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Papadopoulos T, Casemayou A, Neau E, Breuil B, Caubet C, Calise D, Thornhill BA, Bachvarova M, Belliere J, Chevalier RL, Moulos P, Bachvarov D, Buffin-Meyer B, Decramer S, Auriol FC, Bascands JL, Schanstra JP, Klein J. Systems biology combining human- and animal-data miRNA and mRNA data identifies new targets in ureteropelvic junction obstruction. BMC SYSTEMS BIOLOGY 2017; 11:31. [PMID: 28249581 PMCID: PMC5333413 DOI: 10.1186/s12918-017-0411-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 02/22/2017] [Indexed: 12/13/2022]
Abstract
Background Although renal fibrosis and inflammation have shown to be involved in the pathophysiology of obstructive nephropathies, molecular mechanisms underlying evolution of these processes remain undetermined. In an attempt towards improved understanding of obstructive nephropathy and improved translatability of the results to clinical practice we have developed a systems biology approach combining omics data of both human and mouse obstructive nephropathy. Results We have studied in parallel the urinary miRNome of infants with ureteropelvic junction obstruction and the kidney tissue miRNome and transcriptome of the corresponding neonatal partial unilateral ureteral obstruction (UUO) mouse model. Several hundreds of miRNAs and mRNAs displayed changed abundance during disease. Combination of miRNAs in both species and associated mRNAs let to the prioritization of five miRNAs and 35 mRNAs associated to disease. In vitro and in vivo validation identified consistent dysregulation of let-7a-5p and miR-29-3p and new potential targets, E3 ubiquitin-protein ligase (DTX4) and neuron navigator 1 (NAV1), potentially involved in fibrotic processes, in obstructive nephropathy in both human and mice that would not be identified otherwise. Conclusions Our study is the first to correlate a mouse model of neonatal partial UUO with human UPJ obstruction in a comprehensive systems biology analysis. Our data revealed let-7a and miR-29b as molecules potentially involved in the development of fibrosis in UPJ obstruction via the control of DTX4 in both man and mice that would not be identified otherwise. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0411-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Theofilos Papadopoulos
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Metabolic and Cardiovascular Diseases-I2MC, 1 avenue Jean Poulhès, B.P. 84225, 31432, Toulouse Cedex 4, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Audrey Casemayou
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Metabolic and Cardiovascular Diseases-I2MC, 1 avenue Jean Poulhès, B.P. 84225, 31432, Toulouse Cedex 4, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Eric Neau
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Metabolic and Cardiovascular Diseases-I2MC, 1 avenue Jean Poulhès, B.P. 84225, 31432, Toulouse Cedex 4, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Benjamin Breuil
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Metabolic and Cardiovascular Diseases-I2MC, 1 avenue Jean Poulhès, B.P. 84225, 31432, Toulouse Cedex 4, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Cécile Caubet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Metabolic and Cardiovascular Diseases-I2MC, 1 avenue Jean Poulhès, B.P. 84225, 31432, Toulouse Cedex 4, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Denis Calise
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Barbara A Thornhill
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, USA.,Department of Molecular Medicine, Université Laval, Québec, Canada
| | - Magdalena Bachvarova
- Department of Molecular Medicine, Université Laval, Québec, Canada.,Centre de recherche du CHU de Québec, L'Hôtel-Dieu de Québec, Québec, Canada
| | - Julie Belliere
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Metabolic and Cardiovascular Diseases-I2MC, 1 avenue Jean Poulhès, B.P. 84225, 31432, Toulouse Cedex 4, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Robert L Chevalier
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, USA.,Department of Molecular Medicine, Université Laval, Québec, Canada
| | - Panagiotis Moulos
- HybridStat Predictive Analytics, Aiolou 19, 10551, Athens, Greece.,Institute of Molecular Biology and Genetics, Biomedical Sciences Research Center 'Alexander Fleming', Fleming 34, 16672, Vari, Greece
| | - Dimcho Bachvarov
- Department of Molecular Medicine, Université Laval, Québec, Canada.,Centre de recherche du CHU de Québec, L'Hôtel-Dieu de Québec, Québec, Canada
| | - Benedicte Buffin-Meyer
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Metabolic and Cardiovascular Diseases-I2MC, 1 avenue Jean Poulhès, B.P. 84225, 31432, Toulouse Cedex 4, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Stéphane Decramer
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Metabolic and Cardiovascular Diseases-I2MC, 1 avenue Jean Poulhès, B.P. 84225, 31432, Toulouse Cedex 4, France.,Université Toulouse III Paul-Sabatier, Toulouse, France.,Service de Néphrologie-Médecine Interne-Hypertension Pédiatrique, CHU Toulouse, Hôpital des Enfants, 31059, Toulouse, France.,Centre De Référence des Maladies Rénales Rares du Sud Ouest (SORARE), 31059, Toulouse, France
| | - Françoise Conte Auriol
- Unité de recherche clinique pédiatrique, Module plurithémathique pédiatrique du Centre d'Investigation Clinique Toulouse 1436 Hôpital des enfants 330 avenue de grande bretagne, 31059, Toulouse, France
| | - Jean-Loup Bascands
- DéTROI-Inserm U1188-Université de La Réunion, Diabète athérothrombose Thérapies Réunion Océan Indien, CYROI, 2, rue Maxime Rivière, 97490, Sainte Clotilde, La Réunion, France
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Metabolic and Cardiovascular Diseases-I2MC, 1 avenue Jean Poulhès, B.P. 84225, 31432, Toulouse Cedex 4, France. .,Université Toulouse III Paul-Sabatier, Toulouse, France.
| | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Metabolic and Cardiovascular Diseases-I2MC, 1 avenue Jean Poulhès, B.P. 84225, 31432, Toulouse Cedex 4, France. .,Université Toulouse III Paul-Sabatier, Toulouse, France.
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Jaffa MA, Kobeissy F, Al Hariri M, Chalhoub H, Eid A, Ziyadeh FN, Jaffa AA. Global renal gene expression profiling analysis in B2-kinin receptor null mice: impact of diabetes. PLoS One 2012; 7:e44714. [PMID: 23028588 PMCID: PMC3445541 DOI: 10.1371/journal.pone.0044714] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 08/07/2012] [Indexed: 02/06/2023] Open
Abstract
Diabetic nephropathy (DN), the leading cause of end-stage renal failure, is clinically manifested by albuminuria and a progressive decline in glomerular filtration rate. The risk factors and mechanisms that contribute to the development and progression of DN are still incompletely defined. To address the involvement of bradykinin B2-receptors (B2R) in DN, we used a genome wide approach to study the effects of diabetes on differential renal gene expression profile in wild type and B2R knockout (B2R−/−) mice. Diabetes was induced with streptozotocin and plasma glucose levels and albumin excretion rate (AER) were measured at predetermined times throughout the 23 week study period. Longitudinal analysis of AER indicated that diabetic B2R−/−D null mice had a significantly decreased AER levels compared to wild type B2R+/+D mice (P = 0.0005). Results from the global microarray study comparing gene expression profiles among four groups of mice respectively: (B2R+/+C, B2R+/+D, B2R−/−C and B2R−/−D) highlighted the role of several altered pathological pathways in response to disruption of B2R and to the diabetic state that included: endothelial injury, oxidative stress, insulin and lipid metabolism and inflammatory process with a marked alteration in the pro-apoptotic genes. The findings of the present study provide a global genomics view of biomarkers that highlight the mechanisms and putative pathways involved in DN.
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Affiliation(s)
- Miran A. Jaffa
- Epidemiology and Population Health Department, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Firas Kobeissy
- Departments of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Moustafa Al Hariri
- Departments of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Hussein Chalhoub
- Departments of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Assaad Eid
- Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Fuad N. Ziyadeh
- Departments of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Ayad A. Jaffa
- Departments of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
- * E-mail:
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Cervello M, Bachvarov D, Lampiasi N, Cusimano A, Azzolina A, McCubrey JA, Montalto G. Molecular mechanisms of sorafenib action in liver cancer cells. Cell Cycle 2012; 11:2843-55. [PMID: 22801548 DOI: 10.4161/cc.21193] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Sorafenib, a multikinase inhibitor, recently received FDA approval for the treatment of advanced hepatocellular carcinoma (HCC). However, as the clinical application of sorafenib evolves, there is increasing interest in defining the mechanisms underlying its anti-tumor activity. Considering that this specific inhibitor could target unexpected molecules depending on the biologic context, a precise understanding of its mechanism of action could be critical to maximize its treatment efficacy, while minimizing adverse effects. Two human HCC cell lines (HepG2 and Huh7), carrying different biological and genetic characteristics, were used in this study to examine the intracellular events leading to sorafenib-induced HCC cell-growth inhibition. Sorafenib inhibited cell growth in both cell lines in a dose- and time-dependent manner and significantly altered expression levels of 826 and 2011 transcripts in HepG2 and Huh7 cells, respectively. Genes functionally involved in angiogenesis, apoptosis, transcription regulation, signal transduction, protein biosynthesis and modification were predominantly upregulated, while genes implicated in cell cycle control, DNA replication recombination and repair, cell adhesion, metabolism and transport were mainly downregulated upon treatment. However, each sorafenib-treated HCC cell line displayed specificity in the expression and activity of crucial factors involved in hepatocarcinogenesis. The altered expression of some of these genes was confirmed by semiquantitative and quantitative RT-PCR and by western blotting. Many novel genes emerged from our transcriptomics analysis that had not previously been reported to be effected by sorafenib. Further functional analyses may determine whether these genes can serve as potential molecular targets for more effective anti-HCC strategies.
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Affiliation(s)
- Melchiorre Cervello
- Institute of Biomedicine and Molecular Immunology Alberto Monroy, National Research Council (CNR), Palermo, Italy.
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