1
|
Wang X, Huang X, Yang Q, Yan Z, Wang P, Gao X, Luo R, Gun S. TMT labeled comparative proteomic analysis reveals spleen active immune responses during Clostridium perfringens type C infected piglet diarrhea. PeerJ 2022; 10:e13006. [PMID: 35402105 PMCID: PMC8988937 DOI: 10.7717/peerj.13006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/03/2022] [Indexed: 01/11/2023] Open
Abstract
Background Clostridium perfringens (C. perfringens) type C is the principal pathogenic clostridia of swine, frequently causing hemorrhagic diarrhea, even necrotic enteritis in piglets, leading to severe economic loss for swine industr ies worldwide. However, there are no specific and effective prevention measures. Therefore, clarifying the molecular mechanisms of hosts against pathogenesis infection is very important to reduce the incidence of C. perfringens type C infected piglet diarrhea disease. Methods We performed an TMT labeling-based quantitative spleen proteomic analysis of the control group (SC), tolerance group (SR) and susceptible group (SS) to identify the differentially expressed proteins (DEPs), and screened potential molecular markers of piglet spleen tissues in response to C. perfringens type C infection. Results In this study, a total of 115, 176 and 83 DEPs were identified in SR vs SC, SS vs SC, and SR vs SC, respectively, which may play the important regulatory roles in the process of piglet spleens in response toC. perfringens type C-infected diarrhea diseases. GO enrichment analysis revealed that the DEPs were mostly significantly enriched in acute inflammatory response, defense response, antimicrobial response, transporter activity, cellular metabolic process and so on, and KEGG pathway enrichment analysis showed that the significantly enriched immune related pathways of the PPAR signaling pathway, IL-17 signaling pathway, antigen processing and presentation, which hints at the immune defense process of piglet spleen against C. perfringens infection. This study helps to elucidate the protein expressional pattern of piglet spleen against C. perfringens type C-infected diarrhea disease, which can contribute to the prevention and control for pig diarrhea disease and the further development of diarrhea resistant pig breeding.
Collapse
Affiliation(s)
- Xiaoli Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China,Guizhou Institute of Prataculture, Guizhou Academy of Agriculture Science, Guiyang, China
| | - Xiaoyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Qiaoli Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiaoli Gao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Ruirui Luo
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China,Gansu Research Center for Swine Production Engineering and Technology, Lanzhou, Gansu, China
| |
Collapse
|
2
|
Huang X, Yang Q, Yan Z, Wang P, Shi H, Li J, Shang X, Gun S. Combined Analysis of RRBS DNA Methylome and Transcriptome Reveal Novel Candidate Genes Related to Porcine Clostridium perfringens Type C-Induced Diarrhea. Front Genet 2022; 13:803477. [PMID: 35401691 PMCID: PMC8990837 DOI: 10.3389/fgene.2022.803477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/24/2022] [Indexed: 11/29/2022] Open
Abstract
Clostridium perfringens type C (Cp) is one of the principal microorganisms responsible for bacterial diarrhea in neonatal and pre-weaning piglets. To better understand the molecular effects of Cp infection, we performed a genome-wide comparison of the changes in DNA methylation and gene expression in Cp infected resistant and susceptible piglets. We characterized the pattern of changes in methylation and found 6485, 5968, and 6472 differentially methylated regions (DMRs) of piglets infected with Cp in IR vs. IC, IS vs. IC, and IS vs. IR groups, respectively. These methylation changes for genes mainly involved in immune and inflammatory responses, cell adhesion, and activation of transcription factors. Gene ontology and KEGG pathway analyses showed that the differentially methylated genes (DMGs) were associated with negative regulation of transcription, apoptotic processes, protein binding, and kinase activity. In addition, they were enriched in immunity-related pathways, such as MAPK signaling pathway, Toll-like receptor signaling pathway, and NF-kappa B signaling pathway. Integrative analysis identified 168, 198, and 7 mRNAs showing inverse correlations between methylation and expression with Cp infection. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions upon Cp infection, 14 immune-associated mRNAs with differential methylation and transcriptional repression were identified in IS vs. IR, commonly revealing that the differentially expressed genes (DEGs) LBP, TBX21, and LCN2 were likely involved in the piglets against Cp infection. The present results provide further insight into the DNA methylation epigenetic alterations of C. perfringens type C infected piglet ileum tissues, and may advance the identification of biomarkers and drug targets for predicting susceptibility to and controlling C. perfringens type C-induced piglet diarrhea.
Collapse
Affiliation(s)
- Xiaoyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qiaoli Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Hairen Shi
- Tibet Academy of Agricultural and Animal Husbandry Science, Lasa, China
| | - Jie Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xuefeng Shang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Research Center for Swine Production Engineering and Technology, Lanzhou, China
- *Correspondence: Shuangbao Gun,
| |
Collapse
|
3
|
Liu G, Luo S, Lei Y, Wu J, Huang Z, Wang K, Yang P, Huang X. A nine-hub-gene signature of metabolic syndrome identified using machine learning algorithms and integrated bioinformatics. Bioengineered 2021; 12:5727-5738. [PMID: 34516309 PMCID: PMC8806918 DOI: 10.1080/21655979.2021.1968249] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
Early risk assessments and interventions for metabolic syndrome (MetS) are limited because of a lack of effective biomarkers. In the present study, several candidate genes were selected as a blood-based transcriptomic signature for MetS. We collected so far the largest MetS-associated peripheral blood high-throughput transcriptomics data and put forward a novel feature selection strategy by combining weighted gene co-expression network analysis, protein-protein interaction network analysis, LASSO regression and random forest approaches. Two gene modules and 51 hub genes as well as a 9-hub-gene signature associated with metabolic syndrome were identified. Then, based on this 9-hub-gene signature, we performed logistic analysis and subsequently established a web nomogram calculator for metabolic syndrome risk (https://xjtulgz.shinyapps.io/DynNomapp/). This 9-hub-gene signature showed excellent classification and calibration performance (AUC = 0.968 in training set, AUC = 0.883 in internal validation set, AUC = 0.861 in external validation set) as well as ideal potential clinical benefit.
Collapse
Affiliation(s)
- Guanzhi Liu
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Sen Luo
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yutian Lei
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jianhua Wu
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Zhuo Huang
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Kunzheng Wang
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Pei Yang
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xin Huang
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| |
Collapse
|
4
|
Pan YH, Chen J, Sun C, Ma JF, Li X. Effect of Ras-guanine nucleotide release factor 1-mediated H-Ras/ERK signaling pathway on glioma. Brain Res 2021; 1754:147247. [PMID: 33412149 DOI: 10.1016/j.brainres.2020.147247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/29/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To investigate the function of Ras-guanine nucleotide release factor 1 (Ras-GRF1) in glioma through mediating H-Ras/ERK signaling pathway. METHODS Ras-GRF1, H-Ras, K-Ras and N-Ras expressions in glioma and normal brain tissues were detected via Immunohistochemistry. Glioma cells (U87 cells, U251 cells and primary human glioma cells) were transfected with Ras-GRF1 siRNA, H-Ras siRNA and/or Ras-GRF1 lentivirus activation particles. Then, the following aspects were evaluated: cell proliferation by MTT assay, clonogenic ability by the plate clone formation experiment, cell migration and invasion by Wound-healing and Transwell assays, and cell apoptosis by Annexin-V-FITC/PI staining. The protein expressions were measured by Western blotting. Subcutaneous and orthotopic mouse models of glioma were conducted to determine the role of Ras-GRF1 in glioma tumorigenesis. RESULTS Ras-GRF1, H-Ras, K-Ras and N-Ras expressions were upregulated in the glioma tissues, which were correlated with the WHO grade of glioma. Besides, Ras-GRF1 expression was positively related to H-Ras expression. Ras-GRF1 siRNA could reduce the expression of H-Ras and p-ERK/ERK in glioma cell. H-Ras siRNA inhibited the proliferation, clone formation, migration and invasion, and enhance the apoptosis of glioma cells, which, however, were reversed by Ras-GRF1 lentivirus activation particles. In vivo experiments also revealed that Ras-GRF1 shRNA reduced the volume and weight of the tumors in the nude mice, with down-regulations of H-Ras and p-ERK/ERK. CONCLUSION Ras-GRF1 was upregulated in glioma tissues and correlated with its malignancy and prognosis. Silencing Ras-GRF1, through mediating H-Ras/ERK pathway, may suppress the growth and metastasis of glioma.
Collapse
Affiliation(s)
- Yi-Heng Pan
- Center for Diagnosis and Treatment of Neuro-oncology Diseases, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jing Chen
- Center for Diagnosis and Treatment of Neuro-oncology Diseases, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Cui Sun
- Center for Diagnosis and Treatment of Neuro-oncology Diseases, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Ji-Fen Ma
- Center for Diagnosis and Treatment of Neuro-oncology Diseases, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Xia Li
- Center for Diagnosis and Treatment of Neuro-oncology Diseases, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China.
| |
Collapse
|
5
|
Lu Y, Li Y, Li G, Lu H. Identification of potential markers for type 2 diabetes mellitus via bioinformatics analysis. Mol Med Rep 2020; 22:1868-1882. [PMID: 32705173 PMCID: PMC7411335 DOI: 10.3892/mmr.2020.11281] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a multifactorial and multigenetic disease, and its pathogenesis is complex and largely unknown. In the present study, microarray data (GSE201966) of β-cell enriched tissue obtained by laser capture microdissection were downloaded, including 10 control and 10 type 2 diabetic subjects. A comprehensive bioinformatics analysis of microarray data in the context of protein-protein interaction (PPI) networks was employed, combined with subcellular location information to mine the potential candidate genes for T2DM and provide further insight on the possible mechanisms involved. First, differential analysis screened 108 differentially expressed genes. Then, 83 candidate genes were identified in the layered network in the context of PPI via network analysis, which were either directly or indirectly linked to T2DM. Of those genes obtained through literature retrieval analysis, 27 of 83 were involved with the development of T2DM; however, the rest of the 56 genes need to be verified by experiments. The functional analysis of candidate genes involved in a number of biological activities, demonstrated that 46 upregulated candidate genes were involved in ‘inflammatory response’ and ‘lipid metabolic process’, and 37 downregulated candidate genes were involved in ‘positive regulation of cell death’ and ‘positive regulation of cell proliferation’. These candidate genes were also involved in different signaling pathways associated with ‘PI3K/Akt signaling pathway’, ‘Rap1 signaling pathway’, ‘Ras signaling pathway’ and ‘MAPK signaling pathway’, which are highly associated with the development of T2DM. Furthermore, a microRNA (miR)-target gene regulatory network and a transcription factor-target gene regulatory network were constructed based on miRNet and NetworkAnalyst databases, respectively. Notably, hsa-miR-192-5p, hsa-miR-124-5p and hsa-miR-335-5p appeared to be involved in T2DM by potentially regulating the expression of various candidate genes, including procollagen C-endopeptidase enhancer 2, connective tissue growth factor and family with sequence similarity 105, member A, protein phosphatase 1 regulatory inhibitor subunit 1 A and C-C motif chemokine receptor 4. Smad5 and Bcl6, as transcription factors, are regulated by ankyrin repeat domain 23 and transmembrane protein 37, respectively, which might also be used in the molecular diagnosis and targeted therapy of T2DM. Taken together, the results of the present study may offer insight for future genomic-based individualized treatment of T2DM and help determine the underlying molecular mechanisms that lead to T2DM.
Collapse
Affiliation(s)
- Yana Lu
- Key Laboratory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong, Yunnan 666100, P.R. China
| | - Yihang Li
- Key Laboratory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong, Yunnan 666100, P.R. China
| | - Guang Li
- Key Laboratory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong, Yunnan 666100, P.R. China
| | - Haitao Lu
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| |
Collapse
|
6
|
Wang W, Zhou C, Tang H, Yu Y, Zhang Q. Combined Analysis of DNA Methylome and Transcriptome Reveal Novel Candidate Genes Related to Porcine Escherichia coli F4ab/ac-Induced Diarrhea. Front Cell Infect Microbiol 2020; 10:250. [PMID: 32547963 PMCID: PMC7272597 DOI: 10.3389/fcimb.2020.00250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/29/2020] [Indexed: 12/13/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) that express F4 (K88) fimbriae are the principal microorganisms responsible for bacterial diarrhea in neonatal and pre-weaning piglets. To better understand the molecular effects of ETEC F4ab/ac infection, we performed a genome-wide comparison of the changes in DNA methylation and gene expression in ETEC F4ab/ac infected porcine intestinal epithelial cells. We characterized the pattern of changes in methylation and found 3297 and 1593 differentially methylated regions in cells infected with F4ab and F4ac, respectively. Moreover, 606 and 780 differentially expressed genes (DEGs) in ETEC F4ab and F4ac infected cells were detected and these genes were highly enriched in immune/defense response related pathways. Integrative analysis identified 27 and 10 genes showing inverse correlations between promoter methylation and expression with ETEC F4ab/ac infection. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions upon ETEC F4ab/ac infection. Further functional analyses revealed that three DEGs (S100A9, SGO1, and ESPL1) in F4ab infected cells and three DEGs (MAP3K21, PAK6, and MPZL1) in F4ac infected cells are likely involved in the host cells response to ETEC infection. Our data provides further insight into the epigenetic and transcriptomic alterations of ETEC F4ab/ac infected porcine intestinal epithelial cells, and may advance the identification of biomarkers and drug targets for predicting susceptibility to and controlling ETEC F4ab/ac induced diarrhea.
Collapse
Affiliation(s)
- Wenwen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Chuanli Zhou
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hui Tang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Ying Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
7
|
Manyes L, Holst S, Lozano M, Santos E, Fernandez-Medarde A. Spatial learning and long-term memory impairments in RasGrf1 KO, Pttg1 KO, and double KO mice. Brain Behav 2018; 8:e01089. [PMID: 30259712 PMCID: PMC6236249 DOI: 10.1002/brb3.1089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/12/2018] [Accepted: 07/01/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND RasGrf1 is a guanine-nucleotide releasing factor that enhances Ras activity. Human PTTG1 is an oncoprotein found in pituitary tumors and later identified as securin, a protein isolated from yeast with a reported role in chromosome separation. It has been suggested that RasGrf1 is an important upstream component of signal transduction pathways regulating Pttg1 expression and controlling beta cell development and their physiological response. At memory formation level, there are contradictory data regarding the role of RasGrf1, while Pttg1 has not been previously studied. Both proteins are expressed in the mammalian hippocampus, which is one of the key brain areas for spatial learning and memory. OBJECTIVE The aim of this work was to study a potential link between RasGrf1 and Pttg1 in memory formation. METHOD Spatial learning and memory test in the Pttg1 KO, RasGrf1 KO, and Pttg1-RasGrf1 double KO and their correspondent WT mice using a Barnes maze. RESULTS In comparison with the WT control mice, Pttg1 KO mice learned how to solve the task in a less efficient way, suggesting problems in memory consolidation. RasGrf1 KO mice performance was similar to controls, and they learned to use the best searching strategy. Double KO mice reached a better spatial learning level than WT. CONCLUSION A role for Pttg1 in memory consolidation/formation is suggested, while our RasGrf1 KO mice do not show hippocampus associated memory defects.
Collapse
Affiliation(s)
- Lara Manyes
- Lab 1, Cancer Research Center, CSIC-Universidad de Salamanca & CIBERONC, Salamanca, Spain.,Laboratory of Food Sciences and Toxicology, Faculty of Pharmacy, Universitat de València, València, Spain
| | - Sarah Holst
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Manuel Lozano
- Laboratory of Food Sciences and Toxicology, Faculty of Pharmacy, Universitat de València, València, Spain
| | - Eugenio Santos
- Lab 1, Cancer Research Center, CSIC-Universidad de Salamanca & CIBERONC, Salamanca, Spain
| | | |
Collapse
|
8
|
Gómez C, Jimeno D, Fernández-Medarde A, García-Navas R, Calzada N, Santos E. Ras-GRF2 regulates nestin-positive stem cell density and onset of differentiation during adult neurogenesis in the mouse dentate gyrus. Mol Cell Neurosci 2017; 85:127-147. [PMID: 28966131 DOI: 10.1016/j.mcn.2017.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/11/2017] [Accepted: 09/17/2017] [Indexed: 12/12/2022] Open
Abstract
Various parameters of neurogenesis were analyzed in parallel in the two neurogenic areas (the Dentate Gyrus[DG] and the Subventricular Zone[SVZ]/Rostral Migratory Stream[RMS]/Main Olfactory Bulb[MOB] neurogenic system) of adult WT and KO mouse strains for the Ras-GRF1/2 genes (Ras-GRF1-KO, Ras-GRF2-KO, Ras-GRF1/2-DKO). Significantly reduced numbers of doublecortin[DCX]-positive cells were specifically observed in the DG, but not the SVZ/RMS/MOB neurogenic region, of Ras-GRF2-KO and Ras-GRF1/2-DKO mice indicating that this novel Ras-GRF2-dependent phenotype is spatially restricted to a specific neurogenic area. Consistent with a role of CREB as mediator of Ras-GRF2 function in neurogenesis, the density of p-CREB-positive cells was also specifically reduced in all neurogenic regions of Ras-GRF2-KO and DKO mice. Similar levels of early neurogenic proliferation markers (Ki67, BrdU) were observed in all different Ras-GRF genotypes analyzed but significantly elevated levels of nestin-immunolabel, particularly of undifferentiated, highly ramified, A-type nestin-positive neurons were specifically detected in the DG but not the SVZ/RMS/MOB of Ras-GRF2-KO and DKO mice. Together with assays of other neurogenic markers (GFAP, Sox2, Tuj1, NeuN), these observations suggest that the deficit of DCX/p-CREB-positive cells in the DG of Ras-GRF2-depleted mice does not involve impaired neuronal proliferation but rather delayed transition from the stem cell stage to the differentiation stages of the neurogenic process. This model is also supported by functional analyses of DG-derived neurosphere cultures and transcriptional characterization of the neurogenic areas of mice of all relevant Ras-GRF genotypes suggesting that the neurogenic role of Ras-GRF2 is exerted in a cell-autonomous manner through a specific transcriptional program.
Collapse
Affiliation(s)
- Carmela Gómez
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC- Universidad de Salamanca) and CIBERONC, 37007 Salamanca, Spain
| | - David Jimeno
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC- Universidad de Salamanca) and CIBERONC, 37007 Salamanca, Spain
| | - Alberto Fernández-Medarde
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC- Universidad de Salamanca) and CIBERONC, 37007 Salamanca, Spain
| | - Rósula García-Navas
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC- Universidad de Salamanca) and CIBERONC, 37007 Salamanca, Spain
| | - Nuria Calzada
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC- Universidad de Salamanca) and CIBERONC, 37007 Salamanca, Spain
| | - Eugenio Santos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC- Universidad de Salamanca) and CIBERONC, 37007 Salamanca, Spain.
| |
Collapse
|
9
|
Singh V, Saluja N. Phylogenetic and promoter analysis of islet amyloid polypeptide gene causing type 2 diabetes in mammalian species. Int J Diabetes Dev Ctries 2016. [DOI: 10.1007/s13410-016-0508-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
10
|
Hanna CW, Peñaherrera MS, Saadeh H, Andrews S, McFadden DE, Kelsey G, Robinson WP. Pervasive polymorphic imprinted methylation in the human placenta. Genome Res 2016; 26:756-67. [PMID: 26769960 PMCID: PMC4889973 DOI: 10.1101/gr.196139.115] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/07/2016] [Indexed: 01/19/2023]
Abstract
The maternal and paternal copies of the genome are both required for mammalian development, and this is primarily due to imprinted genes, those that are monoallelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are established in the germline and maintained after fertilization. There are a large number of germline DMRs that have not yet been associated with imprinting, and their function in development is unknown. In this study, we developed a genome-wide approach to identify novel imprinted DMRs in the human placenta and investigated the dynamics of these imprinted DMRs during development in somatic and extraembryonic tissues. DNA methylation was evaluated using the Illumina HumanMethylation450 array in 134 human tissue samples, publicly available reduced representation bisulfite sequencing in the human embryo and germ cells, and targeted bisulfite sequencing in term placentas. Forty-three known and 101 novel imprinted DMRs were identified in the human placenta by comparing methylation between diandric and digynic triploid conceptions in addition to female and male gametes. Seventy-two novel DMRs showed a pattern consistent with placental-specific imprinting, and this monoallelic methylation was entirely maternal in origin. Strikingly, these DMRs exhibited polymorphic imprinted methylation between placental samples. These data suggest that imprinting in human development is far more extensive and dynamic than previously reported and that the placenta preferentially maintains maternal germline-derived DNA methylation.
Collapse
Affiliation(s)
- Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Maria S Peñaherrera
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada; Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Heba Saadeh
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Deborah E McFadden
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada; Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| |
Collapse
|
11
|
Jimeno D, Gómez C, Calzada N, de la Villa P, Lillo C, Santos E. RASGRF2 controls nuclear migration in postnatal retinal cone photoreceptors. J Cell Sci 2016; 129:729-42. [PMID: 26743081 DOI: 10.1242/jcs.180919] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/29/2015] [Indexed: 02/04/2023] Open
Abstract
Detailed immunocytochemical analyses comparing wild-type (WT), GRF1-knockout (KO), GRF2-KO and GRF1/2 double-knockout (DKO) mouse retinas uncovered the specific accumulation of misplaced, 'ectopic' cone photoreceptor nuclei in the photoreceptor segment (PS) area of retinas from GRF2-KO and GRF1/2-DKO, but not of WT or GRF1-KO mice. Localization of ectopic nuclei in the PS area of GRF2-depleted retinas occurred postnatally and peaked between postnatal day (P)11 and P15. Mechanistically, the generation of this phenotype involved disruption of the outer limiting membrane and intrusion into the PS layer by cone nuclei displaying significant perinuclear accumulation of signaling molecules known to participate in nuclear migration and cytoskeletal reorganization, such as PAR3, PAR6 and activated, phosphorylated forms of PAK, MLC2 and VASP. Electroretinographic recordings showed specific impairment of cone-mediated retinal function in GRF2-KO and GRF1/2-DKO retinas compared with WT controls. These data identify defective cone nuclear migration as a novel phenotype in mouse retinas lacking GRF2 and support a crucial role of GRF2 in control of the nuclear migration processes required for proper postnatal development and function of retinal cone photoreceptors.
Collapse
Affiliation(s)
- David Jimeno
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC - Universidad de Salamanca), Salamanca 37007, Spain
| | - Carmela Gómez
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC - Universidad de Salamanca), Salamanca 37007, Spain
| | - Nuria Calzada
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC - Universidad de Salamanca), Salamanca 37007, Spain
| | - Pedro de la Villa
- Departamento de Fisiología, Universidad Alcalá, Alcalá de Henares 28871, Spain, Spain
| | | | - Eugenio Santos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC - Universidad de Salamanca), Salamanca 37007, Spain
| |
Collapse
|