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Mavridou D, Psatha K, Aivaliotis M. Integrative Analysis of Multi-Omics Data to Identify Deregulated Molecular Pathways and Druggable Targets in Chronic Lymphocytic Leukemia. J Pers Med 2024; 14:831. [PMID: 39202022 PMCID: PMC11355716 DOI: 10.3390/jpm14080831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 09/03/2024] Open
Abstract
Chronic Lymphocytic Leukemia (CLL) is the most common B-cell malignancy in the Western world, characterized by frequent relapses despite temporary remissions. Our study integrated publicly available proteomic, transcriptomic, and patient survival datasets to identify key differences between healthy and CLL samples. We exposed approximately 1000 proteins that differentiate healthy from cancerous cells, with 608 upregulated and 415 downregulated in CLL cases. Notable upregulated proteins include YEATS2 (an epigenetic regulator), PIGR (Polymeric immunoglobulin receptor), and SNRPA (a splicing factor), which may serve as prognostic biomarkers for this disease. Key pathways implicated in CLL progression involve RNA processing, stress resistance, and immune response deficits. Furthermore, we identified three existing drugs-Bosutinib, Vorinostat, and Panobinostat-for potential further investigation in drug repurposing in CLL. We also found limited correlation between transcriptomic and proteomic data, emphasizing the importance of proteomics in understanding gene expression regulation mechanisms. This generally known disparity highlights once again that mRNA levels do not accurately predict protein abundance due to many regulatory factors, such as protein degradation, post-transcriptional modifications, and differing rates of translation. These results demonstrate the value of integrating omics data to uncover deregulated proteins and pathways in cancer and suggest new therapeutic avenues for CLL.
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Affiliation(s)
- Dimitra Mavridou
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece;
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Konstantina Psatha
- Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece;
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Laboratory of Medical Biology—Genetics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Michalis Aivaliotis
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece;
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
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2
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Qiu Z, Khalife J, Ethiraj P, Jaafar C, Lin AP, Holder KN, Ritter JP, Chiou L, Huelgas-Morales G, Aslam S, Zhang Z, Liu Z, Arya S, Gupta YK, Dahia PLM, Aguiar RC. IRF8-mutant B cell lymphoma evades immunity through a CD74-dependent deregulation of antigen processing and presentation in MHCII complexes. SCIENCE ADVANCES 2024; 10:eadk2091. [PMID: 38996030 PMCID: PMC11244530 DOI: 10.1126/sciadv.adk2091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 06/06/2024] [Indexed: 07/14/2024]
Abstract
The mechanism by which interferon regulatory factor 8 (IRF8) mutation contributes to lymphomagenesis is unknown. We modeled IRF8 variants in B cell lymphomas and found that they affected the expression of regulators of antigen presentation. Expression of IRF8 mutants in murine B cell lymphomas suppressed CD4, but not CD8, activation elicited by antigen presentation and downmodulated CD74 and human leukocyte antigen (HLA) DM, intracellular regulators of antigen peptide processing/loading in the major histocompatibility complex (MHC) II. Concordantly, mutant IRF8 bound less efficiently to the promoters of these genes. Mice harboring IRF8 mutant lymphomas displayed higher tumor burden and remodeling of the tumor microenvironment, typified by depletion of CD4, CD8, and natural killer cells, increase in regulatory T cells and T follicular helper cells. Deconvolution of bulk RNA sequencing data from IRF8-mutant human diffuse large B cell lymphoma (DLBCL) recapitulated part of the immune remodeling detected in mice. We concluded that IRF8 mutations contribute to DLBCL biology by facilitating immune escape.
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MESH Headings
- Interferon Regulatory Factors/genetics
- Interferon Regulatory Factors/metabolism
- Animals
- Antigen Presentation/immunology
- Antigen Presentation/genetics
- Humans
- Mice
- Mutation
- Histocompatibility Antigens Class II/genetics
- Histocompatibility Antigens Class II/immunology
- Histocompatibility Antigens Class II/metabolism
- Antigens, Differentiation, B-Lymphocyte/genetics
- Antigens, Differentiation, B-Lymphocyte/metabolism
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Tumor Microenvironment/immunology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/pathology
- Cell Line, Tumor
- Tumor Escape/genetics
- Gene Expression Regulation, Neoplastic
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Affiliation(s)
- Zhijun Qiu
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Jihane Khalife
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Purushoth Ethiraj
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Carine Jaafar
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - An-Ping Lin
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Kenneth N. Holder
- Department of Pathology, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Jacob P. Ritter
- Department of Pathology, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Lilly Chiou
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Gabriela Huelgas-Morales
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Sadia Aslam
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Zhao Zhang
- Department of Molecular Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Zhijie Liu
- Department of Molecular Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Shailee Arya
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Yogesh K. Gupta
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Patricia L. M. Dahia
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Ricardo C.T. Aguiar
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
- South Texas Veterans Health Care System, Audie Murphy VA Hospital, San Antonio, TX 78229, USA
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3
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Louveau B, Reger De Moura C, Jouenne F, Sadoux A, Allayous C, Da Meda L, Bernard-Cacciarella M, Baroudjian B, Lebbé C, Mourah S, Dumaz N. Combined PDE4+MEK inhibition shows antiproliferative effects in NRASQ61 mutated melanoma preclinical models. Melanoma Res 2024; 34:186-192. [PMID: 38141200 DOI: 10.1097/cmr.0000000000000950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2023]
Abstract
Upregulation of phosphodiesterase type 4 (PDE4) has been associated with worse prognosis in several cancers. In melanomas harboring NRAS mutations, PDE4 upregulation has been shown to trigger a switch in signaling from BRAF to RAF1 which leads to mitogen-activated protein kinase pathway activation. Previous in vitro evidence showed that PDE4 inhibition induced death in NRASQ61mut melanoma cells and such a strategy may thus be a relevant therapeutic option in those cases with no molecular targeted therapies approved to date. In this study, we generated patient-derived xenografts (PDX) from two NRASQ61mut melanoma lesions. We performed ex vivo histoculture drug response assays and in vivo experiments. A significant ex vivo inhibition of proliferation with the combination of roflumilast+cobimetinib was observed compared to dimethyl sulfoxide control in both models (51 and 67%). This antiproliferative effect was confirmed in vivo for PDX-1 with a 56% inhibition of tumor growth. To decipher molecular mechanisms underlying this effect, we performed transcriptomic analyses and revealed a decrease in MKI67, RAF1 and CCND1 expression under bitherapy. Our findings strengthen the therapeutic interest of PDE4 inhibitors and support further experiments to evaluate this approach in metastatic melanoma.
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Affiliation(s)
- Baptiste Louveau
- Department of Pharmacology and Tumor Genomics, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), Paris, France
| | - Coralie Reger De Moura
- Department of Pharmacology and Tumor Genomics, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), Paris, France
| | - Fanélie Jouenne
- Department of Pharmacology and Tumor Genomics, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), Paris, France
| | - Aurélie Sadoux
- Department of Pharmacology and Tumor Genomics, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), Paris, France
| | - Clara Allayous
- Department of Dermatology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laetitia Da Meda
- Department of Dermatology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Mélanie Bernard-Cacciarella
- Université Paris Cité, INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), Paris, France
| | - Barouyr Baroudjian
- Department of Dermatology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Céleste Lebbé
- Université Paris Cité, INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), Paris, France
- Department of Dermatology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Samia Mourah
- Department of Pharmacology and Tumor Genomics, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), Paris, France
| | - Nicolas Dumaz
- Université Paris Cité, INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), Paris, France
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4
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Liu D, Yan B, Yin Y, Chen F, Guo C, Li Q, Liu J, Pu L, Wu W, Luo J. PI3Kδ Mediates Fibrosis by Patient-Derived Vitreous. J Transl Med 2024; 104:102026. [PMID: 38307209 DOI: 10.1016/j.labinv.2024.102026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/23/2023] [Accepted: 01/24/2024] [Indexed: 02/04/2024] Open
Abstract
The epithelial-mesenchymal transition (EMT) is a fundamental process in developing fibrotic diseases, including forming epiretinal membranes (ERMs). ERMs can result in irreversible vision loss. Previous research has demonstrated that vitreous (VIT) derived from patients with proliferative diabetic retinopathy can stimulate angiogenesis through the Axl/PI3K/Akt pathway. Building upon this knowledge, we aimed to explore the influence of VIT from patients with macular membranes in ARPE-19 cells. Our findings reveal that patient-derived VIT from individuals with macular membranes promotes EMT and phosphoinositide 3-kinase-delta (PI3Kδ) expression in ARPE-19 cells. To elucidate the function of PI3Kδ in the ERM, we conducted experiments involving the knockout of p110δ, a key subunit of PI3Kδ, and observed that its absence hinders EMT induced by patient-derived VIT. Moreover, p110δ depletion reduces cell proliferation and migration in ARPE-19 cells. Remarkably, these effects were further corroborated by applying the p110δ inhibitor idelalisib, which blocks fibrosis in the laser-induced fibrosis model. Collectively, our results propose that p110δ plays a critical role in the progression of ERMs. Consequently, targeting p110δ emerges as a promising therapeutic approach for mitigating fibrosis. These findings contribute to a better understanding of the underlying mechanisms involved in ERM formation and highlight the potential for p110δ-directed antifibrotic therapy in retinal diseases.
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Affiliation(s)
- Dan Liu
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bin Yan
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yiwei Yin
- Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Cao Guo
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qin Li
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jia Liu
- School of Medicine, Hunan University of Medicine, Huaihua, Hunan, China
| | - Li Pu
- Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenyi Wu
- Department of Ophthalmology, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Jing Luo
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
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5
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DA Costa Machado AK, Machado CB, DE Pinho Pessoa FMC, Barreto IV, Gadelha RB, DE Sousa Oliveira D, Ribeiro RM, Lopes GS, DE Moraesfilho MO, DE Moraes MEA, Khayat AS, Moreira-Nunes CA. Development and Clinical Applications of PI3K/AKT/mTOR Pathway Inhibitors as a Therapeutic Option for Leukemias. CANCER DIAGNOSIS & PROGNOSIS 2024; 4:9-24. [PMID: 38173664 PMCID: PMC10758851 DOI: 10.21873/cdp.10279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
Leukemias are hematological neoplasms characterized by dysregulations in several cellular signaling pathways, prominently including the PI3K/AKT/mTOR pathway. Since this pathway is associated with several important cellular mechanisms, such as proliferation, metabolism, survival, and cell death, its hyperactivation significantly contributes to the development of leukemias. In addition, it is a crucial prognostic factor, often correlated with therapeutic resistance. Changes in the PI3K/AKT/mTOR pathway are identified in more than 50% of cases of acute leukemia, especially in myeloid lineages. Furthermore, these changes are highly frequent in cases of chronic lymphocytic leukemia, especially those with a B cell phenotype, due to the correlation between the hyperactivation of B cell receptors and the abnormal activation of PI3Kδ. Thus, the search for new therapies that inhibit the activity of the PI3K/AKT/mTOR pathway has become the objective of several clinical studies that aim to replace conventional oncological treatments that have high rates of toxicities and low specificity with target-specific therapies offering improved patient quality of life. In this review we describe the PI3K/AKT/mTOR signal transduction pathway and its implications in leukemogenesis. Furthermore, we provide an overview of clinical trials that employed PI3K/AKT/mTOR inhibitors either as monotherapy or in combination with other cytotoxic agents for treating patients with various types of leukemias. The varying degrees of treatment efficacy are also reported.
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Affiliation(s)
- Anna Karolyna DA Costa Machado
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE, Brazil
| | - Caio Bezerra Machado
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE, Brazil
| | - Flávia Melo Cunha DE Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE, Brazil
| | - Igor Valentim Barreto
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE, Brazil
| | - Renan Brito Gadelha
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE, Brazil
| | | | | | | | - Manoel Odorico DE Moraesfilho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE, Brazil
| | - Maria Elisabete Amaral DE Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE, Brazil
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém, PA, Brazil
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE, Brazil
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém, PA, Brazil
- Clementino Fraga Group, Central Unity, Molecular Biology Laboratory, Fortaleza, CE, Brazil
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6
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Qiu Z, Khalife J, Lin AP, Ethiraj P, Jaafar C, Chiou L, Huelgas-Morales G, Aslam S, Arya S, Gupta YK, Dahia PLM, Aguiar RCT. IRF8-mutant B cell lymphoma evades immunity through a CD74-dependent deregulation of antigen processing and presentation in MHC CII complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.14.560755. [PMID: 37873241 PMCID: PMC10592808 DOI: 10.1101/2023.10.14.560755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
In diffuse large B-cell lymphoma (DLBCL), the transcription factor IRF8 is the target of a series of potentially oncogenic events, including, chromosomal translocation, focal amplification, and super-enhancer perturbations. IRF8 is also frequently mutant in DLBCL, but how these variants contribute to lymphomagenesis is unknown. We modeled IRF8 mutations in DLBCL and found that they did not meaningfully impact cell fitness. Instead, IRF8 mutants, mapping either to the DNA-binding domain (DBD) or c-terminal tail, displayed diminished transcription activity towards CIITA, a direct IRF8 target. In primary DLBCL, IRF8 mutations were mutually exclusive with mutations in genes involved in antigen presentation. Concordantly, expression of IRF8 mutants in murine B cell lymphomas uniformly suppressed CD4, but not CD8, activation elicited by antigen presentation. Unexpectedly, IRF8 mutation did not modify MHC CII expression on the cell surface, rather it downmodulated CD74 and HLA- DM, intracellular regulators of antigen peptide processing/loading in the MHC CII complex. These changes were functionally relevant as, in comparison to IRF8 WT, mice harboring IRF8 mutant lymphomas displayed a significantly higher tumor burden, in association with a substantial remodeling of the tumor microenvironment (TME), typified by depletion of CD4, CD8, Th1 and NK cells, and increase in T-regs and Tfh cells. Importantly, the clinical and immune phenotypes of IRF8-mutant lymphomas were rescued in vivo by ectopic expression of CD74. Deconvolution of bulk RNAseq data from primary human DLBCL recapitulated part of the immune remodeling detected in mice and pointed to depletion of dendritic cells as another feature of IRF8 mutant TME. We concluded that IRF8 mutations contribute to DLBCL biology by facilitating immune escape.
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7
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Guo Q, Cheng ZM, Gonzalez-Cantú H, Rotondi M, Huelgas-Morales G, Ethiraj P, Qiu Z, Lefkowitz J, Song W, Landry BN, Lopez H, Estrada-Zuniga CM, Goyal S, Khan MA, Walker TJ, Wang E, Li F, Ding Y, Mulligan LM, Aguiar RCT, Dahia PLM. TMEM127 suppresses tumor development by promoting RET ubiquitination, positioning, and degradation. Cell Rep 2023; 42:113070. [PMID: 37659079 PMCID: PMC10637630 DOI: 10.1016/j.celrep.2023.113070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/06/2023] [Accepted: 08/18/2023] [Indexed: 09/04/2023] Open
Abstract
The TMEM127 gene encodes a transmembrane protein of poorly known function that is mutated in pheochromocytomas, neural crest-derived tumors of adrenomedullary cells. Here, we report that, at single-nucleus resolution, TMEM127-mutant tumors share precursor cells and transcription regulatory elements with pheochromocytomas carrying mutations of the tyrosine kinase receptor RET. Additionally, TMEM127-mutant pheochromocytomas, human cells, and mouse knockout models of TMEM127 accumulate RET and increase its signaling. TMEM127 contributes to RET cellular positioning, trafficking, and lysosome-mediated degradation. Mechanistically, TMEM127 binds to RET and recruits the NEDD4 E3 ubiquitin ligase for RET ubiquitination and degradation via TMEM127 C-terminal PxxY motifs. Lastly, increased cell proliferation and tumor burden after TMEM127 loss can be reversed by selective RET inhibitors in vitro and in vivo. Our results define TMEM127 as a component of the ubiquitin system and identify aberrant RET stabilization as a likely mechanism through which TMEM127 loss-of-function mutations cause pheochromocytoma.
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Affiliation(s)
- Qianjin Guo
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Zi-Ming Cheng
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Hector Gonzalez-Cantú
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Matthew Rotondi
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Gabriela Huelgas-Morales
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Purushoth Ethiraj
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Zhijun Qiu
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Jonathan Lefkowitz
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Wan Song
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Bethany N Landry
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Hector Lopez
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Cynthia M Estrada-Zuniga
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Shivi Goyal
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Mohammad Aasif Khan
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA
| | - Timothy J Walker
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Exing Wang
- Department Cell Structure and Anatomy, UTHSCSA, San Antonio, TX, USA
| | - Faqian Li
- Department of Pathology, UTHSCSA, San Antonio, TX, USA
| | - Yanli Ding
- Department of Pathology, UTHSCSA, San Antonio, TX, USA
| | - Lois M Mulligan
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Ricardo C T Aguiar
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA; Mays Cancer Center, UTHSCSA, San Antonio, TX, USA; South Texas Veterans Health Care System, Audie Murphy VA Hospital, San Antonio, TX 78229, USA
| | - Patricia L M Dahia
- Division of Hematology/Medical Oncology, Department of Medicine, University of Texas Health San Science Center at Antonio (UTHSCSA), San Antonio, TX, USA; Mays Cancer Center, UTHSCSA, San Antonio, TX, USA.
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8
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Câmara AB, Brandão IA. The Non-Hodgkin Lymphoma Treatment and Side Effects: A Systematic Review and Meta-Analysis. Recent Pat Anticancer Drug Discov 2023; 19:PRA-EPUB-128894. [PMID: 36650656 DOI: 10.2174/1574892818666230117151757] [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: 05/27/2022] [Revised: 10/11/2022] [Accepted: 11/11/2022] [Indexed: 01/19/2023]
Abstract
OBJECTIVE This paper aims to review studies regarding side effects found during Non-Hodgkin Lymphoma treatment, to suggest the drug class most associated with these effects, as well as the most prevalent side effect grade. METHODS This review is registered in PROSPERO (IDCRD42022295774) and followed the PICOS strategy and PRISMA guidelines. The search was carried out in the databases PubMed/MEDLINE, Scientific Electronic Library Online, and DOAJ. Medical Subject Headings Terms were used and quantitative studies with conclusive results regarding side effects during the non-Hodgkin lymphoma treatment were selected. Patent information was obtained from google patents. RESULTS Monoclonal antibodies were the main drug class associated with side effects during NHL therapy. The combination of Rituximab (Rituxan®; patent EP1616572B) and iInotuzumab (Besponsa®; patent EP1504035B3) was associated with a higher incidence of thrombocytopenia (p<0.05), while the combination of Rituximab and Venetoclax (Venclexta®; patent CN107089981A) was associated with a higher incidence of neutropenia (p<0.05) when compared to Bendamustine combinations (Treanda ™; patent US20130253025A1). Meta-analysis revealed a high prevalence of grade 3-4 neutropenia and thrombocytopenia in men. Finally, Americans and Canadians experienced a higher prevalence of these side effects, when compared to others nationalities (p<0.05). CONCLUSION Patents regarding the use of monoclonal antibodies in NHL treatment were published in the last year. Monoclonal antibodies associated with neutropenia (grade 3-4) and thrombocytopenia, especially in North American men treated for NHL, and with an average age of 62 years demonstrated importance in this study.
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Affiliation(s)
- Alice Barros Câmara
- Department of Biophysics and Pharmacology, Federal University of Rio Grande do Norte
| | - Igor Augusto Brandão
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte
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9
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Henderson J, Havranek O, Ma MCJ, Herman V, Kupcova K, Chrbolkova T, Pacheco-Blanco M, Wang Z, Comer JM, Zal T, Davis RE. Detecting Förster resonance energy transfer in living cells by conventional and spectral flow cytometry. Cytometry A 2022; 101:818-834. [PMID: 34128311 DOI: 10.1002/cyto.a.24472] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 01/27/2023]
Abstract
Assays based on Förster resonance energy transfer (FRET) can be used to study many processes in cell biology. Although this is most often done with microscopy for fluorescence detection, we report two ways to measure FRET in living cells by flow cytometry. Using a conventional flow cytometer and the "3-cube method" for intensity-based calculation of FRET efficiency, we measured the enzymatic activity of specific kinases in cells expressing a genetically-encoded reporter. For both AKT and protein kinase A, the method measured kinase activity in time-course, dose-response, and kinetic assays. Using the Cytek Aurora spectral flow cytometer, which applies linear unmixing to emission measured in multiple wavelength ranges, FRET from the same reporters was measured with greater single-cell precision, in real time and in the presence of other fluorophores. Results from gene-knockout studies suggested that spectral flow cytometry might enable the sorting of cells on the basis of FRET. The methods we present provide convenient and flexible options for using FRET with flow cytometry in studies of cell biology.
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Affiliation(s)
- Jared Henderson
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Ondrej Havranek
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA.,BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic.,Department of Hematology, Charles University and General University Hospital, Prague, Czech Republic
| | - Man Chun John Ma
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Vaclav Herman
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic.,Department of Hematology, Charles University and General University Hospital, Prague, Czech Republic
| | - Kristyna Kupcova
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Tereza Chrbolkova
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | | | - Zhiqiang Wang
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Justin M Comer
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Tomasz Zal
- Department of Leukemia, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Richard Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA.,Department of Translational Molecular Pathology, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
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10
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Tong L, Shan M, Zou W, Liu X, Felsher DW, Wang J. Cyclic adenosine monophosphate/phosphodiesterase 4 pathway associated with immune infiltration and PD-L1 expression in lung adenocarcinoma cells. Front Oncol 2022; 12:904969. [PMID: 35978822 PMCID: PMC9376450 DOI: 10.3389/fonc.2022.904969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
Background The cyclic adenosine monophosphate/phosphodiesterase 4 (cAMP/PDE4) pathway is involved in inflammation and immune regulation; however, the effect of cAMP/PDE4 on immune infiltration and immune evasion in lung adenocarcinoma (LUAD) remains unclear. Methods CBioPortal, which is the The Cancer Genome Atlas (TCGA) online database, and the Kaplan Meier plotter were used to analyze the association between genes and the prognosis of TCGA-LUAD. Tumor Immune Estimation Resource (TIMER) was used to analyze the association between gene expression and immune infiltration. The Genecards database was used to identify the transcription factors of related genes. The lung adenocarcinoma cell line H1299 and A549 were treated with cAMP pathway drugs. Flow cytometry and qRT-PCR were used to detect the PD-L1 protein and gene expression, respectively. A one-way analysis of variance with Tukey’s post-hoc test or a Student’s t-test were used. Results It was found that PDE4B and CREB1, which are downstream genes of the cAMP/PDE4 axis, were differentially expressed in LUAD and adjacent tissues and are correlated with the prognosis and immune infiltration of LUAD. In the CBioPortal database, cAMP pathway genes are closely related to programmed cell death-ligand 1 (PD-L1) expression in TCGA-LUAD. The protein-protein interaction revealed that there was a direct interaction between CREB1/CREBBP, which are the downstream molecules of the cAMP/PDE4 axis, and MYC; additionally, MYC was predicted to bind to the PD-L1 transcription site and regulate PD-L1 expression. CREB1 was also predicted to transcriptionally bind to both MYC and PD-L1. These results predicted the interaction network of cAMP/PDE4/CREB1/CREBP/MYC/PD-L1, and the core factor may be related to MYC. In the cell experiment, forskolin (an adenylate cyclase activator) and zardaverine (a PDE4 inhibitor) enhance the cAMP pathway and decrease PD-L1 expression, while SQ2253 (an adenylate cyclase inhibitor) inhibits the cAMP pathway and increases PD-L1 expression of the LUAD cell lines H1299 and A549, and MYC regulation by these drugs was positively correlated with PD-L1 regulation, which verified the regulation of the cAMP/PDE4 pathway on MYC and PD-L1. Conclusions This study showed that the cAMP/PDE4 pathway may play an important role in PD-L1 regulation and immune infiltration in LUAD.
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Affiliation(s)
- Ling Tong
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Minjie Shan
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Wen Zou
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - XianLing Liu
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Dean W. Felsher
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Jingjing Wang
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Jingjing Wang,
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11
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Ethiraj P, Sasi B, Holder KN, Lin AP, Qiu Z, Jaafar C, Elkhalili A, Desai P, Saksena A, Ritter JP, Aguiar RCT. Cyclic-AMP signalling, MYC and hypoxia-inducible factor 1α intersect to regulate angiogenesis in B-cell lymphoma. Br J Haematol 2022; 198:349-359. [PMID: 35411936 DOI: 10.1111/bjh.18196] [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: 12/14/2021] [Revised: 03/08/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023]
Abstract
Angiogenesis and MYC expression associate with poor outcome in diffuse large B-cell lymphoma (DLBCL). MYC promotes neo-vasculature development but whether its deregulation in DLBCL contributes to angiogenesis is unclear. Examination of this relationship may uncover novel pathogenic regulatory circuitry as well as anti-angiogenic strategies in DLBCL. Here, we show that MYC expression positively correlates with vascular endothelial growth factor (VEGF) expression and angiogenesis in primary DLBCL biopsies, independently of dual expressor status or cell-of-origin classification. We found that MYC promotes VEGFA expression, a correlation that was validated in large datasets of mature B-cell tumours. Using DLBCL cell lines and patient-derived xenograft models, we identified the second messenger cyclic-AMP (cAMP) as a potent suppressor of MYC expression, VEGFA secretion and angiogenesis in DLBCL in normoxia. In hypoxia, cAMP switched targets and suppressed hypoxia-inducible factor 1α, a master regulator of VEGFA/angiogenesis in low oxygen environments. Lastly, we used the phosphodiesterase 4b (Pde4b) knockout mouse to demonstrate that the cAMP/PDE4 axis exercises additional anti-angiogenesis by directly targeting the lymphoma microenvironment. In conclusion, MYC could play a direct role in DLBCL angiogenesis, and modulation of cAMP levels, which can be achieved with clinical grade PDE4 inhibitors, has cell and non-cell autonomous anti-angiogenic activity in DLBCL.
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Affiliation(s)
- Purushoth Ethiraj
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - Binu Sasi
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - Kenneth N Holder
- Department of Pathology, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - An-Ping Lin
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - Zhijun Qiu
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - Carine Jaafar
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - Alia Elkhalili
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - Parth Desai
- Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - Annapurna Saksena
- Department of Pathology, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - Jacob P Ritter
- Department of Pathology, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - Ricardo C T Aguiar
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
- South Texas Veterans Health Care System, Audie Murphy VA Hospital, San Antonio, Texas, USA
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12
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Sun SL, Wu SH, Kang JB, Ma YY, Chen L, Cao P, Chang L, Ding N, Xue X, Li NG, Shi ZH. Medicinal Chemistry Strategies for the Development of Bruton's Tyrosine Kinase Inhibitors against Resistance. J Med Chem 2022; 65:7415-7437. [PMID: 35594541 DOI: 10.1021/acs.jmedchem.2c00030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Despite significant efficacy, one of the major limitations of small-molecule Bruton's tyrosine kinase (BTK) agents is the presence of clinically acquired resistance, which remains a major clinical challenge. This Perspective focuses on medicinal chemistry strategies for the development of BTK small-molecule inhibitors against resistance, including the structure-based design of BTK inhibitors targeting point mutations, e.g., (i) developing noncovalent inhibitors from covalent inhibitors, (ii) avoiding steric hindrance from mutated residues, (iii) making interactions with the mutated residue, (iv) modifying the solvent-accessible region, and (v) developing new scaffolds. Additionally, a comparative analysis of multi-inhibitions of BTK is presented based on cross-comparisons between 2916 unique BTK ligands and 283 other kinases that cover 7108 dual/multiple inhibitions. Finally, targeting the BTK allosteric site and uding proteolysis-targeting chimera (PROTAC) as two potential strategies are addressed briefly, while also illustrating the possibilities and challenges to find novel ligands of BTK.
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Affiliation(s)
- Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shi-Han Wu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ji-Bo Kang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yi-Yuan Ma
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lu Chen
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Peng Cao
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, China
| | - Liang Chang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhi-Hao Shi
- Department of Organic Chemistry, China Pharmaceutical University, Nanjing 211198, China
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13
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MYC, mitochondrial metabolism and O-GlcNAcylation converge to modulate the activity and subcellular localization of DNA and RNA demethylases. Leukemia 2022; 36:1150-1159. [PMID: 34997181 PMCID: PMC8983447 DOI: 10.1038/s41375-021-01489-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/17/2021] [Accepted: 11/25/2021] [Indexed: 12/31/2022]
Abstract
Mitochondria can function as signaling organelles, and part of this output leads to epigenetic remodeling. The full extent of this far-reaching interplay remains undefined. Here, we show that MYC transcriptionally activates IDH2 and increases alpha-ketoglutarate (αKG) levels. This regulatory step induces the activity of αKG-dependent DNA hydroxylases and RNA demethylases, thus reducing global DNA and RNA methylation. MYC, in a IDH2-dependent manner, also promotes the nuclear accumulation of TET1-TET2-TET3, FTO and ALKBH5. Notably, this subcellular movement correlated with the ability of MYC, in an IDH2-dependent manner, and, unexpectedly, of αKG to directly induce O-GlcNAcylation. Concordantly, modulation of the activity of OGT and OGA, enzymes that control the cycling of this non-canonical mono-glycosylation, largely recapitulated the effects of the MYC-IDH2-αKG axis on the subcellular movement of DNA and RNA demethylases. Together, we uncovered a hitherto unsuspected crosstalk between MYC, αKG and O-GlcNAcylation which could influence the epigenome and epitranscriptome homeostasis.
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14
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Targeting metabolism to overcome cancer drug resistance: A promising therapeutic strategy for diffuse large B cell lymphoma. Drug Resist Updat 2022; 61:100822. [DOI: 10.1016/j.drup.2022.100822] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 02/07/2023]
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15
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Mavridou D, Psatha K, Aivaliotis M. Proteomics and Drug Repurposing in CLL towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13143391. [PMID: 34298607 PMCID: PMC8303629 DOI: 10.3390/cancers13143391] [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: 05/06/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Despite continued efforts, the current status of knowledge in CLL molecular pathobiology, diagnosis, prognosis and treatment remains elusive and imprecise. Proteomics approaches combined with advanced bioinformatics and drug repurposing promise to shed light on the complex proteome heterogeneity of CLL patients and mitigate, improve, or even eliminate the knowledge stagnation. In relation to this concept, this review presents a brief overview of all the available proteomics and drug repurposing studies in CLL and suggests the way such studies can be exploited to find effective therapeutic options combined with drug repurposing strategies to adopt and accost a more “precision medicine” spectrum. Abstract CLL is a hematological malignancy considered as the most frequent lymphoproliferative disease in the western world. It is characterized by high molecular heterogeneity and despite the available therapeutic options, there are many patient subgroups showing the insufficient effectiveness of disease treatment. The challenge is to investigate the individual molecular characteristics and heterogeneity of these patients. Proteomics analysis is a powerful approach that monitors the constant state of flux operators of genetic information and can unravel the proteome heterogeneity and rewiring into protein pathways in CLL patients. This review essences all the available proteomics studies in CLL and suggests the way these studies can be exploited to find effective therapeutic options combined with drug repurposing approaches. Drug repurposing utilizes all the existing knowledge of the safety and efficacy of FDA-approved or investigational drugs and anticipates drug alignment to crucial CLL therapeutic targets, leading to a better disease outcome. The drug repurposing studies in CLL are also discussed in this review. The next goal involves the integration of proteomics-based drug repurposing in precision medicine, as well as the application of this procedure into clinical practice to predict the most appropriate drugs combination that could ensure therapy and the long-term survival of each CLL patient.
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Affiliation(s)
- Dimitra Mavridou
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Konstantina Psatha
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Greece
- Correspondence: (K.P.); (M.A.)
| | - Michalis Aivaliotis
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Greece
- Correspondence: (K.P.); (M.A.)
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Regulation of PD-L1 expression is a novel facet of cyclic-AMP-mediated immunosuppression. Leukemia 2020; 35:1990-2001. [PMID: 33299141 PMCID: PMC8187478 DOI: 10.1038/s41375-020-01105-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/03/2020] [Accepted: 11/23/2020] [Indexed: 01/13/2023]
Abstract
Cyclic-AMP (cAMP) exerts suppressive effects in the innate and adaptive immune system. The PD-1/PD-L1 immune checkpoint down-regulates T-cell activity. Here, we examined if these two immunosuppressive nodes intersect. Using normal and malignant lymphocytes from humans, and the phosphodiesterase 4b (Pde4b) knockout mouse, we found that cAMP induces PD-L1 transcription and protein expression. Mechanistically, we discovered that the cAMP effectors PKA and CREB induce the transcription/secretion of IL-10, IL-8 and IL-6, which initiate an autocrine loop that activates the JAK/STAT pathway and ultimately increase PD-L1 expression in the cell surface. This signaling axis is disarmed at two specific nodes in subsets of diffuse large B cell lymphoma, which may help explain the variable PD-L1 expression in these tumors. In vivo, we found that despite its immunosuppressive attributes, the PDE4 inhibitor roflumilast did not decrease the clinical activity of checkpoint inhibitors, an important clinical observation given the approved use of these agents in multiple diseases. In summary, we discovered that PD-L1 induction is a part of the repertoire of immunosuppressive actions mediated by cAMP, defined a cytokine-mediated autocrine loop that executes this action and, reassuringly, showed that PDE4 inhibition does not antagonize immune checkpoint blockade in an in vivo syngeneic lymphoma model.
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Phillips TJ, Michot JM, Ribrag V. Can Next-Generation PI3K Inhibitors Unlock the Full Potential of the Class in Patients With B-Cell Lymphoma? CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2020; 21:8-20.e3. [PMID: 33132100 DOI: 10.1016/j.clml.2020.08.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 12/11/2022]
Abstract
Although outcomes after first-line therapy for patients with indolent or aggressive non-Hodgkin lymphoma (NHL) are continually improving, relapse is still common. Current treatment options for patients with relapsed or refractory disease have limited efficacy, and various targeted therapies are under investigation to help improve outcomes in this patient population. The phosphatidylinositol 3-kinase (PI3K) pathway was identified as being involved in hematologic malignancies, leading to significant research for potential therapeutic agents. This has led to 3 PI3K inhibitors (idelalisib, copanlisib, and duvelisib) being approved for the treatment of patients with relapsed or refractory follicular lymphoma who have received at least 2 prior systemic therapies, with reported response rates of 40% to 59%. With potential class-specific and PI3K isoform-related toxicities that may limit clinical utility, the safety of the approved PI3K inhibitors has been carefully evaluated to weigh the risk/benefit ratio of therapy. Currently, there are no approved PI3K inhibitors for patients with aggressive NHL. A number of newer PI3K inhibitors are in clinical development for the treatment of relapsed or refractory NHL, aiming to improve treatment benefit for patients. We discuss a number of attributes that are important to increase the therapeutic potential of newer PI3K inhibitors. More promising results may come from combination trials with these newer PI3K inhibitors, developed to limit toxicities (including long-term adverse events), and other antitumor agents.
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Affiliation(s)
| | | | - Vincent Ribrag
- Institut de Cancérologie Gustave Roussy, Villejuif, France.
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18
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Hsien Lai S, Zervoudakis G, Chou J, Gurney ME, Quesnelle KM. PDE4 subtypes in cancer. Oncogene 2020; 39:3791-3802. [PMID: 32203163 PMCID: PMC7444459 DOI: 10.1038/s41388-020-1258-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/22/2022]
Abstract
Cyclic nucleotide phosphodiesterases (PDE) break down cyclic nucleotides such as cAMP and cGMP, reducing the signaling of these important intracellular second messengers. Several unique families of phosphodiesterases exist, and certain families are clinically important modulators of vasodilation. In the current work, we have summarized the body of literature that describes an emerging role for the PDE4 subfamily of phosphodiesterases in malignancy. We have systematically investigated PDE4A, PDE4B, PDE4C, and PDE4D isoforms and found evidence associating them with several cancer types including hematologic malignancies and lung cancers, among others. In this review, we compare the evidence examining the functional role of each PDE4 subtype across malignancies, looking for common signaling themes, signaling pathways, and establishing the case for PDE4 subtypes as a potential therapeutic target for cancer treatment.
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Affiliation(s)
- Samuel Hsien Lai
- Department of Biomedical Sciences, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, USA
| | - Guston Zervoudakis
- Department of Biomedical Sciences, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, USA
| | - Jesse Chou
- Department of Biomedical Sciences, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, USA
| | | | - Kelly M Quesnelle
- Department of Biomedical Sciences, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, USA.
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MYC Regulation of D2HGDH and L2HGDH Influences the Epigenome and Epitranscriptome. Cell Chem Biol 2020; 27:538-550.e7. [PMID: 32101699 DOI: 10.1016/j.chembiol.2020.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 12/22/2019] [Accepted: 02/05/2020] [Indexed: 02/07/2023]
Abstract
Mitochondrial D2HGDH and L2HGDH catalyze the oxidation of D-2-HG and L-2-HG, respectively, into αKG. This contributes to cellular homeostasis in part by modulating the activity of αKG-dependent dioxygenases. Signals that control the expression/activity of D2HGDH/L2HGDH are presumed to broadly influence physiology and pathology. Using cell and mouse models, we discovered that MYC directly induces D2HGDH and L2HGDH transcription. Furthermore, in a manner suggestive of D2HGDH, L2HGDH, and αKG dependency, MYC activates TET enzymes and RNA demethylases, and promotes their nuclear localization. Consistent with these observations, in primary B cell lymphomas MYC expression positively correlated with enhancer hypomethylation and overexpression of lymphomagenic genes. Together, these data provide additional evidence for the role of mitochondria metabolism in influencing the epigenome and epitranscriptome, and imply that in specific contexts wild-type TET enzymes could demethylate and activate oncogenic enhancers.
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Liu L, Li X, Cheng Y, Wang L, Yang H, Li J, He S, shuangjie Wu, Yin Q, Xiang H. Optimization of novel benzofuro[3,2-b]pyridin-2(1H)-one derivatives as dual inhibitors of BTK and PI3Kδ. Eur J Med Chem 2019; 164:304-316. [DOI: 10.1016/j.ejmech.2018.12.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/08/2018] [Accepted: 12/22/2018] [Indexed: 11/30/2022]
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Identification of novel PI3Kδ inhibitors by docking, ADMET prediction and molecular dynamics simulations. Comput Biol Chem 2018; 78:190-204. [PMID: 30557817 DOI: 10.1016/j.compbiolchem.2018.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/25/2018] [Accepted: 12/06/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND Phosphoinositide-3-kinase Delta (PI3Kδ) plays a key role in B-cell signal transduction and inhibition of PI3Kδ is confirmed to have clinical benefit in certain types of activation of B-cell malignancies. Virtual screening techniques have been used to discover new molecules for developing novel PI3Kδ inhibitors with little side effects. METHOD Computer aided drug design method were used to rapidly screen optimal PI3Kδ inhibitors from the Asinex database. Virtual screening based molecular docking was performed to find novel and potential lead compound targeting PI3Kδ, at first. Subsequently, drug likeness studies were carried out on the retrieved hits to evaluate and analyze their drug like properties such as absorption, distribution, metabolism, excretion, and toxicity (ADMET) for toxicity prediction. Three least toxic compounds were selected for the molecular dynamics (MD) simulations for 30 ns in order to validate its stability inside the active site of PI3Kδ receptor. RESULTS Based on the present in silico analysis, two molecules have been identified which occupied the same binding pocket confirming the selection of active site. ASN 16296138 (Glide score: -12.175 kcal/mol, cdocker binding energy: -42.975 kcal/mol and ΔGbind value: -90.457 kcal/mol) and BAS 00227397 (Glide score: -10.988 kcal/mol, cdocker binding energy: -39.3376 kcal/mol and ΔGbind value: -81.953 kcal/mol) showed docking affinities comparatively much stronger than those of already reported known inhibitors against PI3Kδ. These two ligand's behaviors also showed consistency during the simulation of protein-ligand complexes for 30000 ps respectively, which is indicative of its stability in the receptor pocket. CONCLUSION Compound ASN 16296138 and BAS 00227397 are potential candidates for experimental validation of biological activity against PI3Kδ in future drug discovery studies. This study smoothes the path for the development of novel leads with improved binding properties, high drug likeness, and low toxicity to humans for the treatment of cancer.
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