1
|
Stroedecke K, Meinel S, Markwardt F, Kloeckner U, Straetz N, Quarch K, Schreier B, Kopf M, Gekle M, Grossmann C. The mineralocorticoid receptor leads to increased expression of EGFR and T-type calcium channels that support HL-1 cell hypertrophy. Sci Rep 2021; 11:13229. [PMID: 34168192 PMCID: PMC8225817 DOI: 10.1038/s41598-021-92284-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/05/2021] [Indexed: 11/12/2022] Open
Abstract
The EGF receptor (EGFR) has been extensively studied in tumor biology and recently a role in cardiovascular pathophysiology was suggested. The mineralocorticoid receptor (MR) is an important effector of the renin-angiotensin-aldosterone-system and elicits pathophysiological effects in the cardiovascular system; however, the underlying molecular mechanisms are unclear. Our aim was to investigate the importance of EGFR for MR-mediated cardiovascular pathophysiology because MR is known to induce EGFR expression. We identified a SNP within the EGFR promoter that modulates MR-induced EGFR expression. In RNA-sequencing and qPCR experiments in heart tissue of EGFR KO and WT mice, changes in EGFR abundance led to differential expression of cardiac ion channels, especially of the T-type calcium channel CACNA1H. Accordingly, CACNA1H expression was increased in WT mice after in vivo MR activation by aldosterone but not in respective EGFR KO mice. Aldosterone- and EGF-responsiveness of CACNA1H expression was confirmed in HL-1 cells by Western blot and by measuring peak current density of T-type calcium channels. Aldosterone-induced CACNA1H protein expression could be abrogated by the EGFR inhibitor AG1478. Furthermore, inhibition of T-type calcium channels with mibefradil or ML218 reduced diameter, volume and BNP levels in HL-1 cells. In conclusion the MR regulates EGFR and CACNA1H expression, which has an effect on HL-1 cell diameter, and the extent of this regulation seems to depend on the SNP-216 (G/T) genotype. This suggests that the EGFR may be an intermediate for MR-mediated cardiovascular changes and that SNP analysis can help identify subgroups of patients that will benefit most from MR antagonists.
Collapse
Affiliation(s)
- Katharina Stroedecke
- Julius Bernstein Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06097, Halle, Saale, Germany
| | - Sandra Meinel
- Julius Bernstein Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06097, Halle, Saale, Germany
| | - Fritz Markwardt
- Julius Bernstein Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06097, Halle, Saale, Germany
| | - Udo Kloeckner
- Julius Bernstein Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06097, Halle, Saale, Germany
| | - Nicole Straetz
- Julius Bernstein Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06097, Halle, Saale, Germany
| | - Katja Quarch
- Julius Bernstein Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06097, Halle, Saale, Germany
| | - Barbara Schreier
- Julius Bernstein Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06097, Halle, Saale, Germany
| | - Michael Kopf
- Julius Bernstein Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06097, Halle, Saale, Germany
| | - Michael Gekle
- Julius Bernstein Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06097, Halle, Saale, Germany
| | - Claudia Grossmann
- Julius Bernstein Institute of Physiology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 6, 06097, Halle, Saale, Germany.
| |
Collapse
|
2
|
Oxidative stress induced by palmitic acid modulates K Ca2.3 channels in vascular endothelium. Exp Cell Res 2019; 383:111552. [PMID: 31415760 DOI: 10.1016/j.yexcr.2019.111552] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/27/2019] [Accepted: 08/10/2019] [Indexed: 02/08/2023]
Abstract
Elevated plasma free fatty acids level has been implicated in the development of insulin resistance, inflammation, and endothelial dysfunction in diabetic and nondiabetic individuals. However, the underlying mechanisms still remain to be defined. Herein, we investigated the effect of palmitic acid (PA), the most abundant saturated fatty acid in the human body, on small-conductance Ca2+-activated potassium channels (KCa2.3)-mediated relaxation in rodent resistance arteries and the underlying molecular mechanism. The effect of PA on KCa2.3 in endothelium was evaluated using real-time PCR, Western blotting, whole-cell patch voltage-clamp, wire and pressure myograph system, and reactive oxygen species (ROS) were measured by using dihydroethidium and 2', 7'-dichlorofluorescein diacetate. KCa2.3-mediated vasodilatation responses to acetylcholine and NS309 (agonist of KCa2.3 and KCa3.1) were impaired by incubation of normal mesenteric arteries with 100 μM PA for 24 h. In cultured human umbilical vein endothelial cells (HUVECs), PA decreased KCa2.3 current and expression at mRNA and protein levels. Incubation with the NADPH oxidase (Nox) inhibitor dibenziodolium (DPI) partly inhibited the PA-induced ROS production and restored KCa2.3 expression. Inhibition of either p38-MAPK or NF-κB using specific inhibitors (SB203580, SB202190 or Bay11-7082, pyrrolidinedithiocarbamate) attenuated PA-induced downregulation of KCa2.3 and inhibition of p38-MAPK also attenuated PA-induced phosphorylation of NF-κB p65. Furthermore, DPI reversed the increment of phospho-p38-MAPK by PA. These results demonstrated that PA downregulated KCa2.3 expressions via Nox/ROS/p38-MAPK/NF-κB signaling leading to endothelial vasodilatory dysfunction.
Collapse
|
3
|
Shen Z, Yang X, Chen Y, Shi L. CAPA periviscerokinin-mediated activation of MAPK/ERK signaling through Gq-PLC-PKC-dependent cascade and reciprocal ERK activation-dependent internalized kinetics of Bom-CAPA-PVK receptor 2. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 98:1-15. [PMID: 29730398 DOI: 10.1016/j.ibmb.2018.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/16/2018] [Accepted: 04/28/2018] [Indexed: 06/08/2023]
Abstract
Bombyx mori neuropeptide G protein-coupled receptor (BNGR)-A27 is a specific receptor for B. mori capability (CAPA) periviscerokinin (PVK), that is, Bom-CAPA-PVK receptor 2. Upon stimulation of Bom-CAPA-PVK-1 or -PVK-2, Bom-CAPA-PVK receptor 2 significantly increases cAMP-response element-controlled luciferase activity and Ca2+ mobilization in a Gq inhibitor-sensitive manner. However, the underlying mechanism(s) for CAPA/CAPA receptor system mediation of extracellular signal-regulated kinases1/2 (ERK1/2) activation remains to be explained further. Here, we discovered that Bom-CAPA-PVK receptor 2 stimulated ERK1/2 phosphorylation in a dose- and time-dependent manner in response to Bom-CAPA-PVK-1 or -PVK-2 with similar potencies. Furthermore, ERK1/2 phosphorylation can be inhibited by Gq inhibitor UBO-QIC, PLC inhibitor U73122, protein kinase C (PKC) inhibitor Go 6983, phospholipase D (PLD) inhibitor FIPI and Ca2+ chelators EGTA and BAPTA-AM. Moreover, Bom-CAPA-PVK-R2-induced activation of ERK1/2 was significantly attenuated by treatment with the Gβγ-specific inhibitors, phosphatidylinositol 3-kinase (PI3K)-specific inhibitor Wortmannin and Src-specific inhibitor PP2. Our data also demonstrate that receptor tyrosine kinase (RTK) transactivation pathways are involved in the mechanisms of Bom-CAPA-PVK receptor to ERK1/2 phosphorylation. In addition, β-arrestin1/2 is not involved in Bom-CAPA-PVK-R2-mediated ERK1/2 activation but required for the agonist-independent, ERK1/2 activation-dependent internalization of the G protein-coupled receptor (GPCR).
Collapse
Affiliation(s)
- Zhangfei Shen
- Department of Economic Zoology, College of Animal Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xiaoyuan Yang
- College of Life Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yu Chen
- College of Life Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Liangen Shi
- Department of Economic Zoology, College of Animal Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| |
Collapse
|
4
|
Chen KH, Liu H, Sun HY, Jin MW, Xiao GS, Wang Y, Li GR. The Natural Flavone Acacetin Blocks Small Conductance Ca 2+-Activated K + Channels Stably Expressed in HEK 293 Cells. Front Pharmacol 2017; 8:716. [PMID: 29081746 PMCID: PMC5646423 DOI: 10.3389/fphar.2017.00716] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 09/25/2017] [Indexed: 01/06/2023] Open
Abstract
The natural flavone acacetin inhibits several voltage-gated potassium currents in atrial myocytes, and has anti-atrial fibrillation (AF) effect in experimental AF models. The present study investigates whether acacetin inhibits the Ca2+-activated potassium (KCa) currents, including small conductance (SKCa1, SKCa2, and SKCa3), intermediate conductance (IKCa), and large-conductance (BKCa) channels stably expressed in HEK 293 cells. The effects of acacetin on these KCa channels were determined with a whole-cell patch voltage-clamp technique. The results showed that acacetin inhibited the three subtype SKCa channel currents in concentration-dependent manner with IC50 of 12.4 μM for SKCa1, 10.8 μM for SKCa2, and 11.6 μM for SKCa3. Site-directed mutagenesis of SKCa3 channels generated the mutants H490N, S512T, H521N, and A537V. Acacetin inhibited the mutants with IC50 of 118.5 μM for H490N, 275.2 μM for S512T, 15.3 μM for H521N, and 10.6 μM for A537V, suggesting that acacetin interacts with the P-loop helix of SKCa3 channel. However, acacetin at 3–10 μM did not decrease, but induced a slight increase of BKCa (+70 mV) by 8% at 30 μM. These results demonstrate the novel information that acacetin remarkably inhibits SKCa channels, but not IKCa or BKCa channels, which suggests that blockade of SKCa by acacetin likely contributes to its anti-AF property previously observed in experimental AF.
Collapse
Affiliation(s)
- Kui-Hao Chen
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pharmacology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Liu
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pharmacology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hai-Ying Sun
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Man-Wen Jin
- Department of Pharmacology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guo-Sheng Xiao
- Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, China
| | - Yan Wang
- Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, China
| | - Gui-Rong Li
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong.,Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, China
| |
Collapse
|
5
|
Dai H, Jia G, Wang W, Liang C, Han S, Chu M, Mei X. Genistein inhibited ammonia induced astrocyte swelling by inhibiting NF-κB activation-mediated nitric oxide formation. Metab Brain Dis 2017; 32:841-848. [PMID: 28255863 DOI: 10.1007/s11011-017-9975-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 02/15/2017] [Indexed: 11/27/2022]
Abstract
Our previous study has indicated the involvement of epidermal growth factor receptor (EGFR) transactivation in ammonia-induced astrocyte swelling, which represents a major pathogenesis of brain edema in hepatic encephalopathy. In this study, we examined the effect of genistein, a naturally occurred broad-spectrum protein tyrosine kinase (PTK) inhibitor, on ammonia-induced cell swelling. We found that genistein pretreatment significantly prevented ammonia-induced astrocyte swelling. Mechanistically, ammonia triggered EGFR/extracellular signal-regulated kinase (ERK) association and subsequent ERK phosphorylation were alleviated by genistein pretreatment. Moreover, ammonia-induced NF-κB nuclear location, iNOS expression, and consequent NO production were all prevented by AG1478 and genistein pretreatment. This study suggested that genistein could alleviate ammonia-induced astrocyte swelling, which may be, at least partly, related to its PTK-inhibiting activity and repression of NF-κB mediated iNOS-derived NO accumulation.
Collapse
Affiliation(s)
- Hongliang Dai
- School of Nursing, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Jinzhou, Liaoning, 121001, China.
| | - Guizhi Jia
- Department of Physiology, Jinzhou Medical University, Jinzhou, Liaoning, 121001, People's Republic of China.
| | - Wei Wang
- Department of Orthopedics, First Affiliated Hospital, Jinzhou Medical University, Jinzhou, Liaoning, 121001, People's Republic of China
| | - Chunguang Liang
- School of Nursing, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Jinzhou, Liaoning, 121001, China
| | - Siyu Han
- School of Nursing, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Jinzhou, Liaoning, 121001, China
| | - Minghui Chu
- School of Nursing, Jinzhou Medical University, No. 40, Section 3, Songpo Road, Jinzhou, Liaoning, 121001, China
| | - Xifan Mei
- Department of Orthopedics, First Affiliated Hospital, Jinzhou Medical University, Jinzhou, Liaoning, 121001, People's Republic of China.
| |
Collapse
|
6
|
Zatkova M, Reichova A, Bacova Z, Strbak V, Kiss A, Bakos J. Neurite Outgrowth Stimulated by Oxytocin Is Modulated by Inhibition of the Calcium Voltage-Gated Channels. Cell Mol Neurobiol 2017; 38:371-378. [DOI: 10.1007/s10571-017-0503-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/06/2017] [Indexed: 11/29/2022]
|
7
|
Wang Y, Sun HY, Liu YG, Song Z, She G, Xiao GS, Wang Y, Li GR, Deng XL. Tyrphostin AG556 increases the activity of large conductance Ca 2+ -activated K + channels by inhibiting epidermal growth factor receptor tyrosine kinase. J Cell Mol Med 2017; 21:1826-1834. [PMID: 28294531 PMCID: PMC5571560 DOI: 10.1111/jcmm.13103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 12/28/2016] [Indexed: 01/08/2023] Open
Abstract
The present study was designed to investigate whether large conductance Ca2+‐activated K+ (BK) channels were regulated by epidermal growth factor (EGF) receptor (EGFR) tyrosine kinase. BK current and channel tyrosine phosphorylation level were measured in BK‐HEK 293 cells expressing both functional α‐subunits and the auxiliary β1‐subunits using electrophysiology, immunoprecipitation and Western blotting approaches, respectively, and the function of rat cerebral basilar arteries was determined with a wire myography system. We found that BK current in BK‐HEK 293 cells was increased by the broad spectrum protein tyrosine kinase (PTK) inhibitor genistein and the selective EGFR tyrosine kinase inhibitor AG556, one of the known tyrphostin. The effect of genistein or AG556 was antagonized by the protein tyrosine phosphatase (PTP) inhibitor orthovanadate. On the other hand, orthovanadate or EGF decreased BK current, and the effect was counteracted by AG556. The tyrosine phosphorylation level of BK channels (α‐ and β1‐subunits) was increased by EGF and orthovanadate, while decreased by genistein and AG556, and the reduced tyrosine phosphorylation of BK channels by genistein or AG556 was reversed by orthovanadate. Interestingly, AG556 induced a remarkable enhancement of BK current in rat cerebral artery smooth muscle cells and relaxation of pre‐contracted rat cerebral basilar arteries with denuded endothelium, and these effects were antagonized by the BK channel blocker paxilline or orthovanadate. These results demonstrate that tyrosine phosphorylation of BK channels by EGFR kinase decreases the channel activity, and inhibition of EGFR kinase by AG556 enhances the channel activity and dilates rat cerebral basilar arteries.
Collapse
Affiliation(s)
- Yan Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.,Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hai-Ying Sun
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ying-Guang Liu
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Zheng Song
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Gang She
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Guo-Sheng Xiao
- Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, Fujian, China
| | - Yan Wang
- Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, Fujian, China
| | - Gui-Rong Li
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, Fujian, China
| | - Xiu-Ling Deng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.,Cardiovascular Research Centre, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| |
Collapse
|
8
|
Xiao GS, Zhang YH, Wu W, Sun HY, Wang Y, Li GR. Genistein and tyrphostin AG556 decrease ultra-rapidly activating delayed rectifier K + current of human atria by inhibiting EGF receptor tyrosine kinase. Br J Pharmacol 2017; 174:454-467. [PMID: 28072464 DOI: 10.1111/bph.13710] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 12/16/2016] [Accepted: 01/05/2017] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND AND PURPOSE The ultra-rapidly activating delayed rectifier K+ current IKur (encoded by Kv 1.5 or KCNA5) plays an important role in human atrial repolarization. The present study investigates the regulation of this current by protein tyrosine kinases (PTKs). EXPERIMENTAL APPROACH Whole-cell patch voltage clamp technique and immunoprecipitation and Western blotting analysis were used to investigate whether the PTK inhibitors genistein, tyrphostin AG556 (AG556) and PP2 regulate human atrial IKur and hKv1.5 channels stably expressed in HEK 293 cells. KEY RESULTS Human atrial IKur was decreased by genistein (a broad-spectrum PTK inhibitor) and AG556 (a highly selective EGFR TK inhibitor) in a concentration-dependent manner. Inhibition of IKur induced by 30 μM genistein or 10 μM AG556 was significantly reversed by 1 mM orthovanadate (a protein tyrosine phosphatase inhibitor). Similar results were observed in HEK 293 cells stably expressing hKv 1.5 channels. On the other hand, the Src family kinase inhibitor PP2 (1 μM) slightly enhanced IKur and hKv 1.5 current, and the current increase was also reversed by orthovanadate. Immunoprecipitation and Western blotting analysis showed that genistein, AG556, and PP2 decreased tyrosine phosphorylation of hKv 1.5 channels and that the decrease was countered by orthovanadate. CONCLUSION AND IMPLICATIONS The PTK inhibitors genistein and AG556 decrease human atrial IKur and cloned hKv 1.5 channels by inhibiting EGFR TK, whereas the Src kinase inhibitor PP2 increases IKur and hKv 1.5 current. These results imply that EGFR TK and the soluble Src kinases may have opposite effects on human atrial IKur .
Collapse
Affiliation(s)
- Guo-Sheng Xiao
- Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, Fujian, China
| | - Yan-Hui Zhang
- Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, Fujian, China.,Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Wei Wu
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Hai-Ying Sun
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yan Wang
- Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, Fujian, China
| | - Gui-Rong Li
- Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, Fujian, China.,Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| |
Collapse
|
9
|
Mbogning C, Perdry H, Broët P. A Bagged, Partially Linear, Tree-Based Regression Procedure for Prediction and Variable Selection. Hum Hered 2015. [PMID: 26201703 DOI: 10.1159/000380850] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES In genomics, variable selection and prediction accounting for the complex interrelationships between explanatory variables represent major challenges. Tree-based methods are powerful alternatives to classical regression models. We have recently proposed the generalized, partially linear, tree-based regression (GPLTR) procedure that integrates the advantages of generalized linear regression (allowing the incorporation of confounding variables) and of tree-based models. In this work, we use bagging to address a classical concern of tree-based methods: their instability. METHODS We present a bagged GPLTR procedure and three scores for variable importance. The prediction accuracy and the performance of the scores are assessed by simulation. The use of this procedure is exemplified by the analysis of a lung cancer data set. The aim is to predict the epidermal growth factor receptor (EGFR) mutation based on gene expression measurements, taking into account the ethnicity (confounder variable) and perform variable selection. RESULTS The procedure performs well in terms of prediction accuracy. The scores differentiate predictive variables from noise variables. Based on a lung adenocarcinoma data set, the procedure achieves good predictive performance for EGFR mutation and selects relevant genes. CONCLUSION The proposed bagged GPLTR procedure performs well for prediction and variable selection.
Collapse
|
10
|
Zhao LM, Wang Y, Yang Y, Guo R, Wang NP, Deng XL. Metformin Restores Intermediate-Conductance Calcium-Activated K+ Channel– and Small-Conductance Calcium-Activated K+ Channel–Mediated Vasodilatation Impaired by Advanced Glycation End Products in Rat Mesenteric Artery. Mol Pharmacol 2014; 86:580-91. [DOI: 10.1124/mol.114.092874] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|