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Zhang M, Lang X, Chen X, Lv Y. Prospective Identification of Prognostic Hot-Spot Mutant Gene Signatures for Leukemia: A Computational Study Based on Integrative Analysis of TCGA and cBioPortal Data. Mol Biotechnol 2023; 65:1898-1912. [PMID: 36879146 DOI: 10.1007/s12033-023-00704-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/14/2023] [Indexed: 03/08/2023]
Abstract
The advantage of an increasing amount of bioinformatics data on leukemias intrigued us to explore the hot-spot mutation profiles and investigate the implications of those hot-spot mutations in patient survival. We retrieved somatic mutations and their distribution in protein domains through data analysis of The Cancer Genome Atlas and cBioPortal databases. After determining differentially expressed mutant genes related to leukemia, we further conducted principal component analysis and single-factor Cox regression analyses. Moreover, survival analysis was performed for the obtained candidate genes, followed by a multi-factor Cox proportional hazard model method for the impacts of the candidate genes on the survival and prognosis of patients with leukemia. At last, the signaling pathways involved in leukemia were investigated by gene set enrichment analysis. There were 223 somatic missense mutation hot-spots identified with pertinence to leukemia, which were distributed in 41 genes. Differential expression in leukemia was witnessed in 39 genes. We found a close correlation between seven genes and the prognosis of leukemia patients, among which, three genes could significantly influence the survival rate. In addition, among these three genes, CD74 and P2RY8 were highlighted due to close pertinence with survival conditions of leukemia patients. Finally, data suggested that B cell receptor, Hedgehog, and TGF-beta signaling pathways were enriched in low-hazard patients. In conclusion, these data underline the involvement of hot-spot mutations of CD74 and P2RY8 genes in survival status of leukemia patients, highlighting their as novel therapeutic targets or prognostic indicators for leukemia patients. Summary of Graphical Abstract: We identified 223 leukemia-associated somatic missense mutation hotspots concentrated in 41 different genes from 2297 leukemia patients in the TCGA database. Differential analysis of leukemic and normal samples from the TCGA and GTEx databases revealed that 39 of these 41 genes showed significant differential expression in leukemia. These 39 genes were subjected to PCA analysis, univariate Cox analysis, survival analysis, multivariate Cox regression analysis, GSEA pathway enrichment analysis, and then the association with leukemia survival prognosis and related pathways were investigated.
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Affiliation(s)
- Min Zhang
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China.
| | - Xianghua Lang
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China
| | - Xinyi Chen
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China
| | - Yuke Lv
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China
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Thavayogarajah T, Sinitski D, Bounkari OE, Torres-Garcia L, Lewinsky H, Harjung A, Chen HR, Panse J, Vankann L, Shachar I, Bernhagen J, Koschmieder S. CXCR4 and CD74 together enhance cell survival in response to macrophage migration-inhibitory factor in chronic lymphocytic leukemia. Exp Hematol 2022; 115:30-43. [PMID: 36096455 DOI: 10.1016/j.exphem.2022.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/16/2022] [Accepted: 08/29/2022] [Indexed: 11/04/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of small, mature CD5+ B lymphocytes in the blood, marrow, and lymphoid organs. Cell survival depends on interaction with the leukemic microenvironment. However, the mechanisms controlling CLL cell survival are still incompletely understood. Macrophage migration-inhibitory factor (MIF), a pro-inflammatory and immunoregulatory chemokine-like cytokine, interacts with CXCR4, a major chemokine receptor, as well as with CD74/invariant chain, a single-pass type II receptor. In this study, we analyzed the roles of CXCR4, CD74, and MIF in CLL. Mononuclear cells from patients with hematological malignancies were analyzed for coexpression of CXCR4 and CD74 by flow cytometry. Strong co- and overexpression of CXCR4 and CD74 were observed on B cells of CLL patients (n = 10). Survival and chemotaxis assays indicated that CXCR4 and CD74 work together to enhance the survival and migration of malignant cells in CLL. Blockade of the receptors, either individually or in combination, promoted cell death and led to an abrogation of MIF-driven migration responses in murine and human CLL cells, suggesting that joint activation of both receptors is crucial for CLL cell survival and mobility. These findings indicate that the MIF/CXCR4/CD74 axis represents a novel therapeutic target in CLL.
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Affiliation(s)
- Tharshika Thavayogarajah
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, Rheinisch-Westfälische Technische (RWTH) Aachen University, Aachen, Germany; Department of Vascular Biology, Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, Germany; Department of Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Dzmitry Sinitski
- Department of Vascular Biology, Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, Germany
| | - Omar El Bounkari
- Department of Vascular Biology, Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, Germany
| | - Laura Torres-Garcia
- Department of Vascular Biology, Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, Germany
| | - Hadas Lewinsky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Harjung
- Department of Vascular Biology, Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, Germany
| | - Hong-Ru Chen
- Department of Vascular Biology, Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, Germany
| | - Jens Panse
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, Rheinisch-Westfälische Technische (RWTH) Aachen University, Aachen, Germany
| | - Lucia Vankann
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, Rheinisch-Westfälische Technische (RWTH) Aachen University, Aachen, Germany
| | - Idit Shachar
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Jürgen Bernhagen
- Department of Vascular Biology, Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; SyNergy Excellence Cluster, Munich, Germany.
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, Rheinisch-Westfälische Technische (RWTH) Aachen University, Aachen, Germany.
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Chen BL, Li Y, Xu S, Nie Y, Zhang J. NFAT5 Regulated by STUB1, Facilitates Malignant Cell Survival and p38 MAPK Activation by Upregulating AQP5 in Chronic Lymphocytic Leukemia. Biochem Genet 2021; 59:870-883. [PMID: 33544297 DOI: 10.1007/s10528-021-10040-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is a clonal proliferative disease of mature B lymphocytes. To further improve the prognosis of patients, it is necessary to further elucidate the pathogenesis of CLL and find more effective therapeutic targets. Nuclear Factor of Activated T cells 5 (NFAT5) is the major activated transcription factor (TF) upon osmotic pressure increase in mammalian cells, and it also regulates many target genes to affect various cellular functions. The effects of NFAT5 on tumor growth and metastasis have also been widely revealed. However, the effects of NFAT5 on the progression of CLL are still unclear. In this study, we found abnormally high expression of NFAT5 in human CLL patients. Additionally, NFAT5 depletion suppressed proliferation and stimulated apoptosis of CLL cells. Our data further confirmed NFAT5 regulated AQP5 expression and the phosphorylation of p38 MAPK. We also found that AQP5 overexpression reversed the inhibitory effect of NFAT5 depletion on cell proliferation in CLL cells. Furthermore, we revealed STUB1 directly bound to NFAT5 and promoted its degradation. Taken together, our results indicate the involvement of NFAT5 in CLL progression and suggest that NFAT5 could serve as a promising therapeutic target for CLL treatment.
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Affiliation(s)
- Bei Li Chen
- Department of Hematology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi Zhuang Autonomous Region, China
| | - Yuchuan Li
- Department of Gynaecology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi Zhuang Autonomous Region, China
| | - Shujuan Xu
- Department of Hematology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi Zhuang Autonomous Region, China
| | - Yuwei Nie
- Department of Hematology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi Zhuang Autonomous Region, China
| | - Jiang Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, No. 58 Zhongshan Second Road, Yuexiu District, Guangzhou, 510080, Guangdong, China.
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