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Yu S, Wang XS, Cao KC, Bao XJ, Yu J. Identification of CDK6 and RHOU in Serum Exosome as Biomarkers for the Invasiveness of Non-functioning Pituitary Adenoma. ACTA ACUST UNITED AC 2020; 34:168-176. [PMID: 31601299 DOI: 10.24920/003585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Objective To explore circulating biomarkers for screening the invasiveness of non-functioning pituitary adenomas (NF-PAs). Methods The exosomal RNAs were extracted from serum of patients with invasive NF-PA (INF-PA) or noninvasive NF-PA (NNF-PA). Droplet digital PCR was adapted to detect the mRNA expression of candidate genes related to tumor progression or invasion, such as cyclin dependent kinase 6 (CDK6), ras homolog family member U (RHOU), and spire type actin nucleation factor 2 (SPIRE2). Student's t-test was used to analyze the statistical difference in the mRNA expression of candidate genes between the two groups. Receiver operating characteristic (ROC) curve was used to establish a model for predicting the invasiveness of NF-PAs. The accuracy, sensitivity, specificity and precision of the model were then obtained to evaluate the diagnostic performance. Results CDK6 (0.2600±0.0912 vs. 0.1789±0.0628, t=3.431, P=0.0013) and RHOU mRNA expressions (0.2696±0.1118 vs. 0.1788±0.0857, t=2.946, P=0.0052) were upregulated in INF-PAs patients' serum exosomes as compared to NNF-PAs. For CDK6, the area under the ROC curve (AUC) was 0.772 (95% CI: 0.600-0.943, P=0.005), the accuracy, sensitivity, specificity and precision were 77.27%, 83.33%, 75.00% and 55.56% to predict the invasiveness of NF-PAs. For RHOU, the AUC was 0.757 (95% CI: 0.599-0.915, P=0.007), the accuracy, sensitivity, specificity and precision were 72.73%, 83.33%, 68.75% and 50.00%. In addition, the mRNA levels of CDK6 and RHOU in serum exosomes were significantly positively correlated (r=0.935, P<0.001). After combination of the cut-off scores of the two genes, the accuracy, sensitivity, specificity and precision were 81.82%, 83.33%, 81.25% and 62.50%. Conclusions CDK6 and RHOU mRNA in serum exosomes can be used as markers for predicting invasiveness of NF-PAs. Combination of the two genes performs better in distinguishing INF-PAs from NNF-PAs. These results indicate CDK6 and RHOU play important roles in the invasiveness of NF-PAs, and the established diagnostic method is valuable for directing the clinical screening and postoperative treatment.
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Affiliation(s)
- Shan Yu
- State Key Laboratory of Medical Molecular Biology & Key Laboratory of RNA and Hematopoietic Regulation & Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Xiao-Shuang Wang
- State Key Laboratory of Medical Molecular Biology & Key Laboratory of RNA and Hematopoietic Regulation & Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Kai-Can Cao
- Department of Thoracic Surgery, Nanfang Hospital, Guangzhou 510515, China
| | - Xin-Jie Bao
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology & Key Laboratory of RNA and Hematopoietic Regulation & Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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Koroknai V, Szász I, Hernandez-Vargas H, Fernandez-Jimenez N, Cuenin C, Herceg Z, Vízkeleti L, Ádány R, Ecsedi S, Balázs M. DNA hypermethylation is associated with invasive phenotype of malignant melanoma. Exp Dermatol 2020; 29:39-50. [PMID: 31602702 DOI: 10.1111/exd.14047] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/29/2019] [Accepted: 10/06/2019] [Indexed: 01/01/2023]
Abstract
Tumor cell invasion is one of the key processes during cancer progression, leading to life-threatening metastatic lesions in melanoma. As methylation of cancer-related genes plays a fundamental role during tumorigenesis and may lead to cellular plasticity which promotes invasion, our aim was to identify novel epigenetic markers on selected invasive melanoma cells. Using Illumina BeadChip assays and Affymetrix Human Gene 1.0 microarrays, we explored the DNA methylation landscape of selected invasive melanoma cells and examined the impact of DNA methylation on gene expression patterns. Our data revealed predominantly hypermethylated genes in the invasive cells affecting the neural crest differentiation pathway and regulation of the actin cytoskeleton. Integrative analysis of the methylation and gene expression profiles resulted in a cohort of hypermethylated genes (IL12RB2, LYPD6B, CHL1, SLC9A3, BAALC, FAM213A, SORCS1, GPR158, FBN1 and ADORA2B) with decreased expression. On the other hand, hypermethylation in the gene body of the EGFR and RBP4 genes was positively correlated with overexpression of the genes. We identified several methylation changes that can have role during melanoma progression, including hypermethylation of the promoter regions of the ARHGAP22 and NAV2 genes that are commonly altered in locally invasive primary melanomas as well as during metastasis. Interestingly, the down-regulation of the methylcytosine dioxygenase TET2 gene, which regulates DNA methylation, was associated with hypermethylated promoter region of the gene. This can probably lead to the observed global hypermethylation pattern of invasive cells and might be one of the key changes during the development of malignant melanoma cells.
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Affiliation(s)
- Viktória Koroknai
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - István Szász
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | | | | | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Laura Vízkeleti
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - Róza Ádány
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - Szilvia Ecsedi
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Margit Balázs
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
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Chen K, Liu H, Liu Z, Bloomer W, Amos CI, Lee JE, Li X, Nan H, Wei Q. Genetic variants in glutamine metabolic pathway genes predict cutaneous melanoma-specific survival. Mol Carcinog 2019; 58:2091-2103. [PMID: 31435991 PMCID: PMC7504905 DOI: 10.1002/mc.23100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/23/2019] [Accepted: 08/03/2019] [Indexed: 01/04/2023]
Abstract
Glutamine dependence is a unique metabolic defect seen in cutaneous melanoma (CM), directly influencing the treatment and prognosis. Here, we investigated the associations between 6025 common single-nucleotide polymorphisms (SNPs) in 77 glutamine metabolic pathway genes with CM-specific survival (CMSS) using genotyping datasets from two published genome-wide association studies (GWASs). In the single-locus analysis, 76 SNPs were found to be significantly associated with CMSS (P < .050, false-positive report probability < 0.2 and Bayesian false discovery probability < 0.8) in the discovery dataset, of which seven SNPs were replicated in the validation dataset and three SNPs (HAL rs17676826T > C, LGSN rs12663017T > A, and NOXRED1 rs8012548A > G) independently predicted CMSS, with an effect-allele attributed adjusted hazards ratio of 1.52 (95% confidence interval = 1.19-1.93) and P < .001, 0.68 (0.54-0.87) and P = .002 and 0.62 (0.46-0.83) and P = .002, respectively. The model including the number of unfavorable genotypes (NUGs) of these three SNPs and covariates improved the five-year CMSS prediction (P = .012) than the one with other covariates only. Further expression quantitative trait loci (eQTL) analysis found that the LGSN rs12663017 A allele was significantly associated with increased messenger RNA (mRNA) expression levels (P = 8.89 × 10 -11 ) in lymphoblastoid cell lines of the 1000 Genomes Project database. In the analysis of the genotype tissue expression (GTEx) project datasets, HAL rs17676826 C and NOXRED1 rs8012548 G alleles were significantly associated with their mRNA expression levels in sun-exposed skin of the lower leg (P = 6.62 × 10-6 and 1.37 × 10-7 , respectively) and in sun-not-exposed suprapubic skin (P < .001 and 1.43 × 10-8 , respectively). Taken together, these genetic variants of glutamine-metabolic pathway genes may be promising predictors of survival in patients with CM.
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Affiliation(s)
- Ka Chen
- Research Center for Nutrition and Food Safety, Institute of Military Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wendy Bloomer
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Christopher I. Amos
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, 03755
| | - Jeffrey E. Lee
- Department of Surgical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Xin Li
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN 46202, USA
| | - Hongmei Nan
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN 46202, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC 27710, USA
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Zhao X, Liu X, Zhang A, Chen H, Huo Q, Li W, Ye R, Chen Z, Liang L, Liu QA, Shen J, Jin X, Li W, Nygaard M, Liu X, Hou Y, Ni T, Bolund L, Gottschalk W, Tao W, Gu J, Tian XL, Yang H, Wang J, Xu X, Lutz MW, Min J, Zeng Y, Nie C. The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese. Aging (Albany NY) 2019; 10:1206-1222. [PMID: 29883365 PMCID: PMC6046244 DOI: 10.18632/aging.101461] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/30/2018] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs) have been shown to cause numerous diseases, however, their roles in human lifespan remain elusive. In this study, we investigate the association of CNVs with longevity by comparing the Han Chinese genomes of long-lived individuals from 90 to 117 years of age and the middle-aged from 30 to 65. Our data demonstrate that the numbers of CNVs, especially deletions, increase significantly in a direct correlation with longevity. We identify eleven CNVs that strongly associate with longevity; four of them locate in the chromosome bands, 7p11.2, 20q13.33, 19p12 and 8p23.3 and overlap partially with the CNVs identified in long-lived Danish or U.S. populations, while the other seven have not been reported previously. These CNV regions encode nineteen known genes, and some of which have been shown to affect aging-related phenotypes such as the shortening of telomere length (ZNF208), the risk of cancer (FOXA1, LAMA5, ZNF716), and vascular and immune-related diseases (ARHGEF10, TOR2A, SH2D3C). In addition, we found several pathways enriched in long-lived genomes, including FOXA1 and FOXA transcription factor networks involved in regulating aging or age-dependent diseases such as cancer. Thus, our study has identified longevity-associated CNV regions and their affected genes and pathways. Our results suggest that the human genome structures such as CNVs might play an important role in determining a long life in human.
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Affiliation(s)
- Xin Zhao
- BGI Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.,College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xiaomin Liu
- BGI Shenzhen, Shenzhen 518083, China.,School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | | | - Huashuai Chen
- Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham NC 27710, USA.,Center for Healthy Aging and Development Studies, Raissun Institute for Advanced Studies, National School of Development, Peking University, Beijing 10080, China.,Business School of Xiangtan University, Xiangtan 411105, China
| | - Qing Huo
- BGI Shenzhen, Shenzhen 518083, China
| | | | - Rui Ye
- BGI Shenzhen, Shenzhen 518083, China
| | | | | | | | - Juan Shen
- BGI Shenzhen, Shenzhen 518083, China
| | - Xin Jin
- BGI Shenzhen, Shenzhen 518083, China
| | - Wenwen Li
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Marianne Nygaard
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C 5000, Denmark
| | - Xiao Liu
- BGI Shenzhen, Shenzhen 518083, China
| | - Yong Hou
- BGI Shenzhen, Shenzhen 518083, China
| | - Ting Ni
- State Key Laboratory of Genetics Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Lars Bolund
- BGI Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - William Gottschalk
- Department of Neurology, Medical Center, Duke University, Durham, NC 27704, USA
| | - Wei Tao
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Jun Gu
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Xiao-Li Tian
- Department of Human Population Genetics, Human Aging Research Institute and School of Life Science Nanchang University, Nanchang 330000, China
| | | | - Jian Wang
- BGI Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI Shenzhen, Shenzhen 518083, China
| | - Michael W Lutz
- Department of Neurology, Medical Center, Duke University, Durham, NC 27704, USA
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yi Zeng
- Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham NC 27710, USA.,Center for Healthy Aging and Development Studies, Raissun Institute for Advanced Studies, National School of Development, Peking University, Beijing 10080, China
| | - Chao Nie
- BGI Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
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Hartman ML, Sztiller-Sikorska M, Czyz M. Whole-exome sequencing reveals novel genetic variants associated with diverse phenotypes of melanoma cells. Mol Carcinog 2019; 58:588-602. [DOI: 10.1002/mc.22953] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Mariusz L. Hartman
- Department of Molecular Biology of Cancer; Medical University of Lodz; Lodz Poland
| | | | - Malgorzata Czyz
- Department of Molecular Biology of Cancer; Medical University of Lodz; Lodz Poland
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Dorasamy MS, Ab A, Nellore K, Wong PF. Synergistic inhibition of melanoma xenografts by Brequinar sodium and Doxorubicin. Biomed Pharmacother 2018; 110:29-36. [PMID: 30458345 DOI: 10.1016/j.biopha.2018.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 10/27/2022] Open
Abstract
Malignant melanoma continues to be a fatal disease for which novel and long-term curative breakthroughs are desired. One such innovative idea would be to assess combination therapeutic treatments - by way of combining two potentially effective and very different therapy. Previously, we have shown that DHODH inhibitors, A771726 and Brequinar sodium (BQR) induced cell growth impairment in melanoma cells. Similar results were seen with DHODH RNA interference (shRNA). In the present study, we showed that combination of BQR with doxorubicin resulted in synergistic and additive cell growth inhibition in these cells. In addition, in vivo studies with this combination of drugs demonstrated an almost 90% tumor regression in nude mice bearing melanoma tumors. Cell cycle regulatory proteins, cyclin B1 and its binding partner pcdc-2 and p21 were significantly downregulated and upregulated respectively following the combined treatment. Given that we have observed synergistic effects with BQR and doxorubicin, both in vitro and in vivo, these drugs potentially represent a new combination in the targeted therapy of melanoma.
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Affiliation(s)
- Mathura Subangari Dorasamy
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, 50603, Malaysia; Aurigene Discovery Technologies, IPPP, University Malaya, Kuala Lumpur, 50603, Malaysia
| | - Aravind Ab
- Aurigene Discovery Technologies Limited, Electronic City, Bangalore, 560100, Karnataka, India
| | - Kavitha Nellore
- Aurigene Discovery Technologies Limited, Electronic City, Bangalore, 560100, Karnataka, India
| | - Pooi-Fong Wong
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, 50603, Malaysia.
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