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Cardoso C, Pestana D, Gokuladhas S, Marreiros AD, O'Sullivan JM, Binnie A, TFernandes M, Castelo-Branco P. Identification of Novel DNA Methylation Prognostic Biomarkers for AML With Normal Cytogenetics. JCO Clin Cancer Inform 2024; 8:e2300265. [PMID: 39052947 PMCID: PMC11371081 DOI: 10.1200/cci.23.00265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/08/2024] [Accepted: 05/28/2024] [Indexed: 07/27/2024] Open
Abstract
PURPOSE AML is a hematologic cancer that is clinically heterogeneous, with a wide range of clinical outcomes. DNA methylation changes are a hallmark of AML but are not routinely used as a criterion for risk stratification. The aim of this study was to explore DNA methylation markers that could risk stratify patients with cytogenetically normal AML (CN-AML), currently classified as intermediate-risk. MATERIALS AND METHODS DNA methylation profiles in whole blood samples from 77 patients with CN-AML in The Cancer Genome Atlas (LAML cohort) were analyzed. Individual 5'-cytosine-phosphate-guanine-3' (CpG) sites were assessed for their ability to predict overall survival. The output was validated using DNA methylation profiles from bone marrow samples of 79 patients with CN-AML in a separate data set from the Gene Expression Omnibus. RESULTS In the training set, using DNA methylation data derived from the 450K array, we identified 2,549 CpG sites that could potentially distinguish patients with CN-AML with an adverse prognosis (intermediate-poor) from those with a more favorable prognosis (intermediate-favorable) independent of age. Of these, 25 CpGs showed consistent prognostic potential across both the 450K and 27K array platforms. In a separate validation data set, nine of these 25 CpGs exhibited statistically significant differences in 2-year survival. These nine validated CpGs formed the basis for a combined prognostic biomarker panel, which includes an 8-CpG Somatic Panel and the methylation status of cg23947872. This panel displayed strong predictive ability for 2-year survival, 2-year progression-free survival, and complete remission in the validation cohort. CONCLUSION This study highlights DNA methylation profiling as a promising approach to enhance risk stratification in patients with CN-AML, potentially offering a pathway to more personalized treatment strategies.
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Affiliation(s)
- Cândida Cardoso
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve/Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Faro, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
| | - Daniel Pestana
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve/Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Faro, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
| | | | - Ana D. Marreiros
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve/Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Faro, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
| | - Justin M. O'Sullivan
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve/Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Faro, Portugal
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Australian Parkinson's Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alexandra Binnie
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve/Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Faro, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
- Department of Critical Care, William Osler Health System, Etobicoke, ON, Canada
| | - Mónica TFernandes
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
- School of Health, Universidade do Algarve, Faro, Portugal
| | - Pedro Castelo-Branco
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve/Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Faro, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, Lisbon, Portugal
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Long Y, Mao C, Liu S, Tao Y, Xiao D. Epigenetic modifications in obesity-associated diseases. MedComm (Beijing) 2024; 5:e496. [PMID: 38405061 PMCID: PMC10893559 DOI: 10.1002/mco2.496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
The global prevalence of obesity has reached epidemic levels, significantly elevating the susceptibility to various cardiometabolic conditions and certain types of cancer. In addition to causing metabolic abnormalities such as insulin resistance (IR), elevated blood glucose and lipids, and ectopic fat deposition, obesity can also damage pancreatic islet cells, endothelial cells, and cardiomyocytes through chronic inflammation, and even promote the development of a microenvironment conducive to cancer initiation. Improper dietary habits and lack of physical exercise are important behavioral factors that increase the risk of obesity, which can affect gene expression through epigenetic modifications. Epigenetic alterations can occur in early stage of obesity, some of which are reversible, while others persist over time and lead to obesity-related complications. Therefore, the dynamic adjustability of epigenetic modifications can be leveraged to reverse the development of obesity-associated diseases through behavioral interventions, drugs, and bariatric surgery. This review provides a comprehensive summary of the impact of epigenetic regulation on the initiation and development of obesity-associated cancers, type 2 diabetes, and cardiovascular diseases, establishing a theoretical basis for prevention, diagnosis, and treatment of these conditions.
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Affiliation(s)
- Yiqian Long
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Chao Mao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaChina
| | - Shuang Liu
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Yongguang Tao
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaChina
- Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Department of Thoracic SurgerySecond Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Desheng Xiao
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
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Liu J, Huang B, Ding F, Li Y. Environment factors, DNA methylation, and cancer. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:7543-7568. [PMID: 37715840 DOI: 10.1007/s10653-023-01749-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/30/2023] [Indexed: 09/18/2023]
Abstract
Today, the rapid development of science and technology and the rapid change in economy and society are changing the way of life of human beings and affecting the natural, living, working, and internal environment on which human beings depend. At the same time, the global incidence of cancer has increased significantly yearly, and cancer has become the number one killer that threatens human health. Studies have shown that diet, living habits, residential environment, mental and psychological factors, intestinal flora, genetics, social factors, and viral and non-viral infections are closely related to human cancer. However, the molecular mechanisms of the environment and cancer development remain to be further explored. In recent years, DNA methylation has become a key hub and bridge for environmental and cancer research. Some environmental factors can alter the hyper/hypomethylation of human cancer suppressor gene promoters, proto-oncogene promoters, and the whole genome, causing low/high expression or gene mutation of related genes, thereby exerting oncogenic or anticancer effects. It is expected to develop early warning markers of cancer environment based on DNA methylation, thereby providing new methods for early detection of cancers, diagnosis, and targeted therapy. This review systematically expounds on the internal mechanism of environmental factors affecting cancer by changing DNA methylation, aiming to help establish the concept of cancer prevention and improve people's health.
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Affiliation(s)
- Jie Liu
- Department of General Surgery, Second Hospital of Lanzhou University, Lan Zhou, China
- Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lan Zhou, China
| | - Binjie Huang
- Department of General Surgery, Second Hospital of Lanzhou University, Lan Zhou, China
- Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lan Zhou, China
| | - Feifei Ding
- Department of General Surgery, Second Hospital of Lanzhou University, Lan Zhou, China
- Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lan Zhou, China
| | - Yumin Li
- Department of General Surgery, Second Hospital of Lanzhou University, Lan Zhou, China.
- Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lan Zhou, China.
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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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Wu DL, Wang Y, Zhang TJ, Chu MQ, Xu ZJ, Yuan Q, Ma JC, Lin J, Qian J, Zhou JD. SLIT2 promoter hypermethylation predicts disease progression in chronic myeloid leukemia. Eur J Med Res 2022; 27:259. [PMID: 36411451 PMCID: PMC9677675 DOI: 10.1186/s40001-022-00899-2] [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: 08/04/2022] [Accepted: 11/13/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Aberrant DNA methylation plays a crucial role in the progression of myeloid neoplasms. Previously, our literature reported that slit guidance ligand 2 (SLIT2) promoter methylation was associated with disease progression and indicated a poor prognosis in patients with myelodysplastic syndrome. Herein, we further investigated the clinical implications and role of SLIT2 promoter methylation in patients with chronic myeloid leukemia (CML). METHODS The level of SLIT2 promoter methylation was determined in 104 CML patients, and its clinical significance was analyzed. Moreover, demethylation studies were performed in K562 cells to determine the epigenetic mechanism by which SLIT2 promoter methylation is regulated in CML. RESULTS The level of SLIT2 promoter methylation was similar between CML patients and controls. However, deeper analysis revealed that the SLIT2 promoter methylation level in the accelerated phase (AP) and blast crisis (BC) was markedly higher than that in the chronic phase (CP) and controls. Additionally, a marked difference was identified between the SLIT2 promoter hypermethylated and non-hypermethylated groups among CML patients grouped by clinical stage. The frequency of SLIT2 hypermethylation was markedly increased with the progression of clinical stage, that is, it was the lowest in CP samples (12/80, 15%), higher in AP samples (4/8, 50%) and the highest in BC samples (11/16, 69%). Importantly, the level/density of SLIT2 promoter methylation was significantly higher in the advanced stage than in the early stage among the 6 tested paired CML patients. Epigenetically, the expression of the SLIT2-embedded non-coding genes SLIT2-IT1 and miR-218 expression was decreased in patients with CML. SLIT2 promoter hypermethylated cases had a markedly lower SLIT2-IT1 expression level than SLIT2 promoter non-hypermethylated cases. Moreover, SLIT2-IT1 and miR-218 expression was remarkably upregulated in a dose-dependent manner after demethylation treatment of K562 cells. CONCLUSIONS Hypermethylation of the SLIT2 promoter is correlated with disease progression in CML. Furthermore, SLIT2 promoter methylation may function by regulating the expression of the SLIT2-embedded non-coding genes SLIT2-IT1 and miR-218 during CML progression.
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Affiliation(s)
- De-long Wu
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,Department of Oncology, Dongtai People’s Hospital, Dongtai, Jiangsu People’s Republic of China
| | - Yun Wang
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Ting-juan Zhang
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Department of Oncology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Ming-qiang Chu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Zi-jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Qian Yuan
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Ji-chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Jun Qian
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Jing-dong Zhou
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
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Zhou JD, Zhao YJ, Leng JY, Gu Y, Xu ZJ, Ma JC, Wen XM, Lin J, Zhang TJ, Qian J. DNA methylation-mediated differential expression of DLX4 isoforms has opposing roles in leukemogenesis. Cell Mol Biol Lett 2022; 27:59. [PMID: 35883028 PMCID: PMC9327205 DOI: 10.1186/s11658-022-00358-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/28/2022] [Indexed: 11/14/2022] Open
Abstract
Background Previously, we reported the expression of DLX4 isoforms (BP1 and DLX7) in myeloid leukemia, but the functional role of DLX4 isoforms remains poorly understood. In the work described herein, we further determined the underlying role of DLX4 isoforms in chronic myeloid leukemia (CML) leukemogenesis. Methods The expression and methylation of DLX4 isoforms were detected by real-time quantitative PCR (RT-qPCR) and real-time quantitative methylation-specific PCR (RT-qMSP) in patients with CML. The functional role of DLX4 isoforms was determined in vitro and in vivo. The molecular mechanism of DLX4 isoforms in leukemogenesis was identified based on chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq)/assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) and RNA sequencing (RNA-Seq). Results BP1 expression was increased in patients with CML with unmethylated promoter, but DLX7 expression was decreased with hypermethylated promoter. Functionally, overexpression of BP1 increased the proliferation rate of K562 cells with S/G2 promotion, whereas DLX7 overexpression reduced the proliferation rate of K562 cells with G1 arrest. Moreover, K562 cells with BP1 overexpression increased the tumorigenicity in NCG mice, whereas K562 cells with DLX7 overexpression decreased the tumorigenicity. Mechanistically, a total of 91 genes including 79 messenger RNAs (mRNAs) and 12 long noncoding RNAs (lncRNAs) were discovered by ChIP-Seq and RNA-Seq as direct downstream targets of BP1. Among the downstream genes, knockdown of RREB1 and SGMS1-AS1 partially revived the proliferation caused by BP1 overexpression in K562 cells. Similarly, using ATAC-Seq and RNA-Seq, a total of 282 genes including 151 mRNA and 131 lncRNAs were identified as direct downstream targets of DLX7. Knockdown of downstream genes PTPRB and NEAT1 partially revived the proliferation caused by DLX7 overexpression in K562 cells. Finally, we also identified and validated a SGMS1-AS1/miR-181d-5p/SRPK2 competing endogenous RNA (ceRNA) network caused by BP1 overexpression in K562 cells. Conclusions The current findings reveal that DNA methylation-mediated differential expression of DLX4 isoforms BP1 and DLX7 plays opposite functions in leukemogenesis. BP1 plays an oncogenic role in leukemia development, whereas DLX7 acts as a tumor suppressor gene. These results suggest DLX4 as a therapeutic target for antileukemia therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s11658-022-00358-0.
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Affiliation(s)
- Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Yang-Jing Zhao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Jia-Yan Leng
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Zi-Jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Ji-Chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Xiang-Mei Wen
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Ting-Juan Zhang
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Department of Oncology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
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Zhou JD, Xu ZJ, Jin Y, Zhang XL, Gu Y, Ma JC, Wen XM, Lin J, Zhang TJ, Qian J. Whole-Genome DNA Methylation Sequencing Reveals Epigenetic Changes in Myelodysplastic Syndromes. Front Oncol 2022; 12:897898. [PMID: 35847864 PMCID: PMC9277050 DOI: 10.3389/fonc.2022.897898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022] Open
Abstract
Epigenetic dysregulation of cancer-associated genes has been identified to contribute to the pathogenesis of myelodysplastic syndromes (MDS). However, few studies have elucidated the whole-genome DNA methylation in the initiation pathogenesis of MDS. Reduced representation bisulfite sequencing was performed in five de novo MDS patients and four controls to investigate epigenetic alterations in MDS pathogenesis. The mean global methylation in five MDS patients showed no significant difference compared with the four controls. In depth, a total of 1,459 differentially methylated fragments, including 759 hypermethylated and 700 hypomethylated fragments, were identified between MDS patients and controls. Targeted bisulfite sequencing further identified that hypermethylation of DLEU7, FOXR1, LEP, and PANX2 were frequent events in an additional cohort of MDS patients. Subsequently, LEP hypermethylation was confirmed by real-time quantitative methylation-specific PCR in an expanded cohort of larger MDS patients. In clinics, LEP hypermethylation tended to be associated with lower bone marrow blasts and was significantly correlated with U2AF1 mutation. Survival analysis indicated that LEP hypermethylation was associated with a markedly longer survival time but was not an independent prognostic biomarker in MDS patients. Functional studies revealed pro-proliferative and anti-apoptotic effects of leptin in the MDS cell line SKM-1, and it was significantly associated with cell growth and death as well as the Toll-like receptor and NF-kappa B signaling pathways. Collectively, our findings demonstrated that whole-genome DNA methylation analysis identified novel epigenetic alterations such as DLEU7, FOXR1, LEP, and PANX2 methylations as frequent events in MDS. Moreover, LEP might play a role in MDS pathogenesis, and LEP hypermethylation was associated with longer survival but not as an independent prognostic biomarker in MDS.
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Affiliation(s)
- Jing-dong Zhou
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, China
| | - Zi-jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, China
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Ye Jin
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, China
| | - Xin-long Zhang
- Department of Hematology, The People’s Hospital of Danyang, Zhenjiang, China
| | - Yu Gu
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, China
| | - Ji-chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, China
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Xiang-mei Wen
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, China
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, China
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- *Correspondence: Jun Qian, ; Ting-juan Zhang, ; Jiang Lin,
| | - Ting-juan Zhang
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, China
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Department of Oncology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- *Correspondence: Jun Qian, ; Ting-juan Zhang, ; Jiang Lin,
| | - Jun Qian
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, China
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, China
- *Correspondence: Jun Qian, ; Ting-juan Zhang, ; Jiang Lin,
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8
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Wang Y, Ma X, Huang J, Yang X, Kang M, Sun X, Li H, Wu Y, Zhang H, Zhu Y, Xue Y, Fang Y. Somatic FOXC1 insertion mutation remodels the immune microenvironment and promotes the progression of childhood acute lymphoblastic leukemia. Cell Death Dis 2022; 13:431. [PMID: 35504885 PMCID: PMC9065155 DOI: 10.1038/s41419-022-04873-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/10/2022] [Accepted: 04/20/2022] [Indexed: 12/14/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignant hematological diseases in children. An immunosuppressive microenvironment, particularly regulatory T cell (Treg) infiltration, has been documented to be highly associated with childhood ALL. This present study, based on genetic factors, was aimed at investigating the mutations potentially involved in the immunosuppressive microenvironment in childhood ALL. After whole-exome sequencing was used on DNA extracted from the T cells of ALL bone marrow samples, we found the FOXC1 H446HG induced a increased Treg while decreased cytotoxic T lymphocyte (CTL) in bone marrow. The mutation of FOXC1 in T cell promoted the proliferation of leukemia cells in vitro and in vivo. CpG islands formed by insertion mutation led to an abnormal increase in exon methylation and were associated with the suppression of FOXC1. Decreased FOXC1 attenuated the transcription of HDAC1, thus resulting in the activation of KLF10 through increasing H3K27 acetylation in the promoter region. In conclusion, the de novo insertion mutation in FOXC1 induced suppression of FOXC1, thereby promoting a Treg/CTL shift in the ALL immune microenvironment. The FOXC1 H446HG mutation might be a potential therapeutic target for ALL in the future.
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Affiliation(s)
- Yaping Wang
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Xiaopeng Ma
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Jie Huang
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Xiaoyun Yang
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Meiyun Kang
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Xiaoyan Sun
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Huimin Li
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Yijun Wu
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Heng Zhang
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Yuting Zhu
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Yao Xue
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
| | - Yongjun Fang
- grid.89957.3a0000 0000 9255 8984Department of Hematology and Oncology, Children’s Hospital of Nanjing Medical University, Nanjing Medical University, 72# Guangzhou Road, Nanjing, Jiangsu Province China
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9
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Gu Y, Chu MQ, Xu ZJ, Yuan Q, Zhang TJ, Lin J, Zhou JD. Comprehensive analysis of SPAG1 expression as a prognostic and predictive biomarker in acute myeloid leukemia by integrative bioinformatics and clinical validation. BMC Med Genomics 2022; 15:38. [PMID: 35227274 PMCID: PMC8886923 DOI: 10.1186/s12920-022-01193-0] [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: 07/28/2021] [Accepted: 02/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background Recently, an increasing number of studies have reported that sperm-associated antigen (SPAG) proteins play crucial roles in solid tumorigenesis, and may serve as potentially helpful biomarkers for cancer diagnosis and prognosis. However, very few studies systematically investigated the expression of SPAG family members and their clinical significance in acute myeloid leukemia (AML). Methods The expression of SPAGs and their prognostic significance in AML were determined by a systematic analysis on data gathered from public databases, and the results were validated in clinical samples. Results Using public data, we identified only increased SPAG1 expression negatively associated with survival in AML by Cox regression (P < 0.001) and Kaplan–Meier analysis (P < 0.001). The prognostic value of SPAG1 expression was further confirmed in other independent cohorts. Clinically, higher SPAG1 expression was significantly correlated with white blood cell counts (P = 0.014) and French–American–British (FAB) subtypes (P = 0.024). Moreover, higher SPAG1 expression was more common in + 8 patients (P = 0.034), rarely found with t(8;21) (P = 0.014), and correlated with FLT3 (P < 0.001) and DNMT3A mutations (P = 0.001). Despite these associations, multivariate analysis confirmed the independent prognostic value of SPAG1 expression in AML (P < 0.001). Notably, AML patients with higher SPAG1 expression may benefit from hematopoietic stem cell transplantation (HSCT), whereas patients with lower SPAG1 expression appeared less likely to benefit. Finally, we further validated that SPAG1 expression was significantly increased in newly diagnosed AML patients compared with normal controls (P < 0.001) and with AML patients who achieved complete remission (P < 0.001). Additionally, SPAG1 expression could act as a potentially helpful biomarker for the diagnosis and prognosis of AML (P < 0.001 and = 0.034, respectively). Conclusions Our findings demonstrated that SPAG1 overexpression may serve as an independent prognostic biomarker and may guide the choice between HSCT and chemotherapy in patients with AML. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01193-0.
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Affiliation(s)
- Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Ming-Qiang Chu
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Zi-Jun Xu
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Qian Yuan
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Ting-Juan Zhang
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Department of Oncology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jiang Lin
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
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10
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High Olfactory Receptor-Rich 11q11 Copy Number in Girls and African American Children. Genes (Basel) 2021; 12:genes12121943. [PMID: 34946892 PMCID: PMC8701364 DOI: 10.3390/genes12121943] [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: 10/08/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Copy number variants (CNVs) provide numerous genetic differences between individuals, and they have been linked with multiple human diseases. Obesity is one of the highly heritable complex disorders, which is associated with copy number variance (CNV). A recent report shows that the 11q11 gene, a novel olfactory receptor, and its copy number variants are involved in the early onset of obesity. In the current study, we analyzed the 11q11 gene copy number variance (CNV) based on gender in White/European American (EA) and African American (AA) normal weight and overweight/obese children. Sixty-nine boys and fifty-eight girls between the ages of 6 and 10 years belonging to either EA or AA ethnicity were involved in this study. As per World Health Organization (WHO) guidelines, each participant’s body weight and height were recorded. DNA was extracted from saliva, and the copy number variants for the 11q11 gene were measured using digital PCR. The descriptive analysis of the 11q11 copy number showed significantly more copies in girls compared to boys; similarly, AA participants had significantly increased CNV compared to EA. The normal weight (NW) and overweight/obese (OW/OB) girls were significantly less likely to belong to the low copy number variant (LCNV) group of 11q11 compared to boys; similarly, NW and OW/OB AA children were significantly less likely to belong to the LCNV group. The AA girls in LCNV had significantly higher BMI z-scores. Our findings suggest that the 11q11 copy number in children is race and gender-specific.
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11
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Chu MQ, Zhang LC, Yuan Q, Zhang TJ, Zhou JD. Distinct associations of NEDD4L expression with genetic abnormalities and prognosis in acute myeloid leukemia. Cancer Cell Int 2021; 21:615. [PMID: 34809620 PMCID: PMC8607698 DOI: 10.1186/s12935-021-02327-7] [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: 07/26/2021] [Accepted: 11/10/2021] [Indexed: 12/03/2022] Open
Abstract
Background There is mounting evidence that demonstrated the association of aberrant NEDD4L expression with diverse human cancers. However, the expression pattern and clinical implication of NEDD4L in acute myeloid leukemia (AML) remains poorly defined. Methods We systemically determined NEDD4L expression with its clinical significance in AML by both public data and our research cohort. Moreover, biological functions of NEDD4L in leukemogenesis were further tested by in vitro experiments. Results By the public data, we identified that low NEDD4L expression was correlated with AML among diverse human cancers. Expression of NEDD4L was remarkably decreased in AML compared with controls, and was confirmed by our research cohort. Clinically, low expression of NEDD4L was correlated with greatly lower age, higher white blood cells, and higher bone marrow/peripheral blood blasts. Moreover, NEDD4L underexpression was positively correlated with normal karyotype, FLT3 and NPM1 mutations, but negatively associated with complex karyotype and TP53 mutations. Importantly, the association between NEDD4L expression and survival was also discovered in cytogenetically normal AML patients. Finally, a number of 1024 RNAs and 91 microRNAs were identified to be linked to NEDD4L expression in AML. Among the negatively correlated microRNAs, miR-10a was also discovered as a microRNA that may directly target NEDD4L. Further functional studies revealed that NEDD4L exhibited anti-proliferative and pro-apoptotic effects in leukemic cell line K562. Conclusions Our findings indicated that NEDD4L underexpression, as a frequent event in AML, was associated with genetic abnormalities and prognosis in AML. Moreover, NEDD4L expression may be involved in leukemogenesis with potential therapeutic target value. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02327-7.
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Affiliation(s)
- Ming-Qiang Chu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Liu-Chao Zhang
- Medical Laboratory, Qidong People's Hospital, Qidong, Jiangsu, People's Republic of China
| | - Qian Yuan
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Ting-Juan Zhang
- Department of Oncology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.
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12
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Luo H, Tao C, Long X, Huang K, Zhu X. A risk signature of four aging-related genes has clinical prognostic value and is associated with a tumor immune microenvironment in glioma. Aging (Albany NY) 2021; 13:16198-16218. [PMID: 34114970 PMCID: PMC8266313 DOI: 10.18632/aging.203146] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/20/2021] [Indexed: 01/25/2023]
Abstract
An accumulation of studies has indicated aging to be a significant hazard factor for the development of tumors. Cellular senescence is positively associated with aging progress and aging-related genes (AGs) can regulate cellular senescence and tumor malignancy. While the association between AGs and the prognosis of patients with glioma is still unclear. In our study, we initially selected four survival-associated AGs and performed consensus clustering for these AGs based on The Cancer Genome Atlas (TCGA) database. We then explored the potential biological effects of four selected AGs. A prognostic risk model was constructed according to four selected AGs (LEP, TERT, PON1, and SSTR3) in the TCGA dataset and Chinese Glioma Genome Atlas (CGGA) database. Then we indicated the risk score was an independent prognostic index, and was also positively correlated with immune scores, estimate score, immune cell infiltration level, programmed death ligand 1 (PD-L1) expression, and expression of proinflammatory factors in patients with glioma. Finally, we performed the RT-qPCR and immunohistochemistry assay to validate our bioinformatics results. Thus, this study indicated the risk model was concluded to possibly have potential function as an immune checkpoint inhibitor and to provide promising targets for developing individualized immunotherapies for patients with glioma.
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Affiliation(s)
- Haitao Luo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,East China Institute of Digital Medical Engineering, Shangrao, Jiangxi Province, China
| | - Chuming Tao
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Xiaoyan Long
- East China Institute of Digital Medical Engineering, Shangrao, Jiangxi Province, China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
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