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Lytrivi M, Ghaddar K, Lopes M, Rosengren V, Piron A, Yi X, Johansson H, Lehtiö J, Igoillo-Esteve M, Cunha DA, Marselli L, Marchetti P, Ortsäter H, Eizirik DL, Cnop M. Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity. BMC Genomics 2020; 21:590. [PMID: 32847508 PMCID: PMC7448506 DOI: 10.1186/s12864-020-07003-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Prolonged exposure to elevated free fatty acids induces β-cell failure (lipotoxicity) and contributes to the pathogenesis of type 2 diabetes. In vitro exposure of β-cells to the saturated free fatty acid palmitate is a valuable model of lipotoxicity, reproducing features of β-cell failure observed in type 2 diabetes. In order to map the β-cell response to lipotoxicity, we combined RNA-sequencing of palmitate-treated human islets with iTRAQ proteomics of insulin-secreting INS-1E cells following a time course exposure to palmitate. RESULTS Crossing transcriptome and proteome of palmitate-treated β-cells revealed 85 upregulated and 122 downregulated genes at both transcript and protein level. Pathway analysis identified lipid metabolism, oxidative stress, amino-acid metabolism and cell cycle pathways among the most enriched palmitate-modified pathways. Palmitate induced gene expression changes compatible with increased free fatty acid mitochondrial import and β-oxidation, decreased lipogenesis and modified cholesterol transport. Palmitate modified genes regulating endoplasmic reticulum (ER) function, ER-to-Golgi transport and ER stress pathways. Furthermore, palmitate modulated cAMP/protein kinase A (PKA) signaling, inhibiting expression of PKA anchoring proteins and downregulating the GLP-1 receptor. SLC7 family amino-acid transporters were upregulated in response to palmitate but this induction did not contribute to β-cell demise. To unravel critical mediators of lipotoxicity upstream of the palmitate-modified genes, we identified overrepresented transcription factor binding sites and performed network inference analysis. These identified LXR, PPARα, FOXO1 and BACH1 as key transcription factors orchestrating the metabolic and oxidative stress responses to palmitate. CONCLUSIONS This is the first study to combine transcriptomic and sensitive time course proteomic profiling of palmitate-exposed β-cells. Our results provide comprehensive insight into gene and protein expression changes, corroborating and expanding beyond previous findings. The identification of critical drivers and pathways of the β-cell lipotoxic response points to novel therapeutic targets for type 2 diabetes.
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Affiliation(s)
- Maria Lytrivi
- ULB Center for Diabetes Research, Université Libre de Bruxelles, CP-618, Route de Lennik 808, 1070, Brussels, Belgium.,Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Kassem Ghaddar
- ULB Center for Diabetes Research, Université Libre de Bruxelles, CP-618, Route de Lennik 808, 1070, Brussels, Belgium
| | - Miguel Lopes
- ULB Center for Diabetes Research, Université Libre de Bruxelles, CP-618, Route de Lennik 808, 1070, Brussels, Belgium
| | - Victoria Rosengren
- Diabetes Research Unit, Department of Clinical Science and Education, Sodersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Anthony Piron
- ULB Center for Diabetes Research, Université Libre de Bruxelles, CP-618, Route de Lennik 808, 1070, Brussels, Belgium
| | - Xiaoyan Yi
- ULB Center for Diabetes Research, Université Libre de Bruxelles, CP-618, Route de Lennik 808, 1070, Brussels, Belgium
| | - Henrik Johansson
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, 171 21, Solna, Sweden
| | - Janne Lehtiö
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, 171 21, Solna, Sweden
| | - Mariana Igoillo-Esteve
- ULB Center for Diabetes Research, Université Libre de Bruxelles, CP-618, Route de Lennik 808, 1070, Brussels, Belgium
| | - Daniel A Cunha
- ULB Center for Diabetes Research, Université Libre de Bruxelles, CP-618, Route de Lennik 808, 1070, Brussels, Belgium
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Henrik Ortsäter
- Diabetes Research Unit, Department of Clinical Science and Education, Sodersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, CP-618, Route de Lennik 808, 1070, Brussels, Belgium
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, CP-618, Route de Lennik 808, 1070, Brussels, Belgium. .,Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium.
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Abstract
Amino acid uptake in yeast cells is mediated by about 16 plasma membrane permeases, most of which belong to the amino acid-polyamine-organocation (APC) transporter family. These proteins display various substrate specificity ranges. For instance, the general amino acid permease Gap1 transports all amino acids, whereas Can1 and Lyp1 catalyze specific uptake of arginine and lysine, respectively. Although Can1 and Lyp1 have different narrow substrate specificities, they are close homologs. Here we investigated the molecular rules determining the substrate specificity of the H(+)-driven arginine-specific permease Can1. Using a Can1-Lyp1 sequence alignment as a guideline and a three-dimensional Can1 structural model based on the crystal structure of the bacterial APC family arginine/agmatine antiporter, we introduced amino acid substitutions liable to alter Can1 substrate specificity. We show that the single substitution T456S results in a Can1 variant transporting lysine in addition to arginine and that the combined substitutions T456S and S176N convert Can1 to a Lyp1-like permease. Replacement of a highly conserved glutamate in the Can1 binding site leads to variants (E184Q and E184A) incapable of any amino acid transport, pointing to a potential role for this glutamate in H(+) coupling. Measurements of the kinetic parameters of arginine and lysine uptake by the wild-type and mutant Can1 permeases, together with docking calculations for each amino acid in their binding site, suggest a model in which residues at positions 176 and 456 confer substrate selectivity at the ligand-binding stage and/or in the course of conformational changes required for transport.
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Affiliation(s)
- Kassem Ghaddar
- Laboratoire de Physiologie Moléculaire de la Cellule CP300, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), 11 Rue des Pr. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Eva-Maria Krammer
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Bld. du Triomphe, 1050 Brussels, Belgium
| | - Natalija Mihajlovic
- Laboratoire de Physiologie Moléculaire de la Cellule CP300, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), 11 Rue des Pr. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Sylvain Brohée
- Machine Learning Group, Computer Science Department, Faculté des Sciences, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Bruno André
- Laboratoire de Physiologie Moléculaire de la Cellule CP300, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), 11 Rue des Pr. Jeener et Brachet, 6041 Gosselies, Belgium.
| | - Martine Prévost
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Bld. du Triomphe, 1050 Brussels, Belgium.
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