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Siamoglou S, Boers R, Koromina M, Boers J, Tsironi A, Chatzilygeroudi T, Lazaris V, Verigou E, Kourakli A, van IJcken WFJ, Gribnau J, Symeonidis A, Patrinos GP. Genome-wide analysis toward the epigenetic aetiology of myelodysplastic syndrome disease progression and pharmacoepigenomic basis of hypomethylating agents drug treatment response. Hum Genomics 2023; 17:37. [PMID: 37098643 PMCID: PMC10127336 DOI: 10.1186/s40246-023-00483-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/05/2023] [Indexed: 04/27/2023] Open
Abstract
Myelodysplastic syndromes (MDS) consist of a group of hematological malignancies characterized by ineffective hematopoiesis, cytogenetic abnormalities, and often a high risk of transformation to acute myeloid leukemia (AML). So far, there have been only a very limited number of studies assessing the epigenetics component contributing to the pathophysiology of these disorders, but not a single study assessing this at a genome-wide level. Here, we implemented a generic high throughput epigenomics approach, using methylated DNA sequencing (MeD-seq) of LpnPI digested fragments to identify potential epigenomic targets associated with MDS subtypes. Our results highlighted that PCDHG and ZNF gene families harbor potential epigenomic targets, which have been shown to be differentially methylated in a variety of comparisons between different MDS subtypes. Specifically, CpG islands, transcription start sites and post-transcriptional start sites within ZNF124, ZNF497 and PCDHG family are differentially methylated with fold change above 3,5. Overall, these findings highlight important aspects of the epigenomic component of MDS syndromes pathogenesis and the pharmacoepigenomic basis to the hypomethylating agents drug treatment response, while this generic high throughput whole epigenome sequencing approach could be readily implemented to other genetic diseases with a strong epigenetic component.
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Affiliation(s)
- Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, 265 04, Rion, Patras, Greece
| | - Ruben Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Maria Koromina
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, 265 04, Rion, Patras, Greece
| | - Joachim Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Anna Tsironi
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, 265 04, Rion, Patras, Greece
| | - Theodora Chatzilygeroudi
- Hematology Division, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | - Vasileios Lazaris
- Hematology Division, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | - Evgenia Verigou
- Hematology Division, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | - Alexandra Kourakli
- Hematology Division, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | | | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Argiris Symeonidis
- Hematology Division, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, University Campus, 265 04, Rion, Patras, Greece.
- Department of Genetics and Genomics, United Arab Emirates University, College of Medicine and Health Sciences, Al-Ain, Abu Dhabi, United Arab Emirates.
- Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi, United Arab Emirates.
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Yuan C, Zhang K, Wang Z, Ma X, Liu H, Zhao J, Lu W, Wang J. Dietary flaxseed oil and vitamin E improve semen quality via propionic acid metabolism. Front Endocrinol (Lausanne) 2023; 14:1139725. [PMID: 37124753 PMCID: PMC10140321 DOI: 10.3389/fendo.2023.1139725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/15/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Flaxseed oil (FO) and vitamin E (VE) both have antioxidant effects on sperm. The present study investigated the effects of dietary supplementation with FO and/or VE on semen quality. Methods 16 fertile Simmental bulls were selected and randomly divided into 4 groups (n = 4): the control group (control diet), FO group (control diet containing 24 g/kg FO), VE group (control diet containing 150 mg/kg VE) and FOVE group (control diet containing 150 mg/kg VE and 24 g/kg FO), and the trial lasted 10 weeks. Results The results showed that the addition of FO independently can increase sperm motion parameters, the levels of catalase (CAT), glutathione peroxidase (GSH-Px), testosterone (T) and estradiol (E2), while reduce oxidative stress in seminal plasma (P < 0.05). Supplement of VE independently can increased the motility, motility parameters, CAT and superoxide dismutase (SOD) levels, and reduce oxidative stress in seminal plasma (P < 0.05). There was an interaction effect of FO × VE on motility and reactive oxygen species (ROS), while GSH-Px and ROS were affected by week × VE 2-way interaction, levels of T and E2 were also affected by the dietary FO × week interaction (P < 0.05). The triple interaction effects of FO, VE and week were significant for malondialdehyde (MDA) (P < 0.05). Compared with the control group, sperm from the FOVE group had a significantly higher in vitro fertilization (IVF) rate, and subsequent embryos had increased developmental ability with reduced ROS levels at the eight-cell stage, then increased adenosine triphosphate (ATP) content and gene expression levels of CAT, CDX2, Nanog, and SOD at the blastocyst stage (P < 0.05). Metabolomic and transcriptomic results indicated that dietary supplementation of FO and VE increased the expression of the metabolite aconitic acid, as well as the expression of ABAT and AHDHA genes. Conclusion With in-silico analysis, it can be concluded that the effects of dietary FO and VE on improving semen quality and embryo development may be related to increased aconitic acid via the ABAT and AHDHA genes involved in the propionic acid metabolism pathway.
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Affiliation(s)
- Chongshan Yuan
- Joint Laboratory of the Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Key Lab of the Animal Production, Product Quality, and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
| | - Kaiyan Zhang
- Joint Laboratory of the Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Key Lab of the Animal Production, Product Quality, and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhe Wang
- Joint Laboratory of the Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Key Lab of the Animal Production, Product Quality, and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
| | - Xin Ma
- Joint Laboratory of the Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Key Lab of the Animal Production, Product Quality, and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
| | - Hongyu Liu
- Joint Laboratory of the Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Key Lab of the Animal Production, Product Quality, and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
| | - Jing Zhao
- Joint Laboratory of the Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Key Lab of the Animal Production, Product Quality, and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- *Correspondence: Jing Zhao, ; Wenfa Lu, ; Jun Wang,
| | - Wenfa Lu
- Joint Laboratory of the Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Key Lab of the Animal Production, Product Quality, and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- *Correspondence: Jing Zhao, ; Wenfa Lu, ; Jun Wang,
| | - Jun Wang
- Joint Laboratory of the Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Key Lab of the Animal Production, Product Quality, and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- *Correspondence: Jing Zhao, ; Wenfa Lu, ; Jun Wang,
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Zhao G, Li S, Wang Q, Wu W, Fu X, Zhu C, Wang W, Wang X. ABAT gene expression associated with the sensitivity of hypomethylating agents in myelodysplastic syndrome through CXCR4/mTOR signaling. Cell Death Dis 2022; 8:398. [PMID: 36163180 PMCID: PMC9512903 DOI: 10.1038/s41420-022-01170-7] [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: 04/21/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/09/2022]
Abstract
The factors that affect hypomethylating agents (HMAs) sensitivity in myelodysplastic syndrome (MDS) are complex and multifaceted. They include DNA methylation, gene expression, mutation, etc. However, the underlying mechanisms are still not clearly illustrated. In the present work, ABAT gene expression was associated with HMAs sensitivity. It was found that ABAT gene interference increased the sensitivity of HL-60 and THP-1 cells to HMAs treatment, while ABAT overexpression decreased its sensitivity. RNA-sequencing analysis showed that ABAT knockdown activated both interferon I and interferon-gamma signaling while inhibiting the secondary metabolic synthesis and arginine metabolic process. Gas chromatography-mass spectrometry (GC-MS) based metabolic profiling also demonstrated that ABAT gene knockdown affected arginine, alanine, aspartate, and glutamate metabolism, in addition to the biosynthesis of valine, leucine, and isoleucine, and the metabolism of beta-alanine. The ABAT gene expression downregulation could activate the CXCR4/mTOR signaling pathway, which was related to HMAs sensitivity. CXCR4 expression was regulated by mTOR activity and vice versa. In vivo, mice injected with ABAT gene knockdown cells lived longer than control mice after HMAs treatment. Overall, this study elucidates the novel regulatory mechanisms of HMAs sensitivity and provides a potential therapeutic target in MDS.
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Affiliation(s)
- Guangjie Zhao
- Department of Hematology, Huashan Hospital, Fudan University, No.12 Wulumuqi Middle Road, Shanghai, China
| | - Shuang Li
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University, No.85 Wujin Road, Shanghai, China
| | - Qian Wang
- Department of Hematology, Huashan Hospital, Fudan University, No.12 Wulumuqi Middle Road, Shanghai, China
| | - Wanlin Wu
- Department of Hematology, Huashan Hospital, Fudan University, No.12 Wulumuqi Middle Road, Shanghai, China
| | - Xuewei Fu
- Department of Hematology, Huashan Hospital, Fudan University, No.12 Wulumuqi Middle Road, Shanghai, China
| | - Chen Zhu
- Department of Hematology, Huashan Hospital, Fudan University, No.12 Wulumuqi Middle Road, Shanghai, China
| | - Wei Wang
- Department of Hematology, Huashan Hospital, Fudan University, No.12 Wulumuqi Middle Road, Shanghai, China.
| | - Xiaoqin Wang
- Department of Hematology, Huashan Hospital, Fudan University, No.12 Wulumuqi Middle Road, Shanghai, China.
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Gao X, Jia X, Xu M, Xiang J, Lei J, Li Y, Lu Y, Zuo S. Regulation of Gamma-Aminobutyric Acid Transaminase Expression and Its Clinical Significance in Hepatocellular Carcinoma. Front Oncol 2022; 12:879810. [PMID: 35847853 PMCID: PMC9280914 DOI: 10.3389/fonc.2022.879810] [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: 02/20/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background Gamma-aminobutyric acid transaminase (ABAT) catalyzes the conversion of gamma-aminobutyric acid (GABA) into succinic semialdehyde. Although some evidence supports a key role of ABAT in the progression of hepatocellular carcinoma (HCC), no systematic analysis is available. Thus, this study aimed to investigate the possible mechanisms related to low ABAT expression and the prognostic value and potential functions of ABAT in HCC. Methods We obtained relevant datasets from the Encyclopedia of RNA Interactomes, MethSurv, cBioPortal, TISIDB and The Cancer Genome Atlas and used bioinformatic methods to analyze DNA methylation, copy number variation, gene mutation, and upstream microRNAs (miRNAs) of ABAT, exploring the potential relationship between ABAT expression and the prognosis, glycolysis, and immune infiltration in HCC. Results The results indicated that ABAT expression was lower in HCC tumor tissues than in normal tissues or adjacent tissues. Low ABAT expression was related to patient age, T stage classification, pathologic stage, histological grade, and alpha-fetoprotein level of HCC. Kaplan-Meier survival analyses indicated that low ABAT expression was correlated with poor HCC prognosis. ABAT was also verified as an independent risk factor in HCC via Cox multivariate analysis. Gene set enrichment analysis showed enrichment in various signaling pathways. Furthermore, DNA methylation, copy number variation, and gene mutation potentially induced low ABAT expression; miR-135a-5p was a potential upstream miRNA of ABAT. Additionally, ABAT expression was associated with glycolysis-related genes, infiltrated immune cells, immunoinhibitors, and immunostimulators in HCC. Conclusions Our study reveals that deficient ABAT expression is correlated with disease progression and poor prognosis in HCC because of its role in tumorigenesis and tumor immunity.
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Affiliation(s)
- Xiaoqiang Gao
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xiaodong Jia
- Department of Liver Disease, Fifth Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Moyan Xu
- Health Care Office, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jiao Xiang
- Education Department, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Jin Lei
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Yinyin Li
- Department of Liver Disease, Fifth Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
- *Correspondence: Shi Zuo, ; Yinying Lu, ; Yinyin Li,
| | - Yinying Lu
- Department of Liver Disease, Fifth Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
- Center for Synthetic and Systems Biology (CSSB), Tsinghua University, Beijing, China
- Guangdong Key Laboratory of Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- *Correspondence: Shi Zuo, ; Yinying Lu, ; Yinyin Li,
| | - Shi Zuo
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
- *Correspondence: Shi Zuo, ; Yinying Lu, ; Yinyin Li,
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Chen N, Zheng Q, Wan G, Guo F, Zeng X, Shi P. Impact of posttranslational modifications in pancreatic carcinogenesis and treatments. Cancer Metastasis Rev 2021; 40:739-759. [PMID: 34342796 DOI: 10.1007/s10555-021-09980-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/06/2021] [Indexed: 01/22/2023]
Abstract
Pancreatic cancer (PC) is a highly aggressive cancer, with a 9% 5-year survival rate and a high risk of recurrence. In part, this is because PC is composed of heterogeneous subgroups with different biological and functional characteristics and personalized anticancer treatments are required. Posttranslational modifications (PTMs) play an important role in modifying protein functions/roles and are required for the maintenance of cell viability and biological processes; thus, their dysregulation can lead to disease. Different types of PTMs increase the functional diversity of the proteome, which subsequently influences most aspects of normal cell biology or pathogenesis. This review primarily focuses on ubiquitination, SUMOylation, and NEDDylation, as well as the current understanding of their roles and molecular mechanisms in pancreatic carcinogenesis. Additionally, we briefly summarize studies and clinical trials on PC treatments to advance our knowledge of drugs available to target the ubiquitination, SUMOylation, and NEDDylation PTM types. Further investigation of PTMs could be a critical field of study in relation to PC, as they have been implicated in the initiation and progression of many other types of cancer.
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Affiliation(s)
- Nianhong Chen
- Center Lab of Longhua Branch and Department of Infectious Disease, Shenzhen People's Hospital, 2Nd Clinical Medical College, Jinan University, Guangzhou, People's Republic of China.
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Medicine School, Guangdong Province, Shenzhen University, Shenzhen, 518037, People's Republic of China.
- Department of Cell Biology & University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- Laboratory of Signal Transduction, Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
| | - Qiaoqiao Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Guoqing Wan
- Center Lab of Longhua Branch and Department of Infectious Disease, Shenzhen People's Hospital, 2Nd Clinical Medical College, Jinan University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Medicine School, Guangdong Province, Shenzhen University, Shenzhen, 518037, People's Republic of China
| | - Feng Guo
- Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Xiaobin Zeng
- Center Lab of Longhua Branch and Department of Infectious Disease, Shenzhen People's Hospital, 2Nd Clinical Medical College, Jinan University, Guangzhou, People's Republic of China.
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Medicine School, Guangdong Province, Shenzhen University, Shenzhen, 518037, People's Republic of China.
| | - Ping Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
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Mirsadeghi L, Haji Hosseini R, Banaei-Moghaddam AM, Kavousi K. EARN: an ensemble machine learning algorithm to predict driver genes in metastatic breast cancer. BMC Med Genomics 2021; 14:122. [PMID: 33962648 PMCID: PMC8105935 DOI: 10.1186/s12920-021-00974-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/27/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Today, there are a lot of markers on the prognosis and diagnosis of complex diseases such as primary breast cancer. However, our understanding of the drivers that influence cancer aggression is limited. METHODS In this work, we study somatic mutation data consists of 450 metastatic breast tumor samples from cBio Cancer Genomics Portal. We use four software tools to extract features from this data. Then, an ensemble classifier (EC) learning algorithm called EARN (Ensemble of Artificial Neural Network, Random Forest, and non-linear Support Vector Machine) is proposed to evaluate plausible driver genes for metastatic breast cancer (MBCA). The decision-making strategy for the proposed ensemble machine is based on the aggregation of the predicted scores obtained from individual learning classifiers to be prioritized homo sapiens genes annotated as protein-coding from NCBI. RESULTS This study is an attempt to focus on the findings in several aspects of MBCA prognosis and diagnosis. First, drivers and passengers predicted by SVM, ANN, RF, and EARN are introduced. Second, biological inferences of predictions are discussed based on gene set enrichment analysis. Third, statistical validation and comparison of all learning methods are performed by some evaluation metrics. Finally, the pathway enrichment analysis (PEA) using ReactomeFIVIz tool (FDR < 0.03) for the top 100 genes predicted by EARN leads us to propose a new gene set panel for MBCA. It includes HDAC3, ABAT, GRIN1, PLCB1, and KPNA2 as well as NCOR1, TBL1XR1, SIRT4, KRAS, CACNA1E, PRKCG, GPS2, SIN3A, ACTB, KDM6B, and PRMT1. Furthermore, we compare results for MBCA to other outputs regarding 983 primary tumor samples of breast invasive carcinoma (BRCA) obtained from the Cancer Genome Atlas (TCGA). The comparison between outputs shows that ROC-AUC reaches 99.24% using EARN for MBCA and 99.79% for BRCA. This statistical result is better than three individual classifiers in each case. CONCLUSIONS This research using an integrative approach assists precision oncologists to design compact targeted panels that eliminate the need for whole-genome/exome sequencing. The schematic representation of the proposed model is presented as the Graphic abstract.
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Affiliation(s)
- Leila Mirsadeghi
- Department of Biology, Faculty of Science, Payame Noor University, Tehran, Iran
| | - Reza Haji Hosseini
- Department of Biology, Faculty of Science, Payame Noor University, Tehran, Iran.
| | - Ali Mohammad Banaei-Moghaddam
- Laboratory of Genomics and Epigenomics (LGE), Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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Zhou JD, Zhang TJ, Xu ZJ, Deng ZQ, Gu Y, Ma JC, Wen XM, Leng JY, Lin J, Chen SN, Qian J. Genome-wide methylation sequencing identifies progression-related epigenetic drivers in myelodysplastic syndromes. Cell Death Dis 2020; 11:997. [PMID: 33219204 PMCID: PMC7679421 DOI: 10.1038/s41419-020-03213-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023]
Abstract
The potential mechanism of myelodysplastic syndromes (MDS) progressing to acute myeloid leukemia (AML) remains poorly elucidated. It has been proved that epigenetic alterations play crucial roles in the pathogenesis of cancer progression including MDS. However, fewer studies explored the whole-genome methylation alterations during MDS progression. Reduced representation bisulfite sequencing was conducted in four paired MDS/secondary AML (MDS/sAML) patients and intended to explore the underlying methylation-associated epigenetic drivers in MDS progression. In four paired MDS/sAML patients, cases at sAML stage exhibited significantly increased methylation level as compared with the matched MDS stage. A total of 1090 differentially methylated fragments (DMFs) (441 hypermethylated and 649 hypomethylated) were identified involving in MDS pathogenesis, whereas 103 DMFs (96 hypermethylated and 7 hypomethylated) were involved in MDS progression. Targeted bisulfite sequencing further identified that aberrant GFRA1, IRX1, NPY, and ZNF300 methylation were frequent events in an additional group of de novo MDS and AML patients, of which only ZNF300 methylation was associated with ZNF300 expression. Subsequently, ZNF300 hypermethylation in larger cohorts of de novo MDS and AML patients was confirmed by real-time quantitative methylation-specific PCR. It was illustrated that ZNF300 methylation could act as a potential biomarker for the diagnosis and prognosis in MDS and AML patients. Functional experiments demonstrated the anti-proliferative and pro-apoptotic role of ZNF300 overexpression in MDS-derived AML cell-line SKM-1. Collectively, genome-wide DNA hypermethylation were frequent events during MDS progression. Among these changes, ZNF300 methylation, a regulator of ZNF300 expression, acted as an epigenetic driver in MDS progression. These findings provided a theoretical basis for the usage of demethylation drugs in MDS patients against disease progression.
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Affiliation(s)
- Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 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 in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Ting-Juan Zhang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 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 in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 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 in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Zhao-Qun Deng
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 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 in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 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 in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Xiang-Mei Wen
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Jia-Yan Leng
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 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 in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 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 in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China. .,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.
| | - Su-Ning Chen
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China. .,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, People's Republic of China.
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 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 in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.
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Knott EL, Leidenheimer NJ. A Targeted Bioinformatics Assessment of Adrenocortical Carcinoma Reveals Prognostic Implications of GABA System Gene Expression. Int J Mol Sci 2020; 21:ijms21228485. [PMID: 33187258 PMCID: PMC7697095 DOI: 10.3390/ijms21228485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Adrenocortical carcinoma (ACC) is a rare but deadly cancer for which few treatments exist. Here, we have undertaken a targeted bioinformatics study of The Cancer Genome Atlas (TCGA) ACC dataset focusing on the 30 genes encoding the γ-aminobutyric acid (GABA) system—an under-studied, evolutionarily-conserved system that is an emerging potential player in cancer progression. Our analysis identified a subset of ACC patients whose tumors expressed a distinct GABA system transcriptome. Transcript levels of ABAT (encoding a key GABA shunt enzyme), were upregulated in over 40% of tumors, and this correlated with several favorable clinical outcomes including patient survival; while enrichment and ontology analysis implicated two cancer-related biological pathways involved in metastasis and immune response. The phenotype associated with ABAT upregulation revealed a potential metabolic heterogeneity among ACC tumors associated with enhanced mitochondrial metabolism. Furthermore, many GABAA receptor subunit-encoding transcripts were expressed, including two (GABRB2 and GABRD) prognostic for patient survival. Transcripts encoding GABAB receptor subunits and GABA transporters were also ubiquitously expressed. The GABA system transcriptome of ACC tumors is largely mirrored in the ACC NCI-H295R cell line, suggesting that this cell line may be appropriate for future functional studies investigating the role of the GABA system in ACC cell growth phenotypes and metabolism.
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Unravelling the Epigenome of Myelodysplastic Syndrome: Diagnosis, Prognosis, and Response to Therapy. Cancers (Basel) 2020; 12:cancers12113128. [PMID: 33114584 PMCID: PMC7692163 DOI: 10.3390/cancers12113128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/19/2020] [Accepted: 10/24/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Myelodysplastic syndrome (MDS) is a type of blood cancer that mostly affects older individuals. Invasive tests to obtain bone samples are used to diagnose MDS and many patients do not respond to therapy or stop responding to therapy in the short-term. Less invasive tests to help diagnose, prognosticate, and predict response of patients is a felt need. Factors that influence gene expression without changing the DNA sequence (epigenetic modifiers) such as DNA methylation, micro-RNAs and long-coding RNAs play an important role in MDS, are potential biomarkers and may also serve as targets for therapy. Abstract Myelodysplastic syndrome (MDS) is a malignancy that disrupts normal blood cell production and commonly affects our ageing population. MDS patients are diagnosed using an invasive bone marrow biopsy and high-risk MDS patients are treated with hypomethylating agents (HMAs) such as decitabine and azacytidine. However, these therapies are only effective in 50% of patients, and many develop resistance to therapy, often resulting in bone marrow failure or leukemic transformation. Therefore, there is a strong need for less invasive, diagnostic tests for MDS, novel markers that can predict response to therapy and/or patient prognosis to aid treatment stratification, as well as new and effective therapeutics to enhance patient quality of life and survival. Epigenetic modifiers such as DNA methylation, long non-coding RNAs (lncRNAs) and micro-RNAs (miRNAs) are perturbed in MDS blasts and the bone marrow micro-environment, influencing disease progression and response to therapy. This review focusses on the potential utility of epigenetic modifiers in aiding diagnosis, prognosis, and predicting treatment response in MDS, and touches on the need for extensive and collaborative research using single-cell technologies and multi-omics to test the clinical utility of epigenetic markers for MDS patients in the future.
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Zhang TJ, Xu ZJ, Gu Y, Wen XM, Ma JC, Zhang W, Deng ZQ, Leng JY, Qian J, Lin J, Zhou JD. Identification and validation of prognosis-related DLX5 methylation as an epigenetic driver in myeloid neoplasms. Clin Transl Med 2020; 10:e29. [PMID: 32508046 PMCID: PMC7403826 DOI: 10.1002/ctm2.29] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 12/12/2022] Open
Abstract
The deregulated DLX gene family members DLX1/2/3/4/5/6 (DLXs) caused by DNA methylation has been demonstrated in various cancers with therapeutic target value. However, the potential role of DLXs methylation in myeloid neoplasms such as acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) remains to be elucidated. Clinical significance of DLXs methylation/expression was analyzed in patient with AML and MDS. The functional roles of DLXs were determined in vitro. In the identification stage, we found that lower DLX5 expression was correlated with prognosis in AML among all DLXs analyzed by The Cancer Genome Atlas datasets. In the validation stage, we revealed that reduced DLX5 expression was frequently occurred, and was also correlated with promoter hypermethylation in AML evaluated by targeted bisulfite sequencing. Epigenetic studies also showed that DLX5 promoter DNA methylation was associated with its expression. By quantitative polymerase chain reaction, we also validated that DLX5 hypermethylation was frequent event in both AML and MDS, and also correlated with MDS transformation to leukemia. Moreover, DLX5 hypermethylation was associated with lower rate of complete remission and shorter time of leukemia‐free/overall survival, and was also confirmed by Logistic/Cox regression analysis. Functional studies revealed the antiproliferative and pro‐apoptotic effects of DLX5 in MDS‐derived AML cell‐line SKM‐1. Finally, bioinformatics analysis demonstrated that DLX5 functioned in leukemogenesis may be through the association with PI3K/Akt signaling pathway. Collectively, our findings demonstrated that DLX5 methylation, negatively correlated DLX5 expression, was a potential prognostic and predictive indicator in patients with AML and MDS, which could also act as an epigenetic driver in myeloid neoplasms.
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Affiliation(s)
- Ting-Juan Zhang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
| | - Zi-Jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China
| | - Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
| | - Xiang-Mei Wen
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China
| | - Ji-Chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China
| | - Wei Zhang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
| | - Zhao-Qun Deng
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China
| | - Jia-Yan Leng
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
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Chen Y, Zhao G, Li N, Luo Z, Wang X, Gu J. Role of 4‑aminobutyrate aminotransferase (ABAT) and the lncRNA co‑expression network in the development of myelodysplastic syndrome. Oncol Rep 2019; 42:509-520. [PMID: 31173260 PMCID: PMC6610043 DOI: 10.3892/or.2019.7175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
IncRNAs play an important role in the regulation of gene expression. The present study profiled differentially expressed lncRNAs (DELs) and mRNAs (DEMs) in myelodysplastic syndrome (MDS) to construct a 4-aminobutyrate aminotransferase (ABAT)-DEL-DEM co-expression network in MDS development using the Agilent human BeadChips and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and network analyses. Compared with controls, there were 543 DELs and 2,705 DEMs in MDS patients, among which 285 (52.5%) DELs were downregulated and 258 (47.5%) DELs were upregulated, whereas 1,521 (56.2%) DEMs were downregulated and 1,184 (43.70%) DEMs were upregulated in MDS patients. The ABAT-DEL-DEM co-expression network contained six DELs that were co-expressed with ABAT in MDS. The GO analysis revealed that the co-expression network mainly participated in response to organic cyclic compound, cell proliferation, cell part morphogenesis, regulation of cell proliferation and enzyme-linked receptor protein signaling pathways, while the KEGG database showed that the co-expression network was involved in various pathways, such as phagosome and metabolic pathways. Furthermore, the expression of a selected DEL (lncENST00000444102) and ABAT was shown to be significantly downregulated in MDS patients, and in SKM-1 and THP-1 cells. The selected lncENST00000444102 was then overexpressed and ABAT expression was knocked down in the MDS cell lines using lentiviral transfection. In addition, lncENST00000444102 overexpression reduced the viability and increased the apoptosis of MDS cells, ABAT expression was upregulated by lncENST00000444102.
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Affiliation(s)
- Yanzhen Chen
- WorldWide Medical Center, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
| | - Guangjie Zhao
- Department of Hematology, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
| | - Nianyi Li
- Department of Hematology, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
| | - Zhongguang Luo
- Department of Digestive Diseases, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
| | - Xiaoqin Wang
- Department of Hematology, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
| | - Jingwen Gu
- WorldWide Medical Center, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
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