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Maltseva D, Kirillov I, Zhiyanov A, Averinskaya D, Suvorov R, Gubani D, Kudriaeva A, Belogurov A, Tonevitsky A. Incautious design of shRNAs for stable overexpression of miRNAs could result in generation of undesired isomiRs. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195046. [PMID: 38876159 DOI: 10.1016/j.bbagrm.2024.195046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
shRNA-mediated strategy of miRNA overexpression based on RNA Polymerase III (Pol III) expression cassettes is widely used for miRNA functional studies. For some miRNAs, e.g., encoded in the genome as a part of a polycistronic miRNA cluster, it is most likely the only way for their individual stable overexpression. Here we have revealed that expression of miRNAs longer than 19 nt (e.g. 23 nt in length hsa-miR-93-5p) using such approach could be accompanied by undesired predominant generation of 5' end miRNA isoforms (5'-isomiRs). Extra U residues (up to five) added by Pol III at the 3' end of the transcribed shRNA during transcription termination could cause a shift in the Dicer cleavage position of the shRNA. This results in the formation of 5'-isomiRs, which have a significantly altered seed region compared to the initially encoded canonical hsa-miR-93-5p. We demonstrated that the commonly used qPCR method is insensitive to the formation of 5'-isomiRs and cannot be used to confirm miRNA overexpression. However, the predominant expression of 5'-isomiRs without three or four first nucleotides instead of the canonical isoform could be disclosed based on miRNA-Seq analysis. Moreover, mRNA sequencing data showed that the 5'-isomiRs of hsa-miR-93-5p presumably regulate their own mRNA targets. Thus, omitting miRNA-Seq analysis may lead to erroneous conclusions regarding revealed mRNA targets and possible molecular mechanisms in which studied miRNA is involved. Overall, the presented results show that structures of shRNAs for stable overexpression of miRNAs requires careful design to avoid generation of undesired 5'-isomiRs.
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Affiliation(s)
- Diana Maltseva
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Ivan Kirillov
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Anton Zhiyanov
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Daria Averinskaya
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Roman Suvorov
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Daria Gubani
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia
| | - Anna Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexey Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow 101000, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; Art Photonics GmbH, Berlin 12489, Germany.
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Efimova AS, Antipenko ID, Evtushenko EA, Balan PV, Tonevitskaya SA. Effect of IGFBP6 Knockdown on Proteins Regulating Exosome Synthesis and Secretion in MDA-MB-231 Cell Line. Bull Exp Biol Med 2023:10.1007/s10517-023-05828-9. [PMID: 37336811 DOI: 10.1007/s10517-023-05828-9] [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: 11/03/2022] [Indexed: 06/21/2023]
Abstract
One of the potential causes of cancer recurrence is disruption of the cell-cell communication in the primary tumors that is realized, among other things, through secretion and uptake of exosomes by cells. Low expression of the IGFBP6 gene (insulin-like growth factor binding protein 6) is associated with a high recurrence rate and can serve as a prognostic marker of luminal breast cancer. The knockdown of the IGFBP6 gene leads to significant changes in lipid metabolism. We performed a quantitative analysis of both exosomes and proteins involved in the mechanism of their biogenesis. Changes in the expression profile of mRNAs and their proteins responsible for the synthesis and secretion of exosomes were revealed. We showed a decrease in the expression of the of the VPS28 gene mRNA (vacuolar protein sorting-associated protein 28) and the corresponding protein by 2.3 and 5.6 times, respectively. The secretion of exosomes by MDA-MB-231 cells with IGFBP6 knockdown decreased by 2 times. We discussed a mechanism of disruption of cell-cell communication.
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Affiliation(s)
- A S Efimova
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia.
| | - I D Antipenko
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
| | - E A Evtushenko
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - P V Balan
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
| | - S A Tonevitskaya
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
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3
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Nikulin S, Razumovskaya A, Poloznikov A, Zakharova G, Alekseev B, Tonevitsky A. ELOVL5 and IGFBP6 genes modulate sensitivity of breast cancer cells to ferroptosis. Front Mol Biosci 2023; 10:1075704. [PMID: 36714261 PMCID: PMC9880435 DOI: 10.3389/fmolb.2023.1075704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
Introduction: Relapse of breast cancer is one of the key obstacles to successful treatment. Previously we have shown that low expression of ELOVL5 and IGFBP6 genes in breast cancer tissue corresponded to poor prognosis. ELOVL5 participates directly in the elongation of polyunsaturated fatty acids (PUFAs) that are considered to play an important role in cancer cell metabolism. Thus, in this work we studied the changes in lipid metabolism in breast cancer cells with reduced expression of either ELOVL5 or IGFBP6 gene. Methods: MDA-MB-231 cells with a stable knockdown of either ELOVL5 or IGFBP6 gene were used in this study. Transcriptomic and proteomic analysis as well as RT-PCR were utilized to assess gene expression. Content of individual fatty acids in the cells was measured with HPLC-MS. HPLC was used for analysis of the kinetics of PUFAs uptake. Cell viability was measured with MTS assay. Flow cytometry was used to measure activation of apoptosis. Fluorescent microscopy was utilized to assess accumulation of ROS and formation of lipid droplets. Glutathione peroxidase activity was measured with a colorimetric assay. Results: We found that the knockdown of IGFBP6 gene led to significant changes in the profile of fatty acids in the cells and in the expression of many genes associated with lipid metabolism. As some PUFAs are known to inhibit proliferation and cause death of cancer cells, we also tested the response of the cells to single PUFAs and to combinations of docosahexaenoic acid (DHA, a n-3 PUFA) with standard chemotherapeutic drugs. Our data suggest that external PUFAs cause cell death by activation of ferroptosis, an iron-dependent mechanism of cell death with excessive lipid peroxidation. Moreover, both knockdowns increased cells' sensitivity to ferroptosis, probably due to a significant decrease in the activity of the antioxidant enzyme GPX4. Addition of DHA to commonly used chemotherapeutic drugs enhanced their effect significantly, especially for the cells with low expression of IGFBP6 gene. Discussion: The results of this study suggest that addition of PUFAs to the treatment regimen for the patients with low expression of IGFBP6 and ELOVL5 genes can be potentially beneficial and is worth testing in a clinically relevant setting.
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Affiliation(s)
- Sergey Nikulin
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia,*Correspondence: Sergey Nikulin,
| | | | - Andrey Poloznikov
- P. A. Hertsen Moscow Oncology Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Galina Zakharova
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Boris Alekseev
- P. A. Hertsen Moscow Oncology Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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4
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Wen X, Yang G, Dong Y, Luo L, Cao B, Mengesha BA, Zu R, Liao Y, Liu C, Li S, Deng Y, Zhang K, Ma X, Huang J, Wang D, Zhao K, Leng P, Luo H. Selection and Validation of Reference Genes for Pan-Cancer in Platelets Based on RNA-Sequence Data. Front Genet 2022; 13:913886. [PMID: 35770000 PMCID: PMC9234127 DOI: 10.3389/fgene.2022.913886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Many studies in recent years have demonstrated that some messenger RNA (mRNA) in platelets can be used as biomarkers for the diagnosis of pan-cancer. The quantitative real-time polymerase chain reaction (RT-qPCR) molecular technique is most commonly used to determine mRNA expression changes in platelets. Accurate and reliable relative RT-qPCR is highly dependent on reliable reference genes. However, there is no study to validate the reference gene in platelets for pan-cancer. Given that the expression of some commonly used reference genes is altered in certain conditions, selecting and verifying the most suitable reference gene for pan-cancer in platelets is necessary to diagnose early stage cancer. This study performed bioinformatics and functional analysis from the RNA-seq of platelets data set (GSE68086). We generated 95 candidate reference genes after the primary bioinformatics step. Seven reference genes (YWHAZ, GNAS, GAPDH, OAZ1, PTMA, B2M, and ACTB) were screened out among the 95 candidate reference genes from the data set of the platelets’ transcriptome of pan-cancer and 73 commonly known reference genes. These candidate reference genes were verified by another platelets expression data set (GSE89843). Then, we used RT-qPCR to confirm the expression levels of these seven genes in pan-cancer patients and healthy individuals. These RT-qPCR results were analyzed using the internal stability analysis software programs (the comparative Delta CT method, geNorm, NormFinder, and BestKeeper) to rank the candidate genes in the order of decreasing stability. By contrast, the GAPDH gene was stably and constitutively expressed at high levels in all the tested samples. Therefore, GAPDH was recommended as the most suitable reference gene for platelet transcript analysis. In conclusion, our result may play an essential part in establishing a molecular diagnostic platform based on the platelets to diagnose pan-cancer.
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Affiliation(s)
- Xiaoxia Wen
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guishu Yang
- Department of Clinical Laboratory, Guangyuan Central Hospital, Guangyuan, China
| | | | - Liping Luo
- Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bangrong Cao
- Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Birga Anteneh Mengesha
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruiling Zu
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yulin Liao
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Chang Liu
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shi Li
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yao Deng
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Kaijiong Zhang
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xin Ma
- GenomCan Inc., Chengdu, China
| | - Jian Huang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Keyan Zhao
- GenomCan Inc., Chengdu, China
- *Correspondence: Keyan Zhao, ; Ping Leng, ; Huaichao Luo,
| | - Ping Leng
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Keyan Zhao, ; Ping Leng, ; Huaichao Luo,
| | - Huaichao Luo
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Keyan Zhao, ; Ping Leng, ; Huaichao Luo,
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5
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Zattoni M, Mearelli M, Vanni S, Colini Baldeschi A, Tran TH, Ferracin C, Catania M, Moda F, Di Fede G, Giaccone G, Tagliavini F, Zanusso G, Ironside JW, Ferrer I, Legname G. Serpin Signatures in Prion and Alzheimer's Diseases. Mol Neurobiol 2022; 59:3778-3799. [PMID: 35416570 PMCID: PMC9148297 DOI: 10.1007/s12035-022-02817-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/26/2022] [Indexed: 12/17/2022]
Abstract
Serpins represent the most broadly distributed superfamily of proteases inhibitors. They contribute to a variety of physiological functions and any alteration of the serpin-protease equilibrium can lead to severe consequences. SERPINA3 dysregulation has been associated with Alzheimer's disease (AD) and prion diseases. In this study, we investigated the differential expression of serpin superfamily members in neurodegenerative diseases. SERPIN expression was analyzed in human frontal cortex samples from cases of sporadic Creutzfeldt-Jakob disease (sCJD), patients at early stages of AD-related pathology, and age-matched controls not affected by neurodegenerative disorders. In addition, we studied whether Serpin expression was dysregulated in two animal models of prion disease and AD.Our analysis revealed that, besides the already observed upregulation of SERPINA3 in patients with prion disease and AD, SERPINB1, SERPINB6, SERPING1, SERPINH1, and SERPINI1 were dysregulated in sCJD individuals compared to controls, while only SERPINB1 was upregulated in AD patients. Furthermore, we analyzed whether other serpin members were differentially expressed in prion-infected mice compared to controls and, together with SerpinA3n, SerpinF2 increased levels were observed. Interestingly, SerpinA3n transcript and protein were upregulated in a mouse model of AD. The SERPINA3/SerpinA3nincreased anti-protease activity found in post-mortem brain tissue of AD and prion disease samples suggest its involvement in the neurodegenerative processes. A SERPINA3/SerpinA3n role in neurodegenerative disease-related protein aggregation was further corroborated by in vitro SerpinA3n-dependent prion accumulation changes. Our results indicate SERPINA3/SerpinA3n is a potential therapeutic target for the treatment of prion and prion-like neurodegenerative diseases.
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Affiliation(s)
- Marco Zattoni
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy
| | - Marika Mearelli
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy.,German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
| | - Silvia Vanni
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy.,Osteoncology Unit, Bioscience Laboratory, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Arianna Colini Baldeschi
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy.,Institute of Biomedicine, Department of Pathology and Experimental Therapeutics, Bellvitge University Hospital-IDIBELL, Barcelona, Spain
| | - Thanh Hoa Tran
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy.,VN-UK Institute for Research and Executive Education, The University of Danang, Da Nang, Vietnam
| | - Chiara Ferracin
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy
| | - Marcella Catania
- Division of Neurology 5 and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Fabio Moda
- Division of Neurology 5 and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giuseppe Di Fede
- Division of Neurology 5 and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giorgio Giaccone
- Division of Neurology 5 and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Fabrizio Tagliavini
- Scientific Directorate, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Gianluigi Zanusso
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - James W Ironside
- National CJD Research & Surveillance Unit, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Isidre Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, Spain.,Institute of Biomedical Research of Bellvitge (IDIBELL), Hospitalet de Llobregat, Spain.,Biomedical Research Network Center of Neurodegenerative Diseases (CIBERNED), Hospitalet de Llobregat, Spain
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy.
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6
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Song Q, Dou L, Zhang W, Peng Y, Huang M, Wang M. Public transcriptome database-based selection and validation of reliable reference genes for breast cancer research. Biomed Eng Online 2021; 20:124. [PMID: 34895237 PMCID: PMC8665499 DOI: 10.1186/s12938-021-00963-8] [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: 08/18/2021] [Accepted: 11/21/2021] [Indexed: 11/21/2022] Open
Abstract
Background Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive technique for evaluating gene expression levels. Choosing appropriate reference genes (RGs) is critical for normalizing and evaluating changes in the expression of target genes. However, uniform and reliable RGs for breast cancer research have not been identified, limiting the value of target gene expression studies. Here, we aimed to identify reliable and accurate RGs for breast cancer tissues and cell lines using the RNA-seq dataset. Methods First, we compiled the transcriptome profiling data from the TCGA database involving 1217 samples to identify novel RGs. Next, ten genes with relatively stable expression levels were chosen as novel candidate RGs, together with six conventional RGs. To determine and validate the optimal RGs we performed qRT-PCR experiments on 87 samples from 11 types of surgically excised breast tumor specimens (n = 66) and seven breast cancer cell lines (n = 21). Five publicly available algorithms (geNorm, NormFinder, ΔCt method, BestKeeper, and ComprFinder) were used to assess the expression stability of each RG across all breast cancer tissues and cell lines. Results Our results show that RG combinations SF1 + TRA2B + THRAP3 and THRAP3 + RHOA + QRICH1 showed stable expression in breast cancer tissues and cell lines, respectively, and that they displayed good interchangeability. We propose that these combinations are optimal triplet RGs for breast cancer research. Conclusions In summary, we identified novel and reliable RG combinations for breast cancer research based on a public RNA-seq dataset. Our results lay a solid foundation for the accurate normalization of qRT-PCR results across different breast cancer tissues and cells. Supplementary Information The online version contains supplementary material available at 10.1186/s12938-021-00963-8.
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Affiliation(s)
- Qiang Song
- Department of Central Laboratory, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, 404000, China
| | - Lu Dou
- Department of Central Laboratory, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, 404000, China
| | - Wenjin Zhang
- Department of Central Laboratory, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, 404000, China
| | - Yang Peng
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Man Huang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, No.165, Xin Cheng Lu, Wanzhou, Chongqing, 404000, China.
| | - Mengyuan Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, No.165, Xin Cheng Lu, Wanzhou, Chongqing, 404000, China.
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7
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Gorji-Bahri G, Moradtabrizi N, Hashemi A. Uncovering the stability status of the reputed reference genes in breast and hepatic cancer cell lines. PLoS One 2021; 16:e0259669. [PMID: 34752497 PMCID: PMC8577734 DOI: 10.1371/journal.pone.0259669] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/22/2021] [Indexed: 11/28/2022] Open
Abstract
Accurate and reliable relative gene expression analysis via the Reverse Transcription-quantitative Real Time PCR (RT-qPCR) method strongly depends on employing several stable reference genes as normalizers. Utilization of the reference genes without analyzing their expression stability under each experimental condition causes RT-qPCR analysis error as well as false output. Similar to cancerous tissues, cancer cell lines also exhibit various gene expression profiles. It is crucial to recognize stable reference genes for well-known cancer cell lines to minimize RT-qPCR analysis error. In this study, we showed the expression level and investigated the expression stability of eight common reference genes that are ACTB, YWHAZ, HPRT1, RNA18S, TBP, GAPDH, UBC, and B2M, in two sets of cancerous cell lines. One set contains MCF7, SKBR3, and MDA-MB231 as breast cancer cell lines. Another set includes three hepatic cancer cell lines, including Huh7, HepG2, and PLC-PRF5. Three excel-based softwares comprising geNorm, BestKeeper, and NormFinder, and an online tool, namely RefFinder were used for stability analysis. Although all four algorithms did not show the same stability ranking of nominee genes, the overall results showed B2M and ACTB as the least stable reference genes for the studied breast cancer cell lines. While TBP had the lowest expression stability in the three hepatic cancer cell lines. Moreover, YWHAZ, UBC, and GAPDH showed the highest stability in breast cancer cell lines. Besides that, a panel of five nominees, including ACTB, HPRT1, UBC, YWHAZ, and B2M showed higher stability than others in hepatic cancer cell lines. We believe that our results would help researchers to find and to select the best combination of the reference genes for their own experiments involving the studied breast and hepatic cancer cell lines. To further analyze the reference genes stability for each experimental condition, we suggest researchers to consider the provided stability ranking emphasizing the unstable reference genes.
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Affiliation(s)
- Gilar Gorji-Bahri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Niloofar Moradtabrizi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atieh Hashemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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8
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Arnold S, Kortland J, Maltseva DV, Nersisyan SA, Samatov TR, Lezius S, Tonevitsky AG, Milde-Langosch K, Wicklein D, Schumacher U, Stürken C. Fra-2 overexpression upregulates pro-metastatic cell-adhesion molecules, promotes pulmonary metastasis, and reduces survival in a spontaneous xenograft model of human breast cancer. J Cancer Res Clin Oncol 2021; 148:1525-1542. [PMID: 34693476 PMCID: PMC9114065 DOI: 10.1007/s00432-021-03812-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/22/2021] [Indexed: 11/28/2022]
Abstract
Purpose The transcription factor Fra-2 affects the invasive potential of breast cancer cells by dysregulating adhesion molecules in vitro. Previous results suggested that it upregulates the expression of E- and P-selectin ligands. Such selectin ligands are important members of the leukocyte adhesion cascade, which govern the adhesion and transmigration of cancer cells into the stroma of the host organ of metastasis. As so far, no in vivo data are available, this study was designed to elucidate the role of Fra-2 expression in a spontaneous breast cancer metastasis xenograft model. Methods The effect of Fra-2 overexpression in two stable Fra-2 overexpressing clones of the human breast cancer cell line MDA MB231 on survival and metastatic load was studied after subcutaneous injection into scid and E- and P-selectin-deficient scid mice. Results Fra-2 overexpression leads to a significantly shorter overall survival and a higher amount of spontaneous lung metastases not only in scid mice, but also in E- and P-deficient mice, indicating that it regulates not only selectin ligands, but also selectin-independent adhesion processes. Conclusion Thus, Fra-2 expression influences the metastatic potential of breast cancer cells by changing the expression of adhesion molecules, resulting in increased adherence to endothelial cells in a breast cancer xenograft model. Supplementary Information The online version contains supplementary material available at 10.1007/s00432-021-03812-2.
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Affiliation(s)
- Sabrina Arnold
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Jan Kortland
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Diana V Maltseva
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Myasnitskaya Str. 13/4, 117997, Moscow, Russia
| | - Stepan A Nersisyan
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Myasnitskaya Str. 13/4, 117997, Moscow, Russia
| | - Timur R Samatov
- Evotec International GmbH, Marie-Curie-Str. 7, 37079, Göttingen, Germany
| | - Susanne Lezius
- Department of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Alexander G Tonevitsky
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Myasnitskaya Str. 13/4, 117997, Moscow, Russia.,Scientific Research Center Bioclinicum, Ugreshskaya Str. 2/85, 115088, Moscow, Russia
| | - Karin Milde-Langosch
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Daniel Wicklein
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Udo Schumacher
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Christine Stürken
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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9
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Identification of Novel Endogenous Controls for qPCR Normalization in SK-BR-3 Breast Cancer Cell Line. Genes (Basel) 2021; 12:genes12101631. [PMID: 34681026 PMCID: PMC8535678 DOI: 10.3390/genes12101631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
Normalization of gene expression using internal controls or reference genes (RGs) has been the method of choice for standardizing the technical variations in reverse transcription quantitative polymerase chain reactions (RT-qPCR). Conventionally, ACTB and GAPDH have been used as reference genes despite evidence from literature discouraging their use. Hence, in the present study we identified and investigated novel reference genes in SK-BR-3, an HER2-enriched breast cancer cell line. Transcriptomic data of 82 HER2-E breast cancer samples from TCGA database were analyzed to identify twelve novel genes with stable expression. Additionally, thirteen RGs from the literature were analyzed. The expression variations of the candidate genes were studied over five successive passages (p) in two parallel cultures S1 and S2 and in acute and chronic hypoxia using various algorithms. Finally, the most stable RGs were selected and validated for normalization of the expression of three genes of interest (GOIs) in normoxia and hypoxia. Our results indicate that HSP90AB1, DAD1, PFN1 and PUM1 can be used in any combination of three (triplets) for optimizing intra- and inter-assay gene expression differences in the SK-BR-3 cell line. Additionally, we discourage the use of conventional RGs (ACTB, GAPDH, RPL13A, RNA18S and RNA28S) as internal controls for RT-qPCR in SK-BR-3 cell line.
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10
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Evaluation of Angelica decursiva reference genes under various stimuli for RT-qPCR data normalization. Sci Rep 2021; 11:18993. [PMID: 34556773 PMCID: PMC8460625 DOI: 10.1038/s41598-021-98434-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 08/17/2021] [Indexed: 11/23/2022] Open
Abstract
Angelica decursiva is one of the lending traditional Chinese medicinal plants producing coumarins. Notably, several studies have focused on the biosynthesis and not the RT-qPCR (quantitative real-time reverse transcription polymerase chain reaction) study of coumarins. This RT-qPCR technique has been extensively used to investigate gene expression levels in plants and the selection of reference genes which plays a crucial role in standardizing the data form the RT-qPCR analysis. In our study, 11 candidate reference genes were selected from the existing transcriptome data of Angelica decursiva. Here, four different types of statistical algorithms (geNorm, NormFinder, BestKeeper, and Delta Ct) were used to calculate and evaluate the stability of gene expression under different external treatments. Subsequently, RefFinder analysis was used to determine the geometric average of each candidate gene ranking, and to perform comprehensive index ranking. The obtained results showed that among all the 11 candidate reference genes, SAND family protein (SAND), protein phosphatase 2A gene (PP2A), and polypyrimidine tract-binding protein (PTBP) were the most stable reference genes, where Nuclear cap binding protein 2 (NCBP2), TIP41-like protein (TIP41), and Beta-6-tubulin (TUBA) were the least stable genes. To the best of our knowledge, this work is the first to evaluate the stability of reference genes in the Angelica decursiva which has provided an important foundation on the use of RT-qPCR for an accurate and far-reaching gene expression analysis in this medicinal plant.
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11
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Xiang S, Shao X, Cao J, Yang B, He Q, Ying M. FAT10: Function and Relationship with Cancer. Curr Mol Pharmacol 2021; 13:182-191. [PMID: 31729307 DOI: 10.2174/1874467212666191113130312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 11/22/2022]
Abstract
Posttranslational protein modifications are known to be extensively involved in cancer, and a growing number of studies have revealed that the ubiquitin-like modifier FAT10 is directly involved in cancer development. FAT10 was found to be highly upregulated in various cancer types, such as glioma, hepatocellular carcinoma, breast cancer and gastrointestinal cancer. Protein FAT10ylation and interactions with FAT10 lead to the functional change of proteins, including proteasomal degradation, subcellular delocalization and stabilization, eventually having significant effects on cancer cell proliferation, invasion, metastasis and even tumorigenesis. In this review, we summarized the current knowledge on FAT10 and discussed its biological functions in cancer, as well as potential therapeutic strategies based on the FAT10 pathway.
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Affiliation(s)
- Senfeng Xiang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xuejing Shao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
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12
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Nikulin S, Zakharova G, Poloznikov A, Raigorodskaya M, Wicklein D, Schumacher U, Nersisyan S, Bergquist J, Bakalkin G, Astakhova L, Tonevitsky A. Effect of the Expression of ELOVL5 and IGFBP6 Genes on the Metastatic Potential of Breast Cancer Cells. Front Genet 2021; 12:662843. [PMID: 34149804 PMCID: PMC8206645 DOI: 10.3389/fgene.2021.662843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/20/2021] [Indexed: 12/09/2022] Open
Abstract
Breast cancer (BC) is the leading cause of death from malignant neoplasms among women worldwide, and metastatic BC presents the biggest problems for treatment. Previously, it was shown that lower expression of ELOVL5 and IGFBP6 genes is associated with a higher risk of the formation of distant metastases in BC. In this work, we studied the change in phenotypical traits, as well as in the transcriptomic and proteomic profiles of BC cells as a result of the stable knockdown of ELOVL5 and IGFBP6 genes. The knockdown of ELOVL5 and IGFBP6 genes was found to lead to a strong increase in the expression of the matrix metalloproteinase (MMP) MMP1. These results were in good agreement with the correlation analysis of gene expression in tumor samples from patients and were additionally confirmed by zymography. The knockdown of ELOVL5 and IGFBP6 genes was also discovered to change the expression of a group of genes involved in the formation of intercellular contacts. In particular, the expression of the CDH11 gene was markedly reduced, which also complies with the correlation analysis. The spheroid formation assay showed that intercellular adhesion decreased as a result of the knockdown of the ELOVL5 and IGFBP6 genes. Thus, the obtained data indicate that malignant breast tumors with reduced expression of the ELOVL5 and IGFBP6 genes can metastasize with a higher probability due to a more efficient invasion of tumor cells.
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Affiliation(s)
- Sergey Nikulin
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
| | | | - Andrey Poloznikov
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
- School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Maria Raigorodskaya
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
- Scientific Research Centre Bioclinicum, Moscow, Russia
| | - Daniel Wicklein
- Institute of Anatomy and Experimental Morphology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Udo Schumacher
- Institute of Anatomy and Experimental Morphology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
| | - Jonas Bergquist
- Department of Chemistry – BMC, Uppsala University, Uppsala, Sweden
| | - Georgy Bakalkin
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Lidiia Astakhova
- Scientific Research Centre Bioclinicum, Moscow, Russia
- School of Life Sciences, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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13
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Cole L, Kurscheid S, Nekrasov M, Domaschenz R, Vera DL, Dennis JH, Tremethick DJ. Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells. Nat Commun 2021; 12:2524. [PMID: 33953180 PMCID: PMC8100287 DOI: 10.1038/s41467-021-22688-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/25/2021] [Indexed: 01/02/2023] Open
Abstract
Chromatin accessibility of a promoter is fundamental in regulating transcriptional activity. The histone variant H2A.Z has been shown to contribute to this regulation, but its role has remained poorly understood. Here, we prepare high-depth maps of the position and accessibility of H2A.Z-containing nucleosomes for all human Pol II promoters in epithelial, mesenchymal and isogenic cancer cell lines. We find that, in contrast to the prevailing model, many different types of active and inactive promoter structures are observed that differ in their nucleosome organization and sensitivity to MNase digestion. Key aspects of an active chromatin structure include positioned H2A.Z MNase resistant nucleosomes upstream or downstream of the TSS, and a MNase sensitive nucleosome at the TSS. Furthermore, the loss of H2A.Z leads to a dramatic increase in the accessibility of transcription factor binding sites. Collectively, these results suggest that H2A.Z has multiple and distinct roles in regulating gene expression dependent upon its location in a promoter.
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Affiliation(s)
- Lauren Cole
- College of Arts and Sciences, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
| | - Sebastian Kurscheid
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Maxim Nekrasov
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Renae Domaschenz
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Daniel L Vera
- College of Arts and Sciences, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Jonathan H Dennis
- College of Arts and Sciences, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA.
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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14
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Jain N, Nitisa D, Pirsko V, Cakstina I. Selecting suitable reference genes for qPCR normalization: a comprehensive analysis in MCF-7 breast cancer cell line. BMC Mol Cell Biol 2020; 21:68. [PMID: 32977762 PMCID: PMC7519550 DOI: 10.1186/s12860-020-00313-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/16/2020] [Indexed: 02/08/2023] Open
Abstract
Background MCF-7 breast cancer cell line is undoubtedly amongst the most extensively studied patient-derived research models, providing pivotal results that have over the decades translated to constantly improving patient care. Many research groups, have previously identified suitable reference genes for qPCR normalization in MCF-7 cell line. However, over the course of identification of suitable reference genes, a comparative analysis comprising these genes together in a single study has not been reported. Furthermore, the expression dynamics of these reference genes within sub-clones cultured over multiple passages (p) has attracted limited attention from research groups. Therefore, we investigated the expression dynamics of 12 previously suggested reference genes within two sub-clones (culture A1 and A2) cultured identically over multiple passages. Additionally, the effect of nutrient stress on reference gene expression was examined to postulate an evidence-based recommendation of the least variable reference genes that could be employed in future gene expression studies. Results The analysis revealed the presence of differential reference gene expression within the sub-clones of MCF-7. In culture A1, GAPDH-CCSER2 were identified as the least variable reference genes while for culture A2, GAPDH-RNA28S were identified. However, upon validation using genes of interest, both these pairs were found to be unsuitable control pairs. Normalization of AURKA and KRT19 with triplet pair GAPDH-CCSER2-PCBP1 yielded successful results. The triplet also proved its capability to handle variations arising from nutrient stress. Conclusions The variance in expression behavior amongst sub-clones highlights the potential need for exercising caution while selecting reference genes for MCF-7. GAPDH-CCSER2-PCBP1 triplet offers a reliable alternative to otherwise traditionally used internal controls for optimizing intra- and inter-assay gene expression differences. Furthermore, we suggest avoiding the use of ACTB, GAPDH and PGK1 as single internal controls.
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Affiliation(s)
- Nityanand Jain
- Laboratory of Molecular Genetics, Institute of Oncology, Riga Stradiņš University, Dzirciema street 16, Riga, LV-1007, Latvia
| | - Dina Nitisa
- Laboratory of Molecular Genetics, Institute of Oncology, Riga Stradiņš University, Dzirciema street 16, Riga, LV-1007, Latvia
| | - Valdis Pirsko
- Laboratory of Molecular Genetics, Institute of Oncology, Riga Stradiņš University, Dzirciema street 16, Riga, LV-1007, Latvia
| | - Inese Cakstina
- Laboratory of Molecular Genetics, Institute of Oncology, Riga Stradiņš University, Dzirciema street 16, Riga, LV-1007, Latvia.
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15
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Hahnefeld L, Gruber L, Schömel N, Fischer C, Mattjus P, Gurke R, Beretta M, Ferreirós N, Geisslinger G, Wegner MS. Ether lipid and sphingolipid expression patterns are estrogen receptor-dependently altered in breast cancer cells. Int J Biochem Cell Biol 2020; 127:105834. [PMID: 32827762 DOI: 10.1016/j.biocel.2020.105834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 11/19/2022]
Abstract
Identifying co-expression of lipid species is challenging, but indispensable to identify novel therapeutic targets for breast cancer treatment. Lipid metabolism is often dysregulated in cancer cells, and changes in lipid metabolism affect cellular processes such as proliferation, autophagy, and tumor development. In addition to mRNA analysis of sphingolipid metabolizing enzymes, we performed liquid chromatography time-of-flight mass spectrometry analysis in three breast cancer cell lines. These breast cancer cell lines differ in estrogen receptor and G-protein coupled estrogen receptor 1 status. Our data show that sphingolipids and non-sphingolipids are strongly increased in SKBr3 cells. SKBr3 cells are estrogen receptor negative and G-protein coupled estrogen receptor 1 positive. Treatment with G15, a G-protein coupled estrogen receptor 1 antagonist, abolishes the effect of increased sphingolipid and non-sphingolipid levels in SKBr3 cells. In particular, ether lipids are expressed at much higher levels in cancer compared to normal cells and are strongly increased in SKBr3 cells. Our analysis reveals that this is accompanied by increased sphingolipid levels such as ceramide, sphingadiene-ceramide and sphingomyelin. This shows the importance of focusing on more than one lipid class when investigating molecular mechanisms in breast cancer cells. Our analysis allows unbiased screening for different lipid classes leading to identification of co-expression patterns of lipids in the context of breast cancer. Co-expression of different lipid classes could influence tumorigenic potential of breast cancer cells. Identification of co-regulated lipid species is important to achieve improved breast cancer treatment outcome.
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Affiliation(s)
- Lisa Hahnefeld
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Lisa Gruber
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Nina Schömel
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Caroline Fischer
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Peter Mattjus
- Åbo Akademi University, Biochemistry, Faculty of Science and Engineering Artillerigatan 6A, III, BioCity, FI-20520 Turku, Finland
| | - Robert Gurke
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Martina Beretta
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Nerea Ferreirós
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Gerd Geisslinger
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Marthe-Susanna Wegner
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
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16
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Wang C, Jin F, De Mandal S, Zeng L, Zhang Y, Hua Y, Hong Y, Zhao C, Li J, Li D, Xu X. Insights into the venom protein components of the egg parasitoid Anastatus japonicus (Hymenoptera: Eupelmidae). PEST MANAGEMENT SCIENCE 2020; 76:2113-2126. [PMID: 31951096 DOI: 10.1002/ps.5750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/08/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Parasitoid venom is composed of a complex mixture of various active substances with different biological functions and is injected in the host during the parasitoid oviposition. Anastatus japonicus (Hymenoptera: Eupelmidae) is an egg parasite of Tessaratoma papillosa (Hemiptera: Tessaratomidae). Although the venom of this egg parasitoid plays an important role in the parasitic process, relatively little work has been done to address the mechanism. RESULTS In the present study, proteomic analysis was performed to identify the proteins that play an important role in the parasitic process of A. japonicus. A total of 2084 proteins were identified, including 81 putative venom proteins, most of which were identified as Hexamerin, Chitinase 2, Calreticulin, Heat shock protein 83-like, Serine protease, Arginine kinase, Phosphoserine aminotransferase and Actin protein. Together the before (Be) and after (Af) parasitization venom contains 1628 proteins, including 212 DEPs with 181 and 31 significantly up-regulated and down-regulated respectively. In addition, 10 differentially expressed proteins (DEPs) with fold change ≥8.71 were subjected to RT-qPCR to validate the proteomic data. The differential expression analysis revealed that nine proteins were specifically present in the pre-parasitic venom, whereas 26 proteins were specific to the post-parasitic treatments. Results of RT-qPCR analysis showed high expression of the selected DEPs which further validated our proteomics data. CONCLUSION These new proteomic data greatly enrich our current knowledge about key venom proteins associated with parasitic process in A. japonicus and contribute to better understanding of the parasitic mechanisms leading to the development of new biological control strategies. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Chengxing Wang
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Plant Protection Research Institute, , Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Fengliang Jin
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Surajit De Mandal
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Lu Zeng
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yuxin Zhang
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yanyan Hua
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yingying Hong
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Can Zhao
- Plant Protection Research Institute, , Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Junzhai Li
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Plant Protection Research Institute, , Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Dunsong Li
- Plant Protection Research Institute, , Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Xiaoxia Xu
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
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17
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Wang Z, Xu J, Liu Y, Chen J, Lin H, Huang Y, Bian X, Zhao Y. Selection and validation of appropriate reference genes for real-time quantitative PCR analysis in Momordica charantia. PHYTOCHEMISTRY 2019; 164:1-11. [PMID: 31054374 DOI: 10.1016/j.phytochem.2019.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/21/2019] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
Real time quantitative reverse transcription PCR (RT-qPCR) has been attracting more attention for its high sensitivity in gene expression analysis. Given the widely use of RT-qPCR in normalization, it is playing a pivotal role for seeking suitable reference genes in different species. In current work, 12 candidate reference genes including Actin 2 (ACT2), Cyclophilin 2 (CYP2), Glyceraldehyde-3-phosphate dehydrogenase C2 (GAPC2), Elongation factor 1-α (EF1-α), Nuclear cap binding protein 20 (NCBP20), Serine/threonine-protein phosphatase PP2A (PP2A), Polypyrimidine tract-binding protein 1 (PTBP1), SAND family protein (SNAD), TIP41-like protein (TIP41), Tubulin beta-6 (TUB6), Ubiquitin-conjugating enzyme 9 (UBC9) and Glyceraldehyde-3-phosphatedehydrogenase (GAPDH) were screened from the transcriptome datasets of M. charantia. Afterwards, GeNorm, NormFinder and BestKeeper algorithms were applied to assess the expression stability of these 12 genes under different abiotic stresses including drought, cold, high-salt, hormone, UV, oxidative and metal stress. The results indicated that 12 selected genes exhibited various stability across the samples under different external stress conditions, but TIP41, PTBP1 and PP2A presented high stability among all the reference genes. To validate the suitability of the identified reference genes, the results of hormone subset were compared with RNA sequencing (RNA-seq) data, and the relative abundance of Ascorbate peroxidase 1(APX1)was used to confirm the reliability of the results. This work assesses the stability of reference genes in M. charantia under different abiotic stress conditions, which will be beneficent for accurate normalization of target genes in M. charantia.
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Affiliation(s)
- Zhenglong Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Jiyang Xu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yihan Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Jiyu Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Hanfeng Lin
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yanli Huang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Xiaohong Bian
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
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18
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Ma F, Liu Z, Huang J, Kang Y, Wang J. Evaluation of reference genes for quantitative real-time PCR analysis of messenger RNAs and microRNAs in rainbow trout Oncorhynchus mykiss under heat stress. JOURNAL OF FISH BIOLOGY 2019; 95:540-554. [PMID: 30993691 DOI: 10.1111/jfb.13986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
We assessed the expression stability of several messenger (m)RNAs and micro (mi)RNAs from liver and head kidney of rainbow trout Oncorhynchus mykiss using high-throughput RNA sequencing (RNA-seq) and miRNA-seq data. Additionally, four commonly used reference genes and one small non-coding RNA (u6) were also selected to identify ideal reference mRNAs and miRNAs for quantitative real-time (qrt)-PCR analysis of heat stress responses. GeNorm, NormFinder, BestKeeper and comparative ΔCt were employed for analysis of qrt-PCR data to systematically assess the expression stability of candidate mRNAs and miRNAs and stability was ranked using geometric means. β-actin and ef1-α were the most stably expressed reference mRNAs in liver and head kidney, respectively and ssa-mir-26a-5p and ssa-mir-462b-5p were the most stably expressed miRNAs in these tissues. This is the first identification of appropriate reference mRNAs and miRNAs for qrt-PCR analysis of O. mykiss under heat stress.
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Affiliation(s)
- Fang Ma
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmencun, Anning District, Lanzhou, Gansu, China
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmencun, Anning District, Lanzhou, Gansu, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmencun, Anning District, Lanzhou, Gansu, China
| | - Yujun Kang
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmencun, Anning District, Lanzhou, Gansu, China
| | - Jianfu Wang
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmencun, Anning District, Lanzhou, Gansu, China
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19
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Validation of Reference Genes for Gene Expression Normalization in RAW264.7 Cells under Different Conditions. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6131879. [PMID: 31223620 PMCID: PMC6541955 DOI: 10.1155/2019/6131879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/03/2019] [Accepted: 04/03/2019] [Indexed: 12/17/2022]
Abstract
RAW264.7 is a macrophage strain derived from mice tumour and shows a significant ability in antigen uptake. Real-time quantitative PCR (RT-qPCR) is one of the most commonly used methods in gene studies and requires suitable reference genes to normalize and quantitate the expression of gene of interest with sensitivity and specificity. However, suitable reference genes in RAW264.7 cells have not yet been identified for accurate gene expression quantification. In the current study, we evaluated expression levels of ten candidate reference genes in RAW264.7 cells under different conditions. RT-qPCR results indicated significant differences in the expression levels among the ten reference genes. Statistical analyses were carried out using geNorm, NormFinder, and BestKeeper software to further investigate the stability of the reference genes. Integrating the results from the three analytical methods, cytochrome c-1 and hydroxymethylbilane synthase were found to be the most stable and therefore more suitable reference genes, while ribosomal protein L4 and cyclophilin A were the least stable. This study emphasises the importance of identifying and selecting the most stable reference genes for normalization and provides a basis for future gene expression studies using RAW264.7 cells.
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Jo J, Choi S, Oh J, Lee SG, Choi SY, Kim KK, Park C. Conventionally used reference genes are not outstanding for normalization of gene expression in human cancer research. BMC Bioinformatics 2019; 20:245. [PMID: 31138119 PMCID: PMC6538551 DOI: 10.1186/s12859-019-2809-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The selection of reference genes is essential for quantifying gene expression. Theoretically they should be expressed stably and not regulated by experimental or pathological conditions. However, identification and validation of reference genes for human cancer research are still being regarded as a critical point, because cancerous tissues often represent genetic instability and heterogeneity. Recent pan-cancer studies have demonstrated the importance of the appropriate selection of reference genes for use as internal controls for the normalization of gene expression; however, no stably expressed, consensus reference genes valid for a range of different human cancers have yet been identified. RESULTS In the present study, we used large-scale cancer gene expression datasets from The Cancer Genome Atlas (TCGA) database, which contains 10,028 (9,364 cancerous and 664 normal) samples from 32 different cancer types, to confirm that the expression of the most commonly used reference genes is not consistent across a range of cancer types. Furthermore, we identified 38 novel candidate reference genes for the normalization of gene expression, independent of cancer type. These genes were found to be highly expressed and highly connected to relevant gene networks, and to be enriched in transcription-translation regulation processes. The expression stability of the newly identified reference genes across 29 cancerous and matched normal tissues were validated via quantitative reverse transcription PCR (RT-qPCR). CONCLUSIONS We reveal that most commonly used reference genes in current cancer studies cannot be appropriate to serve as representative control genes for quantifying cancer-related gene expression levels, and propose in this study three potential reference genes (HNRNPL, PCBP1, and RER1) to be the most stably expressed across various cancerous and normal human tissues.
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Affiliation(s)
- Jihoon Jo
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-Ro, Buk-Ku, GwangJu, 61186, Republic of Korea
| | - Sunkyung Choi
- Department of Biochemistry, Chungnam National University, 99 Daehak-Ro, Yuseong-Ku, Daejeon, 34134, Republic of Korea
| | - Jooseong Oh
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-Ro, Buk-Ku, GwangJu, 61186, Republic of Korea
| | - Sung-Gwon Lee
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-Ro, Buk-Ku, GwangJu, 61186, Republic of Korea
| | - Song Yi Choi
- Department of Pathology, Chungnam National University, 282 Munhwa-Ro, Jung-Ku, Daejeon, 35015, Republic of Korea.
| | - Kee K Kim
- Department of Biochemistry, Chungnam National University, 99 Daehak-Ro, Yuseong-Ku, Daejeon, 34134, Republic of Korea.
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-Ro, Buk-Ku, GwangJu, 61186, Republic of Korea.
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Maltseva DV, Makarova JA, Khristichenko AY, Tsypina IM, Tonevitsky E, Rodin SA. Epithelial to Mesenchymal Transition Marker in 2D and 3D Colon Cancer Cell Cultures in the Presence of Laminin 332 and 411. Mol Biol 2019. [DOI: 10.1134/s0026893319020110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Krasnov GS, Kudryavtseva AV, Snezhkina AV, Lakunina VA, Beniaminov AD, Melnikova NV, Dmitriev AA. Pan-Cancer Analysis of TCGA Data Revealed Promising Reference Genes for qPCR Normalization. Front Genet 2019; 10:97. [PMID: 30881377 PMCID: PMC6406071 DOI: 10.3389/fgene.2019.00097] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/29/2019] [Indexed: 11/20/2022] Open
Abstract
Quantitative PCR (qPCR) remains the most widely used technique for gene expression evaluation. Obtaining reliable data using this method requires reference genes (RGs) with stable mRNA level under experimental conditions. This issue is especially crucial in cancer studies because each tumor has a unique molecular portrait. The Cancer Genome Atlas (TCGA) project provides RNA-Seq data for thousands of samples corresponding to dozens of cancers and presents the basis for assessment of the suitability of genes as reference ones for qPCR data normalization. Using TCGA RNA-Seq data and previously developed CrossHub tool, we evaluated mRNA level of 32 traditionally used RGs in 12 cancer types, including those of lung, breast, prostate, kidney, and colon. We developed an 11-component scoring system for the assessment of gene expression stability. Among the 32 genes, PUM1 was one of the most stably expressed in the majority of examined cancers, whereas GAPDH, which is widely used as a RG, showed significant mRNA level alterations in more than a half of cases. For each of 12 cancer types, we suggested a pair of genes that are the most suitable for use as reference ones. These genes are characterized by high expression stability and absence of correlation between their mRNA levels. Next, the scoring system was expanded with several features of a gene: mutation rate, number of transcript isoforms and pseudogenes, participation in cancer-related processes on the basis of Gene Ontology, and mentions in PubMed-indexed articles. All the genes covered by RNA-Seq data in TCGA were analyzed using the expanded scoring system that allowed us to reveal novel promising RGs for each examined cancer type and identify several "universal" pan-cancer RG candidates, including SF3A1, CIAO1, and SFRS4. The choice of RGs is the basis for precise gene expression evaluation by qPCR. Here, we suggested optimal pairs of traditionally used RGs for 12 cancer types and identified novel promising RGs that demonstrate high expression stability and other features of reliable and convenient RGs (high expression level, low mutation rate, non-involvement in cancer-related processes, single transcript isoform, and absence of pseudogenes).
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Affiliation(s)
- George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | | | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Machnik M, Cylwa R, Kiełczewski K, Biecek P, Liloglou T, Mackiewicz A, Oleksiewicz U. The expression signature of cancer-associated KRAB-ZNF factors identified in TCGA pan-cancer transcriptomic data. Mol Oncol 2019; 13:701-724. [PMID: 30444046 PMCID: PMC6442004 DOI: 10.1002/1878-0261.12407] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/03/2018] [Accepted: 10/31/2018] [Indexed: 12/19/2022] Open
Abstract
The KRAB-ZNF (Krüppel-associated box domain zinc finger) gene family is composed of a large number of highly homologous genes, gene isoforms, and pseudogenes. The proteins encoded by these genes, whose expression is often tissue-specific, act as epigenetic suppressors contributing to the addition of repressive chromatin marks and DNA methylation. Due to its high complexity, the KRAB-ZNF family has not been studied in sufficient detail, and the involvement of its members in carcinogenesis remains mostly unexplored. In this study, we aimed to provide a comprehensive description of cancer-associated KRAB-ZNFs using publicly available The Cancer Genome Atlas pan-cancer datasets. We analyzed 6727 tumor and normal tissue samples from 16 cancer types. Here, we showed that a small but distinctive cluster of 16 KRAB-ZNFs is commonly upregulated across multiple cancer cohorts in comparison to normal samples. We confirmed these observations in the independent panels of lung and breast cancer cell lines and tissues. This upregulation was also observed for most of the KRAB-ZNF splicing variants, whose expression is simultaneously upregulated in tumors compared to normal tissues. Finally, by analyzing the clinicopathological data for breast and lung cancers, we demonstrated that the expression of cancer-associated KRAB-ZNFs correlates with patient survival, tumor histology, and molecular subtyping. Altogether, our study allowed the identification and characterization of KRAB-ZNF factors that may have an essential function in cancer biology and thus potential to become novel oncologic biomarkers and treatment targets.
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Affiliation(s)
- Marta Machnik
- Department of Cancer ImmunologyPoznan University of Medical SciencesPoland
- Department of Diagnostics and Cancer ImmunologyGreater Poland Cancer CentrePoznanPoland
| | - Rafał Cylwa
- Faculty of Mathematics, Informatics, and MechanicsUniversity of WarsawWarszawaPoland
| | - Kornel Kiełczewski
- Faculty of Mathematics and Information ScienceWarsaw University of TechnologyWarszawaPoland
| | - Przemysław Biecek
- Faculty of Mathematics and Information ScienceWarsaw University of TechnologyWarszawaPoland
| | | | - Andrzej Mackiewicz
- Department of Cancer ImmunologyPoznan University of Medical SciencesPoland
- Department of Diagnostics and Cancer ImmunologyGreater Poland Cancer CentrePoznanPoland
| | - Urszula Oleksiewicz
- Department of Cancer ImmunologyPoznan University of Medical SciencesPoland
- Department of Diagnostics and Cancer ImmunologyGreater Poland Cancer CentrePoznanPoland
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The effect of ELOVL6 fatty acid elongase inhibition on the expression of genes associated with the metastasis of breast cancer. Russ Chem Bull 2019. [DOI: 10.1007/s11172-018-2374-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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25
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Shkurnikov MY, Maltseva DV, Knyazev EN, Alekseev BY. Expression of Stroma Components in the Lymph Nodes Affected by Prostate Cancer Metastases. Mol Biol 2018. [DOI: 10.1134/s0026893318050126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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26
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Nikulin SV, Mnafki NA, Shilin SA, Gazizov IN, Maltseva DV. Ribosome Inactivation and the Integrity of the Intestinal Epithelial Barrier. Mol Biol 2018. [DOI: 10.1134/s0026893318040143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Fomicheva KA, Knyazev EN, Mal'tseva DV. hsa-miR-1973 MicroRNA is Significantly and Differentially Expressed in MDA-MB-231 Cells of Breast Adenocarcinoma and Xenografts Derived from the Tumor. Bull Exp Biol Med 2017; 163:660-662. [PMID: 28948560 DOI: 10.1007/s10517-017-3873-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 12/21/2022]
Abstract
The gene expression profiles of MDA-MB-231 cell line of breast cancer and xenografts derived from this tumor in murine model were analyzed using GeneChip Human Transcriptome array 2.0 platform (Affymetrix). A more than 1000-fold increase in the MIR1973 gene expression was observed in the xenografts compared to the original cell line. Real-time reverse transcription PCR showed that the content of mature hsa-miR-1973 microRNA encoded by this gene was elevated in the xenografts by more than 300 times. According to microarray analysis, none of hsa-miR-1973 target genes available in the databases changed the expression in the cell line and xenografts. A possible role of hsa-miR-1973 is reduction of apoptosis in the tumor.
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Affiliation(s)
- K A Fomicheva
- P. A. Herzen Moscow Oncology Research Center - Branch of National Medical Radiological Research Center, Ministry of Health of the Russian Federation, Moscow, Russia.
| | - E N Knyazev
- P. A. Herzen Moscow Oncology Research Center - Branch of National Medical Radiological Research Center, Ministry of Health of the Russian Federation, Moscow, Russia.,BioClinicum Research Center, Moscow, Russia
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Khaustova NA, Maltseva DV, Oliveira-Ferrer L, Stürken C, Milde-Langosch K, Makarova JA, Rodin S, Schumacher U, Tonevitsky AG. Selectin-independent adhesion during ovarian cancer metastasis. Biochimie 2017; 142:197-206. [PMID: 28919578 DOI: 10.1016/j.biochi.2017.09.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/12/2017] [Indexed: 12/31/2022]
Abstract
PURPOSE Ovarian cancer (OvCa) progression mainly takes place by intraperitoneal spread. Adhesion of tumor cells to the mesothelial cells which form the inner surface of the peritoneum is a crucial step in this process. Cancer cells use in principle different molecules of the leukocyte adhesion cascade to facilitate adhesion. This cascade is initiated by selectin-ligand interactions followed by integrin - extracellular matrix protein interactions. Here we address the question whether all tumor cells predominantly employ selectin-dependent leukocyte-like adhesion cascade (SDAC) or whether they use integrin mediated adhesion for OvCa progression as well. METHODS A comparative transcriptomic analysis of the human OvCa cell lines OVCAR8 and SKOV3 was performed. Intraperitoneal xenograft model of OVCAR8 cells was used to determine whether there is a correlation between SDAC gene expression and the metastatic potential of the control cells and the cells overexpressing c-Fos. Transcriptomic analysis of OVCAR8 and SKOV3 samples was performed using microarrays. RESULTS One-third of the protein-coding genes involved in SDAC exhibited lower expression levels in OVCAR8 than in SKOV3 cells. In contrast to SKOV3 cells, c-Fos overexpression in OVCAR8 cells did not significantly influence the expression of SDAC genes. Intraperitoneal xenograft model of OVCAR8 cells unexpectedly demonstrated that the aggressiveness of OVCAR8 tumors was not depended on the c-Fos expression level and was comparable to that of SKOV3 control tumors. Gene expression analysis of tumors suggests that SKOV3-derived tumor progression was mainly depended on SDAC. Progression of OVCAR8 tumors relied on other cell adhesion molecules that do not interact with selectins. CONCLUSIONS High expression of c-Fos in ovarian cancer cells is not always associated with reduced metastatic potential. Low expression level of SDAC genes may not ensure low OvCa metastatic potential hence alternative adhesion mechanisms involving laminin-integrin interactions exist as well.
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Affiliation(s)
| | | | - Leticia Oliveira-Ferrer
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, D-20246, Germany.
| | - Christine Stürken
- Department of Anatomy and Experimental Morphology, University Medical Center Hamburg-Eppendorf, Hamburg, D-20246, Germany.
| | - Karin Milde-Langosch
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, D-20246, Germany.
| | - Julia A Makarova
- P. Herzen Moscow Oncology Research Institute, Moscow, 125284, Russia.
| | - Sergey Rodin
- SRC Bioclinicum, Moscow, 115088, Russia; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden.
| | - Udo Schumacher
- Department of Anatomy and Experimental Morphology, University Medical Center Hamburg-Eppendorf, Hamburg, D-20246, Germany.
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Target Cell Glycosylation Determines the Biodistribution of Plant Lectin Viscumin. Bull Exp Biol Med 2017; 163:482-485. [PMID: 28853065 DOI: 10.1007/s10517-017-3833-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Indexed: 10/19/2022]
Abstract
We studied the possibility of using viscumin lectin (MLI) for targeted delivery of antitumor drugs. Affinity of MLI for more than 600 oligosaccharide structures was determined and the glycosylation profiles of cell surface in various mouse tissues were analyzed. It was found that biodistribution of MLI was determined by not only expression of oligosaccharides specifically recognized by the lectin in tissue cells, but also by the structure of glycan in general.
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30
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Maltseva DV, Krainova NA, Khaustova NA, Nikulin SV, Tonevitskaya SA, Poloznikov AA. Biodistribution of Viscumin after Subcutaneous Injection to Mice and In Vitro Modeling of Endoplasmic Reticulum Stress. Bull Exp Biol Med 2017; 163:451-455. [DOI: 10.1007/s10517-017-3826-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 12/01/2022]
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31
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Effect of ketoconazole on the transport and metabolism of drugs in the human liver cell model. Russ Chem Bull 2017. [DOI: 10.1007/s11172-017-1713-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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32
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Kudriaeva A, Galatenko VV, Maltseva DV, Khaustova NA, Kuzina E, Tonevitsky AG, Gabibov A, Belogurov A. The Transcriptome of Type I Murine Astrocytes under Interferon-Gamma Exposure and Remyelination Stimulus. Molecules 2017; 22:molecules22050808. [PMID: 28505143 PMCID: PMC6153759 DOI: 10.3390/molecules22050808] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/30/2017] [Accepted: 05/11/2017] [Indexed: 02/04/2023] Open
Abstract
Astrocytes are considered to be an important contributor to central nervous system (CNS) disorders, particularly multiple sclerosis. The transcriptome of these cells is greatly affected by cytokines released by lymphocytes, penetrating the blood–brain barrier—in particular, the classical pro-inflammatory cytokine interferon-gamma (IFNγ). We report here the transcriptomal profiling of astrocytes treated using IFNγ and benztropine, a putative remyelinization agent. Our findings indicate that the expression of genes involved in antigen processing and presentation in astrocytes are significantly upregulated upon IFNγ exposure, emphasizing the critical role of this cytokine in the redirection of immune response towards self-antigens. Data reported herein support previous observations that the IFNγ-induced JAK-STAT signaling pathway may be regarded as a valuable target for pharmaceutical interventions.
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Affiliation(s)
- Anna Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.
| | - Vladimir V Galatenko
- Department of Mathematical Analysis, Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, 119991 Moscow, Russia.
- Big Data and Information Retrieval School, Faculty of Computer Science, National Research University Higher School of Economics, 125319 Moscow, Russia.
- SRC Bioclinicum, 115088 Moscow, Russia.
| | | | | | - Ekaterina Kuzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.
| | | | - Alexander Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.
- Big Data and Information Retrieval School, Faculty of Computer Science, National Research University Higher School of Economics, 125319 Moscow, Russia.
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia.
| | - Alexey Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.
- Big Data and Information Retrieval School, Faculty of Computer Science, National Research University Higher School of Economics, 125319 Moscow, Russia.
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia.
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Li X, Li J, Li F. P21 activated kinase 4 binds translation elongation factor eEF1A1 to promote gastric cancer cell migration and invasion. Oncol Rep 2017; 37:2857-2864. [PMID: 28393218 DOI: 10.3892/or.2017.5543] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 03/03/2017] [Indexed: 11/05/2022] Open
Abstract
P21 activated kinase 4 (PAK4), as an effector of Cdc42, playing important roles in regulating the processes of cytoskeleton organization. PAK4 has been considered to be an oncogenic protein, which has strong relationship with gastric cancer metastasis. However, the mechanism of PAK4 in regulating gastric cancer metastasis is still not fully understood. In this study, using yeast two-hybrid system, we identified that the eukaryotic elongation factor 1 α1 (eEF1A1) is a new binding partner of PAK4. The interaction between PAK4 and eEF1A1 was confirmed by GST pull-down and co-immunoprecipitation. PAK4 co-localized with eEF1A1 in the cytoplasm of gastric cancer cells. Overexpression of PAK4 enhanced the expression level of eEF1A1 and vice versa. PAK4 and eEF1A1 could cooperate to promote gastric cancer cell migration and invasion. Furthermore, the expression of PAK4 and eEF1A1 in clinical gastric cancer samples were examined by western blotting and immunohistochemistry. Statistical analysis indicated that there was positive correlation between the expression of PAK4 and eEF1A1. This study demonstrated for the first time that PAK4 interacted with eEF1A1 to promote migration and invasion of gastric cancer cells, thereby providing new insights into the function of PAK4 and eEF1A1 in the progression of gastric cancer.
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Affiliation(s)
- Xiang Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, Liaoning, P.R. China
| | - Jiabin Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, Liaoning, P.R. China
| | - Feng Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, Liaoning, P.R. China
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Zakharyants AA, Burmistrova OA, Poloznikov AA. The Use of Human Liver Cell Model and Cytochrome P450 Substrate—Inhibitor Panel for Studies of Dasatinib and Warfarin Interactions. Bull Exp Biol Med 2017; 162:515-519. [DOI: 10.1007/s10517-017-3651-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Indexed: 02/05/2023]
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Wu J, Li S, Ma R, Sharma A, Bai S, Dun B, Cao H, Jing C, She J, Feng J. Tumor profiling of co-regulated receptor tyrosine kinase and chemoresistant genes reveal different targeting options for lung and gastroesophageal cancers. Am J Transl Res 2016; 8:5729-5740. [PMID: 28078044 PMCID: PMC5209524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/10/2016] [Indexed: 06/06/2023]
Abstract
The expression of a number of genes can influence the response rates to chemotherapy while genes encoding receptor tyrosine kinases (RTKs) determine the response to most targeted cancer therapies currently used in clinics. In this study, we evaluated seven genes known to influence chemotherapeutic response (ERCC1, BRCA1, RRM1, TUBB3, STMN1, TYMS, and TOP2A) and five RTKs (EGFR, ERBB2, PDGFRB, VEGFR1 and VEGFR2) in non-small cell lung cancer (NSCLC) and esophagus cancer (EC) and the data are compared to gastric cancer (GC) data reported previously. We demonstrate significant differences in the expression profiles between different cancer types as well as heterogeneity among patients within the same cancer type. In all three cancer types, five chemoresistant genes (TOP2A, STMN1, TYMS, BRCA1 and RRM1) are coordinately up-regulated in almost all EC, approximately 90% of NSCLC and one third of GC patients. Most EC and nearly half of GC patients have increased expression of the three RTKs critical to angiogenesis (PDGFR, VEGFR1 and VEGFR2), while almost none of the NSCLC patients have elevated expression of angiogenic RTKs. A variable percentage of patients in the three cancer types show upregulation of the EGFR family RTKs, EGFR and/or ERBB2. It is of interest to note that approximately 10% of the NSCLC and GC patients are triple-negative for the chemosensitivity genes, angiogenic and EGFR RTK genes. The results suggest significant gene expression differences between different cancer types as well as heterogeneity within each cancer type and therefore different molecules should be targeted for future drug development and clinical trials.
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Affiliation(s)
- Jianzhong Wu
- Clinical Oncology Research Center, Jiangsu Cancer HospitalNanjing, Jiangsu Province, People’s Republic of China
| | - Shuchun Li
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, GA, USA
| | - Rong Ma
- Clinical Oncology Research Center, Jiangsu Cancer HospitalNanjing, Jiangsu Province, People’s Republic of China
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, GA, USA
| | - Shan Bai
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, GA, USA
| | - Boying Dun
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, GA, USA
| | - Haixia Cao
- Clinical Oncology Research Center, Jiangsu Cancer HospitalNanjing, Jiangsu Province, People’s Republic of China
| | - Changwen Jing
- Clinical Oncology Research Center, Jiangsu Cancer HospitalNanjing, Jiangsu Province, People’s Republic of China
| | - Jinxiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, GA, USA
| | - Jifeng Feng
- Clinical Oncology Research Center, Jiangsu Cancer HospitalNanjing, Jiangsu Province, People’s Republic of China
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Chen L, Jin Y, Wang L, Sun F, Yang X, Shi M, Zhan C, Shi Y, Wang Q. Identification of reference genes and miRNAs for qRT-PCR in human esophageal squamous cell carcinoma. Med Oncol 2016; 34:2. [PMID: 27889881 DOI: 10.1007/s12032-016-0860-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/22/2016] [Indexed: 02/06/2023]
Abstract
It is important to select an appropriate reference gene and miRNA when using quantitative real-time polymerase chain reaction (qRT-PCR) to analyze gene and miRNA expression. However, many commonly used reference genes and miRNAs are not stably expressed and therefore not suitable for normalization or quantification of qRT-PCR data. This study aims to identify appropriate reference genes and miRNAs for use in human esophageal squamous carcinoma qRT-PCR analysis. Using data provided by The Cancer Genome Atlas, we identified DDX5, LAPTM4A, P4HB, RHOA, miR-28-5p, miR-34a-5p, and miR-186-5p as candidate reference genes and miRNAs. We used qRT-PCR to verify the expression levels of these candidates and another seven commonly used reference genes and miRNAs. A set of 50 paired human normal esophageal tissues and squamous cell carcinoma samples were used in the analysis. We then used geNorm and NormFinder to analyze the results. DDX5, LAPTM4A, RHOA, ACTB, RNU48, miR-28-5p, miR-34a-5p, and miR-186-5p were stably expressed, indicating they are suitable for used as references in qRT-PCR analysis of esophageal squamous cell carcinoma. However, expression levels of 18s rRNA, GAPDH, P4HB, 5s rRNA, U6, and RNU6B varied greatly between esophageal normal and squamous cell carcinoma samples, indicating that they are not suitable for use as references in the qRT-PCR analysis of esophageal squamous cell carcinoma.
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Affiliation(s)
- Li Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Yulin Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Lin Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Fenghao Sun
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Xiaodong Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Mengkun Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
| | - Yu Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
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Lima L, Gaiteiro C, Peixoto A, Soares J, Neves M, Santos LL, Ferreira JA. Reference Genes for Addressing Gene Expression of Bladder Cancer Cell Models under Hypoxia: A Step Towards Transcriptomic Studies. PLoS One 2016; 11:e0166120. [PMID: 27835695 PMCID: PMC5106008 DOI: 10.1371/journal.pone.0166120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 10/24/2016] [Indexed: 11/18/2022] Open
Abstract
Highly aggressive, rapidly growing tumors contain significant areas of hypoxia or anoxia as a consequence of inadequate and/or irregular blood supply. During oxygen deprivation, tumor cells withstand a panoply of adaptive responses, including a shift towards anaerobic metabolism and the reprogramming of the transcriptome. One of the major mediators of the transcriptional hypoxic response is the hypoxia-inducible factor 1 (HIF-1), whose stabilization under hypoxia acts as an oncogenic stimulus contributing to chemotherapy resistance, invasion and metastasis. Gene expression analysis by qRT-PCR is a powerful tool for cancer cells phenotypic characterization. Nevertheless, as cells undergo a severe transcriptome remodeling.in response to oxygen deficit, the precise identification of reference genes poses a significant challenge for hypoxic studies. Herein, we aim to establish the best reference genes for studying the effects of hypoxia on bladder cancer cells. Accordingly, three bladder cancer cell lines (T24, 5637, and HT1376) representative of two distinct carcinogenesis pathways to invasive cancer (FGFR3/CCND1 and E2F3/RB1) were used. Additionally, we have explored the most suitable control gene when addressing the influence of Deferoxamine Mesilate salt (DFX), an iron chelator often used to avoid the proteasomal degradation of HIF-1α, acting as an hypoxia-mimetic agent. Using bioinformatics tools (GeNorm and NormFinder), we have elected B2M and HPRT as the most stable genes for all cell lines and experimental conditions out of a panel of seven putative candidates (HPRT, ACTB, 18S, GAPDH, TBP, B2M, and SDHA). These observations set the molecular basis for future studies addressing the effect of hypoxia and particularly HIF-1α in bladder cancer cells.
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Affiliation(s)
- Luís Lima
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- * E-mail:
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Janine Soares
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
| | - Manuel Neves
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
- Health School of University of Fernando Pessoa, 4249-004, Porto, Portugal
- Department of Surgical Oncology, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
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Samatov TR, Galatenko VV, Block A, Shkurnikov MY, Tonevitsky AG, Schumacher U. Novel biomarkers in cancer: The whole is greater than the sum of its parts. Semin Cancer Biol 2016; 45:50-57. [PMID: 27639751 DOI: 10.1016/j.semcancer.2016.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/08/2016] [Indexed: 02/07/2023]
Abstract
The major issues hampering progress in the treatment of cancer patients are distant metastases and drug resistance to chemotherapy. Metastasis formation is a very complex process, and looking at gene signatures alone is not enough to get deep insight into it. This paper reviews traditional and novel approaches to identify gene signature biomarkers and intratumoural fluid pressure both as a novel way of creating predictive markers and as an obstacle to cancer therapy. Finally recently developed in vitro systems to predict the response of individual patient derived cancer explants to chemotherapy are discussed.
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Affiliation(s)
- Timur R Samatov
- SRC Bioclinicum, Ugreshskaya str 2/85, 115088, Moscow, Russia; Moscow State University of Mechanical Engineering, Bolshaya Semenovskaya str 38, 107023, Moscow, Russia
| | - Vladimir V Galatenko
- SRC Bioclinicum, Ugreshskaya str 2/85, 115088, Moscow, Russia; Lomonosov Moscow State University, Leninskie Gory, 119991, Moscow, Russia; National Research University Higher School of Economics, Kochnovsky Pass 3, 125319 Moscow, Russia
| | - Andreas Block
- Department of Oncology and Hematology, University Cancer Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Maxim Yu Shkurnikov
- P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, 3 Second Botkinsky Lane, Moscow, 125284, Russia
| | - Alexander G Tonevitsky
- Lomonosov Moscow State University, Leninskie Gory, 119991, Moscow, Russia; P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, 3 Second Botkinsky Lane, Moscow, 125284, Russia
| | - Udo Schumacher
- Department of Anatomy and Experimental Morphology, University Cancer Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany, Germany.
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Kudriaeva AA, Khaustova NA, Maltseva DV, Kuzina ES, Glagoleva IS, Surina EA, Knorre VD, Belogurov AA, Tonevitsky AG, Gabibov AG. mRNA expression profile of mouse oligodendrocytes in inflammatory conditions. DOKL BIOCHEM BIOPHYS 2016; 469:264-8. [PMID: 27599508 DOI: 10.1134/s1607672916040086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 11/23/2022]
Abstract
In this study, we performed transcriptome profiling of oligodendrocyte culture of mice treated with the remyelinating therapeutic agent benztropine in the presence and absence of interferon gamma (IFNγ). The results of this work are important for understanding the expression profile of oligodendrocytes under conditions of systemic inflammation in the central nervous system in multiple sclerosis as well as the mechanisms of cellular response to benztropine in light of its possible use for the treatment of multiple sclerosis.
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Affiliation(s)
- A A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - N A Khaustova
- BioKlinikum Scientific-Technical Center LLC, ul. Ugreshskaya 2, bdg. 85, Moscow, 115088, Russia
| | - D V Maltseva
- BioKlinikum Scientific-Technical Center LLC, ul. Ugreshskaya 2, bdg. 85, Moscow, 115088, Russia
| | - E S Kuzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - I S Glagoleva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, ul. Karla Marksa 74, Kazan, Tatarstan, 420055, Russia
| | - E A Surina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - V D Knorre
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia.
| | - A A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia.,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, ul. Karla Marksa 74, Kazan, Tatarstan, 420055, Russia
| | - A G Tonevitsky
- BioKlinikum Scientific-Technical Center LLC, ul. Ugreshskaya 2, bdg. 85, Moscow, 115088, Russia
| | - A G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia.,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, ul. Karla Marksa 74, Kazan, Tatarstan, 420055, Russia.,Faculty of Chemistry, Moscow State University, Moscow, 119991, Russia
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Semenova OV, Petrov VA, Gerasimenko TN, Aleksandrova AV, Burmistrova OA, Khutornenko AA, Osipyants AI, Poloznikov AA, Sakharov DA. Effect of Circulation Parameters on Functional Status of HepaRG Spheroids Cultured in Microbioreactor. Bull Exp Biol Med 2016; 161:425-9. [PMID: 27496037 DOI: 10.1007/s10517-016-3430-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Indexed: 12/20/2022]
Abstract
We studied the relationship between microcirculation parameters and functional status of HepaRG cells in spheroids and chose an optimal regimen within the physiologically permissible limits of mechanical impact for the cells that maintains the expression of functional genes of the liver.
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Affiliation(s)
- O V Semenova
- Moscow Aircraft Construction Institute (National Research University), Moscow, Russia
| | - V A Petrov
- Moscow Aircraft Construction Institute (National Research University), Moscow, Russia
| | - T N Gerasimenko
- Moscow Aircraft Construction Institute (National Research University), Moscow, Russia
| | - A V Aleksandrova
- Moscow Aircraft Construction Institute (National Research University), Moscow, Russia
| | - O A Burmistrova
- Moscow Aircraft Construction Institute (National Research University), Moscow, Russia
| | - A A Khutornenko
- Moscow Aircraft Construction Institute (National Research University), Moscow, Russia.
| | - A I Osipyants
- Moscow Aircraft Construction Institute (National Research University), Moscow, Russia
| | - A A Poloznikov
- Moscow Aircraft Construction Institute (National Research University), Moscow, Russia
| | - D A Sakharov
- Moscow Aircraft Construction Institute (National Research University), Moscow, Russia
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Maintenance of High Cytochrome P450 Expression in HepaRG Cell Spheroids in DMSO-Free Medium. Bull Exp Biol Med 2016; 161:120-4. [DOI: 10.1007/s10517-016-3360-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Indexed: 01/19/2023]
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Localization and Expression of Nucleoside Transporters ENT1 and ENT2 in Polar Cells of Intestinal Epithelium. Bull Exp Biol Med 2016; 160:771-4. [PMID: 27160886 DOI: 10.1007/s10517-016-3306-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Indexed: 10/21/2022]
Abstract
Сасо-2 cell line is widely used in in vitro studies of the intestinal wall permeability for drugs, but transport activity of these cells has not been thoroughly studied. We analyzed localization and expression of nucleoside transporters of the ENT family transferring a number of anticancer and antiviral drugs. Immunocytochemical staining revealed apical localization of ENT1 and integral expression of ENT2 in Caco-2 cells. Based on these data and on the value of hypoxanthine uptake by these cells, we created a mathematical model allowing quantification of transporter expression on the apical and basolateral membranes of Caco-2 cells. The discrepancy between gene and protein expression of the transporter complicating prediction of patient's sensitivity to the drug upon individual therapy selection is discussed.
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Choe KN, Nicolae CM, Constantin D, Imamura Kawasawa Y, Delgado-Diaz MR, De S, Freire R, Smits VA, Moldovan GL. HUWE1 interacts with PCNA to alleviate replication stress. EMBO Rep 2016; 17:874-86. [PMID: 27146073 DOI: 10.15252/embr.201541685] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/05/2016] [Indexed: 02/01/2023] Open
Abstract
Defects in DNA replication, DNA damage response, and DNA repair compromise genomic stability and promote cancer development. In particular, unrepaired DNA lesions can arrest the progression of the DNA replication machinery during S-phase, causing replication stress, mutations, and DNA breaks. HUWE1 is a HECT-type ubiquitin ligase that targets proteins involved in cell fate, survival, and differentiation. Here, we report that HUWE1 is essential for genomic stability, by promoting replication of damaged DNA We show that HUWE1-knockout cells are unable to mitigate replication stress, resulting in replication defects and DNA breakage. Importantly, we find that this novel role of HUWE1 requires its interaction with the replication factor PCNA, a master regulator of replication fork restart, at stalled replication forks. Finally, we provide evidence that HUWE1 mono-ubiquitinates H2AX to promote signaling at stalled forks. Altogether, our work identifies HUWE1 as a novel regulator of the replication stress response.
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Affiliation(s)
- Katherine N Choe
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Daniel Constantin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yuka Imamura Kawasawa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, USA Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Maria Rocio Delgado-Diaz
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, La Laguna Tenerife, Spain
| | - Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO, USA
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, La Laguna Tenerife, Spain
| | - Veronique Aj Smits
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, La Laguna Tenerife, Spain
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
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Xu L, Fengji L, Changning L, Liangcai Z, Yinghui L, Yu L, Shanguang C, Jianghui X. Comparison of the Prognostic Utility of the Diverse Molecular Data among lncRNA, DNA Methylation, microRNA, and mRNA across Five Human Cancers. PLoS One 2015; 10:e0142433. [PMID: 26606135 PMCID: PMC4659652 DOI: 10.1371/journal.pone.0142433] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/21/2015] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Advances in high-throughput technologies have generated diverse informative molecular markers for cancer outcome prediction. Long non-coding RNA (lncRNA) and DNA methylation as new classes of promising markers are emerging as key molecules in human cancers; however, the prognostic utility of such diverse molecular data remains to be explored. MATERIALS AND METHODS We proposed a computational pipeline (IDFO) to predict patient survival by identifying prognosis-related biomarkers using multi-type molecular data (mRNA, microRNA, DNA methylation, and lncRNA) from 3198 samples of five cancer types. We assessed the predictive performance of both single molecular data and integrated multi-type molecular data in patient survival stratification, and compared their relative importance in each type of cancer, respectively. Survival analysis using multivariate Cox regression was performed to investigate the impact of the IDFO-identified markers and traditional variables on clinical outcome. RESULTS Using the IDFO approach, we obtained good predictive performance of the molecular datasets (bootstrap accuracy: 0.71-0.97) in five cancer types. Impressively, lncRNA was identified as the best prognostic predictor in the validated cohorts of four cancer types, followed by DNA methylation, mRNA, and then microRNA. We found the incorporating of multi-type molecular data showed similar predictive power to single-type molecular data, but with the exception of the lncRNA + DNA methylation combinations in two cancers. Survival analysis of proportional hazard models confirmed a high robustness for lncRNA and DNA methylation as prognosis factors independent of traditional clinical variables. CONCLUSION Our study provides insight into systematically understanding the prognostic performance of diverse molecular data in both single and aggregate patterns, which may have specific reference to subsequent related studies.
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Affiliation(s)
- Li Xu
- School of life science and biotechnology, Harbin Institute of Technology, Harbin, Hei Longjiang Province, China
- State Key Laboratory of Space Medicine Fundamentals and Application, Space Institute of Southern China, China Astronaut Research and Training Center, Beijing, China
- National Key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing, China
| | - Liang Fengji
- State Key Laboratory of Space Medicine Fundamentals and Application, Space Institute of Southern China, China Astronaut Research and Training Center, Beijing, China
| | - Liu Changning
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Zhang Liangcai
- Department of statistics, Rice University, Houston, Texas, United States of America
| | - Li Yinghui
- School of life science and biotechnology, Harbin Institute of Technology, Harbin, Hei Longjiang Province, China
- State Key Laboratory of Space Medicine Fundamentals and Application, Space Institute of Southern China, China Astronaut Research and Training Center, Beijing, China
| | - Li Yu
- School of life science and biotechnology, Harbin Institute of Technology, Harbin, Hei Longjiang Province, China
| | - Chen Shanguang
- School of life science and biotechnology, Harbin Institute of Technology, Harbin, Hei Longjiang Province, China
- National Key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing, China
- * E-mail: (XJH); (CSG)
| | - Xiong Jianghui
- State Key Laboratory of Space Medicine Fundamentals and Application, Space Institute of Southern China, China Astronaut Research and Training Center, Beijing, China
- * E-mail: (XJH); (CSG)
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Suppression of ITGB4 Gene Expression in PC-3 Cells with Short Interfering RNA Induces Changes in the Expression of β-Integrins Associated with RGD-Receptors. Bull Exp Biol Med 2015; 159:541-5. [DOI: 10.1007/s10517-015-3011-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 10/23/2022]
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Sharan RN, Vaiphei ST, Nongrum S, Keppen J, Ksoo M. Consensus reference gene(s) for gene expression studies in human cancers: end of the tunnel visible? Cell Oncol (Dordr) 2015; 38:419-31. [PMID: 26384826 DOI: 10.1007/s13402-015-0244-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gene expression studies are increasingly used to provide valuable information on the diagnosis and prognosis of human cancers. Also, for in vitro and in vivo experimental cancer models gene expression studies are widely used. The complex algorithms of differential gene expression analyses require normalization of data against a reference or normalizer gene, or a set of such genes. For this purpose, mostly invariant housekeeping genes are used. Unfortunately, however, there are no consensus (housekeeping) genes that serve as reference or normalizer for different human cancers. In fact, scientists have employed a wide range of reference genes across different types of cancer for normalization of gene expression data. As a consequence, comparisons of these data and/or data harmonizations are difficult to perform and challenging. In addition, an inadequate choice for a reference gene may obscure genuine changes and/or result in erroneous gene expression data comparisons. METHODS In our effort to highlight the importance of selecting the most appropriate reference gene(s), we have screened the literature for gene expression studies published since the turn of the century on thirteen of the most prevalent human cancers worldwide. CONCLUSIONS Based on the analysis of the data at hand, we firstly recommend that in each study the suitability of candidate reference gene(s) should carefully be evaluated in order to yield reliable differential gene expression data. Secondly, we recommend that a combination of PPIA and either GAPDH, ACTB, HPRT and TBP, or appropriate combinations of two or three of these genes, should be employed in future studies, to ensure that results from different studies on different human cancers can be harmonized. This approach will ultimately increase the depth of our understanding of gene expression signatures across human cancers.
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Affiliation(s)
- R N Sharan
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India.
| | - S Thangminlal Vaiphei
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Saibadaiahun Nongrum
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Joshua Keppen
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Mandahakani Ksoo
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
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Li SC, Ma R, Wu JZ, Xiao X, Wu W, Li G, Chen B, Sharma A, Bai S, Dun BY, She JX, Tang JH. Delineation of gastric cancer subtypes by co-regulated expression of receptor tyrosine kinases and chemosensitivity genes. Am J Transl Res 2015; 7:1429-1439. [PMID: 26396673 PMCID: PMC4568798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 06/22/2015] [Indexed: 06/05/2023]
Abstract
Chemotherapy plays a key role in improving disease-free survival and overall survival of gastric cancer (GC); however, response rates are variable and a non-negligible proportion of patients undergo toxic and costly chemotherapeutic regimens without a survival benefit. Several studies have shown the existence of GC subtypes which may predict survival and respond differently to chemotherapy. It is also known that the expression level of chemotherapy-related and target therapy-related genes correlates with response to specific antitumor drugs. Nevertheless, these genes have not been considered jointly to define GC subtypes. In this study, we evaluated seven genes known to influence chemotherapeutic response (ERCC1, BRCA1, RRM1, TUBB3, STMN1, TYMS and TOP2A) and five receptor tyrosine kinases (RTKs) (EGFR, ERBB2, PDGFRB, VEGFR1 and VEGFR2). We demonstrate significant heterogeneity of gene expression among GC patients and identified four GC subtypes using the expression profiles of eight genes in two co-regulation groups: chemosensitivity (BRCA1, STMN1, TYMS and TOP2A) and RTKs (EGFR, PDGFRB, VEGFR1 and VEGFR2). The results are of immediate translational value regarding GC diagnostics and therapeutics, as many of these genes are curently widely used in relevant clinical testing.
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Affiliation(s)
- Shu-Chun Li
- Clinical Oncology Research Center, Jiangsu Cancer Hospital Nanjing, Jiangsu Province, People's Republic of China ; Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA ; Sino-American Institute of Translational Medicine, Nanjing Tech University Nanjing, Jiangsu Province, People's Republic of China
| | - Rong Ma
- Clinical Oncology Research Center, Jiangsu Cancer Hospital Nanjing, Jiangsu Province, People's Republic of China
| | - Jian-Zhong Wu
- Clinical Oncology Research Center, Jiangsu Cancer Hospital Nanjing, Jiangsu Province, People's Republic of China
| | - Xia Xiao
- Sino-American Institute of Translational Medicine, Nanjing Tech University Nanjing, Jiangsu Province, People's Republic of China
| | - Wei Wu
- Zhenjiang Jintai Life Technologies Zhenjiang, Jiangsu Province, People's Republic of China
| | - Gang Li
- Clinical Oncology Research Center, Jiangsu Cancer Hospital Nanjing, Jiangsu Province, People's Republic of China
| | - Bo Chen
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA ; Sino-American Institute of Translational Medicine, Nanjing Tech University Nanjing, Jiangsu Province, People's Republic of China
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA
| | - Shan Bai
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA
| | - Bo-Ying Dun
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA
| | - Jin-Hai Tang
- Clinical Oncology Research Center, Jiangsu Cancer Hospital Nanjing, Jiangsu Province, People's Republic of China
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López-Cortés A, Echeverría C, Oña-Cisneros F, Sánchez ME, Herrera C, Cabrera-Andrade A, Rosales F, Ortiz M, Paz-Y-Miño C. Breast cancer risk associated with gene expression and genotype polymorphisms of the folate-metabolizing MTHFR gene: a case-control study in a high altitude Ecuadorian mestizo population. Tumour Biol 2015; 36:6451-61. [PMID: 25801246 DOI: 10.1007/s13277-015-3335-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/12/2015] [Indexed: 12/12/2022] Open
Abstract
Breast cancer (BC) is the leading cause of cancer-related death among women in 2014. Methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR), and MTR reductase (MTRR) are enzymes that play an important role in folate metabolism. The single nucleotide polymorphisms, MTHFR C677T, A1298C, MTR A2756G, and MTRR A66G, alter plasmatic folate and homocysteine concentrations, causing problems during the repairment, synthesis, and methylation of the genetic material. Therefore, it is essential to know how BC risk is associated with histopathological and immunohistochemical characteristics, genotype polymorphisms, and gene expression in a high altitude Ecuadorian mestizo population. DNA was extracted from 195 healthy and 114 affected women. Genotypes were determined by restriction enzymes and genomic sequencing. mRNA was extracted from 26 glandular breast tissue samples, both from cancerous tissue and healthy tissue adjacent to the tumor. Relative gene expression was determined with the comparative Livak method (2(-ΔΔCT)). We found significant association between the rs1801133 (A222V) genotypes and an increased risk of BC development: C/T (odds ratio [OR] = 1.8; 95 % confidence interval [CI] = 1.1-3.2; P = 0.039), T/T (OR = 2.9; 95 % CI = 1.2-7.2; P = 0.025), and C/T + T/T (OR = 1.9; 95 % CI = 1.1-3.3; P = 0.019). Regarding relative gene expression, we found significant mRNA subexpression between the combined genotypes C/T + T/T (rs1801133) and triple negative breast cancer (TNBC) (P = 0.034). In brief, the MTHFR gene and its protein could act as potential predictive biomarkers of BC, especially TNBC among the high altitude Ecuadorian mestizo population.
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Affiliation(s)
- Andrés López-Cortés
- Biomedical Research Institute, Faculty of Health Sciences, Universidad de las Americas, Avenue Granados E12-41 and Colimes Street, Quito, 170122, Ecuador,
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Aggerholm-Pedersen N, Safwat A, Bærentzen S, Nordsmark M, Nielsen OS, Alsner J, Sørensen BS. The importance of reference gene analysis of formalin-fixed, paraffin-embedded samples from sarcoma patients - an often underestimated problem. Transl Oncol 2014; 7:687-93. [PMID: 25500077 PMCID: PMC4311021 DOI: 10.1016/j.tranon.2014.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Reverse transcription quantitative real-time polymerase chain reaction is efficient for quantification of gene expression, but the choice of reference genes is of paramount importance as it is essential for correct interpretation of data. This is complicated by the fact that the materials often available are routinely collected formalin-fixed, paraffin-embedded (FFPE) samples in which the mRNA is known to be highly degraded. The purpose of this study was to investigate 22 potential reference genes in sarcoma FFPE samples and to study the variation in expression level within different samples taken from the same tumor and between different histologic types. METHODS Twenty-nine patients treated for sarcoma were enrolled. The samples encompassed 82 (FFPE) specimens. Extraction of total RNA from 7-μm FFPE sections was performed using a fully automated, bead-base RNA isolation procedure, and 22 potential reference genes were analyzed by reverse transcription quantitative real-time polymerase chain reaction. The stability of the genes was analyzed by RealTime Statminer. The intrasamples variation and the interclass correlation coefficients were calculated. The linear regression model was used to calculate the degradation of the mRNA over time. RESULTS The quality of RNA was sufficient for analysis in 84% of the samples. Recommended reference genes differed with histologic types. However, PPIA, SF3A1, and MRPL19 were stably expressed regardless of the histologic type included. The variation in ∆Cq value for samples from the same patients was similar to the variation between patients. It was possible to compensate for the time-dependent degradation of the mRNA when normalization was made using the selected reference genes. CONCLUSION PPIA, SF3A1, and MRPL19 are suitable reference genes for normalization in gene expression studies of FFPE samples from sarcoma regardless of the histology.
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Affiliation(s)
| | - Akmal Safwat
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Steen Bærentzen
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Jan Alsner
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Brita S Sørensen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
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Maltseva DV, Galatenko VV, Samatov TR, Zhikrivetskaya SO, Khaustova NA, Nechaev IN, Shkurnikov MU, Lebedev AE, Mityakina IA, Kaprin AD, Schumacher U, Tonevitsky AG. miRNome of inflammatory breast cancer. BMC Res Notes 2014; 7:871. [PMID: 25471792 PMCID: PMC4289319 DOI: 10.1186/1756-0500-7-871] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/28/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Inflammatory breast cancer (IBC) is an extremely malignant form of breast cancer which can be easily misdiagnosed. Conclusive prognostic IBC molecular biomarkers which are also providing the perspectives for targeted therapy are lacking so far. The aim of this study was to reveal the IBC-specific miRNA expression profile and to evaluate its association with clinicopathological parameters. METHODS miRNA expression profiles of 13 IBC and 17 non-IBC patients were characterized using comprehensive Affymetrix GeneChip miRNA 3.0 microarray platform. Bioinformatic analysis was used to reveal IBC-specific miRNAs, deregulated pathways and potential miRNA targets. RESULTS 31 differentially expressed miRNAs characterize IBC and mRNAs regulated by them and their associated pathways can functionally be attributed to IBC progression. In addition, a minimal predictive set of 4 miRNAs characteristic for the IBC phenotype and associated with the TP53 mutational status in breast cancer patients was identified. CONCLUSIONS We have characterized the complete miRNome of inflammatory breast cancer and found differentially expressed miRNAs which reliably classify the patients to IBC and non-IBC groups. We found that the mRNAs and pathways likely regulated by these miRNAs are highly relevant to cancer progression. Furthermore a minimal IBC-related predictive set of 4 miRNAs associated with the TP53 mutational status and survival for breast cancer patients was identified.
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Affiliation(s)
| | | | - Timur R Samatov
- SRC Bioclinicum, Ugreshskaya str 2/85, 115088 Moscow, Russia.
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