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Zhang G, Diamante G, Ahn IS, Palafox-Sanchez V, Cheng J, Cheng M, Ying Z, Wang SSM, Abuhanna KD, Phi N, Arneson D, Cely I, Arellano K, Wang N, Zhang S, Peng C, Gomez-Pinilla F, Yang X. Thyroid hormone T4 mitigates traumatic brain injury in mice by dynamically remodeling cell type specific genes, pathways, and networks in hippocampus and frontal cortex. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167344. [PMID: 39004380 DOI: 10.1016/j.bbadis.2024.167344] [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: 01/16/2024] [Revised: 05/30/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024]
Abstract
The complex pathology of mild traumatic brain injury (mTBI) is a main contributor to the difficulties in achieving a successful therapeutic regimen. Thyroxine (T4) administration has been shown to prevent the cognitive impairments induced by mTBI in mice but the mechanism is poorly understood. To understand the underlying mechanism, we carried out a single cell transcriptomic study to investigate the spatiotemporal effects of T4 on individual cell types in the hippocampus and frontal cortex at three post-injury stages in a mouse model of mTBI. We found that T4 treatment altered the proportions and transcriptomes of numerous cell types across tissues and timepoints, particularly oligodendrocytes, astrocytes, and microglia, which are crucial for injury repair. T4 also reversed the expression of mTBI-affected genes such as Ttr, mt-Rnr2, Ggn12, Malat1, Gnaq, and Myo3a, as well as numerous pathways such as cell/energy/iron metabolism, immune response, nervous system, and cytoskeleton-related pathways. Cell-type specific network modeling revealed that T4 mitigated select mTBI-perturbed dynamic shifts in subnetworks related to cell cycle, stress response, and RNA processing in oligodendrocytes. Cross cell-type ligand-receptor networks revealed the roles of App, Hmgb1, Fn1, and Tnf in mTBI, with the latter two ligands having been previously identified as TBI network hubs. mTBI and/or T4 signature genes were enriched for human genome-wide association study (GWAS) candidate genes for cognitive, psychiatric and neurodegenerative disorders related to mTBI. Our systems-level single cell analysis elucidated the temporal and spatial dynamic reprogramming of cell-type specific genes, pathways, and networks, as well as cell-cell communications as the mechanisms through which T4 mitigates cognitive dysfunction induced by mTBI.
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Affiliation(s)
- Guanglin Zhang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Graciel Diamante
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Victoria Palafox-Sanchez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jenny Cheng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Cheng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhe Ying
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Susanna Sue-Ming Wang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin Daniel Abuhanna
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Nguyen Phi
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas Arneson
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ingrid Cely
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kayla Arellano
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ning Wang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shujing Zhang
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chao Peng
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Brain Research Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Mary S. Easton Center for Alzheimer's Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Neurosurgery, University of California, Los Angeles, Los Angeles, CA 90095, USA; Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Brain Research Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Veraguas-Dávila D, Zapata-Rojas C, Aguilera C, Saéz-Ruiz D, Saravia F, Castro FO, Rodriguez-Alvarez L. Proteomic Analysis of Domestic Cat Blastocysts and Their Secretome Produced in an In Vitro Culture System without the Presence of the Zona Pellucida. Int J Mol Sci 2024; 25:4343. [PMID: 38673927 PMCID: PMC11050229 DOI: 10.3390/ijms25084343] [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: 03/23/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Domestic cat blastocysts cultured without the zona pellucida exhibit reduced implantation capacity. However, the protein expression profile has not been evaluated in these embryos. The objective of this study was to evaluate the protein expression profile of domestic cat blastocysts cultured without the zona pellucida. Two experimental groups were generated: (1) domestic cat embryos generated by IVF and cultured in vitro (zona intact, (ZI)) and (2) domestic cat embryos cultured in vitro without the zona pellucida (zona-free (ZF group)). The cleavage, morula, and blastocyst rates were estimated at days 2, 5 and 7, respectively. Day 7 blastocysts and their culture media were subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). The UniProt Felis catus database was used to identify the standard proteome. No significant differences were found in the cleavage, morula, or blastocyst rates between the ZI and ZF groups (p > 0.05). Proteomic analysis revealed 22 upregulated and 20 downregulated proteins in the ZF blastocysts. Furthermore, 14 proteins involved in embryo development and implantation were present exclusively in the culture medium of the ZI blastocysts. In conclusion, embryo culture without the zona pellucida did not affect in vitro development, but altered the protein expression profile and release of domestic cat blastocysts.
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Affiliation(s)
- Daniel Veraguas-Dávila
- Escuela de Medicina Veterinaria, Departamento de Ciencias Agrarias, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Km 6 Los Niches, Curicó 3340000, Chile
- Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Méndez 595, Chillan 3780000, Chile; (C.Z.-R.); (D.S.-R.); (F.S.); (F.O.C.); (L.R.-A.)
| | - Camila Zapata-Rojas
- Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Méndez 595, Chillan 3780000, Chile; (C.Z.-R.); (D.S.-R.); (F.S.); (F.O.C.); (L.R.-A.)
| | - Constanza Aguilera
- School of Veterinary Medicine, Faculty of Natural Sciences, San Sebastián University, Concepción 4081339, Chile;
| | - Darling Saéz-Ruiz
- Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Méndez 595, Chillan 3780000, Chile; (C.Z.-R.); (D.S.-R.); (F.S.); (F.O.C.); (L.R.-A.)
| | - Fernando Saravia
- Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Méndez 595, Chillan 3780000, Chile; (C.Z.-R.); (D.S.-R.); (F.S.); (F.O.C.); (L.R.-A.)
| | - Fidel Ovidio Castro
- Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Méndez 595, Chillan 3780000, Chile; (C.Z.-R.); (D.S.-R.); (F.S.); (F.O.C.); (L.R.-A.)
| | - Lleretny Rodriguez-Alvarez
- Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Méndez 595, Chillan 3780000, Chile; (C.Z.-R.); (D.S.-R.); (F.S.); (F.O.C.); (L.R.-A.)
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Edwards GA, Wood CA, Nguyen Q, Kim PJ, Gomez-Gutierrez R, Park KW, Zurhellen C, Al-Ramahi I, Jankowsky JL. TMEM106B coding variant is protective and deletion detrimental in a mouse model of tauopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533978. [PMID: 36993574 PMCID: PMC10055407 DOI: 10.1101/2023.03.23.533978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
TMEM106B is a risk modifier for a growing list of age-associated dementias including Alzheimer’s and frontotemporal dementia, yet its function remains elusive. Two key questions that emerge from past work are whether the conservative T185S coding variant found in the minor haplotype contributes to protection, and whether the presence of TMEM106B is helpful or harmful in the context of disease. Here we address both issues while extending the testbed for study of TMEM106B from models of TDP to tauopathy. We show that TMEM106B deletion accelerates cognitive decline, hindlimb paralysis, neuropathology, and neurodegeneration. TMEM106B deletion also increases transcriptional overlap with human AD, making it a better model of disease than tau alone. In contrast, the coding variant protects against tau-associated cognitive decline, neurodegeneration, and paralysis without affecting tau pathology. Our findings show that the coding variant contributes to neuroprotection and suggest that TMEM106B is a critical safeguard against tau aggregation.
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Liu R, Liu Z, Zhao Y, Cheng X, Liu B, Wang Y, Wang J, Lian X, Zhu Y, Gao Y. GNG12 as A Novel Molecular Marker for the Diagnosis and Treatment of Glioma. Front Oncol 2022; 12:726556. [PMID: 35928884 PMCID: PMC9345608 DOI: 10.3389/fonc.2022.726556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
PurposeGNG12 influences a variety of tumors; however, its relationship with glioma remains unclear. The aim of this study was to comprehensively investigate the relationship between GNG12 and the clinical characteristics and prognosis of glioma patients and reveal the mechanisms causing the malignant process of GNG12.Materials and MethodsWe obtained information on clinical samples from multiple databases. The expression level of GNG12 was validated using a RT-qPCR and IHC. KM curves were used to assess the correlation between the GNG12 expression and OS of glioma patients. An ROC curve was drawn to assess the predictive performance of GNG12. Univariate and multivariate Cox analyses were performed to analyze the factors affecting the prognosis of patients with glioma. GSEA and TIMER databases were used to estimate the relationship between GNG12 expression, possible molecular mechanisms, and immune cell infiltration. CMap analysis was used to screen candidate drugs for glioma. Subsequent in vitro experiments were used to validate the proliferation and migration of glioma cells and to explore the potential mechanisms by which GNG12 causes poor prognosis in gliomas.ResultsGNG12 was overexpressed in glioma patients and GNG12 expression level correlated closely with clinical features, including age and histological type, etc. Subsequently, the K-M survival analysis indicated that the expression level of GNG12 was relevant to the prognosis of glioma, and the ROC curve implied that GNG12 can predict glioma stability. Univariate and multivariate analyses showed that GNG12 represents a risk factor for glioma occurrence. GNG12 expression is closely associated with some immune cells. Additionally, several in vitro experiments demonstrated that down-regulation of GNG12 expression can inhibits the proliferation and migration capacity of glioma cells. Ultimately, the results for the GSEA and WB experiments revealed that GNG12 may promote the malignant progression of gliomas by regulating the cell adhesion molecule cell signaling pathway.ConclusionIn this study, we identified GNG12 as a novel oncogene elevated in gliomas. Reducing GNG12 expression inhibits the proliferation and migration of glioma cells. In summary, GNG12 can be used as a novel biomarker for the early diagnosis of human gliomas and as a potential therapeutic target.
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Affiliation(s)
- Runze Liu
- Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan International Joint Laboratory of Intelligentized Orthopedics Innovation and Transformation, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Yaoye Zhao
- Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Xingbo Cheng
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan International Joint Laboratory of Intelligentized Orthopedics Innovation and Transformation, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Binfeng Liu
- Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Yanbiao Wang
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan International Joint Laboratory of Intelligentized Orthopedics Innovation and Transformation, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Jialin Wang
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan International Joint Laboratory of Intelligentized Orthopedics Innovation and Transformation, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Xiaoyu Lian
- Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Yongjie Zhu
- Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Yanzheng Gao
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, Henan International Joint Laboratory of Intelligentized Orthopedics Innovation and Transformation, Henan Key Laboratory for Intelligent Precision Orthopedics, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
- *Correspondence: Yanzheng Gao,
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Mazzolini J, Le Clerc S, Morisse G, Coulonges C, Zagury J, Sieger D. Wasl is crucial to maintain microglial core activities during glioblastoma initiation stages. Glia 2022; 70:1027-1051. [PMID: 35194846 PMCID: PMC9306864 DOI: 10.1002/glia.24154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/28/2022]
Abstract
Microglia actively promotes the growth of high-grade gliomas. Within the glioma microenvironment an amoeboid microglial morphology has been observed, however the underlying causes and the related impact on microglia functions and their tumor promoting activities is unclear. Using the advantages of the larval zebrafish model, we identified the underlying mechanism and show that microglial morphology and functions are already impaired during glioma initiation stages. The presence of pre-neoplastic HRasV12 expressing cells induces an amoeboid morphology of microglia, increases microglial numbers and decreases their motility and phagocytic activity. RNA sequencing analysis revealed lower expression levels of the actin nucleation promoting factor wasla in microglia. Importantly, a microglia specific rescue of wasla expression restores microglial morphology and functions. This results in increased phagocytosis of pre-neoplastic cells and slows down tumor progression. In conclusion, we identified a mechanism that de-activates core microglial functions within the emerging glioma microenvironment. Restoration of this mechanism might provide a way to impair glioma growth.
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Affiliation(s)
- Julie Mazzolini
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
| | - Sigrid Le Clerc
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et MétiersHESAM UniversitéParisFrance
| | - Gregoire Morisse
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
| | - Cédric Coulonges
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et MétiersHESAM UniversitéParisFrance
| | - Jean‐François Zagury
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et MétiersHESAM UniversitéParisFrance
| | - Dirk Sieger
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
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Checkpoints and Immunity in Cancers: Role of GNG12. Pharmacol Res 2022; 180:106242. [DOI: 10.1016/j.phrs.2022.106242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
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Identification of Novel Key Genes and Pathways in Multiple Sclerosis Based on Weighted Gene Coexpression Network Analysis and Long Noncoding RNA-Associated Competing Endogenous RNA Network. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9328160. [PMID: 35281467 PMCID: PMC8915924 DOI: 10.1155/2022/9328160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/16/2022] [Indexed: 12/15/2022]
Abstract
Objective Multiple sclerosis (MS) is an autoimmune disease of the central nervous system characterized by chronic inflammation and demyelination. This study is aimed at identifying crucial genes and molecular pathways involved in MS pathogenesis. Methods Raw data in GSE52139 were collected from the Gene Expression Omnibus. The top 50% expression variants were subjected to weighted gene coexpression network analysis (WGCNA), and the key module associated with MS occurrence was identified. A long noncoding RNA- (lncRNA-) associated competing endogenous RNA (ceRNA) network was constructed in the key module. The hub gene candidates were subsequently verified in an individual database. Results Of the 18 modules obtained, the cyan module was designated as the key module. The established ceRNA network was composed of seven lncRNAs, 45 mRNAs, and 21 microRNAs (miRNAs), and the FAM13A-AS1 was the lncRNA with the highest centrality. Functional assessments indicated that the genes in the cyan module primarily gathered in ribosome-related functional terms. Interestingly, the targeted mRNAs of the ceRNA network enriched in diverse categories. Moreover, highly expressed CYBRD1, GNG12, and SMAD1, which were identified as hub genes, may be associated with “valine leucine and isoleucine degradation,” “base excision repair,” and “fatty acid metabolism,” respectively, according to the results of single gene-based genomes and gene set enrichment analysis (GSEA). Conclusions Combined with the WGCNA and ceRNA network, our findings provide novel insights into the pathogenesis of MS. The hub genes discovered herein might also serve as novel biomarkers that correlate with the development and management of MS.
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GNG12 Targeted by miR-876-5p Contributes to Glioma Progression Through the Activation of the PI3K/AKT Signaling Pathway. J Mol Neurosci 2022; 72:441-450. [DOI: 10.1007/s12031-021-01956-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
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Yuan J, Yuan Z, Ye A, Wu T, Jia J, Guo J, Zhang J, Li T, Cheng X. Low GNG12 Expression Predicts Adverse Outcomes: A Potential Therapeutic Target for Osteosarcoma. Front Immunol 2021; 12:758845. [PMID: 34691083 PMCID: PMC8527884 DOI: 10.3389/fimmu.2021.758845] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/17/2021] [Indexed: 01/04/2023] Open
Abstract
Background G protein subunit gamma 12 (GNG12) is observed in some types of cancer, but its role in osteosarcoma is unknown. This study hypothesized that GNG12 may be a potential biomarker and therapeutic target. We aimed to identify an association between GNG12 and osteosarcoma based on the Gene Expression Omnibus and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) databases. Methods Osteosarcoma samples in GSE42352 and TARGET database were selected as the test cohorts. As the external validation cohort, 78 osteosarcoma specimens from The Second Affiliated Hospital of Nanchang University were collected. Patients with osteosarcoma were divided into high and low GNG12 mRNA-expression groups; differentially expressed genes were identified as GNG12-related genes. The biological function of GNG12 was annotated using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set enrichment analysis, and immune infiltration analysis. Gene expression correlation analysis and competing endogenous RNA regulatory network construction were used to determine potential biological regulatory relationships of GNG12. Overall survival, Kaplan–Meier analysis, and log-rank tests were calculated to determine GNG12 reliability in predicting survival prognosis. Results GNG12 expression decreased in osteosarcoma samples. GNG12 was a highly effective biomarker for osteosarcoma [area under the receiver operating characteristic (ROC) curve (AUC) = 0.920], and the results of our Kaplan–Meier analysis indicated that overall survival and progression-free survival differed significantly between low and high GNG-expression group (p < 0.05). Functional analyses indicated that GNG12 may promote osteosarcoma through regulating the endoplasmic reticulum. Expression correlation analysis and competing endogenous RNA network construction showed that HOTTIP/miR-27a-3p may regulate GNG12 expression. Furthermore, the subunit suppresses adaptive immunity via inhibiting M1 and M2 macrophage infiltration. GNG12 was inhibited in metastatic osteosarcoma compared with non-metastatic osteosarcoma, and its expression predicted survival of patients (1, 3, and 5-year AUCs were 0.961, 0.826, and 0.808, respectively). Conclusion This study identified GNG12 as a potential biomarker for osteosarcoma prognosis, highlighting its potential as an immunotherapy target.
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Affiliation(s)
- Jinghong Yuan
- Department of Orthopaedics, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhao Yuan
- Clinical Research Center, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Aifang Ye
- Department of Otorhinolaryngology, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Tianlong Wu
- Institute of Orthopaedics of Jiangxi Province, Nanchang, China
| | - Jingyu Jia
- Institute of Minimally Invasive Orthopaedics of Nanchang University, Nanchang University, Nanchang, China
| | - Jia Guo
- Department of Orthopaedics, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Jian Zhang
- Department of Orthopaedics, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tao Li
- Department of Orthopaedics, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xigao Cheng
- Department of Orthopaedics, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Institute of Orthopaedics of Jiangxi Province, Nanchang, China.,Institute of Minimally Invasive Orthopaedics of Nanchang University, Nanchang University, Nanchang, China
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Adulthood systemic inflammation accelerates the trajectory of age-related cognitive decline. Aging (Albany NY) 2021; 13:22092-22108. [PMID: 34587117 PMCID: PMC8507275 DOI: 10.18632/aging.203588] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/20/2021] [Indexed: 11/25/2022]
Abstract
In order to understand the long-term effects of systemic inflammation, it is important to distinguish inflammation-induced changes in baseline cognitive function from changes that interact with aging to influence the trajectory of cognitive decline. Lipopolysaccharide (LPS; 1 mg/kg) or vehicle was administered to young adult (6 months) male rats via intraperitoneal injections, once a week for 7 weeks. Longitudinal effects on cognitive decline were examined 6 and 12 months after the initial injections. Repeated LPS treatment, in adults, resulted in a long-term impairment in memory, examined in aged animals (age 18 months), but not in middle-age (age 12 months). At 12 months following injections, LPS treatment was associated with a decrease in N-methyl-D-aspartate receptor-mediated component of synaptic transmission and altered expression of genes linked to the synapse and to regulation of the response to inflammatory signals. The results of the current study suggest that the history of systemic inflammation is one component of environmental factors that contribute to the resilience or susceptibility to age-related brain changes and associated trajectory of cognitive decline.
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SILAC proteomics implicates SOCS1 in modulating cellular macromolecular complexes and the ubiquitin conjugating enzyme UBE2D involved in MET receptor tyrosine kinase downregulation. Biochimie 2021; 182:185-196. [PMID: 33493533 DOI: 10.1016/j.biochi.2021.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/27/2020] [Accepted: 01/18/2021] [Indexed: 01/25/2023]
Abstract
Suppressor of Cytokine Signaling 1 (SOCS1) functions as a tumor suppressor in hepatocellular carcinoma and many other types of cancers. SOCS1 mediates its functions by inhibiting tyrosine kinases, promoting ubiquitination and proteasomal degradation of signal transducing proteins, and by modulating transcription factors. Here, we studied the impact of SOCS1 on the hepatocyte proteome using Stable Isotopic Labelling of Amino acids in Cell culture (SILAC)-based mass spectrometry on the Hepa1-6 murine HCC cell line stably expressing wildtype SOCS1 or a mutant SOCS1 with impaired SH2 domain. As SOCS1 regulates the hepatocyte growth factor (HGF) receptor, the MET receptor tyrosine kinase (RTK), the SILAC-labelled cells were stimulated or not with HGF. Following mass spectrometry analysis, differentially modulated proteins were identified, quantified and analyzed for pathway enrichment. Of the 3440 proteins identified in Hepa-SOCS1 cells at steady state, 181 proteins were significantly modulated compared to control cells. The SH2 domain mutation and HGF increased the number of differentially modulated proteins. Protein interaction network analysis revealed enrichment of SOCS1-modulated proteins within multiprotein complexes such as ubiquitin conjugating enzymes, proteasome, mRNA spliceosome, mRNA exosome and mitochondrial ribosome. Notably, the expression of UBE2D ubiquitin conjugating enzyme, which is implicated in the control of growth factor receptor tyrosine kinase signaling, was found to be regulated by SOCS1. These findings suggest that SOCS1, induced by cytokines, growth factors and diverse other stimuli, has the potential to dynamically modulate of large macromolecular regulatory complexes to help maintain cellular homeostasis.
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Lazary J, Eszlari N, Kriko E, Tozser D, Dome P, Deakin JFW, Juhasz G, Bagdy G. Genetic analyses of the endocannabinoid pathway in association with affective phenotypic variants. Neurosci Lett 2021; 744:135600. [PMID: 33421489 DOI: 10.1016/j.neulet.2020.135600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/22/2020] [Accepted: 12/26/2020] [Indexed: 12/21/2022]
Abstract
BACKGORUND Increasing experimental data confirm the crucial role of the endocannabinoid (eCB) system in the regulation of stress response and emotional processes. Despite of the fact, that genetically determined vulnerability for stress is a widely accepted concept in the pathomechanism of affective disorders, replicable human genetic results with interaction analyses of early life trauma and eCB genes are rare. The aim of this study is to test the associations between genetic variants of the eCB pathway, childhood trauma and affective phenotypes. METHODS We selected 18,897 SNPs in the eCB pathway of a GWAS dataset in two general population cohorts (BP sample N = 837; MN sample N = 988). Association analyses were performed on the anxious and depressive subscales of the Brief Symptom Inventory (BSI-ANX and BSI-DEP, respectively). Childhood trauma was assessed by the Childhood Adversity Questionnaire (CAQ). Association analyses were performed in the R 2.0. statistical program using the SNPassoc package. REULTS Genetic effect was more robust in the BP sample than in the MN sample. The most comprehensive results showed that SNPs in the CACNA1C gene associated with depressive phenotype in interaction with CAQ in both BP (p = 1.2 × 10-4) and MN samples (p = 1.6 × 10-4). Direct association analyses (without interaction) provided significant associations between SNPs in different genesets of the two study populations. SNPs in KCNJ3 and GNB5 genes on the BSI-DEP (p = 6.1 × 10-5; p = 7.1 × 10-4) and GNG12 gene on the BSI-ANX (p = 7.4 × 10-6) in the BP sample, while GABAergic, ADCY1 and HTR2A gene variants can be outlined from results of MN sample with less strong p-values. CONCLUSION Our results confirmed the prominent role of CACNA1C gene in the pathogenic effect of early life stress in the development of affective vulnerability in two different study populations using GxE interaction analysis. CACNA1C gene, as it encodes for L-type voltage-gated calcium channel, contributes to neuronal excitability, plasticity and neurogenesis being a crucial effector of both eCB signaling and the BDNF-CREB pathway as well. Our findings suggest that childhood trauma related depression may have more robust genetically determined basis than without early life stress.
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Affiliation(s)
- Judit Lazary
- National Institute of Psychiatry and Addictions, Budapest, Hungary; Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary.
| | - Nora Eszlari
- Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
| | - Eszter Kriko
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, Hungary
| | - Dora Tozser
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, Hungary
| | - Peter Dome
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - J F William Deakin
- Neuroscience and Psychiatry Unit, University of Manchester, Manchester, United Kingdom
| | - Gabriella Juhasz
- Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
| | - Gyorgy Bagdy
- Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
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Ma S, Guo Z, Wang B, Yang M, Yuan X, Ji B, Wu Y, Chen S. A Computational Framework to Identify Biomarkers for Glioma Recurrence and Potential Drugs Targeting Them. Front Genet 2021; 12:832627. [PMID: 35116059 PMCID: PMC8804649 DOI: 10.3389/fgene.2021.832627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Recurrence is still a major obstacle to the successful treatment of gliomas. Understanding the underlying mechanisms of recurrence may help for developing new drugs to combat gliomas recurrence. This study provides a strategy to discover new drugs for recurrent gliomas based on drug perturbation induced gene expression changes. Methods: The RNA-seq data of 511 low grade gliomas primary tumor samples (LGG-P), 18 low grade gliomas recurrent tumor samples (LGG-R), 155 glioblastoma multiforme primary tumor samples (GBM-P), and 13 glioblastoma multiforme recurrent tumor samples (GBM-R) were downloaded from TCGA database. DESeq2, key driver analysis and weighted gene correlation network analysis (WGCNA) were conducted to identify differentially expressed genes (DEGs), key driver genes and coexpression networks between LGG-P vs LGG-R, GBM-P vs GBM-R pairs. Then, the CREEDS database was used to find potential drugs that could reverse the DEGs and key drivers. Results: We identified 75 upregulated and 130 downregulated genes between LGG-P and LGG-R samples, which were mainly enriched in human papillomavirus (HPV) infection, PI3K-Akt signaling pathway, Wnt signaling pathway, and ECM-receptor interaction. A total of 262 key driver genes were obtained with frizzled class receptor 8 (FZD8), guanine nucleotide-binding protein subunit gamma-12 (GNG12), and G protein subunit β2 (GNB2) as the top hub genes. By screening the CREEDS database, we got 4 drugs (Paclitaxel, 6-benzyladenine, Erlotinib, Cidofovir) that could downregulate the expression of up-regulated genes and 5 drugs (Fenofibrate, Oxaliplatin, Bilirubin, Nutlins, Valproic acid) that could upregulate the expression of down-regulated genes. These drugs may have a potential in combating recurrence of gliomas. Conclusion: We proposed a time-saving strategy based on drug perturbation induced gene expression changes to find new drugs that may have a potential to treat recurrent gliomas.
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Affiliation(s)
- Shuzhi Ma
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhen Guo
- Academician Workstation, Changsha Medical University, Changsha, China
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Bo Wang
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Min Yang
- Geneis (Beijing) Co., Ltd., Beijing, China
| | | | - Binbin Ji
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Yan Wu
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Size Chen
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precise Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- Central Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- *Correspondence: Size Chen,
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Tu P, Tian R, Lu Y, Zhang Y, Zhu H, Ling L, Li H, Chen D. Beneficial effect of Indigo Naturalis on acute lung injury induced by influenza A virus. Chin Med 2020; 15:128. [PMID: 33349263 PMCID: PMC7750395 DOI: 10.1186/s13020-020-00415-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Background Infections induced by influenza viruses, as well as coronavirus disease 19 (COVID-19) pandemic induced by severe acute respiratory coronavirus 2 (SARS-CoV-2) led to acute lung injury (ALI) and multi organ failure, during which traditional Chinese medicine (TCM) played an important role in treatment of the pandemic. The study aimed to investigate the effect of Indigo Naturalis on ALI induced by influenza A virus (IAV) in mice. Method The anti-influenza and anti-inflammatory properties of aqueous extract of Indigo Naturalis (INAE) were evaluated in vitro. BALB/c mice inoculated intranasally with IAV (H1N1) were treated intragastrically with INAE (40, 80 and 160 mg/kg/day) 2 h later for 4 or 7 days. Animal lifespan and mortality were recorded. Expression of high mobility group box-1 protein (HMGB-1) and toll-like receptor 4 (TLR4) were evaluated through immunohistological staining. Inflammatory cytokines were also monitored by ELISA. Result INAE inhibited virus replication on Madin-Darby canine kidney (MDCK) cells and decreased nitric oxide (NO) production from lipopolysaccharide (LPS)-stimulated peritoneal macrophages in vitro. The results showed that oral administration of 160 mg/kg of INAE significantly improved the lifespan (P < 0.01) and survival rate of IAV infected mice, improved lung injury and lowered viral replication in lung tissue (P < 0.01). Treatment with INAE (40, 80 and 160 mg/kg) significantly increased liver weight and liver index (P < 0.05), as well as weight and organ index of thymus and spleen at 160 mg/kg (P < 0.05). Serum alanine transaminase (ALT) and aspartate aminotransferase (AST) levels were reduced by INAE administration (P < 0.05). The expression of HMGB-1 and TLR4 in lung tissue were also suppressed. The increased production of myeloperoxidase (MPO) and methylene dioxyamphetamine (MDA) in lung tissue were inhibited by INAE treatment (P < 0.05). Treatment with INAE reduced the high levels of interferon α (IFN-α), interferon β (IFN-β), monocyte chemoattractant protein-1 (MCP-1), regulated upon activation normal T cell expressed and secreted factor (RANTES), interferon induced protein-10 (IP-10), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) (P < 0.05), with increased production of interferon γ (IFN-γ) and interleukin-10 (IL-10) (P < 0.05). Conclusion The results showed that INAE alleviated IAV induced ALI in mice. The mechanisms of INAE were associated with its anti-influenza, anti-inflammatory and anti-oxidation properties. Indigo Naturalis might have clinical potential to treat ALI induced by IAV.
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Affiliation(s)
- Peng Tu
- Department of Natural Medicine, School of Pharmacy, Fudan University, No. 826, Zhangheng Road, Shanghai, 201203, People's Republic of China
| | - Rong Tian
- Department of Natural Medicine, School of Pharmacy, Fudan University, No. 826, Zhangheng Road, Shanghai, 201203, People's Republic of China
| | - Yan Lu
- Department of Natural Medicine, School of Pharmacy, Fudan University, No. 826, Zhangheng Road, Shanghai, 201203, People's Republic of China
| | - Yunyi Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, No. 826, Zhangheng Road, Shanghai, 201203, People's Republic of China
| | - Haiyan Zhu
- Department of Microbiological and Biochemical Pharmacy, School of Pharmacy, Fudan University, No. 826, Zhangheng Road, Shanghai, 201203, People's Republic of China
| | - Lijun Ling
- Department of Natural Medicine, School of Pharmacy, Fudan University, No. 826, Zhangheng Road, Shanghai, 201203, People's Republic of China
| | - Hong Li
- Department of Pharmacology, School of Pharmacy, Fudan University, No. 826, Zhangheng Road, Shanghai, 201203, People's Republic of China.
| | - Daofeng Chen
- Department of Natural Medicine, School of Pharmacy, Fudan University, No. 826, Zhangheng Road, Shanghai, 201203, People's Republic of China.
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Chen YC, Hsiao CC, Chen TW, Wu CC, Chao TY, Leung SY, Eng HL, Lee CP, Wang TY, Lin MC. Whole Genome DNA Methylation Analysis of Active Pulmonary Tuberculosis Disease Identifies Novel Epigenotypes: PARP9/ miR-505/ RASGRP4/ GNG12 Gene Methylation and Clinical Phenotypes. Int J Mol Sci 2020; 21:ijms21093180. [PMID: 32365959 PMCID: PMC7246806 DOI: 10.3390/ijms21093180] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
We hypothesized that DNA methylation patterns may contribute to the development of active pulmonary tuberculosis (TB). Illumina’s DNA methylation 450 K assay was used to identify differentially methylated loci (DML) in a discovery cohort of 12 active pulmonary TB patients and 6 healthy subjects (HS). DNA methylation levels were validated in an independent cohort of 64 TB patients and 24 HS. Microarray analysis identified 1028 DMLs in TB patients versus HS, and 3747 DMLs in TB patients after versus before anti-TB treatment, while autophagy was the most enriched signaling pathway. In the validation cohort, PARP9 and miR505 genes were hypomethylated in the TB patients versus HS, while RASGRP4 and GNG12 genes were hypermethylated, with the former two further hypomethylated in those with delayed sputum conversion, systemic symptoms, or far advanced lesions. MRPS18B and RPTOR genes were hypomethylated in TB patients with pleural involvement. RASGRP4 gene hypermethylation and RPTOR gene down-regulation were associated with high mycobacterial burden. TB patients with WIPI2/GNG12 hypermethylation or MRPS18B/FOXO3 hypomethylation had lower one-year survival. In vitro ESAT6 and CFP10 stimuli of THP-1 cells resulted in DNA de-methylation changes of the PARP9, RASGRP4, WIPI2, and FOXO3 genes. In conclusions, aberrant DNA methylation over the PARP9/miR505/RASGRP4/GNG12 genes may contribute to the development of active pulmonary TB disease and its clinical phenotypes, while aberrant DNA methylation over the WIPI2/GNG12/MARPS18B/FOXO3 genes may constitute a determinant of long-term outcomes.
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Affiliation(s)
- Yung-Che Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
- Graduate Institute of Clinical Medical Sciences and Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Correspondence: (Y.-C.C.); (M.-C.L.); Tel.: +886-975056041 (Y.-C.C.); +886-7-731-7123 (ext 8199) (M.-C.L.)
| | - Chang-Chun Hsiao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
- Graduate Institute of Clinical Medical Sciences and Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Ting-Wen Chen
- Molecular Medicine Research Center, and Bioinformatics Center, Chang Gung University, Taoyuan 33302, Taiwan;
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chao-Chien Wu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
| | - Tung-Ying Chao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
| | - Sum-Yee Leung
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
| | - Hock-Liew Eng
- Division of Clinical Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan;
| | - Chiu-Ping Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
| | - Ting-Ya Wang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-C.H.); (C.-C.W.); (T.-Y.C.); (S.-Y.L.); (C.-P.L.); (T.-Y.W.)
- Correspondence: (Y.-C.C.); (M.-C.L.); Tel.: +886-975056041 (Y.-C.C.); +886-7-731-7123 (ext 8199) (M.-C.L.)
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Li J, Jin C, Zou C, Qiao X, Ma P, Hu D, Li W, Jin J, Jin X, Fan P. GNG12 regulates PD-L1 expression by activating NF-κB signaling in pancreatic ductal adenocarcinoma. FEBS Open Bio 2020; 10:278-287. [PMID: 31898405 PMCID: PMC6996305 DOI: 10.1002/2211-5463.12784] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/16/2019] [Accepted: 01/02/2020] [Indexed: 01/09/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive solid tumors in the digestive system. A greater understanding of the pathogenesis of PDAC may facilitate the search for new therapeutic targets. Guanine nucleotide-binding protein subunit gamma-12 (GNG12) belongs to the G protein family and participates in the modulation of the inflammatory signaling cascade. However, the cancer-related function and clinical relevance of GNG12 in PDAC have not previously been reported. Here, we investigated the clinical significance of GNG12 in PDAC using the Oncomine web tool, the gene expression profiling interactive analysis tool and tissue microarray (TMA). GNG12 expression was observed to be higher in PDAC patient specimens than in nontumor pancreatic tissues, and high expression of GNG12 was associated with poor prognosis. We subsequently show that GNG12 promotes pancreatic cancer cell growth in vivo and in vitro, as evaluated using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt assays, colony formation assays and a xenograft mouse model. Furthermore, our results suggest that GNG12 activates nuclear factor-κB signaling and modulates the immune response. Collectively, our findings suggest that GNG12 may be suitable as a new prognosis-related biomarker and a promising target for treatment of pancreatic cancer.
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Affiliation(s)
- Juan Li
- Department of General MedicineThe Second Clinical Medical CollegeJingzhou Central HospitalYangtze UniversityJingzhouChina
| | - Can Jin
- Department of GastroenterologyThe Second Clinical Medical CollegeJingzhou Central HospitalYangtze UniversityJingzhouChina
| | - Chuanxin Zou
- Department of GastroenterologyThe Second Clinical Medical CollegeJingzhou Central HospitalYangtze UniversityJingzhouChina
| | - Xu Qiao
- Digestive Endoscopy CenterThe Second Clinical Medical CollegeJingzhou Central HospitalYangtze UniversityJingzhouChina
| | - Peng Ma
- Department of GastroenterologyThe Second Clinical Medical CollegeJingzhou Central HospitalYangtze UniversityJingzhouChina
| | - Di Hu
- Department of GastroenterologyThe Second Clinical Medical CollegeJingzhou Central HospitalYangtze UniversityJingzhouChina
| | - Wenqin Li
- Department of GastroenterologyThe Second Clinical Medical CollegeJingzhou Central HospitalYangtze UniversityJingzhouChina
| | - Jun Jin
- Department of OncologyNo. 99 Hospital of Joint Logistics Support Force of PLAZhangzhouChina
| | - Xin Jin
- Cancer CenterTongji Medical CollegeUnion HospitalHuazhong University of Science and TechnologyWuhanChina
| | - Ping Fan
- Cancer CenterTongji Medical CollegeUnion HospitalHuazhong University of Science and TechnologyWuhanChina
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Zhang YB, Jiang Y, Wang J, Ma J, Han S. Evaluation of core serous epithelial ovarian cancer genes as potential prognostic markers and indicators of the underlying molecular mechanisms using an integrated bioinformatics analysis. Oncol Lett 2019; 18:5508-5522. [PMID: 31612059 PMCID: PMC6781641 DOI: 10.3892/ol.2019.10884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022] Open
Abstract
Ovarian cancer is a major cause of mortality in women. However, the molecular events underlying the pathogenesis of the disease are yet to be fully elucidated. In the present study, an integrated bioinformatics analysis was performed to identify core genes involved in serous epithelial ovarian cancer. A total of three expression datasets were downloaded from the Gene Expression Omnibus database, and included 46 serous epithelial ovarian cancer and 30 ovarian surface epithelium samples. The three datasets were merged, and batch normalization was performed. The normalized merged data were subsequently analyzed for differentially expressed genes (DEGs). In total, 2,212 DEGs were identified, including 1,300 upregulated and 912 downregulated genes. Gene Ontology analysis revealed that these DEGs were primarily involved in ‘regulation of cell cycle’, ‘mitosis’, ‘DNA packaging’ and ‘nucleosome assembly’. The main cellular components included ‘extracellular region part’, ‘chromosome’, ‘extracellular matrix’ and ‘condensed chromosome kinetochore’, whereas the molecular functions included ‘Calcium ion binding’, ‘polysaccharide binding’, ‘enzyme inhibitor activity’, ‘growth factor activity’, ‘cyclin-dependent protein kinase regulator activity’, ‘microtubule motor activity’ and ‘Wnt receptor activity’. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that these DEGs were predominantly involved in ‘Wnt signaling pathway’, ‘pathways in cancer’, ‘PI3K-Akt signaling pathway’, ‘cell cycle’, ‘ECM-receptor interaction’, ‘p53 signaling pathway’ and ‘focal adhesion’. The 20 most significant DEGs were identified from the protein-protein interaction network, and Oncomine analysis of these core genes revealed that 13 were upregulated and two were downregulated in serous epithelial ovarian cancer. Survival analysis revealed that cyclin B1, polo like kinase 1, G protein subunit γ transducin 1 and G protein subunit γ 12 are key molecules that may be involved in the prognosis of serous epithelial ovarian cancer. These core genes may provide novel treatment targets, although their roles in the carcinogenesis and prognosis of serous epithelial ovarian cancer require further study.
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Affiliation(s)
- Yu-Bo Zhang
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yuhan Jiang
- Department of Gynecology, The Affiliated Hospital of Jining Medical College, Jining, Shandong 272000, P.R. China
| | - Jiao Wang
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Jing Ma
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Shiyu Han
- Department of Gynecology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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Wang Y, Liu Q, Huang S, Yuan B. Learning a Structural and Functional Representation for Gene Expressions: To Systematically Dissect Complex Cancer Phenotypes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1729-1742. [PMID: 28489545 DOI: 10.1109/tcbb.2017.2702161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cancer is a heterogeneous disease, thus one of the central problems is how to dissect the resulting complex phenotypes in terms of their biological building blocks. Computationally, this is to represent and interpret high dimensional observations through a structural and conceptual abstraction into the most influential determinants underlying the problem. The working hypothesis of this report is to consider gene interaction to be largely responsible for the manifestation of complex cancer phenotypes, thus where the representation is to be conceptualized. Here, we report a representation learning strategy combined with regularizations, in which gene expressions are described in terms of a regularized product of meta-genes and their expression levels. The meta-genes are constrained by gene interactions thus representing their original topological contexts. The expression levels are supervised by their conditional dependencies among the observations thus providing a cluster-specific constraint. We obtain both of these structural constraints using a node-based graphical model. Our representation allows the selection of more influential modules, thus implicating their possible roles in neoplastic transformations. We validate our representation strategy by its robust recognitions of various cancer phenotypes comparing with various classical methods. The modules discovered are either shared or specify for different types or stages of human cancers, all of which are consistent with literature and biology.
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Smoking-Related DNA Methylation is Associated with DNA Methylation Phenotypic Age Acceleration: The Veterans Affairs Normative Aging Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16132356. [PMID: 31277270 PMCID: PMC6651499 DOI: 10.3390/ijerph16132356] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/29/2019] [Accepted: 07/01/2019] [Indexed: 12/17/2022]
Abstract
DNA methylation may play a critical role in aging and age-related diseases. DNA methylation phenotypic age (DNAmPhenoAge) is a new aging biomarker and predictor of chronic disease risk. While smoking is a strong risk factor for chronic diseases and influences methylation, its influence on DNAmPhenoAge is unknown. We investigated associations of self-reported and epigenetic smoking indicators with DNAmPhenoAge acceleration in a longitudinal aging study in eastern Massachusetts. DNA methylation was measured in whole blood samples from multiple visits for 692 male participants in the Veterans Affairs Normative Aging Study during 1999–2013. Acceleration was defined using residuals from linear regression of the DNAmPhenoAge on the chronological age. Cumulative smoking (pack-years) was significantly associated with DNAmPhenoAge acceleration, whereas self-reported smoking status was not. We observed significant validated associations between smoking-related loci and DNAmPhenoAge acceleration for 52 CpG sites, where 18 were hypomethylated and 34 were hypermethylated, mapped to 16 genes. The AHRR gene had the most loci (N = 8) among the 16 genes. We generated a smoking aging index based on these 52 loci, which showed positive significant associations with DNAmPhenoAge acceleration. These epigenetic biomarkers may help to predict age-related risks driven by smoking.
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20
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Wiklund P, Karhunen V, Richmond RC, Parmar P, Rodriguez A, De Silva M, Wielscher M, Rezwan FI, Richardson TG, Veijola J, Herzig KH, Holloway JW, Relton CL, Sebert S, Järvelin MR. DNA methylation links prenatal smoking exposure to later life health outcomes in offspring. Clin Epigenetics 2019; 11:97. [PMID: 31262328 PMCID: PMC6604191 DOI: 10.1186/s13148-019-0683-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Maternal smoking during pregnancy is associated with adverse offspring health outcomes across their life course. We hypothesize that DNA methylation is a potential mediator of this relationship. METHODS We examined the association of prenatal maternal smoking with offspring blood DNA methylation in 2821 individuals (age 16 to 48 years) from five prospective birth cohort studies and perform Mendelian randomization and mediation analyses to assess whether methylation markers have causal effects on disease outcomes in the offspring. RESULTS We identify 69 differentially methylated CpGs in 36 genomic regions (P value < 1 × 10-7) associated with exposure to maternal smoking in adolescents and adults. Mendelian randomization analyses provided evidence for a causal role of four maternal smoking-related CpG sites on an increased risk of inflammatory bowel disease or schizophrenia. Further mediation analyses showed some evidence of cg25189904 in GNG12 gene mediating the effect of exposure to maternal smoking on schizophrenia-related outcomes. CONCLUSIONS DNA methylation may represent a biological mechanism through which maternal smoking is associated with increased risk of psychiatric morbidity in the exposed offspring.
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Affiliation(s)
- Petri Wiklund
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Health Sciences, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | | | - Priyanka Parmar
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Alina Rodriguez
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- School of Psychology, University of Lincoln, Lincoln, UK
| | - Maneka De Silva
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Tom G. Richardson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Juha Veijola
- Medical Research Center Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Neuroscience, University of Oulu, Oulu, Finland
| | - Karl-Heinz Herzig
- Medical Research Center Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
- Institute of Biomedicine and Biocenter of Oulu, Oulu, Finland
- Department of Gastroenterology and Metabolism, Poznan University of Medical Sciences, Poznan, Poland
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Institute of Biomedicine and Biocenter of Oulu, Oulu, Finland
- Department for Genomics of Common Diseases, School of Medicine, Imperial College London, London, UK
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Oulu University Hospital, Oulu, Finland
- Institute of Biomedicine and Biocenter of Oulu, Oulu, Finland
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
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21
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Chu Y, Elrod N, Wang C, Li L, Chen T, Routh A, Xia Z, Li W, Wagner EJ, Ji P. Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients. Oncogene 2019; 38:4154-4168. [PMID: 30705404 PMCID: PMC6533131 DOI: 10.1038/s41388-019-0714-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 12/09/2018] [Accepted: 01/18/2019] [Indexed: 02/03/2023]
Abstract
Alternative polyadenylation (APA) has emerged as a prevalent feature associated with cancer development and progression. The advantage of APA to tumor progression is to induce oncogenes through 3'-UTR shortening, and to inactivate tumor suppressor genes via the re-routing of microRNA competition. We previously identified the Mammalian Cleavage Factor I-25 (CFIm25) (encoded by Nudt21 gene) as a master APA regulator whose expression levels directly impact the tumorigenicity of glioblastoma (GBM) in vitro and in vivo. Despite its importance, the role of Nudt21 in GBM development is not known and the genes subject to Nudt21 APA regulation that contribute to GBM progression have not been identified. Here, we find that Nudt21 is reduced in low grade glioma (LGG) and all four subtypes of high grade glioma (GBM). Reduced expression of Nudt21 associates with worse survival in TCGA LGG cohorts and two TCGA GBM cohorts. Moreover, although CFIm25 was initially identified as biochemically associated with both CFIm59 and CFIm68, we observed three CFIm distinct subcomplexes exist and CFIm59 protein level is dependent on Nudt21 expression in GBM cells, but CFIm68 is not, and that only CFIm59 predicts prognosis of GBM patients similar to Nudt21. Through the use of Poly(A)-Click-Seq to characterize APA, we define the mRNAs subject to 3'-UTR shortening upon Nudt21 depletion in GBM cells and observed enrichment in genes important in the Ras signaling pathway, including Pak1. Remarkably, we find that Pak1 expression is regulated by Nudt21 through its 3'-UTR APA, and the combination of Pak1 and Nudt21 expression generates an even stronger prognostic indicator of GBM survival versus either value used alone. Collectively, our data uncover Nudt21 and its downstream target Pak1 as a potential "combination biomarker" for predicting prognosis of GBM patients.
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Affiliation(s)
- Yuan Chu
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA,Endoscopy Center, Zhongshan Hospital and Endoscopy Research Institute, Fudan University, Shanghai, China
| | - Nathan Elrod
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Chaojie Wang
- Department of Molecular Microbiology and Immunology, Computational Biology Program, OHSU, Portland, OR 97273, USA
| | - Lei Li
- Daniel Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Tao Chen
- Endoscopy Center, Zhongshan Hospital and Endoscopy Research Institute, Fudan University, Shanghai, China
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA,Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Zheng Xia
- Department of Molecular Microbiology and Immunology, Computational Biology Program, OHSU, Portland, OR 97273, USA
| | - Wei Li
- Daniel Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric J. Wagner
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA,Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Ji
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
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Luo C, Zhao S, Dai W, Zheng N, Wang J. Proteomic analyses reveal GNG12 regulates cell growth and casein synthesis by activating the Leu-mediated mTORC1 signaling pathway. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:1092-1101. [PMID: 30282607 DOI: 10.1016/j.bbapap.2018.08.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/10/2018] [Accepted: 08/30/2018] [Indexed: 12/01/2022]
Abstract
In cow mammary epithelial cells (CMECs), cell growth and casein synthesis are regulated by amino acids (AAs), and lysosomes are important organelles in this regulatory process, but the mechanisms remain unclear. Herein, lysosomal membrane proteins (LMPs) in CMECs in the presence (Leu+) and absence (Leu-) of leucine were quantitatively analysed using Sequential Windowed Acquisition of All Theoretical Fragment Ion (SWATH) mass spectrometry. In identified LMPs, Guanine nucleotide-binding protein subunit gamma-12 (GNG12) was a markedly up-regulated protein in Leu+ group. CMECs were treated with Leu+ or Leu-, expression and lysosomal localization of GNG12 were decreased in response to Leu absence. Overexpressing or inhibiting GNG12 demonstrated that cell growth, casein synthesis and activation of the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway were all up-regulated by GNG12. Cell growth, casein synthesis and mTORC1 signaling pathway were decreased in response to Leu absence, but these decreases were partially restored by GNG12 overexpression, and those effects were partially reversed by inhibiting GNG12. Co-immunoprecipitation analysis showed that GNG12 activates the mTORC1 pathway via interaction with Ragulator. Taken together, these results suggest that GNG12 is a positive regulator of the Leu-mediated mTORC1 signaling pathway in CMECs that promotes cell growth and casein synthesis.
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Affiliation(s)
- Chaochao Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Wenting Dai
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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23
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Fan L, Wu X, Jin C, Li F, Xiong S, Dong Y. MptpB Promotes Mycobacteria Survival by Inhibiting the Expression of Inflammatory Mediators and Cell Apoptosis in Macrophages. Front Cell Infect Microbiol 2018; 8:171. [PMID: 29888212 PMCID: PMC5981270 DOI: 10.3389/fcimb.2018.00171] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 05/03/2018] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis is a severe contagious disease caused by Mycobacterium tuberculosis (Mtb). To develop new vaccines and medicine against TB, there is an urgent need to provide insights into the mechanisms by which Mtb induces tuberculosis. In this study, we found that secreted Mtb virulence factor MptpB significantly enhanced the survival of H37Rv in macrophages. MptpB suppressed the production of iNOS, the expression of inflammatory factors IL-1β and IL-6, as well as the apoptosis of the macrophage in Mtb infected RAW264.7 cells. Mechanism investigation showed that MptpB simultaneously hampered the NF-κB and MAPK signal pathways, evidenced by its blocking of p65, IKKα, Erk1/2, and p38 phosphorylation induced by Mtb infection. MptpB also inhibited host cell p53 expression. The results demonstrated that MptpB contributed to the survival of H37Rv by inhibiting host inflammatory responses and apoptosis through impeding the NF-κB and MAPK signal pathways and p53 expression in the macrophage.
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Affiliation(s)
- Lingbo Fan
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
| | - Xiaoyu Wu
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
| | - Chunyan Jin
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
| | - Fengge Li
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
| | - Yuanshu Dong
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
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24
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Gao X, Zhang Y, Saum KU, Schöttker B, Breitling LP, Brenner H. Tobacco smoking and smoking-related DNA methylation are associated with the development of frailty among older adults. Epigenetics 2016; 12:149-156. [PMID: 28001461 DOI: 10.1080/15592294.2016.1271855] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Tobacco smoking is a preventable environmental factor that contributes to a wide spectrum of age-related health outcomes; however, its association with the development of frailty is not yet well established. We examined the associations of self-reported smoking indicators, serum cotinine levels and smoking-related DNA methylation biomarkers with a quantitative frailty index (FI) in 2 independent subsets of older adults (age 50-75) recruited in Saarland, Germany in 2000 - 2002 (discovery set: n = 978, validation set: n = 531). We obtained DNA methylation profiles in whole blood samples by Illumina HumanMethylation450 BeadChip and calculated the FI according to the method of Mitnitski and Rockwood. Mixed linear regression models were implemented to assess the associations between smoking indicators and the FI. After controlling for potential covariates, current smoking, cumulative smoking exposure (pack-years), and time after smoking cessation (years) were significantly associated with the FI (P-value < 0.05). In the discovery panel, 17 out of 151 previously identified smoking-related CpG sites were associated with the FI after correction for multiple testing (FDR < 0.05). Nine of them survived in the validation phase and were designated as frailty-associated loci. A smoking index (SI) based on the 9 loci manifested a monotonic association with the FI. In conclusion, this study suggested that epigenetic alterations could play a role in smoking-associated development of frailty. The identified CpG sites have the potential to be prognostic biomarkers of frailty and frailty-related health outcomes. Our findings and the underlying mechanisms should be followed up in further, preferably longitudinal studies.
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Affiliation(s)
- Xu Gao
- a Division of Clinical Epidemiology and Aging Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Yan Zhang
- a Division of Clinical Epidemiology and Aging Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Kai-Uwe Saum
- a Division of Clinical Epidemiology and Aging Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Ben Schöttker
- a Division of Clinical Epidemiology and Aging Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,b Network Aging Research , University of Heidelberg , Heidelberg , Germany
| | - Lutz Philipp Breitling
- a Division of Clinical Epidemiology and Aging Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Hermann Brenner
- a Division of Clinical Epidemiology and Aging Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,b Network Aging Research , University of Heidelberg , Heidelberg , Germany.,c Division of Preventive Oncology , German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) , Heidelberg , Germany.,d German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
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25
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Núñez de Villavicencio-Díaz T, Ramos Gómez Y, Oliva Argüelles B, Fernández Masso JR, Rodríguez-Ulloa A, Cruz García Y, Guirola-Cruz O, Perez-Riverol Y, Javier González L, Tiscornia I, Victoria S, Bollati-Fogolín M, Besada Pérez V, Guerra Vallespi M. Comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells. J Proteomics 2015; 126:163-71. [DOI: 10.1016/j.jprot.2015.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/06/2015] [Accepted: 05/19/2015] [Indexed: 10/25/2022]
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26
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Abstract
The pathogenesis of Alzheimer's disease (AD) is a critical unsolved question; and although recent studies have demonstrated a strong association between altered brain immune responses and disease progression, the mechanistic cause of neuronal dysfunction and death is unknown. We have previously described the unique CVN-AD mouse model of AD, in which immune-mediated nitric oxide is lowered to mimic human levels, resulting in a mouse model that demonstrates the cardinal features of AD, including amyloid deposition, hyperphosphorylated and aggregated tau, behavioral changes, and age-dependent hippocampal neuronal loss. Using this mouse model, we studied longitudinal changes in brain immunity in relation to neuronal loss and, contrary to the predominant view that AD pathology is driven by proinflammatory factors, we find that the pathology in CVN-AD mice is driven by local immune suppression. Areas of hippocampal neuronal death are associated with the presence of immunosuppressive CD11c(+) microglia and extracellular arginase, resulting in arginine catabolism and reduced levels of total brain arginine. Pharmacologic disruption of the arginine utilization pathway by an inhibitor of arginase and ornithine decarboxylase protected the mice from AD-like pathology and significantly decreased CD11c expression. Our findings strongly implicate local immune-mediated amino acid catabolism as a novel and potentially critical mechanism mediating the age-dependent and regional loss of neurons in humans with AD.
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27
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Li X, Li D, Zhuang Y, Shi Q, Wei W, Ju X. Overexpression of miR-708 and its targets in the childhood common precursor B-cell ALL. Pediatr Blood Cancer 2013; 60:2060-7. [PMID: 23970374 DOI: 10.1002/pbc.24583] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/07/2013] [Indexed: 01/08/2023]
Abstract
BACKGROUND The critical function of microRNAs in the pathogenesis and prognosis of hematopoietic cancer has become increasingly apparent. However, only a few miRNAs have been reported to be altered in acute lymphocytic leukemia (ALL). PROCEDURES To uncover aberrantly expressed miRNAs in pediatric B-cell ALL, our study employed genome-wide miRNA microarray analysis and stem-loop real-time quantitative polymerase chain reaction (qRT-PCR) to examine common precursor B-cell ALL samples. The target genes of miRNA-708 were then identified and verified by bioinformatics, dual-luciferase reporter assay, qRT-PCR, and Western blot. RESULTS Significant upregulation of miR-708, miR-210, and miR-181b, and downregulation of miR-345 and miR-27a were observed in common precursor B-cell ALL (common-ALL) samples (P < 0.05). In addition, elevated expression of miR-708 and miR-181b were found in high-risk common-ALL compared to standard and intermediate ones. miR-708 inhibited luciferase reporter activity by binding to the 3'-untranslated regions (3'-UTRs) of CNTFR, NNAT, and GNG12 mRNA in HEK-293 cell line and suppressed the protein levels of CNTFR, NNAT, and GNG12 in Jurkat cells. In addition, mRNA levels of CNTFR and NNAT, but not of GNG12, were found to be downregulated in high risk common-ALL samples. Mutational analysis revealed that miR-708 binds to the 394-400 bp sequence region of the 3'-UTR of CNTFR mRNA. CONCLUSION The expression level of miR-708 reflects differences among the clinical types of common-ALL, and CNTFR, NNAT, and GNG12 were identified as targets of miR-708.
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Affiliation(s)
- Xue Li
- Department of Pediatrics, Cryomedicine Laboratory, Qilu Hospital, Shandong University, Shandong, PR China
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28
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McBride WJ, Kimpel MW, McClintick JN, Ding ZM, Hauser SR, Edenberg HJ, Bell RL, Rodd ZA. Changes in gene expression within the ventral tegmental area following repeated excessive binge-like alcohol drinking by alcohol-preferring (P) rats. Alcohol 2013; 47:367-80. [PMID: 23714385 DOI: 10.1016/j.alcohol.2013.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/02/2013] [Accepted: 04/17/2013] [Indexed: 12/11/2022]
Abstract
The objective of this study was to detect changes in gene expression in the ventral tegmental area (VTA) following repeated excessive binge-like ('loss-of-control') alcohol drinking by alcohol-preferring (P) rats. Adult female P rats (n = 7) were given concurrent access to 10, 20, and 30% EtOH for 4 1-h sessions daily for 10 weeks followed by 2 cycles of 2 weeks of abstinence and 2 weeks of EtOH access. Rats were sacrificed by decapitation 3 h after the 4th daily EtOH-access session at the end of the second 2-week relapse period. A water-control group of female P rats (n = 8) was also sacrificed. RNA was prepared from micro-punch samples of the VTA from individual rats; analyses were conducted with Affymetrix Rat 230.2 GeneChips. Ethanol intakes were 1.2-1.7 g/kg per session, resulting in blood levels >200 mg% at the end of the 4th session. There were 211 unique named genes that significantly differed (FDR = 0.1) between the water and EtOH groups. Bioinformatics analyses indicated alterations in a) transcription factors that reduced excitation-coupled transcription and promoted excitotoxic neuronal damage involving clusters of genes associated with Nfkbia, Fos, and Srebf1, b) genes that reduced cholesterol and fatty acid synthesis, and increased protein degradation, and c) genes involved in cell-to-cell interactions and regulation of the actin cytoskeleton. Among the named genes, there were 62 genes that showed differences between alcohol-naïve P and non-preferring (NP) rats, with 43 of the genes changing toward NP-like expression levels following excessive binge-like drinking in the P rats. These genes are involved in a pro-inflammatory response, and enhanced response to glucocorticoids and steroid hormones. Overall, the results of this study indicate that the repeated excessive binge-like alcohol drinking can change the expression of genes that may alter neuronal function in several ways, some of which may be deleterious.
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Affiliation(s)
- William J McBride
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indiana University-Purdue University at Indianapolis, Indianapolis, IN 46202, USA.
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29
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Niesman IR, Zemke N, Fridolfsson HN, Haushalter KJ, Levy K, Grove A, Schnoor R, Finley JC, Patel PM, Roth DM, Head BP, Patel HH. Caveolin isoform switching as a molecular, structural, and metabolic regulator of microglia. Mol Cell Neurosci 2013; 56:283-97. [PMID: 23851187 DOI: 10.1016/j.mcn.2013.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/11/2013] [Accepted: 07/02/2013] [Indexed: 11/28/2022] Open
Abstract
Microglia are ramified cells that serve as central nervous system (CNS) guardians, capable of proliferation, migration, and generation of inflammatory cytokines. In non-pathological states, these cells exhibit ramified morphology with processes intermingling with neurons and astrocytes. Under pathological conditions, they acquire a rounded amoeboid morphology and proliferative and migratory capabilities. Such morphological changes require cytoskeleton rearrangements. The molecular control points for polymerization states of microtubules and actin are still under investigation. Caveolins (Cavs), membrane/lipid raft proteins, are expressed in inflammatory cells, yet the role of caveolin isoforms in microglia physiology is debatable. We propose that caveolins provide a necessary control point in the regulation of cytoskeletal dynamics, and thus investigated a role for caveolins in microglia biology. We detected mRNA and protein for both Cav-1 and Cav-3. Cav-1 protein was significantly less and localized to plasmalemma (PM) and cytoplasmic vesicles (CVs) in the microglial inactive state, while the active (amoeboid-shaped) microglia exhibited increased Cav-1 expression. In contrast, Cav-3 was highly expressed in the inactive state and localized with cellular processes and perinuclear regions and was detected in active amoeboid microglia. Pharmacological manipulation of the cytoskeleton in the active or non-active state altered caveolin expression. Additionally, increased Cav-1 expression also increased mitochondrial respiration, suggesting possible regulatory roles in cell metabolism necessary to facilitate the morphological changes. The present findings strongly suggest that regulation of microglial morphology and activity are in part due to caveolin isoforms, providing promising novel therapeutic targets in CNS injury or disease.
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Affiliation(s)
- Ingrid R Niesman
- Department of Anesthesiology, University of California, San Diego, La Jolla, CA 92093, USA.
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30
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Lee MS, Kim B, Lee SM, Cho WC, Lee WB, Kang JS, Choi UY, Lyu J, Kim YJ. Genome-wide profiling of in vivo LPS-responsive genes in splenic myeloid cells. Mol Cells 2013; 35:498-513. [PMID: 23666259 PMCID: PMC3887871 DOI: 10.1007/s10059-013-2349-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 04/09/2013] [Accepted: 04/12/2013] [Indexed: 11/24/2022] Open
Abstract
Lipopolysaccharide (LPS), the major causative agent of bacterial sepsis, has been used by many laboratories in genome-wide expression profiling of the LPS response. However, these studies have predominantly used in vitro cultured macrophages (Macs), which may not accurately reflect the LPS response of these innate immune cells in vivo. To overcome this limitation and to identify inflammatory genes in vivo, we have profiled genome-wide expression patterns in non-lymphoid, splenic myeloid cells extracted directly from LPS-treated mice. Genes encoding factors known to be involved in mediating or regulating inflammatory processes, such as cytokines and chemokines, as well as many genes whose immunological functions are not well known, were strongly induced by LPS after 3 h or 8 h of treatment. Most of the highly LPS-responsive genes that we randomly selected from the microarray data were independently confirmed by quantitative RT-PCR, implying that our microarray data are quite reliable. When our in vivo data were compared to previously reported microarray data for in vitro LPS-treated Macs, a significant proportion (∼20%) of the in vivo LPS-responsive genes defined in this study were specific to cells exposed to LPS in vivo, but a larger proportion of them (∼60%) were influenced by LPS in both in vitro and in vivo settings. This result indicates that our in vivo LPS-responsive gene set includes not only previously identified in vitro LPS-responsive genes but also novel LPS-responsive genes. Both types of genes would be a valuable resource in the future for understanding inflammatory responses in vivo.
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Affiliation(s)
- Myeong Sup Lee
- Department of Biochemistry, College of Life Science and Biotechnology, World Class University, Yonsei University, Seoul 120–749,
Korea
| | - Byungil Kim
- Department of Biochemistry, College of Life Science and Biotechnology, World Class University, Yonsei University, Seoul 120–749,
Korea
| | - Sun-Min Lee
- Department of Biochemistry, College of Life Science and Biotechnology, World Class University, Yonsei University, Seoul 120–749,
Korea
| | - Woo-Cheul Cho
- Department of Biochemistry, College of Life Science and Biotechnology, World Class University, Yonsei University, Seoul 120–749,
Korea
| | - Wook-Bin Lee
- Department of Biochemistry, College of Life Science and Biotechnology, World Class University, Yonsei University, Seoul 120–749,
Korea
| | - Ji-Seon Kang
- Department of Biochemistry, College of Life Science and Biotechnology, World Class University, Yonsei University, Seoul 120–749,
Korea
| | - Un Yung Choi
- Department of Biochemistry, College of Life Science and Biotechnology, World Class University, Yonsei University, Seoul 120–749,
Korea
| | - Jaemyun Lyu
- Department of Biochemistry, College of Life Science and Biotechnology, World Class University, Yonsei University, Seoul 120–749,
Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, World Class University, Yonsei University, Seoul 120–749,
Korea
- Department of Integrated OMICS for Biomedical Sciences, World Class University, Yonsei University, Seoul 120–749,
Korea
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31
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Fatemi SH, Folsom TD, Rooney RJ, Mori S, Kornfield TE, Reutiman TJ, Kneeland RE, Liesch SB, Hua K, Hsu J, Patel DH. The viral theory of schizophrenia revisited: abnormal placental gene expression and structural changes with lack of evidence for H1N1 viral presence in placentae of infected mice or brains of exposed offspring. Neuropharmacology 2011; 62:1290-8. [PMID: 21277874 DOI: 10.1016/j.neuropharm.2011.01.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 12/22/2010] [Accepted: 01/10/2011] [Indexed: 12/19/2022]
Abstract
Researchers have long noted an excess of patients with schizophrenia were born during the months of January and March. This winter birth effect has been hypothesized to result either from various causes such as vitamin D deficiency (McGrath, 1999; McGrath et al., 2010), or from maternal infection during pregnancy. Infection with a number of viruses during pregnancy including influenza, and rubella are known to increase the risk of schizophrenia in the offspring (Brown, 2006). Animal models using influenza virus or Poly I:C, a viral mimic, have been able to replicate many of the brain morphological, genetic, and behavioral deficits of schizophrenia (Meyer et al., 2006, 2008a, 2009; Bitanihirwe et al., 2010; Meyer and Feldon, 2010; Short et al., 2010). Using a murine model of prenatal viral infection, our laboratory has shown that viral infection on embryonic days 9, 16, and 18 leads to abnormal expression of brain genes and brain structural abnormalities in the exposed offspring (Fatemi et al., 2005, 2008a,b, 2009a,b). The purpose of the current study was to examine gene expression and morphological changes in the placenta, hippocampus, and prefrontal cortex as a result of viral infection on embryonic day 7 of pregnancy. Pregnant mice were either infected with influenza virus [A/WSN/33 strain (H1N1)] or sham-infected with vehicle solution. At E16, placentas were harvested and prepared for either microarray analysis or for light microscopy. We observed significant, upregulation of 77 genes and significant downregulation of 93 genes in placentas. In brains of exposed offspring following E7 infection, there were changes in gene expression in prefrontal cortex (6 upregulated and 24 downregulated at P0; 5 upregulated and 14 downregulated at P56) and hippocampus (4 upregulated and 6 downregulated at P0; 6 upregulated and 13 downregulated at P56). QRT-PCR verified the direction and magnitude of change for a number of genes associated with hypoxia, inflammation, schizophrenia, and autism. Placentas from infected mice showed a number of morphological abnormalities including presence of thrombi and increased presence of immune cells. Additionally, we searched for presence of H1N1 viral-specific genes for M1/M2, NA, and NS1 in placentas of infected mice and brains of exposed offspring and found none. Our results demonstrate that prenatal viral infection disrupts structure and gene expression of the placenta, hippocampus, and prefrontal cortex potentially explaining deleterious effects in the exposed offspring without evidence for presence of viral RNAs in the target tissues.
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Affiliation(s)
- S Hossein Fatemi
- Department of Psychiatry, Division of Neuroscience Research, University of Minnesota Medical School, 420 Delaware St SE, MMC 392, Minneapolis, MN 55455, USA.
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Bigler Wang D, Sherman NE, Shannon JD, Leonhardt SA, Mayeenuddin LH, Yeager M, McIntire WE. Binding of β4γ5 by adenosine A1 and A2A receptors determined by stable isotope labeling with amino acids in cell culture and mass spectrometry. Biochemistry 2010; 50:207-20. [PMID: 21128647 DOI: 10.1021/bi101227y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Characterization of G protein βγ dimer isoform expression in different cellular contexts has been impeded by low levels of protein expression, broad isoform heterogeneity, and antibodies of limited specificity, sensitivity, or availability. As a new approach, we used quantitative mass spectrometry to characterize native βγ dimers associated with adenosine A(1):α(i1) and adenosine A(2A):α(S) receptor fusion proteins expressed in HEK-293 cells. Cells expressing A(1):α(i1) were cultured in media containing [(13)C(6)]Arg and [(13)C(6)]Lys and βγ labeled with heavy isotopes purified. Heavy βγ was combined with either recombinant βγ purified from Sf9 cells, βγ purified from the A(2A):α(S) expressed in HEK-293 cells cultured in standard media, or an enriched βγ fraction from HEK-293 cells. Samples were separated by SDS-PAGE, protein bands containing β and γ were excised, digested with trypsin, and separated by HPLC, and isotope ratios were analyzed by mass spectrometry. Three β isoforms, β(1), β(2), and β(4), and seven γ isoforms, γ(2), γ(4), γ(5), γ(7), γ(10), γ(11), and γ(12), were identified in the analysis. β(1) and γ(5) were most abundant in the enriched βγ fraction, and this βγ profile was generally mirrored in the fusion proteins. However, both A(2A):α(S) and A(1):α(i1) bound more β(4) and γ(5) compared to the enriched βγ fraction; also, more β(4) was associated with A(2A):α(S) than A(1):α(i1). Both fusion proteins also contained less γ(2), γ(10), and γ(12) than the enriched βγ fraction. These results suggest that preferences for particular βγ isoforms may be driven in part by structural motifs common to adenosine receptor family members.
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Affiliation(s)
- Dora Bigler Wang
- Department of Pharmacology, University of Virginia Health System, Charlottesville, 22908, United States
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