1
|
Hu YB, Deng X, Liu L, Cao CC, Su YW, Gao ZJ, Cheng X, Kong D, Li Q, Shi YW, Wang XG, Ye X, Zhao H. Distinct roles of excitatory and inhibitory neurons in the medial prefrontal cortex in the expression and reconsolidation of methamphetamine-associated memory in male mice. Neuropsychopharmacology 2024:10.1038/s41386-024-01879-2. [PMID: 38730034 DOI: 10.1038/s41386-024-01879-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Methamphetamine, a commonly abused drug, is known for its high relapse rate. The persistence of addictive memories associated with methamphetamine poses a significant challenge in preventing relapse. Memory retrieval and subsequent reconsolidation provide an opportunity to disrupt addictive memories. However, the key node in the brain network involved in methamphetamine-associated memory retrieval has not been clearly defined. In this study, using the conditioned place preference in male mice, whole brain c-FOS mapping and functional connectivity analysis, together with chemogenetic manipulations of neural circuits, we identified the medial prefrontal cortex (mPFC) as a critical hub that integrates inputs from the retrosplenial cortex and the ventral tegmental area to support both the expression and reconsolidation of methamphetamine-associated memory during its retrieval. Surprisingly, with further cell-type specific analysis and manipulation, we also observed that methamphetamine-associated memory retrieval activated inhibitory neurons in the mPFC to facilitate memory reconsolidation, while suppressing excitatory neurons to aid memory expression. These findings provide novel insights into the neural circuits and cellular mechanisms involved in the retrieval process of addictive memories. They suggest that targeting the balance between excitation and inhibition in the mPFC during memory retrieval could be a promising treatment strategy to prevent relapse in methamphetamine addiction.
Collapse
Affiliation(s)
- Yu-Bo Hu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Xi Deng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Lu Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Can-Can Cao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Ya-Wen Su
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zhen-Jie Gao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Xin Cheng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Deshan Kong
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Qi Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Yan-Wei Shi
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Xiao-Guang Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Xiaojing Ye
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| | - Hu Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| |
Collapse
|
2
|
Wang J, Gao M, Cheng M, Luo J, Lu M, Xing X, Sun Y, Lu Y, Li X, Shi C, Wang J, Wang N, Yang W, Jiang Y, Huang H, Yang G, Zeng Y, Wang C, Cao X. Single-Cell Transcriptional Analysis of Lamina Propria Lymphocytes in the Jejunum Reveals Innate Lymphoid Cell-like Cells in Pigs. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:130-142. [PMID: 37975680 DOI: 10.4049/jimmunol.2300463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
Pigs are the most suitable model to study various therapeutic strategies and drugs for human beings, although knowledge about cell type-specific transcriptomes and heterogeneity is poorly available. Through single-cell RNA sequencing and flow cytometry analysis of the types in the jejunum of pigs, we found that innate lymphoid cells (ILCs) existed in the lamina propria lymphocytes (LPLs) of the jejunum. Then, through flow sorting of live/dead-lineage (Lin)-CD45+ cells and single-cell RNA sequencing, we found that ILCs in the porcine jejunum were mainly ILC3s, with a small number of NK cells, ILC1s, and ILC2s. ILCs coexpressed IL-7Rα, ID2, and other genes and differentially expressed RORC, GATA3, and other genes but did not express the CD3 gene. ILC3s can be divided into four subgroups, and genes such as CXCL8, CXCL2, IL-22, IL-17, and NCR2 are differentially expressed. To further detect and identify ILC3s, we verified the classification of ILCs in the porcine jejunum subgroup and the expression of related hallmark genes at the protein level by flow cytometry. For systematically characterizing ILCs in the porcine intestines, we combined our pig ILC dataset with publicly available human and mice ILC data and identified that the human and pig ILCs shared more common features than did those mouse ILCs in gene signatures and cell states. Our results showed in detail for the first time (to our knowledge) the gene expression of porcine jejunal ILCs, the subtype classification of ILCs, and the markers of various ILCs, which provide a basis for an in-depth exploration of porcine intestinal mucosal immunity.
Collapse
Affiliation(s)
- Junhong Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Ming Gao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Mingyang Cheng
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jiawei Luo
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Mei Lu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xinyuan Xing
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yu Sun
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yiyuan Lu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xiaoxu Li
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chunwei Shi
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jianzhong Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Nan Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Wentao Yang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yanlong Jiang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Haibin Huang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Guilian Yang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yan Zeng
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chunfeng Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xin Cao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| |
Collapse
|
3
|
Fernandes HB, de Oliveira IM, Postler TS, Lima SQ, Santos CAC, Oliveira MS, Leão FB, Ghosh S, Souza MC, Andrade W, Silva AM. Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophages. Sci Rep 2023; 13:19614. [PMID: 37950057 PMCID: PMC10638313 DOI: 10.1038/s41598-023-47040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
Ras guanine nucleotide exchange factor member 1b (RasGEF1b) of the RasGEF/CDC25 domain-containing family is preferentially expressed by macrophages. However, information is lacking about its role in macrophage function. In this study, we generated mice with ubiquitous deletion of Rasgef1b and used RNA-seq-based transcriptomics to compare the global gene expression in wild-type and knock-out primary bone-marrow-derived macrophages under basal conditions and after lipopolysaccharide (LPS) treatment. Transcriptional filtering identified several genes with significantly different transcript levels between wild-type and knock-out macrophages. In total, 49 and 37 differentially expressed genes were identified at baseline and in LPS-activated macrophages, respectively. Distinct biological processes were significantly linked to down-regulated genes at the basal condition only, and largely included chemotaxis, response to cytokines, and positive regulation of GTPase activity. Importantly, validation by RT-qPCR revealed that the expression of genes identified as down-regulated after LPS stimulation was also decreased in the knock-out cells under basal conditions. We used a luciferase-based reporter assay to showcase the capability of RasGEF1b in activating the Serpinb2 promoter. Notably, knockdown of RasGEF1b in RAW264.7 macrophages resulted in impaired transcriptional activation of the Serpinb2 promoter, both in constitutive and LPS-stimulated conditions. This study provides a small collection of genes that shows relative expression changes effected by the absence of RasGEF1b in macrophages. Thus, we present the first evidence that RasGEF1b mediates the regulation of both steady-state and signal-dependent expression of genes and propose that this GEF plays a role in the maintenance of the basal transcriptional level in macrophages.
Collapse
Affiliation(s)
- Heliana B Fernandes
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Isadora Mafra de Oliveira
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Faculdade de Medicina de Ribeirão Preto, Av. Bandeirantes, 3900 - Campus da USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Thomas S Postler
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Design and Development Laboratory, International AIDS Vaccine Initiative, Brooklyn, NY, USA
| | - Sérgio Q Lima
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Cícera A C Santos
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia de Rondônia (IFRO), Guajará-Mirim, RO, Brazil
| | - Michaelle S Oliveira
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Felipe B Leão
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Sankar Ghosh
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Maria C Souza
- Faculdade de Medicina de Ribeirão Preto, Av. Bandeirantes, 3900 - Campus da USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Warrison Andrade
- Faculdade de Medicina de Ribeirão Preto, Av. Bandeirantes, 3900 - Campus da USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Aristóbolo M Silva
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.
| |
Collapse
|
4
|
Ventham NT, Kennedy NA, Kalla R, Adams AT, Noble A, Ennis H, Mowat C, Dunlop MG, Satsangi J. Genome-Wide Methylation Profiling in 229 Patients With Crohn's Disease Requiring Intestinal Resection: Epigenetic Analysis of the Trial of Prevention of Post-operative Crohn's Disease (TOPPIC). Cell Mol Gastroenterol Hepatol 2023; 16:431-450. [PMID: 37331566 PMCID: PMC10372903 DOI: 10.1016/j.jcmgh.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/20/2023]
Abstract
BACKGROUND & AIMS DNA methylation alterations may provide important insights into gene-environment interaction in cancer, aging, and complex diseases, such as inflammatory bowel disease (IBD). We aim first to determine whether the circulating DNA methylome in patients requiring surgery may predict Crohn's disease (CD) recurrence following intestinal resection; and second to compare the circulating methylome seen in patients with established CD with that we had reported in a series of inception cohorts. METHODS TOPPIC was a placebo-controlled, randomized controlled trial of 6-mercaptopurine at 29 UK centers in patients with CD undergoing ileocolic resection between 2008 and 2012. Genomic DNA was extracted from whole blood samples from 229 of the 240 patients taken before intestinal surgery and analyzed using 450KHumanMethylation and Infinium Omni Express Exome arrays (Illumina, San Diego, CA). Coprimary objectives were to determine whether methylation alterations may predict clinical disease recurrence; and to assess whether the epigenetic alterations previously reported in newly diagnosed IBD were present in the patients with CD recruited into the TOPPIC study. Differential methylation and variance analysis was performed comparing patients with and without clinical evidence of recurrence. Secondary analyses included investigation of methylation associations with smoking, genotype (MeQTLs), and chronologic age. Validation of our previously published case-control observation of the methylome was performed using historical control data (CD, n = 123; Control, n = 198). RESULTS CD recurrence in patients following surgery is associated with 5 differentially methylated positions (Holm P < .05), including probes mapping to WHSC1 (P = 4.1 × 10-9, Holm P = .002) and EFNA3 (P = 4.9 × 10-8, Holm P = .02). Five differentially variable positions are demonstrated in the group of patients with evidence of disease recurrence including a probe mapping to MAD1L1 (P = 6.4 × 10-5). DNA methylation clock analyses demonstrated significant age acceleration in CD compared with control subjects (GrimAge + 2 years; 95% confidence interval, 1.2-2.7 years), with some evidence for accelerated aging in patients with CD with disease recurrence following surgery (GrimAge +1.04 years; 95% confidence interval, -0.04 to 2.22). Significant methylation differences between CD cases and control subjects were seen by comparing this cohort in conjunction with previously published control data, including validation of our previously described differentially methylated positions (RPS6KA2 P = 1.2 × 10-19, SBNO2 = 1.2 × 10-11) and regions (TXK [false discovery rate, P = 3.6 × 10-14], WRAP73 [false discovery rate, P = 1.9 × 10-9], VMP1 [false discovery rate, P = 1.7 × 10-7], and ITGB2 [false discovery rate, P = 1.4 × 10-7]). CONCLUSIONS We demonstrate differential methylation and differentially variable methylation in patients developing clinical recurrence within 3 years of surgery. Moreover, we report replication of the CD-associated methylome, previously characterized only in adult and pediatric inception cohorts, in patients with medically refractory disease needing surgery.
Collapse
Affiliation(s)
- Nicholas T Ventham
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom.
| | - Nicholas A Kennedy
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Rahul Kalla
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Alex T Adams
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Alexandra Noble
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Holly Ennis
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Craig Mowat
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Malcolm G Dunlop
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Jack Satsangi
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| |
Collapse
|
5
|
Gonzalez TL, Schaub AM, Lee B, Cui J, Taylor KD, Dorfman AE, Goodarzi MO, Wang ET, Chen YDI, Rotter JI, Hussaini R, Harakuni PM, Khan MH, Rich SS, Farber CR, Williams J, Pisarska MD. Infertility and treatments used have minimal effects on first-trimester placental DNA methylation and gene expression. Fertil Steril 2023; 119:301-312. [PMID: 36379261 DOI: 10.1016/j.fertnstert.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To determine whether deoxyribonucleic acid (DNA) methylation alterations exist in the first-trimester human placenta between conceptions using fertility treatments and those that do not and, if so, whether they are the result of underlying infertility or fertility treatments. We also assessed whether significant alterations led to changes in gene expression. DESIGN We compared DNA methylation of the first-trimester placenta from singleton pregnancies that resulted in live births from unassisted, in vitro fertilization (IVF), and non-IVF fertility treatment (NIFT) conceptions using the Infinium MethylationEPIC BeadChip array. Significant CpG sites were compared with corresponding ribonucleic acid sequencing analysis in similar cohorts to determine whether methylation alterations lead to differences in gene expression. SETTING Academic medical center. PATIENT(S) A total of 138 singleton pregnancies undergoing chorionic villus sampling resulting in a live birth were recruited for methylation analysis (56 unassisted, 38 NIFT, and 44 IVF conceptions). Ribonucleic acid-sequencing data consisted of 141 subjects (74 unassisted, 33 NIFT, and 34 IVF conceptions) of which 116 overlapped with the methylation cohort. INTERVENTION(S) In vitro fertilization-conceived pregnancy or pregnancy conceived via NIFT, such as ovulation induction and intrauterine insemination. MAIN OUTCOME MEASURE(S) Significant methylation changes at CpG sites after adjustment for multiple comparisons. The secondary outcome was gene expression changes of significant CpG sites. RESULT(S) Of the 741,145 probes analyzed in the placenta, few were significant at Bonferroni <0.05: 185 CpG sites (0.025%) significant in pregnancies conceived with the fertility treatments (NIFT + IVF) vs. unassisted conceptions; 28 in NIFT vs. unassisted; 195 in IVF vs. unassisted; and only 13 (0.0018%) in IVF vs. NIFT conceptions. Of all significant CpG sites combined, 10% (35) were located in genes with suggestive gene expression changes, but none were significant after adjustment for multiple comparisons (ribonucleic acid sequencing false discovery rate <0.05). None of the 13 differentially methylated probes in the IVF vs. NIFT placenta were located in genes with suggestive IVF vs. NIFT gene expression differences. CONCLUSION(S) Underlying infertility is the most significant contributor to the minimal differences in first-trimester placental methylation, and not the specific fertility treatment used, such as IVF.
Collapse
Affiliation(s)
- Tania L Gonzalez
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Amelia M Schaub
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Bora Lee
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Jinrui Cui
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, Cedars Sinai Medical Center, Los Angeles, California
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Anna E Dorfman
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, Cedars Sinai Medical Center, Los Angeles, California
| | - Erica T Wang
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California; David Geffen School of Medicine, University of California, Los Angeles, California
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Rimsha Hussaini
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Paige M Harakuni
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Mayaal H Khan
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - John Williams
- David Geffen School of Medicine, University of California, Los Angeles, California; Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California
| | - Margareta D Pisarska
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars Sinai Medical Center, Los Angeles, California; David Geffen School of Medicine, University of California, Los Angeles, California; Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, California.
| |
Collapse
|
6
|
He X, Zhang W, Fu W, Liu X, Yang P, Wang J, Zhu M, Li S, Zhang W, Zhang X, Dong G, Yan C, Zhao Y, Zeng Z, Jing H. The prognostic value of RASGEF1A RNA expression and DNA methylation in cytogenetically normal acute myeloid leukemia. Cancer Biomark 2022; 36:103-116. [PMID: 36404533 DOI: 10.3233/cbm-210407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a significantly heterogeneous malignancy of the blood. Cytogenetic abnormalities are crucial for the prognosis of AML. However, since more than half of patients with AML are cytogenetically normal AML (CN-AML), predictive prognostic indicators need to be further refined. In recent years, gene abnormalities are considered to be strong prognostic factors of CN-AML, already having clinical significance for treatment. In addition, the relationship of methylation in some genes and AML prognosis predicting has been discovered. RASGEF1A is a guanine nucleotide exchange factors of Ras and widely expressed in brain tissue, bone marrow and 17 other tissues. RASGEF1A has been reported to be associated with a variety of malignant tumors, examples include Hirschsprung disease, renal cell carcinoma, breast cancer, diffuse large B cell lymphoma, intrahepatic cholangiocarcinoma and so on [1, 2]. However, the relationship between the RASGEF1A gene and CN-AML has not been reported. METHODS By integrating the Cancer Genome Atlas (TCGA) database 75 patients with CN-AML and 240 Gene Expression Omnibus (GEO) database CN-AML samples, we examined the association between RASGEF1A's RNA expression level and DNA methylation of and AML patients' prognosis. Then, we investigated the RASGEF1A RNA expression and DNA methylation's prognostic value in 77 patients with AML after allogeneic hematopoietic stem cell transplantation (Allo-HSCT) as well as 101 AML patients after chemotherapy respectively. We investigated the association between sensitivity to Crenolanib and expression level of RASGED1A in patients by integrating 191 CN-AML patients from BeatAML dadataset. We integrated the expression and methylation of RASGEF1A to predict the CN-AML patients' prognosis and investigated the relationship between prognostic of AML patients with different risk classification and expression levels or methylation levels of RASGEF1A. RESULTS We found that RASGEF1A gene high expression group predicted poorer event-free survival (EFS) (P< 0.0001) as well as overall survival (OS) (P< 0.0001) in CN-AML samples, and the identical results were found in AML patients receiving chemotherapy (P< 0.0001) and Allo-HSCT (P< 0.0001). RASGEF1A RNA expression level is an CN-AML patients' independent prognostic factor (EFS: HR = 5.5534, 95% CI: 1.2982-23.756, P= 0.0208; OS: HR = 5.3615, 95% CI: 1.1014-26.099, P= 0.0376). The IC50 (half maximal inhibitory concentration) of Crenolanib of CN-AML samples with RASGEF1A high expression level is lower. In addition, patients with high RASGEF1A methylation level had significant favorable prognosis (EPS: P< 0.0001, OS: P< 0.0001). Furthermore, the integrative analysis of expression and methylation of RASGEF1A could classify CN-AML patients into subgroups with different prognosis (EFS: P= 0.034, OS: P= 0.0024). Expression levels or methylation levels of RASGEF1A help to improve risk classification of 2010 European Leukemia Net. CONCLUSION Higher RASGEF1A RNA expression and lower DNA methylation predicts CN-AML patients' poorer prognosis. The RASGEF1A high expression level from patients with CN-AML have better sensitivity to Crenolanib. The integrative analysis of RASGEF1A RNA expression and DNA methylation can provide a more accurate classification for prognosis. Lower RASGEF1A expression is a favorable prognostic factor for AML patients receiving chemotherapy or Allo-HSCT. 2010 European Leukemia Net's risk classification can be improved by RASGEF1A expression levels or methylation levels.
Collapse
Affiliation(s)
- Xue He
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China.,Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Weilong Zhang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China.,Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wei Fu
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China.,Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaoni Liu
- The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Ping Yang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| | - Jing Wang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| | - Mingxia Zhu
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| | - Shaoxiang Li
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China
| | - Wei Zhang
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China
| | - Xiuru Zhang
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Pathology, Capital Medical University, Beijing, China
| | | | - Yali Zhao
- General Practice Medicine, The First People's Hospital of Huzhou, Huzhou, Zhejiang, China
| | - Zhiping Zeng
- The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Hongmei Jing
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| |
Collapse
|
7
|
Leung HW, Foo G, VanDongen A. Arc Regulates Transcription of Genes for Plasticity, Excitability and Alzheimer’s Disease. Biomedicines 2022; 10:biomedicines10081946. [PMID: 36009494 PMCID: PMC9405677 DOI: 10.3390/biomedicines10081946] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023] Open
Abstract
The immediate early gene Arc is a master regulator of synaptic function and a critical determinant of memory consolidation. Here, we show that Arc interacts with dynamic chromatin and closely associates with histone markers for active enhancers and transcription in cultured rat hippocampal neurons. Both these histone modifications, H3K27Ac and H3K9Ac, have recently been shown to be upregulated in late-onset Alzheimer’s disease (AD). When Arc induction by pharmacological network activation was prevented using a short hairpin RNA, the expression profile was altered for over 1900 genes, which included genes associated with synaptic function, neuronal plasticity, intrinsic excitability, and signalling pathways. Interestingly, about 100 Arc-dependent genes are associated with the pathophysiology of AD. When endogenous Arc expression was induced in HEK293T cells, the transcription of many neuronal genes was increased, suggesting that Arc can control expression in the absence of activated signalling pathways. Taken together, these data establish Arc as a master regulator of neuronal activity-dependent gene expression and suggest that it plays a significant role in the pathophysiology of AD.
Collapse
Affiliation(s)
| | - Gabriel Foo
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Antonius VanDongen
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
- Correspondence:
| |
Collapse
|
8
|
Trusov NV, Apryatin SA, Shipelin VA, Shumakova AA, Gmoshinski IV, Nikityuk DB, Tutelyan VA. Effect of Administration of Carnitine, Resveratrol, and Aromatic Amino Acids with High-Fat-High-Fructose Diet on Gene Expression in Liver of Rats: Full Transcriptome Analysis. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421100136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
9
|
Carvalho BC, Oliveira LC, Rocha CD, Fernandes HB, Oliveira IM, Leão FB, Valverde TM, Rego IMG, Ghosh S, Silva AM. Both knock-down and overexpression of Rap2a small GTPase in macrophages result in impairment of NF-κB activity and inflammatory gene expression. Mol Immunol 2019; 109:27-37. [PMID: 30851634 DOI: 10.1016/j.molimm.2019.02.015] [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: 09/09/2018] [Revised: 01/12/2019] [Accepted: 02/17/2019] [Indexed: 02/08/2023]
Abstract
Small Ras GTPases are key molecules that regulate a variety of cellular responses in different cell types. Rap1 plays important functions in the regulation of macrophage biology during inflammation triggered by toll-like receptors (TLRs). However, despite sharing a relatively high degree of similarity with Rap1, no studies concerning Rap2 in macrophages and innate immunity have been reported yet. In this work, we show that either way alterations in the levels of Rap2a hampers proper macrophages response to TLR stimulation. Rap2a is activated by LPS in macrophages, and although putative activator TLR-inducible Ras guanine exchange factor RasGEF1b was sufficient to induce, it was not fully required for Rap2a activation. Silencing of Rap2a impaired LPS-induced production of IL-6 cytokine and KC/Cxcl1 chemokine, and also NF-κB activity as measured by reporter gene studies. Surprisingly, overexpression of Rap2a did also lead to marked inhibition of NF-κB activation induced by LPS, Pam3CSK4 and downstream TLR signaling molecules. We also found that Rap2a can inhibit the LPS-induced phosphorylation of the NF-κB subunit p65 at serine 536. Collectively, our data suggest that expression levels of Rap2a in macrophages might be tightly regulated to avoid unbalanced immune response. Our results implicate Rap2a in TLR-mediated responses by contributing to balanced NF-κB activity status in macrophages.
Collapse
Affiliation(s)
- Brener C Carvalho
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Leonardo C Oliveira
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Carolina D Rocha
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Heliana B Fernandes
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Isadora M Oliveira
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Felipe B Leão
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Thalita M Valverde
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Igor M G Rego
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Sankar Ghosh
- Department of Microbiology & Immunology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Aristóbolo M Silva
- Laboratory of Inflammatory Genes, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
| |
Collapse
|
10
|
Matana A, Brdar D, Torlak V, Boutin T, Popović M, Gunjača I, Kolčić I, Boraska Perica V, Punda A, Polašek O, Barbalić M, Hayward C, Zemunik T. Genome-wide meta-analysis identifies novel loci associated with parathyroid hormone level. Mol Med 2018; 24:15. [PMID: 30134803 PMCID: PMC6016867 DOI: 10.1186/s10020-018-0018-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/02/2018] [Indexed: 02/08/2023] Open
Abstract
Background Parathyroid hormone (PTH) is one of the principal regulators of calcium homeostasis. Although serum PTH level is mostly accounted by genetic factors, genetic background underlying PTH level is insufficiently known. Therefore, the aim of this study was to identify novel genetic variants associated with PTH levels. Methods We performed GWAS meta-analysis within two genetically isolated Croatian populations followed by replication analysis in a Croatian mainland population and we also combined results across all three analyzed populations. The analyses included 2596 individuals. A total of 7,411,206 variants, imputed using the 1000 Genomes reference panel, were analysed for the association. In addition, a sex-specific GWAS meta-analyses were performed. Results Polymorphisms with the lowest P-values were located on chromosome 4 approximately 84 kb of the 5′ of RASGEF1B gene. The most significant SNP was rs11099476 (P = 1.15 × 10−8). Sex-specific analysis identified genome-wide significant association of the variant rs77178854, located within DPP10 gene in females only (P = 2.21 × 10− 9). There were no genome-wide significant findings in the meta-analysis of males. Conclusions We identified two biologically plausible novel loci associated with PTH levels, providing us with further insights into the genetics of this complex trait. Electronic supplementary material The online version of this article (10.1186/s10020-018-0018-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Antonela Matana
- Department of Medical Biology, University of Split, School of Medicine, Šoltanska 2, Split, Croatia
| | - Dubravka Brdar
- Department of Nuclear Medicine, University Hospital Split, Spinciceva 1, Split, Croatia
| | - Vesela Torlak
- Department of Nuclear Medicine, University Hospital Split, Spinciceva 1, Split, Croatia
| | - Thibaud Boutin
- MRC Human Genetics Unit, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Marijana Popović
- Department of Medical Biology, University of Split, School of Medicine, Šoltanska 2, Split, Croatia
| | - Ivana Gunjača
- Department of Medical Biology, University of Split, School of Medicine, Šoltanska 2, Split, Croatia
| | - Ivana Kolčić
- Department of Public Health, University of Split, School of Medicine Split, Šoltanska 2, Split, Croatia
| | - Vesna Boraska Perica
- Department of Medical Biology, University of Split, School of Medicine, Šoltanska 2, Split, Croatia
| | - Ante Punda
- Department of Nuclear Medicine, University Hospital Split, Spinciceva 1, Split, Croatia
| | - Ozren Polašek
- Department of Public Health, University of Split, School of Medicine Split, Šoltanska 2, Split, Croatia
| | - Maja Barbalić
- Department of Medical Biology, University of Split, School of Medicine, Šoltanska 2, Split, Croatia
| | - Caroline Hayward
- MRC Human Genetics Unit, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Tatijana Zemunik
- Department of Medical Biology, University of Split, School of Medicine, Šoltanska 2, Split, Croatia.
| |
Collapse
|
11
|
Shah B, Püschel AW. Regulation of Rap GTPases in mammalian neurons. Biol Chem 2017; 397:1055-69. [PMID: 27186679 DOI: 10.1515/hsz-2016-0165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/06/2016] [Indexed: 12/15/2022]
Abstract
Small GTPases are central regulators of many cellular processes. The highly conserved Rap GTPases perform essential functions in the mammalian nervous system during development and in mature neurons. During neocortical development, Rap1 is required to regulate cadherin- and integrin-mediated adhesion. In the adult nervous system Rap1 and Rap2 regulate the maturation and plasticity of dendritic spine and synapses. Although genetic studies have revealed important roles of Rap GTPases in neurons, their regulation by guanine nucleotide exchange factors (GEFs) that activate them and GTPase activating proteins (GAPs) that inactivate them by stimulating their intrinsic GTPase activity is just beginning to be explored in vivo. Here we review how GEFs and GAPs regulate Rap GTPases in the nervous system with a focus on their in vivo function.
Collapse
|
12
|
McDermott N, Meunier A, Wong S, Buchete V, Marignol L. Profiling of a panel of radioresistant prostate cancer cells identifies deregulation of key miRNAs. Clin Transl Radiat Oncol 2017; 2:63-68. [PMID: 29658003 PMCID: PMC5893531 DOI: 10.1016/j.ctro.2017.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/13/2017] [Accepted: 01/13/2017] [Indexed: 12/15/2022] Open
Abstract
Background miRNAs are increasingly associated with the aggressive phenotype of prostate tumours. Their ability to control radiobiologically-relevant cellular processes strengthens their potential as novel markers of response to radiation therapy. Purpose To identify miRNAs associated with increased clonogenic survival following radiation exposure. Material and methods The miRNA expression profiles of a panel of 22RV1 cells with varying levels of radiosensitivities (hypoxic H-22Rv1 cells, RR-22Rv1 cells derived from WT-22Rv1 cells through 2-Gy fractionated repeated exposure, the associated aged matched cells (AMC-22Rv1) and the WT-22Rv1 cell lines) were generated and cross-analysed to identify common miRNAs associated with a radioresistant phenotype. Results Increased clonogenic survival following irradiation was associated with significant modifications in miRNA expression pattern. miR-221 (up) and miR-4284 (down) in RR-22Rv1 and MiR-31 and miR-200c in AMC-22Rv1 were the most uniquely significantly deregulated miRNAs when compared to WT-22Rv1 cells. miR-200c ranked as the most downregulated miRNAs in hypoxic, when compared to RR-22Rv1 cells. miR-200a was the only differentially expressed miRNA between RR-22Rv1 and AMC-22Rv1 cells. miR-210 yielded the highest fold change in expression in H-22Rv1, when compared to WT-22RV1 cells. Conclusion This study identifies candidate miRNAs for the development of novel prognostic biomarkers for radiotherapy prostate cancer patients.
Collapse
Affiliation(s)
- Niamh McDermott
- Trinity Translational Medicine Institute, Translational Radiobiology and Molecular Oncology, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Ireland
| | - Armelle Meunier
- Trinity Translational Medicine Institute, Translational Radiobiology and Molecular Oncology, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Ireland
| | - Simon Wong
- Irish Centre for High-End Computing, National University of Ireland, Galway, Ireland
| | - Vio Buchete
- School of Physics & Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Laure Marignol
- Trinity Translational Medicine Institute, Translational Radiobiology and Molecular Oncology, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Ireland
| |
Collapse
|
13
|
Halder P, Kumar R, Jana K, Chakraborty S, Ghosh Z, Kundu M, Basu J. Gene expression profiling of Mycobacterium tuberculosis Lipoarabinomannan-treated macrophages: A role of the Bcl-2 family member A1 in inhibition of apoptosis in mycobacteria-infected macrophages. IUBMB Life 2015; 67:726-36. [PMID: 26337784 DOI: 10.1002/iub.1430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 08/17/2015] [Indexed: 01/02/2023]
Abstract
Macrophages play an important role in the establishment of infection by intracellular pathogens. Mycobacterium tuberculosis is known to inhibit apoptosis and to downregulate immune responses of host cells using various strategies, including activation of peroxisome proliferator-activated receptor (PPAR)γ. Mannose-capped lipoarabinomannan (ManLAM) is one of the known bacterial effectors that plays a role in subversion of host immunity and activation of PPARγ. Here, we have used an unbiased global gene expression profiling approach to understand (a) how ManLAM regulates host cell immune responses and (b) the role of PPARγ in modulating ManLAM-induced host cell signaling. We have demonstrated that ManLAM-dependent inhibition of macrophage apoptosis is mediated by the upregulation of the antiapoptotic B-cell CLL/lymphoma 2 (Bcl2) family member A1. Our in silico analyses suggested that ManLAM-mediated PPARγ signaling is linked to important functions such as phagocytosis, cytoskeleton remodeling, cell survival, and autophagy. We have validated that ManLAM upregulates signal transducer and activator of transcription (STAT5)α, an important transcriptional regulator of cell survival in a PPARγ-dependent manner.
Collapse
Affiliation(s)
- Priyanka Halder
- Department of Chemistry, Bose Institute, Kolkata, West Bengal, India
| | - Ranjeet Kumar
- Department of Chemistry, Bose Institute, Kolkata, West Bengal, India
| | - Kuladip Jana
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | | | - Zhumur Ghosh
- Bioinformatics Centre, Bose Institute, Kolkata, West Bengal, India
| | - Manikuntala Kundu
- Department of Chemistry, Bose Institute, Kolkata, West Bengal, India
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, West Bengal, India
| |
Collapse
|
14
|
Jarosova M, Kriegova E, Schneiderova P, Fillerova R, Prochazka V, Mikesova M, Flodr P, Indrak K, Papajik T. A Novel Non-Immunoglobulin (non-Ig)/BCL6 Translocation in Diffuse Large B-Cell Lymphoma Involving Chromosome 10q11.21 Loci and Review on Clinical Consequences of BCL6 Rearrangements. Pathol Oncol Res 2015; 22:233-43. [DOI: 10.1007/s12253-015-9972-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/19/2015] [Indexed: 11/30/2022]
|
15
|
Walkup WG, Washburn L, Sweredoski MJ, Carlisle HJ, Graham RL, Hess S, Kennedy MB. Phosphorylation of synaptic GTPase-activating protein (synGAP) by Ca2+/calmodulin-dependent protein kinase II (CaMKII) and cyclin-dependent kinase 5 (CDK5) alters the ratio of its GAP activity toward Ras and Rap GTPases. J Biol Chem 2014; 290:4908-4927. [PMID: 25533468 DOI: 10.1074/jbc.m114.614420] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
synGAP is a neuron-specific Ras and Rap GTPase-activating protein (GAP) found in high concentrations in the postsynaptic density (PSD) fraction from the mammalian forebrain. We have previously shown that, in situ in the PSD fraction or in recombinant form in Sf9 cell membranes, synGAP is phosphorylated by Ca(2+)/calmodulin-dependent protein kinase II (CaMKII), another prominent component of the PSD. Here, we show that recombinant synGAP (r-synGAP), lacking 102 residues at the N terminus, can be purified in soluble form and is phosphorylated by cyclin-dependent kinase 5 (CDK5) as well as by CaMKII. Phosphorylation of r-synGAP by CaMKII increases its HRas GAP activity by 25% and its Rap1 GAP activity by 76%. Conversely, phosphorylation by CDK5 increases r-synGAP's HRas GAP activity by 98% and its Rap1 GAP activity by 20%. Thus, phosphorylation by both kinases increases synGAP activity; CaMKII shifts the relative GAP activity toward inactivation of Rap1, and CDK5 shifts the relative activity toward inactivation of HRas. GAP activity toward Rap2 is not altered by phosphorylation by either kinase. CDK5 phosphorylates synGAP primarily at two sites, Ser-773 and Ser-802. Phosphorylation at Ser-773 inhibits r-synGAP activity, and phosphorylation at Ser-802 increases it. However, the net effect of concurrent phosphorylation of both sites, Ser-773 and Ser-802, is an increase in GAP activity. synGAP is phosphorylated at Ser-773 and Ser-802 in the PSD fraction, and its phosphorylation by CDK5 and CaMKII is differentially regulated by activation of NMDA-type glutamate receptors in cultured neurons.
Collapse
Affiliation(s)
| | | | - Michael J Sweredoski
- Proteome Exploration Laboratory of the Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | | | - Robert L Graham
- Proteome Exploration Laboratory of the Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Sonja Hess
- Proteome Exploration Laboratory of the Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | | |
Collapse
|
16
|
Gasper R, Sot B, Wittinghofer A. GTPase activity of Di-Ras proteins is stimulated by Rap1GAP proteins. Small GTPases 2014; 1:133-141. [PMID: 21686267 DOI: 10.4161/sgtp.1.3.14742] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 01/06/2011] [Accepted: 01/06/2011] [Indexed: 11/19/2022] Open
Abstract
The Ras family is the largest and most diverse sub-group of Ras-like G proteins. This complexity is further increased by the high number of regulatory Guanine nucleotide Exchange Factors (GEFs) and GTPase Activating Proteins (GAPs) that target specific members of this subfamily. Di-Ras1 and Di-Ras2 are little characterized members of the Ras-like sub-group with still unidentified regulatory and effector proteins. Here we determined the nucleotide binding properties of Di-Ras1/Di-Ras2. The above nanomolar affinity and the inability to react with members of the Cdc25 RasGEF family might suggest that activation does not require a GEF. We identified Rap1GAP1 and Rap1GAP2 as specific GTPase activating proteins of the Di-Ras family. Dual-specificity GAPs of the GAP1(m) family could not activate Di-Ras proteins, despite the presence of the required catalytic residue. Although Di-Ras proteins share GAPs with Rap G proteins, no common effectors could be identified in vitro.
Collapse
Affiliation(s)
- Raphael Gasper
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Strukturelle Biologie; Dortmund, Germany
| | | | | |
Collapse
|
17
|
Telkoparan P, Erkek S, Yaman E, Alotaibi H, Bayık D, Tazebay UH. Coiled-coil domain containing protein 124 is a novel centrosome and midbody protein that interacts with the Ras-guanine nucleotide exchange factor 1B and is involved in cytokinesis. PLoS One 2013; 8:e69289. [PMID: 23894443 PMCID: PMC3716640 DOI: 10.1371/journal.pone.0069289] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 06/06/2013] [Indexed: 01/11/2023] Open
Abstract
Cytokinetic abscission is the cellular process leading to physical separation of two postmitotic sister cells by severing the intercellular bridge. The most noticeable structural component of the intercellular bridge is a transient organelle termed as midbody, localized at a central region marking the site of abscission. Despite its major role in completion of cytokinesis, our understanding of spatiotemporal regulation of midbody assembly is limited. Here, we report the first characterization of coiled-coil domain-containing protein-124 (Ccdc124), a eukaryotic protein conserved from fungi-to-man, which we identified as a novel centrosomal and midbody protein. Knockdown of Ccdc124 in human HeLa cells leads to accumulation of enlarged and multinucleated cells; however, centrosome maturation was not affected. We found that Ccdc124 interacts with the Ras-guanine nucleotide exchange factor 1B (RasGEF1B), establishing a functional link between cytokinesis and activation of localized Rap2 signaling at the midbody. Our data indicate that Ccdc124 is a novel factor operating both for proper progression of late cytokinetic stages in eukaryotes, and for establishment of Rap2 signaling dependent cellular functions proximal to the abscission site.
Collapse
Affiliation(s)
- Pelin Telkoparan
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
| | - Serap Erkek
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
| | - Elif Yaman
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
| | - Hani Alotaibi
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
| | - Defne Bayık
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
| | - Uygar H. Tazebay
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
- Department of Molecular Biology and Genetics, Gebze Institute of Technology, Kocaeli, Turkey
- * E-mail:
| |
Collapse
|
18
|
Pannekoek WJ, Linnemann JR, Brouwer PM, Bos JL, Rehmann H. Rap1 and Rap2 antagonistically control endothelial barrier resistance. PLoS One 2013; 8:e57903. [PMID: 23469100 PMCID: PMC3585282 DOI: 10.1371/journal.pone.0057903] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 01/30/2013] [Indexed: 11/19/2022] Open
Abstract
Rap1 and Rap2 are closely related proteins of the Ras family of small G-proteins. Rap1 is well known to regulate cell-cell adhesion. Here, we have analysed the effect of Rap-mediated signalling on endothelial permeability using electrical impedance measurements of HUVEC monolayers and subsequent determination of the barrier resistance, which is a measure for the ease with which ions can pass cell junctions. In line with its well-established effect on cell-cell junctions, depletion of Rap1 decreases, whereas activation of Rap1 increases barrier resistance. Despite its high sequence homology with Rap1, depletion of Rap2 has an opposite, enhancing, effect on barrier resistance. This effect can be mimicked by depletion of the Rap2 specific activator RasGEF1C and the Rap2 effector MAP4K4, establishing Rap2 signalling as an independent pathway controlling barrier resistance. As simultaneous depletion or activation of both Rap1 and Rap2 results in a barrier resistance comparable to control cells, Rap1 and Rap2 control barrier resistance in a reciprocal manner. This Rap1-antagonizing effect of Rap2 is established independent of junctional actin formation. These data establish that endothelial barrier resistance is determined by the combined antagonistic actions of Rap1 and Rap2.
Collapse
Affiliation(s)
- Willem-Jan Pannekoek
- Molecular Cancer Research, Centre of Biomedical Genetics and Cancer Genomics Centre, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jelena R. Linnemann
- Molecular Cancer Research, Centre of Biomedical Genetics and Cancer Genomics Centre, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Patricia M. Brouwer
- Molecular Cancer Research, Centre of Biomedical Genetics and Cancer Genomics Centre, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johannes L. Bos
- Molecular Cancer Research, Centre of Biomedical Genetics and Cancer Genomics Centre, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Holger Rehmann
- Molecular Cancer Research, Centre of Biomedical Genetics and Cancer Genomics Centre, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
| |
Collapse
|
19
|
Fernández RM, Bleda M, Núñez-Torres R, Medina I, Luzón-Toro B, García-Alonso L, Torroglosa A, Marbà M, Enguix-Riego MV, Montaner D, Antiñolo G, Dopazo J, Borrego S. Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung's disease. Orphanet J Rare Dis 2012; 7:103. [PMID: 23270508 PMCID: PMC3575329 DOI: 10.1186/1750-1172-7-103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 12/19/2012] [Indexed: 12/23/2022] Open
Abstract
Finding gene associations in rare diseases is frequently hampered by the reduced numbers of patients accessible. Conventional gene-based association tests rely on the availability of large cohorts, which constitutes a serious limitation for its application in this scenario. To overcome this problem we have used here a combined strategy in which a pathway-based analysis (PBA) has been initially conducted to prioritize candidate genes in a Spanish cohort of 53 trios of short-segment Hirschsprung’s disease. Candidate genes have been further validated in an independent population of 106 trios. The study revealed a strong association of 11 gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other HSCR-related processes. Among the preselected candidates, a total of 4 loci, RASGEF1A, IQGAP2, DLC1 and CHRNA7, related to signal transduction and migration processes, were found to be significantly associated to HSCR. Network analysis also confirms their involvement in the network of already known disease genes. This approach, based on the study of functionally-related gene sets, requires of lower sample sizes and opens new opportunities for the study of rare diseases.
Collapse
Affiliation(s)
- Raquel Ma Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Friocourt G, Parnavelas JG. Identification of Arx targets unveils new candidates for controlling cortical interneuron migration and differentiation. Front Cell Neurosci 2011; 5:28. [PMID: 22355284 PMCID: PMC3280452 DOI: 10.3389/fncel.2011.00028] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/08/2011] [Indexed: 11/13/2022] Open
Abstract
Mutations in the homeobox transcription factor ARX have been found to be responsible for a wide spectrum of disorders extending from phenotypes with severe neuronal migration defects, such as lissencephaly, to mild forms of intellectual disabilities without apparent brain abnormalities, but with associated features of dystonia and epilepsy. Arx expression is mainly restricted to populations of GABA-containing neurons. Studies of the effects of ARX loss of function, either in humans or mutant mice, revealed varying defects, suggesting multiple roles of this gene in brain patterning, neuronal proliferation and migration, cell maturation and differentiation, as well as axonal outgrowth and connectivity. However, to date, little is known about how Arx functions as a transcription factor or which genes it binds and regulates. Recently, we combined chromatin immunoprecipitation and mRNA expression with microarray analysis and identified approximately 1000 gene promoters bound by Arx in transfected neuroblastoma N2a cells and mouse embryonic brain. To narrow the analysis of Arx targets to those most likely to control cortical interneuron migration and/or differentiation, we compare here our data to previously published studies searching for genes enriched or down-regulated in cortical interneurons between E13.5 and E15.5. We thus identified 14 Arx-target genes enriched (Cxcr7, Meis1, Ppap2a, Slc 12a5, Ets2, Phlda1, Egr1, Igf1, Lmo3, Sema6, Lgi1, Alk, Tgfb3, and Napb) and 5 genes specifically down-regulated (Hmgn3, Lmo1, Ebf3, Rasgef1b, and Slit2) in cortical migrating neurons. In this review, we present these genes and discuss how their possible regulation by Arx may lead to the dysfunction of GABAergic neurons, resulting in mental retardation and epilepsy.
Collapse
Affiliation(s)
- Gaëlle Friocourt
- Laboratory of Molecular Genetics and Histocompatibility Inserm U613, Brest, France
| | | |
Collapse
|
21
|
Huang M, Anand S, Murphy EA, Desgrosellier JS, Stupack DG, Shattil SJ, Schlaepfer DD, Cheresh DA. EGFR-dependent pancreatic carcinoma cell metastasis through Rap1 activation. Oncogene 2011; 31:2783-93. [PMID: 21963850 PMCID: PMC3711644 DOI: 10.1038/onc.2011.450] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Tyrosine kinase receptors play an essential role in various aspects of tumor progression. In particular, epidermal growth factor receptor (EGFR) and its ligands have been implicated in the growth and dissemination of a wide array of human carcinomas. Here, we describe an EGFR-mediated signaling pathway that regulates human pancreatic carcinoma cell invasion and metastasis, yet does not influence the growth of primary tumors. In fact, ligation/activation of EGFR induces Src-dependent phosphorylation of two critical tyrosine residues of p130CAS, leading to assembly of a CAS/Nck1 complex that promotes Rap1 signaling. Importantly, GTP loading of Rap1 is specifically required for pancreatic carcinoma cell migration on vitronectin, but not on collagen. Furthermore, Rap1 activation is required for EGFR-mediated metastasis in vivo without impacting primary tumor growth. These findings identify a molecular pathway that promotes the invasive/metastatic properties of human pancreatic carcinomas driven by EGFR.
Collapse
Affiliation(s)
- M Huang
- Department of Pathology, Moores University of California San Diego Cancer Center, La Jolla, CA 92093-1503, USA
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Gloerich M, Bos JL. Regulating Rap small G-proteins in time and space. Trends Cell Biol 2011; 21:615-23. [PMID: 21820312 DOI: 10.1016/j.tcb.2011.07.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 06/29/2011] [Accepted: 07/05/2011] [Indexed: 11/25/2022]
Abstract
Signaling by the small G-protein Rap is under tight regulation by its GEFs and GAPs. These are multi-domain proteins that are themselves controlled by distinct upstream pathways, and thus couple different extra- and intracellular cues to Rap. The individual RapGEFs and RapGAPs are, in addition, targeted to specific cellular locations by numerous anchoring mechanisms and, consequently, may control different pools of Rap. Here, we review the various activating signals and targeting mechanisms of these proteins and discuss their contribution to the spatiotemporal regulation and biological functions of the Rap proteins.
Collapse
Affiliation(s)
- Martijn Gloerich
- Molecular Cancer Research, Centre for Biomedical Genetics and Cancer Genomics Centre, University Medical Center Utrecht, Utrecht, The Netherlands
| | | |
Collapse
|
23
|
Abstract
Small Rap guanosine-tri-phosphate (GTP)ases are crucially involved in many cellular processes, including cell proliferation, differentiation, survival, adhesion and movement. In line, it has been shown that Rap signalling is involved in various aspects of neuronal differentiation, like the establishment of neuronal polarity or axonal growth cone movement. Rap GTPases can be activated by a wide variety of external stimuli, and this is mediated by specific guanine nucleotide exchange factors (RapGEFs). Inactivation of RapGTP can be achieved with the aid of specific GTPase-activating proteins (RapGAPs). In the brain, the most prominent RapGAPs are Rap1GAP and those of the spine-associated RapGAP (SPAR) family. This latter family consists of three members (SPAR1-3), from which two of them, namely SPAR1 and 2, have been investigated in more detail. As such, the localization of RapGAPs is crucially important in regulating Rap signalling at various sites in the cell and, for both SPAR1 and 2, enrichment at synaptic sites has been demonstrated. In recent years particularly the role of SPAR1 in shaping dendritic spine morphology has attracted considerable interest. In this review we will summarize the described actions of different RapGAPs expressed in the brain, and we will focus in particular on the SPAR family members.
Collapse
Affiliation(s)
- Christina Spilker
- Project Group Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | | |
Collapse
|
24
|
Andrade WA, Silva AM, Alves VS, Salgado APC, Melo MB, Andrade HM, Dall'Orto FV, Garcia SA, Silveira TN, Gazzinelli RT. Early endosome localization and activity of RasGEF1b, a toll-like receptor-inducible Ras guanine-nucleotide exchange factor. Genes Immun 2010; 11:447-57. [PMID: 20090772 DOI: 10.1038/gene.2009.107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Guanine-nucleotide exchange factors (GEFs) stimulate the intrinsic GDP/GTP exchange activity of Ras and promote the formation of active Ras-GTP, which in turn controls diverse signalling networks important for the regulation of cell proliferation, survival, differentiation, vesicular trafficking, and gene expression. RasGEF1b is a GEF, whose expression is induced in macrophages on stimulation with toll-like receptor (TLR) agonists. Here, we showed that in vitro RasGEF1b expression by macrophages is mostly induced by TLR3 (poly I:C) and TLR4 (lipopolysaccharyde) through the MyD88-independent pathway. In vivo infection with the protozoan parasites Trypanosoma cruzi and Plasmodium chabaudi induced RasGEF1b in an MyD88-, TRIF-, and IFN-gamma-dependent manner. Ectopically expressed RasGEF1b was found, mostly, in the heavy membrane fraction of HEK 293T, and by confocal microscopy, it was found to be located at early endosomes. Computational modelling of the RasGEF1b-Ras interaction revealed that RasGEF1b interacts with the binding domain site of Ras, a critical region for interacting with GEFs involved in the activation of Ras-Raf-MEK-ERK pathway. More important, RasGEF1b was found to be closely associated with Ras in live cells and to trigger Ras activity. Altogether, these results indicate that on TLR activation, RasGEF1b may trigger Ras-like proteins and regulate specific biological activities described for this subtype of GTPases.
Collapse
Affiliation(s)
- W A Andrade
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | | | | | | | | | | | | |
Collapse
|