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Bao X, Chi J, Zhu Y, Yang M, Du J, Tang Z, Xu X, Mao G, Wu Z, Chen J, Hua J, Xu T, Liu SB. High FAAP24 expression reveals poor prognosis and an immunosuppressive microenvironment shaping in AML. Cancer Cell Int 2023; 23:117. [PMID: 37328842 DOI: 10.1186/s12935-023-02937-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/04/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND As a core member of the FA complex, in the Fanconi anemia pathway, FAAP24 plays an important role in DNA damage repair. However, the association between FAAP24 and patient prognosis in AML and immune infiltration remains unclear. The purpose of this study was to explore its expression characteristics, immune infiltration pattern, prognostic value and biological function using TCGA-AML and to verify it in the Beat AML cohort. METHODS In this study, we examined the expression and prognostic value of FAAP24 across cancers using data from TCGA, TARGET, GTEx, and GEPIA2. To further investigate the prognosis in AML, development and validation of a nomogram containing FAAP24 were performed. GO/KEGG, ssGSEA, GSVA and xCell were utilized to explore the functional enrichment and immunological features of FAAP24 in AML. Drug sensitivity analysis used data from the CellMiner website, and the results were confirmed in vitro. RESULTS Integrated analysis of the TCGA, TARGET and GTEx databases showed that FAAP24 is upregulated in AML; meanwhile, high FAAP24 expression was associated with poor prognosis according to GEPIA2. Gene set enrichment analysis revealed that FAAP24 is implicated in pathways involved in DNA damage repair, the cell cycle and cancer. Components of the immune microenvironment using xCell indicate that FAAP24 shapes an immunosuppressive tumor microenvironment (TME) in AML, which helps to promote AML progression. Drug sensitivity analysis showed a significant correlation between high FAAP24 expression and chelerythrine resistance. In conclusion, FAAP24 could serve as a novel prognostic biomarker and play an immunomodulatory role in AML. CONCLUSIONS In summary, FAAP24 is a promising prognostic biomarker in AML that requires further exploration and confirmation.
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Affiliation(s)
- Xiebing Bao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215006, China
| | - Jingyun Chi
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, 28 Kehua Road, Suzhou, 215009, China
| | - Yiwei Zhu
- Suzhou Medical College, Soochow University, Suzhou, 215006, China
| | - Minfeng Yang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, P.R. China
| | - Jiahui Du
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, 28 Kehua Road, Suzhou, 215009, China
| | - Zaixiang Tang
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, China
| | - Xiaogang Xu
- Zhejiang Provincial Key Lab of Geriatrics & Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Genxiang Mao
- Zhejiang Provincial Key Lab of Geriatrics & Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Zhibing Wu
- Department of Oncology, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Jun Chen
- Zhejiang Provincial Key Lab of Geriatrics & Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Jingsheng Hua
- Department of Hematology, Taizhou Municipal Hospital Affiliated to Taizhou University, Taizhou, 318000, China.
| | - Ting Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215006, China.
| | - Song-Bai Liu
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, 28 Kehua Road, Suzhou, 215009, China.
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Ameri M, Alipour M, Madihi M, Nezafat N. Identification of intrinsically disordered regions in hub genes of acute myeloid leukemia: A bioinformatics approach. Biotechnol Appl Biochem 2022; 69:2304-2322. [PMID: 34812529 DOI: 10.1002/bab.2287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/30/2021] [Indexed: 12/27/2022]
Abstract
Acute myeloid leukemia (AML) is the most common acute leukemia in adults. Over the past decades, there has been a great challenge in the treatment of AML. A combination of gene expression profiling with computational approaches can lead to the identification of hub genes in AML. However, it is important to study the structure of these hub genes considering their importance in the protein-protein interaction (PPI) network of specific cancer. In this study, we designed an integrated method to analyze the presence of intrinsically disordered regions (IDRs) in selected hub genes of AML. A gene expression profile of AML was obtained from Gene Expression Omnibus (GEO) database. Further analysis identified differentially expressed genes (DEGs) in AML. Additionally, the top 15 hub genes following construction and analysis of the PPI network of DEGs were selected. Validation of hub genes revealed that there is a reverse relationship between overexpression of FLT3, PPBP, and PF4 genes and the survival of AML patients. Based on IDRs investigation, FLT3 and PF4 are partially disordered, while PPBP is mostly disordered. Through clustering the network into structural modules, we identified two important modules in the PPI network of DEGs that showed the important position of PPBP in module 1. Based on further analysis of protein flexibility and its important role in biological processes, we suggest that PPBP can be considered as a potential drug target in AML.
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Affiliation(s)
- Mehrdad Ameri
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maedeh Alipour
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mobina Madihi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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Schwarz A, Roeder I, Seifert M. Comparative Gene Expression Analysis Reveals Similarities and Differences of Chronic Myeloid Leukemia Phases. Cancers (Basel) 2022; 14:cancers14010256. [PMID: 35008420 PMCID: PMC8750437 DOI: 10.3390/cancers14010256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/25/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a slowly progressing blood cancer that primarily affects elderly people. Without successful treatment, CML progressively develops from the chronic phase through the accelerated phase to the blast crisis, and ultimately to death. Nowadays, the availability of targeted tyrosine kinase inhibitor (TKI) therapies has led to long-term disease control for the vast majority of patients. Nevertheless, there are still patients that do not respond well enough to TKI therapies and available targeted therapies are also less efficient for patients in accelerated phase or blast crises. Thus, a more detailed characterization of molecular alterations that distinguish the different CML phases is still very important. We performed an in-depth bioinformatics analysis of publicly available gene expression profiles of the three CML phases. Pairwise comparisons revealed many differentially expressed genes that formed a characteristic gene expression signature, which clearly distinguished the three CML phases. Signaling pathway expression patterns were very similar between the three phases but differed strongly in the number of affected genes, which increased with the phase. Still, significant alterations of MAPK, VEGF, PI3K-Akt, adherens junction and cytokine receptor interaction signaling distinguished specific phases. Our study also suggests that one can consider the phase-wise CML development as a three rather than a two-step process. This is in accordance with the phase-specific expression behavior of 24 potential major regulators that we predicted by a network-based approach. Several of these genes are known to be involved in the accumulation of additional mutations, alterations of immune responses, deregulation of signaling pathways or may have an impact on treatment response and survival. Importantly, some of these genes have already been reported in relation to CML (e.g., AURKB, AZU1, HLA-B, HLA-DMB, PF4) and others have been found to play important roles in different leukemias (e.g., CDCA3, RPL18A, PRG3, TLX3). In addition, increased expression of BCL2 in the accelerated and blast phase indicates that venetoclax could be a potential treatment option. Moreover, a characteristic signaling pathway signature with increased expression of cytokine and ECM receptor interaction pathway genes distinguished imatinib-resistant patients from each individual CML phase. Overall, our comparative analysis contributes to an in-depth molecular characterization of similarities and differences of the CML phases and provides hints for the identification of patients that may not profit from an imatinib therapy, which could support the development of additional treatment strategies.
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Affiliation(s)
- Annemarie Schwarz
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, D-01307 Dresden, Germany; (A.S.); (I.R.)
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, D-01307 Dresden, Germany; (A.S.); (I.R.)
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany: German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany; Helmholtz-Zentrum Dresden—Rossendorf (HZDR), D-01328 Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, D-01307 Dresden, Germany; (A.S.); (I.R.)
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany: German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany; Helmholtz-Zentrum Dresden—Rossendorf (HZDR), D-01328 Dresden, Germany
- Correspondence:
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