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Aslan B, Manyam G, Iles LR, Tantawy SI, Desikan SP, Wierda WG, Gandhi V. Transcriptomic and proteomic differences in BTK-WT and BTK-mutated CLL and their changes during therapy with pirtobrutinib. Blood Adv 2024; 8:4487-4501. [PMID: 38968154 PMCID: PMC11395759 DOI: 10.1182/bloodadvances.2023012360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/07/2024] Open
Abstract
ABSTRACT Covalent Bruton tyrosine kinase inhibitors (cBTKis), which bind to the BTK C481 residue, are now primary therapeutics for chronic lymphocytic leukemia (CLL). Alterations at C481, primarily C481S, prevent cBTKi binding and lead to the emergence of resistant clones. Pirtobrutinib is a noncovalent BTKi that binds to both wild-type (WT) and C481S-mutated BTK and has shown efficacy in BTK-WT and -mutated CLL patient groups. To compare baseline clinical, transcriptomic, and proteomic characteristics and their changes during treatment in these 2 groups, we used 67 longitudinal peripheral blood samples obtained during the first 3 cycles of treatment with pirtobrutinib from 18 patients with CLL (11 BTK-mutated, 7 BTK-WT) enrolled in the BRUIN (pirtobrutinib in relapsed or refractory B-cell malignancies) trial. Eastern Cooperative Oncology Group performance status, age, and Rai stage were similar in both groups. At baseline, lymph nodes were larger in the BTK-mutated cohort. All patients achieved partial remission within 4 cycles of pirtobrutinib. Lactate dehydrogenase and β2-microglobulin levels decreased in both cohorts after 1 treatment cycle. Expression analysis demonstrated upregulation of 35 genes and downregulation of 6 in the BTK-mutated group. Gene set enrichment analysis revealed that the primary pathways enriched in BTK-mutated cells were involved in cell proliferation, metabolism, and stress response. Pathways associated with metabolism and proliferation were downregulated in both groups during pirtobrutinib treatment. Proteomic data corroborated transcriptomic findings. Our data identified inherent differences between BTK-mutated and -WT CLL and demonstrated molecular normalization of plasma and omics parameters with pirtobrutinib treatment in both groups.
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MESH Headings
- Humans
- Agammaglobulinaemia Tyrosine Kinase/antagonists & inhibitors
- Agammaglobulinaemia Tyrosine Kinase/metabolism
- Agammaglobulinaemia Tyrosine Kinase/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Mutation
- Middle Aged
- Transcriptome
- Pyrimidines/therapeutic use
- Pyrimidines/pharmacology
- Proteomics/methods
- Female
- Male
- Aged
- Piperidines/therapeutic use
- Piperidines/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Protein Kinase Inhibitors/pharmacology
- Proteome
- Adenine/analogs & derivatives
- Adenine/therapeutic use
- Pyrazoles/therapeutic use
- Pyrazoles/pharmacology
- Aged, 80 and over
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Affiliation(s)
- Burcu Aslan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ganiraju Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lakesla R Iles
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shady I Tantawy
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sai Prasad Desikan
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - William G Wierda
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Varsha Gandhi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
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2
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López C, Silkenstedt E, Dreyling M, Beà S. Biological and clinical determinants shaping heterogeneity in mantle cell lymphoma. Blood Adv 2024; 8:3652-3664. [PMID: 38748869 DOI: 10.1182/bloodadvances.2023011763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/03/2024] [Indexed: 07/12/2024] Open
Abstract
ABSTRACT Mantle cell lymphoma (MCL) is an uncommon mature B-cell lymphoma that presents a clinical spectrum ranging from indolent to aggressive disease, with challenges in disease management and prognostication. MCL is characterized by significant genomic instability, affecting various cellular processes, including cell cycle regulation, cell survival, DNA damage response and telomere maintenance, NOTCH and NF-κB/ B-cell receptor pathways, and chromatin modification. Recent molecular and next-generation sequencing studies unveiled a broad genetic diversity among the 2 molecular subsets, conventional MCL (cMCL) and leukemic nonnodal MCL (nnMCL), which may partially explain their clinical heterogeneity. Some asymptomatic and genetically stable nnMCL not requiring treatment at diagnosis may eventually progress clinically. Overall, the high proliferation of tumor cells, blastoid morphology, TP53 and/or CDKN2A/B inactivation, and high genetic complexity influence treatment outcome in cases treated with standard regimens. Emerging targeted and immunotherapeutic strategies are promising for refractory or relapsed cases and a few genetic and nongenetic determinants of refractoriness have been reported. This review summarizes the recent advances in MCL biology, focusing on molecular insights, prognostic markers, and novel therapeutic approaches.
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Affiliation(s)
- Cristina López
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Pathology Department, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Departament de Fonaments Clínics, Universitat de Barcelona, Barcelona, Spain
| | - Elisabeth Silkenstedt
- Department of Medicine III, Ludwig-Maximilians-University Munich University Hospital, Munich, Germany
| | - Martin Dreyling
- Department of Medicine III, Ludwig-Maximilians-University Munich University Hospital, Munich, Germany
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Pathology Department, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Departament de Fonaments Clínics, Universitat de Barcelona, Barcelona, Spain
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3
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Yu G, Zhang W, Basyal M, Nishida Y, Mizumo H, Ly C, Zhang H, Rice WG, Andreeff M. The multi-kinase inhibitor CG-806 exerts anti-cancer activity against acute myeloid leukemia by co-targeting FLT3, BTK, and aurora kinases. Leuk Lymphoma 2024:1-16. [PMID: 38871487 DOI: 10.1080/10428194.2024.2364839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/01/2024] [Indexed: 06/15/2024]
Abstract
Despite the development of several Fms-like tyrosine kinase 3 (FLT3) inhibitors that have improved outcomes in patients with FLT3-mutant acute myeloid leukemia (AML), drug resistance is frequently observed, which may be associated with the activation of additional pro-survival pathways, such as those regulated by BTK, aurora kinases (AuroK), and potentially others, in addition to acquired tyrosine kinase domain (TKD) mutations of FLT3 gene. FLT3 may not always be a driver mutation. We evaluated the anti-leukemia efficacy of the novel multi-kinase inhibitor CG-806, which targets FLT3 and other kinases, to circumvent drug resistance and target FLT3 wild-type (WT) cells. The anti-leukemia activity of CG-806 was investigated by measuring apoptosis induction and analyzing the cell cycle using flow cytometry in vitro. CG-806 demonstrated superior anti-leukemia efficacy compared to commercially available FLT3 inhibitors, both in vitro and in vivo, regardless of FLT3 mutational status. The mechanism of action of CG-806 may involve its broad inhibitory profile against FLT3, BTK, and AuroK. In FLT3 mutant cells, CG-806 induced G1 phase blockage, whereas in FLT3 WT cells, it resulted in G2/M phase arrest. Targeting FLT3 and Bcl-2 and/or Mcl-1 simultaneously results in a synergistic pro-apoptotic effect in FLT3 mutant leukemia cells. The results of this study suggest that CG-806 is a promising multi-kinase inhibitor with anti-leukemic efficacy regardless of FLT3 mutational status. A phase 1 clinical trial of CG-806 for the treatment of AML has been initiated (NCT04477291).Key pointsThe multi-kinase inhibitor CG-806 exerts superior anti-leukemic activity in AML, regardless of its FLT3 status.CG-806 triggered G1 arrest in FLT3 mutated cells and G2/M arrest in FLT3 WT cells through the suppression of FLT3/BTK and aurora kinases.Concomitantly targeting FLT3 and Bcl-2 and/or Mcl-1 exerted synergistic pro-apoptotic effects on both FLT3 WT and mutated AML cells.
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Affiliation(s)
- Guopan Yu
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weiguo Zhang
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mahesh Basyal
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuki Nishida
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hideaki Mizumo
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charlie Ly
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Michael Andreeff
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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4
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Jin Y, Wu H, Liu J, Cho WC, Song G. Application and progress of CRISPR/Cas9 gene editing in B-cell lymphoma: a narrative review. Transl Cancer Res 2024; 13:1584-1595. [PMID: 38617522 PMCID: PMC11009809 DOI: 10.21037/tcr-23-1146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
Background and Objective Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) gene editing and CRISPR/Cas9 screening libraries are hot topics, and have high application values in the diagnosis and treatment of genetic diseases, and the improvement of prognosis. The major treatment of B-cell lymphoma is chemotherapy combined with biological therapy. Due to the individual specificity and the emergence of drug resistance, the therapeutic efficacy varies. The objective of this article is to explore potential targets to enhance therapeutic effects, optimize treatment plans, and improve the prognosis of patients with B-cell lymphoma. Methods We undertook a comprehensive, narrative review of the latest literature to define the current application and progress of CRISPR/Cas9 in B-cell lymphoma. Key Content and Findings The concepts of CRISPR/Cas9, the mechanism of gene editing, and the procedures of CRISPR/Cas9 screening libraries are investigated for candidate genes. We mainly focus on application and progress of CRISPR/Cas9 in B-cell lymphoma and screen out some genes, signaling pathways, and cytokines, which may become potential targets for clinical treatment. Conclusions CRISPR/Cas9 gene editing has great promise in the treatment of B-cell lymphoma. This article reviews some genes, signaling pathways, and cytokines related to the progression and prognosis of B-cell lymphoma to provide a strong theoretical basis.
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Affiliation(s)
- Ying Jin
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Haiyi Wu
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Jianzhao Liu
- Department of Hematology, Affiliated Hospital of Nantong University, Dalian Medical University, Dalian, China
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | - Guoqi Song
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
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5
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Gambino S, Quaglia FM, Galasso M, Cavallini C, Chignola R, Lovato O, Giacobazzi L, Caligola S, Adamo A, Putta S, Aparo A, Ferrarini I, Ugel S, Giugno R, Donadelli M, Dando I, Krampera M, Visco C, Scupoli MT. B-cell receptor signaling activity identifies patients with mantle cell lymphoma at higher risk of progression. Sci Rep 2024; 14:6595. [PMID: 38503806 PMCID: PMC10951201 DOI: 10.1038/s41598-024-55728-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024] Open
Abstract
Mantle cell lymphoma (MCL) is an incurable B-cell malignancy characterized by a high clinical variability. Therefore, there is a critical need to define parameters that identify high-risk patients for aggressive disease and therapy resistance. B-cell receptor (BCR) signaling is crucial for MCL initiation and progression and is a target for therapeutic intervention. We interrogated BCR signaling proteins (SYK, LCK, BTK, PLCγ2, p38, AKT, NF-κB p65, and STAT5) in 30 primary MCL samples using phospho-specific flow cytometry. Anti-IgM modulation induced heterogeneous BCR signaling responses among samples allowing the identification of two clusters with differential responses. The cluster with higher response was associated with shorter progression free survival (PFS) and overall survival (OS). Moreover, higher constitutive AKT activity was predictive of inferior response to the Bruton's tyrosine kinase inhibitor (BTKi) ibrutinib. Time-to-event analyses showed that MCL international prognostic index (MIPI) high-risk category and higher STAT5 response were predictors of shorter PFS and OS whilst MIPI high-risk category and high SYK response predicted shorter OS. In conclusion, we identified BCR signaling properties associated with poor clinical outcome and resistance to ibrutinib, thus highlighting the prognostic and predictive significance of BCR activity and advancing our understanding of signaling heterogeneity underlying clinical behavior of MCL.
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Affiliation(s)
- Simona Gambino
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy
| | | | - Marilisa Galasso
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy
| | - Chiara Cavallini
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Roberto Chignola
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Ornella Lovato
- Research Center LURM (Interdepartmental Laboratory of Medical Research), University of Verona, Verona, Italy
| | - Luca Giacobazzi
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | | | - Annalisa Adamo
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | | | - Antonino Aparo
- Research Center LURM (Interdepartmental Laboratory of Medical Research), University of Verona, Verona, Italy
| | - Isacco Ferrarini
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy
- Hematology Unit, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Stefano Ugel
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Ilaria Dando
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Mauro Krampera
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy
- Hematology Unit, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Carlo Visco
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy.
- Hematology Unit, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy.
| | - Maria Teresa Scupoli
- Department of Engineering for Innovation Medicine, Section of Biomedicine, University of Verona, Verona, Italy.
- Research Center LURM (Interdepartmental Laboratory of Medical Research), University of Verona, Verona, Italy.
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6
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Stergiou IE, Tsironis C, Papadakos SP, Tsitsilonis OE, Dimopoulos MA, Theocharis S. Unraveling the Role of the NLRP3 Inflammasome in Lymphoma: Implications in Pathogenesis and Therapeutic Strategies. Int J Mol Sci 2024; 25:2369. [PMID: 38397043 PMCID: PMC10889189 DOI: 10.3390/ijms25042369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Inflammasomes are multimeric protein complexes, sensors of intracellular danger signals, and crucial components of the innate immune system, with the NLRP3 inflammasome being the best characterized among them. The increasing scientific interest in the mechanisms interconnecting inflammation and tumorigenesis has led to the study of the NLRP3 inflammasome in the setting of various neoplasms. Despite a plethora of data regarding solid tumors, NLRP3 inflammasome's implication in the pathogenesis of hematological malignancies only recently gained attention. In this review, we investigate its role in normal lymphopoiesis and lymphomagenesis. Considering that lymphomas comprise a heterogeneous group of hematologic neoplasms, both tumor-promoting and tumor-suppressing properties were attributed to the NLRP3 inflammasome, affecting neoplastic cells and immune cells in the tumor microenvironment. NLRP3 inflammasome-related proteins were associated with disease characteristics, response to treatment, and prognosis. Few studies assess the efficacy of NLRP3 inflammasome therapeutic targeting with encouraging results, though most are still at the preclinical level. Further understanding of the mechanisms regulating NLRP3 inflammasome activation during lymphoma development and progression can contribute to the investigation of novel treatment approaches to cover unmet needs in lymphoma therapeutics.
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Affiliation(s)
- Ioanna E. Stergiou
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (I.E.S.); (C.T.)
| | - Christos Tsironis
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (I.E.S.); (C.T.)
| | - Stavros P. Papadakos
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 10679 Athens, Greece;
| | - Ourania E. Tsitsilonis
- Flow Cytometry Unit, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece;
| | - Meletios Athanasios Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra Hospital, 11528 Athens, Greece;
| | - Stamatios Theocharis
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 10679 Athens, Greece;
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7
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Jain N, Mamgain M, Chowdhury SM, Jindal U, Sharma I, Sehgal L, Epperla N. Beyond Bruton's tyrosine kinase inhibitors in mantle cell lymphoma: bispecific antibodies, antibody-drug conjugates, CAR T-cells, and novel agents. J Hematol Oncol 2023; 16:99. [PMID: 37626420 PMCID: PMC10463717 DOI: 10.1186/s13045-023-01496-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023] Open
Abstract
Mantle cell lymphoma is a B cell non-Hodgkin lymphoma (NHL), representing 2-6% of all NHLs and characterized by overexpression of cyclin D1. The last decade has seen the development of many novel treatment approaches in MCL, most notably the class of Bruton's tyrosine kinase inhibitors (BTKi). BTKi has shown excellent outcomes for patients with relapsed or refractory MCL and is now being studied in the first-line setting. However, patients eventually progress on BTKi due to the development of resistance. Additionally, there is an alteration in the tumor microenvironment in these patients with varying biological and therapeutic implications. Hence, it is necessary to explore novel therapeutic strategies that can be effective in those who progressed on BTKi or potentially circumvent resistance. In this review, we provide a brief overview of BTKi, then discuss the various mechanisms of BTK resistance including the role of genetic alteration, cancer stem cells, tumor microenvironment, and adaptive reprogramming bypassing the effect of BTK inhibition, and then provide a comprehensive review of current and emerging therapeutic options beyond BTKi including novel agents, CAR T cells, bispecific antibodies, and antibody-drug conjugates.
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Affiliation(s)
- Neeraj Jain
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002 India
| | - Mukesh Mamgain
- Department of Medical Oncology and Hematology, All India Institute of Medical Sciences, Rishikesh, India
| | - Sayan Mullick Chowdhury
- Division of Hematology, Department of Medicine, Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH USA
| | - Udita Jindal
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002 India
| | - Isha Sharma
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh India
| | - Lalit Sehgal
- Division of Hematology, Department of Medicine, Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH USA
| | - Narendranath Epperla
- The Ohio State University Comprehensive Cancer Center, Suite 7198, 2121 Kenny Rd, Columbus, OH 43221 USA
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8
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Li G, Li J, Tian Y, Zhao Y, Pang X, Yan A. Machine learning-based classification models for non-covalent Bruton's tyrosine kinase inhibitors: predictive ability and interpretability. Mol Divers 2023:10.1007/s11030-023-10696-6. [PMID: 37479824 DOI: 10.1007/s11030-023-10696-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023]
Abstract
In this study, we built classification models using machine learning techniques to predict the bioactivity of non-covalent inhibitors of Bruton's tyrosine kinase (BTK) and to provide interpretable and transparent explanations for these predictions. To achieve this, we gathered data on BTK inhibitors from the Reaxys and ChEMBL databases, removing compounds with covalent bonds and duplicates to obtain a dataset of 3895 inhibitors of non-covalent. These inhibitors were characterized using MACCS fingerprints and Morgan fingerprints, and four traditional machine learning algorithms (decision trees (DT), random forests (RF), support vector machines (SVM), and extreme gradient boosting (XGBoost)) were used to build 16 classification models. In addition, four deep learning models were developed using deep neural networks (DNN). The best model, Model D_4, which was built using XGBoost and MACCS fingerprints, achieved an accuracy of 94.1% and a Matthews correlation coefficient (MCC) of 0.75 on the test set. To provide interpretable explanations, we employed the SHAP method to decompose the predicted values into the contributions of each feature. We also used K-means dimensionality reduction and hierarchical clustering to visualize the clustering effects of molecular structures of the inhibitors. The results of this study were validated using crystal structures, and we found that the interaction between the BTK amino acid residue and the important features of clustered scaffold was consistent with the known properties of the complex crystal structures. Overall, our models demonstrated high predictive ability and a qualitative model can be converted to a quantitative model to some extent by SHAP, making them valuable for guiding the design of new BTK inhibitors with desired activity.
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Affiliation(s)
- Guo Li
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Jiaxuan Li
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Yujia Tian
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Yunyang Zhao
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Xiaoyang Pang
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China.
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9
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Fakhri B, Danilov A. SOHO State of the Art Updates and Next Questions: New Targetable Pathways in Chronic Lymphocytic Leukemia. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2023; 23:232-237. [PMID: 36754692 DOI: 10.1016/j.clml.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
Regulatory approvals of Bruton tyrosine kinase (BTK) inhibitors and BCL2 inhibitors have transformed the therapeutic paradigm in chronic lymphocytic leukemia (CLL). However, despite significant improvement, treatment discontinuations due to an acquired resistance mutation or intolerance to these agents are common. Those who are refractory and/or intolerant to both these classes of drugs - the "double exposed/refractory" patients - pose a real challenge in clinical practice and are in dire need of novel therapeutic approaches. In this manuscript, we review the ongoing efforts addressing this unmet clinical need including the ongoing development of non-covalent BTK inhibitors, BTK degraders, novel BH3-mimetics, therapeutic antibodies targeting novel antigens and immune cell enabling therapies.
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Affiliation(s)
- Bita Fakhri
- Division of Hematology, Department of Medicine, Stanford University, Palo Alto, CA
| | - Alexey Danilov
- Department of Hematology and Hematopoietic Stem Cell Transplant, City of Hope National Medical Center, Duarte, CA.
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10
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Dong Z, Song JY, Thieme E, Anderson A, Oh E, Cheng WA, Kuang BZ, Lee V, Zhang T, Wang Z, Szymura S, Smith DL, Zhang J, Nian W, Zheng X, He F, Zhou Q, Cha SC, Danilov AV, Qin H, Kwak LW. Generation of a humanized afucosylated BAFF-R antibody with broad activity against human B-cell malignancies. Blood Adv 2023; 7:918-932. [PMID: 36469551 PMCID: PMC10027513 DOI: 10.1182/bloodadvances.2022008560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
B-cell activating factor receptor (BAFF-R) is a mature B-cell survival receptor, which is highly expressed in a wide variety of B-cell malignancies but with minimal expression in immature B cells. These properties make BAFF-R an attractive target for therapy of B-cell lymphomas. We generated a novel humanized anti BAFF-R monoclonal antibody (mAb) with high specificity and potent in vitro and in vivo activity against B-cell lymphomas and leukemias. The humanized variants of an original chimeric BAFF-R mAb retained BAFF-R binding affinity and antibody-dependent cellular cytotoxicity (ADCC) against a panel of human cell lines and primary lymphoma samples. Furthermore, 1 humanized BAFF-R mAb clone and its afucosylated version, glycoengineered to optimize the primary mechanism of action, prolonged survival of immunodeficient mice bearing human tumor cell lines or patient-derived lymphoma xenografts in 3 separate models, compared with controls. Finally, the tissue specificity of this humanized mAb was confirmed against a broad panel of normal human tissues. Taken together, we have identified a robust lead-candidate BAFF-R mAb for clinical development.
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Affiliation(s)
- Zhenyuan Dong
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Joo Y. Song
- Department of Pathology, City of Hope Medical Center, Duarte, CA
| | - Elana Thieme
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Aaron Anderson
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Elizabeth Oh
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Wesley A. Cheng
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Benjamin Z. Kuang
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Vincent Lee
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Tiantian Zhang
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Zhe Wang
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Szymon Szymura
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - D. Lynne Smith
- Clinical and Translational Project Development, City of Hope Medical Center, Duarte, CA
| | | | - Weihong Nian
- Shanghai Escugen Biotechnology Co, Ltd, Shanghai, China
| | - Xintong Zheng
- Shanghai Escugen Biotechnology Co, Ltd, Shanghai, China
| | - Feng He
- Shanghai Escugen Biotechnology Co, Ltd, Shanghai, China
| | - Qing Zhou
- Shanghai Escugen Biotechnology Co, Ltd, Shanghai, China
| | - Soung-chul Cha
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Alexey V. Danilov
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Hong Qin
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Larry W. Kwak
- Toni Stephenson Lymphoma Center, Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
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11
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Sonowal H, Rice WG, Howell SB. Luxeptinib interferes with LYN-mediated activation of SYK and modulates BCR signaling in lymphoma. PLoS One 2023; 18:e0277003. [PMID: 36888611 PMCID: PMC9994718 DOI: 10.1371/journal.pone.0277003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/19/2023] [Indexed: 03/09/2023] Open
Abstract
Luxeptinib (LUX) is a novel oral kinase inhibitor that inhibits FLT3 and also interferes with signaling from the BCR and cell surface TLRs, as well as activation of the NLRP3 inflammasome. Ongoing clinical trials are testing its activity in patients with lymphoma and AML. This study sought to refine understanding of how LUX modulates the earliest steps downstream of the BCR following its activation by anti-IgM in lymphoma cells in comparison to ibrutinib (IB). LUX decreased anti-IgM-induced phosphorylation of BTK at Y551 and Y223 but its ability to reduce phosphorylation of kinases further upstream suggests that BTK is not the primary target. LUX was more effective than IB at reducing both steady state and anti-IgM-induced phosphorylation of LYN and SYK. LUX decreased phosphorylation of SYK (Y525/Y526) and BLNK (Y96) which are necessary regulators of BTK activation. Further upstream, LUX blunted the anti-IgM-induced phosphorylation of LYN (Y397) whose activation is required for phosphorylation of SYK and BLNK. These results indicate that LUX is targeting autophosphorylation of LYN or a step further upstream of LYN in the cascade of signal generated by BCR and that it does so more effectively than IB. The fact that LUX has activity at or upstream of LYN is important because LYN is an essential signaling intermediate in multiple cellular signaling processes that regulate growth, differentiation, apoptosis, immunoregulation, migration and EMT in normal and cancer cells.
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Affiliation(s)
- Himangshu Sonowal
- Moores Cancer Center, Division of Hematology, Department of Medicine, University of California, San Diego, San Diego, California, United States of America
| | - William G. Rice
- Aptose Biosciences, Inc., San Diego, California, United States of America
| | - Stephen B. Howell
- Moores Cancer Center, Division of Hematology, Department of Medicine, University of California, San Diego, San Diego, California, United States of America
- * E-mail:
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12
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Ancos-Pintado R, Bragado-García I, Morales ML, García-Vicente R, Arroyo-Barea A, Rodríguez-García A, Martínez-López J, Linares M, Hernández-Sánchez M. High-Throughput CRISPR Screening in Hematological Neoplasms. Cancers (Basel) 2022; 14:3612. [PMID: 35892871 PMCID: PMC9329962 DOI: 10.3390/cancers14153612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
CRISPR is becoming an indispensable tool in biological research, revolutionizing diverse fields of medical research and biotechnology. In the last few years, several CRISPR-based genome-targeting tools have been translated for the study of hematological neoplasms. However, there is a lack of reviews focused on the wide uses of this technology in hematology. Therefore, in this review, we summarize the main CRISPR-based approaches of high throughput screenings applied to this field. Here we explain several libraries and algorithms for analysis of CRISPR screens used in hematology, accompanied by the most relevant databases. Moreover, we focus on (1) the identification of novel modulator genes of drug resistance and efficacy, which could anticipate relapses in patients and (2) new therapeutic targets and synthetic lethal interactions. We also discuss the approaches to uncover novel biomarkers of malignant transformations and immune evasion mechanisms. We explain the current literature in the most common lymphoid and myeloid neoplasms using this tool. Then, we conclude with future directions, highlighting the importance of further gene candidate validation and the integration and harmonization of the data from CRISPR screening approaches.
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Affiliation(s)
- Raquel Ancos-Pintado
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Irene Bragado-García
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Luz Morales
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Roberto García-Vicente
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Andrés Arroyo-Barea
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Alba Rodríguez-García
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Joaquín Martínez-López
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain
| | - María Linares
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
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