1
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Wang Y, Flowers CR, Wang M, Huang X, Li Z. CASi: A framework for cross-timepoint analysis of single-cell RNA sequencing data. Sci Rep 2024; 14:10633. [PMID: 38724550 PMCID: PMC11082156 DOI: 10.1038/s41598-024-58566-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/01/2024] [Indexed: 05/12/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technology has been widely used to study the differences in gene expression at the single cell level, providing insights into the research of cell development, differentiation, and functional heterogeneity. Various pipelines and workflows of scRNA-seq analysis have been developed but few considered multi-timepoint data specifically. In this study, we develop CASi, a comprehensive framework for analyzing multiple timepoints' scRNA-seq data, which provides users with: (1) cross-timepoint cell annotation, (2) detection of potentially novel cell types emerged over time, (3) visualization of cell population evolution, and (4) identification of temporal differentially expressed genes (tDEGs). Through comprehensive simulation studies and applications to a real multi-timepoint single cell dataset, we demonstrate the robust and favorable performance of the proposal versus existing methods serving similar purposes.
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Affiliation(s)
- Yizhuo Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, 77030, USA
| | - Christopher R Flowers
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, 77030, USA
| | - Michael Wang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, 77030, USA
| | - Xuelin Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, 77030, USA.
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, 77030, USA.
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2
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Zhuang H, Ji Z. PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns. bioRxiv 2024:2024.03.20.585926. [PMID: 38585819 PMCID: PMC10996487 DOI: 10.1101/2024.03.20.585926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Modeling temporal and spatial gene expression patterns in large-scale single-cell and spatial transcriptomics data is a computationally intensive task. We present PreTSA, a method that offers computational efficiency in modeling these patterns and is applicable to single-cell and spatial transcriptomics data comprising millions of cells. PreTSA consistently matches the results of state-of-the-art methods while significantly reducing computational time. PreTSA provides a unique solution for studying gene expression patterns in extremely large datasets.
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Affiliation(s)
- Haotian Zhuang
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
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3
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Nylund P, Nikkarinen A, Ek S, Glimelius I. Empowering macrophages: the cancer fighters within the tumour microenvironment in mantle cell lymphoma. Front Immunol 2024; 15:1373269. [PMID: 38566987 PMCID: PMC10985169 DOI: 10.3389/fimmu.2024.1373269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
In Mantle Cell Lymphoma (MCL), the role of macrophages within the tumour microenvironment (TME) has recently gained attention due to their impact on prognosis and response to therapy. Despite their low absolute number in MCL tumour tissue, recent findings reveal an association between the levels of macrophages and prognosis, consistent with trends observed in other lymphoma subtypes. M2-like macrophages, identified by markers such as CD163, contribute to angiogenesis and suppression of the immune response. Clinical trials with MCL patients treated with chemoimmunotherapy and targeted treatments underscore the adverse impact of high levels of M2-like macrophages. Immunomodulatory drugs like lenalidomide reduce the levels of MCL-associated CD163+ macrophages and enhance macrophage phagocytic activity. Similarly, clinical approaches targeting the CD47 "don't eat me" signalling, in combination with the anti-CD20-antibody rituximab, demonstrate increased macrophage activity and phagocytosis of MCL tumour cells. Cell-based therapies such as chimeric antigen receptor (CAR) T-cell have shown promise but various challenges persist, leading to a potential interest in CAR-macrophages (CAR-M). When macrophages are recruited to the TME, they offer advantages including phagocytic function and responsiveness to microenvironment alterations, suggesting their potential as a manipulable and inducible alternative when CAR T-cell therapies fails in the complex landscape of MCL treatment.
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Affiliation(s)
- Patrick Nylund
- Department of Immunology, Genetics and Pathology, Cancer Precision Medicine Unit, Uppsala University, Uppsala, Sweden
| | - Anna Nikkarinen
- Department of Immunology, Genetics and Pathology, Cancer Precision Medicine Unit, Uppsala University, Uppsala, Sweden
| | - Sara Ek
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Ingrid Glimelius
- Department of Immunology, Genetics and Pathology, Cancer Precision Medicine Unit, Uppsala University, Uppsala, Sweden
- Division of Clinical Epidemiology, Department of Medicine, Karolinska Institute, Stockholm, Sweden
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4
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Lantermans HC, Ma F, Kuil A, van Kesteren S, Yasinoglu S, Yang G, Buhrlage SJ, Wang J, Gray NS, Kersten MJ, Treon SP, Pals ST, Spaargaren M. The dual HCK/BTK inhibitor KIN-8194 impairs growth and integrin-mediated adhesion of BTKi-resistant mantle cell lymphoma. Leukemia 2024:10.1038/s41375-024-02207-9. [PMID: 38454120 DOI: 10.1038/s41375-024-02207-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024]
Abstract
Although Bruton's tyrosine kinase (BTK) inhibitors (BTKi) have significantly improved patient prognosis, mantle cell lymphoma (MCL) is still considered incurable due to primary and acquired resistance. We have recently shown that aberrant expression of the Src-family tyrosine kinase hematopoietic cell kinase (HCK) in MCL correlates with poor prognosis, and that genetic HCK perturbation impairs growth and integrin-mediated adhesion of MCL cells. Here, we show that KIN-8194, a dual inhibitor of BTK and HCK with in vivo activity against Myd88-L265P-driven diffuse large B-cell lymphoma and Waldenström Macroglobulinemia, has a potent growth inhibitory effect in MCL cell lines and primary MCL cells, irrespective of their sensitivity to BTKi (ibrutinib and acalabrutinib). In BTKi-resistant cells this is mediated by inhibition of HCK, which results in repression of AKT-S6 signaling. In addition, KIN-8194 inhibits integrin-mediated adhesion of BTKi-sensitive and insensitive MCL cells to fibronectin and stromal cells in an HCK-dependent manner. Finally, we show that MCL cells with acquired BTKi resistance retain their sensitivity to KIN-8194. Taken together, our data demonstrate that KIN-8194 inhibits growth and integrin-mediated adhesion of BTKi-sensitive MCL cells, as well as MCL cells with primary or acquired BTKi resistance. This renders KIN-8194 a promising novel treatment for MCL patients.
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Affiliation(s)
- Hildo C Lantermans
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Lymphoma and Myeloma Center Amsterdam - LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target & Therapy Discovery, Amsterdam, The Netherlands
| | - Fangxue Ma
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Lymphoma and Myeloma Center Amsterdam - LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target & Therapy Discovery, Amsterdam, The Netherlands
| | - Annemieke Kuil
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Lymphoma and Myeloma Center Amsterdam - LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target & Therapy Discovery, Amsterdam, The Netherlands
| | - Sanne van Kesteren
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Lymphoma and Myeloma Center Amsterdam - LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target & Therapy Discovery, Amsterdam, The Netherlands
| | - Sevtap Yasinoglu
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Lymphoma and Myeloma Center Amsterdam - LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target & Therapy Discovery, Amsterdam, The Netherlands
| | - Guang Yang
- Bing Center for Waldenström Macroglobulinemia, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Blueprint Medicines, Cambridge, MA, USA
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Marie José Kersten
- Lymphoma and Myeloma Center Amsterdam - LYMMCARE, Amsterdam, The Netherlands
- Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Steven P Treon
- Bing Center for Waldenström Macroglobulinemia, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Steven T Pals
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Lymphoma and Myeloma Center Amsterdam - LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target & Therapy Discovery, Amsterdam, The Netherlands
| | - Marcel Spaargaren
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
- Lymphoma and Myeloma Center Amsterdam - LYMMCARE, Amsterdam, The Netherlands.
- Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target & Therapy Discovery, Amsterdam, The Netherlands.
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5
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Playa-Albinyana H, Arenas F, Royo R, Giró A, López-Oreja I, Aymerich M, López-Guerra M, Frigola G, Beà S, Delgado J, Garcia-Roves PM, Campo E, Nadeu F, Colomer D. Chronic lymphocytic leukemia patient-derived xenografts recapitulate clonal evolution to Richter transformation. Leukemia 2024; 38:557-569. [PMID: 38017105 PMCID: PMC10912031 DOI: 10.1038/s41375-023-02095-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/08/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is a B-cell neoplasm with a heterogeneous clinical behavior. In 5-10% of patients the disease transforms into a diffuse large-B cell lymphoma known as Richter transformation (RT), which is associated with dismal prognosis. Here, we aimed to establish patient-derived xenograft (PDX) models to study the molecular features and evolution of CLL and RT. We generated two PDXs by injecting CLL (PDX12) and RT (PDX19) cells into immunocompromised NSG mice. Both PDXs were morphologically and phenotypically similar to RT. Whole-genome sequencing analysis at different time points of the PDX evolution revealed a genomic landscape similar to RT tumors from both patients and uncovered an unprecedented RT subclonal heterogeneity and clonal evolution during PDX generation. In PDX12, the transformed cells expanded from a very small subclone already present at the CLL stage. Transcriptomic analysis of PDXs showed a high oxidative phosphorylation (OXPHOS) and low B-cell receptor (BCR) signaling similar to the RT in the patients. IACS-010759, an OXPHOS inhibitor, reduced proliferation, and circumvented resistance to venetoclax. In summary, we have generated new RT-PDX models, one of them from CLL cells that mimicked the evolution of CLL to RT uncovering intrinsic features of RT cells of therapeutical value.
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MESH Headings
- Humans
- Animals
- Mice
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Heterografts
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Clonal Evolution/genetics
- Prognosis
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
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Affiliation(s)
- Heribert Playa-Albinyana
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Fabian Arenas
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Barcelona, Spain
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Ariadna Giró
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Irene López-Oreja
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Barcelona, Spain
- Hematopathology Section, Pathology Department, Hospital Clínic, Barcelona, Spain
| | - Marta Aymerich
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Barcelona, Spain
- Hematopathology Section, Pathology Department, Hospital Clínic, Barcelona, Spain
| | - Mònica López-Guerra
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Barcelona, Spain
- Hematopathology Section, Pathology Department, Hospital Clínic, Barcelona, Spain
| | - Gerard Frigola
- Hematopathology Section, Pathology Department, Hospital Clínic, Barcelona, Spain
- Molecular Pathology of Lymphoid Neoplasms Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sílvia Beà
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Hematopathology Section, Pathology Department, Hospital Clínic, Barcelona, Spain
- Molecular Pathology of Lymphoid Neoplasms Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Julio Delgado
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
- Lymphoid Neoplasms Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pablo M Garcia-Roves
- University of Barcelona, Barcelona, Spain
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Elías Campo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Hematopathology Section, Pathology Department, Hospital Clínic, Barcelona, Spain
- Molecular Pathology of Lymphoid Neoplasms Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ferran Nadeu
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Barcelona, Spain
- Molecular Pathology of Lymphoid Neoplasms Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Dolors Colomer
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Barcelona, Spain.
- University of Barcelona, Barcelona, Spain.
- Hematopathology Section, Pathology Department, Hospital Clínic, Barcelona, Spain.
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6
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Yan F, Jiang V, Jordan A, Che Y, Liu Y, Cai Q, Xue Y, Li Y, McIntosh J, Chen Z, Vargas J, Nie L, Yao Y, Lee HH, Wang W, Bigcal JR, Badillo M, Meena J, Flowers C, Zhou J, Zhao Z, Simon LM, Wang M. The HSP90-MYC-CDK9 network drives therapeutic resistance in mantle cell lymphoma. Exp Hematol Oncol 2024; 13:14. [PMID: 38326887 PMCID: PMC10848414 DOI: 10.1186/s40164-024-00484-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
Brexucabtagene autoleucel CAR-T therapy is highly efficacious in overcoming resistance to Bruton's tyrosine kinase inhibitors (BTKi) in mantle cell lymphoma. However, many patients relapse post CAR-T therapy with dismal outcomes. To dissect the underlying mechanisms of sequential resistance to BTKi and CAR-T therapy, we performed single-cell RNA sequencing analysis for 66 samples from 25 patients treated with BTKi and/or CAR-T therapy and conducted in-depth bioinformatics™ analysis. Our analysis revealed that MYC activity progressively increased with sequential resistance. HSP90AB1 (Heat shock protein 90 alpha family class B member 1), a MYC target, was identified as early driver of CAR-T resistance. CDK9 (Cyclin-dependent kinase 9), another MYC target, was significantly upregulated in Dual-R samples. Both HSP90AB1 and CDK9 expression were correlated with MYC activity levels. Pharmaceutical co-targeting of HSP90 and CDK9 synergistically diminished MYC activity, leading to potent anti-MCL activity. Collectively, our study revealed that HSP90-MYC-CDK9 network is the primary driving force of therapeutic resistance.
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Affiliation(s)
- Fangfang Yan
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivian Jiang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Alexa Jordan
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuxuan Che
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yang Liu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qingsong Cai
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Xue
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Yijing Li
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph McIntosh
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhihong Chen
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jovanny Vargas
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lei Nie
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yixin Yao
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heng-Huan Lee
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei Wang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - JohnNelson R Bigcal
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Badillo
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jitendra Meena
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
| | - Lukas M Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Michael Wang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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7
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Long ME, Koirala S, Sloan S, Brown-Burke F, Weigel C, Villagomez L, Corps K, Sharma A, Hout I, Harper M, Helmig-Mason J, Tallada S, Chen Z, Scherle P, Vaddi K, Chen-Kiang S, Di Liberto M, Meydan C, Foox J, Butler D, Mason C, Alinari L, Blaser BW, Baiocchi R. Resistance to PRMT5-targeted therapy in mantle cell lymphoma. Blood Adv 2024; 8:150-163. [PMID: 37782774 PMCID: PMC10787272 DOI: 10.1182/bloodadvances.2023010554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/16/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023] Open
Abstract
ABSTRACT Mantle cell lymphoma (MCL) is an incurable B-cell non-Hodgkin lymphoma, and patients who relapse on targeted therapies have poor prognosis. Protein arginine methyltransferase 5 (PRMT5), an enzyme essential for B-cell transformation, drives multiple oncogenic pathways and is overexpressed in MCL. Despite the antitumor activity of PRMT5 inhibition (PRT-382/PRT-808), drug resistance was observed in a patient-derived xenograft (PDX) MCL model. Decreased survival of mice engrafted with these PRMT5 inhibitor-resistant cells vs treatment-naive cells was observed (P = .005). MCL cell lines showed variable sensitivity to PRMT5 inhibition. Using PRT-382, cell lines were classified as sensitive (n = 4; 50% inhibitory concentration [IC50], 20-140 nM) or primary resistant (n = 4; 340-1650 nM). Prolonged culture of sensitive MCL lines with drug escalation produced PRMT5 inhibitor-resistant cell lines (n = 4; 200-500 nM). This resistant phenotype persisted after prolonged culture in the absence of drug and was observed with PRT-808. In the resistant PDX and cell line models, symmetric dimethylarginine reduction was achieved at the original PRMT5 inhibitor IC50, suggesting activation of alternative resistance pathways. Bulk RNA sequencing of resistant cell lines and PDX relative to sensitive or short-term-treated cells, respectively, highlighted shared upregulation of multiple pathways including mechanistic target of rapamycin kinase [mTOR] signaling (P < 10-5 and z score > 0.3 or < 0.3). Single-cell RNA sequencing analysis demonstrated a strong shift in global gene expression, with upregulation of mTOR signaling in resistant PDX MCL samples. Targeted blockade of mTORC1 with temsirolimus overcame the PRMT5 inhibitor-resistant phenotype, displayed therapeutic synergy in resistant MCL cell lines, and improved survival of a resistant PDX.
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Affiliation(s)
- Mackenzie Elizabeth Long
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Shirsha Koirala
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
| | - Shelby Sloan
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Fiona Brown-Burke
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
| | - Christoph Weigel
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
| | - Lynda Villagomez
- Division of Hematology and Oncology, Department of Pediatrics, The Ohio State University and Nationwide Children’s Hospital, Columbus, OH
| | - Kara Corps
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Archisha Sharma
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
| | - Ian Hout
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
| | - Margaret Harper
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
| | - JoBeth Helmig-Mason
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
| | - Sheetal Tallada
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
| | - Zhengming Chen
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY
| | | | | | - Selina Chen-Kiang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Maurizio Di Liberto
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Cem Meydan
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
| | - Jonathan Foox
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
| | - Daniel Butler
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
| | - Christopher Mason
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
| | - Lapo Alinari
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
| | - Bradley W. Blaser
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
| | - Robert Baiocchi
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
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8
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Sun L, Wan AH, Yan S, Liu R, Li J, Zhou Z, Wu R, Chen D, Bu X, Ou J, Li K, Lu X, Wan G, Ke Z. A multidimensional platform of patient-derived tumors identifies drug susceptibilities for clinical lenvatinib resistance. Acta Pharm Sin B 2024; 14:223-240. [PMID: 38261805 PMCID: PMC10793100 DOI: 10.1016/j.apsb.2023.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 01/25/2024] Open
Abstract
Lenvatinib, a second-generation multi-receptor tyrosine kinase inhibitor approved by the FDA for first-line treatment of advanced liver cancer, facing limitations due to drug resistance. Here, we applied a multidimensional, high-throughput screening platform comprising patient-derived resistant liver tumor cells (PDCs), organoids (PDOs), and xenografts (PDXs) to identify drug susceptibilities for conquering lenvatinib resistance in clinically relevant settings. Expansion and passaging of PDCs and PDOs from resistant patient liver tumors retained functional fidelity to lenvatinib treatment, expediting drug repurposing screens. Pharmacological screening identified romidepsin, YM155, apitolisib, NVP-TAE684 and dasatinib as potential antitumor agents in lenvatinib-resistant PDC and PDO models. Notably, romidepsin treatment enhanced antitumor response in syngeneic mouse models by triggering immunogenic tumor cell death and blocking the EGFR signaling pathway. A combination of romidepsin and immunotherapy achieved robust and synergistic antitumor effects against lenvatinib resistance in humanized immunocompetent PDX models. Collectively, our findings suggest that patient-derived liver cancer models effectively recapitulate lenvatinib resistance observed in clinical settings and expedite drug discovery for advanced liver cancer, providing a feasible multidimensional platform for personalized medicine.
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Affiliation(s)
- Lei Sun
- Department of Pathology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Arabella H. Wan
- Department of Pathology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Shijia Yan
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ruonian Liu
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiarui Li
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhuolong Zhou
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ruirui Wu
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Dongshi Chen
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Xianzhang Bu
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingxing Ou
- Department of Hepatic Surgery and Liver Transplantation Center, Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou 510630, China
| | - Kai Li
- Department of Ultrasound, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Xiongbin Lu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN 46202, USA
| | - Guohui Wan
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zunfu Ke
- Department of Pathology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
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9
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Gribbin C, Chen J, Martin P, Ruan J. Novel treatment for mantle cell lymphoma - impact of BTK inhibitors and beyond. Leuk Lymphoma 2024; 65:1-13. [PMID: 37800170 DOI: 10.1080/10428194.2023.2264430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
Mantle cell lymphoma (MCL) primarily affects older adults, accounting for 3-10% of all non-Hodgkin lymphoma (NHL) in western countries. The disease course of MCL is heterogenous; driven by clinical, cytogenetics, and molecular features that shape differences in outcomes, including proliferation index, MIPI scores, and mutational profile such as TP53 aberration. The advent of novel agents has fundamentally evolved the treatment landscape for MCL with treatment strategies that can now be more effectively tailored based on both patient- and disease-specific factors. In this review, we discuss the major classes of novel agents used for the treatment of MCL, focusing on efficacy and notable toxicities of BTK inhibitors. We further examine effective novel combination regimens and, lastly, discuss future directions for the evolution of targeted approaches for the treatment of MCL.
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Affiliation(s)
- Caitlin Gribbin
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Jane Chen
- The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Peter Martin
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Jia Ruan
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
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10
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Li Y, Lee HH, Jiang VC, Che Y, McIntosh J, Jordan A, Vargas J, Zhang T, Yan F, Simmons ME, Wang W, Nie L, Yao Y, Jain P, Wang M, Liu Y. Potentiation of apoptosis in drug-resistant mantle cell lymphoma cells by MCL-1 inhibitor involves downregulation of inhibitor of apoptosis proteins. Cell Death Dis 2023; 14:714. [PMID: 37919300 PMCID: PMC10622549 DOI: 10.1038/s41419-023-06233-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Bruton's tyrosine kinase inhibitors (BTKi) and CAR T-cell therapy have demonstrated tremendous clinical benefits in mantle cell lymphoma (MCL) patients, but intrinsic or acquired resistance inevitably develops. In this study, we assessed the efficacy of the highly potent and selective MCL-1 inhibitor AZD5991 in various therapy-resistant MCL cell models. AZD5991 markedly induced apoptosis in these cells. In addition to liberating BAK from the antiapoptotic MCL-1/BAK complex for the subsequent apoptosis cascade, AZD5991 downregulated inhibitor of apoptosis proteins (IAPs) through a BAK-dependent mechanism to amplify the apoptotic signal. The combination of AZD5991 with venetoclax enhanced apoptosis and reduced mitochondrial oxygen consumption capacity in MCL cell lines irrespective of their BTKi or venetoclax sensitivity. This combination also dramatically inhibited tumor growth and prolonged mouse survival in two aggressive MCL patient-derived xenograft models. Mechanistically, the augmented cell lethality was accompanied by the synergistic suppression of IAPs. Supporting this notion, the IAP antagonist BV6 induced dramatic apoptosis in resistant MCL cells and sensitized the resistant MCL cells to venetoclax. Our study uncovered another unique route for MCL-1 inhibitor to trigger apoptosis, implying that the pro-apoptotic combination of IAP antagonists and apoptosis inducers could be further exploited for MCL patients with multiple therapeutic resistance.
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Affiliation(s)
- Yijing Li
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Heng-Huan Lee
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vivian Changying Jiang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yuxuan Che
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Joseph McIntosh
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexa Jordan
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jovanny Vargas
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Tianci Zhang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Fangfang Yan
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Margaret Elizabeth Simmons
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wei Wang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lei Nie
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yixin Yao
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Preetesh Jain
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Michael Wang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yang Liu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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11
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Maura F, Adams RM, Aoki T. Scientific techniques in adolescent and young adult classic Hodgkin lymphoma. EJHaem 2023; 4:902-907. [PMID: 38024640 PMCID: PMC10660113 DOI: 10.1002/jha2.786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 12/01/2023]
Abstract
Understanding the tumor microenvironment and genomic landscape is crucial for better prediction of treatment outcomes and developing novel therapies in Hodgkin lymphoma (HL). Recent advancements in genomics have enabled researchers to gain deeper insights into the genomic characteristics of HL at both single-cell resolution and the whole genome level. The use of noninvasive methods such as liquid biopsies and formalin-fixed paraffin-embedded-based imaging techniques has expanded the possibilities of applying cutting-edge analyses to routine clinically available samples. Collaborative efforts between adult and pediatric group are imperative to translate novel findings into routine patient care.
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Affiliation(s)
- Francesco Maura
- Sylvester Comprehensive Cancer CenterUniversity of MiamiMiamiFloridaUSA
| | - Ragini M. Adams
- Division of Pediatric Hematology, OncologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Tomohiro Aoki
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoOntarioCanada
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12
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Jain P, Nomie K, Kotlov N, Segodin V, Hill H, Ok CY, Fetooh A, Kanagal-Shamanna R, Vega F, Bagaev A, Fowler N, Flowers CR, Wang M. Immune-depleted tumor microenvironment is associated with poor outcomes and BTK inhibitor resistance in mantle cell lymphoma. Blood Cancer J 2023; 13:156. [PMID: 37821434 PMCID: PMC10567800 DOI: 10.1038/s41408-023-00927-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/08/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Affiliation(s)
- Preetesh Jain
- Department of Lymphoma and Myeloma from The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | | | | | | | - Holly Hill
- Department of Lymphoma and Myeloma from The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi Young Ok
- Department of Hematopathology at The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ahmed Fetooh
- Department of Lymphoma and Myeloma from The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology at The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francisco Vega
- Department of Hematopathology at The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Nathan Fowler
- Department of Lymphoma and Myeloma from The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- BostonGene Corporation, Boston, MA, USA
| | - Christopher R Flowers
- Department of Lymphoma and Myeloma from The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Wang
- Department of Lymphoma and Myeloma from The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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13
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Liu L, Zhang Q, Wang C, Guo H, Mukwaya V, Chen R, Xu Y, Wei X, Chen X, Zhang S, Zhou M, Dou H. Single-Cell Diagnosis of Cancer Drug Resistance through the Differential Endocytosis of Nanoparticles between Drug-Resistant and Drug-Sensitive Cancer Cells. ACS Nano 2023; 17:19372-19386. [PMID: 37781914 DOI: 10.1021/acsnano.3c07030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Single-cell diagnosis of cancer drug resistance is highly relevant for cancer treatment, as it can be used to identify the subpopulations of drug-resistant cancer cells, reveal the sensitivity of cancer cells to treatment, and monitor the progress of cancer drug resistance. However, simple and effective methods for cancer drug resistance detection at the single-cell level are still lacking in laboratory and clinical studies. Inspired by the fact that nanoparticles with diverse physicochemical properties would generate distinct and specific interactions with drug-resistant and drug-sensitive cancer cells, which have distinctive molecular signatures, here, we have synthesized a library of fluorescent nanoparticles with various sizes, surface charges, and compositions (SiO2 nanoparticles (SNPs), organic PS-co-PAA nanoparticles (ONPs), and ZIF-8 nanoparticles (ZNPs)), thus demonstrating that the composition has a critical influence on the interaction of nanoparticles with drug-resistant cancer cells. Furthermore, the clathrin/caveolae-independent endocytosis of ZNPs together with the P-glycoprotein-related decreased cell membrane fluidity resulted in a lower cellular accumulation of ZNPs in drug-resistant cancer cells, consequently causing the distinct cellular accumulation of ZNPs between the drug-resistant and drug-sensitive cancer cells. This difference was further quantified by detecting the fluorescence signals generated by the accumulation of nanoparticles at the single-cell level via flow cytometry. Our findings provide another insight into the nanoparticle-cell interactions and offer a promising platform for the diagnosis of cancer drug resistance of various cancer cells and clinical cancer samples at the single-cell level.
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Affiliation(s)
- Lingshan Liu
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
| | - Qiurui Zhang
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, China
| | - Chenglong Wang
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
| | - Heze Guo
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
| | - Vincent Mukwaya
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
| | - Rong Chen
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, China
| | - Yichun Xu
- Shanghai Biochip Co. Ltd. and National Engineering Center for Biochip at Shanghai, 151 Libing Road, Shanghai 201203, China
| | - Xiaohui Wei
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaoyan Chen
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, China
| | - Sujiang Zhang
- 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, 197 Ruijin 2nd Road, Shanghai 200025, China
| | - Min Zhou
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, China
| | - Hongjing Dou
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
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14
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Raghani NR, Shah DD, Shah TS, Chorawala MR, Patel RB. Combating relapsed and refractory Mantle cell lymphoma with novel therapeutic armamentarium: Recent advances and clinical prospects. Crit Rev Oncol Hematol 2023; 190:104085. [PMID: 37536448 DOI: 10.1016/j.critrevonc.2023.104085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/05/2023] Open
Abstract
Mantle cell lymphoma (MCL) is a rare, aggressive subtype of non-Hodgkin's lymphoma (NHL), accounting for 5% of all cases. Due to its virulence factor, it is an incurable disease and keeps relapsing despite an intensive treatment regimen. Advancements in research and drug discovery have shifted the treatment strategy from conventional chemotherapy to targeted agents and immunotherapies. The establishment of the role of Bruton tyrosine kinase led to the development of ibrutinib, a first-generation BTK inhibitor, and its successors. A conditioning regimen based immunotherapeutic agent like ibritumumob, has also demonstrated a viable response with a favorable toxicity profile. Brexucabtagene Autoleucel, the only approved CAR T-cell therapy, has proven advantageous for relapsed/refractory MCL in both children and adults. This article reviews certain therapies that could help update the current approach and summarizes a few miscellaneous agents, which, seldom studied in trials, could alleviate the regression observed in traditional therapies. DATA AVAILABILITY: The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.
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Affiliation(s)
- Neha R Raghani
- Department of Pharmacology and Pharmacy practice, L. M. College of Pharmacy, Opp. Gujarat University, Navrangpura, Ahmedabad 380009, Gujarat, India.
| | - Disha D Shah
- Department of Pharmacology and Pharmacy practice, L. M. College of Pharmacy, Opp. Gujarat University, Navrangpura, Ahmedabad 380009, Gujarat, India.
| | - Tithi S Shah
- Department of Pharmacology and Pharmacy practice, L. M. College of Pharmacy, Opp. Gujarat University, Navrangpura, Ahmedabad 380009, Gujarat, India.
| | - Mehul R Chorawala
- Department of Pharmacology and Pharmacy practice, L. M. College of Pharmacy, Opp. Gujarat University, Navrangpura, Ahmedabad 380009, Gujarat, India.
| | - Rakesh B Patel
- Department of Internal Medicine, Division of Hematology and Oncology, UI Carver College of Medicine: The University of Iowa Roy J and Lucille A Carver College of Medicine, 375 Newton Rd, Iowa City, IA 52242, USA.
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Dang M, Wang R, Lee HC, Patel KK, Becnel MR, Han G, Thomas SK, Hao D, Chu Y, Weber DM, Lin P, Lutter-Berka Z, Berrios Nolasco DA, Huang M, Bansal H, Song X, Zhang J, Futreal A, Moreno Rueda LY, Symer DE, Green MR, Rojas Hernandez CM, Kroll M, Afshar-Khargan V, Ndacayisaba LJ, Kuhn P, Neelapu SS, Orlowski RZ, Wang L, Manasanch EE. Single cell clonotypic and transcriptional evolution of multiple myeloma precursor disease. Cancer Cell 2023; 41:1032-1047.e4. [PMID: 37311413 DOI: 10.1016/j.ccell.2023.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/02/2023] [Accepted: 05/09/2023] [Indexed: 06/15/2023]
Abstract
Multiple myeloma remains an incurable disease, and the cellular and molecular evolution from precursor conditions, including monoclonal gammopathy of undetermined significance and smoldering multiple myeloma, is incompletely understood. Here, we combine single-cell RNA and B cell receptor sequencing from fifty-two patients with myeloma precursors in comparison with myeloma and normal donors. Our comprehensive analysis reveals early genomic drivers of malignant transformation, distinct transcriptional features, and divergent clonal expansion in hyperdiploid versus non-hyperdiploid samples. Additionally, we observe intra-patient heterogeneity with potential therapeutic implications and identify distinct patterns of evolution from myeloma precursor disease to myeloma. We also demonstrate distinctive characteristics of the microenvironment associated with specific genomic changes in myeloma cells. These findings add to our knowledge about myeloma precursor disease progression, providing valuable insights into patient risk stratification, biomarker discovery, and possible clinical applications.
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Affiliation(s)
- Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hans C Lee
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krina K Patel
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melody R Becnel
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sheeba K Thomas
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yanshuo Chu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Donna M Weber
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pei Lin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zuzana Lutter-Berka
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David A Berrios Nolasco
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mei Huang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hima Bansal
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luz Yurany Moreno Rueda
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David E Symer
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael R Green
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cristhiam M Rojas Hernandez
- Department of Internal Medicine, Section of Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Kroll
- Department of Internal Medicine, Section of Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vahid Afshar-Khargan
- Department of Internal Medicine, Section of Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Peter Kuhn
- University of Southern California, Los Angeles, CA, USA
| | - Sattva S Neelapu
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Z Orlowski
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
| | - Elisabet E Manasanch
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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17
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Li L, Nie L, Jordan A, Cai Q, Liu Y, Li Y, Che Y, Vargas J, Chen Z, Leeming A, Wang W, Yao Y, Wang M, Jiang VC. Targeting glutaminase is therapeutically effective in ibrutinib-resistant mantle cell lymphoma. Haematologica 2023; 108:1616-1627. [PMID: 36420799 PMCID: PMC10230437 DOI: 10.3324/haematol.2022.281538] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2023] Open
Abstract
Mantle cell lymphoma (MCL) is an incurable B-cell non-Hodgkin lymphoma characterized by frequent relapses. The development of resistance to ibrutinib therapy remains a major challenge in MCL. We previously showed that glutaminolysis is associated with resistance to ibrutinib. In this study, we confirmed that glutaminase (GLS), the first enzyme in glutaminolysis, is overexpressed in ibrutinib-resistant MCL cells, and that its expression correlates well with elevated glutamine dependency and glutaminolysis. Furthermore, we discovered that GLS expression correlates with MYC expression and the functioning of the glutamine transporter ASCT2. Depletion of glutamine or GLS significantly reduced cell growth, while GLS overexpression enhanced glutamine dependency and ibrutinib resistance. Consistent with this, GLS inhibition by its specific inhibitor telaglenastat suppressed MCL cell growth both in vitro and in vivo. Moreover, telaglenastat showed anti-MCL synergy when combined with ibrutinib or venetoclax in vitro, which was confirmed using an MCL patient-derived xenograft model. Our study provides the first evidence that targeting GLS with telaglenastat, alone or in combination with ibrutinib or venetoclax, is a promising strategy to overcome ibrutinib resistance in MCL.
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Affiliation(s)
- Lingzhi Li
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Lei Nie
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Alexa Jordan
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Qingsong Cai
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Yang Liu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Yijing Li
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Yuxuan Che
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Jovanny Vargas
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Zhihong Chen
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Angela Leeming
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Wei Wang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Yixin Yao
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center
| | - Michael Wang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center
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18
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Chu Y, Dai E, Li Y, Han G, Pei G, Ingram DR, Thakkar K, Qin JJ, Dang M, Le X, Hu C, Deng Q, Sinjab A, Gupta P, Wang R, Hao D, Peng F, Yan X, Liu Y, Song S, Zhang S, Heymach JV, Reuben A, Elamin YY, Pizzi MP, Lu Y, Lazcano R, Hu J, Li M, Curran M, Futreal A, Maitra A, Jazaeri AA, Ajani JA, Swanton C, Cheng XD, Abbas HA, Gillison M, Bhat K, Lazar AJ, Green M, Litchfield K, Kadara H, Yee C, Wang L. Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance. Nat Med 2023; 29:1550-1562. [PMID: 37248301 DOI: 10.1038/s41591-023-02371-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Tumor-infiltrating T cells offer a promising avenue for cancer treatment, yet their states remain to be fully characterized. Here we present a single-cell atlas of T cells from 308,048 transcriptomes across 16 cancer types, uncovering previously undescribed T cell states and heterogeneous subpopulations of follicular helper, regulatory and proliferative T cells. We identified a unique stress response state, TSTR, characterized by heat shock gene expression. TSTR cells are detectable in situ in the tumor microenvironment across various cancer types, mostly within lymphocyte aggregates or potential tertiary lymphoid structures in tumor beds or surrounding tumor edges. T cell states/compositions correlated with genomic, pathological and clinical features in 375 patients from 23 cohorts, including 171 patients who received immune checkpoint blockade therapy. We also found significantly upregulated heat shock gene expression in intratumoral CD4/CD8+ cells following immune checkpoint blockade treatment, particularly in nonresponsive tumors, suggesting a potential role of TSTR cells in immunotherapy resistance. Our well-annotated T cell reference maps, web portal and automatic alignment/annotation tool could provide valuable resources for T cell therapy optimization and biomarker discovery.
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Affiliation(s)
- Yanshuo Chu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yating Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangsheng Pei
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davis R Ingram
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krupa Thakkar
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Jiang-Jiang Qin
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Can Hu
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Qing Deng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pravesh Gupta
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fuduan Peng
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinmiao Yan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melissa P Pizzi
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Hu
- Department of Human Genetics, Emory School of Medicine, Atlanta, GA, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Curran
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Xiang-Dong Cheng
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maura Gillison
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krishna Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Michael Green
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin Litchfield
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
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19
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Aoki T, Steidl C. Novel insights into Hodgkin lymphoma biology by single-cell analysis. Blood 2023; 141:1791-1801. [PMID: 36548960 PMCID: PMC10646771 DOI: 10.1182/blood.2022017147] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence and rapid development of single-cell technologies mark a paradigm shift in cancer research. Various technology implementations represent powerful tools to understand cellular heterogeneity, identify minor cell populations that were previously hard to detect and define, and make inferences about cell-to-cell interactions at single-cell resolution. Applied to lymphoma, recent advances in single-cell RNA sequencing have broadened opportunities to delineate previously underappreciated heterogeneity of malignant cell differentiation states and presumed cell of origin, and to describe the composition and cellular subsets in the ecosystem of the tumor microenvironment (TME). Clinical deployment of an expanding armamentarium of immunotherapy options that rely on targets and immune cell interactions in the TME emphasizes the requirement for a deeper understanding of immune biology in lymphoma. In particular, classic Hodgkin lymphoma (CHL) can serve as a study paradigm because of its unique TME, featuring infrequent tumor cells among numerous nonmalignant immune cells with significant interpatient and intrapatient variability. Synergistic to advances in single-cell sequencing, multiplexed imaging techniques have added a new dimension to describing cellular cross talk in various lymphoma entities. Here, we comprehensively review recent progress using novel single-cell technologies with an emphasis on the TME biology of CHL as an application field. The described technologies, which are applicable to peripheral blood, fresh tissues, and formalin-fixed samples, hold the promise to accelerate biomarker discovery for novel immunotherapeutic approaches and to serve as future assay platforms for biomarker-informed treatment selection, including immunotherapies.
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Affiliation(s)
- Tomohiro Aoki
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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20
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Vasaikar SV, Savage AK, Gong Q, Swanson E, Talla A, Lord C, Heubeck AT, Reading J, Graybuck LT, Meijer P, Torgerson TR, Skene PJ, Bumol TF, Li XJ. A comprehensive platform for analyzing longitudinal multi-omics data. Nat Commun 2023; 14:1684. [PMID: 36973282 PMCID: PMC10041512 DOI: 10.1038/s41467-023-37432-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
Longitudinal bulk and single-cell omics data is increasingly generated for biological and clinical research but is challenging to analyze due to its many intrinsic types of variations. We present PALMO ( https://github.com/aifimmunology/PALMO ), a platform that contains five analytical modules to examine longitudinal bulk and single-cell multi-omics data from multiple perspectives, including decomposition of sources of variations within the data, collection of stable or variable features across timepoints and participants, identification of up- or down-regulated markers across timepoints of individual participants, and investigation on samples of same participants for possible outlier events. We have tested PALMO performance on a complex longitudinal multi-omics dataset of five data modalities on the same samples and six external datasets of diverse background. Both PALMO and our longitudinal multi-omics dataset can be valuable resources to the scientific community.
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Affiliation(s)
| | - Adam K Savage
- Allen Institute for Immunology, Seattle, WA, 98109, USA
| | - Qiuyu Gong
- Allen Institute for Immunology, Seattle, WA, 98109, USA
| | - Elliott Swanson
- Allen Institute for Immunology, Seattle, WA, 98109, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Aarthi Talla
- Allen Institute for Immunology, Seattle, WA, 98109, USA
| | - Cara Lord
- Allen Institute for Immunology, Seattle, WA, 98109, USA
- GlaxoSmithKline, Collegeville, PA, 19426, USA
| | | | | | | | - Paul Meijer
- Allen Institute for Immunology, Seattle, WA, 98109, USA
| | | | - Peter J Skene
- Allen Institute for Immunology, Seattle, WA, 98109, USA
| | | | - Xiao-Jun Li
- Allen Institute for Immunology, Seattle, WA, 98109, USA.
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21
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Jiang VC, Liu Y, Lian J, Huang S, Jordan A, Cai Q, Lin R, Yan F, McIntosh J, Li Y, Che Y, Chen Z, Vargas J, Badillo M, Bigcal JN, Lee HH, Wang W, Yao Y, Nie L, Flowers CR, Wang M. Cotargeting of BTK and MALT1 overcomes resistance to BTK inhibitors in mantle cell lymphoma. J Clin Invest 2023; 133:165694. [PMID: 36719376 PMCID: PMC9888382 DOI: 10.1172/jci165694] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/07/2022] [Indexed: 02/01/2023] Open
Abstract
Bruton's tyrosine kinase (BTK) is a proven target in mantle cell lymphoma (MCL), an aggressive subtype of non-Hodgkin lymphoma. However, resistance to BTK inhibitors is a major clinical challenge. We here report that MALT1 is one of the top overexpressed genes in ibrutinib-resistant MCL cells, while expression of CARD11, which is upstream of MALT1, is decreased. MALT1 genetic knockout or inhibition produced dramatic defects in MCL cell growth regardless of ibrutinib sensitivity. Conversely, CARD11-knockout cells showed antitumor effects only in ibrutinib-sensitive cells, suggesting that MALT1 overexpression could drive ibrutinib resistance via bypassing BTK/CARD11 signaling. Additionally, BTK knockdown and MALT1 knockout markedly impaired MCL tumor migration and dissemination, and MALT1 pharmacological inhibition decreased MCL cell viability, adhesion, and migration by suppressing NF-κB, PI3K/AKT/mTOR, and integrin signaling. Importantly, cotargeting MALT1 with safimaltib and BTK with pirtobrutinib induced potent anti-MCL activity in ibrutinib-resistant MCL cell lines and patient-derived xenografts. Therefore, we conclude that MALT1 overexpression associates with resistance to BTK inhibitors in MCL, targeting abnormal MALT1 activity could be a promising therapeutic strategy to overcome BTK inhibitor resistance, and cotargeting of MALT1 and BTK should improve MCL treatment efficacy and durability as well as patient outcomes.
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Affiliation(s)
| | - Yang Liu
- Department of Lymphoma and Myeloma and
| | | | | | | | | | - Ruitao Lin
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Fangfang Yan
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Yijing Li
- Department of Lymphoma and Myeloma and
| | | | | | | | | | | | | | - Wei Wang
- Department of Lymphoma and Myeloma and
| | - Yixin Yao
- Department of Lymphoma and Myeloma and
| | - Lei Nie
- Department of Lymphoma and Myeloma and
| | | | - Michael Wang
- Department of Lymphoma and Myeloma and.,Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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22
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Zhang W, Shi JN, Wang HN, Zhang T, Zhou X, Zhang HM, Zhu F. Identification of immune-related genes and development of a prognostic model in mantle cell lymphoma. Ann Transl Med 2022; 10:1323. [PMID: 36660618 PMCID: PMC9843426 DOI: 10.21037/atm-22-5815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Background The immune landscape, prognostic model, and molecular variations of mantle cell lymphoma (MCL) remain unclear. Hence, an integrated bioinformatics analysis of MCL datasets is required for the development of immunotherapy and the optimization of targeted therapies. Methods Data were obtained from the Gene Expression Omnibus (GEO) database (GSE32018, GSE45717 and GSE93291). The differentially expressed immune-related genes were selected, and the hub genes were screened by three machine learning algorithms, followed by enrichment and correlation analyses. Next, MCL molecular clusters based on the hub genes were identified by K-Means clustering, the probably approximately correct (PAC) algorithm, and principal component analysis (PCA). The landscape of immune cell infiltration and immune checkpoint molecules in distinct clusters was explored by single-sample gene-set enrichment analysis (ssGSEA) as well as the CIBERSORT and xCell algorithms. The prognostic genes and prognostic risk score model for MCL clusters were identified by least absolute shrinkage and selection operator (LASSO)-Cox analysis and cross-validation for lambda. Correlation analysis was performed to explore the correlation between the screened prognostic genes and immune cells or immune checkpoint molecules. Results Four immune-related hub genes (CD247, CD3E, CD4, and GATA3) were screened in MCL, mainly enriched in the T-cell receptor signaling pathway. Based on the hub genes, two MCL molecular clusters were recognized. The cluster 2 group had a significantly worse overall survival (OS), with down-regulated hub genes, and a variety of activated immune effector cells declined. The majority of immune checkpoint molecules had also decreased. An efficient prognostic model was established, including six prognostic genes (LGALS2, LAMP3, ICOS, FCAMR, IGFBP4, and C1QA) differentially expressed between two MCL clusters. Patients with a higher risk score in the prognostic model had a poor prognosis. Furthermore, most types of immune cells and a range of immune checkpoint molecules were positively correlated with the prognostic genes. Conclusions Our study identified distinct molecular clusters based on the immune-related hub genes, and showed that the prognostic model affected the prognosis of MCL patients. These hub genes, modulated immune cells, and immune checkpoint molecules might be involved in oncogenesis and could be potential prognostic biomarkers in MCL.
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Affiliation(s)
- Wei Zhang
- Department of Hematology, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Jin-Ning Shi
- Department of Hematology, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Hai-Ning Wang
- Department of Blood Supply, Nanjing Red Cross Blood Center, Nanjing, China
| | - Ting Zhang
- Department of Hematology, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Xuan Zhou
- Department of Hematology, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Mei Zhang
- Department of Blood Transfusion, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Zhu
- Department of Blood Transfusion, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
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23
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de Leval L, Alizadeh AA, Bergsagel PL, Campo E, Davies A, Dogan A, Fitzgibbon J, Horwitz SM, Melnick AM, Morice WG, Morin RD, Nadel B, Pileri SA, Rosenquist R, Rossi D, Salaverria I, Steidl C, Treon SP, Zelenetz AD, Advani RH, Allen CE, Ansell SM, Chan WC, Cook JR, Cook LB, d’Amore F, Dirnhofer S, Dreyling M, Dunleavy K, Feldman AL, Fend F, Gaulard P, Ghia P, Gribben JG, Hermine O, Hodson DJ, Hsi ED, Inghirami G, Jaffe ES, Karube K, Kataoka K, Klapper W, Kim WS, King RL, Ko YH, LaCasce AS, Lenz G, Martin-Subero JI, Piris MA, Pittaluga S, Pasqualucci L, Quintanilla-Martinez L, Rodig SJ, Rosenwald A, Salles GA, San-Miguel J, Savage KJ, Sehn LH, Semenzato G, Staudt LM, Swerdlow SH, Tam CS, Trotman J, Vose JM, Weigert O, Wilson WH, Winter JN, Wu CJ, Zinzani PL, Zucca E, Bagg A, Scott DW. Genomic profiling for clinical decision making in lymphoid neoplasms. Blood 2022; 140:2193-2227. [PMID: 36001803 PMCID: PMC9837456 DOI: 10.1182/blood.2022015854] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/15/2022] [Indexed: 01/28/2023] Open
Abstract
With the introduction of large-scale molecular profiling methods and high-throughput sequencing technologies, the genomic features of most lymphoid neoplasms have been characterized at an unprecedented scale. Although the principles for the classification and diagnosis of these disorders, founded on a multidimensional definition of disease entities, have been consolidated over the past 25 years, novel genomic data have markedly enhanced our understanding of lymphomagenesis and enriched the description of disease entities at the molecular level. Yet, the current diagnosis of lymphoid tumors is largely based on morphological assessment and immunophenotyping, with only few entities being defined by genomic criteria. This paper, which accompanies the International Consensus Classification of mature lymphoid neoplasms, will address how established assays and newly developed technologies for molecular testing already complement clinical diagnoses and provide a novel lens on disease classification. More specifically, their contributions to diagnosis refinement, risk stratification, and therapy prediction will be considered for the main categories of lymphoid neoplasms. The potential of whole-genome sequencing, circulating tumor DNA analyses, single-cell analyses, and epigenetic profiling will be discussed because these will likely become important future tools for implementing precision medicine approaches in clinical decision making for patients with lymphoid malignancies.
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Affiliation(s)
- Laurence de Leval
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Ash A. Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University, Stanford, CA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - P. Leif Bergsagel
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Phoenix, AZ
| | - Elias Campo
- Haematopathology Section, Hospital Clínic, Institut d'Investigaciones Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Andrew Davies
- Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jude Fitzgibbon
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Steven M. Horwitz
- Lymphoma Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ari M. Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - William G. Morice
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Ryan D. Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Bertrand Nadel
- Aix Marseille University, CNRS, INSERM, CIML, Marseille, France
| | - Stefano A. Pileri
- Haematopathology Division, IRCCS, Istituto Europeo di Oncologia, IEO, Milan, Italy
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
| | - Davide Rossi
- Institute of Oncology Research and Oncology Institute of Southern Switzerland, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Itziar Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, Vancouver, Canada
| | | | - Andrew D. Zelenetz
- Lymphoma Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Ranjana H. Advani
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
| | - Carl E. Allen
- Division of Pediatric Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | | | - Wing C. Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - James R. Cook
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Lucy B. Cook
- Centre for Haematology, Imperial College London, London, United Kingdom
| | - Francesco d’Amore
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Stefan Dirnhofer
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Kieron Dunleavy
- Division of Hematology and Oncology, Georgetown Lombardi Comprehensive Cancer Centre, Georgetown University Hospital, Washington, DC
| | - Andrew L. Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Falko Fend
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Philippe Gaulard
- Department of Pathology, University Hospital Henri Mondor, AP-HP, Créteil, France
- Faculty of Medicine, IMRB, INSERM U955, University of Paris-Est Créteil, Créteil, France
| | - Paolo Ghia
- Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milan, Italy
| | - John G. Gribben
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Olivier Hermine
- Service D’hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Daniel J. Hodson
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Eric D. Hsi
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Elaine S. Jaffe
- Hematopathology Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Kennosuke Karube
- Department of Pathology and Laboratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Toyko, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Wolfram Klapper
- Hematopathology Section and Lymph Node Registry, Department of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Won Seog Kim
- Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, South Korea
| | - Rebecca L. King
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Young H. Ko
- Department of Pathology, Cheju Halla General Hospital, Jeju, Korea
| | | | - Georg Lenz
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
| | - José I. Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Miguel A. Piris
- Department of Pathology, Jiménez Díaz Foundation University Hospital, CIBERONC, Madrid, Spain
| | - Stefania Pittaluga
- Hematopathology Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Pathology & Cell Biology, Columbia University, New York, NY
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Scott J. Rodig
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | | | - Gilles A. Salles
- Lymphoma Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jesus San-Miguel
- Clínica Universidad de Navarra, Navarra, Cancer Center of University of Navarra, Cima Universidad de NavarraI, Instituto de Investigacion Sanitaria de Navarra, Centro de Investigación Biomédica en Red de Céncer, Pamplona, Spain
| | - Kerry J. Savage
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, Vancouver, Canada
| | - Laurie H. Sehn
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, Vancouver, Canada
| | - Gianpietro Semenzato
- Department of Medicine, University of Padua and Veneto Institute of Molecular Medicine, Padova, Italy
| | - Louis M. Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Steven H. Swerdlow
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Judith Trotman
- Haematology Department, Concord Repatriation General Hospital, Sydney, Australia
| | - Julie M. Vose
- Department of Internal Medicine, Division of Hematology-Oncology, University of Nebraska Medical Center, Omaha, NE
| | - Oliver Weigert
- Department of Medicine III, LMU Hospital, Munich, Germany
| | - Wyndham H. Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jane N. Winter
- Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | - Pier L. Zinzani
- IRCCS Azienda Ospedaliero-Universitaria di Bologna Istitudo di Ematologia “Seràgnoli” and Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale Università di Bologna, Bologna, Italy
| | - Emanuele Zucca
- Institute of Oncology Research and Oncology Institute of Southern Switzerland, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, Vancouver, Canada
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Liu L, Cheng M, Guo H, Guan Q, You J, Dou H. Multidimensional Quantitative Measurement of Cancer Chemoresistance through Differential ZIF-8 Nanoparticle Cellular Retention. ACS Appl Mater Interfaces 2022; 14:51798-51807. [PMID: 36367515 DOI: 10.1021/acsami.2c17692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Chemoresistance of cancer cells is conventionally quantified by half-maximal inhibitory concentration (IC50) or multidrug resistance gene 1 (MDR1) values, but these metrics can only reflect the overall drug resistance level of a cancer cell line. Meanwhile, the multidimensional evaluation of both the heterogeneity in a cell line and the drug resistance degree of each cell still presents a daunting challenge. We report here that the cellular heterogeneity, cellular cross contamination, and the proportion of chemoresistant cancer cells can be visualized via flow cytometry through the differential cellular retention of fluorescent ZIF-8 nanoparticles. In addition, we show that the degree of drug resistance exhibited by each cell subpopulation can be quantified by differing fluorescence of the drug-resistant and drug-sensitive cells in the corresponding flow cytometry profile, and the quantified metric S is highly consistent with the MDR1 expression results. Importantly, this novel strategy is applicable to various cancer cell lines, thus demonstrating a universal diagnosis platform for multidimensional, quantitative, and highly efficient diagnosis of cancer chemoresistance.
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Affiliation(s)
- Lingshan Liu
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai201203, China
| | - Meng Cheng
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
| | - Heze Guo
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai201203, China
| | - Qixiao Guan
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai201203, China
| | - Jiayi You
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
| | - Hongjing Dou
- The State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai201203, China
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25
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Qualls D, Kumar A, Epstein-Peterson Z. Targeting the immune microenvironment in mantle cell lymphoma: implications for current and emerging therapies. Leuk Lymphoma 2022; 63:2515-2527. [PMID: 35704674 PMCID: PMC9741766 DOI: 10.1080/10428194.2022.2086244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/21/2022] [Accepted: 05/27/2022] [Indexed: 12/14/2022]
Abstract
Mantle cell lymphoma (MCL) is a morphologically and phenotypically heterogeneous subtype of non-Hodgkin lymphoma, and has historically been associated with poor outcomes. However, recent advances in our understanding of this disease have yielded new targeted and immune-based therapies with promising activity. Immune-based therapies such as monoclonal antibodies, immunomodulators, and CAR T cells have significantly improved outcomes and are now standard of care in MCL. In this review, we describe our current understanding of the immune microenvironment of MCL, discuss current immunotherapeutic approaches, and highlight promising novel immune-based therapies and combination therapies that may further improve outcomes for patients with MCL.
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Affiliation(s)
- David Qualls
- Lymphoma Service, Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center. New York, NY, USA
| | - Anita Kumar
- Lymphoma Service, Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center. New York, NY, USA
| | - Zachary Epstein-Peterson
- Lymphoma Service, Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center. New York, NY, USA
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Liu Z, Li H, Dang Q, Weng S, Duo M, Lv J, Han X. Integrative insights and clinical applications of single-cell sequencing in cancer immunotherapy. Cell Mol Life Sci 2022; 79:577. [DOI: 10.1007/s00018-022-04608-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/03/2022]
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Abstract
PURPOSE OF REVIEW This review focuses on the feasibility of combining Bruton's tyrosine kinase (BTK) inhibitors (BTKis) with chimeric antigen receptor (CAR) T-cell therapy in patients with relapsed or refractory (R/R) mantle cell lymphoma (MCL). Potential scenarios for combination treatment with these agents are presented. RECENT FINDINGS BTKis and CAR T-cell therapy have revolutionized the treatment paradigm for R/R MCL. Ibrutinib, acalabrutinib, and zanubrutinib are covalent irreversible BTKis approved for R/R MCL. Brexucabtagene autoleucel was the first CAR T-cell therapy approved for R/R MCL based on findings from the ZUMA-2 trial. There is evidence to suggest that combination treatment with BTKis and CAR T-cell therapy may improve CAR T-cell efficacy. As BTKis and CAR T-cell therapy become mainstays in R/R MCL therapy, combination treatment strategies should be evaluated for their potential benefit in R/R MCL.
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Affiliation(s)
| | | | - Preetesh Jain
- Department of Lymphoma-Myeloma, Division of Cancer Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA.
| | - Michael Wang
- Department of Lymphoma-Myeloma, Division of Cancer Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
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Jiang VC, Hao D, Jain P, Li Y, Cai Q, Yao Y, Nie L, Liu Y, Jin J, Wang W, Lee HH, Che Y, Dai E, Han G, Wang R, Rai K, Futreal A, Flowers C, Wang L, Wang M. TIGIT is the central player in T-cell suppression associated with CAR T-cell relapse in mantle cell lymphoma. Mol Cancer 2022; 21:185. [PMID: 36163179 PMCID: PMC9513944 DOI: 10.1186/s12943-022-01655-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chimeric antigen receptor (CAR) T-cell therapy using brexucabtagene autoleucel (BA) induces remission in many patients with mantle cell lymphoma (MCL), and BA is the only CAR T-cell therapy approved by the FDA for MCL. However, development of relapses to BA is recognized with poor patient outcomes. Multiple CAR T-cell therapies have been approved for other lymphomas and the resistance mechanisms have been investigated. However, the mechanisms underlying BA relapse in MCL have not been investigated and whether any previously reported resistance mechanisms apply to BA-relapsed patients with MCL is unknown. METHODS To interrogate BA resistance mechanisms in MCL, we performed single-cell RNA sequencing on 39 longitudinally collected samples from 15 BA-treated patients, and multiplex cytokine profiling on 80 serial samples from 20 patients. RESULTS We demonstrate that after BA relapse, the proportion of T cells, especially cytotoxic T cells (CTLs), decreased among non-tumor cells, while the proportion of myeloid cells correspondingly increased. TIGIT, LAG3, and CD96 were the predominant checkpoint molecules expressed on exhausted T cells and CTLs; only TIGIT was significantly increased after relapse. CTLs expanded during remission, and then contracted during relapse with upregulated TIGIT expression. Tumor cells also acquired TIGIT expression after relapse, leading to the enhanced interaction of tumor cell TIGIT with monocyte CD155/PVR. In myeloid cells, post-relapse HLA-II expression was reduced relative to pretreatment and during remission. Myeloid-derived suppressor cells (MDSCs) were enriched after relapse with elevated expression of activation markers, including CLU (clusterin) and VCAN (versican). Extracellular chemokines (CCL4, CXCL9, CXCL13), soluble checkpoint inhibitors (sPD-L1, sTIM3, s4-1BB), and soluble receptors (sIL-2R, sTNFRII) were decreased during remission but elevated after relapse. CONCLUSIONS Our data demonstrate that multiple tumor-intrinsic and -extrinsic factors are associated with T-cell suppression and BA relapse. Among these, TIGIT appears to be the central player given its elevated expression after BA relapse in not only CTLs but also MCL cells. The acquisition of TIGIT expression on tumor cells is MCL-specific and has not been reported in other CAR T-treated diseases. Together, our data suggest that co-targeting TIGIT may prevent CAR T relapses and thus promote long-term progression-free survival in MCL patients.
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Affiliation(s)
- Vivian Changying Jiang
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dapeng Hao
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Preetesh Jain
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yijing Li
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Qingsong Cai
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yixin Yao
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lei Nie
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yang Liu
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jingling Jin
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wei Wang
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Heng-Huan Lee
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yuxuan Che
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Enyu Dai
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Guangchun Han
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ruiping Wang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kunal Rai
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Andrew Futreal
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Christopher Flowers
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (GSBS), Houston, TX, 77030, USA.
| | - Michael Wang
- Department of Lymphoma and Myeloma, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Stem Cell Transplantation and Cellular Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Hino C, Pham B, Gray AL, Wang J, Castillo DR, Akhtari M, Liu Y. Clinicopathologic Features and Treatment of CD10-Positive Mantle Cell Lymphoma: A Case Report and Review of Literature. Pathol Oncol Res 2022; 28:1610588. [PMID: 36091937 PMCID: PMC9454308 DOI: 10.3389/pore.2022.1610588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Mantle cell lymphoma (MCL) is a rare and aggressive non-Hodgkin’s B cell lymphoma characterized by the translocation t(11;14) (q13;32) and overexpression of CCND1. MCL is immunophenotypically identified as CD20+, CD5+, CyclinD1+, CD43+, CD10−, BCL6−, and CD23−. It is often distinguished from B cell lymphomas of germinal center cell origin by the absence of CD10 expression. Here we report the unique clinicopathologic features of a patient with CD10+ MCL with gastrointestinal involvement and review current literature identifying this unique immunophenotype.
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Affiliation(s)
- Christopher Hino
- Department of Internal Medicine, Loma Linda University Medical Center, Loma Linda, CA, United States
| | - Bryan Pham
- Department of Internal Medicine, Loma Linda University Medical Center, Loma Linda, CA, United States
| | - Austin L. Gray
- Department of Pathology, Loma Linda University, Loma Linda, CA, United States
| | - Jun Wang
- Department of Pathology, Loma Linda University, Loma Linda, CA, United States
| | - Dan Ran Castillo
- Department of Oncology/Hematology, Loma Linda University, Loma Linda, CA, United States
| | - Mojtaba Akhtari
- Department of Oncology/Hematology, Loma Linda University, Loma Linda, CA, United States
| | - Yan Liu
- Department of Pathology, Loma Linda University, Loma Linda, CA, United States
- *Correspondence: Yan Liu,
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30
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Abstract
Careful histopathologic examination remains the cornerstone in the diagnosis of the clinically and biologically heterogeneous group of lymphoid malignancies. However, recent advances in genomic and epigenomic characterization using high-throughput technologies have significantly improved our understanding of these tumors. Although no single genomic alteration is completely specific for a lymphoma entity, some alterations are highly recurrent in certain entities and thus can provide complementary diagnostic information when integrated in the hematopathological diagnostic workup. Moreover, other alterations may provide important information regarding the clinical course, that is, prognostic or risk-stratifying markers, or response to treatment, that is, predictive markers, which may allow tailoring of the patient's treatment based on (epi)genetic characteristics. In this review, we will focus on clinically relevant diagnostic, prognostic, and predictive biomarkers identified in more common types of B-cell malignancies, and discuss how diagnostic assays designed for comprehensive molecular profiling may pave the way for the implementation of precision diagnostics/medicine approaches. We will also discuss future directions in this rapidly evolving field, including the application of single-cell sequencing and other omics technologies, to decipher clonal dynamics and evolution in lymphoid malignancies.
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Affiliation(s)
- Marco M Bühler
- Department of Pathology and Molecular Pathology, University Hospital of Zurich, Zurich, Switzerland.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Section, Laboratory of Pathology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - José I Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Section, Laboratory of Pathology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Section, Laboratory of Pathology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
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31
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Cao YH, Ding J, Tang QH, Zhang J, Huang ZY, Tang XM, Liu JB, Ma YS, Fu D. Deciphering cell-cell interactions and communication in the tumor microenvironment and unraveling intratumoral genetic heterogeneity via single-cell genomic sequencing. Bioengineered 2022; 13:14974-14986. [PMID: 37105769 DOI: 10.1080/21655979.2023.2185434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
A tumor's heterogeneity has important implications in terms of its clonal origin, progression, stemness, and drug resistance. Therefore, because of its significance in treatment, it is important to understand the gene expression pattern of a single cell, track gene expression or mutation in heterogeneous cells, evaluate the clonal origin of cancer cells, and determine the selective evolution of different subpopulations of cancer cells. Researchers are able to trace a cell's mutation and identify different types of tumor cells by measuring the whole transcriptome with single-cell sequencing (scRNA-seq). This technology provides a better understanding of the molecular mechanisms driving tumor growth than that offered by traditional RNA sequencing methods. In addition, it has revealed changes in the mutations and functions of somatic cells as a tumor evolves; it has also clarified immune cell infiltration and activation. Research on scRNA-seq technology has recently advanced significantly, suggesting new strategies for the treatment of cancer. In short, cancer researchers have become increasingly dependent on scRNA-seq. This paper reviews the development, detection principles, and processes of scRNA-seq technology and their application in tumor research. It also considers potential clinical applications.
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Affiliation(s)
- Ya-Hong Cao
- Department of Respiratory, Nantong Traditional Chinese Medicine Hospital, Affiliated Nantong Traditional Chinese Medicine Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jie Ding
- Department of Clinical Laboratory, Jingjiang Traditional Chinese Medicine Hospital, Jingjiang, Jiangsu, China
| | - Qing-Hai Tang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region and College of Life Sciences and Environment, Hengyang Normal University, Hengyang, Hunan, China
| | - Jie Zhang
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Zhong-Yan Huang
- Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, Huangpu, China
| | - Xiao-Mei Tang
- Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, Huangpu, China
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yu-Shui Ma
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
| | - Da Fu
- Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, Huangpu, China
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Jain P, Wang ML. Mantle cell lymphoma in 2022-A comprehensive update on molecular pathogenesis, risk stratification, clinical approach, and current and novel treatments. Am J Hematol 2022; 97:638-656. [PMID: 35266562 DOI: 10.1002/ajh.26523] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/21/2022]
Abstract
The field of mantle cell lymphoma (MCL) has witnessed remarkable progress due to relentless advances in molecular pathogenesis, prognostication, and newer treatments. MCL consists of a spectrum of clinical subtypes. Rarely, atypical cyclin D1-negative MCL and in situ MCL neoplasia are identified. Prognostication of MCL is further refined by identifying somatic mutations (such as TP53, NSD2, KMT2D), methylation status, chromatin organization pattern, SOX-11 expression, minimal residual disease (MRD), and genomic clusters. Lymphoid tissue microenvironment studies demonstrated the role of B-cell receptor signaling, nuclear factor kappa B (NF-kB), colony-stimulating factor (CSF)-1, the CD70-SOX-11 axis. Molecular mechanism of resistance, mutation dynamics, and pathogenic pathways (B-cell receptor (BCR), oxidative phosphorylation, and MYC) were identified in mediating resistance to various treatments (bruton tyrosine kinase (BTK) inhibitors [ibrutinib, acalabrutinib]. Treatment options range from conventional chemoimmunotherapy and stem cell transplantation (SCT) to targeted therapies against BTK (covalent and noncovalent), Bcl2, ROR1, cellular therapy such as anti-CD19 chimeric antigen receptor therapy (CAR-T), and most recently bispecific antibodies against CD19 and CD20. MCL patients frequently relapse. Complex pathogenesis and the management of patients with progression after treatment with BTK/Bcl2 inhibitors and CAR-T (triple-resistant MCL) remain a challenge. Next-generation clinical trials incorporating newer agents and concurrent translational and molecular investigations are ongoing.
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Affiliation(s)
- Preetesh Jain
- Department of Lymphoma/Myeloma. Mantle cell lymphoma center of excellence The University of Texas MD Anderson Cancer Center Houston Texas USA
| | - Michael L. Wang
- Department of Lymphoma/Myeloma. Mantle cell lymphoma center of excellence The University of Texas MD Anderson Cancer Center Houston Texas USA
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Eyre TA, Cheah CY, Wang ML. Therapeutic options for relapsed/refractory mantle cell lymphoma. Blood 2022; 139:666-77. [PMID: 34679161 DOI: 10.1182/blood.2021013326] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/20/2021] [Indexed: 02/05/2023] Open
Abstract
Mantle cell lymphoma (MCL) is an uncommon subtype of non-Hodgkin lymphoma in which immunochemotherapy, with or without high-dose therapy, and autologous stem cell transplantation remain standard frontline therapies. Despite their clear efficacy, patients inevitably relapse and require subsequent therapy. In this review, we discuss the key therapeutic approaches in the management of relapsed MCL, covering in depth the data supporting the use of covalent Bruton tyrosine kinase (BTK) inhibitors at first or subsequent relapse. We describe the outcomes of patients progressing through BTK inhibitors and discuss the mechanisms of covalent BTKi resistance and treatment options after covalent treatment with BTKi. Options in this setting may depend on treatment availability, patient's and physician's preference, and the patient's age and comorbidity status. We discuss the rapid recent development of anti-CD19 chimeric antigen receptor T-cell therapy, as well as the utility of allogenic stem cell transplantation and novel therapies, such as noncovalent, reversible BTK inhibitors; ROR1 antibody drug conjugates; and bispecific antibodies.
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Alpár D, Egyed B, Bödör C, Kovács GT. Single-Cell Sequencing: Biological Insight and Potential Clinical Implications in Pediatric Leukemia. Cancers (Basel) 2021; 13:5658. [PMID: 34830811 PMCID: PMC8616124 DOI: 10.3390/cancers13225658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 01/15/2023] Open
Abstract
Single-cell sequencing (SCS) provides high-resolution insight into the genomic, epigenomic, and transcriptomic landscape of oncohematological malignancies including pediatric leukemia, the most common type of childhood cancer. Besides broadening our biological understanding of cellular heterogeneity, sub-clonal architecture, and regulatory network of tumor cell populations, SCS can offer clinically relevant, detailed characterization of distinct compartments affected by leukemia and identify therapeutically exploitable vulnerabilities. In this review, we provide an overview of SCS studies focused on the high-resolution genomic and transcriptomic scrutiny of pediatric leukemia. Our aim is to investigate and summarize how different layers of single-cell omics approaches can expectedly support clinical decision making in the future. Although the clinical management of pediatric leukemia underwent a spectacular improvement during the past decades, resistant disease is a major cause of therapy failure. Currently, only a small proportion of childhood leukemia patients benefit from genomics-driven therapy, as 15-20% of them meet the indication criteria of on-label targeted agents, and their overall response rate falls in a relatively wide range (40-85%). The in-depth scrutiny of various cell populations influencing the development, progression, and treatment resistance of different disease subtypes can potentially uncover a wider range of driver mechanisms for innovative therapeutic interventions.
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Affiliation(s)
- Donát Alpár
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary; (D.A.); (B.E.); (C.B.)
| | - Bálint Egyed
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary; (D.A.); (B.E.); (C.B.)
- 2nd Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary; (D.A.); (B.E.); (C.B.)
| | - Gábor T. Kovács
- 2nd Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
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Valentin Hansen S, Høy Hansen M, Cédile O, Møller MB, Haaber J, Abildgaard N, Guldborg Nyvold C. Detailed characterization of the transcriptome of single B cells in mantle cell lymphoma suggesting a potential use for SOX4. Sci Rep 2021; 11:19092. [PMID: 34580376 DOI: 10.1038/s41598-021-98560-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/07/2021] [Indexed: 01/04/2023] Open
Abstract
Mantle cell lymphoma (MCL) is a malignancy arising from naive B lymphocytes with common bone marrow (BM) involvement. Although t(11;14) is a primary event in MCL development, the highly diverse molecular etiology and causal genomic events are still being explored. We investigated the transcriptome of CD19+ BM cells from eight MCL patients at single-cell level. The transcriptomes revealed marked heterogeneity across patients, while general homogeneity and clonal continuity was observed within the patients with no clear evidence of subclonal involvement. All patients were SOX11+CCND1+CD20+. Despite monotypic surface immunoglobulin (Ig) κ or λ protein expression in MCL, 10.9% of the SOX11 + malignant cells expressed both light chain transcripts. The early lymphocyte transcription factor SOX4 was expressed in a fraction of SOX11 + cells in two patients and co-expressed with the precursor lymphoblastic marker, FAT1, in a blastoid case, suggesting a potential prognostic role. Additionally, SOX4 was found to identify non-malignant SOX11– pro-/pre-B cell populations. Altogether, the observed expression of markers such as SOX4, CD27, IgA and IgG in the SOX11+ MCL cells, may suggest that the malignant cells are not fixed in the differentiation state of naïve mature B cells, but instead the patients carry B lymphocytes of different differentiation stages.
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