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Affiliation(s)
- Sean Hockney
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Jessica Parker
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Jasmin E Turner
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle Upon Tyne NE1 4EP, UK
| | - Xanthea Todd
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Stephen Todryk
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Roben Ger Gieling
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Gerrit Hilgen
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Biosciences Institute, Newcastle University, International Centre for Life, Newcastle Upon Tyne NE1 4EP, UK
| | - Davina Camargo Madeira Simoes
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Deepali Pal
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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28
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Le Floch AC, Rouvière MS, Salem N, Ben Amara A, Orlanducci F, Vey N, Gorvel L, Chretien AS, Olive D. Prognostic Immune Effector Signature in Adult Acute Lymphoblastic Leukemia Patients Is Dominated by γδ T Cells. Cells 2023; 12:1693. [PMID: 37443727 PMCID: PMC10340700 DOI: 10.3390/cells12131693] [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: 03/26/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
The success of immunotherapy has highlighted the critical role of the immune microenvironment in acute lymphoblastic leukemia (ALL); however, the immune landscape in ALL remains incompletely understood and most studies have focused on conventional T cells or NK cells. This study investigated the prognostic impact of circulating γδ T-cell alterations using high-dimensional analysis in a cohort of newly diagnosed adult ALL patients (10 B-ALL; 9 Philadelphia+ ALL; 9 T-ALL). Our analysis revealed common alterations in CD8+ T cells and γδ T cells of relapsed patients, including accumulation of early stage differentiation and increased expression of BTLA and CD73. We demonstrated that the circulating γδ T-cell signature was the most discriminating between relapsed and disease-free groups. In addition, Vδ2 T-cell alterations strongly discriminated patients by relapse status. Taken together, these data highlight the role of ɣδ T cells in adult ALL patients, among whom Vδ2 T cells may be a pivotal contributor to T-cell immunity in ALL. Our findings provide a strong rationale for further monitoring and potentiating Vδ2 T cells in ALL, including in the autologous setting.
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Affiliation(s)
- Anne-Charlotte Le Floch
- Equipe Immunité et Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, 13009 Marseille, France; (A.-C.L.F.)
- Plateforme d’Immunomonitoring, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Marie-Sarah Rouvière
- Equipe Immunité et Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, 13009 Marseille, France; (A.-C.L.F.)
- Plateforme d’Immunomonitoring, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Nassim Salem
- Equipe Immunité et Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, 13009 Marseille, France; (A.-C.L.F.)
- Plateforme d’Immunomonitoring, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Amira Ben Amara
- Equipe Immunité et Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, 13009 Marseille, France; (A.-C.L.F.)
- Plateforme d’Immunomonitoring, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Florence Orlanducci
- Equipe Immunité et Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, 13009 Marseille, France; (A.-C.L.F.)
- Plateforme d’Immunomonitoring, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Norbert Vey
- Département d’Hématologie, CRCM, INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, 13009 Marseille, France
| | - Laurent Gorvel
- Equipe Immunité et Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, 13009 Marseille, France; (A.-C.L.F.)
- Plateforme d’Immunomonitoring, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Anne-Sophie Chretien
- Equipe Immunité et Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, 13009 Marseille, France; (A.-C.L.F.)
- Plateforme d’Immunomonitoring, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Daniel Olive
- Equipe Immunité et Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, 13009 Marseille, France; (A.-C.L.F.)
- Plateforme d’Immunomonitoring, Institut Paoli-Calmettes, 13009 Marseille, France
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29
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Ma B, Liu X, Zhang Z, Ma C, Chand R, Patwardhan S, Wang C, Thamphiwatana SD, Chen P, Chen W. A digital nanoplasmonic microarray immunosensor for multiplexed cytokine monitoring during CAR T-cell therapy from a leukemia tumor microenvironment model. Biosens Bioelectron 2023; 230:115247. [PMID: 37023552 PMCID: PMC10103176 DOI: 10.1016/j.bios.2023.115247] [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: 10/31/2022] [Revised: 03/07/2023] [Accepted: 03/20/2023] [Indexed: 03/28/2023]
Abstract
The release of cytokines by chimeric antigen receptor (CAR) T-cells and tumor resident immune cells defines a significant part of CAR T-cell functional activity and patient immune responses during CAR T-cell therapy. However, few studies have so far precisely characterized the cytokine secretion dynamics in the tumor niche during CAR T-cell therapy, which requires multiplexed, and timely biosensing platforms and integration with biomimetic tumor microenvironment. Herein, we implemented a digital nanoplasmonic microarray immunosensor with a microfluidic biomimetic Leukemia-on-a-Chip model to monitor cytokine secretion dynamics during CD19 CAR T-cell therapy against precursor B-cell acute lymphocytic leukemia (B-ALL). The integrated nanoplasmonic biosensors achieved precise multiplexed cytokine measurements with low operating sample volume, short assay time, heightened sensitivity, and negligible sensor crosstalk. Using the digital nanoplasmonic biosensing approach, we measured the concentrations of six cytokines (TNF-α, IFN-γ, MCP-1, GM-CSF, IL-1β, and IL-6) during first 5 days of CAR T-cell treatment in the microfluidic Leukemia-on-a-Chip model. Our results revealed a heterogeneous secretion profile of various cytokines during CAR T-cell therapy and confirmed a correlation between the cytokine secretion profile and the CAR T-cell cytotoxic activity. The capability to monitor immune cell cytokine secretion dynamics in a biomimetic tumor microenvironment could further help in study of cytokine release syndrome during CAR T-cell therapy and in development of more efficient and safer immunotherapies.
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Affiliation(s)
- Benteng Ma
- Department of Biomedical Engineering, New York University, Brooklyn, NY, 11201, USA
| | - Xinya Liu
- Department of Biomedical Engineering, New York University, Brooklyn, NY, 11201, USA
| | - Zhuoyu Zhang
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY, 11201, USA
| | - Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY, 11201, USA
| | - Rashik Chand
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Saee Patwardhan
- Department of Biomedical Engineering, New York University, Brooklyn, NY, 11201, USA
| | - Chuanyu Wang
- Department of Material Engineering, Auburn University, Auburn, AL, 36849, USA
| | - Soracha D Thamphiwatana
- Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakorn Pathom, 73170, Thailand
| | - Pengyu Chen
- Department of Material Engineering, Auburn University, Auburn, AL, 36849, USA
| | - Weiqiang Chen
- Department of Biomedical Engineering, New York University, Brooklyn, NY, 11201, USA; Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY, 11201, USA; Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA.
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30
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Wu M, Zhang S, Chi C, Zhu H, Ma H, Liu L, Shi Q, Li D, Ju X. 1,5-AG suppresses pro-inflammatory polarization of macrophages and promotes the survival of B-ALL in vitro by upregulating CXCL14. Mol Immunol 2023; 158:91-102. [PMID: 37178520 DOI: 10.1016/j.molimm.2023.05.003] [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: 01/14/2023] [Revised: 03/30/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023]
Abstract
B-lineage acute lymphoblastic leukemia (B-ALL) is one of the most common malignancies in children. Despite advances in treatment, the role of the tumor microenvironment in B-ALL remains poorly understood. Among the key components of the immune microenvironment, macrophages play a critical role in the progression of the disease. However, recent research has suggested that abnormal metabolites may influence the function of macrophages, altering the immune microenvironment and promoting tumor growth. Our previous non-targeted metabolomic detection revealed that the metabolite 1,5-anhydroglucitol (1,5-AG) level in the peripheral blood of children newly diagnosed with B-ALL was significantly elevated. Except for its direct influence on leukemia cells, the effect of 1,5-AG on macrophages is still unclear. Herein, we demonstrated new potential therapeutic targets by focusing on the effect of 1,5-AG on macrophages. We used polarization-induced macrophages to determine how 1,5-AG acted on M1-like polarization and screened out the target gene CXCL14 via transcriptome sequencing. Furthermore, we constructed CXCL14 knocked-down macrophages and a macrophage-leukemia cell coculture model to validate the interaction between macrophages and leukemia cells. We discovered that 1,5-AG upregulated the CXCL14 expression, thereby inhibiting M1-like polarization. CXCL14 knockdown restored the M1-like polarization of macrophages and induced leukemia cells apoptosis in the coculture model. Our findings offer new possibilities for the genetic engineering of human macrophages to rehabilitate their immune activity against B-ALL in cancer immunotherapy.
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Affiliation(s)
- Min Wu
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Shule Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Cheng Chi
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Huasu Zhu
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Huixian Ma
- Cryomedicine Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Linghong Liu
- Cryomedicine Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Qing Shi
- Cryomedicine Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Dong Li
- Cryomedicine Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xiuli Ju
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan 250012, China; Cryomedicine Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China.
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31
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Cai Y, Chen X, Lu T, Yu Z, Hu S, Liu J, Zhou X, Wang X. Single-cell transcriptome analysis profiles the expression features of TMEM173 in BM cells of high-risk B-cell acute lymphoblastic leukemia. BMC Cancer 2023; 23:372. [PMID: 37095455 PMCID: PMC10123968 DOI: 10.1186/s12885-023-10830-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 04/08/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND As an essential regulator of type I interferon (IFN) response, TMEM173 participates in immune regulation and cell death induction. In recent studies, activation of TMEM173 has been regarded as a promising strategy for cancer immunotherapy. However, transcriptomic features of TMEM173 in B-cell acute lymphoblastic leukemia (B-ALL) remain elusive. METHODS Quantitative real-time PCR (qRT-PCR) and western blotting (WB) were applied to determine the mRNA and protein levels of TMEM173 in peripheral blood mononuclear cells (PBMCs). TMEM173 mutation status was assessed by Sanger sequencing. Single-cell RNA sequencing (scRNA-seq) analysis was performed to explore the expression of TMEM173 in different types of bone marrow (BM) cells. RESULTS The mRNA and protein levels of TMEM173 were increased in PBMCs from B-ALL patients. Besides, frameshift mutation was presented in TMEM173 sequences of 2 B-ALL patients. ScRNA-seq analysis identified the specific transcriptome profiles of TMEM173 in the BM of high-risk B-ALL patients. Specifically, expression levels of TMEM173 in granulocytes, progenitor cells, mast cells, and plasmacytoid dendritic cells (pDCs) were higher than that in B cells, T cells, natural killer (NK) cells, and dendritic cells (DCs). Subset analysis further revealed that TMEM173 and pyroptosis effector gasdermin D (GSDMD) restrained in precursor-B (pre-B) cells with proliferative features, which expressed nuclear factor kappa-B (NF-κB), CD19, and Bruton's tyrosine kinase (BTK) during the progression of B-ALL. In addition, TMEM173 was associated with the functional activation of NK cells and DCs in B-ALL. CONCLUSIONS Our findings provide insights into the transcriptomic features of TMEM173 in the BM of high-risk B-ALL patients. Targeted activation of TMEM173 in specific cells might provide new therapeutic strategies for B-ALL patients.
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Affiliation(s)
- Yiqing Cai
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Xiaomin Chen
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Tiange Lu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Zhuoya Yu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Shunfeng Hu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Jiarui Liu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Xiangxiang Zhou
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, Shandong, 250021, China.
- Shandong Provincial Engineering Research Center of Lymphoma, Jinan, Shandong, 250021, China.
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, Shandong, 250021, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, Shandong, 250021, China.
- Shandong Provincial Engineering Research Center of Lymphoma, Jinan, Shandong, 250021, China.
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, Shandong, 250021, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
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32
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Zhang X, Hou Z, Huang D, Wang F, Gao B, Zhang C, Zhou D, Lou J, Wang H, Gao Y, Kang Z, Lu Y, Liu Q, Yan J. Single-cell heterogeneity and dynamic evolution of Ph-like acute lymphoblastic leukemia patient with novel TPR-PDGFRB fusion gene. Exp Hematol Oncol 2023; 12:19. [PMID: 36797781 PMCID: PMC9936632 DOI: 10.1186/s40164-023-00380-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a refractory and recurrent subtype of B-cell ALL enriched with kinase-activating rearrangements. Incomplete understanding of the heterogeneity within the tumor cells presents a major challenge for the diagnosis and therapy of Ph-like ALL. Here, we exhibited a comprehensive cell atlas of one Ph-like ALL patient with a novel TPR-PDGFRB fusion gene at diagnosis and relapse by using single-cell RNA sequencing (scRNA-seq). Twelve heterogeneous B-cell clusters, four with strong MKI67 expression indicating highly proliferating B cells, were identified. A relapse-enriched B-cell subset associated with poor prognosis was discovered, implicating the transcriptomic evolution during disease progression. Integrative single-cell analysis was performed on Ph-like ALL and Ph+ ALL patients, and revealed Ph-like specific B-cell subpopulations and shared malignant B cells characterized by the ectopic expression of the inhibitory receptor CLEC2D. Collectively, scRNA-seq of Ph-like ALL with a novel TPR-PDGFRB fusion gene provides valuable insights into the underlying heterogeneity associated with disease progression and offers useful information for the development of immunotherapeutic techniques in the future.
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Affiliation(s)
- Xuehong Zhang
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China. .,Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China.
| | - Zhijie Hou
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China ,grid.411971.b0000 0000 9558 1426Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Dan Huang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Furong Wang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Beibei Gao
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Chengtao Zhang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Dong Zhou
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Jiacheng Lou
- grid.452828.10000 0004 7649 7439Department of Neurosurgery, the Second Hospital of Dalian Medical University, Dalian, China
| | - Haina Wang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Yuan Gao
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Zhijie Kang
- grid.452828.10000 0004 7649 7439Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Ying Lu
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China. .,Institute of Dermatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Quentin Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China. .,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Jinsong Yan
- Department of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, Dalian Key Laboratory of Hematology, Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Diamond Bay Institute of Hematology, The Second Hospital of Dalian Medical University, Dalian, China.
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Liu Y, Zhao X, Bian J, Wang G. Feature selection combined with top-down and bottom-up strategies for survival analysis: A case of prognostic prediction in glioblastoma. Comput Biol Med 2023; 153:106486. [PMID: 36603438 DOI: 10.1016/j.compbiomed.2022.106486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/18/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022]
Abstract
Over the last decades, molecular signatures have attracted extensive attention in cancer research. However, most of the reported biomarkers show a weak distinguishing ability in predicting the survival risks of patients. Actually, univariate analysis is generally considered in regression analysis, which makes the existing statistical methods ineffective. Furthermore, there is too much human involvement in the ways of classifying patients with high and low risk. Last but not least, the participation of therapy after conservative surgery also makes the survival analysis more complex. In order to solve these problems, we propose a solid method of feature selection which combines top-down and bottom-up strategies. The top-down strategy is to randomly extract some genes each time and select candidate genes through cumulative voting. The bottom-up strategy is to fully enumerate the selected genes and to use a clustering algorithm to classify samples. We analyzed glioblastoma data from the Cancer Genome Atlas (TCGA) and got candidate signatures. The results of simulation data, as well as an independent test set the Chinese Glioma Genome Atlas (CGGA), verified the reliability of the method and validity of the selected features.
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Affiliation(s)
- Yanan Liu
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Xudong Zhao
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China.
| | - Jilong Bian
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Guohua Wang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
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Iacobucci I, Witkowski MT, Mullighan CG. Single-cell analysis of acute lymphoblastic and lineage-ambiguous leukemia: approaches and molecular insights. Blood 2023; 141:356-368. [PMID: 35926109 PMCID: PMC10023733 DOI: 10.1182/blood.2022016954] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/13/2022] [Accepted: 07/23/2022] [Indexed: 01/31/2023] Open
Abstract
Despite recent progress in identifying the genetic drivers of acute lymphoblastic leukemia (ALL), prognosis remains poor for those individuals who experience disease recurrence. Moreover, acute leukemias of ambiguous lineage lack a biologically informed framework to guide classification and therapy. These needs have driven the adoption of multiple complementary single-cell sequencing approaches to explore key issues in the biology of these leukemias, including cell of origin, developmental hierarchy and ontogeny, and the molecular heterogeneity driving pathogenesis, progression, and therapeutic responsiveness. There are multiple single-cell techniques for profiling a specific modality, including RNA, DNA, chromatin accessibility and methylation; and an expanding range of approaches for simultaneous analysis of multiple modalities. Single-cell sequencing approaches have also enabled characterization of cell-intrinsic and -extrinsic features of ALL biology. In this review we describe these approaches and highlight the extensive heterogeneity that underpins ALL gene expression, cellular differentiation, and clonal architecture throughout disease pathogenesis and treatment resistance. In addition, we discuss the importance of the dynamic interactions that occur between leukemia cells and the nonleukemia microenvironment. We discuss potential opportunities and limitations of single-cell sequencing for the study of ALL biology and treatment responsiveness.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN
| | - Matthew T. Witkowski
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Charles G. Mullighan
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN
- Hematological Malignancies Program, St Jude Children’s Research Hospital, Memphis, TN
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35
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Yanir AD, Izraeli S. Inflammation meets translation in AML. NATURE CANCER 2023; 4:3-4. [PMID: 36721071 DOI: 10.1038/s43018-022-00499-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Asaf D Yanir
- Schneider Children's Medical Center, Petach Tikva, Israel
| | - Shai Izraeli
- Schneider Children's Medical Center, Petach Tikva, Israel.
- Felsentein Research Institute, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Beckman Research Institute, City of Hope, Duarte, CA, USA.
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Lasry A, Nadorp B, Fornerod M, Nicolet D, Wu H, Walker CJ, Sun Z, Witkowski MT, Tikhonova AN, Guillamot-Ruano M, Cayanan G, Yeaton A, Robbins G, Obeng EA, Tsirigos A, Stone RM, Byrd JC, Pounds S, Carroll WL, Gruber TA, Eisfeld AK, Aifantis I. An inflammatory state remodels the immune microenvironment and improves risk stratification in acute myeloid leukemia. NATURE CANCER 2023; 4:27-42. [PMID: 36581735 PMCID: PMC9986885 DOI: 10.1038/s43018-022-00480-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/04/2022] [Indexed: 12/31/2022]
Abstract
Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. Here we provide a comprehensive census of the bone marrow immune microenvironment in adult and pediatric patients with AML. We characterize unique inflammation signatures in a subset of AML patients, associated with inferior outcomes. We identify atypical B cells, a dysfunctional B-cell subtype enriched in patients with high-inflammation AML, as well as an increase in CD8+GZMK+ and regulatory T cells, accompanied by a reduction in T-cell clonal expansion. We derive an inflammation-associated gene score (iScore) that associates with poor survival outcomes in patients with AML. Addition of the iScore refines current risk stratifications for patients with AML and may enable identification of patients in need of more aggressive treatment. This work provides a framework for classifying patients with AML based on their immune microenvironment and a rationale for consideration of the inflammatory state in clinical settings.
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Affiliation(s)
- Audrey Lasry
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Bettina Nadorp
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Maarten Fornerod
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher J Walker
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Zhengxi Sun
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Matthew T Witkowski
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Anastasia N Tikhonova
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Maria Guillamot-Ruano
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Geraldine Cayanan
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Anna Yeaton
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Gabriel Robbins
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Esther A Obeng
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John C Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William L Carroll
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Tanja A Gruber
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Ann-Kathrin Eisfeld
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA.
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, USA.
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY, USA.
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.
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Single-cell technologies uncover intra-tumor heterogeneity in childhood cancers. Semin Immunopathol 2023; 45:61-69. [PMID: 36625902 DOI: 10.1007/s00281-022-00981-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/11/2022] [Indexed: 01/11/2023]
Abstract
Childhood cancer is the second leading cause of death in children aged 1 to 14. Although survival rates have vastly improved over the past 40 years, cancer resistance and relapse remain a significant challenge. Advances in single-cell technologies enable dissection of tumors to unprecedented resolution. This facilitates unraveling the heterogeneity of childhood cancers to identify cell subtypes that are prone to treatment resistance. The rapid accumulation of single-cell data from different modalities necessitates the development of novel computational approaches for processing, visualizing, and analyzing single-cell data. Here, we review single-cell approaches utilized or under development in the context of childhood cancers. We review computational methods for analyzing single-cell data and discuss best practices for their application. Finally, we review the impact of several studies of childhood tumors analyzed with these approaches and future directions to implement single-cell studies into translational cancer research in pediatric oncology.
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Lai W, Wang X, Liu L, Xu L, Mao L, Tan J, Zha X, Zhan H, Lei W, Lan Y, Chen G, Li Y, Luo OJ. Single-cell profiling of T cells uncovers a tissue-resident memory-like T-cell subset associated with bidirectional prognosis for B-cell acute lymphoblastic leukemia. Front Immunol 2022; 13:957436. [PMID: 36532049 PMCID: PMC9757161 DOI: 10.3389/fimmu.2022.957436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction The character and composition of leukemia-related T cells are closely related to the treatment response and prognosis for patients. Though B cell-acute lymphoblastic leukemia (B-ALL) patients have benefited from immune-based approaches, such as chimeric antigen receptor T cells therapy, some of them still end with poor prognosis, especially for adult patients. Therefore, deep understanding of the developmental relationship between T cell subtypes in relation to B-ALL patient prognosis is urgently needed. Methods We analyzed the peripheral blood T cell single-cell RNA sequencing data of three B-ALL patients, using data from 11 healthy individuals as controls. In total, 16,143 and 53,701 T cells from B-ALL patients and healthy adults, respectively, were objectively analyzed for detailed delineation of 13 distinct T cell clusters. Cluster-specific genes were used as marker genes to annotate each T cell subtype. Results Unbiased analysis enabled the discovery of circulating CD103+ T cell (CD3+CD103+MKI67+), also defined as tissue-resident memory-like T (Trm-like) cell, populations were elevated in B-ALL patients, which expressed high level of cell proliferation and exhaustion related genes. In addition, cell fate trajectory analysis showed these Trm-like cells, which shared T-cell receptor (TCR) clonotypes with exhausted T (Tex) cells and effector T (Teff) cells, were supposed to transition into Teff cells; however, mainly transformed into Tex cells in leukemia environment. More importantly, Trm-like cells transformation into Teff cells and Tex cells potentially led to favorable or poor prognosis for B-ALL patients, respectively. Conclusion In sum, a circulating Trm-like cell subset with high level expression of cell proliferation and exhaustion related genes was elevated in B-ALL patients. The bidirectional developmental potential of these T cells into Teff or Tex is closely associated with favorable or poor prognosis, respectively. Together, our study provided a unique insight of alteration of leukemia related T cells, also showed a potential immunotherapy direction and prognosis assessment model for B-ALL patients.
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Affiliation(s)
- Wenpu Lai
- 1Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China,2Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China,3Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
| | - Xiaofang Wang
- 4Department of Hematology/Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lian Liu
- 2Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Ling Xu
- 2Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Lipeng Mao
- 5Department of Microbiology and Immunology, School of Medicine, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
| | - Jiaxiong Tan
- 1Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Xianfeng Zha
- 6Department of Clinical Laboratory, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Huien Zhan
- 1Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Wen Lei
- 5Department of Microbiology and Immunology, School of Medicine, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
| | - Yu Lan
- 2Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Guobing Chen
- 5Department of Microbiology and Immunology, School of Medicine, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
| | - Yangqiu Li
- 1Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China,2Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China,*Correspondence: Yangqiu Li, ; Oscar Junhong Luo,
| | - Oscar Junhong Luo
- 3Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China,*Correspondence: Yangqiu Li, ; Oscar Junhong Luo,
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Liu L, Ma C, Zhang Z, Witkowski MT, Aifantis I, Ghassemi S, Chen W. Computational model of CAR T-cell immunotherapy dissects and predicts leukemia patient responses at remission, resistance, and relapse. J Immunother Cancer 2022; 10:e005360. [PMID: 36600553 PMCID: PMC9730379 DOI: 10.1136/jitc-2022-005360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Adaptive CD19-targeted chimeric antigen receptor (CAR) T-cell transfer has become a promising treatment for leukemia. Although patient responses vary across different clinical trials, reliable methods to dissect and predict patient responses to novel therapies are currently lacking. Recently, the depiction of patient responses has been achieved using in silico computational models, with prediction application being limited. METHODS We established a computational model of CAR T-cell therapy to recapitulate key cellular mechanisms and dynamics during treatment with responses of continuous remission (CR), non-response (NR), and CD19-positive (CD19+) and CD19-negative (CD19-) relapse. Real-time CAR T-cell and tumor burden data of 209 patients were collected from clinical studies and standardized with unified units in bone marrow. Parameter estimation was conducted using the stochastic approximation expectation maximization algorithm for nonlinear mixed-effect modeling. RESULTS We revealed critical determinants related to patient responses at remission, resistance, and relapse. For CR, NR, and CD19+ relapse, the overall functionality of CAR T-cell led to various outcomes, whereas loss of the CD19+ antigen and the bystander killing effect of CAR T-cells may partly explain the progression of CD19- relapse. Furthermore, we predicted patient responses by combining the peak and accumulated values of CAR T-cells or by inputting early-stage CAR T-cell dynamics. A clinical trial simulation using virtual patient cohorts generated based on real clinical patient datasets was conducted to further validate the prediction. CONCLUSIONS Our model dissected the mechanism behind distinct responses of leukemia to CAR T-cell therapy. This patient-based computational immuno-oncology model can predict late responses and may be informative in clinical treatment and management.
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Affiliation(s)
- Lunan Liu
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, New York, USA
| | - Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, New York, USA
- Department of Biomedical Engineering, New York University, Brooklyn, New York, USA
| | - Zhuoyu Zhang
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, New York, USA
| | - Matthew T Witkowski
- Perlmutter Cancer Center, NYU Langone Health, New York City, New York, USA
- Department of Pathology, NYU Langone Health, New York City, New York, USA
| | - Iannis Aifantis
- Perlmutter Cancer Center, NYU Langone Health, New York City, New York, USA
- Department of Pathology, NYU Langone Health, New York City, New York, USA
| | - Saba Ghassemi
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, New York, USA
- Department of Biomedical Engineering, New York University, Brooklyn, New York, USA
- Perlmutter Cancer Center, NYU Langone Health, New York City, New York, USA
- Department of Pathology, NYU Langone Health, New York City, New York, USA
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40
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Migliaccio AR, Balduini A, Zhan H. Editorial: Megakaryocytes as regulators of tumor microenvironments. Front Oncol 2022; 12:1090658. [PMID: 36505825 PMCID: PMC9732936 DOI: 10.3389/fonc.2022.1090658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Affiliation(s)
- Anna Rita Migliaccio
- Center for Integrated Biomedical Research, Campus Bio-medico, Rome, Italy
- Altius Institute for Biomedical Sciences, Seattle, WA, United States
| | - Alessandra Balduini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
| | - Huichun Zhan
- Department of Medicine, Stony Brook School of Medicine, Stony Brook, NY, United States
- Medical Service, Northport VA Medical Center, Northport, NY, United States
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Jia R, Ji M, Li G, Xia Y, Guo S, Li P, Sun Y, Lu F, Zhang J, Zang S, Yan S, Ye J, Xue F, Ma D, Sun T, Ji C. Subclones of bone marrow CD34 + cells in acute myeloid leukemia at diagnosis confer responses of patients to induction chemotherapy. Cancer 2022; 128:3929-3942. [PMID: 36197314 PMCID: PMC9828578 DOI: 10.1002/cncr.34481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/01/2022] [Accepted: 08/22/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a hematopoietic malignancy with a prognosis that varies with genetic heterogeneity of hematopoietic stem/progenitor cells (HSPCs). Induction chemotherapy with cytarabine and anthracycline has been the standard care for newly diagnosed AML, but about 30% of patients have no response to this regimen. The resistance mechanisms require deeper understanding. METHODS In our study, using single-cell RNA sequencing, we analyzed the heterogeneity of bone marrow CD34+ cells from newly diagnosed patients with AML who were then divided into sensitive and resistant groups according to their responses to induction chemotherapy with cytarabine and anthracycline. We verified our findings by TCGA database, GEO datasets, and multiparameter flow cytometry. RESULTS We established a landscape for AML CD34+ cells and identified HSPC types based on the lineage signature genes. Interestingly, we found a cell population with CRIP1high LGALS1high S100Ashigh showing features of granulocyte-monocyte progenitors was associated with poor prognosis of AML. And two cell populations marked by CD34+ CD52+ or CD34+ CD74+ DAP12+ were related to good response to induction therapy, showing characteristics of hematopoietic stem cells. CONCLUSION Our study indicates the subclones of CD34+ cells confers for outcomes of AML and provides biomarkers to predict the response of patients with AML to induction chemotherapy.
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Affiliation(s)
- Ruinan Jia
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina
| | - Min Ji
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina
| | - Guosheng Li
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina,Shandong Key Laboratory of ImmunohematologyQilu HospitalShandong UniversityJinanChina
| | - Yuan Xia
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina
| | - Shouhui Guo
- Department of BiostatisticsSchool of Public HealthCheeloo College of MedicineShandong UniversityJinanChina,National Institute of Health Data Science of ChinaShandong UniversityJinanChina
| | - Peng Li
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina
| | - Yanping Sun
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina
| | - Fei Lu
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina
| | - Jingru Zhang
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina
| | - Shaolei Zang
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina
| | - Shuxin Yan
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina
| | - Jingjing Ye
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina,Shandong Key Laboratory of ImmunohematologyQilu HospitalShandong UniversityJinanChina
| | - Fuzhong Xue
- Department of BiostatisticsSchool of Public HealthCheeloo College of MedicineShandong UniversityJinanChina,National Institute of Health Data Science of ChinaShandong UniversityJinanChina
| | - Daoxin Ma
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina,Shandong Key Laboratory of ImmunohematologyQilu HospitalShandong UniversityJinanChina
| | - Tao Sun
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina,Shandong Key Laboratory of ImmunohematologyQilu HospitalShandong UniversityJinanChina
| | - Chunyan Ji
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanChina,Shandong Key Laboratory of ImmunohematologyQilu HospitalShandong UniversityJinanChina
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Raufaste-Cazavieille V, Santiago R, Droit A. Multi-omics analysis: Paving the path toward achieving precision medicine in cancer treatment and immuno-oncology. Front Mol Biosci 2022; 9:962743. [PMID: 36304921 PMCID: PMC9595279 DOI: 10.3389/fmolb.2022.962743] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
The acceleration of large-scale sequencing and the progress in high-throughput computational analyses, defined as omics, was a hallmark for the comprehension of the biological processes in human health and diseases. In cancerology, the omics approach, initiated by genomics and transcriptomics studies, has revealed an incredible complexity with unsuspected molecular diversity within a same tumor type as well as spatial and temporal heterogeneity of tumors. The integration of multiple biological layers of omics studies brought oncology to a new paradigm, from tumor site classification to pan-cancer molecular classification, offering new therapeutic opportunities for precision medicine. In this review, we will provide a comprehensive overview of the latest innovations for multi-omics integration in oncology and summarize the largest multi-omics dataset available for adult and pediatric cancers. We will present multi-omics techniques for characterizing cancer biology and show how multi-omics data can be combined with clinical data for the identification of prognostic and treatment-specific biomarkers, opening the way to personalized therapy. To conclude, we will detail the newest strategies for dissecting the tumor immune environment and host–tumor interaction. We will explore the advances in immunomics and microbiomics for biomarker identification to guide therapeutic decision in immuno-oncology.
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Affiliation(s)
| | - Raoul Santiago
- CHU de Québec Research Center, Université Laval, Québec, QC, Canada
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire de L’Université Laval, Charles Bruneau Cancer Center, Québec, QC, Canada
- *Correspondence: Raoul Santiago, ; Arnaud Droit,
| | - Arnaud Droit
- CHU de Québec Research Center, Université Laval, Québec, QC, Canada
- *Correspondence: Raoul Santiago, ; Arnaud Droit,
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43
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Witkowski MT, Lee S, Wang E, Lee AK, Talbot A, Ma C, Tsopoulidis N, Brumbaugh J, Zhao Y, Roberts KG, Hogg SJ, Nomikou S, Ghebrechristos YE, Thandapani P, Mullighan CG, Hochedlinger K, Chen W, Abdel-Wahab O, Eyquem J, Aifantis I. NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia. Nat Immunol 2022; 23:1424-1432. [PMID: 36138187 PMCID: PMC9611506 DOI: 10.1038/s41590-022-01314-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/11/2022] [Indexed: 02/04/2023]
Abstract
B cell progenitor acute lymphoblastic leukemia (B-ALL) treatment has been revolutionized by T cell-based immunotherapies-including chimeric antigen receptor T cell therapy (CAR-T) and the bispecific T cell engager therapeutic, blinatumomab-targeting surface glycoprotein CD19. Unfortunately, many patients with B-ALL will fail immunotherapy due to 'antigen escape'-the loss or absence of leukemic CD19 targeted by anti-leukemic T cells. In the present study, we utilized a genome-wide CRISPR-Cas9 screening approach to identify modulators of CD19 abundance on human B-ALL blasts. These studies identified a critical role for the transcriptional activator ZNF143 in CD19 promoter activation. Conversely, the RNA-binding protein, NUDT21, limited expression of CD19 by regulating CD19 messenger RNA polyadenylation and stability. NUDT21 deletion in B-ALL cells increased the expression of CD19 and the sensitivity to CD19-specific CAR-T and blinatumomab. In human B-ALL patients treated with CAR-T and blinatumomab, upregulation of NUDT21 mRNA coincided with CD19 loss at disease relapse. Together, these studies identify new CD19 modulators in human B-ALL.
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Affiliation(s)
- Matthew T Witkowski
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, USA.
| | - Soobeom Lee
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
- Department of Biology, New York University (NYU), New York, NY, USA
| | - Eric Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - Anna K Lee
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Alexis Talbot
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY, USA
- Department of Biomedical Engineering, New York University, New York, NY, USA
| | - Nikolaos Tsopoulidis
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Yaqi Zhao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Simon J Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sofia Nomikou
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Yohana E Ghebrechristos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Palaniraja Thandapani
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY, USA
- Department of Biomedical Engineering, New York University, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justin Eyquem
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Parker Institute of Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.
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44
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Li Y, Yang X, Sun Y, Li Z, Yang W, Ju B, Easton J, Pei D, Cheng C, Lee S, Pui CH, Yu J, Chi H, Yang JJ. Impact of T-cell immunity on chemotherapy response in childhood acute lymphoblastic leukemia. Blood 2022; 140:1507-1521. [PMID: 35675514 PMCID: PMC9523375 DOI: 10.1182/blood.2021014495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/29/2022] [Indexed: 11/20/2022] Open
Abstract
Although acute lymphoblastic leukemia (ALL) is highly responsive to chemotherapy, it is unknown how or which host immune factors influence the long-term remission of this cancer. To this end, we systematically evaluated the effects of T-cell immunity on Ph+ ALL therapy outcomes. Using a murine Arf-/-BCR-ABL1 B-cell ALL model, we showed that loss of T cells in the host drastically increased leukemia relapse after dasatinib or cytotoxic chemotherapy. Although ABL1 mutations emerged early during dasatinib treatment in both immunocompetent and immunocompromised hosts, T-cell immunity was essential for suppressing the outgrowth of drug-resistant leukemia. Bulk and single-cell transcriptome profiling of T cells during therapy pointed to the activation of type 1 immunity-related cytokine signaling being linked to long-term leukemia remission in mice. Consistent with these observations, interferon γ and interleukin 12 directly modulated dasatinib antileukemia efficacy in vivo. Finally, we evaluated peripheral blood immune cell composition in 102 children with ALL during chemotherapy and observed a significant association of T-cell abundance with treatment outcomes. Together, these results suggest that T-cell immunity plays pivotal roles in maintaining long-term remission of ALL, highlighting that the interplay between host immunity and drug resistance can be harnessed to improve ALL chemotherapy outcomes.
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Affiliation(s)
- Yizhen Li
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Xu Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Yu Sun
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
| | - Zhenhua Li
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenjian Yang
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Bensheng Ju
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Shawn Lee
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J Yang
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
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45
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Identification of immune and stromal cell infiltration-related gene signature for prognosis prediction in acute lymphoblastic leukemia. Aging (Albany NY) 2022; 14:7470-7504. [PMID: 36126190 PMCID: PMC9550239 DOI: 10.18632/aging.204292] [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: 04/26/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a common and life-threatening hematologic malignancy, its occurrence and progression are closely related to immune/stromal cell infiltration in the bone marrow (BM) microenvironment. However, no studies have described an immune/stromal cell infiltration-related gene (ISCIRG)-based prognostic signature for ALL. A total of 444 patients involving 437 bulk and 7 single-cell RNA-seq datasets were included in this study. Eligible datasets were searched and reviewed from the database of TCGA, TARGET project and GEO. Then an integrated bioinformatics analysis was performed to select optimal prognosis-related genes from ISCIRGs, construct a nomogram model for predicting prognosis, and assess the predictive power. After LASSO and multivariate Cox regression analyses, a seven ISCIRGs-based signature was proved to be able to significantly stratify patients into high- and low-risk groups in terms of OS. The seven genes were confirmed that directly related to the composition and status of immune/stromal cells in BM microenvironment by analyzing bulk and single-cell RNA-seq datasets. The calibration plot showed that the predicted results of the nomogram were consistent with the actual observation results of training/validation cohort. This study offers a reference for future research regarding the role of ISCIRGs in ALL and the clinical care of patients.
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46
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Ma R, Liu XT, Chang YJ. Allogeneic haematopoietic stem cell transplantation for acute lymphoblastic leukaemia: current status and future directions mainly focusing on a Chinese perspective. Expert Rev Hematol 2022; 15:789-803. [DOI: 10.1080/17474086.2022.2125375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Rui Ma
- Peking University People’s Hospital & Peking University Institute of Hematology
- National Clinical Research Center for Hematologic Disease
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Xin-Tong Liu
- Peking University People’s Hospital & Peking University Institute of Hematology
- National Clinical Research Center for Hematologic Disease
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Ying-Jun Chang
- Peking University People’s Hospital & Peking University Institute of Hematology
- National Clinical Research Center for Hematologic Disease
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
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47
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Baumann N, Arndt C, Petersen J, Lustig M, Rösner T, Klausz K, Kellner C, Bultmann M, Bastian L, Vogiatzi F, Leusen JHW, Burger R, Schewe DM, Peipp M, Valerius T. Myeloid checkpoint blockade improves killing of T-acute lymphoblastic leukemia cells by an IgA2 variant of daratumumab. Front Immunol 2022; 13:949140. [PMID: 36052078 PMCID: PMC9427194 DOI: 10.3389/fimmu.2022.949140] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Antibody-based immunotherapy is increasingly employed to treat acute lymphoblastic leukemia (ALL) patients. Many T-ALL cells express CD38 on their surface, which can be targeted by the CD38 antibody daratumumab (DARA), approved for the treatment of multiple myeloma. Tumor cell killing by myeloid cells is relevant for the efficacy of many therapeutic antibodies and can be more efficacious with human IgA than with IgG antibodies. This is demonstrated here by investigating antibody-dependent cellular phagocytosis (ADCP) by macrophages and antibody-dependent cell-mediated cytotoxicity (ADCC) by polymorphonuclear (PMN) cells using DARA (human IgG1) and an IgA2 isotype switch variant (DARA-IgA2) against T-ALL cell lines and primary patient-derived tumor cells. ADCP and ADCC are negatively regulated by interactions between CD47 on tumor cells and signal regulatory protein alpha (SIRPα) on effector cells. In order to investigate the impact of this myeloid checkpoint on T-ALL cell killing, CD47 and glutaminyl-peptide cyclotransferase like (QPCTL) knock-out T-ALL cells were employed. QPTCL is an enzymatic posttranslational modifier of CD47 activity, which can be targeted by small molecule inhibitors. Additionally, we used an IgG2σ variant of the CD47 blocking antibody magrolimab, which is in advanced clinical development. Moreover, treatment of T-ALL cells with all-trans retinoic acid (ATRA) increased CD38 expression leading to further enhanced ADCP and ADCC, particularly when DARA-IgA2 was applied. These studies demonstrate that myeloid checkpoint blockade in combination with IgA2 variants of CD38 antibodies deserves further evaluation for T-ALL immunotherapy.
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Affiliation(s)
- Niklas Baumann
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Christian Arndt
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Judith Petersen
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Marta Lustig
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Thies Rösner
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Katja Klausz
- Division of Antibody-Based Immunotherapy, Department of Medicine II, Christian- Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Christian Kellner
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, LMU Munich, Munich, Germany
| | - Miriam Bultmann
- Department of Medicine II, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Lorenz Bastian
- Department of Medicine II, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Fotini Vogiatzi
- Pediatric Hematology/Oncology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jeanette H. W. Leusen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Renate Burger
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Denis M. Schewe
- Children’s Hospital, University Medical Center Magdeburg, Magdeburg, Germany
| | - Matthias Peipp
- Division of Antibody-Based Immunotherapy, Department of Medicine II, Christian- Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Thomas Valerius
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- *Correspondence: Thomas Valerius,
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48
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Gao X, Hong F, Hu Z, Zhang Z, Lei Y, Li X, Cheng T. ABC portal: a single-cell database and web server for blood cells. Nucleic Acids Res 2022; 51:D792-D804. [PMID: 35920330 PMCID: PMC9825444 DOI: 10.1093/nar/gkac646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 01/30/2023] Open
Abstract
ABC portal (http://abc.sklehabc.com) is a database and web portal containing 198 single-cell transcriptomic datasets of development, differentiation and disorder of blood/immune cells. All the datasets were re-annotated with a manually curated and unified single-cell reference, especially for the haematopoietic stem and progenitor cells. ABC portal provides web-based interactive analysis modules, especially a comprehensive cell-cell communication analysis and disease-related gene signature analysis. Importantly, ABC portal allows customized sample selection based on a combination of several metadata for downstream analysis and comparison analysis across datasets. ABC portal also allows users to select multiple cell types for analysis in the modules. Together, ABC portal provides an interactive interface of single-cell data exploration and re-analysis with customized analysis modules for the researchers and clinicians, and will facilitate understanding of haematopoiesis and blood/immune disorders.
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Affiliation(s)
- Xin Gao
- To whom correspondence should be addressed. Tel: +86 22 2390 9006; Fax: +86 22 2390 9006;
| | - Fang Hong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Zhenyu Hu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Zilong Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yang Lei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Xiaoyun Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- Correspondence may also be addressed to Tao Cheng.
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Singh VK, Seed TM. Acute radiation syndrome drug discovery using organ-on-chip platforms. Expert Opin Drug Discov 2022; 17:865-878. [PMID: 35838021 DOI: 10.1080/17460441.2022.2099833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION : The high attrition rate during drug development remains a challenge that costs a significant amount of time and money. Improving the probabilities of success during the early stages of radiation medical countermeasure (MCM) development for approval by the United States Food and Drug Administration (US FDA) following the Animal Rule will reduce this burden. For optimal development of MCMs, we need suitable and efficient radiation injury models with high biological relevance for evaluating drug efficacy as well as biomarker discovery and validation. AREA COVERED This article focuses on new technologies involving various organs-on-chip platforms. Of late, there have been rapid development of these technologies, especially in terms of mimicking both normal and abnormal physiological conditions. Here, we suggest possible applications of these novel systems for the discovery and development of radiation MCMs for the acute radiation syndrome (ARS). We offer preliminary information on the utility of one such system for MCM research and discovery for the ARS condition. EXPERT OPINION : Each organ-on-a-chip system has its own strengths and shortcomings. As such, the system selected for MCM discovery, development, and regulatory approval should be carefully considered and optimized to the fullest extent in order to augment successful drug testing and the minimization of attrition rates of candidate agents. The recent encouraging progress with organ-on-a-chip technology will likely lead to additional radiation MCMs for ARS approved by the US FDA. The acceptance of organ-on-a-chip technology may be a promising step toward improving the success rate of pharmaceuticals in MCM development.
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Affiliation(s)
- Vijay K Singh
- Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Thomas M Seed
- Tech Micro Services, 4417 Maple Avenue, Bethesda, MD, USA
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50
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B-cell acute lymphoblastic leukemia promotes an immune suppressive microenvironment that can be overcome by IL-12. Sci Rep 2022; 12:11870. [PMID: 35831470 PMCID: PMC9279427 DOI: 10.1038/s41598-022-16152-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/05/2022] [Indexed: 12/14/2022] Open
Abstract
Immunotherapies have revolutionized the treatment of B-cell acute lymphoblastic leukemia (B-ALL), but the duration of responses is still sub-optimal. We sought to identify mechanisms of immune suppression in B-ALL and strategies to overcome them. Plasma collected from children with B-ALL with measurable residual disease after induction chemotherapy showed differential cytokine expression, particularly IL-7, while single-cell RNA-sequencing revealed the expression of genes associated with immune exhaustion in immune cell subsets. We also found that the supernatant of leukemia cells suppressed T-cell function ex vivo. Modeling B-ALL in mice, we observed an altered tumor immune microenvironment, including compromised activation of T-cells and dendritic cells (DC). However, recombinant IL-12 (rIL-12) treatment of mice with B-ALL restored the levels of several pro-inflammatory cytokines and chemokines in the bone marrow and increased the number of splenic and bone marrow resident T-cells and DCs. RNA-sequencing of T-cells isolated from vehicle and rIL-12 treated mice with B-ALL revealed that the leukemia-induced increase in genes associated with exhaustion, including Lag3, Tigit, and Il10, was abrogated with rIL-12 treatment. In addition, the cytolytic capacity of T-cells co-cultured with B-ALL cells was enhanced when IL-12 and blinatumomab treatments were combined. Overall, these results demonstrate that the leukemia immune suppressive microenvironment can be restored with rIL-12 treatment which has direct therapeutic implications.
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