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Müller-Dott S, Tsirvouli E, Vazquez M, Ramirez Flores R, Badia-i-Mompel P, Fallegger R, Türei D, Lægreid A, Saez-Rodriguez J. Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities. Nucleic Acids Res 2023; 51:10934-10949. [PMID: 37843125 PMCID: PMC10639077 DOI: 10.1093/nar/gkad841] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/08/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023] Open
Abstract
Gene regulation plays a critical role in the cellular processes that underlie human health and disease. The regulatory relationship between transcription factors (TFs), key regulators of gene expression, and their target genes, the so called TF regulons, can be coupled with computational algorithms to estimate the activity of TFs. However, to interpret these findings accurately, regulons of high reliability and coverage are needed. In this study, we present and evaluate a collection of regulons created using the CollecTRI meta-resource containing signed TF-gene interactions for 1186 TFs. In this context, we introduce a workflow to integrate information from multiple resources and assign the sign of regulation to TF-gene interactions that could be applied to other comprehensive knowledge bases. We find that the signed CollecTRI-derived regulons outperform other public collections of regulatory interactions in accurately inferring changes in TF activities in perturbation experiments. Furthermore, we showcase the value of the regulons by examining TF activity profiles in three different cancer types and exploring TF activities at the level of single-cells. Overall, the CollecTRI-derived TF regulons enable the accurate and comprehensive estimation of TF activities and thereby help to interpret transcriptomics data.
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Affiliation(s)
- Sophia Müller-Dott
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Eirini Tsirvouli
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Ricardo O Ramirez Flores
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Pau Badia-i-Mompel
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Robin Fallegger
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Dénes Türei
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Astrid Lægreid
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
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2
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Xie J, Zhang H, Wang K, Ni J, Ma X, Khoury CJ, Prifti V, Hoard B, Cerenzia EG, Yin L, Zhang H, Wang R, Zhuo D, Mao W, Peng B. M6A-mediated-upregulation of lncRNA BLACAT3 promotes bladder cancer angiogenesis and hematogenous metastasis through YBX3 nuclear shuttling and enhancing NCF2 transcription. Oncogene 2023; 42:2956-2970. [PMID: 37612524 PMCID: PMC10541332 DOI: 10.1038/s41388-023-02814-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023]
Abstract
Lymphatic metastasis is recognized as the leading manner of metastasis in bladder cancer (BLCa), but hematogenous metastasis accounts for a majority of cancer-associated deaths. The past two decades have witnessed tremendous attention in long non-coding RNAs (lncRNAs), which are a new hope for the development of targeted drug therapy for metastatic cancers; however, the underlying mechanism of lncRNAs involved in BLCa hematogenous metastasis remains to be elucidated. Here, we identified BLCa-associated transcript 3 (BLACAT3), a lncRNA, which was aberrantly upregulated in BLCa and corelated with poor prognosis of patients with muscle-invasive bladder cancer. Methodologically, m6A epitranscriptomic microarray, RNA sequencing and mass spectrometry (MS) were used to screen the key molecules of the regulatory axis. Functional assays, animal models and clinical samples were used to explore the roles of BLACAT3 in BLCa in vitro and in vivo. Mechanistically, m6A modification contributes to BLACAT3 upregulation by stabilizing RNA structure. BLACAT3 recruits YBX3 to shuttle into the nucleus, synergistically enhances NCF2 transcription, and promotes BLCa angiogenesis and hematogenous metastasis by activating downstream NF-κB signaling. Our findings will develop prognosis prediction tools for BLCa patients and discover novel therapeutic biological targets for metastatic BLCa.
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Affiliation(s)
- Jinbo Xie
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Department of Urology, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, China
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Department of Laboratory Medicine, LKSKI-Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
| | - Hui Zhang
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
| | - Keyi Wang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Jinliang Ni
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Xiaoying Ma
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Department of Laboratory Medicine, LKSKI-Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
| | - Christopher J Khoury
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Department of Laboratory Medicine, LKSKI-Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
| | - Viktor Prifti
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Department of Laboratory Medicine, LKSKI-Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
| | - Brock Hoard
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Department of Laboratory Medicine, LKSKI-Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
| | - Eric G Cerenzia
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Department of Laboratory Medicine, LKSKI-Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
| | - Lei Yin
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Houliang Zhang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China
| | - Ruiliang Wang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Dong Zhuo
- Department of Urology, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, China.
| | - Weipu Mao
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China.
| | - Bo Peng
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
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3
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Spourquet C, Delcorte O, Lemoine P, Dauguet N, Loriot A, Achouri Y, Hollmén M, Jalkanen S, Huaux F, Lucas S, Meerkeeck PV, Knauf JA, Fagin JA, Dessy C, Mourad M, Henriet P, Tyteca D, Marbaix E, Pierreux CE. BRAFV600E Expression in Thyrocytes Causes Recruitment of Immunosuppressive STABILIN-1 Macrophages. Cancers (Basel) 2022; 14:cancers14194687. [PMID: 36230610 PMCID: PMC9563029 DOI: 10.3390/cancers14194687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/22/2022] Open
Abstract
Simple Summary Incidence of thyroid cancer, including papillary thyroid cancer, is rapidly increasing. Oncogenes, such as the BRAFV600E, have been identified, and their effect on thyroid cancer cells have been studied in vitro and in mouse models. What is less understood is the impact of these mutations on thyroid cancer microenvironment and, in turn, the effect of changes in the microenvironment on tumor progression. We investigated the modifications in the cellular composition of thyroid cancer microenvironment using an inducible mouse model. We focused on a subpopulation of macrophages, expressing the STABILIN-1 protein, recruited in the thyroid tumor microenvironment following BRAFV600E expression. CRISPR/Cas9 genetic inactivation of Stablin-1 did not change macrophage recruitment but highlighted the immunosuppressive role of STABILIN-1-expressing macrophages. The identification of a similar subpopulation of STABILIN-1 macrophages in human thyroid diseases supports a conserved role for these macrophages and offers an opportunity for intervention. Abstract Papillary thyroid carcinoma (PTC) is the most frequent histological subtype of thyroid cancers (TC), and BRAFV600E genetic alteration is found in 60% of this endocrine cancer. This oncogene is associated with poor prognosis, resistance to radioiodine therapy, and tumor progression. Histological follow-up by anatomo-pathologists revealed that two-thirds of surgically-removed thyroids do not present malignant lesions. Thus, continued fundamental research into the molecular mechanisms of TC downstream of BRAFV600E remains central to better understanding the clinical behavior of these tumors. To study PTC, we used a mouse model in which expression of BRAFV600E was specifically switched on in thyrocytes by doxycycline administration. Upon daily intraperitoneal doxycycline injection, thyroid tissue rapidly acquired histological features mimicking human PTC. Transcriptomic analysis revealed major changes in immune signaling pathways upon BRAFV600E induction. Multiplex immunofluorescence confirmed the abundant recruitment of macrophages, among which a population of LYVE-1+/CD206+/STABILIN-1+ was dramatically increased. By genetically inactivating the gene coding for the scavenger receptor STABILIN-1, we showed an increase of CD8+ T cells in this in situ BRAFV600E-dependent TC. Lastly, we demonstrated the presence of CD206+/STABILIN-1+ macrophages in human thyroid pathologies. Altogether, we revealed the recruitment of immunosuppressive STABILIN-1 macrophages in a PTC mouse model and the interest to further study this macrophage subpopulation in human thyroid tissues.
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Affiliation(s)
- Catherine Spourquet
- CELL Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Ophélie Delcorte
- CELL Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Pascale Lemoine
- CELL Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Nicolas Dauguet
- CYTF Platform, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Axelle Loriot
- CBIO Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Younes Achouri
- Transgenesis Platform, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Maija Hollmén
- MediCity Research Laboratory and InFLAMES Flagship, University of Turku, 20500 Turku, Finland
| | - Sirpa Jalkanen
- MediCity Research Laboratory and InFLAMES Flagship, University of Turku, 20500 Turku, Finland
| | - François Huaux
- LTAP Unit, IREC, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Sophie Lucas
- GECE Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
| | - Pierre Van Meerkeeck
- GECE Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Jeffrey A. Knauf
- Department of Otolaryngology Head & Neck Surgery in the Cleveland Clinic Lerner, College of Medicine of Case Western Reserve University, Cleveland, OH 44106, USA
| | - James A. Fagin
- Department of Medicine and Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chantal Dessy
- FATH & MORF Unit, IREC, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Michel Mourad
- Surgery and Abdominal Transplantation Division, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Patrick Henriet
- CELL Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Donatienne Tyteca
- CELL Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Etienne Marbaix
- CELL Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Christophe E. Pierreux
- CELL Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
- Correspondence: ; Tel.:+32-2-764-65-22
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Xu C, Zhan C, Huang S, Xu Q, Tang T, Wang Y, Luo J, Zeng X. Resistance to Powdery Mildew in Qingke Involves the Accumulation of Aromatic Phenolamides Through Jasmonate-Mediated Activation of Defense-Related Genes. FRONTIERS IN PLANT SCIENCE 2022; 13:900345. [PMID: 35845698 PMCID: PMC9280689 DOI: 10.3389/fpls.2022.900345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/25/2022] [Indexed: 05/08/2023]
Abstract
Powdery mildew (PM) leads to severe yield reduction in qingke (Hordeum vulgare L. var. nudum). Although studies have focused on identifying PM-related resistance genes, mechanistic insights into the metabolic regulation networks of resistance against PM have rarely been explored in qingke. Here, we integrated transcriptomic, proteomic and metabolomic data using PM-susceptible (G72) and PM-resistant (K69) accessions to systemically explore the mechanisms of PM resistance. The integrated results show that a rapidly transduction of jasmonic acid (JA) and (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile), and importantly, a inducing accumulation of aromatic PAs conferred qingke-specific resistance for PM stress. Functional analysis revealed that the four BAHD N-acyltransferase genes were responsible for the synthesis of aliphatic and aromatic PAs. The expression of the four genes are induced by methyl jasmonate (MeJA) and PM treatment. Co-expression network analysis shows that a histone lysine demethylase, JMJ705 gene, also induced by MeJA and PM treatment, had highly correlation with PAs biosynthesis. Chromatin immunoprecipitation (ChIP)-seq assays revealed that the level of trimethylated histone H3 lysine 27 (H3K27me3) of the four genes in MeJA and PM-treated plants was significantly reduced. Overall, our results suggest that a novel strategy for jasmonic acid signal-mediated demethylation controlling the accumulation of aromatic PAs to enhance plant immune resistance through removal of H3K27me3 and activating defense-related gene expression.
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Affiliation(s)
- Congping Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet, China
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Chuansong Zhan
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Sishu Huang
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Qijun Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet, China
| | - Tang Tang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- *Correspondence: Jie Luo,
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet, China
- Plant Sciences College, Tibet Agriculture and Animal Husbandry University, Tibet, China
- Xingquan Zeng,
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5
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Strauss P, Mikkelsen H, Furriol J. Variable expression of eighteen common housekeeping genes in human non-cancerous kidney biopsies. PLoS One 2021; 16:e0259373. [PMID: 34882702 PMCID: PMC8659319 DOI: 10.1371/journal.pone.0259373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/18/2021] [Indexed: 11/24/2022] Open
Abstract
Housekeeping, or reference genes (RGs) are, by definition, loci with stable expression profiles that are widely used as internal controls to normalize mRNA levels. However, due to specific events, such as pathological changes, or technical procedures, their expression might be altered, failing to fulfil critical normalization pre-requisites. To identify RG genes suitable as internal controls in human non-cancerous kidney tissue, we selected 18 RG candidates based on previous data and screen them in 30 expression datasets (>800 patients), including our own, publicly available or provided by independent groups. Datasets included specimens from patients with hypertensive and diabetic nephropathy, Fabry disease, focal segmental glomerulosclerosis, IgA nephropathy, membranous nephropathy, and minimal change disease. We examined both microdissected and whole section-based datasets. Expression variability of 4 candidate genes (YWHAZ, SLC4A1AP, RPS13 and ACTB) was further examined by qPCR in biopsies from patients with hypertensive nephropathy (n = 11) and healthy controls (n = 5). Only YWHAZ gene expression remained stable in all datasets whereas SLC4A1AP was stable in all but one Fabry dataset. All other RGs were differentially expressed in at least 2 datasets, and in 4.5 datasets on average. No differences in YWHAZ, SLC4A1AP, RPS13 and ACTB gene expression between hypertensive and control biopsies were detected by qPCR. Although RGs suitable to all techniques and tissues are unlikely to exist, our data suggest that in non-cancerous kidney biopsies expression of YWHAZ and SLC4AIAP genes is stable and suitable for normalization purposes.
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Affiliation(s)
- Philipp Strauss
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- * E-mail:
| | - Håvard Mikkelsen
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Jessica Furriol
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Rashid M, Shah SG, Natu A, Verma T, Rauniyar S, Gera PB, Gupta S. RPS13, a potential universal reference gene for normalisation of gene expression in multiple human normal and cancer tissue samples. Mol Biol Rep 2021; 48:7967-7974. [PMID: 34657252 DOI: 10.1007/s11033-021-06828-6] [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: 03/10/2021] [Accepted: 09/24/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Reference genes are considered stable genes and are used for normalizing the gene expression profile across different cell types; as well as, in normal and diseased samples. However, these gene associates with different biological processes, and hence expression vary in different pathological conditions. Therefore, in the present study, eight different reference genes were used and compared to identify common reference gene usable for an array of different cell types and human cancers. METHODS AND RESULTS The expression stability of the eight reference genes across eleven normal and cancerous tissues was confirmed through real time-qPCR. Ribosomal protein S13 (RPS13) was found to be a common and stable reference gene across intra- and inter-comparison between various normal and tumor tissue types. Further, TCGA data analysis across and between normal and tumor tissue types also showed minimum deviation in expression of RPS13 gene out of eight routinely used reference genes. CONCLUSION RPS13 is the common stable reference gene in normalization for gene expression based analysis in cancer research.
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Affiliation(s)
- Mudasir Rashid
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sanket Girish Shah
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Abhiram Natu
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Tripti Verma
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sukanya Rauniyar
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Poonam B Gera
- Biorepository, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
| | - Sanjay Gupta
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India.
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7
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Ppia is the most stable housekeeping gene for qRT-PCR normalization in kidneys of three Pkd1-deficient mouse models. Sci Rep 2021; 11:19798. [PMID: 34611276 PMCID: PMC8492864 DOI: 10.1038/s41598-021-99366-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/13/2021] [Indexed: 01/08/2023] Open
Abstract
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most common inherited renal disorder, characterized by renal cyst development leading to end-stage renal disease. Although the appropriate choice of suitable reference is critical for quantitative RNA analysis, no comparison of frequently used “housekeeping” genes is available. Here, we determined the validity of 7 candidate housekeeping genes (Actb, Actg1, B2m, Gapdh, Hprt, Pgam1 and Ppia) in kidney tissues from mouse models orthologous to ADPKD, including a cystic mice (CY) 10–12 weeks old (Pkd1flox/flox:Nestincre/Pkd1flox/−:Nestincre, n = 10) and non-cystic (NC) controls (Pkd1flox/flox/Pkd1flox/-, n = 10), Pkd1-haploinsufficient (HT) mice (Pkd1+/−, n = 6) and wild-type (WT) controls (Pkd1+/+, n = 6) and a severely cystic (SC) mice 15 days old (Pkd1V/V, n = 7) and their controls (CO, n = 5). Gene expression data were analyzed using six distinct statistical softwares. The estimation of the ideal number of genes suggested the use of Ppia alone as sufficient, although not ideal, to analyze groups altogether. Actb, Hprt and Ppia expression profiles were correlated in all samples. Ppia was identified as the most stable housekeeping gene, while Gapdh was the least stable for all kidney samples. Stat3 expression level was consistent with upregulation in SC compared to CO when normalized by Ppia expression. In conclusion, present findings identified Ppia as the best housekeeping gene for CY + NC and SC + CO groups, while Hprt was the best for the HT + WT group.
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8
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Fan X, Xie X, Yang M, Wang Y, Wu H, Deng T, Weng X, Wen W, Nie G. YBX3 Mediates the Metastasis of Nasopharyngeal Carcinoma via PI3K/AKT Signaling. Front Oncol 2021; 11:617621. [PMID: 33816248 PMCID: PMC8010247 DOI: 10.3389/fonc.2021.617621] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/02/2021] [Indexed: 01/11/2023] Open
Abstract
The metastasis of nasopharyngeal carcinoma (NPC) is a complex process associated with oncogenic dysfunction, the deciphering of which remains a challenge and requires more in-depth studies. Y-box protein 3 (YBX3) is a DNA/RNA binding protein associated with gene transcription, DNA repair, and the progression of various diseases. However, whether and how YBX3 affects the metastasis of NPC remains unknown. Thus, in this study, we aimed to investigate the role of YBX3 in the metastasis of NPC and determine its underlying mechanism. Interestingly, it was found that the expression of YBX3, which was associated with NPC metastasis, was upregulated in the clinical NPC tissues and cell lines. Moreover, we found that knockdown of YBX3 expression by lentivirus shRNA significantly suppressed NPC cells migration in vitro and metastasis in vivo. Mechanistically, RNA sequencing results suggested that the genes regulated by YBX3 were significantly enriched in cell adhesion molecules, cAMP signaling pathway, calcium signaling pathway, focal adhesion, PI3K/AKT signaling pathway, Ras signaling pathway, Rap1 signaling pathway, NF-κB signaling pathway, and Chemokine signaling pathway. Of these, PI3K/AKT signaling pathway contained the most genes. Accordingly, YBX3 knockdown decreased the activation of PI3K/AKT signaling pathway, thereby inhibit epithelial-to-mesenchymal transition (EMT) and MMP1. These results have demonstrated that YBX3 are involved in the metastasis of NPC through regulating PI3K/AKT signaling pathway, and serve as a potential therapeutic target for patients with NPC.
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Affiliation(s)
- Xiaoqin Fan
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.,Department of Otolaryngology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xina Xie
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ming Yang
- Department of Otolaryngology, Shenzhen First People's Hospital, The Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yujie Wang
- Department of Otolaryngology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Hanwei Wu
- Department of Otolaryngology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Tingting Deng
- Department of Otolaryngology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xin Weng
- Department of Pathology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Weiping Wen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Guohui Nie
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.,Department of Otolaryngology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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9
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Nowak I, Brożyna AA, Zabłocka M, Student S, Durbas M, Bugara B, Rokita H. MCPIP1 expression positively correlates with melanoma-specific survival of patients, and its overexpression affects vital intracellular pathways of human melanoma cells. Mol Carcinog 2021; 60:227-241. [PMID: 33544962 DOI: 10.1002/mc.23286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/14/2023]
Abstract
The suppressive activity of monocyte chemoattractant protein 1-induced protein 1 (MCPIP1) an inflammation-related ribonuclease, has been described in a few cancer types but has yet to be assessed in the most common subtype of skin cancer: melanoma. Here, we have evaluated the MCPIP1 expression in melanoma tissues by reanalysis of publicly available transcriptome data from 89 melanoma samples, and immunohistochemical staining of 21 primary and 81 metastatic melanomas. Our data implicated decreased MCPIP1 expression in melanoma tumors compared to normal tissues, and positive correlation between high ribonuclease expression and melanoma-specific survival of patients. To investigate the ribonuclease activity in melanoma cells, MCPIP1 was ectopically expressed in the MV3 human melanoma cell line. Following the transcriptome, proteome, and intracellular signaling of MCPIP1-overexpressing MV3 cells was assessed via real-time quantitative polymerase chain reaction, Western blot analysis, and RNAseq. MV3 cells overexpressing MCPIP1 exhibited a broad range of alterations in the transcriptome and proteome, as well as in the phosphorylation status of a number of proteins, strongly indicating MCPIP1-dependent cell cycle arrest and inhibition of Akt/mTOR signaling in these cells. Moreover, we have shown, that MCPIP1 overexpression downregulates miRNA-193a-3p expression in MV3 cells. Furthermore, the majority of the described effects were dependent on the ribonucleolytic activity of the protein. The presented body of data strongly suggests a potential tumor suppressor role and possible future application as a positive prognostic marker of MCPIP1 protein in melanoma.
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Affiliation(s)
- Iwona Nowak
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna A Brożyna
- Department of Human Biology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland.,Department of Tumour Pathology and Pathomorphology, Oncology Centre-Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Marzena Zabłocka
- Department of Tumour Pathology and Pathomorphology, Oncology Centre-Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Sebastian Student
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland.,Department of System Biology and Engineering, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Małgorzata Durbas
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Beata Bugara
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Hanna Rokita
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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10
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Ordikhani F, Kasinath V, Uehara M, Akbarzadeh A, Yilmam OA, Dai L, Aksu H, Jung S, Jiang L, Li X, Zhao J, Bahmani B, Ichimura T, Fiorina P, Annabi N, Abdi R. Selective Trafficking of Light Chain-Conjugated Nanoparticles to the Kidney and Renal Cell Carcinoma. NANO TODAY 2020; 35:100990. [PMID: 33244320 PMCID: PMC7685247 DOI: 10.1016/j.nantod.2020.100990] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Specific delivery platforms for drugs to the kidney and diagnostic agents to renal cell carcinoma (RCC) constitute urgent but unfulfilled clinical needs. To address these challenges, we engineered nanocarriers that interact selectively for the first time with proximal tubule epithelial cells (PTECs) in the kidney and with RCC through the interplay between lambda light chains (LCs) attached to PEGylated polylactic-co-glycolic acid (PLGA) nanoparticles and the membrane protein megalin. Systemic administration of these light chain-conjugated nanoparticles (LC-NPs) to mice resulted in their specific retention by megalin-expressing PTECs for seven days. Repetitive dosing of LC-NPs demonstrated no renal toxicity. LC-NPs also localized selectively to megalin-expressing RCC tumors in mice. Moreover, we confirmed that both the primary tumor and lymph node metastases of human RCC express megalin, reinforcing the potential of LC-NPs for clinical use. Thus, LC-NPs can contribute potentially to improving the management of both non-oncologic and oncologic renal disorders.
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Affiliation(s)
- Farideh Ordikhani
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Vivek Kasinath
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mayuko Uehara
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Aram Akbarzadeh
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Osman A Yilmam
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Li Dai
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hamza Aksu
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sungwook Jung
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Liwei Jiang
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaofei Li
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jing Zhao
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Baharak Bahmani
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Takaharu Ichimura
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Paolo Fiorina
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Nephrology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nasim Annabi
- Chemical and Biomolecular Engineering Department and Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute (CNSI), University of California - Los Angeles, Los Angeles, CA, USA
| | - Reza Abdi
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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11
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Hua X, Chen J, Ge S, Xiao H, Zhang L, Liang C. Integrated analysis of the functions of RNA binding proteins in clear cell renal cell carcinoma. Genomics 2020; 113:850-860. [PMID: 33169673 DOI: 10.1016/j.ygeno.2020.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/16/2020] [Indexed: 12/29/2022]
Abstract
RNA binding proteins (RBPs) dysregulation is involved in the processes of various tumors. However, the roles of RBPs in clear cell renal cell carcinoma (ccRCC) remain poorly understand. In present study, we first performed consensus clustering and identified two clusters, of which cluster 2 was closely correlated with the malignancy of ccRCC. Differentially expressed RBPs between normal and tumor tissues were obtained, comprising 71 up-regulated and 44 down-regulated ones. Then, ten hub genes were selected and validated using The Human Protein Atlas database and receiver operating characteristic curves, showing good diagnostic value for cancers. Besides, we identified ten RBPs with the most useful prognostic values, and were used to construct a risk score model. The model could be used to stratify patients with different prognosis and phenotype distributions. The model showed good performance and can be used as a complementation for clinical factors to guide clinical practice in the future.
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Affiliation(s)
- Xiaoliang Hua
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China
| | - Juan Chen
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, the College of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, China
| | - Shengdong Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China
| | - Haibing Xiao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China.
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China.
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12
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Asiabi P, Ambroise J, Giachini C, Coccia ME, Bearzatto B, Chiti MC, Dolmans MM, Amorim CA. Assessing and validating housekeeping genes in normal, cancerous, and polycystic human ovaries. J Assist Reprod Genet 2020; 37:2545-2553. [PMID: 32729067 DOI: 10.1007/s10815-020-01901-8] [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: 03/31/2020] [Accepted: 07/23/2020] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Housekeeping genes (HKGs), reference or endogenous control genes, are vital to normalize mRNA levels between different samples. Since using inappropriate HKGs can lead to unreliable results, selecting the proper ones is critical for gene expression studies. To this end, normal human ovaries, as well as those from patients diagnosed with ovarian endometrioid adenocarcinoma (OEA), ovarian mucinous adenocarcinoma (OMA), ovarian serous papillary carcinoma (OSPC), and polycystic ovary syndrome (PCOS), were used to identify the most suitable housekeeping genes. METHODS RNA was isolated from 5 normal human ovaries (52-79 years of age), 9 cancerous ovaries (3 OEA, 3 OMA, 3 OSPC; 49-75 years of age), and 4 PCOS ovaries (18-35 years of age) in women undergoing hysterectomy. cDNA was synthesized using a whole transcriptome kit, and quantitative real-time PCR was performed using TaqMan array 96-well plates containing 32 human endogenous controls in triplicate. RESULTS Among 32 HKGs studied, RPS17, RPL37A, PPIA, 18srRNA, B2M, RPLP0, RPLP30, HPRT1, POP4, CDKN1B, and ELF1 were selected as the best reference genes. CONCLUSIONS This study confirms recent investigations demonstrating that conventional HKGs, such as GAPDH and beta-actin, are not suitable reference genes for specific pathological conditions, emphasizing the importance of determining the best HKGs on a case-by-case basis and according to tissue type. Our results have identified reliable HKGs for studies of normal human ovaries and those affected by OEA, OMA, OSPC, or PCOS, as well as combined studies of control subjects vs. each cancer or PCOS group.
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Affiliation(s)
- P Asiabi
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Avenue Mounier 52, bte B1.52.02, 1200, Brussels, Belgium
| | - J Ambroise
- Centre de Technologies Moléculaires Appliquées, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - C Giachini
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - M E Coccia
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - B Bearzatto
- Centre de Technologies Moléculaires Appliquées, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - M C Chiti
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Avenue Mounier 52, bte B1.52.02, 1200, Brussels, Belgium
| | - M M Dolmans
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Avenue Mounier 52, bte B1.52.02, 1200, Brussels, Belgium
- Gynecology Department, Cliniques Universitaires Saint-Luc, 1200, Brussels, Belgium
| | - C A Amorim
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Avenue Mounier 52, bte B1.52.02, 1200, Brussels, Belgium.
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13
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Boratyn E, Nowak I, Karnas E, Ryszawy D, Wnuk D, Polus A, Durbas M, Horwacik I, Rokita H. MCPIP1 overexpression in human neuroblastoma cell lines causes cell‐cycle arrest by G1/S checkpoint block. J Cell Biochem 2020; 121:3406-3425. [DOI: 10.1002/jcb.29614] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/11/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Elżbieta Boratyn
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics, and BiotechnologyJagiellonian University Kraków Poland
| | - Iwona Nowak
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics, and BiotechnologyJagiellonian University Kraków Poland
| | - Elżbieta Karnas
- Laboratory of Stem Cell Biotechnology, Malopolska Centre of BiotechnologyJagiellonian University Kraków Poland
- Department of Cell Biology, Faculty of Biochemistry, Biophysics, and BiotechnologyJagiellonian University Kraków Poland
| | - Damian Ryszawy
- Department of Cell Biology, Faculty of Biochemistry, Biophysics, and BiotechnologyJagiellonian University Kraków Poland
| | - Dawid Wnuk
- Department of Cell Biology, Faculty of Biochemistry, Biophysics, and BiotechnologyJagiellonian University Kraków Poland
| | - Anna Polus
- Department of Clinical Biochemistry, Medical CollegeJagiellonian University Kraków Poland
| | - Małgorzata Durbas
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics, and BiotechnologyJagiellonian University Kraków Poland
| | - Irena Horwacik
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics, and BiotechnologyJagiellonian University Kraków Poland
| | - Hanna Rokita
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics, and BiotechnologyJagiellonian University Kraków Poland
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14
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Trott JF, Abu Aboud O, McLaughlin B, Anderson KL, Modiano JF, Kim K, Jen KY, Senapedis W, Chang H, Landesman Y, Baloglu E, Pili R, Weiss RH. Anti-Cancer Activity of PAK4/NAMPT Inhibitor and Programmed Cell Death Protein-1 Antibody in Kidney Cancer. KIDNEY360 2020; 1:376-388. [PMID: 35224510 PMCID: PMC8809296 DOI: 10.34067/kid.0000282019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/12/2020] [Indexed: 06/14/2023]
Abstract
BACKGROUND Kidney cancer (or renal cell carcinoma, RCC) is the sixth most common malignancy in the United States and is increasing in incidence. Despite new therapies, including targeted therapies and immunotherapies, most RCCs are resistant to treatment. Thus, several laboratories have been evaluating new approaches to therapy, both with single agents as well as combinations. Although we have previously shown efficacy of the dual PAK4/nicotinamide phosphoribosyltransferase (NAMPT) inhibitor KPT-9274, and the immune checkpoint inhibitors (CPI) have shown utility in the clinic, there has been no evaluation of this combination either clinically or in an immunocompetent animal model of kidney cancer. METHODS In this study, we use the renal cell adenocarcinoma (RENCA) model of spontaneous murine kidney cancer. Male BALB/cJ mice were injected subcutaneously with RENCA cells and, after tumors were palpable, they were treated with KPT-9274 and/or anti-programmed cell death 1 (PDCD1; PD1) antibody for 21 days. Tumors were measured and then removed at animal euthanasia for subsequent studies. RESULTS We demonstrate a significant decrease in allograft growth with the combination treatment of KPT-9274 and anti-PD1 antibody without significant weight loss by the animals. This is associated with decreased (MOUSE) Naprt expression, indicating dependence of these tumors on NAMPT in parallel to what we have observed in human RCC. Histology of the tumors showed substantial necrosis regardless of treatment condition, and flow cytometry of antibody-stained tumor cells revealed that the enhanced therapeutic effect of KPT-9274 and anti-PD1 antibody was not driven by infiltration of T cells into tumors. CONCLUSIONS This study highlights the potential of the RENCA model for evaluating immunologic responses to KPT-9274 and checkpoint inhibitor (CPI) and suggests that therapy with this combination could improve efficacy in RCC beyond what is achievable with CPI alone.
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Affiliation(s)
- Josephine F. Trott
- Division of Nephrology, Department of Internal Medicine, University of California, Davis, California
| | - Omran Abu Aboud
- Division of Nephrology, Department of Internal Medicine, University of California, Davis, California
| | - Bridget McLaughlin
- Comprehensive Cancer Center, University of California, Davis, California
| | - Katie L. Anderson
- Animal Cancer Care and Research Program, College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota
| | - Jaime F. Modiano
- Animal Cancer Care and Research Program, College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota
| | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, California
| | - Kuang-Yu Jen
- Department of Pathology and Laboratory Medicine, University of California, Davis, California
| | - William Senapedis
- Research and Translational Development, Karyopharm Therapeutics Inc., Newton, Massachusetts
| | - Hua Chang
- Research and Translational Development, Karyopharm Therapeutics Inc., Newton, Massachusetts
| | - Yosef Landesman
- Research and Translational Development, Karyopharm Therapeutics Inc., Newton, Massachusetts
| | - Erkan Baloglu
- Research and Translational Development, Karyopharm Therapeutics Inc., Newton, Massachusetts
| | - Roberto Pili
- Simon Cancer Center, School of Medicine, Indiana University, Indianapolis, Indiana
| | - Robert H. Weiss
- Division of Nephrology, Department of Internal Medicine, University of California, Davis, California
- Comprehensive Cancer Center, University of California, Davis, California
- Medical Service, Veterans Affairs Northern California Health Care System, Sacramento, California
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15
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Cox A, Zhao C, Tolkach Y, Nettersheim D, Schmidt D, Kristiansen G, Hauser S, Müller SC, Ritter M, Ellinger J. The contrasting roles of Dysferlin during tumor progression in renal cell carcinoma. Urol Oncol 2020; 38:687.e1-687.e11. [PMID: 32430251 DOI: 10.1016/j.urolonc.2020.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND The vesicle fusion protein Dysferlin (DYSF) is mainly known as a membrane repair protein in muscle cells. Mutations of DYSF lead to muscular dystrophies and cardiomyopathies. In contrast to other members of the Ferlin protein family, few is known about its role in cancer. Our study was designed to investigate the expression and functional properties of DYSF in ccRCC and its association with clinicopathological parameters and survival. MATERIAL AND METHODS TCGA cohort: mRNA expression data of DYSF were extracted from TCGA for patients with ccRCC (n = 603; ccRCC n = 522, benign n = 81). Study cohort: mRNA expression of DYSF in ccRCC was determined using qPCR (n = 126; ccRCC n = 82, benign n = 44). Immunohistochemical staining against DYSF was performed on tissue microarrays to validate protein expression (n = 172; ccRCC n = 142, benign n = 30). Correlations between mRNA/protein expression and clinicopathological data were statistically tested. Following siRNA-mediated knockdown of DYSF in ccRCC cell line ACHN, cell migration, invasion and proliferation were investigated. RESULTS Both DYSF mRNA and protein expression are significantly up-regulated in ccRCC tissue. DYSF mRNA expression decreased during tumor progression: lower expression levels were measured in higher stage/grade and metastatic ccRCC with independent prognostic significance for overall and cancer-specific survival. In contrast, protein expression correlated positively with pathological parameters. Overexpression showed tendency toward poor survival. Accordingly, knockdown of DYSF suppressed migration and invasion of ccRCC cells. CONCLUSION DYSF mRNA and protein expression are opposingly involved in tumor progression of ccRCC. DYSF could be used as a prognostic biomarker to predict survival of patients with ccRCC.
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Affiliation(s)
- Alexander Cox
- Department of Urology, University Hospital Bonn, Bonn, Germany.
| | - Chenming Zhao
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Yuri Tolkach
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Daniel Nettersheim
- Department of Urology, Urological Research Lab, Translational Uro-oncology, University Medical School Düsseldorf, Düsseldorf, Germany
| | - Doris Schmidt
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | | | - Stefan Hauser
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Stefan C Müller
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Manuel Ritter
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Jörg Ellinger
- Department of Urology, University Hospital Bonn, Bonn, Germany
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16
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Cox A, Tolkach Y, Kristiansen G, Ritter M, Ellinger J. The lncRNA Fer1L4 is an adverse prognostic parameter in clear-cell renal-cell carcinoma. Clin Transl Oncol 2020; 22:1524-1531. [PMID: 31965534 PMCID: PMC7381450 DOI: 10.1007/s12094-020-02291-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/06/2020] [Indexed: 01/10/2023]
Abstract
Purpose Long non-coding RNAs (lncRNA) are involved in oncogenesis and tumor progression in various tumor entities. At present, little is known about the role in tumor biology of the lncRNA Fer-1 like family member 4 (Fer1L4) in clear-cell renal-cell carcinoma (ccRCC). The aim of this study is to evaluate the expression of Fer1L4 in patients with ccRCC, its association with clinicopathological parameters, and value as prognostic biomarker. Material and methods The expression of Fer1L4 was analyzed in the TCGA ccRCC cohort (n = 603; ccRCC n = 522, normal n = 81) and subsequently validated by quantitative real-time PCR in an independent cohort (n = 103, ccRCC n = 69, normal n = 34). Expression profiles were statistically correlated with clinicopathological and survival data. Results Fer1L4 lncRNA is overexpressed in ccRCC compared to adjacent normal tissues. Increased expression significantly correlates with tumor aggressiveness: high expression levels of Fer1L4 RNA were found in higher grade, higher stage, and metastatic tumors. Furthermore, Fer1L4 overexpression is an independent prognostic factor for overall, cancer-specific, and progression-free survival of patients with ccRCC. Conclusion Fer1L4 expression significantly correlates with aspects of tumor aggressiveness. Based on this impact on tumor progression and its influence as an independent prognostic factor, Fer1L4 appears to exert properties as an oncogene in ccRCC. As a prognostic tissue biomarker, further functional investigations are warranted to investigate Fer1L4 as a potential therapeutic target.
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Affiliation(s)
- A Cox
- Department of Urology, University Hospital Bonn, Bonn, Germany.
| | - Y Tolkach
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - G Kristiansen
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - M Ritter
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - J Ellinger
- Department of Urology, University Hospital Bonn, Bonn, Germany
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17
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Grieco G, Wang T, Delcorte O, Spourquet C, Janssens V, Strickaert A, Gaide Chevronnay HP, Liao XH, Bilanges B, Refetoff S, Vanhaesebroeck B, Maenhaut C, Courtoy PJ, Pierreux CE. Class III PI3K Vps34 Controls Thyroid Hormone Production by Regulating Thyroglobulin Iodination, Lysosomal Proteolysis, and Tissue Homeostasis. Thyroid 2020; 30:133-146. [PMID: 31650902 PMCID: PMC6983755 DOI: 10.1089/thy.2019.0182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background: The production of thyroid hormones [triiodothyronine (T3), thyroxine (T4)] depends on the organization of the thyroid in follicles, which are lined by a monolayer of thyrocytes with strict apicobasal polarity. This polarization supports vectorial transport of thyroglobulin (Tg) for storage into, and recapture from, the colloid. It also allows selective addressing of channels, transporters, ion pumps, and enzymes to their appropriate basolateral [Na+/I- symporter (NIS), SLC26A7, and Na+/K+-ATPase] or apical membrane domain (anoctamin, SLC26A4, DUOX2, DUOXA2, and thyroperoxidase). How these actors of T3/T4 synthesis reach their final destination remains poorly understood. The PI 3-kinase isoform Vps34/PIK3C3 is now recognized as a main component in the general control of vesicular trafficking and of cell homeostasis through the regulation of endosomal trafficking and autophagy. We recently reported that conditional Vps34 inactivation in proximal tubular cells in the kidney prevents normal addressing of apical membrane proteins and causes abortive macroautophagy. Methods:Vps34 was inactivated using a Pax8-driven Cre recombinase system. The impact of Vps34 inactivation in thyrocytes was analyzed by histological, immunolocalization, and messenger RNA expression profiling. Thyroid hormone synthesis was assayed by 125I injection and plasma analysis. Results:Vps34 conditional knockout (Vps34cKO) mice were born at the expected Mendelian ratio and showed normal growth until postnatal day 14 (P14), then stopped growing and died at ∼1 month of age. We therefore analyzed thyroid Vps34cKO at P14. We found that loss of Vps34 in thyrocytes causes (i) disorganization of thyroid parenchyma, with abnormal thyrocyte and follicular shape and reduced PAS+ colloidal spaces; (ii) severe noncompensated hypothyroidism with extremely low T4 levels (0.75 ± 0.62 μg/dL) and huge thyrotropin plasma levels (19,300 ± 10,500 mU/L); (iii) impaired 125I organification at comparable uptake and frequent occurrence of follicles with luminal Tg but nondetectable T4-bearing Tg; (iv) intense signal in thyrocytes for the lysosomal membrane marker, LAMP-1, as well as Tg and the autophagy marker, p62, indicating defective lysosomal proteolysis; and (v) presence of macrophages in the colloidal space. Conclusions: We conclude that Vps34 is crucial for thyroid hormonogenesis, at least by controlling epithelial organization, Tg iodination as well as proteolytic T3/T4 excision in lysosomes.
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Affiliation(s)
- Giuseppina Grieco
- Cell Biology Unit, de Duve Institute and Université Catholique de Louvain, Brussels, Belgium
| | - Tongsong Wang
- Cell Biology Unit, de Duve Institute and Université Catholique de Louvain, Brussels, Belgium
| | - Ophélie Delcorte
- Cell Biology Unit, de Duve Institute and Université Catholique de Louvain, Brussels, Belgium
| | - Catherine Spourquet
- Cell Biology Unit, de Duve Institute and Université Catholique de Louvain, Brussels, Belgium
| | - Virginie Janssens
- Cell Biology Unit, de Duve Institute and Université Catholique de Louvain, Brussels, Belgium
| | - Aurélie Strickaert
- Thyroid Cancer Group, Faculty of Medecine, Institute of Interdisciplinary Research (IRIBHM), Université libre de Bruxelles, Brussels, Belgium
| | | | - Xiao-Hui Liao
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Benoît Bilanges
- Cell Signalling, UCL Cancer Institute, University College London, London, United Kingdom
| | - Samuel Refetoff
- Department of Medicine, The University of Chicago, Chicago, Illinois
- Department of Pediatrics and Genetics, The University of Chicago, Chicago, Illinois
| | - Bart Vanhaesebroeck
- Cell Signalling, UCL Cancer Institute, University College London, London, United Kingdom
| | - Carine Maenhaut
- Thyroid Cancer Group, Faculty of Medecine, Institute of Interdisciplinary Research (IRIBHM), Université libre de Bruxelles, Brussels, Belgium
| | - Pierre J. Courtoy
- Cell Biology Unit, de Duve Institute and Université Catholique de Louvain, Brussels, Belgium
| | - Christophe E. Pierreux
- Cell Biology Unit, de Duve Institute and Université Catholique de Louvain, Brussels, Belgium
- Address correspondence to: Christophe E. Pierreux, PhD, Cell Biology Unit, de Duve Institute and Université Catholique de Louvain, 75, Avenue Hippocrate, Brussels B-1200, Belgium
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Hamilton MJ, Young M, Jang K, Sauer S, Neang VE, King AT, Girke T, Martinez E. HOTAIRM1 lncRNA is downregulated in clear cell renal cell carcinoma and inhibits the hypoxia pathway. Cancer Lett 2019; 472:50-58. [PMID: 31862408 DOI: 10.1016/j.canlet.2019.12.022] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022]
Abstract
HOXA Transcript Antisense RNA, Myeloid-Specific 1 (HOTAIRM1) is a conserved long non-coding RNA (lncRNA) involved in myeloid and neural differentiation that is deregulated in acute myeloid leukemia and other cancers. Previous studies focused on the nuclear unspliced HOTAIRM1 transcript, however cytoplasmic splice variants exist whose roles have remained unknown. Here, we report novel functions of HOTAIRM1 in the kidney. HOTAIRM1 transcripts are induced during renal lineage differentiation of embryonic stem cells and required for expression of specific renal differentiation genes. We show that the major HOTAIRM1 transcript in differentiated cells is the spliced cytoplasmic HM1-3 isoform and that HM1-3 is downregulated in >90% of clear cell renal cell carcinomas (ccRCCs). Knockdown of HM1-3 in renal cells deregulates hypoxia-responsive and angiogenic genes, including ANGPTL4. Furthermore, HOTAIRM1 transcripts are downregulated by hypoxia-mimetic stress and knockdown of the cytoplasmic HM1-3 isoform in normoxic cells post-transcriptionally induces Hypoxia-Inducible Factor 1α (HIF1α) protein, a key activator of ANGPTL4. Our results demonstrate the pervasive downregulation of the specific HOTAIRM1 cytoplasmic isoform HM1-3 in ccRCC and suggest possible roles of HOTAIRM1 in kidney differentiation and suppression of HIF1-dependent angiogenic pathways.
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Affiliation(s)
- Michael J Hamilton
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Matthew Young
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Kay Jang
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Silvia Sauer
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Vanessa E Neang
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Alexia T King
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Thomas Girke
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California, Riverside, CA, USA.
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Validation of Reference Genes for Normalization of Relative qRT-PCR Studies in Papillary Thyroid Carcinoma. Sci Rep 2019; 9:15241. [PMID: 31645594 PMCID: PMC6811563 DOI: 10.1038/s41598-019-49247-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
Quantitative reverse transcription polymerase chain reaction (qRT-PCR) in thyroid tumors require accurate data normalization, however, there are no sufficient studies addressing the suitable reference genes for gene expression analysis in malignant and normal thyroid tissue specimens. The purpose of this study was to identify valid internal control genes for normalization of relative qRT-PCR studies in human papillary thyroid carcinoma tissue samples. The expression characteristics of 12 candidate reference genes (GAPDH, ACTB, HPRT1, TBP, B2M, PPIA, 18SrRNA, HMBS, GUSB, PGK1, RPLP0, and PGM1) were assessed by qRT-PCR in 45 thyroid tissue samples (15 papillary thyroid carcinoma, 15 paired normal tissues and 15 multinodular goiters). These twelve candidate reference genes were selected by a systematic literature search. GeNorm, NormFinder, and BestKeeper statistical algorithms were applied to determine the most stable reference genes. The three algorithms were in agreement in identifying GUSB and HPRT1 as the most stably expressed genes in all thyroid tumors investigated. According to the NormFinder software, the pair of genes including ‘GUSB and HPRT1’ or ‘GUSB and HMBS’ or ‘GUSB and PGM1’ were the best combinations for selection of pair reference genes. The optimal number of genes required for reliable normalization of qPCR data in thyroid tissues would be three according to calculations made by GeNorm algorithm. These results suggest that GUSB and HPRT1 are promising reference genes for normalization of relative qRT-PCR studies in papillary thyroid carcinoma.
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20
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Durbas M, Pabisz P, Wawak K, Wiśniewska A, Boratyn E, Nowak I, Horwacik I, Woźnicka O, Rokita H. GD2 ganglioside-binding antibody 14G2a and specific aurora A kinase inhibitor MK-5108 induce autophagy in IMR-32 neuroblastoma cells. Apoptosis 2019; 23:492-511. [PMID: 30027525 PMCID: PMC6153511 DOI: 10.1007/s10495-018-1472-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The process of autophagy and its role in survival of human neuroblastoma cell cultures was studied upon addition of an anti-GD2 ganglioside (GD2) 14G2a mouse monoclonal antibody (14G2a mAb) and an aurora A kinase specific inhibitor, MK-5108. It was recently shown that combination of these agents significantly potentiates cytotoxicity against IMR-32 and CHP-134 neuroblastoma cells in vitro, as compared to the inhibitor used alone. In this study we gained mechanistic insights on autophagy in the observed cytotoxic effects exerted by both agents using cytotoxicity assays, RT-qPCR, immunoblotting, and autophagy detection methods. Enhancement of the autophagy process in the 14G2a mAb- and MK-5108-treated IMR-32 cells was documented by assessing autophagic flux. Application of a lysosomotropic agent-chloroquine (CQ) affected the 14G2a mAb- and MK-5108-stimulated autophagic flux. It is our conclusion that the 14G2a mAb (40 μg/ml) and MK-5108 inhibitor (0.1 μM) induce autophagy in IMR-32 cells. Moreover, the combinatorial treatment of IMR-32 cells with the 14G2a mAb and CQ significantly potentiates cytotoxic effect, as compared to CQ used alone. Most importantly, we showed that interfering with autophagy at its early and late step augments the 14G2a mAb-induced apoptosis, therefore we can conclude that inhibition of autophagy is the primary mechanism of the CQ-mediated sensitization to the 14G2a mAb-induced apoptosis. Although, there was no virtual stimulation of autophagy in the 14G2a mAb-treated CHP-134 neuroblastoma cells, we were able to show that PHLDA1 protein positively regulates autophagy and this process exists in a mutually exclusive manner with apoptosis in PHLDA1-silenced CHP-134 cells.
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Affiliation(s)
- Małgorzata Durbas
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
| | - Paweł Pabisz
- Departament of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Katarzyna Wawak
- Departament of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Aneta Wiśniewska
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Elżbieta Boratyn
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Iwona Nowak
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Irena Horwacik
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Olga Woźnicka
- Department of Cell Biology and Imaging, Faculty of Biology, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland
| | - Hanna Rokita
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
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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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22
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Diagnostic and prognostic value of the detection of hTERT mRNA in renal tumors. Urol Oncol 2019; 37:749-757. [PMID: 30975552 DOI: 10.1016/j.urolonc.2019.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/06/2019] [Accepted: 03/13/2019] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Elevated mRNA expression of human telomerase reverse transcriptase (hTERT mRNA) is common in many types of tumors, participating in tumor growth and progression. Such expression has not been sufficiently examined in renal cancer. The goal of the present study was to quantify it and analyze its possible clinical value in the management of this pathology. PATIENTS AND METHODS The study included 111 patients who underwent surgery for renal cell carcinoma (RCC) between 2015 and 2017. Tumor samples were taken from all patients and, in 94 of them, healthy renal tissue adjacent to the tumor was also sampled. The 2 types of tissue were histologically confirmed, after which mRNA was extracted. Using real-time quantitative PCR, the expression of hTERT and glyceraldehyde-3-phosphate dehydrogenase (as endogenous control) were indirectly quantified using the crossing point (CP), which is inversely correlated with the number of sample replicates yielding positive results. These values were correlated with patient socio-demographic variables and clinical-pathological factors of the RCC. RESULTS The majority of patients were males, with an average age of 60.5 years (SD: 14.02). Most tumors (69.4%) were clear cell carcinomas. The most frequent stages were pT2 or lower (73%), while 5% were pN1 and 12% pM1. The majority of tumors (58%) were Fuhrman grades 1 or 2 (low grade). All samples of tumor and nontumor tissue expressed glyceraldehyde-3-phosphate dehydrogenase mRNA, with the CP in the tumor sample significantly lower than in the nontumor tissue (P < 0.001). The expression of hTERT mRNA was detected in 68% of tumor tissues and significantly correlated with histopathology: 100% in sarcomatoid RCC and 77.9% in clear cell carcinomas (P < 0.0001). The CP was lower in pN1 (P = 0.018), pM1 (P = 0.046), and TNM IV stages (P = 0,041). A greater number of hTERT mRNA replicas were detected in M1 patients (P = 0.0005) and TNM IV stage (P = 0.017). There was no correlation of hTERT mRNA expression with Fuhrman grade. CONCLUSIONS The quantitation of hTERT mRNA expression in RCC might be useful as a complementary diagnostic tool as well as for assessing aggressiveness of the tumor.
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23
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Pancreatic acinar differentiation is guided by differential laminin deposition. Sci Rep 2019; 9:2711. [PMID: 30804366 PMCID: PMC6389953 DOI: 10.1038/s41598-019-39077-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/12/2018] [Indexed: 01/03/2023] Open
Abstract
Endothelial cells play multiple roles during pancreas organogenesis. First, they are required to instruct endoderm-derived pancreatic progenitor cells to initiate branching morphogenesis. Later, blood vessels promote β-cell differentiation but also limit acinar development. In this work, we show how endothelial cells might signal to pancreatic progenitors and spatially regulate acinar differentiation. Using an ex vivo culture system of undifferentiated E12.5 pancreata, we demonstrate that embryonic endothelial progenitor cells and their conditioned medium prevent the expression of two members of the pro-acinar transcriptional PTF1L-complex. This effect is not mediated by SPARC, a protein abundantly released in the medium conditioned by endothelial progenitors. On the contrary, heterotrimeric laminin-α1β1γ1, also produced by endothelial progenitor cells, can repress acinar differentiation when used on its own on pancreatic explants. Lastly, we found that laminin-α1 is predominantly found in vivo around the pancreatic trunk cells, as compared to the tip cells, at E14.5. In conclusion, we propose that expression or deposition of laminin-α1β1γ1 around the trunk cells, where blood vessels are predominantly localized, prevent acinar differentiation of these cells. On the contrary, transient decreased expression or deposition of laminin-α1β1γ1 around the tip cells would allow PTF1L-complex formation and acinar differentiation.
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24
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Courtoy GE, Donnez J, Ambroise J, Arriagada P, Luyckx M, Marbaix E, Dolmans MM. Gene expression changes in uterine myomas in response to ulipristal acetate treatment. Reprod Biomed Online 2018; 37:224-233. [DOI: 10.1016/j.rbmo.2018.04.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 01/25/2023]
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25
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Visentin M, Torozi A, Gai Z, Häusler S, Li C, Hiller C, Schraml PH, Moch H, Kullak-Ublick GA. Fluorocholine Transport Mediated by the Organic Cation Transporter 2 (OCT2, SLC22A2): Implication for Imaging of Kidney Tumors. Drug Metab Dispos 2018; 46:1129-1136. [DOI: 10.1124/dmd.118.081091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
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Hamilton MJ, Girke T, Martinez E. Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma. Oncotarget 2018; 9:23670-23680. [PMID: 29805765 PMCID: PMC5955119 DOI: 10.18632/oncotarget.25330] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/19/2018] [Indexed: 11/25/2022] Open
Abstract
Extensive genome-wide analyses of deregulated gene expression have now been performed for many types of cancer. However, most studies have focused on deregulation at the gene-level, which may overlook the alterations of specific transcripts for a given gene. Clear cell renal cell carcinoma (ccRCC) is one of the best-characterized and most pervasive renal cancers, and ccRCCs are well-documented to have aberrant RNA processing. In the present study, we examine the extent of aberrant isoform-specific RNA expression by reporting a comprehensive transcript-level analysis, using the new kallisto-sleuth-RATs pipeline, investigating coding and non-coding differential transcript expression in ccRCC. We analyzed 50 ccRCC tumors and their matched normal samples from The Cancer Genome Altas datasets. We identified 7,339 differentially expressed transcripts and 94 genes exhibiting differential transcript isoform usage in ccRCC. Additionally, transcript-level coexpression network analyses identified vasculature development and the tricarboxylic acid cycle as the most significantly deregulated networks correlating with ccRCC progression. These analyses uncovered several uncharacterized transcripts, including lncRNAs FGD5-AS1 and AL035661.1, as potential regulators of the tricarboxylic acid cycle associated with ccRCC progression. As ccRCC still presents treatment challenges, our results provide a new resource of potential therapeutics targets and highlight the importance of exploring alternative methodologies in transcriptome-wide studies.
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Affiliation(s)
- Michael J. Hamilton
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - Thomas Girke
- Department of Botany and Plant Sciences, University of California at Riverside, Riverside, CA, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
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Inhibiting tryptophan metabolism enhances interferon therapy in kidney cancer. Oncotarget 2018; 7:66540-66557. [PMID: 27572319 PMCID: PMC5341819 DOI: 10.18632/oncotarget.11658] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/01/2016] [Indexed: 12/28/2022] Open
Abstract
Renal cell carcinoma (RCC) is increasing in incidence, and a complete cure remains elusive. While immune-checkpoint antibodies are promising, interferon-based immunotherapy has been disappointing. Tryptophan metabolism, which produces immunosuppressive metabolites, is enhanced in RCC. Here we show indolamine-2,3-dioxygenase-1 (IDO1) expression, a kynurenine pathway enzyme, is increased not only in tumor cells but also in the microenvironment of human RCC compared to normal kidney tissues. Neither kynurenine metabolites nor IDO inhibitors affected the survival or proliferation of human RCC or murine renal cell adenocarcinoma (RENCA) cells in vitro. However, interferon-gamma (IFNγ) induced high levels of IDO1 in both RCC and RENCA cells, concomitant with enhanced kynurenine levels in conditioned media. Induction of IDO1 by IFNα was weaker than by IFNγ. Neither the IDO1 inhibitor methyl-thiohydantoin-DL-tryptophan (MTH-trp) nor IFNα alone inhibited RENCA tumor growth, however the combination of MTH-trp and IFNα reduced tumor growth compared to IFNα. Thus, the failure of IFNα therapy for human RCC is likely due to its inability to overcome the immunosuppressive environment created by increased IDO1. Based on our data, and given that IDO inhibitors are already in clinical trials for other malignancies, IFNα therapy with an IDO inhibitor should be revisited for RCC.
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Carmona R, Arroyo M, Jiménez-Quesada MJ, Seoane P, Zafra A, Larrosa R, Alché JDD, Claros MG. Automated identification of reference genes based on RNA-seq data. Biomed Eng Online 2017; 16:65. [PMID: 28830520 PMCID: PMC5568602 DOI: 10.1186/s12938-017-0356-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background Gene expression analyses demand appropriate reference genes (RGs) for normalization, in order to obtain reliable assessments. Ideally, RG expression levels should remain constant in all cells, tissues or experimental conditions under study. Housekeeping genes traditionally fulfilled this requirement, but they have been reported to be less invariant than expected; therefore, RGs should be tested and validated for every particular situation. Microarray data have been used to propose new RGs, but only a limited set of model species and conditions are available; on the contrary, RNA-seq experiments are more and more frequent and constitute a new source of candidate RGs. Results An automated workflow based on mapped NGS reads has been constructed to obtain highly and invariantly expressed RGs based on a normalized expression in reads per mapped million and the coefficient of variation. This workflow has been tested with Roche/454 reads from reproductive tissues of olive tree (Olea europaea L.), as well as with Illumina paired-end reads from two different accessions of Arabidopsis thaliana and three different human cancers (prostate, small-cell cancer lung and lung adenocarcinoma). Candidate RGs have been proposed for each species and many of them have been previously reported as RGs in literature. Experimental validation of significant RGs in olive tree is provided to support the algorithm. Conclusion Regardless sequencing technology, number of replicates, and library sizes, when RNA-seq experiments are designed and performed, the same datasets can be analyzed with our workflow to extract suitable RGs for subsequent PCR validation. Moreover, different subset of experimental conditions can provide different suitable RGs. Electronic supplementary material The online version of this article (doi:10.1186/s12938-017-0356-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosario Carmona
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Macarena Arroyo
- Servicio de Neumología, Hospital Regional Universitario de Málaga, Avda Carlos Haya s/n, Malaga, Spain
| | - María José Jiménez-Quesada
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Pedro Seoane
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Malaga, Spain
| | - Adoración Zafra
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Rafael Larrosa
- Departamento de Arquitectura de Computadores, Universidad de Málaga, Malaga, Spain
| | - Juan de Dios Alché
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Malaga, Spain.
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Expression of long non-coding RNA MFI2-AS1 is a strong predictor of recurrence in sporadic localized clear-cell renal cell carcinoma. Sci Rep 2017; 7:8540. [PMID: 28819235 PMCID: PMC5561098 DOI: 10.1038/s41598-017-08363-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/06/2017] [Indexed: 01/09/2023] Open
Abstract
Prediction of recurrence is a challenge for the development of adjuvant treatments in clear-cell renal cell carcinoma (ccRCC). In these tumors, expression of long non-coding RNAs (lncRNAs) are deregulated and closely associated with prognosis. Thus, we aimed to predict ccRCC recurrence risk using lncRNA expression. We identified prognostic lncRNAs in a training set of 351 localized ccRCCs from The Cancer Genome Atlas and validated lncRNA-based recurrence classification in an independent cohort of 167 localized ccRCCs. We identified lncRNA MFI2-AS1 as best candidate in the training set. In the validation cohort, MFI2-AS1 expression was independently associated with shorter disease-free survival (Hazard Ratio (HR) for relapse 3.5, p = 0.0001). Combined with Leibovich classification, MFI2-AS1 status improved prediction of recurrence (C-index 0.70) compared to MFI2-AS1 alone (0.67) and Leibovich classification alone (0.66). In patients with aggressive tumors (Leibovich ≥5), MFI2-AS1 expression was associated with dramatically increased risk of relapse (HR 12.16, p < 0.0001) compared to patients with undetectable MFI2-AS1 who had favorable outcomes. Compared to normal samples, MFI2-AS1 was upregulated in tumor tissue, and higher expression was associated with metastatic dissemination. Overall, MFI2-AS1 status improves patient stratification in localized ccRCC, which supports further integration of lncRNAs in molecular cancer classifications.
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Brüggemann M, Gromes A, Poss M, Schmidt D, Klümper N, Tolkach Y, Dietrich D, Kristiansen G, Müller SC, Ellinger J. Systematic Analysis of the Expression of the Mitochondrial ATP Synthase (Complex V) Subunits in Clear Cell Renal Cell Carcinoma. Transl Oncol 2017; 10:661-668. [PMID: 28672194 PMCID: PMC5496479 DOI: 10.1016/j.tranon.2017.06.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 05/31/2017] [Accepted: 06/05/2017] [Indexed: 01/16/2023] Open
Abstract
Mitochondrial dysfunction is common in cancer and the mitochondrial electron transport chain is often affected in carcinogenesis. To date, little is known about the expression of the ATP synthase subunits in clear cell renal cell carcinoma (ccRCC). The NextBio database was used to determine an expression profile of the ATP synthase subunits based on published microarray studies. We observed down-regulation of 23 out of 29 subunits of the ATP synthase. Differential expression was validated exemplarily for 12 genes (ATP5A1, ATP5B, ATPAF1, ATP5C1, ATP5D, ATP5O, ATP5F1, ATP5G1, ATP5G2, ATP5G3, ATP5I, ATP5S; screening cohort ccRCC n = 18 and normal renal tissue n = 10) using real-time PCR. Additional eight genes (ATP5A1, ATP5B, ATPAF1, ATP5F1, ATP5G1, ATP5G2, ATP5G3, ATP5S) were internally validated within an enlarged cohort (ccRCC n = 74; normal renal tissue n = 36). Furthermore, down-regulation of ATP5A1, ATPAF1, ATP5G1/G2/G3 was confirmed on the protein level using Western Blot and immunohistochemistry. We observed that altered expression of ATPAF1 and ATP5G1/G2/G3 was correlated with overall survival in patients with ccRCC. In conclusion, down-regulation of many ATP Synthase subunits occurs in ccRCC and is the basis for the reduced activity of the mitochondrial electron chain. Alteration of the expression of ATP5A1, ATPAF1, and ATP5G1/G2/G3 is characteristic for ccRCC and may be prognostic for ccRCC patients' outcome.
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Affiliation(s)
- Maria Brüggemann
- University Hospital Bonn, Department of Urology, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Arabella Gromes
- University Hospital Bonn, Department of Urology, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Mirjam Poss
- University Hospital Bonn, Department of Urology, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Doris Schmidt
- University Hospital Bonn, Department of Urology, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Niklas Klümper
- University Hospital Bonn, Department of Urology, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Yuri Tolkach
- University Hospital Bonn, Institute of Pathology, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Dimo Dietrich
- University Hospital Bonn, Institute of Pathology, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany; University Hospital Bonn, Department of Otorhinolaryngology/Head and Neck Surgery, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Glen Kristiansen
- University Hospital Bonn, Institute of Pathology, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Stefan C Müller
- University Hospital Bonn, Department of Urology, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Jörg Ellinger
- University Hospital Bonn, Department of Urology, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany.
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31
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Gholami K, Loh SY, Salleh N, Lam SK, Hoe SZ. Selection of suitable endogenous reference genes for qPCR in kidney and hypothalamus of rats under testosterone influence. PLoS One 2017; 12:e0176368. [PMID: 28591185 PMCID: PMC5462341 DOI: 10.1371/journal.pone.0176368] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 04/10/2017] [Indexed: 12/21/2022] Open
Abstract
Real-time quantitative PCR (qPCR) is the most reliable and accurate technique for analyses of gene expression. Endogenous reference genes are being used to normalize qPCR data even though their expression may vary under different conditions and in different tissues. Nonetheless, verification of expression of reference genes in selected studied tissue is essential in order to accurately assess the level of expression of target genes of interest. Therefore, in this study, we attempted to examine six commonly used reference genes in order to identify the gene being expressed most constantly under the influence of testosterone in the kidneys and hypothalamus. The reference genes include glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin beta (ACTB), beta-2 microglobulin (B2m), hypoxanthine phosphoribosyltransferase 1 (HPRT), peptidylprolylisomerase A (Ppia) and hydroxymethylbilane synthase (Hmbs). The cycle threshold (Ct) value for each gene was determined and data obtained were analyzed using the software programs NormFinder, geNorm, BestKeeper, and rank aggregation. Results showed that Hmbs and Ppia genes were the most stably expressed in the hypothalamus. Meanwhile, in kidneys, Hmbs and GAPDH appeared to be the most constant genes. In conclusion, variations in expression levels of reference genes occur in kidneys and hypothalamus under similar conditions; thus, it is important to verify reference gene levels in these tissues prior to commencing any studies.
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Affiliation(s)
- Khadijeh Gholami
- Division of Human Biology, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
- * E-mail:
| | - Su Yi Loh
- Division of Human Biology, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Naguib Salleh
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sau Kuen Lam
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - See Ziau Hoe
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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32
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MicroRNA expression profiling defines the impact of electronic cigarettes on human airway epithelial cells. Sci Rep 2017. [PMID: 28439113 DOI: 10.1038/s41598‐017‐01167‐8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
While all forms of tobacco exposure have negative health effects, the significance of exposure to electronic cigarettes (eCig) is not fully understood. Here, we studied the global effects of eCig on the micro RNA (miRNA) transcriptome in human lung epithelial cells. Primary human bronchial epithelial (NHBE) cells differentiated at air-liquid interface were exposed to eCig liquid. Exposure of NHBE to any eCig liquid resulted in the induction of oxidative stress-response genes including GCLM, GCLC, GPX2, NQO1 and HO-1. Vaporization of, and/or the presence of nicotine in, eCig liquid was associated with a greater response. We identified 578 miRNAs dysregulated by eCig exposure in NHBE, and 125 miRNA affected by vaporization of eCig liquid. Nicotine containing eCig vapor displayed the most profound effects upon miRNA expression. We selected 8 miRNAs (29A, 140, 126, 374A, 26A-2, 147B, 941 and 589) for further study. We validated increased expression of multiple miRNAs, including miR126, following eCig exposure. We also found significant reduction in the expression of two miR126 target genes, MYC and MRGPRX3, following exposure. These data demonstrated that eCig exposure has profound effects upon gene expression in human lung epithelial cells, some of which are epigenetically programmed at the level of miRNA regulation.
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33
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MicroRNA expression profiling defines the impact of electronic cigarettes on human airway epithelial cells. Sci Rep 2017; 7:1081. [PMID: 28439113 PMCID: PMC5430826 DOI: 10.1038/s41598-017-01167-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/27/2017] [Indexed: 01/18/2023] Open
Abstract
While all forms of tobacco exposure have negative health effects, the significance of exposure to electronic cigarettes (eCig) is not fully understood. Here, we studied the global effects of eCig on the micro RNA (miRNA) transcriptome in human lung epithelial cells. Primary human bronchial epithelial (NHBE) cells differentiated at air-liquid interface were exposed to eCig liquid. Exposure of NHBE to any eCig liquid resulted in the induction of oxidative stress-response genes including GCLM, GCLC, GPX2, NQO1 and HO-1. Vaporization of, and/or the presence of nicotine in, eCig liquid was associated with a greater response. We identified 578 miRNAs dysregulated by eCig exposure in NHBE, and 125 miRNA affected by vaporization of eCig liquid. Nicotine containing eCig vapor displayed the most profound effects upon miRNA expression. We selected 8 miRNAs (29A, 140, 126, 374A, 26A-2, 147B, 941 and 589) for further study. We validated increased expression of multiple miRNAs, including miR126, following eCig exposure. We also found significant reduction in the expression of two miR126 target genes, MYC and MRGPRX3, following exposure. These data demonstrated that eCig exposure has profound effects upon gene expression in human lung epithelial cells, some of which are epigenetically programmed at the level of miRNA regulation.
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34
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Boratyn E, Nowak I, Durbas M, Horwacik I, Sawicka A, Rokita H. MCPIP1 Exogenous Overexpression Inhibits Pathways Regulating MYCN Oncoprotein Stability in Neuroblastoma. J Cell Biochem 2017; 118:1741-1755. [DOI: 10.1002/jcb.25832] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 12/07/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Elżbieta Boratyn
- Faculty of Biochemistry, Biophysics and Biotechnology; Laboratory of Molecular Genetics and Virology, Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Iwona Nowak
- Faculty of Biochemistry, Biophysics and Biotechnology; Laboratory of Molecular Genetics and Virology, Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Małgorzata Durbas
- Faculty of Biochemistry, Biophysics and Biotechnology; Laboratory of Molecular Genetics and Virology, Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Irena Horwacik
- Faculty of Biochemistry, Biophysics and Biotechnology; Laboratory of Molecular Genetics and Virology, Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Anna Sawicka
- Faculty of Biochemistry, Biophysics and Biotechnology; Laboratory of Molecular Genetics and Virology, Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Hanna Rokita
- Faculty of Biochemistry, Biophysics and Biotechnology; Laboratory of Molecular Genetics and Virology, Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
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35
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Bustin SA, Huggett JF. Reproducibility of biomedical research - The importance of editorial vigilance. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 11:1-3. [PMID: 28331813 PMCID: PMC5348116 DOI: 10.1016/j.bdq.2017.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Many journal editors are a failing to implement their own authors' instructions, resulting in the publication of many articles that do not meet basic standards of transparency, employ unsuitable data analysis methods and report overly optimistic conclusions. This problem is particularly acute where quantitative measurements are made and results in the publication of papers that lack scientific rigor and contributes to the concerns with regard to the reproducibility of biomedical research. This hampers research areas such as biomarker identification, as reproducing all but the most striking changes is challenging and translation to patient care rare.
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Affiliation(s)
- Stephen A Bustin
- Faculty of Medical Science , Anglia Ruskin University, Chelmsford, CM1 1SQ, United Kingdom
| | - Jim F Huggett
- Analytical Microbiology, School of Bioscience and Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, GU2 7XH, United Kingdom
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36
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Marsh APL, Heron D, Edwards TJ, Quartier A, Galea C, Nava C, Rastetter A, Moutard ML, Anderson V, Bitoun P, Bunt J, Faudet A, Garel C, Gillies G, Gobius I, Guegan J, Heide S, Keren B, Lesne F, Lukic V, Mandelstam SA, McGillivray G, McIlroy A, Méneret A, Mignot C, Morcom LR, Odent S, Paolino A, Pope K, Riant F, Robinson GA, Spencer-Smith M, Srour M, Stephenson SEM, Tankard R, Trouillard O, Welniarz Q, Wood A, Brice A, Rouleau G, Attié-Bitach T, Delatycki MB, Mandel JL, Amor DJ, Roze E, Piton A, Bahlo M, Billette de Villemeur T, Sherr EH, Leventer RJ, Richards LJ, Lockhart PJ, Depienne C. Mutations in DCC cause isolated agenesis of the corpus callosum with incomplete penetrance. Nat Genet 2017; 49:511-514. [PMID: 28250454 DOI: 10.1038/ng.3794] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/25/2017] [Indexed: 12/15/2022]
Abstract
Brain malformations involving the corpus callosum are common in children with developmental disabilities. We identified DCC mutations in four families and five sporadic individuals with isolated agenesis of the corpus callosum (ACC) without intellectual disability. DCC mutations result in variable dominant phenotypes with decreased penetrance, including mirror movements and ACC associated with a favorable developmental prognosis. Possible phenotypic modifiers include the type and location of mutation and the sex of the individual.
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Affiliation(s)
- Ashley P L Marsh
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Delphine Heron
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,Groupe de Recherche Clinique (GRC) `Déficience Intellectuelle et Autisme' UPMC, Paris, France.,Centre de Référence `Déficiences Intellectuelles de Causes Rares', Paris, France
| | - Timothy J Edwards
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia.,School of Medicine, University of Queensland, Herston, Brisbane, Australia
| | - Angélique Quartier
- IGBMC, Université de Strasbourg, CNRS, INSERM, UMR7104 U964, Strasbourg, France
| | - Charles Galea
- Drug Delivery, Disposition and Dynamics (D4), Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Caroline Nava
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Agnès Rastetter
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Marie-Laure Moutard
- AP-HP, Hôpital Trousseau, Service de Neuropédiatrie, Paris, France.,UPMC, GRC ConCer-LD, Sorbonne Université, Paris, France.,Centre de Référence `Neurogénétique', Paris, France
| | - Vicki Anderson
- Developmental Imaging and Child Neuropsychology Research Groups, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Pierre Bitoun
- Génétique Médicale, CHU Paris Nord, Hôpital Jean Verdier, Bondy, France
| | - Jens Bunt
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | - Anne Faudet
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Catherine Garel
- AP-HP GHUEP, Hôpital Armand Trousseau, Service de Radiologie, Paris, France
| | - Greta Gillies
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Ilan Gobius
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | | | - Solveig Heide
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,Groupe de Recherche Clinique (GRC) `Déficience Intellectuelle et Autisme' UPMC, Paris, France
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Fabien Lesne
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Vesna Lukic
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Simone A Mandelstam
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia.,Department of Radiology, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Alissandra McIlroy
- Developmental Imaging and Child Neuropsychology Research Groups, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Aurélie Méneret
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France.,AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Neurologie, Paris, France
| | - Cyril Mignot
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,Groupe de Recherche Clinique (GRC) `Déficience Intellectuelle et Autisme' UPMC, Paris, France.,Centre de Référence `Déficiences Intellectuelles de Causes Rares', Paris, France
| | - Laura R Morcom
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de Référence CLAD-Ouest, CHU Rennes, Rennes, France.,UMR 6290 CNRS, IGDR Institut de Génétique et Développement de Rennes, Université de Rennes 1, Rennes, France
| | - Annalisa Paolino
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia
| | - Kate Pope
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Florence Riant
- AP-HP, Groupe Hospitalier Saint-Louis -La Riboisière -Fernand Vidal, Laboratoire de Génétique, Paris, France
| | - Gail A Robinson
- Neuropsychology Research Unit, School of Psychology, University of Queensland, Brisbane, Australia
| | - Megan Spencer-Smith
- Developmental Imaging and Child Neuropsychology Research Groups, Murdoch Childrens Research Institute, Parkville, Victoria, Australia.,School of Psychological Sciences and Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Clayton, Victoria, Australia
| | - Myriam Srour
- Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University Health Center, Montreal, Quebec, Canada
| | - Sarah E M Stephenson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Rick Tankard
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Oriane Trouillard
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Quentin Welniarz
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France.,Institut de Biologie Paris Seine, Neuroscience Paris Seine, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Paris, France
| | - Amanda Wood
- Developmental Imaging and Child Neuropsychology Research Groups, Murdoch Childrens Research Institute, Parkville, Victoria, Australia.,School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Alexis Brice
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
| | - Guy Rouleau
- Department of Neurology and Neurosurgery, McGill University Health Center, Montreal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Tania Attié-Bitach
- INSERM U1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris-Descartes University, Sorbonne Paris Cité and Imagine Institute, Paris, France.,AP-HP, Hôpital Necker-Enfants Malades, Département de Génétique, Paris, France
| | - Martin B Delatycki
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Parkville, Victoria, Australia
| | - Jean-Louis Mandel
- IGBMC, Université de Strasbourg, CNRS, INSERM, UMR7104 U964, Strasbourg, France.,Laboratoires de Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - David J Amor
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Emmanuel Roze
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France.,AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Neurologie, Paris, France
| | - Amélie Piton
- IGBMC, Université de Strasbourg, CNRS, INSERM, UMR7104 U964, Strasbourg, France.,Laboratoires de Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Thierry Billette de Villemeur
- Centre de Référence `Déficiences Intellectuelles de Causes Rares', Paris, France.,AP-HP, Hôpital Trousseau, Service de Neuropédiatrie, Paris, France.,UPMC, GRC ConCer-LD, Sorbonne Université, Paris, France.,INSERM U1141, Paris, France
| | - Elliott H Sherr
- Department of Neurology, UCSF Benioff Children's Hospital, San Francisco, California, USA
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Neuroscience Research Group, Murdoch Childrens Research Institute, Parkville, Victoria, Australia.,Department of Neurology, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Linda J Richards
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Australia.,University of Queensland, School of Biomedical Sciences, St. Lucia, Brisbane, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Christel Depienne
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,IGBMC, Université de Strasbourg, CNRS, INSERM, UMR7104 U964, Strasbourg, France.,INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France.,Laboratoires de Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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37
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Afsharpad M, Nowroozi MR, Safari M, Nekoohesh L, sohrabi A, Zendehdel K, Modarressi MH. Reference gene validation for relative quantification analysis of transcripts in urinary exfoliated cells among urothelial bladder carcinoma patients. Meta Gene 2017. [DOI: 10.1016/j.mgene.2016.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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38
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Robichaux S, Lacour N, Bagby GJ, Amedee AM. Validation of RPS13 as a reference gene for absolute quantification of SIV RNA in tissue of rhesus macaques. J Virol Methods 2016; 236:245-251. [PMID: 27510462 PMCID: PMC5010941 DOI: 10.1016/j.jviromet.2016.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/02/2016] [Accepted: 08/02/2016] [Indexed: 01/08/2023]
Abstract
Persistent HIV reservoirs and the absolute quantification of viral RNA copies in tissues have become a prominent focus of multiple areas ofHIV/SIV research. Absolute quantification of viral RNA via reverse transcription, quantitative PCR (RT-qPCR) necessitates the use of an appropriate RNA reference gene whose expression is unaffected by both experimental and confounding conditions. In this study, we demonstrate the utility of ribosomal protein S13 mRNA (RPS13) as a stable, medium abundance reference gene for RT-qPCR normalization of HIV/SIV RNA copy number. We developed a RPS13 RNA standard assay utilizing an in vitro RNA transcript for normalization of absolute SIV RNA quantities in tissues reservoirs. The RT-qPCR assay showed a high degree of repeatability and reproducibility across RNA levels appropriate for absolute SIV quantification. In assessing the utility of RPS13 as a reference gene, limited variation in the absolute, inter-tissue quantities of RPS13 mRNA was observed within multiple tissue samples obtained from rhesus macaques (average CV=2.86%). We demonstrate rhesus macaque RPS13 mRNA expression is not affected by alcohol administration, SIV infection, or antiviral therapy (PMPA/FTC). Additionally, assay functionality was validated for normalization of SIV copy number using cellular RNA prepared from samples of variable RNA integrity. RPS13 is a suitable reference gene for normalization of absolute SIV RNA quantities in tissues and is most appropriate for intra-tissue or similar tissue type comparisons of SIV copy number.
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Affiliation(s)
- Spencer Robichaux
- Louisiana State University Health Sciences Center, New Orleans, United States
| | - Nedra Lacour
- Louisiana State University Health Sciences Center, New Orleans, United States
| | - Gregory J Bagby
- Louisiana State University Health Sciences Center, New Orleans, United States
| | - Angela M Amedee
- Louisiana State University Health Sciences Center, New Orleans, United States.
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39
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Peng X, McCormick DL. Identification of reliable reference genes for quantitative gene expression studies in oral squamous cell carcinomas compared to adjacent normal tissues in the F344 rat model. Oncol Rep 2016; 36:1076-84. [PMID: 27375172 DOI: 10.3892/or.2016.4883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/28/2016] [Indexed: 11/06/2022] Open
Abstract
Oral squamous cell carcinomas (OSCCs) induced in F344 rats by 4-nitroquinoline-1-oxide (4-NQO) demonstrate considerable phenotypic similarity to human oral cancers and the model has been widely used for carcinogenesis and chemoprevention studies. Molecular characterization of this model needs reliable reference genes (RGs) to avoid false- positive and -negative results for proper interpretation of gene expression data between tumor and adjacent normal tissues. Microarray analysis of 11 pairs of OSCC and site-matched phenotypically normal oral tissues from 4-NQO-treated rats identified 10 stably expressed genes in OSCC compared to adjacent normal tissues (p>0.5, CV<15%) that could serve as potential RGs in this model. The commonly used 27 RGs in the rat were also analyzed based on microarray data and most of them were found unsuitable for RGs in this model. Traditional RGs such as ACTB and GAPDH were significantly altered in OSCC compared to adjacent normal tissues (p<0.01, n=11); however, the Hsp90ab1 was ranked as the best RG candidate and the combination of Hsp90ab1 and HPRT1 was identified by NormFinder to be a superior reference for gene normalization among the commonly used RGs. This result was also validated by RT-PCR based on the selected top RG candidate pool. These data suggest that there are no common RGs suitable for different models and RG(s) should be identified before gene expression analysis. We successfully identified Hsp90ab1 as a stable RG in 4-NQO-induced OSCC compared to adjacent normal tissues in F344 rats. The combination of two stably expressed genes may be a better option for gene normalization in tissue samples.
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Affiliation(s)
- Xinjian Peng
- Life Sciences Group, IIT Research Institute, Chicago, IL 60616, USA
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Durbas M, Horwacik I, Boratyn E, Rokita H. Downregulation of the PHLDA1 gene in IMR-32 neuroblastoma cells increases levels of Aurora A, TRKB and affects proteins involved in apoptosis and autophagy pathways. Int J Oncol 2016; 49:823-37. [PMID: 27278006 DOI: 10.3892/ijo.2016.3572] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/20/2016] [Indexed: 11/06/2022] Open
Abstract
We have recently shown that mRNA and protein of PHLDA1 (pleckstrin-homology-like domain family A, member 1) were by far the most upregulated molecules upon treatment of IMR-32 cells with the anti-GD2 ganglioside monoclonal antibody 14G2a. Hence, we decided to study functions of PHLDA1 using human neuroblastoma IMR-32 cells as a model. Here, we show that constitutive expression of mRNA and protein of the PHLDA1 gene in IMR-32 cells was inversely correlated with transcript of the AURKA gene and Aurora A oncoprotein. Next, we silenced PHLDA1 expression in IMR-32 cells using an shRNA interference method. We report that IMR-32 cells with stable downregulation of PHLDA1 showed enhanced cellular ATP levels and an increase in mitochondrial membrane potential, as compared to control and non-transduced cells. We demonstrated that downregulation of PHLDA1 leads to a significant increase in expression of Aurora A and TRKB that are markers of poor prognosis in neuroblastoma. Also, we measured an increase in Aurora A and Akt kinases phosphorylation in the cells. Most importantly, PHLDA1-silenced cells were less susceptible to apoptosis than control cells, as shown by the lower expression of cleaved caspase-3 and PARP as well as a decreased activity of caspase-3 and -7. Our study negatively correlates expression of PHLDA1 and Aurora A in IMR-32 cells and sheds new light on functions of PHLDA1 in the neuroblastoma tumor cells, suggesting its role as a pro-apoptotic protein. Additionally, our results show possible links of the protein to regulation of features of mitochondria and formation of autophagosomes.
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Affiliation(s)
- Małgorzata Durbas
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Irena Horwacik
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Elżbieta Boratyn
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Hanna Rokita
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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Villacorte M, Delmarcelle AS, Lernoux M, Bouquet M, Lemoine P, Bolsée J, Umans L, de Sousa Lopes SC, Van Der Smissen P, Sasaki T, Bommer G, Henriet P, Refetoff S, Lemaigre FP, Zwijsen A, Courtoy PJ, Pierreux CE. Thyroid follicle development requires Smad1/5- and endothelial cell-dependent basement membrane assembly. Development 2016; 143:1958-70. [PMID: 27068110 DOI: 10.1242/dev.134171] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/01/2016] [Indexed: 12/12/2022]
Abstract
Thyroid follicles, the functional units of the thyroid gland, are delineated by a monolayer of thyrocytes resting on a continuous basement membrane. The developmental mechanisms of folliculogenesis, whereby follicles are formed by the reorganization of a non-structured mass of non-polarized epithelial cells, are largely unknown. Here we show that assembly of the epithelial basement membrane is crucial for folliculogenesis and is controlled by endothelial cell invasion and by BMP-Smad signaling in thyrocytes. Thyroid-specific Smad1 and Smad5 double-knockout (Smad1/5(dKO)) mice displayed growth retardation, hypothyroidism and defective follicular architecture. In Smad1/5(dKO) embryonic thyroids, epithelial cells remained associated in large clusters and formed small follicles. Although similar follicular defects are found in Vegfa knockout (Vegfa(KO)) thyroids, Smad1/5(dKO) thyroids had normal endothelial cell density yet impaired endothelial differentiation. Interestingly, both Vegfa(KO) and Smad1/5(dKO) thyroids displayed impaired basement membrane assembly. Furthermore, conditioned medium (CM) from embryonic endothelial progenitor cells (eEPCs) rescued the folliculogenesis defects of both Smad1/5(dKO) and Vegfa(KO) thyroids. Laminin α1, β1 and γ1, abundantly released by eEPCs into CM, were crucial for folliculogenesis. Thus, epithelial Smad signaling and endothelial cell invasion promote folliculogenesis via assembly of the basement membrane.
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Affiliation(s)
- Mylah Villacorte
- de Duve Institute and Université Catholique de Louvain, 1200 Brussels, Belgium
| | | | - Manon Lernoux
- de Duve Institute and Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Mahé Bouquet
- de Duve Institute and Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Pascale Lemoine
- de Duve Institute and Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Jennifer Bolsée
- de Duve Institute and Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Lieve Umans
- VIB Center for the Biology of Disease, KU Leuven, 3000 Leuven, Belgium Laboratory of Molecular Biology (Celgen), Stem Cell Biology and Embryology, KU Leuven, 2333 Leuven, Belgium
| | | | | | - Takako Sasaki
- Department of Matrix Medicine, Faculty of Medicine, Oita University, 879-5593 Oita, Japan
| | - Guido Bommer
- de Duve Institute and Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Patrick Henriet
- de Duve Institute and Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Samuel Refetoff
- Department of Medicine, Pediatrics and Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Frédéric P Lemaigre
- de Duve Institute and Université Catholique de Louvain, 1200 Brussels, Belgium
| | - An Zwijsen
- VIB Center for the Biology of Disease, KU Leuven, 3000 Leuven, Belgium Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Pierre J Courtoy
- de Duve Institute and Université Catholique de Louvain, 1200 Brussels, Belgium
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Guo J, Jing R, Lv X, Wang X, Li J, Li L, Li C, Wang D, Bi B, Chen X, Yang JH. H2A/K pseudogene mutation may promote cell proliferation. Mutat Res 2016; 787:32-42. [PMID: 26953487 DOI: 10.1016/j.mrfmmm.2016.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 01/01/2016] [Accepted: 02/28/2016] [Indexed: 11/16/2022]
Abstract
Little attention has been paid to the histone H2A/K pseudogene. Results from our laboratory showed that 7 of 10 kidney cancer patients carried a mutant H2A/K pseudogene; therefore, we were interested in determining the relationship between mutant H2A/K and cell proliferation. We used shotgun and label-free proteomics methods to study whether mutant H2A/K lncRNAs affected cell proliferation. Quantitative proteomic analysis indicated that the expression of mutant H2A/K lncRNAs resulted in the upregulation of many oncogenes, which promoted cell proliferation. Further interaction analyses revealed that a proliferating cell nuclear antigen (PCNA)-protein interaction network, with PCNA in the center, contributes to cell proliferation in cells expressing the mutant H2A/K lncRNAs. Western blotting confirmed the critical upregulation of PCNA by mutant H2A/K lncRNA expression. Finally, the promotion of cell proliferation by mutant H2A/K lncRNAs (C290T, C228A and A45G) was confirmed using cell proliferation assays. Although we did not determine the exact mechanism by which the oncogenes were upregulated by the mutant H2A/K lncRNAs, we confirmed that the mutant H2A/K lncRNAs promoted cell proliferation by upregulating PCNA and other oncogenes. The hypothesis that cell proliferation is promoted by the mutant H2A/K lncRNAs was supported by the protein expression and cell proliferation assay results. Therefore, mutant H2A/K lncRNAs may be a new factor in renal carcinogenesis.
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Affiliation(s)
- Jisheng Guo
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Ruirui Jing
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Xin Lv
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Xiaoyue Wang
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Junqiang Li
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Lin Li
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Cuiling Li
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Daoguang Wang
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Baibing Bi
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Xinjun Chen
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China
| | - Jing-Hua Yang
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China; Department of Surgery, VA Boston Healthcare System, Boston University School of Medicine, Boston 510660, MA, USA.
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Elsamanoudy AZ, Abdalla HA, Hassanien M, Gaballah MA. Spermatozoal cell death-inducing DNA fragmentation factor-α-like effector A (CIDEA) gene expression and DNA fragmentation in infertile men with metabolic syndrome and normal seminogram. Diabetol Metab Syndr 2016; 8:76. [PMID: 27891185 PMCID: PMC5112663 DOI: 10.1186/s13098-016-0192-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 11/10/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This is the first study to investigate spermatozoal cell death-inducing DNA fragmentation factor-α-like effector A (CIDEA) gene expression and DNA fragmentations in the spermatozoa of men diagnosed with metabolic syndrome (MS) who have normal seminograms with unexplained infertility, and to correlate these parameters with seminal glucose concentration. METHODS This study included 120 participants: 75 male subjects with MS (38 fertile and 37 infertile), and a control group of 45 fertile males without MS. HOMA-IR, semen analysis, and biochemical measurement of seminal plasma insulin and glucose levels were carried out. Spermatozoal insulin gene and CIDEA gene expressions were performed by the RT-PCR method. The percentage of spermatozoal DNA fragmentation was also estimated. RESULTS The spermatozoal insulin and CIDEA gene expression, as well as the DNA fragmentation, were significantly higher in the infertile MS group than in the fertile MS group, and significantly higher in both the MS groups than in the control group. Seminal glucose concentration showed significant positive correlations with seminal insulin level, spermatozoa insulin, CIDEA gene expression, and DNA fragmentation. Moreover, there was a positive correlation between spermatozoa CIDEA gene expression and DNA fragmentation. CONCLUSIONS It can be concluded that MS may affect male fertility at the molecular level, through its possible inducing effect of spermatozoa CIDEA and insulin gene expression, DNA fragmentation, and increased seminal glucose.
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Affiliation(s)
- Ayman Z. Elsamanoudy
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Biochemistry, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | | | - Mohammed Hassanien
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Biochemistry, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Mohammad A. Gaballah
- Department of Dermatology, Andrology and STDs, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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Inoue R, Tsukahara T, Nakatani M, Okutani M, Nishibayashi R, Ogawa S, Harayama T, Nagino T, Hatanaka H, Fukuta K, Romero-Pérez GA, Ushida K, Kelly D. Weaning Markedly Affects Transcriptome Profiles and Peyer's Patch Development in Piglet Ileum. Front Immunol 2015; 6:630. [PMID: 26697021 PMCID: PMC4678207 DOI: 10.3389/fimmu.2015.00630] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/30/2015] [Indexed: 12/22/2022] Open
Abstract
Transcriptome analyses were conducted on the ileal mucosa of 14- to 35-day-old piglets to investigate postnatal gut development during suckling and postweaning. The transcriptome profiles of 14-day-old suckling piglets showed a considerably higher number of differentially expressed genes than did those of 21-, 28-, and 35-day olds, indicating an intensive gut development during the first 14–21 postnatal days. In addition, the analysis of biological pathways indicated that Chemotaxis Leucocyte chemotaxis was the most significantly affected pathway in suckling piglets between 14 and 21 days of age. Weaning negatively affected pathways associated with acquired immunity, but positively affected those associated with innate immunity. Interestingly, pathway Chemotaxis Leucocyte chemotaxis was found positively affected when comparing 14- and 21-day-old suckling piglets, but negatively affected in 28-day-old piglets weaned at 21 days of age, when compared with 28-day-old suckling piglets. Genes CXCL13, SLA-DOA (MHC class II), ICAM1, VAV1, and VCAM1 were involved in the pathway Chemotaxis Leukocyte chemotaxis and they were found to significantly change between 14- and 21-day-old suckling piglets and between groups of suckling and weaned piglets. The expression of these genes significantly declined after weaning at 14, 21, and 28 days of age. This decline indicated that CXCL13, SLA-DOA, ICAM1, VAV1, and VCAM1 may be involved in the development of Peyer’s patches (PP) because lower gene expression clearly corresponded with smaller areas of PP in the ileal mucosa of piglets. Moreover, weaning piglets prior to a period of intensive gut development, i.e., 14 days of age, caused significant adverse effects on the size of PP, which were not reverted even 14 days postweaning.
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Affiliation(s)
- Ryo Inoue
- Laboratory of Animal Science, Kyoto Prefectural University , Kyoto , Japan ; Gut Immunology Group, Rowett Institute of Nutrition and Health, University of Aberdeen , Aberdeen , UK
| | - Takamitsu Tsukahara
- Laboratory of Animal Science, Kyoto Prefectural University , Kyoto , Japan ; Kyoto Institute of Nutrition and Pathology , Kyoto , Japan
| | - Masako Nakatani
- Laboratory of Animal Science, Kyoto Prefectural University , Kyoto , Japan
| | - Mie Okutani
- Laboratory of Animal Science, Kyoto Prefectural University , Kyoto , Japan
| | | | - Shohei Ogawa
- Laboratory of Animal Science, Kyoto Prefectural University , Kyoto , Japan
| | - Tomoko Harayama
- Laboratory of Animal Science, Kyoto Prefectural University , Kyoto , Japan
| | - Takayuki Nagino
- Laboratory of Animal Science, Kyoto Prefectural University , Kyoto , Japan
| | - Hironori Hatanaka
- Laboratory of Animal Science, Kyoto Prefectural University , Kyoto , Japan
| | - Kikuto Fukuta
- Technical Center, Toyohashi Feed Mills , Shinshiro , Japan
| | | | - Kazunari Ushida
- Laboratory of Animal Science, Kyoto Prefectural University , Kyoto , Japan
| | - Denise Kelly
- Gut Immunology Group, Rowett Institute of Nutrition and Health, University of Aberdeen , Aberdeen , UK
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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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Oliveira SR, Vieira HLA, Duarte CB. Effect of carbon monoxide on gene expression in cerebrocortical astrocytes: Validation of reference genes for quantitative real-time PCR. Nitric Oxide 2015. [PMID: 26196856 DOI: 10.1016/j.niox.2015.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is a widely used technique to characterize changes in gene expression in complex cellular and tissue processes, such as cytoprotection or inflammation. The accurate assessment of changes in gene expression depends on the selection of adequate internal reference gene(s). Carbon monoxide (CO) affects several metabolic pathways and de novo protein synthesis is crucial in the cellular responses to this gasotransmitter. Herein a selection of commonly used reference genes was analyzed to identify the most suitable internal control genes to evaluate the effect of CO on gene expression in cultured cerebrocortical astrocytes. The cells were exposed to CO by treatment with CORM-A1 (CO releasing molecule A1) and four different algorithms (geNorm, NormFinder, Delta Ct and BestKeeper) were applied to evaluate the stability of eight putative reference genes. Our results indicate that Gapdh (glyceraldehyde-3-phosphate dehydrogenase) together with Ppia (peptidylpropyl isomerase A) is the most suitable gene pair for normalization of qRT-PCR results under the experimental conditions used. Pgk1 (phosphoglycerate kinase 1), Hprt1 (hypoxanthine guanine phosphoribosyl transferase I), Sdha (Succinate Dehydrogenase Complex, Subunit A), Tbp (TATA box binding protein), Actg1 (actin gamma 1) and Rn18s (18S rRNA) genes presented less stable expression profiles in cultured cortical astrocytes exposed to CORM-A1 for up to 60 min. For validation, we analyzed the effect of CO on the expression of Bdnf and bcl-2. Different results were obtained, depending on the reference genes used. A significant increase in the expression of both genes was found when the results were normalized with Gapdh and Ppia, in contrast with the results obtained when the other genes were used as reference. These findings highlight the need for a proper and accurate selection of the reference genes used in the quantification of qRT-PCR results in studies on the effect of CO in gene expression.
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Affiliation(s)
- Sara R Oliveira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal; Chronic Diseases Research Center (CEDOC), NOVA Medical School, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Helena L A Vieira
- Chronic Diseases Research Center (CEDOC), NOVA Medical School, Universidade Nova de Lisboa, Lisbon, Portugal; Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
| | - Carlos B Duarte
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
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Baranoski A, Tempesta Oliveira M, Semprebon SC, Niwa AM, Ribeiro LR, Mantovani MS. Effects of sulfated and non-sulfated β-glucan extracted from Agaricus brasiliensis in breast adenocarcinoma cells – MCF-7. Toxicol Mech Methods 2015; 25:672-9. [DOI: 10.3109/15376516.2015.1043762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Adrivanio Baranoski
- Department of General Biology, State University of Londrina, Londrina, Brazil and
| | | | | | - Andressa Megumi Niwa
- Department of General Biology, State University of Londrina, Londrina, Brazil and
| | - Lúcia Regina Ribeiro
- Department of Pathology, São Paulo State University “Júlio de Mesquita Filho”, São Paulo, Brazil
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Joseph S, Nicolson TJ, Hammons G, Word B, Green-Knox B, Lyn-Cook B. Expression of drug transporters in human kidney: impact of sex, age, and ethnicity. Biol Sex Differ 2015; 6:4. [PMID: 25750709 PMCID: PMC4352278 DOI: 10.1186/s13293-015-0020-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/10/2015] [Indexed: 11/25/2022] Open
Abstract
Background Differences in expression of drug transporters in human kidney contribute to changes in pharmacokinetics and toxicokinetics of a variety of drug compounds. The basal expression levels of genes involved in drug transport processes in the kidney introduces differences in bioavailability, distribution, and clearance of drugs, possibly influencing drug efficacy and adverse reactions. Sex differences in gene expression of transporters are a key cause of differences in sex-dependent pharmacokinetics, which may characterize many drugs and contribute to individual differences in drug efficacy and toxicity. Therefore, evaluating the expression of drug transporters in normal human kidneys is important to better understand differences in drug bioavailability, distribution, and clearance of drugs in humans. Other factors such as age and ethnicity may also contribute to individual differences in gene expression of drug transporters in the human kidney. Methods Quantitative real-time PCR (QRT-PCR) was performed to determine the gene expression of 30 drug transporters in 95 age-matched normal human kidney tissues. Multiple Student’s t-tests (Sidak-Bonferroni correction) and two-way ANOVA (Bonferroni correction) analyses were used to determine statistically significant differences. Results In the 30 transporter genes examined, sex, ethnicity, and age differences in gene expression were exhibited in normal human kidney tissue. These changes in expression were not found to be differentially significant. However, sex-age and sex-ethnicity interactions were found to be statistically significant. For sex-age interactions, SCL22A12 was found to be significantly higher expressed in females <50 years compared to males <50 years. Expression levels of SLC22A2, SLC22A12, SLC6A16, and ABCB6 were significantly higher in females <50 years compared to females ≥50 years. In sex-ethnicity interactions, expression levels of ATP7B and KCNJ8 were found to be significantly higher in African American females compared to European American females. Also, the expression of SLC31A2 was significantly higher in European American males compared to European American females. Conclusions Sex, age, and ethnic differences impacted the expression of drug transporters in normal human kidneys, which suggests that the analysis of gene expression of drug transporters will aid in improving the usage/dosage of drug therapies influencing personalized medicine and susceptibility to adverse drug reactions.
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Affiliation(s)
- Stancy Joseph
- Division of Biochemical Toxicology, National Center for Toxicological Research, Food and Drug Administration, Building 50, Room 630, HFT 100, 3900 NCTR Road, Jefferson, AR 72079 USA
| | | | - George Hammons
- Division of Biochemical Toxicology, National Center for Toxicological Research, Food and Drug Administration, Building 50, Room 630, HFT 100, 3900 NCTR Road, Jefferson, AR 72079 USA
| | - Beverly Word
- Division of Biochemical Toxicology, National Center for Toxicological Research, Food and Drug Administration, Building 50, Room 630, HFT 100, 3900 NCTR Road, Jefferson, AR 72079 USA
| | - Bridgett Green-Knox
- Divison of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079-9502 USA
| | - Beverly Lyn-Cook
- Division of Biochemical Toxicology, National Center for Toxicological Research, Food and Drug Administration, Building 50, Room 630, HFT 100, 3900 NCTR Road, Jefferson, AR 72079 USA
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Wierzbicki PM, Klacz J, Rybarczyk A, Slebioda T, Stanislawowski M, Wronska A, Kowalczyk A, Matuszewski M, Kmiec Z. Identification of a suitable qPCR reference gene in metastatic clear cell renal cell carcinoma. Tumour Biol 2014; 35:12473-87. [PMID: 25225161 PMCID: PMC4275580 DOI: 10.1007/s13277-014-2566-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/27/2014] [Indexed: 11/20/2022] Open
Abstract
There is no data on reference gene (RG) selection in metastatic clear-cell renal cell carcinoma (mccRCC) for quantitative PCR (qPCR) data normalization. We aimed at selecting the most stable RG for further determination of new prognostic markers. Thirty-five nonmetastatic and 35 mccRCC patients undergoing radical nephrectomy were included. Paired primary tumor (T, n = 70) and normal (C, n = 70) kidney fragments were collected; from 12 out of 35 mccRCC cases, we also collected metastasized regional lymph nodes and adrenal gland tissues (M, n = 12). After RNA extraction, reverse transcription and qPCR were performed. Samples were divided into four analyzed groups. Fifteen candidate RGs were tested by RefFinder tool and manual statistics. To present the importance of RG selection, TP53 gene expression levels in samples were normalized with the use of RG data. RPL13 gene was the most stable RG in analysis of 35 primary tumor nonmetastatic versus 35 mccRCC samples and matched metastasized T/C/M samples (n = 12, each group). GUSB was the most suitable RG in total 152 samples and in paired T and C (n = 140) kidney samples. Expression of GUSB, RPL13, and the RPL13 + RPLP0 pair were independent of clinical/sample variables. Normalization of TP53 expression levels showed variability of GAPDH and ACTB assays. GUSB or RPL13 assays should be used in mccRCC for qPCR data normalization whereas GAPDH and ACTB assays should be avoided. Prior RG studies should precede each qPCR gene expression study since RG selection is associated with the origin and proportion of specimens.
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Affiliation(s)
- Piotr M Wierzbicki
- Department of Histology, Faculty of Medicine, Medical University of Gdansk, ul. Dębinki 1, PL 80-211, Gdańsk, Poland,
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