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Toker L, Tran GT, Sundaresan J, Tysnes OB, Alves G, Haugarvoll K, Nido GS, Dölle C, Tzoulis C. Genome-wide histone acetylation analysis reveals altered transcriptional regulation in the Parkinson's disease brain. Mol Neurodegener 2021; 16:31. [PMID: 33947435 PMCID: PMC8097820 DOI: 10.1186/s13024-021-00450-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a complex, age-related neurodegenerative disorder of largely unknown etiology. PD is strongly associated with mitochondrial respiratory dysfunction, which can lead to epigenetic dysregulation and specifically altered histone acetylation. Nevertheless, and despite the emerging role of epigenetics in age-related brain disorders, the question of whether aberrant histone acetylation is involved in PD remains unresolved. METHODS We studied fresh-frozen brain tissue from two independent cohorts of individuals with idiopathic PD (n = 28) and neurologically healthy controls (n = 21). We performed comprehensive immunoblotting to identify histone sites with altered acetylation levels in PD, followed by chromatin immunoprecipitation sequencing (ChIP-seq). RNA sequencing data from the same individuals was used to assess the impact of altered histone acetylation on gene expression. RESULTS Immunoblotting analyses revealed increased acetylation at several histone sites in PD, with the most prominent change observed for H3K27, a marker of active promoters and enhancers. ChIP-seq analysis further indicated that H3K27 hyperacetylation in the PD brain is a genome-wide phenomenon with a strong predilection for genes implicated in the disease, including SNCA, PARK7, PRKN and MAPT. Integration of the ChIP-seq with transcriptomic data from the same individuals revealed that the correlation between promoter H3K27 acetylation and gene expression is attenuated in PD patients, suggesting that H3K27 acetylation may be decoupled from transcription in the PD brain. Strikingly, this decoupling was most pronounced among nuclear-encoded mitochondrial genes, corroborating the notion that impaired crosstalk between the nucleus and mitochondria is involved in the pathogenesis of PD. Our findings independently replicated in the two cohorts. CONCLUSIONS Our findings strongly suggest that aberrant histone acetylation and altered transcriptional regulation are involved in the pathophysiology of PD. We demonstrate that PD-associated genes are particularly prone to epigenetic dysregulation and identify novel epigenetic signatures associated with the disease.
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Affiliation(s)
- Lilah Toker
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Gia T. Tran
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Janani Sundaresan
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Ole-Bjørn Tysnes
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Guido Alves
- The Norwegian Centre for Movement Disorders and Department of Neurology, Stavanger University Hospital, Pb 8100, 4068 Stavanger, Norway
- Department of Mathematics and Natural Sciences, University of Stavanger, 4062 Stavanger, Norway
| | - Kristoffer Haugarvoll
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Gonzalo S. Nido
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Christian Dölle
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
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Yin J, Reiman EM, Beach TG, Serrano GE, Sabbagh MN, Nielsen M, Caselli RJ, Shi J. Effect of ApoE isoforms on mitochondria in Alzheimer disease. Neurology 2020; 94:e2404-e2411. [PMID: 32457210 PMCID: PMC7455369 DOI: 10.1212/wnl.0000000000009582] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/26/2019] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE To test the hypothesis that ApoE isoforms affect mitochondrial structure and function that are related to cognitive impairment in Alzheimer disease (AD), we systematically investigated the effects of ApoE isoforms on mitochondrial biogenesis and dynamics, oxidative stress, synapses, and cognitive performance in AD. METHODS We obtained postmortem human brain tissues and measured proteins that are responsible for mitochondrial biogenesis (peroxisome proliferator-activated receptor-gamma coactivator-1α [PGC-1α] and sirtuin 3 [SIRT3]), for mitochondrial dynamics (mitofusin 1 [MFN1], mitofusin 2 [MFN2], and dynamin-like protein 1 [DLP1]), for oxidative stress (superoxide dismutase 2 [SOD2] and forkhead-box protein O3a [Foxo3a]), and for synapses (postsynaptic density protein 95 [PSD95] and synapsin1 [Syn1]). A total of 46 cases were enrolled, including ApoE-ɛ4 carriers (n = 21) and noncarriers (n = 25). RESULTS Levels of these proteins were compared between ApoE-ɛ4 carriers and noncarriers. ApoE-ɛ4 was associated with impaired mitochondrial structure and function, oxidative stress, and synaptic integrity in the human brain. Correlation analysis revealed that mitochondrial proteins and the synaptic protein were strongly associated with cognitive performance. CONCLUSION ApoE isoforms influence mitochondrial structure and function, which likely leads to alteration in oxidative stress, synapses, and cognitive function. These mitochondria-related proteins may be a harbinger of cognitive decline in ApoE-ɛ4 carriers and provide novel therapeutic targets for prevention and treatment of AD.
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Affiliation(s)
- Junxiang Yin
- From the Barrow Neurological Institute (J.Y., M.N.S., M.N., J.S.), St. Joseph Hospital and Medical Center, Phoenix, AZ; Banner Alzheimer's Institute (E.M.R.), Phoenix, AZ; Civin Laboratory for Neuropathology (T.G.B., G.E.S.), Banner Sun Health Research Institute, Sun City, AZ; Cleveland Clinic Lou Ruvo Center for Brain Health (M.N.S.), Las Vegas, NV; School of Life Sciences (M.N.), Arizona State University, Tempe; Department of Neurology (R.J.C.), Mayo Clinic Arizona, Scottsdale; Advanced Innovation Center for Human Brain Protection (J.S.), Capital Medical University, Beijing, China; and China National Clinical Research Center for Neurological Diseases (J.S.), Beijing Tiantan Hospital, Capital Medical University, Beijing
| | - Eric M Reiman
- From the Barrow Neurological Institute (J.Y., M.N.S., M.N., J.S.), St. Joseph Hospital and Medical Center, Phoenix, AZ; Banner Alzheimer's Institute (E.M.R.), Phoenix, AZ; Civin Laboratory for Neuropathology (T.G.B., G.E.S.), Banner Sun Health Research Institute, Sun City, AZ; Cleveland Clinic Lou Ruvo Center for Brain Health (M.N.S.), Las Vegas, NV; School of Life Sciences (M.N.), Arizona State University, Tempe; Department of Neurology (R.J.C.), Mayo Clinic Arizona, Scottsdale; Advanced Innovation Center for Human Brain Protection (J.S.), Capital Medical University, Beijing, China; and China National Clinical Research Center for Neurological Diseases (J.S.), Beijing Tiantan Hospital, Capital Medical University, Beijing
| | - Thomas G Beach
- From the Barrow Neurological Institute (J.Y., M.N.S., M.N., J.S.), St. Joseph Hospital and Medical Center, Phoenix, AZ; Banner Alzheimer's Institute (E.M.R.), Phoenix, AZ; Civin Laboratory for Neuropathology (T.G.B., G.E.S.), Banner Sun Health Research Institute, Sun City, AZ; Cleveland Clinic Lou Ruvo Center for Brain Health (M.N.S.), Las Vegas, NV; School of Life Sciences (M.N.), Arizona State University, Tempe; Department of Neurology (R.J.C.), Mayo Clinic Arizona, Scottsdale; Advanced Innovation Center for Human Brain Protection (J.S.), Capital Medical University, Beijing, China; and China National Clinical Research Center for Neurological Diseases (J.S.), Beijing Tiantan Hospital, Capital Medical University, Beijing
| | - Geidy E Serrano
- From the Barrow Neurological Institute (J.Y., M.N.S., M.N., J.S.), St. Joseph Hospital and Medical Center, Phoenix, AZ; Banner Alzheimer's Institute (E.M.R.), Phoenix, AZ; Civin Laboratory for Neuropathology (T.G.B., G.E.S.), Banner Sun Health Research Institute, Sun City, AZ; Cleveland Clinic Lou Ruvo Center for Brain Health (M.N.S.), Las Vegas, NV; School of Life Sciences (M.N.), Arizona State University, Tempe; Department of Neurology (R.J.C.), Mayo Clinic Arizona, Scottsdale; Advanced Innovation Center for Human Brain Protection (J.S.), Capital Medical University, Beijing, China; and China National Clinical Research Center for Neurological Diseases (J.S.), Beijing Tiantan Hospital, Capital Medical University, Beijing
| | - Marwan N Sabbagh
- From the Barrow Neurological Institute (J.Y., M.N.S., M.N., J.S.), St. Joseph Hospital and Medical Center, Phoenix, AZ; Banner Alzheimer's Institute (E.M.R.), Phoenix, AZ; Civin Laboratory for Neuropathology (T.G.B., G.E.S.), Banner Sun Health Research Institute, Sun City, AZ; Cleveland Clinic Lou Ruvo Center for Brain Health (M.N.S.), Las Vegas, NV; School of Life Sciences (M.N.), Arizona State University, Tempe; Department of Neurology (R.J.C.), Mayo Clinic Arizona, Scottsdale; Advanced Innovation Center for Human Brain Protection (J.S.), Capital Medical University, Beijing, China; and China National Clinical Research Center for Neurological Diseases (J.S.), Beijing Tiantan Hospital, Capital Medical University, Beijing
| | - Megan Nielsen
- From the Barrow Neurological Institute (J.Y., M.N.S., M.N., J.S.), St. Joseph Hospital and Medical Center, Phoenix, AZ; Banner Alzheimer's Institute (E.M.R.), Phoenix, AZ; Civin Laboratory for Neuropathology (T.G.B., G.E.S.), Banner Sun Health Research Institute, Sun City, AZ; Cleveland Clinic Lou Ruvo Center for Brain Health (M.N.S.), Las Vegas, NV; School of Life Sciences (M.N.), Arizona State University, Tempe; Department of Neurology (R.J.C.), Mayo Clinic Arizona, Scottsdale; Advanced Innovation Center for Human Brain Protection (J.S.), Capital Medical University, Beijing, China; and China National Clinical Research Center for Neurological Diseases (J.S.), Beijing Tiantan Hospital, Capital Medical University, Beijing
| | - Richard J Caselli
- From the Barrow Neurological Institute (J.Y., M.N.S., M.N., J.S.), St. Joseph Hospital and Medical Center, Phoenix, AZ; Banner Alzheimer's Institute (E.M.R.), Phoenix, AZ; Civin Laboratory for Neuropathology (T.G.B., G.E.S.), Banner Sun Health Research Institute, Sun City, AZ; Cleveland Clinic Lou Ruvo Center for Brain Health (M.N.S.), Las Vegas, NV; School of Life Sciences (M.N.), Arizona State University, Tempe; Department of Neurology (R.J.C.), Mayo Clinic Arizona, Scottsdale; Advanced Innovation Center for Human Brain Protection (J.S.), Capital Medical University, Beijing, China; and China National Clinical Research Center for Neurological Diseases (J.S.), Beijing Tiantan Hospital, Capital Medical University, Beijing
| | - Jiong Shi
- From the Barrow Neurological Institute (J.Y., M.N.S., M.N., J.S.), St. Joseph Hospital and Medical Center, Phoenix, AZ; Banner Alzheimer's Institute (E.M.R.), Phoenix, AZ; Civin Laboratory for Neuropathology (T.G.B., G.E.S.), Banner Sun Health Research Institute, Sun City, AZ; Cleveland Clinic Lou Ruvo Center for Brain Health (M.N.S.), Las Vegas, NV; School of Life Sciences (M.N.), Arizona State University, Tempe; Department of Neurology (R.J.C.), Mayo Clinic Arizona, Scottsdale; Advanced Innovation Center for Human Brain Protection (J.S.), Capital Medical University, Beijing, China; and China National Clinical Research Center for Neurological Diseases (J.S.), Beijing Tiantan Hospital, Capital Medical University, Beijing.
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Casadei Gardini A, Faloppi L, De Matteis S, Foschi FG, Silvestris N, Tovoli F, Palmieri V, Marisi G, Brunetti O, Vespasiani-Gentilucci U, Perrone G, Valgiusti M, Granato AM, Ercolani G, Negrini G, Tamburini E, Aprile G, Passardi A, Santini D, Cascinu S, Frassineti GL, Scartozzi M. Metformin and insulin impact on clinical outcome in patients with advanced hepatocellular carcinoma receiving sorafenib: Validation study and biological rationale. Eur J Cancer 2017; 86:106-114. [PMID: 28985579 DOI: 10.1016/j.ejca.2017.09.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/28/2017] [Accepted: 09/04/2017] [Indexed: 02/07/2023]
Abstract
PURPOSE In 2015, we published a study on a small series of patients with hepatocellular carcinoma (HCC) treated chronically with metformin for type II diabetes mellitus (DM2) who showed a poorer response to sorafenib. The aim of the present study was to validate the prognostic significance of metformin in HCC patients treated with sorafenib, providing a biological rationale for the mechanism of resistance to sorafenib in patients on chronic metformin therapy, and to clarify the role of sirtuin-3 (SIRT-3), a protein involved in metabolic diseases and acknowledged as a tumour suppressor in HCC, in this resistance. PATIENTS AND METHODS We analysed 279 patients consecutively treated with sorafenib for the clinical analysis. Of the 86 (30%) patients with DM2, 52 (19%) were on chronic treatment with metformin and 34 (12%) with insulin. We included 43 patients with HCC for the biological study: 19 (44.1%) were diabetic and 14 (73.7%) of these received metformin for DM2. SIRT-3 expression was investigated by immunohistochemistry (IHC) in formalin-fixed and paraffin-embedded (FFPE) samples. RESULTS In HCC patients undergoing chronic treatment with metformin, the use of sorafenib was associated with poor progression-free survival (PFS) and overall survival (OS) (1.9 and 6.6 months, respectively) compared to 3.7 months and 10.8 months, respectively, for patients without DM2 and 8.4 months and 16.6 months, respectively, for patients on insulin (P < .0001). We also observed that SIRT-3 protein expression was significantly higher in patients treated with metformin than in those not taking this medication (65% versus 25%, respectively) (P = .013). CONCLUSIONS Our findings could be attributed to increased tumour aggressiveness and resistance to sorafenib caused by chronic treatment with metformin.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Agents/adverse effects
- Antineoplastic Agents/therapeutic use
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/pathology
- Databases, Factual
- Diabetes Mellitus, Type 2/diagnosis
- Diabetes Mellitus, Type 2/drug therapy
- Diabetes Mellitus, Type 2/mortality
- Disease-Free Survival
- Drug Interactions
- Drug Resistance, Neoplasm
- Female
- Humans
- Hypoglycemic Agents/adverse effects
- Hypoglycemic Agents/therapeutic use
- Immunohistochemistry
- Insulin/adverse effects
- Insulin/therapeutic use
- Italy
- Kaplan-Meier Estimate
- Liver Neoplasms/drug therapy
- Liver Neoplasms/enzymology
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- Male
- Metformin/adverse effects
- Metformin/therapeutic use
- Middle Aged
- Niacinamide/adverse effects
- Niacinamide/analogs & derivatives
- Niacinamide/therapeutic use
- Phenylurea Compounds/adverse effects
- Phenylurea Compounds/therapeutic use
- Protein Kinase Inhibitors/adverse effects
- Protein Kinase Inhibitors/therapeutic use
- Retrospective Studies
- Sirtuin 3/analysis
- Sorafenib
- Time Factors
- Treatment Outcome
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Affiliation(s)
- Andrea Casadei Gardini
- Department of Medical Oncology, Istituto Scientifico Romagnolo per Lo Studio e Cura Dei Tumori (IRST) IRCCS, Meldola, Italy.
| | - Luca Faloppi
- Department of Medical Oncology, University of Cagliari, Italy
| | - Serena De Matteis
- Biosciences Laboratory, Istituto Scientifico Romagnolo per Lo Studio e La Cura Dei Tumori (IRST) IRCCS, Meldola, Italy
| | | | - Nicola Silvestris
- Department of Medical Oncology, National Cancer Institute Giovanni Paolo II, Bari, Italy
| | - Francesco Tovoli
- Department of Medical and Surgical Sciences, Sant'Orsola-Malpighi Hospital, University of Bologna, Italy
| | - Vincenzo Palmieri
- Department of Biomedical Sciences and Human Oncology, Clinica Medica A. Murri, University of Bari Medical School, Italy
| | - Giorgia Marisi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per Lo Studio e La Cura Dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Oronzo Brunetti
- Department of Medical Oncology, National Cancer Institute Giovanni Paolo II, Bari, Italy
| | | | - Giuseppe Perrone
- Department of Pathology, Università Campus Bio-Medico, Rome, Italy
| | - Martina Valgiusti
- Department of Medical Oncology, Istituto Scientifico Romagnolo per Lo Studio e Cura Dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Anna Maria Granato
- Immunotherapy Unit, Istituto Scientifico Romagnolo per Lo Studio e Cura Dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giorgio Ercolani
- Department of Medical and Surgical Sciences, Sant'Orsola-Malpighi Hospital, University of Bologna, Italy; Department of General Surgery, Morgagni-Pierantoni Hospital, Forlì, Italy
| | - Giulia Negrini
- Department of Medical and Surgical Sciences, Sant'Orsola-Malpighi Hospital, University of Bologna, Italy
| | | | - Giuseppe Aprile
- Department of Oncology, University and General Hospital, Udine, Italy
| | - Alessandro Passardi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per Lo Studio e Cura Dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Daniele Santini
- Medical Oncology Unit, Università Campus Bio-Medico, Rome, Italy
| | - Stefano Cascinu
- Modena Cancer Center, Policlinico di Modena, Università di Modena e Reggio Emilia, Italy
| | - Giovanni Luca Frassineti
- Department of Medical Oncology, Istituto Scientifico Romagnolo per Lo Studio e Cura Dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Mario Scartozzi
- Department of Medical Oncology, University of Cagliari, Italy
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Abstract
Sirtuin-3 (SIRT3) is a major mitochondrial NAD(+)-dependent deacetylase and plays a key role in the progression and development of human cancers. Although the prognostic and clinicopathological features of SIRT3 expression in various cancers have been investigated by different research groups, however, inconsistent and opposing results can be observed. In this study, we therefore performed a meta-analysis to evaluate the significance of SIRT3 expression in various cancers. Systematic literature searching was performed in PubMed, Embase, China National Knowledge Infrastructure, and Wanfang Data up to November 2015. Total effect analyses and subgroup analyses were performed to evaluate the relationship between SIRT3 expression and overall survival, cancer/non-cancer tissues, lymph node metastasis, pathological differentiation, tumor node metastasis (TNM) stage, tumor size, and gender, in various cancer patients. Hazard ratios (HRs) or odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to clarify the risk or hazard association. A total of 14 studies comprising 2165 cancer patients were included to assess the association between SIRT3 immunohistochemical expression and overall survival or clinicopathological characteristics. SIRT3 expression was significantly associated with overall survival in gastric cancer (HR = 0.62, 95% CI = 0.43-0.89, P = 0.009) and hepatocellular carcinoma patients (HR = 0.56, 95% CI = 0.42-0.74, P<0.0001), cancer/non-cancer tissues in hepatocellular carcinoma patients (OR = 0.04, 95% CI = 0.01-0.16, P<0.0001), lymph node metastasis in breast cancer patients (OR = 2.20, 95% CI = 1.49-3.26, P<0.0001), and also pathological differentiation in hepatocellular carcinoma patients (OR = 0.69, 95% CI = 0.48-0.98, P = 0.04) and gastric cancer patients (OR = 0.33, 95% CI = 0.21-0.50, P<0.00001), by subgroup analyses. Furthermore, SIRT3 expression was significantly associated with pathological differentiation in total effect analysis (OR = 0.46, 95% CI = 0.29-0.74, P = 0.001). No detectable relation between SIRT3 expression and other clinicopathological parameters were found. This meta-analysis indicates that SIRT3 expression level is associated with prognostic and clinical features in specific cancers.
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Affiliation(s)
- Fei-Yuan Yu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, P. R. China
| | - Qian Xu
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, 515041, P. R. China
| | - Dan-Dan Wu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, P. R. China
| | - Andy T. Y. Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, P. R. China
- * E-mail: (YMX); (ATYL)
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, P. R. China
- * E-mail: (YMX); (ATYL)
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