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Confocal Laser Scanning Microscopy and Fluorescence Correlation Methods for the Evaluation of Molecular Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1310:1-30. [PMID: 33834430 DOI: 10.1007/978-981-33-6064-8_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Confocal laser scanning microscopy (CLSM) and related microscopic techniques allow a unique and versatile approach to image and analyze living cells due to their specificity and high sensitivity. Among confocal related techniques, fluorescence correlation methods, such as fluorescence correlation spectroscopy (FCS) and dual-color fluorescence cross-correlation spectroscopy (FCCS), are highly sensitive biophysical methods for analyzing the complex dynamic events of molecular diffusion and interaction change in live cells as well as in solution by exploiting the characteristics of fluorescence signals. Analytical and quantitative information from FCS and FCCS coupled with fluorescence images obtained from CLSM can now be applied in convergence science such as drug delivery and nanomedicine, as well as in basic cell biology. In this chapter, a brief introduction into the physical parameters that can be obtained from FCS and FCCS is first provided. Secondly, experimental examples of the methods for evaluating the parameters is presented. Finally, two potential FCS and FCCS applications for convergence science are introduced in more detail.
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52
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Huang Q, Read M, Gold JS, Zou XP. Unraveling the identity of gastric cardiac cancer. J Dig Dis 2020; 21:674-686. [PMID: 32975049 DOI: 10.1111/1751-2980.12945] [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] [Received: 06/06/2020] [Revised: 08/11/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022]
Abstract
The classification of gastric cardiac carcinoma (GCC) is controversial. It is currently grouped with esophageal adenocarcinoma (EAC) as an adenocarcinoma of the gastroesophageal junction (GEJ). Recently, diagnostic criteria for adenocarcinoma in the GEJ were established and GCC was separated from EAC. We viewed published evidence to clarify the GCC entity for better patient management. GCC arises in the cardiac mucosa located from 3 cm below and 2 cm above the GEJ line. Compared with EAC, GCC is more like gastric cancer and affects a higher proportion of female patients, younger patients, those with a lower propensity for reflux disease, a wider histopathologic spectrum, and more complex genomic profiles. Although GCC pathogenesis mechanisms remain unknown, the two-etiology proposal is appealing: in high-risk regions, the Correa pathway with Helicobacter pylori infection, chronic inflammation, low acid and intestinal metaplasia, dysplasia and carcinoma may apply, while in low-risk regions the sequence from reflux toxin-induced mucosal injury and high acid, to intestinal metaplasia, dysplasia and carcinoma may occur. In early GCC a minimal risk of nodal metastasis argues for a role of endoscopic therapy, whereas in advanced GCC, gastric cancer staging rules and treatment strategy appear to be more appropriate than the esophageal cancer staging scheme and therapy for better prognosis stratification and treatment. In this brief review we share recent insights into the epidemiology, histopathology and genetics of GCC and hope that this will stimulate further investigations in order to improve the clinical management of patients with GCC.
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Affiliation(s)
- Qin Huang
- Department of Pathology, Nanjing Drum Tower Hospital affiliated to Nanjing University Medical School, Nanjing, Jiangsu Province, China.,Department of Pathology and Laboratory Medicine, Veterans Affairs Boston Healthcare System, Harvard Medical School/Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Matthew Read
- Department of Surgery, St Vincent's Hospital, Melbourne, Victoria, Australia
| | - Jason S Gold
- Department of Surgery, Veterans Affairs Boston Healthcare System, Harvard Medical School/Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Xiao Ping Zou
- Department of Gastroenterology, Nanjing Drum Tower Hospital affiliated to Nanjing University Medical School, Nanjing, Jiangsu Province, China
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53
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Wang L, Li C, Song Y, Yan Z. Inhibition of carnitine palmitoyl transferase 1A-induced fatty acid oxidation suppresses cell progression in gastric cancer. Arch Biochem Biophys 2020; 696:108664. [PMID: 33157102 DOI: 10.1016/j.abb.2020.108664] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/04/2020] [Accepted: 10/30/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Gastric cancer (GC) has a high rate of metastasis which thereason leading to death. Carnitine palmitoyl transferase 1a (CPT1A) has been reported to play a critical obstacle to various types of cancer progression, which is an attractive focus in anti-cancer therapy. However, the underlying molecular mechanisms of CPT1A involved in GC have not been clarified clear. METHODS To determine the expression of CPT1A in human GC tissues and cells and illustrate whether it is correlated with the clinical pathologic characteristics and prognosis in GC patients. Its roles and potential mechanisms in regulating tumor growth and invasion were evaluated by CPT1A knockdown/overexpression of GC cells in vitro. RESULTS Marked upregulation of CPT1A protein expression was observed in GC cells and tissues, which was associated with grade, pathological stage, lymph node metastasis and poor prognosis in patients with GC. CPT1A overexpression also promoted the proliferation, invasion, EMT process of GC cells. In addition, CPT1A upregulation activated GC cell fatty acid oxidation (FAO) via increasing NADP+/NADPH ratio, whereas inhibiting of FAO abolished the effects of CPT1A on GC cell proliferation and migration. CONCLUSION Our results examine that CPT1A-mediated FAO activation increases GC cell proliferation and migration, supporting that CPT1A is a useful prognostic biomarker and an attractive focus for GC.
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Affiliation(s)
- Liqiang Wang
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin Province, 130033, China
| | - Changfeng Li
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin Province, 130033, China
| | - Yumei Song
- Department of Thoracic Oncology, Tumor Hospital of Jilin Province, Changchun, Jilin Province, 130033, China
| | - ZhenKun Yan
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin Province, 130033, China.
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54
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Feng H, Jin Z, Liu K, Peng Y, Jiang S, Wang C, Hu J, Shen X, Qiu W, Cheng X, Zhao R. Identification and validation of critical alternative splicing events and splicing factors in gastric cancer progression. J Cell Mol Med 2020; 24:12667-12680. [PMID: 32939931 PMCID: PMC7686978 DOI: 10.1111/jcmm.15835] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 08/12/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
Gene expression and alternative splicing (AS) interact in complex ways to regulate biological process which is associated with cancer development. Here, by integrated analysis of gene expression and AS events, we aimed to identify the hub AS events and splicing factors relevant in gastric cancer development (GC). RNA‐seq data, clinical data and AS events of 348 GC samples were obtained from the TCGA and TCGASpliceSeq databases. Cox univariable and multivariable analyses, KEGG and GO pathway analyses were performed to identify hub AS events and splicing factor/spliceosome genes, which were further validated in 53 GCs. By bioinformatics methods, we found that gene AS event‐ and gene expression‐mediated GC progression shared the same mechanisms, such as PI3K/AKT pathway, but the involved genes were different. Though expression of 17 hub AS events were confirmed in 53 GC tissues, only 10 AS events in seven genes were identified as critical candidates related to GC progression, notably the AS events (Exon Skip) in CLSTN1 and SEC16A. Expression of these AS events in GC correlated with activation of the PI3K/AKT pathway. Genes with AS events associated with clinical parameters and prognosis were different from the genes whose mRNA levels were related to clinical parameters and prognosis. Besides, we further revealed that QKI and NOVA1 were the crucial splicing factors regulating expression of AS events in GC, but not spliceosome genes. Our integrated analysis revealed hub AS events in GC development, which might be the potential therapeutic targets for GC.
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Affiliation(s)
- Haoran Feng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of General Surgery, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhijian Jin
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kun Liu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of General Surgery, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Peng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of General Surgery, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Songyao Jiang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of General Surgery, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changgang Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of General Surgery, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiele Hu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of General Surgery, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyun Shen
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of General Surgery, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weihua Qiu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi Cheng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ren Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of General Surgery, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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55
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Zhou S, Fang J, Sun Y, Li H. Integrated Analysis of a Risk Score System Predicting Prognosis and a ceRNA Network for Differentially Expressed lncRNAs in Multiple Myeloma. Front Genet 2020; 11:934. [PMID: 33193574 PMCID: PMC7481452 DOI: 10.3389/fgene.2020.00934] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein-coding RNAs longer than 200 nucleotides. Accumulating evidence demonstrates that lncRNA is a potential biomarker for cancer diagnosis and prognosis. However, there are no prognostic biomarkers and lncRNA models for multiple myeloma (MM). Hence, it is necessary to screen novel lncRNA that can potentially participate in the initiation and progression of MM and consequently construct a risk score system for the disease. Raw microarray datasets were obtained from the Gene Expression Omnibus website. Weighted gene co-expression network analysis and principal component analysis identified 12 lncRNAs of interest. Then, univariate, least absolute shrinkage and selection operator Cox regression and multivariate Cox hazard regression analysis identified two lncRNAs (LINC00996 and LINC00525) that were formulated to construct a risk score system to predict survival. Receiver operating characteristic analysis certificated the superior performance in predicting 3-year overall survival (area under the curve = 0.829). The similar prognostic values of the two-lncRNA signature were also observed in the tested The Cancer Genome Atlas dataset. Furthermore, two other lncRNAs (LINC00324 and LINC01128) were differentially expressed between CD138+ plasma cells from normal donors and MM patients and were verified to be associated with cancer stage in the Gene Expression Omnibus dataset. A lncRNA-mediated competing endogenous RNA network, including 2 lncRNAs, 12 mitochondrial RNAs, and 103 target messenger RNAs, was constructed. In conclusion, we developed a two-lncRNA expression signature to predict the prognosis of MM and constructed a key lncRNA-based competing endogenous RNA network in MM. These lncRNAs were associated with survival and are probably involved in the occurrence and progression of MM.
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Affiliation(s)
- Sijie Zhou
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiuyuan Fang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yan Sun
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huixiang Li
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
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56
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Tanida T, Matsuda KI, Tanaka M. Novel metabolic system for lactic acid via LRPGC1/ERRγ signaling pathway. FASEB J 2020; 34:13239-13256. [PMID: 32851675 DOI: 10.1096/fj.202000492r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/25/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022]
Abstract
Lactic acid (LA) is a byproduct of glycolysis resulting from intense exercise or a metabolic defect in aerobic processes. LA metabolism is essential to prevent lactic acidosis, but the mechanism through which LA regulates its own metabolism is largely unknown. Here, we identified a LA-responsive protein, named LRPGC1, which has a distinct role from PGC1α, a key metabolic regulator, and report that LRPGC1 particularly mediates LA response to activate liver LA metabolism. Following LA stimulation, LRPGC1, but not PGC1α, translocates from the cytoplasm to the nucleus through deactivation of nuclear export signals, interacts with the nuclear receptor ERRγ, and upregulates TFAM, which ensures mitochondrial biogenesis. Knockout of PGC1 gene in HepG2 hepatocarcinoma cells decreased the LA consumption and TFAM expression, which were rescued by LRPGC1 expression, but not by PGC1α. These LRPGC1-induced effects were mediated by ERRγ, concomitantly with mitochondrial activation. The response element for LRPGC1/ERRγ signaling pathway was identified in TFAM promoter. Notably, the survival rate of a mouse model of lactic acidosis was reduced by the liver-targeted silencing of Lrpgc1, while it was significantly ameliorated by the pharmacological activation of ERRγ. These findings demonstrate LA-responsive transactivation via LRPGC1 that highlight an intrinsic molecular mechanism for LA homeostasis.
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Affiliation(s)
- Takashi Tanida
- Department of Anatomy and Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ken Ichi Matsuda
- Department of Anatomy and Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masaki Tanaka
- Department of Anatomy and Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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57
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Gallagher KM, Roderick JE, Tan SH, Tan TK, Murphy L, Yu J, Li R, O'Connor KW, Zhu J, Green MR, Sanda T, Kelliher MA. ESRRB regulates glucocorticoid gene expression in mice and patients with acute lymphoblastic leukemia. Blood Adv 2020; 4:3154-3168. [PMID: 32658986 PMCID: PMC7362368 DOI: 10.1182/bloodadvances.2020001555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/21/2020] [Indexed: 12/20/2022] Open
Abstract
Synthetic glucocorticoids (GCs), such as dexamethasone and prednisone, remain key components of therapy for patients with lymphoid malignancies. For pediatric patients with acute lymphoblastic leukemia (ALL), response to GCs remains the most reliable prognostic indicator; failure to respond to GC correlates with poor event-free survival. To uncover GC resistance mechanisms, we performed a genome-wide, survival-based short hairpin RNA screen and identified the orphan nuclear receptor estrogen-related receptor-β (ESRRB) as a critical transcription factor that cooperates with the GC receptor (GR) to mediate the GC gene expression signature in mouse and human ALL cells. Esrrb knockdown interfered with the expression of genes that were induced and repressed by GR and resulted in GC resistance in vitro and in vivo. Dexamethasone treatment stimulated ESRRB binding to estrogen-related receptor elements (ERREs) in canonical GC-regulated genes, and H3K27Ac Hi-chromatin immunoprecipitation revealed increased interactions between GR- and ERRE-containing regulatory regions in dexamethasone-treated human T-ALL cells. Furthermore, ESRRB agonists enhanced GC target gene expression and synergized with dexamethasone to induce leukemic cell death, indicating that ESRRB agonists may overcome GC resistance in ALL, and potentially, in other lymphoid malignancies.
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Affiliation(s)
- Kayleigh M Gallagher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Justine E Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, Center of Translational Medicine, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, Center of Translational Medicine, Singapore
| | - Leonard Murphy
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Kevin W O'Connor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Michael R Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, Center of Translational Medicine, Singapore
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
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58
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Kim SJ, Ju JS, Kang MH, Won JE, Kim YH, Raninga PV, Khanna KK, Győrffy B, Pack CG, Han HD, Lee HJ, Gong G, Shin Y, Mills GB, Eyun SI, Park YY. RNA-binding protein NONO contributes to cancer cell growth and confers drug resistance as a theranostic target in TNBC. Theranostics 2020; 10:7974-7992. [PMID: 32724453 PMCID: PMC7381744 DOI: 10.7150/thno.45037] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/15/2020] [Indexed: 12/22/2022] Open
Abstract
Breast cancer (BC) is one of the most common cancers in women. TNBC (Triple-negative breast cancer) has limited treatment options and still lacks viable molecular targets, leading to poor outcomes. Recently, RNA-binding proteins (RBPs) have been shown to play crucial roles in human cancers, including BC, by modulating a number of oncogenic phenotypes. This suggests that RBPs represent potential molecular targets for BC therapy. Methods: We employed genomic data to identify RBPs specifically expressed in TNBC. NONO was silenced in TNBC cell lines to examine cell growth, colony formation, invasion, and migration. Gene expression profiles in NONO-silenced cells were generated and analyzed. A high-throughput screening for NONO-targeted drugs was performed using an FDA-approved library. Results: We found that the NONO RBP is highly expressed in TNBC and is associated with poor patient outcomes. NONO binds to STAT3 mRNA, increasing STAT3 mRNA levels in TNBC. Surprisingly, NONO directly interacts with STAT3 protein increasing its stability and transcriptional activity, thus contributing to its oncogenic function. Importantly, high-throughput drug screening revealed that auranofin is a potential NONO inhibitor and inhibits cell growth in TNBC. Conclusions: NONO is an RBP upstream regulator of both STAT3 RNA and protein levels and function. It represents an important and clinically relevant promoter of growth and resistance of TNBCs. NONO is also therefore a potential therapeutic target in TNBC.
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59
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Peng Z, Guan Q, Luo J, Deng W, Liu J, Yan R, Wang W. Sophoridine exerts tumor-suppressive activities via promoting ESRRG-mediated β-catenin degradation in gastric cancer. BMC Cancer 2020; 20:582. [PMID: 32571331 PMCID: PMC7310191 DOI: 10.1186/s12885-020-07067-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
Background As a natural alkaloid product isolated from Sophora alopecuroides. L, Sophoridine reshapes gastric cancer immune microenvironment via inhibiting chemotaxis and M2 polarization of tumor-associated macrophages (TAMs). However, the exact effects and underlying mechanism of Sophoridine on gastric cancer cells remains poorly known. Methods The potential anti-tumor effects of Sophoridine on gastric cancer cell lines, including AGS and SGC7901 cells, were detected by CCK-8, EDU and colony forming assay, immunofluorescence, transwell assay, and flow cytometry. Molecular mechanisms of Sophoridine were investigated by siRNA transfection, nuclear/cytoplasmic extraction and western blot. The synergistic effects of Sophoridine with cisplatin on gastric cancer cells were further investigated in in vitro functional studies. Results Sophoridine exhibited potent tumor-suppressive activities in gastric cancer cells, including inhibition of proliferation, colony formulation, migration and invasion, as well as induction of apoptosis. In addition, we further showed that Sophoridine induced G2/M cell cycle arrest via inhibiting double-stranded DNA breaks repair and enhanced the efficacy of cisplatin in gastric cancer cells. Molecular studies further revealed that Sophoridine promoted β-catenin degradation by enhancing Estrogen-related receptor gamma (ESRRG) expression, but not depended on ubiquitination-proteasome pathway, either TRIM33-mediated (GSK3β-independent) or altered GSK3β activity, and thus exerted potent tumor-suppressive activities. Conclusion Sophoridine depends on targeting ESRRG/β-catenin pathway to exert tumor-suppressive activities in gastric cancer cells and enhances the anti-tumor effect of cisplatin. Our study provided the promising preclinical anti-tumor evidence for the potential application of Sophoridine against gastric cancer.
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Affiliation(s)
- Zhiyang Peng
- Department of Gastrointestinal Surgery in East Hospital, Renmin Hospital of Wuhan University, No. 6 Gaoxin Road, East Lake High-tech Development Zone District, Wuhan, 430205, P.R. China
| | - Qing Guan
- Department of Laboratory Medicine, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, 441021, P.R. China
| | - Jianfei Luo
- Department of Gastrointestinal Surgery in East Hospital, Renmin Hospital of Wuhan University, No. 6 Gaoxin Road, East Lake High-tech Development Zone District, Wuhan, 430205, P.R. China
| | - Wenhong Deng
- Department of Gastrointestinal Surgery in East Hospital, Renmin Hospital of Wuhan University, No. 6 Gaoxin Road, East Lake High-tech Development Zone District, Wuhan, 430205, P.R. China
| | - Jiasheng Liu
- Department of Gastrointestinal Surgery in East Hospital, Renmin Hospital of Wuhan University, No. 6 Gaoxin Road, East Lake High-tech Development Zone District, Wuhan, 430205, P.R. China
| | - Ruicheng Yan
- Department of Gastrointestinal Surgery in East Hospital, Renmin Hospital of Wuhan University, No. 6 Gaoxin Road, East Lake High-tech Development Zone District, Wuhan, 430205, P.R. China
| | - Weixing Wang
- Department of Gastrointestinal Surgery in East Hospital, Renmin Hospital of Wuhan University, No. 6 Gaoxin Road, East Lake High-tech Development Zone District, Wuhan, 430205, P.R. China.
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60
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Singh NP, Vinod PK. Integrative analysis of DNA methylation and gene expression in papillary renal cell carcinoma. Mol Genet Genomics 2020; 295:807-824. [PMID: 32185457 DOI: 10.1007/s00438-020-01664-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
Abstract
Patterns of DNA methylation are significantly altered in cancers. Interpreting the functional consequences of DNA methylation requires the integration of multiple forms of data. The recent advancement in the next-generation sequencing can help to decode this relationship and in biomarker discovery. In this study, we investigated the methylation patterns of papillary renal cell carcinoma (PRCC) and its relationship with the gene expression using The Cancer Genome Atlas (TCGA) multi-omics data. We found that the promoter and body of tumor suppressor genes, microRNAs and gene clusters and families, including cadherins, protocadherins, claudins and collagens, are hypermethylated in PRCC. Hypomethylated genes in PRCC are associated with the immune function. The gene expression of several novel candidate genes, including interleukin receptor IL17RE and immune checkpoint genes HHLA2, SIRPA and HAVCR2, shows a significant correlation with DNA methylation. We also developed machine learning models using features extracted from single and multi-omics data to distinguish early and late stages of PRCC. A comparative study of different feature selection algorithms, predictive models, data integration techniques and representations of methylation data was performed. Integration of both gene expression and DNA methylation features improved the performance of models in distinguishing tumor stages. In summary, our study identifies PRCC driver genes and proposes predictive models based on both DNA methylation and gene expression. These results on PRCC will aid in targeted experiments and provide a strategy to improve the classification accuracy of tumor stages.
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Affiliation(s)
- Noor Pratap Singh
- Center for Computational Natural Sciences and Bioinformatics, IIIT Hyderabad, Hyderabad, 500032, India
| | - P K Vinod
- Center for Computational Natural Sciences and Bioinformatics, IIIT Hyderabad, Hyderabad, 500032, India.
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61
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Kim SJ, Ju JS, Park SS, Suh YA, Yoo HJ, Choi EK, Shin Y, Park YY. An RNA-binding-protein, NONO governs energy metabolism by regulating NAMPT in lung cancer. Biochem Biophys Res Commun 2020; 528:376-382. [PMID: 32087970 DOI: 10.1016/j.bbrc.2020.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/06/2020] [Indexed: 12/17/2022]
Abstract
The RNA binding proteins (RBPs) have multiple roles in human cancer. However, their molecular target and function have not been clearly identified. Our genomic analysis derived from patients reveals that NONO is a potential oncogenic gene in lung cancer. NONO is highly expressed in lung cancer tissues compared with normal tissues, and its expression has been correlated with the prognosis of lung cancer patients. We found that NONO significantly influences cancer cell proliferation in lung cancer. Gene expression profiles with NONO-depleted cells revealed that the sirtuin signaling pathway is highly correlated with NONO. Thus, NONO-silenced cells caused reduction of the TCA cycle and glycolysis metabolism. We identified that NONO regulated NAMPT, which is a well-known gene involved in sirtuin signaling, and NONO has a significant correlation with NAMPT in lung cancer patients. We propose that NONO modulates energy metabolism by direct interaction with NAMPT and suggest that a functional relationship between NONO and NAMPT contributes to lung cancer cell survival. Targeting the axis can be a promising approach for patient treatment in lung cancer.
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Affiliation(s)
- Seong-Jin Kim
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, South Korea; Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Jin-Sung Ju
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, South Korea; Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Seok Soon Park
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Young-Ah Suh
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Hyun Ju Yoo
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, South Korea; Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Eun Kyung Choi
- Department of Radiation Oncology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Yong Shin
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, South Korea.
| | - Yun-Yong Park
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, South Korea; Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea.
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Chen Z, Wu L, Zhou J, Lin X, Peng Y, Ge L, Chiang CM, Huang H, Wang H, He W. N6-methyladenosine-induced ERRγ triggers chemoresistance of cancer cells through upregulation of ABCB1 and metabolic reprogramming. Theranostics 2020; 10:3382-3396. [PMID: 32206097 PMCID: PMC7069076 DOI: 10.7150/thno.40144] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/25/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Drug resistance severely reduces treatment efficiency of chemotherapy and leads to poor prognosis. However, regulatory factors of chemoresistant cancer cells are largely unknown. Methods: The expression of estrogen receptor related receptors (ERRs) in chemoresistant cancer cells are checked. The roles of ERRγ in chemoresistance are confirmed by in vitro and in vivo studies. The mechanisms responsible for ERRγ-regulated expression of ABCB1 and CPT1B are investigated. Results: The expression of ERRγ is upregulated in chemoresistant cancer cells. Targeted inhibition of ERRγ restores the chemosensitivity. ERRγ can directly bind to the promoter of ABCB1 to increase its transcription. An elevated interaction between ERRγ and p65 in chemoresistant cells further strengthens transcription of ABCB1. Further, ERRγ can increase the fatty acid oxidation (FAO) in chemoresistant cells via regulation of CPT1B, the rate-limiting enzyme of FAO. The upregulated ERRγ in chemoresistant cancer cells might be due to increased levels of N6-methyladenosine (m6A) can trigger the splicing of precursor ESRRG mRNA. Conclusions: m6A induced ERRγ confers chemoresistance of cancer cells through upregulation of ABCB1 and CPT1B.
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Affiliation(s)
- Zhuojia Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Long Wu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jiawang Zhou
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Xinyao Lin
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yanxi Peng
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Lichen Ge
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- Department of Clinical Laboratory, Jinling Hospital, Nanjing University School of Medicine, 305 East Zhongshan Road, Nanjing 210002, China
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Department of Pharmacology, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Hui Huang
- Cardiovascular Department, The Eighth Affiliated Hospital, Sun Yat-sen University, Shennan Middle Road 3025#, Shenzhen, 518033, China
| | - Hongsheng Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Weiling He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
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Kim TK, Lee BW, Fujii F, Lee KH, Lee S, Park Y, Kim JK, Lee SW, Pack CG. Mitotic Chromosomes in Live Cells Characterized Using High-Speed and Label-Free Optical Diffraction Tomography. Cells 2019; 8:cells8111368. [PMID: 31683735 PMCID: PMC6912651 DOI: 10.3390/cells8111368] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 12/16/2022] Open
Abstract
The cell nucleus is a three-dimensional, dynamic organelle organized into subnuclear compartments such as chromatin and nucleoli. The structure and function of these compartments are maintained by diffusion and interactions between related factors as well as by dynamic and structural changes. Recent studies using fluorescent microscopic techniques suggest that protein factors can access and are freely mobile in heterochromatin and in mitotic chromosomes, despite their densely packed structure. However, the physicochemical properties of the chromosome during cell division are not fully understood. In the present study, characteristic properties such as the refractive index (RI), volume of the mitotic chromosomes, and diffusion coefficient (D) of fluorescent probes inside the chromosome were quantified using an approach combining label-free optical diffraction tomography with complementary confocal laser-scanning microscopy and fluorescence correlation spectroscopy. Variations in these parameters correlated with osmotic conditions, suggesting that changes in RI are consistent with those of the diffusion coefficient for mitotic chromosomes and cytosol. Serial RI tomography images of chromosomes in live cells during mitosis were compared with three-dimensional confocal micrographs to demonstrate that compaction and decompaction of chromosomes induced by osmotic change were characterized by linked changes in chromosome RI, volume, and the mobilities of fluorescent proteins.
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Affiliation(s)
- Tae-Keun Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea.
| | - Byong-Wook Lee
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea.
| | - Fumihiko Fujii
- Division of Physical Pharmacy, Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Kobe 650-8586, Japan.
| | | | - Sanghwa Lee
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea.
| | - YongKeun Park
- Tomocube Inc., Daejeon 34051, Korea.
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea.
| | - Jun Ki Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea.
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 05505, Korea.
| | - Sang-Wook Lee
- Department of Radiation Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea.
| | - Chan-Gi Pack
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea.
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 05505, Korea.
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Chen EB, Qin X, Peng K, Li Q, Tang C, Wei YC, Yu S, Gan L, Liu TS. HnRNPR-CCNB1/CENPF axis contributes to gastric cancer proliferation and metastasis. Aging (Albany NY) 2019; 11:7473-7491. [PMID: 31527303 PMCID: PMC6782008 DOI: 10.18632/aging.102254] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023]
Abstract
Gastric cancer (GC) is a common disease globally with high mortality rate. It is therefore necessary to develop novel therapies targeting specific events in the pathogenesis of GC. Some hnRNP family members are involved in multiple cancer biological behaviors. However, the potential function and mechanism of hnRNPR, a new molecule of hnRNP family in GC remains unknown. We found that the expression of hnRNPR was significantly overexpressed in multiple cancers compared to the normal tissues. Functionally, hnRNPR promoted cancer cell proliferation, migration, and invasion. Knockdown of hnRNPR in two type mice models, with two types of tumors models decreased the tumor aggressiveness and metastasis. Mechanistically, hnRNPR targeted oncogenic pathways by stabilizing the expression of CCNB1 and CENPF mRNA level. Knockdown of CCNB1 and CENPF abolished the hnRNPR-induced cell growth and invasion, respectively. Furthermore, the protein level of hnRNPR in the tumor was positively correlated with the expression of CCNB1 and CENPF in clinical samples. Together, these results indicate that overexpression of hnRNPR promoted the aggressiveness of GC by increasing the mRNA expression of CCNB1 and CENPF. HnRNPR-CCNB1/CENPF axis may be a potential therapeutic target for GC treatment.
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Affiliation(s)
- Er-Bao Chen
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xuan Qin
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, China
| | - Ke Peng
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qian Li
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Tang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yi-Chou Wei
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shan Yu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lu Gan
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tian-Shu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.,Center of Evidence-based Medicine, Fudan University, Shanghai, China
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Chen X, Yu X, Shen E. Overexpression of CDKN2B is involved in poor gastric cancer prognosis. J Cell Biochem 2019; 120:19825-19831. [PMID: 31297846 DOI: 10.1002/jcb.29287] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/28/2019] [Indexed: 12/13/2022]
Abstract
The objective of this investigation is to elucidate the clinical significance of cyclin-dependent kinase inhibitor 2B (CDKN2B) expression regarding gastric cancer (GC), as well as to detect the involvement of CDKN2B expression in the clinicopathological indexes and prognosis of GC. Immunohistochemical analysis was used for identification of CDKN2B expression in GC specimens. Chi-square (χ2 ) test was applied to detect the association of CDKN2B expression and clinicopathological parameters of GC. The involvement of CDKN2B expression in the prognosis was analyzed via univariate and multivariate analysis. It was indicated that relative to the corresponding para-carcinoma tissues, CDKN2B expression was notably upregulated in GC specimens. Moreover, the expression of CDKN2B was strongly correlated with the differentiation (r = -0.182; P = .015), invasion (r = -0.157; P = .038), distant metastases (r = -0.196; P = .004), and TNM stage (r = -0.204; P = .005). Nevertheless, no remarkable variance was related to age, tumor loci, or sex. Kaplan-Meier survival curve and univariate analysis showed that CDKN2B overexpression predicted poorer disease-free survival (P = .007) and overall survival (P = .005) in those with GC. In addition, Cox proportional hazards regression model revealed that CDKN2B was an isolated biomarker of disease-free survival and overall survival in patients with GC. Taken together, our data demonstrated that the overexpression of CDKN2B could be an isolated factor for GC prognostic in patients. CDKN2B gene may be a useful target and new treatment for improving the prognosis of GC.
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Affiliation(s)
- Xi Chen
- Department of Pathology, Taizhou Municipal Hospital, Taizhou, Zhejiang, China
| | - Xingtong Yu
- Department of Pathology, Taizhou Municipal Hospital, Taizhou, Zhejiang, China
| | - Enjian Shen
- Department of Pathology, Taizhou Municipal Hospital, Taizhou, Zhejiang, China
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66
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Gonzalez TL, Rae JM, Colacino JA, Richardson RJ. Homology models of mouse and rat estrogen receptor- α ligand-binding domain created by in silico mutagenesis of a human template: molecular docking with 17ß-estradiol, diethylstilbestrol, and paraben analogs. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 10:1-16. [PMID: 30740556 PMCID: PMC6363358 DOI: 10.1016/j.comtox.2018.11.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Crystal structures exist for human, but not rodent, estrogen receptor-α ligand-binding domain (ERα-LBD). Consequently, rodent studies involving binding of compounds to ERα-LBD are limited in their molecular-level interpretation and extrapolation to humans. Because the sequences of rodent and human ERα-LBDs are > 95% identical, we expected their 3D structures and ligand binding to be highly similar. To test this hypothesis, we used the human ERα-LBD structure (PDB 3UUD) as a template to produce rat and mouse homology models. Employing the rodent models and human structure, we generated docking poses of 23 Group A ligands (17ß-estradiol, diethylstilbestrol, and 21 paraben analogs) in AutoDock Vina for interspecies comparisons. Ligand RMSDs (Å) (median, 95% CI) were 0.49 (0.21-1.82) (human-mouse) and 1.19 (0.22-1.82) (human-rat), well below the 2.0-2.5 Å range for equivalent docking poses. Numbers of interspecies ligand-receptor residue contacts were highly similar, with Sorensen Sc (%) = 96.8 (90.0-100) (human-mouse) and 97.7 (89.5-100) (human-rat). Likewise, numbers of interspecies ligand-receptor residue contacts were highly correlated: Pearson r = 0.913 (human-mouse) and 0.925 (human-rat). Numbers of interspecies ligand-receptor atom contacts were even more tightly correlated: r = 0.979 (human-mouse) and 0.986 (human-rat). Pyramid plots of numbers of ligand-receptor atom contacts by residue exhibited high interspecies symmetry and had Spearman r s = 0.977 (human-mouse) and 0.966 (human-rat). Group B ligands included 15 ring-substituted parabens recently shown experimentally to exhibit decreased binding to human ERα and to exert increased antimicrobial activity. Ligand efficiencies calculated from docking ligands into human ERα-LBD were well correlated with those derived from published experimental data (Pearson partial r p = 0.894 and 0.918; Groups A and B, respectively). Overall, the results indicate that our constructed rodent ERα-LBDs interact with ligands in like manner to the human receptor, thus providing a high level of confidence in extrapolations of rodent to human ligand-receptor interactions.
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Affiliation(s)
- Thomas L. Gonzalez
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - James M. Rae
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Rudy J. Richardson
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Tian S, Zhan N, Li R, Dong W. Downregulation of G Protein-Coupled Estrogen Receptor (GPER) is Associated with Reduced Prognosis in Patients with Gastric Cancer. Med Sci Monit 2019; 25:3115-3126. [PMID: 31028714 PMCID: PMC6503750 DOI: 10.12659/msm.913634] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND This study is aimed to investigate the prognostic significance of the expression of G protein-coupled estrogen receptor (GPER) in gastric cancer tissue using bioinformatics data and immunohistochemistry. MATERIAL AND METHODS Expression of GPER mRNA in gastric cancer tissues and normal adjacent tissues was investigated using data from The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO), and Oncomine database. Kaplan-Meier Plotter identified the association between GPER mRNA and prognosis. Correlation between GPER mRNA and DNA methylation used the cBioPortal for Cancer Genomics and the MethHC website. Genes co-expressed with GPER were identified from The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) underwent FunRich analysis. Immunohistochemistry and Western blot evaluated GPER protein expression in tissue microarrays (TMAs) and gastric cancer cell lines. RESULTS GPER mRNA and protein levels were significantly lower in gastric cancer tissue and cells lined when compared with normal tissues and cells. The results from GSE15459 showed that patients with low levels of GPER mRNA had a reduced overall survival (OS) (P=0.013) and disease-free survival (DFS) (P=0.019). A negative correlation (r=-0.611) between GPER mRNA and DNA methylation was found using the cBioPortal and MethHC. Co-expressed epithelial-mesenchymal transformation (EMT) genes were enriched with GPER (P<0.0001). Cox regression analysis showed that GPER protein expression was an independent prognostic factor (P=0.035) CONCLUSIONS Downregulation of GPER predicts poor prognosis in gastric cancer. GPER may act as a tumor suppressor through the regulation of EMT in gastric cancer.
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Affiliation(s)
- Shan Tian
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Na Zhan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Ruixue Li
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Weiguo Dong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
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De Vitto H, Bode AM, Dong Z. The PGC-1/ERR network and its role in precision oncology. NPJ Precis Oncol 2019; 3:9. [PMID: 30911677 PMCID: PMC6428848 DOI: 10.1038/s41698-019-0081-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Transcriptional regulators include a superfamily of nuclear proteins referred to as co-activators and co-repressors, both of which are involved in controlling the functions of several nuclear receptors (NRs). The Nuclear Receptor Signaling Atlas (NURSA) has cataloged the composition of NRs, co-regulators, and ligands present in the human cell and their effort has been identified in more than 600 potential molecules. Given the importance of co-regulators in steroid, retinoid, and thyroid hormone signaling networks, hypothesizing that NRs/co-regulators are implicated in a wide range of pathologies are tempting. The co-activators known as peroxisome proliferator-activated receptor gamma co-activator 1 (PGC-1) and their key nuclear partner, the estrogen-related receptor (ERR), are emerging as pivotal transcriptional signatures that regulate an extremely broad repertoire of mitochondrial and metabolic genes, making them very attractive drug targets for cancer. Several studies have provided an increased understanding of the functional and structural biology of nuclear complexes. However, more comprehensive work is needed to create different avenues to explore the therapeutic potential of NRs/co-activators in precision oncology. Here, we discuss the emerging data associated with the structure, function, and molecular biology of the PGC-1/ERR network and address how the concepts evolving from these studies have deepened our understanding of how to develop more effective treatment strategies. We present an overview that underscores new biological insights into PGC-1/ERR to improve cancer outcomes against therapeutic resistance. Finally, we discuss the importance of exploiting new technologies such as single-particle cryo-electron microscopy (cryo-EM) to develop a high-resolution biological structure of PGC-1/ERR, focusing on novel drug discovery for precision oncology.
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Affiliation(s)
- Humberto De Vitto
- The Hormel Institute, University of Minnesota, 801 16th Avenue, Austin, NE 55912 USA
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, 801 16th Avenue, Austin, NE 55912 USA
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, 801 16th Avenue, Austin, NE 55912 USA
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69
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Yan P, He Y, Xie K, Kong S, Zhao W. In silico analyses for potential key genes associated with gastric cancer. PeerJ 2018; 6:e6092. [PMID: 30568862 PMCID: PMC6287586 DOI: 10.7717/peerj.6092] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/09/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Understanding hub genes involved in gastric cancer (GC) metastasis could lead to effective approaches to diagnose and treat cancer. In this study, we aim to identify the hub genes and investigate the underlying molecular mechanisms of GC. METHODS To explore potential therapeutic targets for GC,three expression profiles (GSE54129, GSE33651, GSE81948) of the genes were extracted from the Gene Expression Omnibus (GEO) database. The GEO2R online tool was applied to screen out differentially expressed genes (DEGs) between GC and normal gastric samples. Database for Annotation, Visualization and Integrated Discovery was applied to perform Gene Ontology (GO) and KEGG pathway enrichment analysis. The protein-protein interaction (PPI) network of these DEGs was constructed using a STRING online software. The hub genes were identified by the CytoHubba plugin of Cytoscape software. Then, the prognostic value of these identified genes was verified by gastric cancer database derived from Kaplan-Meier plotter platform. RESULTS A total of 85 overlapped upregulated genes and 44 downregulated genes were identified. The majority of the DEGs were enriched in extracellular matrix organization, endodermal cell differentiation, and endoderm formation. Moreover, five KEGG pathways were significantly enriched, including ECM-receptor interaction, amoebiasis, AGE-RAGE signaling pathway in diabetic complications, focal adhesion, protein digestion and absorption. By combining the results of PPI network and CytoHubba, a total of nine hub genes including COL1A1, THBS1, MMP2, CXCL8, FN1, TIMP1, SPARC, COL4A1, and ITGA5 were selected. The Kaplan-Meier plotter database confirmed that overexpression levels of these genes were associated with reduced overall survival, except for THBS1 and CXCL8. CONCLUSIONS Our study suggests that COL1A1, MMP2, FN1, TIMP1, SPARC, COL4A1, and ITGA5 may be potential biomarkers and therapeutic targets for GC. Further study is needed to assess the effect of THBS1 and CXCL8 on GC.
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Affiliation(s)
- Ping Yan
- Department of Gastroenterology, Clinical College, Dali University, Dali, Yunnan, China
| | - Yingchun He
- Department of Clinical Laboratory, Clinical College, Dali University, Dali, Yunnan, China
| | - Kexin Xie
- Department of Clinical Laboratory, Clinical College, Dali University, Dali, Yunnan, China
| | - Shan Kong
- Department of Clinical Laboratory, Clinical College, Dali University, Dali, Yunnan, China
| | - Weidong Zhao
- Department of Clinical Laboratory, Clinical College, Dali University, Dali, Yunnan, China
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Zheng L, Liang X, Li S, Li T, Shang W, Ma L, Jia X, Shao W, Sun P, Chen C, Jia J. CHAF1A interacts with TCF4 to promote gastric carcinogenesis via upregulation of c-MYC and CCND1 expression. EBioMedicine 2018; 38:69-78. [PMID: 30449701 PMCID: PMC6306399 DOI: 10.1016/j.ebiom.2018.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/29/2018] [Accepted: 11/05/2018] [Indexed: 12/15/2022] Open
Abstract
Background Histones chaperones have been found to play critical roles in tumor development and progression. However, the role of histone chaperone CHAF1A in gastric carcinogenesis and its underlying mechanisms remain elusive. Methods CHAF1A expression in gastric cancer (GC) was analyzed in GEO datasets and clinical specimens. CHAF1A knockdown and overexpression were used to explore its functions in gastric cancer cells. The regulation and potential molecular mechanism of CHAF1A expression in gastric cancer cells were studied by using cell and molecular biological methods. Findings CHAF1A was upregulated in GC tissues and its high expression predicted poor prognosis in GC patients. Overexpression of CHAF1A promoted gastric cancer cell proliferation both in vitro and in vivo, whereas CHAF1A suppression exhibited the opposite effects. Mechanistically, CHAF1A acted as a co-activator in the Wnt pathway. CHAF1A directly interacted with TCF4 to enhance the expression of c-MYC and CCND1 through binding to their promoter regions. In addition, the overexpression of CHAF1A was modulated by specificity protein 1 (Sp1) in GC. Sp1 transcriptionally enhanced the expression of CHAF1A in GC. Furthermore, CHAF1A expression induced by Helicobacter pylori was Sp1 dependent. Interpretation CHAF1A is a potential oncogene in GC, and may serve as a novel therapeutic target for GC treatment.
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Affiliation(s)
- Lixin Zheng
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China; Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China
| | - Xiuming Liang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China; Shandong University-Karolinska Institutet Collaborative Laboratory for Cancer Research, Jinan, Shandong 250012, PR China
| | - Shuyan Li
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China
| | - Tongyu Li
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China
| | - Wenjing Shang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China
| | - Lin Ma
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China
| | - Xiaxia Jia
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China
| | - Wei Shao
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China
| | - Pengpeng Sun
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China
| | - Chunyan Chen
- Cancer Center, Qilu Hospital, Shandong University, Jinan, Shandong 250012, PR China
| | - Jihui Jia
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China; Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, PR China; Shandong University-Karolinska Institutet Collaborative Laboratory for Cancer Research, Jinan, Shandong 250012, PR China.
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Liu X, Wu J, Zhang D, Bing Z, Tian J, Ni M, Zhang X, Meng Z, Liu S. Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis. Front Genet 2018; 9:265. [PMID: 30065754 PMCID: PMC6056647 DOI: 10.3389/fgene.2018.00265] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/02/2018] [Indexed: 12/23/2022] Open
Abstract
Background and Objective: Despite striking advances in multimodality management, gastric cancer (GC) remains the third cause of cancer mortality globally and identifying novel diagnostic and prognostic biomarkers is urgently demanded. The study aimed to identify potential key genes associated with the pathogenesis and prognosis of GC. Methods: Differentially expressed genes between GC and normal gastric tissue samples were screened by an integrated analysis of multiple gene expression profile datasets. Key genes related to the pathogenesis and prognosis of GC were identified by employing protein–protein interaction network and Cox proportional hazards model analyses. Results: We identified nine hub genes (TOP2A, COL1A1, COL1A2, NDC80, COL3A1, CDKN3, CEP55, TPX2, and TIMP1) which might be tightly correlated with the pathogenesis of GC. A prognostic gene signature consisted of CST2, AADAC, SERPINE1, COL8A1, SMPD3, ASPN, ITGBL1, MAP7D2, and PLEKHS1 was constructed with a good performance in predicting overall survivals. Conclusion: The findings of this study would provide some directive significance for further investigating the diagnostic and prognostic biomarkers to facilitate the molecular targeting therapy of GC.
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Affiliation(s)
- Xinkui Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jiarui Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Dan Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhitong Bing
- Evidence Based Medicine Center, School of Basic Medical Science, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China.,Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Jinhui Tian
- Evidence Based Medicine Center, School of Basic Medical Science, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
| | - Mengwei Ni
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaomeng Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Ziqi Meng
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shuyu Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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