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Zhao Q, Wang Y, Yu D, Leng JY, Zhao Y, Chu M, Xu Z, Ding H, Zhou J, Zhang T. Comprehensive analysis of ID genes reveals the clinical and prognostic value of ID3 expression in acute myeloid leukemia using bioinformatics identification and experimental validation. BMC Cancer 2022; 22:1229. [PMID: 36443709 PMCID: PMC9707109 DOI: 10.1186/s12885-022-10352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Dysregulation of inhibitor of differentiation/DNA binding (ID) genes is linked to cancer growth, angiogenesis, invasiveness, metastasis and patient survival. Nevertheless, few investigations have systematically determined the expression and prognostic value of ID genes in acute myeloid leukemia (AML). METHODS The expression and clinical prognostic value of ID genes in AML were first identified by public databases and further validated by our research cohort. RESULTS Using public data, the expression of ID1/ID3 was markedly downregulated in AML, and the expression of ID2 was greatly upregulated in AML, whereas ID4 showed no significant difference. Among the ID genes, only ID3 expression may be the most valuable prognostic biomarker in both total AML and cytogenetically normal AML (CN-AML) and especially in CN-AML. Clinically, reduced ID3 expression was greatly associated with higher white blood cell counts, peripheral blood/bone marrow blasts, normal karyotypes and intermediate cytogenetic risk. In addition, low ID3 expression was markedly related to FLT3 and NPM1 mutations as well as wild-type TP53. Despite these associations, multivariate Cox regression analysis revealed that ID3 expression was an independent risk factor affecting overall survival (OS) and disease free survival (DFS) in CN-AML patients. Biologically, a total of 839 mRNAs/lncRNAs and 72 microRNAs were found to be associated with ID3 expression in AML. Importantly, the expression of ID3 with discriminative value in AML was further confirmed in our research cohort. CONCLUSION The bioinformatics analysis and experimental verification demonstrate that low ID3 expression independently affects OS and DFS in patients with CN-AML, which might be seen as a potential prognostic indicator in CN-AML.
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Affiliation(s)
- Qi Zhao
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.,Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 212002, Zhenjiang, Jiangsu, P. R. China.,Department of Respiratory Disease, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China
| | - Yun Wang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.,Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China
| | - Di Yu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.,Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China
| | - Jia-Yan Leng
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.,Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China
| | - Yangjing Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 212013, Zhenjiang, Jiangsu, P. R. China
| | - Mingqiang Chu
- Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 212002, Zhenjiang, Jiangsu, P. R. China.,Department of Respiratory Disease, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China
| | - Zijun Xu
- Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 212002, Zhenjiang, Jiangsu, P. R. China
| | - Hao Ding
- Department of Respiratory Disease, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.
| | - Jingdong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China. .,Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China. .,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China.
| | - Tingjuan Zhang
- Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China. .,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China. .,Department of Oncology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.
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Li JF, Ma XJ, Ying LL, Tong YH, Xiang XP. Multi-Omics Analysis of Acute Lymphoblastic Leukemia Identified the Methylation and Expression Differences Between BCP-ALL and T-ALL. Front Cell Dev Biol 2021; 8:622393. [PMID: 33553159 PMCID: PMC7859262 DOI: 10.3389/fcell.2020.622393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/15/2020] [Indexed: 02/06/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) as a common cancer is a heterogeneous disease which is mainly divided into BCP-ALL and T-ALL, accounting for 80–85% and 15–20%, respectively. There are many differences between BCP-ALL and T-ALL, including prognosis, treatment, drug screening, gene research and so on. In this study, starting with methylation and gene expression data, we analyzed the molecular differences between BCP-ALL and T-ALL and identified the multi-omics signatures using Boruta and Monte Carlo feature selection methods. There were 7 expression signature genes (CD3D, VPREB3, HLA-DRA, PAX5, BLNK, GALNT6, SLC4A8) and 168 methylation sites corresponding to 175 methylation signature genes. The overall accuracy, accuracy of BCP-ALL, accuracy of T-ALL of the RIPPER (Repeated Incremental Pruning to Produce Error Reduction) classifier using these signatures evaluated with 10-fold cross validation repeated 3 times were 0.973, 0.990, and 0.933, respectively. Two overlapped genes between 175 methylation signature genes and 7 expression signature genes were CD3D and VPREB3. The network analysis of the methylation and expression signature genes suggested that their common gene, CD3D, was not only different on both methylation and expression levels, but also played a key regulatory role as hub on the network. Our results provided insights of understanding the underlying molecular mechanisms of ALL and facilitated more precision diagnosis and treatment of ALL.
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Affiliation(s)
- Jin-Fan Li
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao-Jing Ma
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lin-Lin Ying
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ying-Hui Tong
- Department of Pharmacy, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Xue-Ping Xiang
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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