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Kokot A, Gadakh S, Saha I, Gajda E, Łaźniewski M, Rakshit S, Sengupta K, Mollah AF, Denkiewicz M, Górczak K, Claesen J, Burzykowski T, Plewczynski D. Unveiling the Molecular Mechanism of Trastuzumab Resistance in SKBR3 and BT474 Cell Lines for HER2 Positive Breast Cancer. Curr Issues Mol Biol 2024; 46:2713-2740. [PMID: 38534787 DOI: 10.3390/cimb46030171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024] Open
Abstract
HER2-positive breast cancer is one of the most prevalent forms of cancer among women worldwide. Generally, the molecular characteristics of this breast cancer include activation of human epidermal growth factor receptor-2 (HER2) and hormone receptor activation. HER2-positive is associated with a higher death rate, which led to the development of a monoclonal antibody called trastuzumab, specifically targeting HER2. The success rate of HER2-positive breast cancer treatment has been increased; however, drug resistance remains a challenge. This fact motivated us to explore the underlying molecular mechanisms of trastuzumab resistance. For this purpose, a two-fold approach was taken by considering well-known breast cancer cell lines SKBR3 and BT474. In the first fold, trastuzumab treatment doses were optimized separately for both cell lines. This was done based on the proliferation rate of cells in response to a wide variety of medication dosages. Thereafter, each cell line was cultivated with a steady dosage of herceptin for several months. During this period, six time points were selected for further in vitro analysis, ranging from the untreated cell line at the beginning to a fully resistant cell line at the end of the experiment. In the second fold, nucleic acids were extracted for further high throughput-based microarray experiments of gene and microRNA expression. Such expression data were further analyzed in order to infer the molecular mechanisms involved in the underlying development of trastuzumab resistance. In the list of differentially expressed genes and miRNAs, multiple genes (e.g., BIRC5, E2F1, TFRC, and USP1) and miRNAs (e.g., hsa miR 574 3p, hsa miR 4530, and hsa miR 197 3p) responsible for trastuzumab resistance were found. Downstream analysis showed that TFRC, E2F1, and USP1 were also targeted by hsa-miR-8485. Moreover, it indicated that miR-4701-5p was highly expressed as compared to TFRC in the SKBR3 cell line. These results unveil key genes and miRNAs as molecular regulators for trastuzumab resistance.
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Affiliation(s)
- Anna Kokot
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-089 Bialystok, Poland
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
| | - Sachin Gadakh
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
| | - Indrajit Saha
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata 700106, India
| | - Ewa Gajda
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Michał Łaźniewski
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
| | - Somnath Rakshit
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
| | - Kaustav Sengupta
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warszawa, Poland
| | | | - Michał Denkiewicz
- Centre of New Technologies, University of Warsaw, 02-097 Warszawa, Poland
| | - Katarzyna Górczak
- Department of Mathematics and Statistics, Hasselt University, 3500 Hasselt, Belgium
| | - Jürgen Claesen
- Department of Epidemiology and Data Science, Amsterdam Universitair Medische Centra, VU University, 1081 HV Amsterdam, The Netherlands
| | - Tomasz Burzykowski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-089 Bialystok, Poland
- Department of Mathematics and Statistics, Hasselt University, 3500 Hasselt, Belgium
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Capoferri D, Mignani L, Manfredi M, Presta M. Proteomic Analysis Highlights the Impact of the Sphingolipid Metabolizing Enzyme β-Galactosylceramidase on Mitochondrial Plasticity in Human Melanoma. Int J Mol Sci 2024; 25:3062. [PMID: 38474307 DOI: 10.3390/ijms25053062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Mitochondrial plasticity, marked by a dynamism between glycolysis and oxidative phosphorylation due to adaptation to genetic and microenvironmental alterations, represents a characteristic feature of melanoma progression. Sphingolipids play a significant role in various aspects of cancer cell biology, including metabolic reprogramming. Previous observations have shown that the lysosomal sphingolipid-metabolizing enzyme β-galactosylceramidase (GALC) exerts pro-oncogenic functions in melanoma. Here, mining the cBioPortal for a Cancer Genomics data base identified the top 200 nuclear-encoded genes whose expression is negatively correlated with GALC expression in human melanoma. Their categorization indicated a significant enrichment in Gene Ontology terms and KEGG pathways related to mitochondrial proteins and function. In parallel, proteomic analysis by LC-MS/MS of two GALC overexpressing human melanoma cell lines identified 98 downregulated proteins when compared to control mock cells. Such downregulation was confirmed at a transcriptional level by a Gene Set Enrichment Analysis of the genome-wide expression profiling data obtained from the same cells. Among the GALC downregulated proteins, we identified a cluster of 42 proteins significantly associated with GO and KEGG categorizations related to mitochondrion and energetic metabolism. Overall, our data indicate that changes in GALC expression may exert a significant impact on mitochondrial plasticity in human melanoma cells.
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Affiliation(s)
- Davide Capoferri
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Luca Mignani
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, University of Piemonte Orientale, 13100 Novara, Italy
| | - Marco Presta
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Consorzio Interuniversitario Biotecnologie (CIB), Unit of Brescia, 25123 Brescia, Italy
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Faida P, Attiogbe MKI, Majeed U, Zhao J, Qu L, Fan D. Lung cancer treatment potential and limits associated with the STAT family of transcription factors. Cell Signal 2023:110797. [PMID: 37423343 DOI: 10.1016/j.cellsig.2023.110797] [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: 04/06/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
Lung cancer is one of the mortal cancers and the leading cause of cancer-related mortality, with a cancer survival rate of fewer than 5% in developing nations. This low survival rate can be linked to things like late-stage detection, quick postoperative recurrences in patients receiving therapy, and chemoresistance developing against various lung cancer treatments. Signal transducer and activator of transcription (STAT) family of transcription factors are involved in lung cancer cell proliferation, metastasis, immunological control, and treatment resistance. By interacting with specific DNA sequences, STAT proteins trigger the production of particular genes, which in turn result in adaptive and incredibly specific biological responses. In the human genome, seven STAT proteins have been discovered (STAT1 to STAT6, including STAT5a and STAT5b). Many external signaling proteins can activate unphosphorylated STATs (uSTATs), which are found inactively in the cytoplasm. When STAT proteins are activated, they can increase the transcription of several target genes, which leads to unchecked cellular proliferation, anti-apoptotic reactions, and angiogenesis. The effects of STAT transcription factors on lung cancer are variable; some are either pro- or anti-tumorigenic, while others maintain dual, context-dependent activities. Here, we give a succinct summary of the various functions that each member of the STAT family plays in lung cancer and go into more detail about the advantages and disadvantages of pharmacologically targeting STAT proteins and their upstream activators in the context of lung cancer treatment.
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Affiliation(s)
- Paison Faida
- Shaanxi Key Laboratory of Degradable Biomedical Materials and Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Taibai North Road 229, Xi'an, Shaanxi 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Taibai North Road 229, Xi'an, Shaanxi 710069, China
| | - Mawusse K I Attiogbe
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Usman Majeed
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jing Zhao
- Shaanxi Key Laboratory of Degradable Biomedical Materials and Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Taibai North Road 229, Xi'an, Shaanxi 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Taibai North Road 229, Xi'an, Shaanxi 710069, China
| | - Linlin Qu
- Shaanxi Key Laboratory of Degradable Biomedical Materials and Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Taibai North Road 229, Xi'an, Shaanxi 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Taibai North Road 229, Xi'an, Shaanxi 710069, China
| | - Daidi Fan
- Shaanxi Key Laboratory of Degradable Biomedical Materials and Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Taibai North Road 229, Xi'an, Shaanxi 710069, China; Biotech. & Biomed. Research Institute, Northwest University, Taibai North Road 229, Xi'an, Shaanxi 710069, China.
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Li YJ, Zhang C, Martincuks A, Herrmann A, Yu H. STAT proteins in cancer: orchestration of metabolism. Nat Rev Cancer 2023; 23:115-134. [PMID: 36596870 DOI: 10.1038/s41568-022-00537-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/14/2022] [Indexed: 01/04/2023]
Abstract
Reprogrammed metabolism is a hallmark of cancer. However, the metabolic dependency of cancer, from tumour initiation through disease progression and therapy resistance, requires a spectrum of distinct reprogrammed cellular metabolic pathways. These pathways include aerobic glycolysis, oxidative phosphorylation, reactive oxygen species generation, de novo lipid synthesis, fatty acid β-oxidation, amino acid (notably glutamine) metabolism and mitochondrial metabolism. This Review highlights the central roles of signal transducer and activator of transcription (STAT) proteins, notably STAT3, STAT5, STAT6 and STAT1, in orchestrating the highly dynamic metabolism not only of cancer cells but also of immune cells and adipocytes in the tumour microenvironment. STAT proteins are able to shape distinct metabolic processes that regulate tumour progression and therapy resistance by transducing signals from metabolites, cytokines, growth factors and their receptors; defining genetic programmes that regulate a wide range of molecules involved in orchestration of metabolism in cancer and immune cells; and regulating mitochondrial activity at multiple levels, including energy metabolism and lipid-mediated mitochondrial integrity. Given the central role of STAT proteins in regulation of metabolic states, they are potential therapeutic targets for altering metabolic reprogramming in cancer.
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Affiliation(s)
- Yi-Jia Li
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Chunyan Zhang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Antons Martincuks
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Andreas Herrmann
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
- Sorrento Therapeutics, San Diego, CA, USA
| | - Hua Yu
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA.
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Cansaran-Duman D, Yangın S, Çolak B. The role of vulpinic acid as a natural compound in the regulation of breast cancer-associated miRNAs. Biol Res 2021; 54:37. [PMID: 34743742 PMCID: PMC8574026 DOI: 10.1186/s40659-021-00360-4] [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: 03/30/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022] Open
Abstract
Background Breast cancer is the most frequently diagnosed cancer, and no effective treatment solution has yet been found. The number of studies based on the research of novel natural compounds in the treatment of breast cancer has been increasing in recent years. The anticancer properties of natural compounds are related to the regulation of microRNA (miRNA) expression. Therefore, changing the profile of miRNAs with the use of natural products is very important in cancer treatment. However, the role of vulpinic acid and related miRNAs in breast cancer progression remains unknown. Vulpinic acid, methyl (as2E)-2-(3-hydroxy-5-oxo-4-phenylfuran-2-ylidene)-2 phenylacetate, is a natural product extracted from the lichen species and shows an anticancer effect on different cancer cells. Methods This study examines the effects of vulpinic acid on the miRNA levels of breast cancer (MCF-7) cells and its relationship with cell proliferation and apoptosis levels. The antiproliferative effect of vulpinic acid was screened against MCF-7 breast cancer cells and MCF-12A breast epithelial cells using the xCELLigence real-time cell analysis system. We analyzed the altered miRNA expression profile in MCF-7 breast cancer cells versus MCF-12A cells following their response to vulpinic acid through microarray analysis. The microarray analysis results were confirmed through quantitative real-time PCR and bioinformatics analysis. Results The results of the miRNA array and bioinformatic analyses demonstrated that 12 miRNAs were specifically responsive to vulpinic acid in MCF-7 breast cancer cells. This is the first study to reveal that vulpinic acid inhibits the expression of 12 miRNAs and suppresses breast cancer cell proliferation. The study also revealed that vulpinic acid may downregulate the expression of 12 miRNAs by repressing the FOXO-3 gene. The miRNA targets were mainly found to play a role in the apoptosis, cell cycle and MAPK pathways. Moreover, Bcl-2, Bax, procaspase-3 and procaspase-9 protein levels were assessed by western blot analysis for validation of apoptosis at the protein level. Conclusion This study revealed the molecular mechanisms of vulpinic acid on breast cancer and showed that vulpinic acid regulates apoptosis signaling pathways by decreasing the expression of miRNAs. The miRNA expression patterns illuminate the underlying effect of vulpinic acid in breast cancer treatment. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s40659-021-00360-4.
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Affiliation(s)
| | - Sevcan Yangın
- Ankara University, Biotechnology Institute, Keçiören, Ankara, 06135, Turkey
| | - Betül Çolak
- Ankara University, Biotechnology Institute, Keçiören, Ankara, 06135, Turkey
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Liu C, Yang D, Wang H, Hu S, Xie X, Zhang L, Jia H, Qi Q. MicroRNA-197-3p mediates damage to human coronary artery endothelial cells via targeting TIMP3 in Kawasaki disease. Mol Cell Biochem 2021; 476:4245-4263. [PMID: 34351574 DOI: 10.1007/s11010-021-04238-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/28/2021] [Indexed: 11/29/2022]
Abstract
Kawasaki disease (KD) causes cardiovascular system injury in children. However, the pathogenic mechanisms of KD have not been well defined. Recently, strong correlation between aberrant microRNAs and KD nosogenesis has been revealed. A role of microRNA-197-3p (miR-197-3p) in the pathogenesis of KD is identified in the present study. Cell proliferation assay showed human coronary artery endothelial cells (HCAECs) were suppressed by serum from KD patients, which was correlated with high levels of miR-197-3p in both KD serum and HCAECs cultured with KD serum. The inhibition of HCAECs by miR-197-3p was confirmed by cells expressing miR-197-3p mimic and miR-197-3p inhibitor. Comparative proteomics analysis and Ingenuity Pathway Analysis (IPA) revealed TIMP3 as a potential target of miR-197-3p, which was demonstrated by western blot and dual-luciferase reporter assays. Subsequently, by detecting the endothelium damage markers THBS1, VWF, and HSPG2, the role of miR-197-3p/TIMP3 in KD-induced damage to HCAECs was confirmed, which was further validated by a KD mouse model in vivo. The expressions of miR-197-3p and its target, TIMP3, are dramatically variational in KD serum and HCAECs cultured with KD serum. Increased miR-197-3p induces HCAECs abnormal by restraining TIMP3 expression directly. Hence, dysregulation of miR-197-3p/TIMP3 expression in HCAECs may be an important mechanism in cardiovascular endothelium injury in KD patients, which offers a feasible therapeutic target for KD treatment.
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Affiliation(s)
- Chaowu Liu
- Institute of Mass Spectrometer and Atmospheric Environment, Jinan University, Guangzhou, 510632, China
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, Guangdong, China
| | - Deguang Yang
- Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou, 510632, Guangdong, China
| | - Hong Wang
- Guangdong Province Engineering Research Center for Antibody Drug and Immunoassay, Colleges of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Shengwei Hu
- MOE Key Laboratory of Tumor Molecular Biology, Clinical Translational Center for Targeted Drug, Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Xiaofei Xie
- Department of Pediatric Cardiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Li Zhang
- Department of Pediatric Cardiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Hongling Jia
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China.
| | - Qi Qi
- MOE Key Laboratory of Tumor Molecular Biology, Clinical Translational Center for Targeted Drug, Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China.
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Wang IH, Huang TT, Chen JL, Chu LW, Ping YH, Hsu KW, Huang KH, Fang WL, Lee HC, Chen CF, Liao CC, Hsieh RH, Yeh TS. Mevalonate Pathway Enzyme HMGCS1 Contributes to Gastric Cancer Progression. Cancers (Basel) 2020; 12:cancers12051088. [PMID: 32349352 PMCID: PMC7281414 DOI: 10.3390/cancers12051088] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/24/2020] [Accepted: 04/25/2020] [Indexed: 01/26/2023] Open
Abstract
The 3-hydroxy-3-methylglutaryl-CoA synthase 1 (HMGCS1) is a potential regulatory node in the mevalonate pathway that is frequently dysregulated in tumors. This study found that HMGCS1 expression is upregulated in stomach adenocarcinoma samples of patients and tumorspheres of gastric cancer cells. HMGCS1 elevates the expression levels of the pluripotency genes Oct4 and SOX-2 and contributes to tumorsphere formation ability in gastric cancer cells. HMGCS1 also promotes in vitro cell growth and progression and the in vivo tumor growth and lung metastasis of gastric cancer cells. After blocking the mevalonate pathway by statin and dipyridamole, HMGCS1 exerts nonmetabolic functions in enhancing gastric cancer progression. Furthermore, the level and nuclear translocation of HMGCS1 in gastric cancer cells are induced by serum deprivation. HMGCS1 binds to and activates Oct4 and SOX-2 promoters. HMGCS1 also enhances the integrated stress response (ISR) and interacts with the endoplasmic reticulum (ER) stress transducer protein kinase RNA-like endoplasmic reticulum kinase (PERK). Our results reveal that HMGCS1 contributes to gastric cancer progression in both metabolic and nonmetabolic manners.
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Affiliation(s)
- I-Han Wang
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 112, Taiwan;
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (T.-T.H.); (J.-L.C.)
| | - Tzu-Ting Huang
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (T.-T.H.); (J.-L.C.)
| | - Ji-Lin Chen
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (T.-T.H.); (J.-L.C.)
| | - Li-Wei Chu
- Department and Institute of Pharmacology, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (L.-W.C.); (Y.-H.P.); (H.-C.L.)
| | - Yueh-Hsin Ping
- Department and Institute of Pharmacology, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (L.-W.C.); (Y.-H.P.); (H.-C.L.)
| | - Kai-Wen Hsu
- Research Center for Tumor Medical Science, China Medical University, Taichung 404, Taiwan;
- Graduate Institutes of New Drug Development, China Medical University, Taichung 404, Taiwan
| | - Kuo-Hung Huang
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (K.-H.H.); (W.-L.F.)
- Department of Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Wen-Liang Fang
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (K.-H.H.); (W.-L.F.)
- Department of Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Hsin-Chen Lee
- Department and Institute of Pharmacology, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (L.-W.C.); (Y.-H.P.); (H.-C.L.)
| | - Chian-Feng Chen
- Cancer Progression Research Center, National Yang-Ming University, Taipei 112, Taiwan;
| | - Chen-Chung Liao
- Proteomics Research Center, National Yang-Ming University, Taipei 112, Taiwan;
| | - Rong-Hong Hsieh
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan;
| | - Tien-Shun Yeh
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (T.-T.H.); (J.-L.C.)
- Cancer Progression Research Center, National Yang-Ming University, Taipei 112, Taiwan;
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Correspondence: ; Tel.: +886-2-2826-7070; Fax: +886-2-2821-2884
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Liu S, Wang X, Qin W, Genchev GZ, Lu H. Transcription Factors Contribute to Differential Expression in Cellular Pathways in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. Interdiscip Sci 2018; 10:836-847. [PMID: 30039492 DOI: 10.1007/s12539-018-0300-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/25/2022]
Abstract
Lung cancers are broadly classified into small cell lung cancers and non-small cell lung cancers (NSCLC). Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are two common subtypes of NSCLC, and despite the fact that both occur in lung tissues, these two subtypes show a number of different pathological characteristics. To investigate the differences and seek potential therapy targets, we used bioinformatics methods to analyze RNA-Seq data from different aspects. The previous studies and comparative pathway enrichment analysis on publicly available data showed that expressed or inhibited genes are different in two cancer subtypes through important pathways. Some of these genes could not only affect cell function through expression, but also could regulate other genes' expression by binding to a specific DNA sequence. This kind of genes is called transcription factor (TF) or sequence-specific DNA-binding factor. Transcription factors play important roles in controlling gene expression in carcinoma pathways. Our results revealed transcription factors that may cause differential expression of genes in cellular pathways of LUAD and LUSC, which provide new clues for study and treatment. Once such TF is NFE2l2 which may regulate genes in the Wnt signaling pathway, and the MAPK signaling pathway, thus leading to an increase the cell growth, cell division, and gene transcription. Another TF-XBP1 has high correlation with genes related to cell adhesion molecules and cytokine-cytokine receptor interaction pathways that may further affect the immune system. Moreover, the two TF and high correlated genes also show similar patterns in an independent GEO data set.
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Affiliation(s)
- Shiyi Liu
- Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, China
| | - Xujun Wang
- Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, China.,SJTU-Yale Joint Center for Biostatistics, Shanghai Jiaotong University, Shanghai, China
| | - Wenyi Qin
- SJTU-Yale Joint Center for Biostatistics, Shanghai Jiaotong University, Shanghai, China.,Department of Bioengineering, University of Illinois at Chicago, 851 S. Morgan, Rm 218, Chicago, IL, 60607, USA
| | - Georgi Z Genchev
- SJTU-Yale Joint Center for Biostatistics, Shanghai Jiaotong University, Shanghai, China
| | - Hui Lu
- Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, China. .,SJTU-Yale Joint Center for Biostatistics, Shanghai Jiaotong University, Shanghai, China. .,Department of Bioengineering, University of Illinois at Chicago, 851 S. Morgan, Rm 218, Chicago, IL, 60607, USA.
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Dubey R, Malhotra SS, Gupta SK. Forskolin-mediated BeWo cell fusion involves down-regulation of miR-92a-1-5p that targets dysferlin and protein kinase cAMP-activated catalytic subunit alpha. Am J Reprod Immunol 2018; 79:e12834. [PMID: 29484758 DOI: 10.1111/aji.12834] [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: 12/07/2017] [Accepted: 02/04/2018] [Indexed: 12/16/2022] Open
Abstract
PROBLEM To study the role of miRNA(s) during trophoblastic BeWo cell fusion. METHOD OF STUDY Changes in miRNA(s) profile of BeWo cells treated with forskolin were analyzed using Affymetrix miRNA microarray platform. Down-regulated miRNA, miR-92a-1-5p, was overexpressed in BeWo cells followed by forskolin treatment to understand its relevance in the process of BeWo cell fusion by desmoplakin I+II staining and hCG secretion by ELISA. Predicted targets of miR-92a-1-5p were also confirmed by qRT-PCR/Western blotting. RESULTS The miRNA profiling of BeWo cells after forskolin (25 μmol/L) treatment identified miR-92a-1-5p as the most significantly down-regulated miRNA both at 24 and 48 hours time points. Overexpression of miR-92a-1-5p in these cells led to a significant decrease in forskolin-mediated cell fusion and hCG secretion. miRNA target prediction software, TargetScan, revealed dysferlin (DYSF) and protein kinase cAMP-activated catalytic subunit alpha (PRKACA), as target genes of miR-92a-1-5p. Overexpression of miR-92a-1-5p in BeWo cells showed reduction in forskolin-induced transcripts for DYSF and PRKACA. Further, reduction in DYSF (~2.6-fold) at protein level and PRKACA-encoded protein kinase A catalytic subunit alpha (PKAC-α; ~1.6-fold) were also observed. CONCLUSION These observations suggest that miR-92a-1-5p regulates forskolin-mediated BeWo cell fusion and hCG secretion by regulating PKA signaling pathway and dysferlin expression.
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Affiliation(s)
- Richa Dubey
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
| | - Sudha S Malhotra
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
| | - Satish K Gupta
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
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10
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Wang Y, Wang JH, Zhang XL, Wang XL, Yang L. Endoplasmic reticulum chaperone glucose-regulated protein 78 in gastric cancer: An emerging biomarker. Oncol Lett 2018; 15:6087-6093. [PMID: 29616092 DOI: 10.3892/ol.2018.8114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/15/2017] [Indexed: 12/17/2022] Open
Abstract
The endoplasmic reticulum (ER) is the principal organelle responsible for the synthesis, initial post-translational modification, folding, export and secretion of proteins. It is also responsible for the maintenance of cellular homeostasis. In response to cellular stress conditions including glucose deprivation, hypoxia and changes in calcium homeostasis, ER stress machinery is activated and triggers the unfolded protein response, resulting in the restoration of homeostasis or activation of cell death. Glucose-regulated protein 78 (GRP78), a molecular chaperone, may be induced by ER stress at the transcriptional and translational level. A number of studies have demonstrated that GRP78 serves an important role in tumor cell proliferation, metastasis, angiogenesis and drug-resistance. The present review systematically describes the association between GRP78 expression and gastric cancer pathogenesis, and emphasizes that GRP78 is a novel diagnostic and therapeutic biomarker of gastric cancer.
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Affiliation(s)
- Yan Wang
- Department of Medical Oncology, Nantong University Affiliated Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Jian-Hong Wang
- Department of Medical Oncology, Nantong University Affiliated Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Xun-Lei Zhang
- Department of Medical Oncology, Nantong University Affiliated Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Xiao-Li Wang
- Department of Medical Oncology, Nantong University Affiliated Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Lei Yang
- Department of Medical Oncology, Nantong University Affiliated Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
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11
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Bononi I, Comar M, Puozzo A, Stendardo M, Boschetto P, Orecchia S, Libener R, Guaschino R, Pietrobon S, Ferracin M, Negrini M, Martini F, Bovenzi M, Tognon M. Circulating microRNAs found dysregulated in ex-exposed asbestos workers and pleural mesothelioma patients as potential new biomarkers. Oncotarget 2018; 7:82700-82711. [PMID: 27716620 PMCID: PMC5347725 DOI: 10.18632/oncotarget.12408] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/16/2016] [Indexed: 12/12/2022] Open
Abstract
Malignant pleural mesothelioma (MPM), a fatal cancer, is an occupational disease mostly affecting workers ex-exposed to asbestos fibers. The asbestos, a cancerogenic mineral of different chemical composition, was widely employed in western Countries in industrial manufactures of different types. MPM may arise after a long latency period, up to five decades. MPM is resistant to conventional chemo- and radio-therapies. Altogether, these data indicate that the identification of new and specific markers are of a paramount importance for an early diagnosis and treatment of MPM. In recent years, microRNAs expression was found dysregulated in patients, both in cancer cells and sera, affected by tumors of different histotypes, including MPM. Cell and circulanting microRNAs, found to be dysregulated in this neoplasia, were proposed as new biomarkers. It has been reported that circulating microRNAs are stable in biological fluids and could be employed as potential MPM biomarkers. In this investigation, circulating microRNAs (miR) from serum samples of MPM patients and workers ex-exposed to asbestos fibers (WEA) and healthy subjects (HS) were comparatively analyzed by microarray and RT-qPCR technologies. Our results allowed (i) to select MiR-3665, an endogenous stable microRNA, as the internal control to quantify in our analyses circulating miRNAs; to detect (ii) miR-197-3p, miR-1281 and miR 32-3p up-regulated in MPM compared to HS; (iii) miR-197-3p and miR-32-3p up-regulated in MPM compared to WEA; (iv) miR-1281 up-regulated in both MPM and WEA compared to HS. In conclusion, three circulating up-regulated microRNAs, i.e. miR-197-3p, miR-1281 and miR-32-3p are proposed as potential new MPM biomarkers.
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Affiliation(s)
- Ilaria Bononi
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy
| | - Manola Comar
- Institute for Maternal and Child Health - IRCCS "Burlo-Garofolo"- Trieste, University of Trieste, Trieste, Italy
| | - Andrea Puozzo
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy
| | - Mariarita Stendardo
- Department of Medical Sciences, School of Medicine, University of Ferrara, Ferrara, Italy
| | - Piera Boschetto
- Department of Medical Sciences, School of Medicine, University of Ferrara, Ferrara, Italy
| | - Sara Orecchia
- Mesothelioma BioBank, Pathology Unit and City Hospital, Alessandria, Italy
| | - Roberta Libener
- Mesothelioma BioBank, Pathology Unit and City Hospital, Alessandria, Italy
| | | | - Silvia Pietrobon
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine - DIMES, University of Bologna, Bologna, Italy
| | - Massimo Negrini
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy.,Laboratory for Technologies of Advances Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - Fernanda Martini
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy
| | - Massimo Bovenzi
- Clinical Unit of Occupational Medicine, Department of Medical Sciences, School of Medicine, University of Trieste, Trieste, Italy
| | - Mauro Tognon
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, School of Medicine, University of Ferrara, Ferrara, Italy
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12
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Chowdhari S, Sardana K, Saini N. miR-4516, a microRNA downregulated in psoriasis inhibits keratinocyte motility by targeting fibronectin/integrin α9 signaling. Biochim Biophys Acta Mol Basis Dis 2017; 1863:3142-3152. [DOI: 10.1016/j.bbadis.2017.08.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 07/28/2017] [Accepted: 08/16/2017] [Indexed: 12/13/2022]
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13
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Yang S, Shao F, Duan W, Zhao Y, Chen F. Variance component testing for identifying differentially expressed genes in RNA-seq data. PeerJ 2017; 5:e3797. [PMID: 28929020 PMCID: PMC5592911 DOI: 10.7717/peerj.3797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/21/2017] [Indexed: 01/28/2023] Open
Abstract
RNA sequencing (RNA-Seq) enables the measurement and comparison of gene expression with isoform-level quantification. Differences in the effect of each isoform may make traditional methods, which aggregate isoforms, ineffective. Here, we introduce a variance component-based test that can jointly test multiple isoforms of one gene to identify differentially expressed (DE) genes, especially those with isoforms that have differential effects. We model isoform-level expression data from RNA-Seq using a negative binomial distribution and consider the baseline abundance of isoforms and their effects as two random terms. Our approach tests the global null hypothesis of no difference in any of the isoforms. The null distribution of the derived score statistic is investigated using empirical and theoretical methods. The results of simulations suggest that the performance of the proposed set test is superior to that of traditional algorithms and almost reaches optimal power when the variance of covariates is large. This method is also applied to analyze real data. Our algorithm, as a supplement to traditional algorithms, is superior at selecting DE genes with sparse or opposite effects for isoforms.
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Affiliation(s)
- Sheng Yang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, China
| | - Fang Shao
- Department of Biostatistics, School of Public Health, Nanjing Medical University, China
| | - Weiwei Duan
- Department of Biostatistics, School of Public Health, Nanjing Medical University, China
| | - Yang Zhao
- Department of Biostatistics, School of Public Health, Nanjing Medical University, China
| | - Feng Chen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, China
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14
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Qing T, Yamin Z, Guijie W, Yan J, Zhongyang S. STAT6 silencing induces hepatocellular carcinoma-derived cell apoptosis and growth inhibition by decreasing the RANKL expression. Biomed Pharmacother 2017; 92:1-6. [DOI: 10.1016/j.biopha.2017.05.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 05/05/2017] [Accepted: 05/06/2017] [Indexed: 12/22/2022] Open
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15
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Shan Y, Chang T, Shi S, Tang M, Bao L, Li L, You B, You Y. Foxj2 overexpression is associated with poor prognosis, progression, and metastasis in nasopharyngeal carcinoma. Onco Targets Ther 2017; 10:3733-3741. [PMID: 28769576 PMCID: PMC5533490 DOI: 10.2147/ott.s134915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Foxj2, a novel member of Forkhead box family, has been reported to play an important role in tumorigenesis, progression, and metastasis of certain cancers. However, the expression status and effects of Foxj2 on nasopharyngeal carcinoma (NPC) progression and metastasis remain debated. In this study, we first examined the expression of Foxj2 in NPC by immunohistochemistry and Western blotting analysis. We confirmed significantly elevated expression of Foxj2 in NPC tissues and cell lines. Next, the relationships between Foxj2 expression levels and the clinicopathological factors were investigated. Its expression level correlated with T-classification (P=0.026), distant metastasis (P=0.004), and clinical stage (P=0.029). In addition, high expression of Foxj2 was associated with poor prognosis in NPC patients. The effects of Foxj2 on cell proliferation and migration were explored by RNA interference (RNAi) with CCK-8 assay, cell cycle analyses, wound healing, and transwell assay. In conclusion, our data indicate that Foxj2 upregulation promotes the progression and migration of NPC. It makes Foxj2 serve as a potential therapeutic target for the treatment of NPC.
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Affiliation(s)
- Ying Shan
- Department of Otorhinolaryngology, Head and Neck Surgery, Affiliated Hospital of Nantong University, Nantong
| | - Tao Chang
- Department of Otorhinolaryngology, Head and Neck Surgery, The First People's Hospital of Wujiang, Wujiang
| | - Si Shi
- Department of Otorhinolaryngology, Head and Neck Surgery, Affiliated Hospital of Nantong University, Nantong
| | - Mingming Tang
- Department of Otorhinolaryngology, Head and Neck Surgery, Affiliated Cancer Hospital of Nantong University, Nantong, Jiangsu Province, People's Republic of China
| | - Lili Bao
- Department of Otorhinolaryngology, Head and Neck Surgery, Affiliated Hospital of Nantong University, Nantong
| | - Li Li
- Department of Otorhinolaryngology, Head and Neck Surgery, Affiliated Hospital of Nantong University, Nantong
| | - Bo You
- Department of Otorhinolaryngology, Head and Neck Surgery, Affiliated Hospital of Nantong University, Nantong
| | - Yiwen You
- Department of Otorhinolaryngology, Head and Neck Surgery, Affiliated Hospital of Nantong University, Nantong
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16
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Miao H, Miao CX, Li N, Han J. FOXJ2 controls meiosis during spermatogenesis in male mice. Mol Reprod Dev 2016; 83:684-91. [PMID: 27316861 DOI: 10.1002/mrd.22671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 06/13/2016] [Indexed: 12/17/2022]
Abstract
Spermatogenesis is a highly complex cell differentiation process necessary for production of haploid spermatozoa. Central to this unique process is spermatocyte meiosis. FOXJ2 (Forkhead box J2), a FOX transcription factor, is specifically expressed in meiotic spermatocytes in adult mouse testes, so we used a germ cell specific conditional knockout model (Foxj2(flox/flox) , Mvh-Cre) to explore its role in spermatogenesis. Loss of FOXJ2 in the male germ line led to meiotic arrest and complete infertility. Although, DNA double-strand breaks (DSBs) were initiated, Foxj2-deficient spermatocytes failed to form chromosomal synapses and perform DSB repair. Furthermore, Foxj2-deficient spermatocytes contained significantly less mRNA encoding DSB repair-associated factors (Rad18, Rad51, Brca1, Brca2, and Tex15) and meiotic arrest-related proteins (Fzr1, Hsp70-2, Spata22, Eif4g3, and Zpac); in contrast, no change was observed in the expression of spermatogonia markers (Gfra1, Zbtb16, and c-Kit) and germ cell markers (Dazl, Mvh, and Tra98). Taken together, FOXJ2 appears to promote meiotic progression in male mice by a mechanism that needs further investigation. Mol. Reprod. Dev. 83: 684-691, 2016 © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hui Miao
- Department of, Reproduction and Genetics, ChangZhi Medical College Affiliated HePing Hospital, ShanXi Province, China
| | - Cong-Xiu Miao
- Department of, Reproduction and Genetics, ChangZhi Medical College Affiliated HePing Hospital, ShanXi Province, China
| | - Na Li
- Department of, Reproduction and Genetics, ChangZhi Medical College Affiliated HePing Hospital, ShanXi Province, China
| | - Jing Han
- Department of, Reproduction and Genetics, ChangZhi Medical College Affiliated HePing Hospital, ShanXi Province, China
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17
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Wang DD, Chen X, Yu DD, Yang SJ, Shen HY, Sha HH, Zhong SL, Zhao JH, Tang JH. miR-197: A novel biomarker for cancers. Gene 2016; 591:313-9. [PMID: 27320730 DOI: 10.1016/j.gene.2016.06.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/06/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
microRNAs (miRNAs) are small noncoding RNAs that could regulate post-transcription level through binding to 3' untranslated region (3'UTR) of target messenger RNAs (mRNAs), which were reported to be related with the incidence and development of diverse neoplasms. Among them, miR-197 was confirmed to play a vital role of oncogene or anti-oncogene in different cancers via targeting key tumorigenic or tumor-suppressive genes. Additionally, miR-197 had extensively been studied in carcinogenesis progression of cancers through various mechanisms, including apoptosis, proliferation, angiogenesis, metastasis, drug resistance and tumor suppressor, and also played a role in prognosis of cancers. In this review, we summarized the roles of miR-197 in cancers and considered it as a potentially novel biomarker for different cancers, offering an alternatively secure and effective tool in molecular targeting cancer treatment.
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Affiliation(s)
- Dan-Dan Wang
- The First Clinical School of Nanjing Medical University, Nanjing 210009, China; The Forth Clinical School of Nanjing Medical University, Nanjing 210009, China
| | - Xiu Chen
- The Forth Clinical School of Nanjing Medical University, Nanjing 210009, China; Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China
| | - Dan-Dan Yu
- The First Clinical School of Nanjing Medical University, Nanjing 210009, China; Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China
| | - Su-Jin Yang
- The Forth Clinical School of Nanjing Medical University, Nanjing 210009, China; Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China
| | - Hong-Yu Shen
- The Forth Clinical School of Nanjing Medical University, Nanjing 210009, China; Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China
| | - Huan-Huan Sha
- The Forth Clinical School of Nanjing Medical University, Nanjing 210009, China; Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China
| | - Shan-Liang Zhong
- Center of Clinical Laboratory, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China
| | - Jian-Hua Zhao
- Center of Clinical Laboratory, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China
| | - Jin-Hai Tang
- Department of General Surgery, the First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China; Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Baiziting 42, Nanjing 210009, China.
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18
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Isoquercetin ameliorates tunicamycin-induced apoptosis in rat dorsal root ganglion neurons via suppressing ROS-dependent endoplasmic reticulum stress. Biomed Pharmacother 2016; 80:343-351. [DOI: 10.1016/j.biopha.2016.03.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 03/28/2016] [Accepted: 03/28/2016] [Indexed: 11/18/2022] Open
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19
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Meckbach C, Tacke R, Hua X, Waack S, Wingender E, Gültas M. PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information. BMC Bioinformatics 2015; 16:400. [PMID: 26627005 PMCID: PMC4667426 DOI: 10.1186/s12859-015-0827-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 11/17/2015] [Indexed: 01/06/2023] Open
Abstract
Background Transcription factors (TFs) are important regulatory proteins that govern transcriptional regulation. Today, it is known that in higher organisms different TFs have to cooperate rather than acting individually in order to control complex genetic programs. The identification of these interactions is an important challenge for understanding the molecular mechanisms of regulating biological processes. In this study, we present a new method based on pointwise mutual information, PC-TraFF, which considers the genome as a document, the sequences as sentences, and TF binding sites (TFBSs) as words to identify interacting TFs in a set of sequences. Results To demonstrate the effectiveness of PC-TraFF, we performed a genome-wide analysis and a breast cancer-associated sequence set analysis for protein coding and miRNA genes. Our results show that in any of these sequence sets, PC-TraFF is able to identify important interacting TF pairs, for most of which we found support by previously published experimental results. Further, we made a pairwise comparison between PC-TraFF and three conventional methods. The outcome of this comparison study strongly suggests that all these methods focus on different important aspects of interaction between TFs and thus the pairwise overlap between any of them is only marginal. Conclusions In this study, adopting the idea from the field of linguistics in the field of bioinformatics, we develop a new information theoretic method, PC-TraFF, for the identification of potentially collaborating transcription factors based on the idiosyncrasy of their binding site distributions on the genome. The results of our study show that PC-TraFF can succesfully identify known interacting TF pairs and thus its currently biologically uncorfirmed predictions could provide new hypotheses for further experimental validation. Additionally, the comparison of the results of PC-TraFF with the results of previous methods demonstrates that different methods with their specific scopes can perfectly supplement each other. Overall, our analyses indicate that PC-TraFF is a time-efficient method where its algorithm has a tractable computational time and memory consumption. The PC-TraFF server is freely accessible at http://pctraff.bioinf.med.uni-goettingen.de/ Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0827-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cornelia Meckbach
- Institute of Bioinformatics, University of Göttingen, Goldschmidtstr. 1, Göttingen, 37077, Germany.
| | - Rebecca Tacke
- Institute of Bioinformatics, University of Göttingen, Goldschmidtstr. 1, Göttingen, 37077, Germany.
| | - Xu Hua
- Institute of Bioinformatics, University of Göttingen, Goldschmidtstr. 1, Göttingen, 37077, Germany.
| | - Stephan Waack
- Institute of Computer Science, University of Göttingen, Goldschmidtstr. 7, Göttingen, 37077, Germany.
| | - Edgar Wingender
- Institute of Bioinformatics, University of Göttingen, Goldschmidtstr. 1, Göttingen, 37077, Germany.
| | - Mehmet Gültas
- Institute of Bioinformatics, University of Göttingen, Goldschmidtstr. 1, Göttingen, 37077, Germany.
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20
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DiMarco DM, Fernandez ML. The Regulation of Reverse Cholesterol Transport and Cellular Cholesterol Homeostasis by MicroRNAs. BIOLOGY 2015; 4:494-511. [PMID: 26226008 PMCID: PMC4588146 DOI: 10.3390/biology4030494] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that have the ability to post-transcriptionally regulate gene expression. Hundreds of miRNAs have been identified in humans and they are involved in the regulation of almost every process, including cholesterol transport, metabolism, and maintenance of cholesterol homeostasis. Because of their small size and their ability to very specifically regulate gene expression, miRNAs are attractive targets for the regulation of dyslipidemias and other lipid-related disorders. However, the complex interactions between miRNAs, transcription factors, and gene expression raise great potential for side effects as a result of miRNA overexpression or inhibition. Many dietary components can also target specific miRNAs, altering the expression of downstream genes. Therefore, much more research is necessary to fully understand the role(s) of each miRNA in the body and how they may be impacted by diet and health. The present review aims to summarize the known roles of miRNAs in the regulation of reverse cholesterol transport and the maintenance of cholesterol homeostasis, as well as the potential clinical consequences of their manipulation.
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Affiliation(s)
- Diana M DiMarco
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT 06269, USA.
| | - Maria Luz Fernandez
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT 06269, USA.
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21
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RETRACTED ARTICLE: TN-2 Ameliorates Tunicamycin-Induced Mitochondria and Endoplasmic Reticulum Stress-Associated Apoptosis in Rat Dorsal Root Ganglion Neurons. J Mol Neurosci 2015; 57:314. [DOI: 10.1007/s12031-015-0599-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/03/2015] [Indexed: 11/27/2022]
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22
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Gu S, Yang XC, Xiang XY, Wu Y, Zhang Y, Yan XY, Xue YN, Sun LK, Shao GG. Sanguinarine-induced apoptosis in lung adenocarcinoma cells is dependent on reactive oxygen species production and endoplasmic reticulum stress. Oncol Rep 2015; 34:913-9. [PMID: 26081590 DOI: 10.3892/or.2015.4054] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 04/30/2015] [Indexed: 11/05/2022] Open
Abstract
Sanguinarine (SAN), an alkaloid isolated from plants of the Papaveraceae family, is a compound with multiple biological activities. In the present study, we explored the anticancer properties of SAN in lung cancer using the human lung adenocarcinoma cell line SPC-A1. Our results revealed that SAN inhibited SPC-A1 cell growth and induced apoptosis in a dose-dependent manner. We found that SAN triggered reactive oxygen species (ROS) production, while elimination of ROS by N-acetylcysteine (NAC) reversed the growth inhibition and apoptosis induced by SAN. SAN-induced endoplasmic reticulum (ER) stress resulted in the upregulation of many genes and proteins involved in the unfolded protein response (UPR) pathway, including glucose-regulated protein 78 (GRP78), p-protein kinase R (PKR)-like ER kinase (PERK), p-eukaryotic translation initiation factor 2α (eIF2α), activating transcription factor 4 (ATF4) and CCAAT/enhancer binding protein homologous protein (CHOP). Blocking ER stress with tauroursodeoxycholic acid (TUDCA) markedly reduced SAN-induced inhibition of growth and apoptosis. Furthermore, TUDCA decreased SAN-induced ROS production, and NAC attenuated SAN-induced GRP78 and CHOP expression. Overall, our data indicate that the anticancer effects of SAN in lung cancer cells depend on ROS production and ER stress and that SAN may be a potential agent against lung cancer.
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Affiliation(s)
- Shuang Gu
- Department of Thoracic Surgery, First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xiao-Chun Yang
- Department of Pathophysiology, Basic College of Medicine, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xi-Yan Xiang
- Department of Pathophysiology, Basic College of Medicine, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Yao Wu
- Department of Pathophysiology, Basic College of Medicine, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Yu Zhang
- Department of Pathophysiology, Basic College of Medicine, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xiao-Yu Yan
- Department of Pathophysiology, Basic College of Medicine, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Ya-Nan Xue
- Department of Pathophysiology, Basic College of Medicine, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Lian-Kun Sun
- Department of Pathophysiology, Basic College of Medicine, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Guo-Guang Shao
- Department of Thoracic Surgery, First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China
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