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Kosvyra Α, Karadimitris Α, Papaioannou Μ, Chouvarda I. Machine learning and integrative multi-omics network analysis for survival prediction in acute myeloid leukemia. Comput Biol Med 2024; 178:108735. [PMID: 38875909 DOI: 10.1016/j.compbiomed.2024.108735] [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: 02/20/2024] [Revised: 05/14/2024] [Accepted: 06/08/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is the most common malignant myeloid disorder in adults and the fifth most common malignancy in children, necessitating advanced technologies for outcome prediction. METHOD This study aims to enhance prognostic capabilities in AML by integrating multi-omics data, especially gene expression and methylation, through network-based feature selection methodologies. By employing artificial intelligence and network analysis, we are exploring different methods to build a machine learning model for predicting AML patient survival. We evaluate the effectiveness of combining omics data, identify the most informative method for network integration and compare the performance with standard feature selection methods. RESULTS Our findings demonstrate that integrating gene expression and methylation data significantly improves prediction accuracy compared to single omics data. Among network integration methods, our study identifies the best approach that improves informative feature selection for predicting patient outcomes in AML. Comparative analyses demonstrate the superior performance of the proposed network-based methods over standard techniques. CONCLUSIONS This research presents an innovative and robust methodology for building a survival prediction model tailored to AML patients. By leveraging multilayer network analysis for feature selection, our approach contributes to improving the understanding and prognostic capabilities in AML and laying the foundation for more effective personalized therapeutic interventions in the future.
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Affiliation(s)
- Α Kosvyra
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Α Karadimitris
- Centre for Haematology and Hugh and Josseline Langmuir Centre for Myeloma Research, Department of Immunology and Inflammation, Imperial College London, Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, Du Cane Road, London, W12 0NN, UK
| | - Μ Papaioannou
- Hematology Unit, 1st Dept of Internal Medicine, AHEPA Hospital, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - I Chouvarda
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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XIA ZHIGANG, TIAN MENGYAO, CHENG YUCAI, YI WENFANG, DU ZEFAN, LI TIANWEN, WEN YUCHEN, LI LINDI, LIU YONG, CHEN CHUN. Preclinical evaluation of cyclophosphamide and fludarabine combined with CD19 CAR-T in the treatment of B-cell hematologic malignancies in vivo. Oncol Res 2024; 32:1109-1118. [PMID: 38827326 PMCID: PMC11136684 DOI: 10.32604/or.2024.049792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 06/04/2024] Open
Abstract
Background Chimeric antigen receptor T (CAR-T) cell therapy has achieved marked therapeutic success in ameliorating hematological malignancies. However, there is an extant void in the clinical guidelines concerning the most effective chemotherapy regimen prior to chimeric antigen receptor T (CAR-T) cell therapy, as well as the optimal timing for CAR-T cell infusion post-chemotherapy. Materials and Methods We employed cell-derived tumor xenograft (CDX) murine models to delineate the optimal pre-conditioning chemotherapy regimen and timing for CAR-T cell treatment. Furthermore, transcriptome sequencing was implemented to identify the therapeutic targets and elucidate the underlying mechanisms governing the treatment regimen. Results Our preclinical in vivo evaluation determined that a combination of cyclophosphamide and fludarabine, followed by the infusion of CD19 CAR-T cells five days subsequent to the chemotherapy, exerts the most efficacious therapeutic effect in B-cell hematological malignancies. Concurrently, RNA-seq data indicated that the therapeutic efficacy predominantly perturbs tumor cell metabolism, primarily through the inhibition of key mitochondrial targets, such as C-Jun Kinase enzyme (C-JUN). Conclusion In summary, the present study offers critical clinical guidance and serves as an authoritative reference for the deployment of CD19 CAR-T cell therapy in the treatment of B-cell hematological malignancies.
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Affiliation(s)
- ZHIGANG XIA
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - MENGYAO TIAN
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - YUCAI CHENG
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - WENFANG YI
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - ZEFAN DU
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - TIANWEN LI
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - YUCHEN WEN
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - LINDI LI
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - YONG LIU
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - CHUN CHEN
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
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Novikova S, Tolstova T, Kurbatov L, Farafonova T, Tikhonova O, Soloveva N, Rusanov A, Zgoda V. Systems Biology for Drug Target Discovery in Acute Myeloid Leukemia. Int J Mol Sci 2024; 25:4618. [PMID: 38731835 PMCID: PMC11083274 DOI: 10.3390/ijms25094618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
Combining new therapeutics with all-trans-retinoic acid (ATRA) could improve the efficiency of acute myeloid leukemia (AML) treatment. Modeling the process of ATRA-induced differentiation based on the transcriptomic profile of leukemic cells resulted in the identification of key targets that can be used to increase the therapeutic effect of ATRA. The genome-scale transcriptome analysis revealed the early molecular response to the ATRA treatment of HL-60 cells. In this study, we performed the transcriptomic profiling of HL-60, NB4, and K562 cells exposed to ATRA for 3-72 h. After treatment with ATRA for 3, 12, 24, and 72 h, we found 222, 391, 359, and 1032 differentially expressed genes (DEGs) in HL-60 cells, as well as 641, 1037, 1011, and 1499 DEGs in NB4 cells. We also found 538 and 119 DEGs in K562 cells treated with ATRA for 24 h and 72 h, respectively. Based on experimental transcriptomic data, we performed hierarchical modeling and determined cyclin-dependent kinase 6 (CDK6), tumor necrosis factor alpha (TNF-alpha), and transcriptional repressor CUX1 as the key regulators of the molecular response to the ATRA treatment in HL-60, NB4, and K562 cell lines, respectively. Mapping the data of TMT-based mass-spectrometric profiling on the modeling schemes, we determined CDK6 expression at the proteome level and its down-regulation at the transcriptome and proteome levels in cells treated with ATRA for 72 h. The combination of therapy with a CDK6 inhibitor (palbociclib) and ATRA (tretinoin) could be an alternative approach for the treatment of acute myeloid leukemia (AML).
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Tretinoin/pharmacology
- Systems Biology/methods
- HL-60 Cells
- Gene Expression Profiling
- K562 Cells
- Drug Discovery/methods
- Transcriptome
- Cell Line, Tumor
- Cyclin-Dependent Kinase 6/metabolism
- Cyclin-Dependent Kinase 6/genetics
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Gene Expression Regulation, Leukemic/drug effects
- Tumor Necrosis Factor-alpha/metabolism
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Affiliation(s)
| | | | | | | | | | | | | | - Victor Zgoda
- Institute of Biomedical Chemistry, Pogodinskaya 10, 119121 Moscow, Russia; (S.N.) (T.T.); (L.K.); (T.F.); (O.T.); (N.S.); (A.R.)
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Lim S, Lee KW, Kim JY, Kim KD. Consideration of SHP-1 as a Molecular Target for Tumor Therapy. Int J Mol Sci 2023; 25:331. [PMID: 38203502 PMCID: PMC10779157 DOI: 10.3390/ijms25010331] [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: 12/01/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Abnormal activation of receptor tyrosine kinases (RTKs) contributes to tumorigenesis, while protein tyrosine phosphatases (PTPs) contribute to tumor control. One of the most representative PTPs is Src homology region 2 (SH2) domain-containing phosphatase 1 (SHP-1), which is associated with either an increased or decreased survival rate depending on the cancer type. Hypermethylation in the promoter region of PTPN6, the gene for the SHP-1 protein, is a representative epigenetic regulation mechanism that suppresses the expression of SHP-1 in tumor cells. SHP-1 comprises two SH2 domains (N-SH2 and C-SH2) and a catalytic PTP domain. Intramolecular interactions between the N-SH2 and PTP domains inhibit SHP-1 activity. Opening of the PTP domain by a conformational change in SHP-1 increases enzymatic activity and contributes to a tumor control phenotype by inhibiting the activation of the Janus kinase/signal transducer and activator of transcription (JAK/STAT3) pathway. Although various compounds that increase SHP-1 activation or expression have been proposed as tumor therapeutics, except sorafenib and its derivatives, few candidates have demonstrated clinical significance. In some cancers, SHP-1 expression and activation contribute to a tumorigenic phenotype by inducing a tumor-friendly microenvironment. Therefore, developing anticancer drugs targeting SHP-1 must consider the effect of SHP-1 on both cell biological mechanisms of SHP-1 in tumor cells and the tumor microenvironment according to the target cancer type. Furthermore, the use of combination therapies should be considered.
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Affiliation(s)
- Seyeon Lim
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Ki Won Lee
- Anti-Aging Bio Cell Factory—Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Jeong Yoon Kim
- Department of Pharmaceutical Engineering, Institute of Agricultural and Life Science (IALS), Gyeongsang National University, Jinju 52725, Republic of Korea;
| | - Kwang Dong Kim
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea;
- Anti-Aging Bio Cell Factory—Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea;
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea
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Ma L, Liu Y, Wang Y, Yang J, Lu J, Feng H, Ye S, Liu Y. Identification of PTPN20 as an innate immunity-related gene in gastric cancer with Helicobacter pylori infection. Front Immunol 2023; 14:1212692. [PMID: 37359510 PMCID: PMC10287967 DOI: 10.3389/fimmu.2023.1212692] [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: 04/26/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
Background Gastric cancer (GC) is among the deadliest diseases with countless incidences and deaths each year. Helicobacter pylori (Hp) is the primary type of microbe that colonizes the stomach. In recent years, increasing evidence has demonstrated that Hp infection is one of the main risk factors for GC. Elucidating the molecular mechanism of how Hp leads to GC will not only benefit the treatment of GC, but also boost the development of therapeutics for other gastric disorders caused by Hp infection. In this study, we aimed to identify innate immunity-related genes in GC and investigate their potentials as prognostic markers and therapeutic targets for Hp-related GC. Methods Firstly, we analyzed the differentially expressed innate immunity-related genes in GC samples from the TCGA database. Then prognostic correlation analysis was carried out to explore the prognostic value of these candidate genes. By combing transcriptome data, somatic mutation data, and clinical data, co-expression analysis, functional enrichment analysis, tumor mutational burden analysis, and immune infiltration analysis were performed to reveal the pathological relevance of the candidate gene. Finally, ceRNA network was constructed to identify the genes and pathways for the regulation of the candidate gene. Results We revealed that protein tyrosine phosphatase non-receptor type 20 (PTPN20) is a significant prognostic marker in Hp-related GC. Thus, PTPN20 levels have the potential to efficiently predict the survival of Hp-related GC patients. In addition, PTPN20 is associated with immune cell infiltration and tumor mutation burden in these GC patients. Moreover, we have also identified PTPN20-related genes, PTPN20 protein-protein interactions, and the PTPN20 ceRNA network. Conclusion Our data suggest that PTPN20 may have critical functions in Hp-related GC. Targeting PTPN20 may be a promising way to treat Hp-related GC.
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Affiliation(s)
- Lianjun Ma
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yang Liu
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yizhao Wang
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Jiaxing Yang
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
| | - Jordan Lu
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
| | - Huijin Feng
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
| | - Shujun Ye
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yanqing Liu
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
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