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Souza JLN, Lopes CDA, Leal-Silva T, Vieira-Santos F, Amorim CCO, Padrão LDLS, Antunes Porto AR, Fujiwara RT, Russo RC, Bueno LL. Evaluation of reference genes for gene expression analysis by real-time quantitative PCR (qPCR) in different tissues from mice infected by Ascaris suum. Microb Pathog 2024; 189:106567. [PMID: 38364877 DOI: 10.1016/j.micpath.2024.106567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/19/2024] [Accepted: 01/31/2024] [Indexed: 02/18/2024]
Abstract
Human ascariasis is the most prevalent helminth infection, affecting 445 million people worldwide. To better understand the impact of the immune system on the pathophysiology of individuals infected with Ascaris suum, mice have been used as experimental models. The RT-qPCR technique is a critical auxiliary tool of investigation used to quantify mRNA levels. However, proper normalization using reference genes is essential to ensure reliable outcomes to avoid analytical errors and false results. Despite the importance of reference genes for experimental A. suum infection studies, no specific reference genes have been identified yet. Therefore, we conducted a study to assess five potential reference genes (GAPDH, 18s, ACTB, B2M, and HPRT1) in different tissues (liver, lungs, small and large intestines) affected by A. suum larval migration in C57BL/6j mice. Tissue collection was carried out to analyze parasite burden and confirm the presence of larvae during the peak of migration in each tissue. Upon confirmation, we analyzed different genes in the tissues and found no common gene with stable expression. Our results highlight the importance of analyzing different genes and using different software programs to ensure reliable relative expression results. Based on our findings, B2M was ranked as the ideal reference gene for the liver, while 18S was the most stable gene in the lung and small intestine. ACTB, or a combination of ACTB with GAPDH, was deemed suitable as reference genes for the large intestine due to their stable expression and less variation between the control and infected groups. To further demonstrate the impact of using different reference genes, we normalized the expression of a chemokine gene (CXCL9) in all tissues. Significant differences in CXCL9 expression levels were observed between different groups in all tissues except for the large intestine. This underscores the importance of selecting appropriate reference genes to avoid overestimating target gene expression levels and encountering normalization-related issues that can lead to false results. In conclusion, our study highlights the significance of using reliable reference genes for accurate RT-qPCR analysis, especially in the context of A. suum infection studies in different tissues. Proper normalization is crucial to ensure the validity of gene expression data and avoid potential pitfalls in interpreting results.
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Affiliation(s)
- Jorge Lucas Nascimento Souza
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Laboratory of Pulmonary Immunology and Mechanics, Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Camila de Almeida Lopes
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thais Leal-Silva
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flaviane Vieira-Santos
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Chiara Cássia Oliveira Amorim
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luiza de Lima Silva Padrão
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Rafaela Antunes Porto
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ricardo Toshio Fujiwara
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Remo Castro Russo
- Laboratory of Pulmonary Immunology and Mechanics, Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lilian Lacerda Bueno
- Laboratory of Immunobiology and Control of Parasites, Department of Parasitology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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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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3
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Ahn HR, Baek GO, Yoon MG, Son JA, You D, Yoon JH, Cho HJ, Kim SS, Cheong JY, Eun JW. HMBS is the most suitable reference gene for RT-qPCR in human HCC tissues and blood samples. Oncol Lett 2021; 22:791. [PMID: 34584568 PMCID: PMC8461756 DOI: 10.3892/ol.2021.13052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
Reverse transcription-quantitative (RT-q) PCR is the most feasible and useful technique for identifying and evaluating cancer biomarkers; however, the method requires suitable reference genes for gene expression analysis. The aim of the present study was to identify the most suitable reference gene for the normalization of relative gene expression in human hepatocellular carcinoma (HCC) tissue and blood samples. First, 14 candidate reference genes were selected through a systematic literature search. The expression levels of these genes (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, PGK1, PPIA, RPLP0, RPL13A, SDHA, TBP, TFRC and YWHAZ) were evaluated using human multistage HCC transcriptome data (dataset GSE114564), which included normal liver (n=15), chronic hepatitis (n=20), liver cirrhosis (n=10), and early (n=18) and advanced HCC (n=45). From the 14 selected genes, five genes, whose expression levels were stable in all liver disease statuses (ACTB, GAPDH, HMBS, PPIA and RPLP0), were further assessed using RT-qPCR in 40 tissues (20 paired healthy tissues and 20 tissues from patients with HCC) and 40 blood samples (20 healthy controls and 20 samples from patients with HCC). BestKeeper statistical algorithms were used to identify the most stable reference genes, of which HMBS was found to be the most stable in both HCC tissues and blood samples. Therefore, the results of the present study suggest HMBS as a promising reference gene for the normalization of relative RT-qPCR techniques in HCC-related studies.
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Affiliation(s)
- Hye Ri Ahn
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea
| | - Geum Ok Baek
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Moon Gyeong Yoon
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Ju A Son
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea
| | - Donglim You
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea
| | - Jung Hwan Yoon
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Hyo Jung Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Soon Sun Kim
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Jae Yeon Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
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Bujnakova Mlynarcikova A, Scsukova S. Bisphenol analogs AF and S: Effects on cell status and production of angiogenesis-related factors by COV434 human granulosa cell line. Toxicol Appl Pharmacol 2021; 426:115634. [PMID: 34174261 DOI: 10.1016/j.taap.2021.115634] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/25/2021] [Accepted: 06/18/2021] [Indexed: 12/19/2022]
Abstract
While Bisphenol A (BPA) has been a requisite plastic additive, as an endocrine disruptor it has been associated with adverse health effects including ovarian disorders. Following implemented restrictions on BPA usage, it is replaced by alternative bisphenols, biological effects of which have not been adequately investigated. Our study examined effects of bisphenols AF (BPAF) and S (BPS), on the human ovarian granulosa cell line COV434, and compared them with BPA, with the focus on cell viability (10-9-10-4 M) and angiogenesis-related factors (10-9-10-5 M), relevant for both the follicle development and ovarian pathologies: vascular endothelial growth factor A (VEGF-A), platelet-derived growth factor AA (PDGF-AA), and matrix metalloproteinase 9 (MMP-9). Each bisphenol impaired cell viability and increased generation of intracellular reactive oxygen species at the highest concentration (10-4 M). While VEGF-A production in BPAF-treated groups did not differ from the control, all doses of BPS and BPA caused a marked reduction in VEGF-A output. Nevertheless, the alterations in VEGF-A production were not caused by the impact on VEGFA gene expression since there were no indications of VEGFA downregulation in the presence of either BPS or BPA. Interestingly, we observed a similar pattern of PDGF-AA output reduction in BPS- and BPA-treated groups to that of VEGF-A production. BPAF and BPS (10-5 M) increased MMP9 expression, however, this effect was not reflected by the increase in MMP-9 production. The results obtained demonstrate that the novel bisphenol analogs are not inert with respect to the ovarian cells, and their effects might contribute to dysregulation of granulosa cells functions.
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Affiliation(s)
| | - Sona Scsukova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
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5
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Effect of selected bisphenol derivatives on nuclear receptor expression in ovarian cell line COV434. Endocr Regul 2020; 54:275-283. [PMID: 33885253 DOI: 10.2478/enr-2020-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Objectives. Bisphenol A (BPA), as an indispensable plastic additive, has also been proven as an endocrine disruptor associated with adverse health effects including impaired ovarian function and cancer. Due to the restrictions of its usage, several analogs have been employed to replace BPA. Although many studies revealed a harmfulness in the biological effects of BPA analogs, their specific targets remain largely unknown. Nuclear receptors (NRs) may be one of the most important targets of bisphenols. Therefore, in this study, our attention was directed to explore the effect of BPA and its analogs, AF and S, on the mRNA expression of selected NRs involved in the steroidogenic and carcinogenic pathways in the human granulosa cell line COV434. The NRs investigated included: thyroid hormone receptor α (THRA), peroxisome proliferator activating receptor β/δ (PPARD), retinoid X receptor α (RXRA), chicken ovalbumin upstream promoter-transcription factor II (COUPTFII), nuclear receptor-related protein 1 (NURR1), and liver receptor homolog-1 (LRH1).Methods. COV434 cells were treated with the bisphenols at the concentrations of 10-9 M, 10-7 M, and 10-5 M, and after 24 and 48 h, cell viability was monitored by the MTS assay and gene expressions were analyzed using RT-qPCR.Results. Bisphenol treatment did not alter the COV434 cell viability. After 24 h, the expression of neither of the NRs was changed. Likewise, after 48 h, the expression of the selected genes was not altered. However, both BPAF and BPS increased, at the highest concentration (10-5 M) used, the mRNA levels of both PPARD and NURR1 NRs after 48 h of the treatment. In the BPA-treated groups, no significant upregulation was observed.Conclusions. In the present study, the effect of bisphenols on COUP-TFII, Nurr1, and LRH-1 NRs was investigated for the first time. Although generally we did not observe that BPs provoked any alterations in the expression of the selected NRs in COV434 cells, at specific concentrations and time points they might alter mRNA expression of certain NRs (NURR1, PPARD).
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Shaw P, Sen A, Mondal P, Dey Bhowmik A, Rath J, Chattopadhyay A. Shinorine ameliorates chromium induced toxicity in zebrafish hepatocytes through the facultative activation of Nrf2-Keap1-ARE pathway. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 228:105622. [PMID: 32947073 DOI: 10.1016/j.aquatox.2020.105622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 06/11/2023]
Abstract
Hexavalent chromium, a heavy metal toxicant, abundantly found in the environment showed hepatotoxic potential in zebrafish liver and instigated the Nrf2-Keap1-ARE pathway as a cellular stress response as reported in our previous studies. In the present study we have evaluated the ameliorating effect of shinorine, a mycosporine like amino acid (MAAs) and a mammalian Keap1 antagonist against chromium induced stress in zebrafish hepatocytes. Shinorine was found to be effective in increasing the cell viability of chromium treated hepatocytes through curtailing the cellular ROS content. Trigonelline, an Nrf2 inhibitor was found to reduce the viability of hepatocyte cultures co-exposed to shinorine and chromium. In other words, trigonelline being an Nrf2 blocker neutralised the alleviating effect of shinorine. This indicated that shinorine mediated cyto-protection in Cr [VI]-intoxicated cells is Nrf2 dependent. Further, qRT-PCR analysis revealed comparatively higher expression of nfe2l2 and nqo1 in shinorine + chromium treated hepatocytes than cells exposed to chromium alone indicating a better functioning of Nrf2-Keap1-Nqo1 axis. To further confirm if shinorine can lead to disruption of Nrf2-Keap1 interaction in zebrafish hepatocytes and render cytoprotection to chromium exposure, our in silico analysis through molecular docking revealed that shinorine could bind to the active amino acid residues of the DGR domain, responsible for Nrf2-Keap1 interaction of all the three Keap1s evaluated. This is the first report about shinorine that ameliorates chromium induced toxicity through acting as an Nrf2-Keap1 interaction disruptor. We additionally carried out in-silico pharmacokinetic and ADMET studies to evaluate druglikeness of shinorine whose promising results indicated its potential to be developed as an ideal therapeutic candidate against toxicant induced pathological conditions.
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Affiliation(s)
- Pallab Shaw
- Department of Zoology, Visva-Bharati, Santiniketan 731235, West Bengal, India
| | - Animesh Sen
- Department of Botany, Visva-Bharati, Santiniketan 731235, West Bengal, India
| | - Paritosh Mondal
- Department of Zoology, Visva-Bharati, Santiniketan 731235, West Bengal, India
| | - Arpan Dey Bhowmik
- Department of Zoology, Visva-Bharati, Santiniketan 731235, West Bengal, India
| | - Jnanendra Rath
- Department of Botany, Visva-Bharati, Santiniketan 731235, West Bengal, India
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Marczell I, Balogh P, Nyiro G, Kiss AL, Kovacs B, Bekesi G, Racz K, Patocs A. Membrane-bound estrogen receptor alpha initiated signaling is dynamin dependent in breast cancer cells. Eur J Med Res 2018; 23:31. [PMID: 29880033 PMCID: PMC5992704 DOI: 10.1186/s40001-018-0328-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 05/19/2018] [Indexed: 01/22/2023] Open
Abstract
Background Although membrane-associated estrogen receptors (mERs) have been known to play important role in steroid-induced signal transmission, we still know little about their function in the estrogen-induced proliferation of breast cancer cells. Methods In our current work we tried to separate membrane-initiated estrogen receptor signaling from the overall estrogenic effect in MCF-7 breast carcinoma cells. Re-analyzing expression data from multiple microarray experiments, we selected a set of key regulatory genes involved in proliferation regulation and estrogen signaling to monitor estrogen-induced transcription changes. We then compared these expression changes after 17β-estradiol and a membrane receptor selective estrogen–BSA treatment using quantitative real-time PCR. In order to follow receptor trafficking we used light and electron microscopy. Results Our quantitative real-time PCR results confirmed that the selective membrane receptor agonist, estrogen–BSA induces similarly pronounced expression changes regarding these genes as 17β-estradiol. Morphological study revealed that the membrane-bound form of classical estrogen receptor alpha is internalized after ligand binding via dynamin-dependent, caveola-mediated endocytosis. Inhibition of this internalization with dynamin inhibitor, dynasore practically abolished the regulatory effect of E2-BSA, suggesting that interaction and internalization with the scaffold protein is necessary for effective signaling. Conclusions The physiological role of plasma membrane estrogen receptor alpha is intensively studied, yet there are still several aspects of it to be resolved. The dynamin-dependent, ligand-mediated internalization of mERs seems to play an important role in estrogen signaling. Our results may serve as another example of how membrane initiated estrogen signaling and nuclear receptor initiated signaling overlap and form an intertwined system. Electronic supplementary material The online version of this article (10.1186/s40001-018-0328-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Istvan Marczell
- 2nd Department of Medicine, Semmelweis University, Budapest, Szentkirályi utca 46., 1088, Hungary
| | - Petra Balogh
- Department of Human Morphology and Developmental Biology, Semmelweis University, Budapest, Hungary
| | - Gabor Nyiro
- 2nd Department of Medicine, Semmelweis University, Budapest, Szentkirályi utca 46., 1088, Hungary.,Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Szentkirályi str. 46., 1088, Hungary
| | - Anna L Kiss
- Department of Human Morphology and Developmental Biology, Semmelweis University, Budapest, Hungary
| | - Balazs Kovacs
- Department of Aquaculture, Szent Istvan University, Godollo, Hungary
| | - Gabor Bekesi
- 2nd Department of Medicine, Semmelweis University, Budapest, Szentkirályi utca 46., 1088, Hungary
| | - Karoly Racz
- 2nd Department of Medicine, Semmelweis University, Budapest, Szentkirályi utca 46., 1088, Hungary.,Department of Human Morphology and Developmental Biology, Semmelweis University, Budapest, Hungary
| | - Attila Patocs
- 2nd Department of Medicine, Semmelweis University, Budapest, Szentkirályi utca 46., 1088, Hungary. .,HAS-SE 'Lendület' Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, 46. Szentkiralyi str, 1088, Hungary. .,Department of Laboratory Medicine, Semmelweis University, Budapest, Nagyvárad sq 4, 1089, Hungary.
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9
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Stork CT, Bocek M, Crossley MP, Sollier J, Sanz LA, Chédin F, Swigut T, Cimprich KA. Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage. eLife 2016; 5. [PMID: 27552054 PMCID: PMC5030092 DOI: 10.7554/elife.17548] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/18/2016] [Indexed: 12/19/2022] Open
Abstract
The hormone estrogen (E2) binds the estrogen receptor to promote transcription of E2-responsive genes in the breast and other tissues. E2 also has links to genomic instability, and elevated E2 levels are tied to breast cancer. Here, we show that E2 stimulation causes a rapid, global increase in the formation of R-loops, co-transcriptional RNA-DNA products, which in some instances have been linked to DNA damage. We show that E2-dependent R-loop formation and breast cancer rearrangements are highly enriched at E2-responsive genomic loci and that E2 induces DNA replication-dependent double-strand breaks (DSBs). Strikingly, many DSBs that accumulate in response to E2 are R-loop dependent. Thus, R-loops resulting from the E2 transcriptional response are a significant source of DNA damage. This work reveals a novel mechanism by which E2 stimulation leads to genomic instability and highlights how transcriptional programs play an important role in shaping the genomic landscape of DNA damage susceptibility. DOI:http://dx.doi.org/10.7554/eLife.17548.001 The hormone estrogen controls the development of breast tissue. However too much estrogen can damage the DNA in human cells and may be linked to an increased risk of breast cancer. In breast cells, estrogen activates many genes via a process called transcription. The transcription process results in the production of an RNA molecule that contains a copy of the instructions encoded within the gene. Previous studies have found that, in certain cases, a new RNA molecule can stick to the matching DNA from which it was made. This creates a structure known as an R-loop, which can lead the DNA to break. DNA breaks are particularly harmful because they can dramatically alter the cell’s genome in ways that allow it to become cancerous. However, it was not clear if the large increase in transcription triggered by estrogen causes an increase in R-loops, which could help to explain the DNA damage that has been reported to occur when cells are treated with estrogen. Now, Stork et al. show that treating human breast cancer cells with estrogen causes an increase in R-loops and DNA breaks. The R-loops occurred particularly in regions of the genome that contain estrogen-activated genes. Stork et al. also found that regions of estrogen-activated transcription were more frequently mutated in breast cancers, and further experiments confirmed that the R-loops were responsible for many of the DNA breaks that occurred following estrogen treatment. Taken together, these findings demonstrate that the changes in transcription due to estrogen lead to increased R-loops and DNA breaks, which may make the cells vulnerable to becoming cancerous. The next challenge is to determine precisely where these DNA breaks that result from estrogen occur on the DNA. Knowing the location of the DNA breaks will be useful in determining what additional factors or genomic features make an R-loop more prone to being broken. This in turn might help explain how the R-loops lead to DNA damage. In addition, further studies are also needed to determine if tumor samples from breast cancer patients also contain increased levels of R-loops. DOI:http://dx.doi.org/10.7554/eLife.17548.002
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Affiliation(s)
- Caroline Townsend Stork
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Michael Bocek
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Madzia P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Julie Sollier
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
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10
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Shah KN, Wilson EA, Malla R, Elford HL, Faridi JS. Targeting Ribonucleotide Reductase M2 and NF-κB Activation with Didox to Circumvent Tamoxifen Resistance in Breast Cancer. Mol Cancer Ther 2015; 14:2411-21. [PMID: 26333382 DOI: 10.1158/1535-7163.mct-14-0689] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/28/2015] [Indexed: 12/31/2022]
Abstract
Tamoxifen is widely used as an adjuvant therapy for patients with estrogen receptor (ERα)-positive tumors. However, the clinical benefit is often limited because of the emergence of drug resistance. In this study, overexpression of ribonucleotide reductase M2 (RRM2) in MCF-7 breast cancer cells resulted in a reduction in the effectiveness of tamoxifen, through downregulation of ERα66 and upregulation of the 36-kDa variant of ER (ERα36). We identified that NF-κB, HIF1α, and MAPK/JNK are the major pathways that are affected by RRM2 overexpression and result in increased NF-κB activity and increased protein levels of EGFR, HER2, IKKs, Bcl-2, RelB, and p50. RRM2-overexpressing cells also exhibited higher migratory and invasive properties. Through time-lapse microscopy and protein profiling studies of tamoxifen-treated MCF-7 and T-47D cells, we have identified that RRM2, along with other key proteins, is altered during the emergence of acquired tamoxifen resistance. Inhibition of RRM2 using siRRM2 or the ribonucleotide reductase (RR) inhibitor didox not only eradicated and effectively prevented the emergence of tamoxifen-resistant populations but also led to the reversal of many of the proteins altered during the process of acquired tamoxifen resistance. Because didox also appears to be a potent inhibitor of NF-κB activation, combining didox with tamoxifen treatment cooperatively reverses ER-α alterations and inhibits NF-κB activation. Finally, inhibition of RRM2 by didox reversed tamoxifen-resistant in vivo tumor growth and decreased in vitro migratory and invasive properties, revealing a beneficial effect of combination therapy that includes RRM2 inhibition to delay or abrogate tamoxifen resistance.
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Affiliation(s)
- Khyati N Shah
- Department of Physiology and Pharmacology, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, California
| | - Elizabeth A Wilson
- Department of Physiology and Pharmacology, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, California
| | - Ritu Malla
- Department of Physiology and Pharmacology, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, California
| | | | - Jesika S Faridi
- Department of Physiology and Pharmacology, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, California.
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Bian Z, Yu Y, Quan C, Guan R, Jin Y, Wu J, Xu L, Chen F, Bai J, Sun W, Fu S. RPL13A as a reference gene for normalizing mRNA transcription of ovarian cancer cells with paclitaxel and 10-hydroxycamptothecin treatments. Mol Med Rep 2014; 11:3188-94. [PMID: 25523336 DOI: 10.3892/mmr.2014.3108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 12/03/2014] [Indexed: 11/06/2022] Open
Abstract
Gene transcription analysis is important in cancer research, and reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) has been demonstrated to be an effective method to evaluate gene transcription in cancer. RT‑qPCR requires an internal reference gene with a consistent level of mRNA transcription across various experimental conditions. However, it has been suggested that different treatments, including anticancer therapy, may influence the transcriptional stability of internal reference genes. Paclitaxel (PTX) and 10‑hydroxycamptothecin (HCPT) are widely used to treat various types of cancer, and a suitable internal reference gene is required in order to analyze the transcription profiles of the cells following treatment. In the current study, the transcriptional stability of 30 candidate reference genes was investigated in cancer cells following treatment with PTX and HCPT. The two ovarian cancer cell lines, UACC‑1598 and SKOV3, were treated with PTX and HCPT for 24 and 48 h, and the transcriptional levels of the candidate reference genes were subsequently evaluated by RT‑qPCR analysis. The transcriptional stability of the selected genes was then analyzed using qbase+ and NormFinder software. A total of 9 genes were demonstrated to exhibit high transcriptional stability and one of these genes, ribosomal protein L13a (RPL13A), was identified to exhibit high transcriptional stability in every group. The current study identified various reference genes suitable under different circumstances, while RPL13A was indicated to be the most suitable reference gene for analyzing the transcription profile of ovarian cancer cells following treatment with PTX and HCPT.
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Affiliation(s)
- Zehua Bian
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Yang Yu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Chao Quan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Rongwei Guan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Yan Jin
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Lidan Xu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Feng Chen
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Jing Bai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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12
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Zhan C, Zhang Y, Ma J, Wang L, Jiang W, Shi Y, Wang Q. Identification of reference genes for qRT-PCR in human lung squamous-cell carcinoma by RNA-Seq. Acta Biochim Biophys Sin (Shanghai) 2014; 46:330-7. [PMID: 24457517 DOI: 10.1093/abbs/gmt153] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although the accuracy of quantitative real-time polymerase chain reaction (qRT-PCR) is highly dependent on the reliable reference genes, many commonly used reference genes are not stably expressed and as such are not suitable for quantification and normalization of qRT-PCR data. The aim of this study was to identify novel reliable reference genes in lung squamous-cell carcinoma. We used RNA sequencing (RNA-Seq) to survey the whole genome expression in 5 lung normal samples and 44 lung squamous-cell carcinoma samples. We evaluated the expression profiles of 15 commonly used reference genes and identified five additional candidate reference genes. To validate the RNA-Seq dataset, we used qRT-PCR to verify the expression levels of these 20 genes in a separate set of 100 pairs of normal lung tissue and lung squamous-cell carcinoma samples, and then analyzed these results using geNorm and NormFinder. With respect to 14 of the 15 common reference genes (B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC, and YWHAZ), the expression levels were either too low to be easily detected, or exhibited a high degree of variability either between lung normal and squamous-cell carcinoma samples, or even among samples of the same tissue type. In contrast, 1 of the 15 common reference genes (ACTB) and the 5 additional candidate reference genes (EEF1A1, FAU, RPS9, RPS11, and RPS14) were stably and constitutively expressed at high levels in all the samples tested. ACTB, EEF1A1, FAU, RPS9, RPS11, and RPS14 are ideal reference genes for qRT-PCR analysis of lung squamous-cell carcinoma, while 14 commonly used qRT-PCR reference genes are less appropriate in this context.
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Affiliation(s)
- Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200031, China
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13
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Shah KN, Mehta KR, Peterson D, Evangelista M, Livesey JC, Faridi JS. AKT-induced tamoxifen resistance is overturned by RRM2 inhibition. Mol Cancer Res 2013; 12:394-407. [PMID: 24362250 DOI: 10.1158/1541-7786.mcr-13-0219] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Acquired tamoxifen resistance develops in the majority of hormone-responsive breast cancers and frequently involves overexpression of the PI3K/AKT axis. Here, breast cancer cells with elevated endogenous AKT or overexpression of activated AKT exhibited tamoxifen-stimulated cell proliferation and enhanced cell motility. To gain mechanistic insight on AKT-induced endocrine resistance, gene expression profiling was performed to determine the transcripts that are differentially expressed post-tamoxifen therapy under conditions of AKT overexpression. Consistent with the biologic outcome, many of these transcripts function in cell proliferation and cell motility networks and were quantitatively validated in a larger panel of breast cancer cells. Moreover, ribonucleotide reductase M2 (RRM2) was revealed as a key contributor to AKT-induced tamoxifen resistance. Inhibition of RRM2 by RNA interference (RNAi)-mediated approaches significantly reversed the tamoxifen-resistant cell growth, inhibited cell motility, and activated DNA damage and proapoptotic pathways. In addition, treatment of tamoxifen-resistant breast cancer cells with the small molecule RRM inhibitor didox significantly reduced in vitro and in vivo growth. Thus, AKT-expressing breast cancer cells upregulate RRM2 expression, leading to increased DNA repair and protection from tamoxifen-induced apoptosis. IMPLICATIONS These findings identify RRM2 as an AKT-regulated gene, which plays a role in tamoxifen resistance and may prove to be a novel target for effective diagnostic and preventative strategies.
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Affiliation(s)
- Khyati N Shah
- Thomas J. Long School of Pharmacy & Health Sciences, University of the Pacific, 751 Brookside Road, Stockton, CA 95211.
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Kolkova Z, Arakelyan A, Casslén B, Hansson S, Kriegova E. Normalizing to GADPH jeopardises correct quantification of gene expression in ovarian tumours - IPO8 and RPL4 are reliable reference genes. J Ovarian Res 2013; 6:60. [PMID: 24001041 PMCID: PMC3766134 DOI: 10.1186/1757-2215-6-60] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/18/2013] [Indexed: 11/10/2022] Open
Abstract
Background To ensure a correct interpretation of results obtained with quantitative real-time reverse transcription-polymerase chain reaction (RT-qPCR), it is critical to normalize to a reference gene with stable mRNA expression in the tissue of interest. GADPH is widely used as a reference gene in ovarian tumour studies, although lacking tissue-specific stability. The aim of this study was to identify alternative suitable reference genes for RT-qPCR studies on benign, borderline, and malignant ovarian tumours. Methods We assayed mRNA levels for 13 potential reference genes – ABL1, ACTB, CDKN1A, GADPH, GUSB, HPRT1, HSP90AB, IPO8, PPIA, RPL30, RPL4, RPLPO, and TBP –with RT-qPCR in 42 primary ovarian tumours, using commercially pre-designed RT-qPCR probes. Expression stability was subsequently analysed with four different statistical programs (GeNorm, NormFinder, BestKeeper, and the Equivalence test). Results Expression of IPO8, RPL4, TBP, RPLPO, and ACTB had the least variation in expression across the tumour samples according to GeNorm, NormFinder, and BestKeeper. The Equivalence test found variation in expression within a 3-fold expression change between tumour groups for: IPO8, RPL40, RPL30, GUSB, TBP, RPLPO, ACTB, ABL1, and CDKN1A. However, only IPO8 satisfied at a 2-fold change as a cut-off. Overall, IPO8 and RPL4 had the highest, whereas GADPH and HPRT1 the lowest expression stability. Employment of suitable reference genes (IPO8, RPL4) in comparison with unsuitable ones (GADPH, HPRT1), demonstrated divergent influence on the mRNA expression pattern of our target genes − GPER and uPAR. Conclusions We found IPO8 and RPL4 to be suitable reference genes for normalization of target gene expression in benign, borderline, and malignant ovarian tumours. Moreover, IPO8 can be recommended as a single reference gene. Neither GADPH nor HPRT1 should be used as reference genes in studies on ovarian tumour tissue.
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Affiliation(s)
- Zuzana Kolkova
- Department of Obstetrics & Gynaecology, Lund University, Skåne University Hospital Lund, Lund, SE 221 85, Sweden.
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15
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Kılıç Y, Çelebiler AÇ, Sakızlı M. Selecting housekeeping genes as references for the normalization of quantitative PCR data in breast cancer. Clin Transl Oncol 2013; 16:184-90. [PMID: 23720140 DOI: 10.1007/s12094-013-1058-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/21/2013] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The common reference genes of choice in relative gene expression studies based on quantitative real time polymerase chain reaction, ACTB and B2M, were shown to be regulated differently in respect to tissue type. In this study, the stability of the selected housekeeping genes for normalizing the qPCR data were identified in the tumor and its adjacent tissues in invasive breast cancer, and the variability of their levels according to the stages and the histopathologic subtypes was analyzed. METHODS Four housekeeping genes: PUM1, RPL13A, B2M, and ACTB were analyzed in 99 surgically excised tissue specimens (50 tumor, 45 tumor adjacent and 4 normal breast tissues). Three of the most common softwares (GeNorm, NormFinder, and BestKeeper) were used for calculation purposes. RESULTS When all of the tissue samples were included in analyses, PUM1 was the most stable gene according to calculations made with both NormFinder and BestKeeper; while PUM1/RPL13A combination was the most stable by GeNorm software. The PUM1 gene was also identified as the most stable gene among the four in all sample groups (in both Estrogen Receptor positive and Estrogen Receptor negative subgroups of invasive breast carcinoma and in normal breast tissue) according to calculations made using the NormFinder software. CONCLUSION While suggesting PUM1 is one of the most stable single gene and the PUM1/RPL13A pair as one of the best housekeeping genes for the normalization of expression studies in invasive breast tumor studies, it will be more practical to evaluate stability once more and decide upon the reference gene accordingly within the sample group itself.
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Affiliation(s)
- Y Kılıç
- Department of Medical Biology and Genetics, Faculty of Medicine, Dokuz Eylül University, Konak, İzmir, Turkey,
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