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Gao C, Fan X, Liu Y, Han Y, Liu S, Li H, Zhang Q, Wang Y, Xue F. Comprehensive Analysis Reveals the Potential Roles of CDKN3 in Pancancer and Verification in Endometrial Cancer. Int J Gen Med 2023; 16:5817-5839. [PMID: 38106976 PMCID: PMC10723185 DOI: 10.2147/ijgm.s438479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
Background Cyclin-dependent kinase inhibitor 3 (CDKN3) has been studied in many cancers. However, the comprehensive and systematic pancancer analysis of CDKN3 genes is still lacking. Methods Data were downloaded from online databases. R was used for analysis of the differential expression and gene alteration of CDKN3 and of the associations between CDKN3 expression and survival, signaling pathways, and drug sensitivity. Clinical samples and in vitro experiments were selected for verification. Results CDKN3 expression was higher in most types of cancers, and this phenotype was significantly correlated with poor survival. CDKN3 showed gene alterations and copy number alterations in many cancers and associated with some immune-related pathways and factors. Drug sensitivity analysis elucidated that CDKN3 could be a useful marker for therapy selection. Clinical samples elucidated CDKN3 expressed high in endometrial cancer tissue. In vitro studies showed that CDKN3 induced pro-tumor effect in immune environment and facilitated endometrial cancer cell proliferation and G1/S phase transition. Conclusion CDKN3 has been shown to be highly expressed in most types of cancers and promoted cancer cell progression. CDKN3 may serve as a novel marker in clinical diagnosis, treatment, and prognosis prediction in future.
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Affiliation(s)
- Chao Gao
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Xiangqin Fan
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Department of Obstetrics and Gynecology, Zaozhuang Municipal Hospital, Shandong, People’s Republic of China
| | - Yanyan Liu
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Yanyan Han
- Department of Pathology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, People’s Republic of China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, People’s Republic of China
| | - Shiqi Liu
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Huanrong Li
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Qiaoling Zhang
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Yingmei Wang
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Fengxia Xue
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
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2
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Chen B, Dong L, Zhang J, Hao Y, Chi W, Song D. Exploring shared pathways and the shared biomarker ERRFI1 in Obstructive sleep apnoea and atherosclerosis using integrated bioinformatics analysis. Sci Rep 2023; 13:15103. [PMID: 37699925 PMCID: PMC10497545 DOI: 10.1038/s41598-023-42184-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023] Open
Abstract
Obstructive sleep apnea (OSA) is an upper airway disorder occurring during sleep and is associated with atherosclerosis (AS). AS is a cardiovascular disease caused by environmental and genetic factors, with a high global mortality rate. This study investigated common pathways and potential biomarkers of OSA and AS. Microarray data were downloaded from the Gene Expression Omnibus (GEO) database and used to screen for differentially expressed genes (DEGs) in the OSA and AS datasets. A weighted gene co-expression network analysis (WGCNA) was used to identify the co-expression modules of OSA and AS. The least absolute shrinkage and selection operators (LASSO) were used to determine critical biomarkers. Immune cell infiltration analysis was used to investigate the correlation between immune cell infiltration and common biomarkers of OSA and AS. Results revealed that differentially expressed genes may be involved in inflammatory processes, chemokine signaling pathways, and molecular changes in cell adhesion. ERBB receptor feedback inhibitor 1 (ERRFI1) was the best-shared biomarker for OSA and AS. Immune infiltration analysis showed that ERRFI1 expression was correlated with immune cell changes. Changes in immune pathways, inflammatory processes, and cell adhesion molecules may underlie the pathogenesis of both diseases, and ERRFI1 may be a potential diagnostic marker for patients with OSA and AS.
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Affiliation(s)
- Bowen Chen
- Clinical Biobank, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Liping Dong
- Clinical Biobank, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jihua Zhang
- Department of Otolaryngology, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ying Hao
- Clinical Biobank, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Weiwei Chi
- Clinical Biobank, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Dongmei Song
- Clinical Biobank, The First Hospital of Hebei Medical University, Shijiazhuang, China.
- Department of Otolaryngology, The First Hospital of Hebei Medical University, Shijiazhuang, China.
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3
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Ye H, Wang R, Wei J, Wang Y, Wang L, Zhang X. HADH may be the target molecule of early vascular endothelial impairment in T2DM. Front Cardiovasc Med 2022; 9:963916. [PMID: 36035955 PMCID: PMC9399638 DOI: 10.3389/fcvm.2022.963916] [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: 06/08/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) will significantly increase the risk of atherosclerosis (AS). Vascular endothelial cell dysfunction (VECD) is the foundation of AS. Early identification and intervention of VECD caused by T2DM can help us effectively delay or even suppress the occurrence of AS. Methods We downloaded the gene expression profiles from the Gene Expression Omnibus (GEO). The differential expression genes (DEGs) were identified in R software and weighted gene co-expression network analysis (WGCNA) was performed to further screen the target genes. In addition, we used the receiver operating characteristic curve (ROC curve) to verify the diagnostic efficiency of target genes. Finally, target genes were validated by quantitative polymerase chain reaction (qPCR). Results Four target genes (CLUH, COG4, HADH, and MPZL2) were discovered in early vascular endothelial impairment caused by T2DM through differential expression analysis and WGCNA. The ROC curve of target genes showed that HADH had the best diagnostic efficacy in VECD and AS. qPCR showed that the mRNA level expression of HADH and MPZL2 were decreased in human coronary artery endothelial cells (HCAECs) treated with high glucose and palmitic acid. Conclusion HADH may be the target gene in early VECD caused by T2DM.
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Affiliation(s)
- Haowen Ye
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Ruxin Wang
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jinjing Wei
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Ying Wang
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Lihong Wang
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Jinan University, Guangzhou, China
- *Correspondence: Lihong Wang
| | - Xiaofang Zhang
- Department Clinical Experimental Center, First Affiliated Hospital of Jinan University, Guangzhou, China
- Xiaofang Zhang
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4
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Wang K, Liu Y, Lu G, Xiao J, Huang J, Lei L, Peng J, Li Y, Wei S. A functional methylation signature to predict the prognosis of Chinese lung adenocarcinoma based on TCGA. Cancer Med 2021; 11:281-294. [PMID: 34854250 PMCID: PMC8704183 DOI: 10.1002/cam4.4431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 01/16/2023] Open
Abstract
Background Lung cancer is the leading cause of cancer morbidity and mortality worldwide, however, the individualized treatment is still unsatisfactory. DNA methylation can affect gene regulation and may be one of the most valuable biomarkers in predicting the prognosis of lung adenocarcinoma. This study was aimed to identify methylation CpG sites that may be used to predict lung adenocarcinoma prognosis. Methods The Cancer Genome Atlas (TCGA) database was used to detect methylation CpG sites associated with lung adenocarcinoma prognosis and construct a methylation signature model. Then, a Chinese cohort was carried out to estimate the association between methylation and lung adenocarcinoma prognosis. Biological function studies, including demethylation treatment, cell proliferative capacity, and gene expression changes in lung adenocarcinoma cell lines, were further performed. Results In the TCGA set, three methylation CpG sites were selected that were associated with lung adenocarcinoma prognosis (cg14517217, cg15386964, and cg18878992). The risk of mortality was increased in lung adenocarcinoma patients with the gradual increase level of methylation signature based on three methylation sites levels (HR = 45.30, 95% CI = 26.69–66.83; p < 0.001). The C‐statistic value increased to 0.77 when age, gender, and other clinical variables were added to the signature to prediction model. A similar situation was confirmed in Chinese lung adenocarcinoma cohort. In the biological function studies, the proliferative capacity of cell lines was inhibited when the cells were demethylated with 5‐aza‐2'‐deoxycytidine (5‐aza‐2dC). The mRNA and protein expression levels of SEPT9 and HIST1H2BH (cg14517217 and cg15386964) were downregulated with different concentrations of 5‐aza‐2dC treatment, while cg18878992 showed the opposite result. Conclusion This study is the first to develop a three‐CpG‐based model for lung adenocarcinoma, which is a practical and useful tool for prognostic prediction that has been validated in a Chinese population.
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Affiliation(s)
- Ke Wang
- Medical College, Hubei University of Arts and Science, Xiangyang, Hubei, China.,Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ying Liu
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guanzhong Lu
- Medical College, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Jinrong Xiao
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiao Huang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lin Lei
- Department of Cancer Control, Shenzhen Center for Chronic Disease Control, Shenzhen, Guangdong, China
| | - Ji Peng
- Department of Cancer Control, Shenzhen Center for Chronic Disease Control, Shenzhen, Guangdong, China
| | - Yangkai Li
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Sheng Wei
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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5
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Liang W, He X, Bi J, Hu T, Sun Y. Role of reactive oxygen species in tumors based on the 'seed and soil' theory: A complex interaction (Review). Oncol Rep 2021; 46:208. [PMID: 34328200 PMCID: PMC8329912 DOI: 10.3892/or.2021.8159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
Tumor microenvironment (TME) can serve as the 'soil' for the growth and survival of tumor cells and function synergically with tumor cells to mediate tumor progression and therapeutic resistance. Reactive oxygen species (ROS) is somewhat of a double‑edged sword for tumors. Accumulating evidence has reported that regulating ROS levels can serve an anti‑tumor role in the TME, including the promotion of cancer cell apoptosis, inhibition of angiogenesis, preventing immune escape, manipulating tumor metabolic reorganization and improving drug resistance. In the present review, the potential role of ROS in anti‑tumor therapy was summarized, including the possibility of directly or indirectly targeting the TME.
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Affiliation(s)
- Wei Liang
- Department of Radiation Oncology, Hebei Province Cangzhou Hospital of Integrated Traditional and Western Medicine, Affiliated Hospital of Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Xinying He
- Department of Radiation Oncology, Hebei Province Cangzhou Hospital of Integrated Traditional and Western Medicine, Affiliated Hospital of Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Jianqiang Bi
- Department of Radiation Oncology, Hebei Province Cangzhou Hospital of Integrated Traditional and Western Medicine, Affiliated Hospital of Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Tingting Hu
- Department of Radiation Oncology, Hebei Province Cangzhou Hospital of Integrated Traditional and Western Medicine, Affiliated Hospital of Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
| | - Yunchuan Sun
- Department of Radiation Oncology, Hebei Province Cangzhou Hospital of Integrated Traditional and Western Medicine, Affiliated Hospital of Hebei Medical University, Cangzhou, Hebei 061000, P.R. China
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6
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Jamin SP, Hikmet F, Mathieu R, Jégou B, Lindskog C, Chalmel F, Primig M. Combined RNA/tissue profiling identifies novel Cancer/testis genes. Mol Oncol 2021; 15:3003-3023. [PMID: 33426787 PMCID: PMC8564638 DOI: 10.1002/1878-0261.12900] [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: 07/20/2020] [Revised: 11/19/2020] [Accepted: 12/24/2020] [Indexed: 11/14/2022] Open
Abstract
Cancer/Testis (CT) genes are induced in germ cells, repressed in somatic cells, and derepressed in somatic tumors, where these genes can contribute to cancer progression. CT gene identification requires data obtained using standardized protocols and technologies. This is a challenge because data for germ cells, gonads, normal somatic tissues, and a wide range of cancer samples stem from multiple sources and were generated over substantial periods of time. We carried out a GeneChip‐based RNA profiling analysis using our own data for testis and enriched germ cells, data for somatic cancers from the Expression Project for Oncology, and data for normal somatic tissues from the Gene Omnibus Repository. We identified 478 candidate loci that include known CT genes, numerous genes associated with oncogenic processes, and novel candidates that are not referenced in the Cancer/Testis Database (www.cta.lncc.br). We complemented RNA expression data at the protein level for SPESP1, GALNTL5, PDCL2, and C11orf42 using cancer tissue microarrays covering malignant tumors of breast, uterus, thyroid, and kidney, as well as published RNA profiling and immunohistochemical data provided by the Human Protein Atlas (www.proteinatlas.org). We report that combined RNA/tissue profiling identifies novel CT genes that may be of clinical interest as therapeutical targets or biomarkers. Our findings also highlight the challenges of detecting truly germ cell‐specific mRNAs and the proteins they encode in highly heterogenous testicular, somatic, and tumor tissues.
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Affiliation(s)
- Soazik P Jamin
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
| | - Feria Hikmet
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Sweden
| | - Romain Mathieu
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France.,Department of Urology, University Hospital, Rennes, France
| | - Bernard Jégou
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Sweden
| | - Frédéric Chalmel
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
| | - Michael Primig
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
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7
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Pecyna P, Wargula J, Murias M, Kucinska M. More Than Resveratrol: New Insights into Stilbene-Based Compounds. Biomolecules 2020; 10:E1111. [PMID: 32726968 PMCID: PMC7465418 DOI: 10.3390/biom10081111] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
The concept of a scaffold concerns many aspects at different steps on the drug development path. In medicinal chemistry, the choice of relevant "drug-likeness" scaffold is a starting point for the design of the structure dedicated to specific molecular targets. For many years, the chemical uniqueness of the stilbene structure has inspired scientists from different fields such as chemistry, biology, pharmacy, and medicine. In this review, we present the outstanding potential of the stilbene-based derivatives. Naturally occurring stilbenes, together with powerful synthetic chemistry possibilities, may offer an excellent approach for discovering new structures and identifying their therapeutic targets. With the development of scientific tools, sophisticated equipment, and a better understanding of the disease pathogenesis at the molecular level, the stilbene scaffold has moved innovation in science. This paper mainly focuses on the stilbene-based compounds beyond resveratrol, which are particularly attractive due to their biological activity. Given the "fresh outlook" about different stilbene-based compounds starting from stilbenoids with particular regard to isorhapontigenin and methoxy- and hydroxyl- analogues, the update about the combretastatins, and the very often overlooked and underestimated benzanilide analogues, we present a new story about this remarkable structure.
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Affiliation(s)
- Paulina Pecyna
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences, Swiecickiego 4 Street, 60-781 Poznan, Poland;
| | - Joanna Wargula
- Department of Organic Chemistry, University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznan, Poland;
| | - Marek Murias
- Department of Toxicology, University of Medical Sciences, Dojazd 30 Street, 60-631 Poznan, Poland;
| | - Malgorzata Kucinska
- Department of Toxicology, University of Medical Sciences, Dojazd 30 Street, 60-631 Poznan, Poland;
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8
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Abstract
The concept of a scaffold concerns many aspects at different steps on the drug development path. In medicinal chemistry, the choice of relevant "drug-likeness" scaffold is a starting point for the design of the structure dedicated to specific molecular targets. For many years, the chemical uniqueness of the stilbene structure has inspired scientists from different fields such as chemistry, biology, pharmacy, and medicine. In this review, we present the outstanding potential of the stilbene-based derivatives. Naturally occurring stilbenes, together with powerful synthetic chemistry possibilities, may offer an excellent approach for discovering new structures and identifying their therapeutic targets. With the development of scientific tools, sophisticated equipment, and a better understanding of the disease pathogenesis at the molecular level, the stilbene scaffold has moved innovation in science. This paper mainly focuses on the stilbene-based compounds beyond resveratrol, which are particularly attractive due to their biological activity. Given the "fresh outlook" about different stilbene-based compounds starting from stilbenoids with particular regard to isorhapontigenin and methoxy- and hydroxyl- analogues, the update about the combretastatins, and the very often overlooked and underestimated benzanilide analogues, we present a new story about this remarkable structure.
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9
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Cardinale CJ, March ME, Lin X, Liu Y, Spruce LA, Bradfield JP, Wei Z, Seeholzer SH, Grant SFA, Hakonarson H. Regulation of Janus Kinase 2 by an Inflammatory Bowel Disease Causal Non-coding Single Nucleotide Polymorphism. J Crohns Colitis 2020; 14:646-653. [PMID: 32271392 DOI: 10.1093/ecco-jcc/jjz213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Among the >240 genetic loci described to date which confer susceptibility to inflammatory bowel disease, a small subset have been fine-mapped to an individual, non-coding single nucleotide polymorphism [SNP]. To illustrate a model mechanism by which a presumed-causal non-coding SNP can function, we analysed rs1887428, located in the promoter region of the Janus kinase 2 [JAK2] gene. METHODS We utilized comparative affinity purification-mass spectrometry, DNA-protein binding assays, CRISPR/Cas9 genome editing, transcriptome sequencing and methylome quantitative trait locus methods to characterize the role of this SNP. RESULTS We determined that the risk allele of rs1887428 is bound by the transcription factor [TF] RBPJ, while the protective allele is bound by the homeobox TF CUX1. While rs188748 only has a very modest influence on JAK2 expression, this effect was amplified downstream through the expression of pathway member STAT5B and epigenetic modification of the JAK2 locus. CONCLUSION Despite the absence of a consensus TF-binding motif or expression quantitative trait locus, we have used improved methods to characterize a putatively causal SNP to yield insight into inflammatory bowel disease mechanisms. PODCAST This article has an associated podcast which can be accessed at https://academic.oup.com/ecco-jcc/pages/podcast.
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Affiliation(s)
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiang Lin
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lynn A Spruce
- Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Steven H Seeholzer
- Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Struan F A Grant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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10
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Induced pluripotency and spontaneous reversal of cellular aging in supercentenarian donor cells. Biochem Biophys Res Commun 2020; 525:563-569. [DOI: 10.1016/j.bbrc.2020.02.092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/12/2020] [Indexed: 12/14/2022]
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11
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Jing C, Wang T, Ma R, Cao H, Wang Z, Liu S, Chen D, Zhang J, Wu Y, Zhang Y, Wu J, Feng J. New genetic variations discovered in KRAS wild-type cetuximab resistant chinese colorectal cancer patients. Mol Carcinog 2020; 59:478-491. [PMID: 32141150 DOI: 10.1002/mc.23172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022]
Abstract
To perform a comprehensive genomic analysis of colorectal cancer (CRC) tumor to detect genetic variants and identify novel resistant mutations associated with cetuximab-resistance in CRC patients. A retrospective study was performed using whole exome sequencing (WES) to identify common genetic factors from 22 cetuximab-sensitive and 10 cetuximab-resistant patients. In all 10 cetuximab-resistant patients, we discovered there are 37 significantly mutated genes (SMGs). CYP4A11 was the most frequently mutated gene in cetuximab-resistant patients. BCAS1 and GOLGA6L1 were found to be among the second group of frequently mutated genes with a frequency of 60%. After cosine similarity analysis, three mutational signatures (signature a, b, and c) were found in all CRC tumors, similar to signature 1, 5, and 6 in COSMIC, respectively. Gene ontology analysis was performed on SMGs and found 12 enriched GO terms. Four genes are enriched in six specific Kyoto Encyclopedia of Genes and Genomes pathway groups, including the metabolism of xenobiotics by cytochrome P450, steroid hormone biosynthesis, retinol metabolism, and drug metabolism. Our data supports a network composed of SMGs and cellular signaling pathways that have been positively linked to the mechanisms of cetuximab resistance. These involve DNA damage repair, angiogenesis, invasion, drug metabolism, and the CRC tumor microenvironment. There is a SMG, OR9G1 correlated with survival rates of KRAS wild-type colon adenocarcinoma patients. These findings support further investigation using WES in a prospective clinical study of cetuximab resistance CRC, to further identify, confirm, and extend the clinical significance of these and other potentially important new candidate predictive biomarkers of cetuximab response.
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Affiliation(s)
- Changwen Jing
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Ting Wang
- Department of Cell Biology, Nanjing Medical University, Nanjing, China
| | - Rong Ma
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Haixia Cao
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Zhuo Wang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Siwen Liu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Dan Chen
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Junying Zhang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Department of Chemotherapy, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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The Effect of 3'-Hydroxy-3,4,5,4'-Tetramethoxy -stilbene, the Metabolite of the Resveratrol Analogue DMU-212, on the Motility and Proliferation of Ovarian Cancer Cells. Int J Mol Sci 2020; 21:ijms21031100. [PMID: 32046103 PMCID: PMC7037107 DOI: 10.3390/ijms21031100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/24/2022] Open
Abstract
Targeting tumor cell motility and proliferation is an extremely important challenge in the prevention of metastasis and improving the effectiveness of cancer treatment. We recently published data revealing that DMU-214, the metabolite of firmly cytotoxic resveratrol analogue DMU-212, exerted significantly higher biological activity than the parent compound in ovarian cancer cells. The aim of the present study was to assess the molecular mechanism of the potential anti-migration and anti-proliferative effect of DMU-214 in ovarian cancer cell line SKOV-3. We showed that DMU-214 reduced the migratory capacity of SKOV-3 cells. The microarray analysis indicated ontology groups of genes involved in processes of negative regulation of cell motility and proliferation. Furthermore, we found DMU-214 triggered changes in expression of several migration- and proliferation-related genes (SMAD7, THBS1, IGFBP3, KLF4, Il6, ILA, SOX4, IL15, SRF, RGCC, GPR56) and proteins (GPR56, RGCC, SRF, SMAD7, THBS1), which have been shown to interact to each other to reduce cell proliferation and motility. Our study showed for the first time that DMU-214 displayed anti-migratory and anti-proliferative activity in SKOV-3 ovarian cancer cells. On the basis of whole transcriptome analysis of these cells, we provide new insight into the role of DMU-214 in inhibition of processes related to metastasis.
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Singh R, Bassett E, Chakravarti A, Parthun MR. Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function. Nucleic Acids Res 2019; 46:8665-8678. [PMID: 30165676 PMCID: PMC6158624 DOI: 10.1093/nar/gky768] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/24/2018] [Indexed: 12/11/2022] Open
Abstract
Replication-dependent histones are expressed in a cell cycle regulated manner and supply the histones necessary to support DNA replication. In mammals, the replication-dependent histones are encoded by a family of genes that are located in several clusters. In humans, these include 16 genes for histone H2A, 22 genes for histone H2B, 14 genes for histone H3, 14 genes for histone H4 and 6 genes for histone H1. While the proteins encoded by these genes are highly similar, they are not identical. For many years, these genes were thought to encode functionally equivalent histone proteins. However, several lines of evidence have emerged that suggest that the replication-dependent histone genes can have specific functions and may constitute a novel layer of chromatin regulation. This Survey and Summary reviews the literature on replication-dependent histone isoforms and discusses potential mechanisms by which the small variations in primary sequence between the isoforms can alter chromatin function. In addition, we summarize the wealth of data implicating altered regulation of histone isoform expression in cancer.
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Affiliation(s)
- Rajbir Singh
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Emily Bassett
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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Elkahloun AG, Rodriguez Y, Alaiyed S, Wenzel E, Saavedra JM. Telmisartan Protects a Microglia Cell Line from LPS Injury Beyond AT1 Receptor Blockade or PPARγ Activation. Mol Neurobiol 2018; 56:3193-3210. [PMID: 30105672 DOI: 10.1007/s12035-018-1300-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/02/2018] [Indexed: 01/12/2023]
Abstract
The Angiotensin II Receptor Blocker (ARB) Telmisartan reduces inflammation through Angiotensin II AT1 receptor blockade and peroxisome proliferator-activated receptor gamma (PPARγ) activation. However, in a mouse microglia-like BV2 cell line, imitating primary microglia responses with high fidelity and devoid of AT1 receptor gene expression or PPARγ activation, Telmisartan reduced gene expression of pro-injury factors, enhanced that of anti-inflammatory genes, and prevented LPS-induced increase in inflammatory markers. Using global gene expression profiling and pathways analysis, we revealed that Telmisartan normalized the expression of hundreds of genes upregulated by LPS and linked with inflammation, apoptosis and neurodegenerative disorders, while downregulating the expression of genes associated with oncological, neurodegenerative and viral diseases. The PPARγ full agonist Pioglitazone had no neuroprotective effects. Surprisingly, the PPARγ antagonists GW9662 and T0070907 were neuroprotective and enhanced Telmisartan effects. GW9226 alone significantly reduced LPS toxic effects and enhanced Telmisartan neuroprotection, including downregulation of pro-inflammatory TLR2 gene expression. Telmisartan and GW9662 effects on LPS injury negatively correlated with pro-inflammatory factors and upstream regulators, including TLR2, and positively with known neuroprotective factors and upstream regulators. Gene Set Enrichment Analysis (GSEA) of the Telmisartan and GW9662 data revealed negative correlations with sets of genes associated with neurodegenerative and metabolic disorders and toxic treatments in cultured systems, while demonstrating positive correlations with gene sets associated with neuroprotection and kinase inhibition. Our results strongly suggest that novel neuroprotective effects of Telmisartan and GW9662, beyond AT1 receptor blockade or PPARγ activation, include downregulation of the TLR2 signaling pathway, findings that may have translational relevance.
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Affiliation(s)
- Abdel G Elkahloun
- Microarray Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 50 South Dr, MSC 4435, Bethesda, MD, 20892-4435, USA
| | - Yara Rodriguez
- Laboratory of Neuroprotection, Department of Pharmacology and Physiology, Georgetown University Medical Center, SE402 Med/Dent, 3900 Reservoir Road, Washington, DC, 20057, USA
| | - Seham Alaiyed
- Laboratory of Neuroprotection, Department of Pharmacology and Physiology, Georgetown University Medical Center, SE402 Med/Dent, 3900 Reservoir Road, Washington, DC, 20057, USA
| | - Erin Wenzel
- Laboratory of Neuroprotection, Department of Pharmacology and Physiology, Georgetown University Medical Center, SE402 Med/Dent, 3900 Reservoir Road, Washington, DC, 20057, USA
| | - Juan M Saavedra
- Laboratory of Neuroprotection, Department of Pharmacology and Physiology, Georgetown University Medical Center, SE402 Med/Dent, 3900 Reservoir Road, Washington, DC, 20057, USA.
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Zhao J, Cheng W, He X, Liu Y, Li J, Sun J, Li J, Wang F, Gao Y. Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network. Onco Targets Ther 2018; 11:3129-3140. [PMID: 29872324 PMCID: PMC5975616 DOI: 10.2147/ott.s151121] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Novel diagnostic predictors and drug targets are needed for LUAD (lung adenocarcinoma). We aimed to build a specific SVM (support vector machine) classifier for diagnosis of LUAD and identify molecular markers with prognostic value for LUAD. Methods The expression differences of miRNAs, lncRNAs and mRNAs between LUAD and normal samples were compared using data from TCGA (The Cancer Genome Atlas) database. A LUAD related miRNA-lncRNA-mRNA network was constructed, based on which feature genes were selected for the construction of LUAD specific SVM classifier. The robustness and transferability of SVM classifier were validated using gene expression profile datasets GSE43458 and GSE10072. Prognostic markers were identified from the network. A set of LUAD-related differentially expressed miRNAs, lncRNAs and miRNAs were identified and a LUAD related miRNA-lncRNA-mRNA network was obtained. The LUAD specific SVM classifier constructed on the basis of the network was robust and efficient for classification of samples from TCGA dataset and two independent validation datasets. Results Eight RNAs with prognostic value were identified, including hsa-miR-96, hsa-miR-204, PGM5P2 (phosphoglucomutase 5 pseudogene 2), SFTA1P (surfactant associated 1), RGS20 (regulator of G protein signaling 20), RGS9BP (RGS9-binding protein), FGB (fibrinogen beta chain) and INA (alpha-internexin). Among them, RGS20 and INA were regulated by hsa-miR-96. RGS20 was also regulated by hsa-miR-204, which was a potential target of SFTA1P. Conclusion The LUAD specific SVM classifier may serve as a novel diagnostic predictor. hsa-miR-96, hsa-miR-204, PGM5P2, SFTA1P, RGS20, RGS9BP, FGB and INA may serve as prognostic markers in clinical practice.
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Affiliation(s)
- Jingming Zhao
- Department of Respiratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Wei Cheng
- Department of Respiratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Xigang He
- Department of Respiratory Medicine, People's Hospital of Rizhao Lanshan, Lanshan District, Rizhao, P.R. China
| | - Yanli Liu
- Department of Respiratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Ji Li
- Department of Pharmacy, Qilu Hospital of Shandong University (Qingdao), Qingdao, P.R. China
| | - Jiaxing Sun
- Department of Respiratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Jinfeng Li
- Department of Respiratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Fangfang Wang
- Department of Respiratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Yufang Gao
- Department of President's Office, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
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Riemer D, Mandaviya B, Schilling W, Götz AC, Kühl T, Finger M, Das S. CO2-Catalyzed Oxidation of Benzylic and Allylic Alcohols with DMSO. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04390] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Daniel Riemer
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Bhavdip Mandaviya
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Waldemar Schilling
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Anne Charlotte Götz
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Torben Kühl
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Markus Finger
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Shoubhik Das
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
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Anwar T, Sen B, Aggarwal S, Nath R, Pathak N, Katoch A, Aiyaz M, Trehanpati N, Khosla S, Ramakrishna G. Differentially regulated gene expression in quiescence versus senescence and identification of ARID5A as a quiescence associated marker. J Cell Physiol 2017; 233:3695-3712. [PMID: 29044508 DOI: 10.1002/jcp.26227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 09/29/2017] [Indexed: 01/20/2023]
Abstract
In multicellular organisms majority of the cells remain in a non-dividing states of either quiescence (reversible) or senescence (irreversible). In the present study, gene expression signatures unique to quiescence and senescence were identified using microarray in osteosarcoma cell line, U2OS. It was noted that certain genes and pathways like NOD pathway was shared by both the growth arrest conditions. A major highlight of the present study was increased expression of number of chemokines and cytokines in both quiescence and senescence. While senescence-associated secretory phenotype (SASP) is well known, the quiescence-associated secretory phenotype (QASP) is relatively unknown and appeared novel in this study. ARID5A, a subunit of SWI/SNF complex was identified as a quiescence associated gene. The endogenous expression of ARID5A increased during serum starved condition of quiescence. Overexpression of ARID5A resulted in more number of cells in G0/G1 phase of cell cycle. Further ARID5A overexpressing cells when subjected to serum starvation showed a pronounced secretory phenotype. Overall, the present work has identified gene expression signatures which can distinguish quiescence from senescence.
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Affiliation(s)
- Tarique Anwar
- Institute of Liver and Biliary Sciences, Vasant Kunj, Delhi, India.,Cedars-Sinai Advanced Health Sciences Pavilion, Los Angeles, California, USA
| | - Bijoya Sen
- Institute of Liver and Biliary Sciences, Vasant Kunj, Delhi, India
| | - Savera Aggarwal
- Institute of Liver and Biliary Sciences, Vasant Kunj, Delhi, India
| | - Rhisita Nath
- Institute of Liver and Biliary Sciences, Vasant Kunj, Delhi, India
| | - Niteen Pathak
- Centre for DNA Fingerprinting and Diagnostics, Laboratory Block, Nampally 2, Hyderabad, Telangana, India
| | | | | | | | - Sanjeev Khosla
- Centre for DNA Fingerprinting and Diagnostics, Laboratory Block, Nampally 2, Hyderabad, Telangana, India
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Klupczynska A, Sulej-Suchomska AM, Piotrowska-Kempisty H, Wierzchowski M, Jodynis-Liebert J, Kokot ZJ. Development and validation of HPLC-MS/MS procedure for determination of 3,4,4',5-tetra-methoxystilbene (DMU-212) and its metabolites in ovarian cancer cells and culture medium. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1060:30-35. [PMID: 28582662 DOI: 10.1016/j.jchromb.2017.05.015] [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: 03/14/2017] [Revised: 05/08/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
Abstract
The synthetic resveratrol analogue DMU-212 (3,4,4',5-tetramethoxystilbene) has been shown to possess stronger anticancer activity than resveratrol in a variety of tumour cells. To date, there has been no appropriate procedure that would ensure a reliable data about levels of metabolic products of DMU-212 in cancer cell lines. The purpose of this study was to develop a new procedure for determination of DMU-212 and its three metabolites (DMU-214, DMU-281, DMU-291) in cell lines. Analyses were performed using an HPLC system coupled with a triple quadrupole mass spectrometer operating in multiple reaction monitoring mode. Separation was conducted using a C18 column at a flow rate 800μL/min with a mobile phase consisting of 5mM ammonium acetate with 0.1% formic acid (solvent A) and acetonitrile (solvent B). The new methodology is fast, simple and has excellent specificity. Moreover, it showed good linearity in two matrices - cell lysates and culture media. Accuracy values for analytes evaluated at different concentration levels ranged from 0.43 to 18% (%bias). The intra-day and inter-day precision, expressed as CV, was in a range 0.49-5.5% and 0.83-13%, respectively. The validated procedure was successfully applied to quantify the resveratrol analogues in the human ovarian cancer cell line SKOV3.
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Affiliation(s)
- Agnieszka Klupczynska
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Str., 60-780 Poznan, Poland
| | - Anna Maria Sulej-Suchomska
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Str., 60-780 Poznan, Poland
| | - Hanna Piotrowska-Kempisty
- Department of Toxicology, Poznan University of Medical Sciences, 30 Dojazd Str., 60-631 Poznan, Poland
| | - Marcin Wierzchowski
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, 6 Grunwaldzka Str., 60-780 Poznan, Poland
| | - Jadwiga Jodynis-Liebert
- Department of Toxicology, Poznan University of Medical Sciences, 30 Dojazd Str., 60-631 Poznan, Poland
| | - Zenon J Kokot
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Str., 60-780 Poznan, Poland.
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Ung C, Sanchez AV, Shen L, Davoudi S, Ahmadi T, Navarro-Gomez D, Chen CJ, Hancock H, Penman A, Hoadley S, Consugar M, Restrepo C, Shah VA, Arboleda-Velasquez JF, Sobrin L, Gai X, Kim LA. Whole exome sequencing identification of novel candidate genes in patients with proliferative diabetic retinopathy. Vision Res 2017; 139:168-176. [PMID: 28431867 DOI: 10.1016/j.visres.2017.03.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 10/19/2022]
Abstract
Rare or novel gene variants in patients with proliferative diabetic retinopathy may contribute to disease development. We performed whole exome sequencing (WES) on patients at the phenotypic extremes of diabetic retinal complications: 57 patients diagnosed with proliferative diabetic retinopathy (PDR) as cases and 13 patients with no diabetic retinopathy despite at least 10years of type 2 diabetes as controls. Thirty-one out of the 57 cases and all 13 controls were from the African American Proliferative Diabetic Retinopathy Study (AA). The rest of the cases were of mixed ethnicities (ME). WES identified 721 candidate genes with rare or novel non-synonymous variants found in at least one case with PDR and not present in any controls. After filtering for genes with null alleles in greater than two cases, 28 candidate genes were identified in our ME cases and 16 genes were identified in our AA cases. Our analysis showed rare and novel variants within these genes that could contribute to the development of PDR, including rare non-synonymous variants in FAM132A, SLC5A9, ZNF600, and TMEM217. We also found previously unidentified variants in VEGFB and APOB. We found that VEGFB, VPS13B, PHF21A, NAT1, ZNF600, PKHD1L1 expression was reduced in human retinal endothelial cells (HRECs) cultured under high glucose conditions. In an exome sequence analysis of patients with PDR, we identified variants in genes that could contribute to pathogenesis. Six of these genes were further validated and found to have reduced expression in HRECs under high glucose conditions, suggestive of an important role in the development of PDR.
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Affiliation(s)
- Cindy Ung
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Angie V Sanchez
- Schepens Eye Research Institute, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Samaneh Davoudi
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Tina Ahmadi
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Daniel Navarro-Gomez
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Ching J Chen
- Department of Ophthalmology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Heather Hancock
- Department of Ophthalmology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Alan Penman
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Suzanne Hoadley
- Department of Ophthalmology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Mark Consugar
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Carlos Restrepo
- Basic Science Group, School of Medicine, CES University, Medellin, Colombia
| | - Vinay A Shah
- Department of Ophthalmology, Dean McGee Eye Institute, University of Oklahoma, OK, USA
| | - Joseph F Arboleda-Velasquez
- Schepens Eye Research Institute, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
| | - Lucia Sobrin
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA.
| | - Xiaowu Gai
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA.
| | - Leo A Kim
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA.
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