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Sarlo Davila KM, Boggiatto P, Olsen S, Lippolis JD, Crooker BA, Putz EJ. Effect of selection genotype on immune response to Brucella abortus RB51 in Holstein cattle. Anim Genet 2024; 55:47-54. [PMID: 37946616 DOI: 10.1111/age.13372] [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: 07/10/2023] [Revised: 09/11/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Genetic selection for milk production traits in US Holsteins has affected numerous genes associated with reproduction and immunity. This study compares the transcriptomic response of peripheral blood mononuclear cells to an in vitro Brucella abortus strain RB51 (RB51) bacterial challenge between contemporary Holsteins and Holsteins that have not been selected for milk production traits since the mid-1960s. Total RNA was extracted from peripheral blood mononuclear cells from four contemporary and four unselected lactating, primiparous cows following 24-h incubation with or without stimulation with RB51 bacteria. RNA was sequenced and reads analyzed using tools from galaxy.scinet.usda.gov. A total of 412 differentially expressed genes (false discovery rate p < 0.05, log fold change > |1|) were identified. The upregulated genes (genes with higher expression in contemporary than unselected cattle) were enriched for 19 terms/pathways, including alanine, aspartate, and glutamate metabolism, indicating a cellular stress response. Downregulated genes (genes with higher expression in unselected than contemporary cows) were enriched for 37 terms/pathways, representing diverse immune responses, including natural killer cell-mediated immunity, interferon-γ production, negative regulation of interleukin-10 production, and cytokine receptor activity indicating a broad immune response with an emphasis on immune defense. These results provide evidence that differences exist between the two genotypes in response to in vitro bacterial challenge. This suggests that contemporary cows, genetically selected for milk production, may have reduced immune function, including limitations in response to intracellular bacteria.
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Affiliation(s)
- Kaitlyn M Sarlo Davila
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA
| | - Paola Boggiatto
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA
| | - Steven Olsen
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA
| | - John D Lippolis
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA
| | - Brian A Crooker
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - Ellie J Putz
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA
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Chen X, Li Z, Wang X, Zhou J, Wei Q, Chen K, Jiang R. Investigation and verification of GIMAP6 as a robust biomarker for prognosis and tumor immunity in lung adenocarcinoma. J Cancer Res Clin Oncol 2023; 149:11041-11055. [PMID: 37338641 DOI: 10.1007/s00432-023-04980-z] [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: 03/18/2023] [Accepted: 06/10/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND AND AIM According to previous reports, GTPase of immunity-associated protein 6 (GIMAP6) is essential for autophagy. However, it is unclear how GIMAP6 affects the development and tumor immunity of lung adenocarcinoma (LUAD). METHODS In the present study, the role of GIMAP6 in vivo and in vitro was examined using reverse transcription-quantitative PCR, western blotting, and Cell Counting Kit-8, colony formation and Transwell assays. Datasets from The Cancer Genome Atlas and Genotype-Tissue Expression databases were thoroughly analyzed using R software. A nomogram was created using GIMAP6 and prognostic characteristics. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and Gene Set Enrichment Analysis were applied to explore the potential mechanism of GIMAP6 in lung cancer. The link between GIMAP6 and the immunological landscape was studied using single-cell RNA sequencing datasets from Tumor Immune Estimation Resource (TIMER) 2.0 and Tumor Immune Single-cell Hub. RESULTS Patients with high GIMAP6 expression had improved overall and disease-specific survival compared with those patients with low GIMAP6 expression. According to the receiver operating characteristic and calibration curve, the nomogram based on T stage, N stage and GIMAP6 had predictive value for prognosis. According to functional enrichment analysis, GIMAP6 was primarily involved in T-cell receptor signaling pathway, chemokine signaling pathway, cytokine and cytokine receptor interaction. GIMAP6 was shown to be favorably linked with the infiltration of immune cells and immune-related molecules, including cytotoxic T-lymphocyte associated protein 4, programmed death-ligand 1, and T cell immunoreceptor with Ig and ITIM domains, by single-cell sequencing and TIMER2.0 analysis. The role of GIMAP6 in lung cancer cell proliferation, invasion, migration and immunity was experimentally verified. CONCLUSION These findings confirmed that GIMAP6 was an effective prognostic molecule that was involved in the regulation of the immune microenvironment of LUAD, and may become a predictor for the efficacy of immunotherapy.
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Affiliation(s)
- Xiuqiong Chen
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute and Hospital, Tianjin Medical University, Tianjin, 300060, People's Republic of China
| | - Zhaona Li
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute and Hospital, Tianjin Medical University, Tianjin, 300060, People's Republic of China
| | - Xinyue Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute and Hospital, Tianjin Medical University, Tianjin, 300060, People's Republic of China
| | - Jing Zhou
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute and Hospital, Tianjin Medical University, Tianjin, 300060, People's Republic of China
| | - Qianhui Wei
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute and Hospital, Tianjin Medical University, Tianjin, 300060, People's Republic of China
| | - Kaidi Chen
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute and Hospital, Tianjin Medical University, Tianjin, 300060, People's Republic of China
| | - Richeng Jiang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, China.
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute and Hospital, Tianjin Medical University, Tianjin, 300060, People's Republic of China.
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Prognostic Value of GIMAP4 and Its Role in Promoting Immune Cell Infiltration into Tumor Microenvironment of Lung Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7440189. [PMID: 36246963 PMCID: PMC9560834 DOI: 10.1155/2022/7440189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/24/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
GIMAPs are recognized as an important regulator in the carcinogenesis and development of lung cancer, but the function of GIMAP4 in the tumor microenvironment (TME) of lung cancers is unclear. In this study, we investigated the expression and variation of GIMAP4 in lung adenocarcinoma (LUAD), to explore its association with infiltration of immune cells. The Cancer Genome Atlas (TCGA) data and Gene Expression Omnibus (GEO) data were analyzed. Infiltration of immune cells was identified with TIMER (Tumor Immune Estimation Resource) and TISIDB (an integrated repository portal for tumor-immune system interactions). GIMAP4 expression declined in non-small-cell lung cancer (NSCLC), correlated with a poor overall survival (OS) in LUAD, indicating that GIMAP4 was a promising prognostic biomarker in LUAD. GIMAP4 mutation frequency was 1.76% in TCGA cohort and was relevant to the expression of immune components. TIMER and CIBERSORT analysis further confirmed that high GIMAP4 expression possibly promoted immune cell infiltration into the TME, with low GIMAP4 impairing the efficacy of immunotherapies targeting common immune check point inhibitors (ICI). GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses were performed to provide insights into biological processes involved in LUAD. GIMAP4 was expected to be a prognostic biomarker in LUAD and provides potential adjuvant or neoadjuvant therapeutic strategies for targeting ICIs.
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Li Q, Jiang Y, Song N, Zhou B, Li Z, Lin L. An Immune-Related Genetic Feature Depicted the Heterogeneous Nature of Lung Adenocarcinoma and Squamous Cell Carcinoma and Their Distinctive Predicted Drug Responses. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8447083. [PMID: 36071867 PMCID: PMC9442502 DOI: 10.1155/2022/8447083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Abstract
One of the primary causes of global cancer-associated mortality is lung cancer (LC). Current improvements in the management of LC rely mainly on the advancement of patient stratification, both molecularly and clinically, to achieve the maximal therapeutic benefit, while most LC screening protocols remain underdeveloped. In this research, we first employed two algorithms (ESTIMATE and xCell) to calculate the immune/stromal infiltration scores. This helped identify the altered immune infiltration landscapes in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). Afterward, based on their immune-related characteristics, we successfully stratified the LUAD and LUSC into 2 and 3 clusters, respectively. Different from the conventional bioinformatic approaches that start from the investigation of differential expression of single genes, differentially enriched curated gene sets identified through gene set variation analyses (GSVA) were curated, and gene names were reconstructed afterward. Furthermore, weighted gene correlation network analyses (WGCNA) were used to reveal hub genes highly connected with the clustering process. Actual expression levels of critical hub genes among different clusters were compared and so were the functional pathways these genes enriched into. Lastly, a computational method was applied to predict and compare the responses of each cluster to primary therapeutic agents. The heterogeneity presented in our study, along with the drug responses expected for identified clusters, may shed light on future exploration of combination immunochemotherapy that facilitates the optimization of individualized therapy.
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Affiliation(s)
- Qiuyuan Li
- Department of Thoracic Surgery, Tongji University Shanghai Pulmonary Hospital, No. 507 Zhengmin Rd., Shanghai, China
| | - Yan Jiang
- Department of Thoracic Surgery, Tongji University Shanghai Pulmonary Hospital, No. 507 Zhengmin Rd., Shanghai, China
| | - Nan Song
- Department of Thoracic Surgery, Tongji University Shanghai Pulmonary Hospital, No. 507 Zhengmin Rd., Shanghai, China
| | - Bin Zhou
- Department of Thoracic Surgery, Tongji University Shanghai Pulmonary Hospital, No. 507 Zhengmin Rd., Shanghai, China
| | - Zhao Li
- Department of Thoracic Surgery, Tongji University Shanghai Pulmonary Hospital, No. 507 Zhengmin Rd., Shanghai, China
| | - Lei Lin
- Department of Thoracic Surgery, Tongji University Shanghai Pulmonary Hospital, No. 507 Zhengmin Rd., Shanghai, China
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5
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Cui H, Ma R, Hu T, Xiao GG, Wu C. Bioinformatics Analysis Highlights Five Differentially Expressed Genes as Prognostic Biomarkers of Cervical Cancer and Novel Option for Anticancer Treatment. Front Cell Infect Microbiol 2022; 12:926348. [PMID: 35782114 PMCID: PMC9247199 DOI: 10.3389/fcimb.2022.926348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Cervical cancer is one of the most common gynecological malignancies and is related to human papillomavirus (HPV) infection, especially high-risk type HPV16 and HPV18. Aberrantly expressed genes are involved in the development of cervical cancer, which set a genetic basis for patient prognosis. In this study, we identified a set of aberrantly expressed key genes from The Cancer Genome Atlas (TCGA) database, which could be used to accurately predict the survival rate of patients with cervical squamous cell carcinoma (CESC). A total of 3,570 genes that are differentially expressed between normal and cancerous samples were analyzed by the algorithm of weighted gene co-expression network analysis (WGCNA): 1,606 differentially expressed genes (DEGs) were upregulated, while 1,964 DEGs were downregulated. Analysis of these DEGs divided them into 7 modules including 76 hub genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis revealed a significant increase of genes related to cell cycle, DNA replication, p53 signaling pathway, cGMP-PKG signaling pathway, and Fanconi anemia (FA) pathway in CESC. These biological activities are previously reported to associate with cervical cancer or/and HPV infection. Finally, we highlighted 5 key genes (EMEMP2, GIMAP4, DYNC2I2, FGF13-AS1, and GIMAP1) as robust prognostic markers to predict patient’s survival rate (p = 3.706e-05) through univariate and multivariate regression analyses. Thus, our study provides a novel option to set up several biomarkers for cervical cancer prognosis and anticancer drug targets.
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Affiliation(s)
- Hongtu Cui
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
| | - Ruilin Ma
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
| | - Tao Hu
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
| | - Gary Guishan Xiao
- School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian, China
| | - Chengjun Wu
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
- *Correspondence: Chengjun Wu,
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Dong H, Dong Z, Wang F, Wang G, Luo X, Lei C, Chen J. Whole Genome Sequencing Provides New Insights Into the Genetic Diversity and Coat Color of Asiatic Wild Ass and Its Hybrids. Front Genet 2022; 13:818420. [PMID: 35646088 PMCID: PMC9135160 DOI: 10.3389/fgene.2022.818420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
The diversity of livestock coat color results from human positive selection and is an indispensable part of breed registration. As an important biodiversity resource, Asiatic wild ass has many special characteristics, including the most visualized feature, its yellowish-brown coat color, and excellent adaptation. To explore the genetic mechanisms of phenotypic characteristics in Asiatic wild ass and its hybrids, we resequenced the whole genome of one Mongolian Kulan (a subspecies of Asiatic wild ass) and 29 Kulan hybrids (Mongolian Kulan ♂×Xinjiang♀), and the ancestor composition indicated the true lineage of the hybrids. XP-EHH (Cross Population Extended Haplotype Homozygosity), θπ-ratio (Nucleotide Diversity Ratio), CLR (Composite Likelihood Ratio) and θπ (Nucleotide Diversity) methods were used to detect the candidate regions of positive selection in Asiatic wild ass and its hybrids. Several immune genes (DEFA1, DEFA5, DEFA7, GIMAP4, GIMAP1, IGLC1, IGLL5, GZMB and HLA) were observed by the CLR and θπ methods. XP-EHH and θπ-ratio revealed that these genes are potentially responsible for coat color (KITLG) and meat quality traits (PDE1B and MYLK2). Furthermore, the heatmap was able to show the clear difference in the haplotype of the KITLG gene between the Kulan hybrids and Asiatic wild ass group and the Guanzhong black donkey group, which is a powerful demonstration of the key role of KITLG in donkey color. Therefore, our study may provide new insights into the genetic basis of coat color, meat quality traits and immunity of Asiatic wild ass and its hybrids.
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Affiliation(s)
- Hong Dong
- College of Animal Science and Technology, SHIHEZI University, Shihezi, China
| | - Zheng Dong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Gang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jingbo Chen
- College of Animal Science and Technology, SHIHEZI University, Shihezi, China
- *Correspondence: Jingbo Chen,
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7
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Liu L, Chen J, Zhang H, Ye J, Moore C, Lu C, Fang Y, Fu YX, Li B. Concurrent delivery of immune checkpoint blockade modulates T cell dynamics to enhance neoantigen vaccine-generated antitumor immunity. NATURE CANCER 2022; 3:437-452. [PMID: 35393580 PMCID: PMC9050907 DOI: 10.1038/s43018-022-00352-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 02/24/2022] [Indexed: 12/30/2022]
Abstract
Neoantigen vaccines aiming to induce tumor-specific T cell responses have achieved promising antitumor effects in early clinical trials. However, the underlying mechanism regarding response or resistance to this treatment is unclear. Here we observe that neoantigen vaccine-generated T cells can synergize with the immune checkpoint blockade for effective tumor control. Specifically, we performed single-cell sequencing on over 100,000 T cells and uncovered that combined therapy induces an antigen-specific CD8 T cell population with active chemokine signaling (Cxcr3+/Ccl5+), lower co-inhibitory receptor expression (Lag3-/Havcr2-) and higher cytotoxicity (Fasl+/Gzma+). Furthermore, generation of neoantigen-specific T cells in the draining lymph node is required for combination treatment. Signature genes of this unique population are associated with T cell clonal frequency and better survival in humans. Our study profiles the dynamics of tumor-infiltrating T cells during neoantigen vaccine and immune checkpoint blockade treatments and high-dimensionally identifies neoantigen-reactive T cell signatures for future development of therapeutic strategies.
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Affiliation(s)
- Longchao Liu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jiahui Chen
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hongyi Zhang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jianfeng Ye
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Casey Moore
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Changzheng Lu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Fang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang-Xin Fu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Bo Li
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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8
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Revealing therapeutic targets and mechanism of baicalin for anti-chronic gastritis using proteomic analysis of the gastric tissue. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1196:123214. [DOI: 10.1016/j.jchromb.2022.123214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 02/19/2022] [Accepted: 03/04/2022] [Indexed: 11/24/2022]
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Diaz-Lundahl S, Sundaram AYM, Gillund P, Gilfillan GD, Olsaker I, Krogenæs A. Gene Expression in Embryos From Norwegian Red Bulls With High or Low Non Return Rate: An RNA-Seq Study of in vivo-Produced Single Embryos. Front Genet 2022; 12:780113. [PMID: 35096004 PMCID: PMC8795813 DOI: 10.3389/fgene.2021.780113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/13/2021] [Indexed: 11/24/2022] Open
Abstract
During the last decade, paternal effects on embryo development have been found to have greater importance than previously believed. In domestic cattle, embryo mortality is an issue of concern, causing huge economical losses for the dairy cattle industry. In attempts to reveal the paternal influence on embryo death, recent approaches have used transcriptome profiling of the embryo to find genes and pathways affected by different phenotypes in the bull. For practical and economic reasons, most such studies have used in vitro produced embryos. The aim of the present study was to investigate the differences in the global transcriptome of in vivo produced embryos, derived from sires with either high or low field fertility measured as the non-return rate (NRR) on day 56 after first AI of the inseminated cows. Superovulated heifers (n = 14) in the age span of 12–15 months were artificially inseminated with semen from either high fertility (n = 6) or low fertility (n = 6) bulls. On day seven after insemination, embryos were retrieved through uterine flushing. Embryos with first grade quality and IETS stage 5 (early blastocyst), 6 (blastocyst) or 7 (expanded blastocyst) were selected for further processing. In total, RNA extracted from 24 embryos was sequenced using Illumina sequencing, followed by differential expression analysis and gene set enrichment analysis. We found 62 genes differentially expressed between the two groups (adj.p-value<0.05), of which several genes and their linked pathways could explain the different developmental capacity. Transcripts highly expressed in the embryos from low fertility bulls were related to sterol metabolism and terpenoid backbone synthesis, while transcripts highly expressed in the high fertility embryos were linked to anti-apoptosis and the regulation of cytokine signaling. The leukocyte transendothelial migration and insulin signaling pathways were associated with enrichments in both groups. We also found some highly expressed transcripts in both groups which can be considered as new candidates in the regulation of embryo development. The present study is an important step in defining the paternal influence in embryonic development. Our results suggest that the sire’s genetic contribution affects several important processes linked to pre-and peri implantation regulation in the developing embryo.
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Affiliation(s)
- Sofia Diaz-Lundahl
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Arvind Y M Sundaram
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Per Gillund
- Geno Breeding and AI Association, Hamar, Norway
| | - Gregor Duncan Gilfillan
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ingrid Olsaker
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Anette Krogenæs
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
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Kron NS, Fieber LA. Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica. PLoS One 2021; 16:e0252647. [PMID: 34116561 PMCID: PMC8195618 DOI: 10.1371/journal.pone.0252647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/20/2021] [Indexed: 01/08/2023] Open
Abstract
Aging of the nervous system is typified by depressed metabolism, compromised proteostasis, and increased inflammation that results in cognitive impairment. Differential expression analysis is a popular technique for exploring the molecular underpinnings of neural aging, but technical drawbacks of the methodology often obscure larger expression patterns. Co-expression analysis offers a robust alternative that allows for identification of networks of genes and their putative central regulators. In an effort to expand upon previous work exploring neural aging in the marine model Aplysia californica, we used weighted gene correlation network analysis to identify co-expression networks in a targeted set of aging sensory neurons in these animals. We identified twelve modules, six of which were strongly positively or negatively associated with aging. Kyoto Encyclopedia of Genes analysis and investigation of central module transcripts identified signatures of metabolic impairment, increased reactive oxygen species, compromised proteostasis, disrupted signaling, and increased inflammation. Although modules with immune character were identified, there was no correlation between genes in Aplysia that increased in expression with aging and the orthologous genes in oyster displaying long-term increases in expression after a virus-like challenge. This suggests anti-viral response is not a driver of Aplysia sensory neuron aging.
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Affiliation(s)
- N. S. Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
| | - L. A. Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
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Limoges MA, Cloutier M, Nandi M, Ilangumaran S, Ramanathan S. The GIMAP Family Proteins: An Incomplete Puzzle. Front Immunol 2021; 12:679739. [PMID: 34135906 PMCID: PMC8201404 DOI: 10.3389/fimmu.2021.679739] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022] Open
Abstract
Overview: Long-term survival of T lymphocytes in quiescent state is essential to maintain their cell numbers in secondary lymphoid organs and in peripheral circulation. In the BioBreeding diabetes-prone strain of rats (BB-DP), loss of functional GIMAP5 (GTPase of the immune associated nucleotide binding protein 5) results in profound peripheral T lymphopenia. This discovery heralded the identification of a new family of proteins initially called Immune-associated nucleotide binding protein (IAN) family. In this review we will use ‘GIMAP’ to refer to this family of proteins. Recent studies suggest that GIMAP proteins may interact with each other and also be involved in the movement of the cellular cargo along the cytoskeletal network. Here we will summarize the current knowledge on the characteristics and functions of GIMAP family of proteins.
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Affiliation(s)
- Marc-André Limoges
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Maryse Cloutier
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Madhuparna Nandi
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
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12
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Xu F, Shen J, Xu S. Multi-Omics Data Analyses Construct a Six Immune-Related Genes Prognostic Model for Cervical Cancer in Tumor Microenvironment. Front Genet 2021; 12:663617. [PMID: 34108992 PMCID: PMC8181403 DOI: 10.3389/fgene.2021.663617] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/15/2021] [Indexed: 12/26/2022] Open
Abstract
The cross-talk between tumor cells and the tumor microenvironment (TME) is an important factor in determining the tumorigenesis and progression of cervical cancer (CC). However, clarifying the potential mechanisms which trigger the above biological processes remains a challenge. The present study focused on immune-relevant differences at the transcriptome and somatic mutation levels through an integrative multi-omics analysis based on The Cancer Genome Atlas database. The objective of the study was to recognize the specific immune-related prognostic factors predicting the survival and response to immunotherapy of patients with CC. Firstly, eight hub immune-related prognostic genes were ultimately identified through construction of a protein–protein interaction network and Cox regression analysis. Secondly, 32 differentially mutated genes were simultaneously identified based on the different levels of immune infiltration. As a result, an immune gene-related prognostic model (IGRPM), including six factors (chemokine receptor 7 [CCR7], CD3d molecule [CD3D], CD3e molecule [CD3E], and integrin subunit beta 2 [ITGB2], family with sequence similarity 133 member A [FAM133A], and tumor protein p53 [TP53]), was finally constructed to forecast clinical outcomes of CC. Its predictive capability was further assessed and validated using the Gene Expression Omnibus validation set. In conclusion, IGRPM may be a promising prognostic signature to predict the prognoses and responses to immunotherapy of patients with CC. Moreover, the multi-omics study showed that IGRPM could be a novel therapeutic target for CC, which is a promising biomarker for indicating the immune-dominant status of the TME and revealing the potential mechanisms responsible for the tumorigenesis and progression of CC.
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Affiliation(s)
- Fangfang Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Jiacheng Shen
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Tongji University, Shanghai, China
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13
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Abstract
The CD8+ T cell noncytotoxic antiviral response (CNAR) was discovered during studies of asymptomatic HIV-infected subjects more than 30 years ago. In contrast to CD8+ T cell cytotoxic lymphocyte (CTL) activity, CNAR suppresses HIV replication without target cell killing. This activity has characteristics of innate immunity: it acts on all retroviruses and thus is neither epitope specific nor HLA restricted. The HIV-associated CNAR does not affect other virus families. It is mediated, at least in part, by a CD8+ T cell antiviral factor (CAF) that blocks HIV transcription. A variety of assays used to measure CNAR/CAF and the effects on other retrovirus infections are described. Notably, CD8+ T cell noncytotoxic antiviral responses have now been observed with other virus families but are mediated by different cytokines. Characterizing the protein structure of CAF has been challenging despite many biologic, immunologic, and molecular studies. It represents a low-abundance protein that may be identified by future next-generation sequencing approaches. Since CNAR/CAF is a natural noncytotoxic activity, it could provide promising strategies for HIV/AIDS therapy, cure, and prevention.
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Affiliation(s)
- Maelig G Morvan
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Fernando C Teque
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Jay A Levy
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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14
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Ortutay Z, Grönholm A, Laitinen M, Keresztes-Andrei M, Hermelo I, Pesu M. Identification of Novel Genetic Regulatory Region for Proprotein Convertase FURIN and Interferon Gamma in T Cells. Front Immunol 2021; 12:630389. [PMID: 33679774 PMCID: PMC7930619 DOI: 10.3389/fimmu.2021.630389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/22/2021] [Indexed: 12/30/2022] Open
Abstract
The proprotein convertase enzyme FURIN promotes the proteolytic maturation of pro-proteins and thereby it serves as an important factor for maintaining cellular homeostasis. In T cells, FURIN is critical for maintaining the T regulatory cell dependent peripheral immune tolerance and intact T helper cell polarization. The enzymatic activity of FURIN is directly associated with its expression levels, but genetic determinants for cell-type specific Furin gene regulation have remained elusive. By exploring the histone acetyltransferase p300 binding patterns in T helper cells, a putative regulatory region at ca. 20kB upstream of Furin gene was identified. When this region was deleted with CRISPR/Cas9 the production of Furin mRNA was significantly reduced in activated mouse T cells. Genome-wide RNA profiling by sequencing revealed that the novel Furin regulator region also impacted the expression of several genes that have previously been associated with the Th1 type hall mark cytokine IFNγ regulation or function. Finally, Furin genetic regulatory region was found to specifically promote the secretion of IFNγ by activated T cells. In sum, our data unravels the presence of Furin expression regulatory region in T cells that has characteristics of a super-enhancer for Th1 cell fate.
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Affiliation(s)
- Zsuzsanna Ortutay
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anna Grönholm
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Melina Laitinen
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Melinda Keresztes-Andrei
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Ismail Hermelo
- Computational Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Marko Pesu
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Laboratories, Tampere, Finland
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15
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Xu F, Shen J, Xu S. Integrated Bioinformatical Analysis Identifies GIMAP4 as an Immune-Related Prognostic Biomarker Associated With Remodeling in Cervical Cancer Tumor Microenvironment. Front Cell Dev Biol 2021; 9:637400. [PMID: 33553190 PMCID: PMC7858649 DOI: 10.3389/fcell.2021.637400] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022] Open
Abstract
Tumor microenvironment (TME) is emerging as an essential part of cervical cancer (CC) tumorigenesis and development, becoming a hotspot of research these years. However, comprehending the specific composition of TME is still facing enormous challenges, especially the immune and stromal components. In this study, we downloaded the RNA-seq profiles and somatic mutation data of 309 CC cases from The Cancer Genome Atlas (TCGA) database, which were analyzed by integrative bioinformatical methods. Initially, ESTIMATE computational method was employed to calculate the amount of immune and stromal components. Then, based on the high- and low-immunity cohorts, we recognized the differentially expressed genes (DEGs) as well as the differentially mutated genes (DMGs). Additionally, we conducted an intersection analysis of DEGs and DMGs, ultimately determining an immune-related prognostic signature, GTPase, IMAP Family Member 4 (GIMAP4). Moreover, sequential analyses demonstrated that GIMAP4 was a protective factor in CC, positively correlated with the overall survival (OS) and negatively with distant metastasis. Besides, we utilized the Gene Set Enrichment Analysis (GSEA) to explore the enrichment-pathways in high and low-expression cohorts of GIMAP4. The results indicated that the genes of the high-expression cohort had a high enrichment in immune-related biological processes and metabolic activities in the low one. Furthermore, CIBERSORT analysis was applied to evaluate the proportion of tumor-infiltrating immune cells (TICs), illustrating that several activated TICs were strongly associated with GIMAP4 expression, which suggested that GIMAP4 had the potential to be an indicator for the immune state in TME of CC. Hence, GIMAP4 contributed to predicting the CC patients’ clinical outcomes, such as survival rate, distant metastasis and immunotherapy response. Moreover, GIMAP4 could serve as a promising biomarker for TME remodeling, suggesting the possible underlying mechanisms of tumorigenesis and CC progression, which may provide different therapeutic perceptions of CC, and therefore improve treatment.
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Affiliation(s)
- Fangfang Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiacheng Shen
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
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16
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Martos SN, Campbell MR, Lozoya OA, Wang X, Bennett BD, Thompson IJB, Wan M, Pittman GS, Bell DA. Single-cell analyses identify dysfunctional CD16 + CD8 T cells in smokers. CELL REPORTS MEDICINE 2020; 1. [PMID: 33163982 PMCID: PMC7644053 DOI: 10.1016/j.xcrm.2020.100054] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tobacco smoke exposure contributes to the global burden of communicable and chronic diseases. To identify the immune cells affected by smoking, we use single-cell RNA sequencing on peripheral blood from smokers and nonsmokers. Transcriptomes reveal a subpopulation of FCGR3A (CD16)-expressing natural killer (NK)-like CD8 T lymphocytes that increase in smokers. Mass cytometry confirms elevated CD16+ CD8 T cells in smokers. Inferred as highly differentiated by pseudotime analysis, NK-like CD8 T cells express markers that are characteristic of effector memory re-expressing CD45RA T (TEMRA) cells. Indicative of immune aging, smokers’ CD8 T cells are biased toward differentiated cells, and smokers have fewer naive cells than nonsmokers. DNA methylation-based models show that smoking dose is associated with accelerated aging and decreased telomere length, a biomarker of T cell senescence. Immune aging accompanies T cell senescence, which can ultimately lead to impaired immune function. This suggests a role for smoking-induced, senescence-associated immune dysregulation in smoking-mediated pathologies. Smoking shifts the composition of CD8 T cells from naive to differentiated states NK-like CD16+ CD8 TEMRA cells are elevated in smokers and express GZMB and PRF1 DNA methylation links smoking dose with age acceleration and shortened telomeres CD8 T, CD4 T, NKT, NK, and monocytes express senescence-linked genes in smokers
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Affiliation(s)
- Suzanne N Martos
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, 27709.,These authors contributed equally
| | - Michelle R Campbell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, 27709.,These authors contributed equally
| | - Oswaldo A Lozoya
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Xuting Wang
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Brian D Bennett
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Isabel J B Thompson
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Ma Wan
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Gary S Pittman
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Douglas A Bell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, 27709
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17
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Mégarbané A, Piquemal D, Rebillat AS, Stora S, Pierrat F, Bruno R, Noguier F, Mircher C, Ravel A, Vilaire-Meunier M, Durand S, Lefranc G. Transcriptomic study in women with trisomy 21 identifies a possible role of the GTPases of the immunity-associated proteins (GIMAP) in the protection of breast cancer. Sci Rep 2020; 10:9447. [PMID: 32523132 PMCID: PMC7286899 DOI: 10.1038/s41598-020-66469-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/22/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND People with trisomy 21 (T21) are predisposed to developing hematological tumors, but have significantly lower-than-expected age-adjusted incidence rates of having a solid tumor. MATERIAL AND METHODS To identify novel genetic factors implicated in the lower breast cancer (BC) frequency observed in women with T21 than in the general population, we compared the transcriptome pattern of women with a homogeneous T21, aged more than 30 years, with or without BC, and tumoral BC tissue of control women with a normal karyotype from the study of Varley et al. (2014). RESULTS Differential analysis of gene expression between the 15 women in the T21 without BC group and BC patients in the other groups (two women with T21 and fifteen control women, respectively) revealed 154 differentially expressed genes, of which 63 were found to have similar expression profile (up- or downregulated). Of those 63 genes, four were in the same family, namely GIMAP4, GIMAP6, GIMAP7 and GIMAP8, and were strongly upregulated in the T21 without BC group compared to the other groups. A significant decrease in mRNA levels of these genes in BC tissues compared to non-tumor breast tissues was also noted. CONCLUSION We found that the expression of some GIMAPs is significantly higher in women with T21 without BC than in patients with sporadic BC. Our findings support the hypothesis that GIMAPs may play a tumor-suppressive role against BC, and open the possibility that they may also have the same role for other solid tumors in T21 patients. The search for new prognostic factors and hopefully new therapeutic or preventive strategies against BC are discussed.
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Affiliation(s)
- André Mégarbané
- Institut Jérôme Lejeune, CRB BioJeL, Paris, France. .,Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon.
| | | | | | | | | | | | | | | | - Aimé Ravel
- Institut Jérôme Lejeune, CRB BioJeL, Paris, France
| | | | | | - Gérard Lefranc
- Institut de Génétique Humaine, UMR 9002 CNRS-Université de Montpellier, Montpellier, France
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18
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Paluschinski M, Castoldi M, Schöler D, Bardeck N, Oenarto J, Görg B, Häussinger D. Tauroursodeoxycholate protects from glycochenodeoxycholate-induced gene expression changes in perfused rat liver. Biol Chem 2020; 400:1551-1565. [PMID: 31152635 DOI: 10.1515/hsz-2019-0204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/16/2019] [Indexed: 02/07/2023]
Abstract
Tauroursodeoxycholate (TUDC) is well known to protect against glycochenodeoxycholate (GCDC)-induced apoptosis in rat hepatocytes. In the present study, we analyzed whether TUDC also exerts protective effects by modulating GCDC-induced gene expression changes. For this, gene array-based transcriptome analysis and quantitative polymerase chain reaction (qPCR) were performed on RNA isolated from rat livers perfused with GCDC, TUDC or a combination of both (each 20 μm for 2 h). GCDC led to a significant increase of lactate dehydrogenase (LDH) into the effluent perfusate, which was prevented by TUDC. GCDC, TUDC and co-perfusion induced distinct gene expression changes. While GCDC upregulated the expression of several pro-inflammatory genes, co-perfusion with TUDC increased the expression of pro-proliferative and anti-apoptotic p53 target genes. In line with this, levels of serine20-phosphorylated p53 and of its target gene p21 were elevated by GCDC in a TUDC-sensitive way. GCDC upregulated the oxidative stress surrogate marker 8OH(d)G and the pro-apoptotic microRNAs miR-15b/16 and these effects were prevented by TUDC. The upregulation of miR-15b and miR-16 in GCDC-perfused livers was accompanied by a downregulation of several potential miR-15b and miR-16 target genes. The present study identified changes in the transcriptome of the rat liver which suggest, that TUDC is hepatoprotective by counteracting GCDC-induced gene expression changes.
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Affiliation(s)
- Martha Paluschinski
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Mirco Castoldi
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - David Schöler
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Nils Bardeck
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Jessica Oenarto
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Boris Görg
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
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19
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Tong DL, Kempsell KE, Szakmany T, Ball G. Development of a Bioinformatics Framework for Identification and Validation of Genomic Biomarkers and Key Immunopathology Processes and Controllers in Infectious and Non-infectious Severe Inflammatory Response Syndrome. Front Immunol 2020; 11:380. [PMID: 32318053 PMCID: PMC7147506 DOI: 10.3389/fimmu.2020.00380] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Sepsis is defined as dysregulated host response caused by systemic infection, leading to organ failure. It is a life-threatening condition, often requiring admission to an intensive care unit (ICU). The causative agents and processes involved are multifactorial but are characterized by an overarching inflammatory response, sharing elements in common with severe inflammatory response syndrome (SIRS) of non-infectious origin. Sepsis presents with a range of pathophysiological and genetic features which make clinical differentiation from SIRS very challenging. This may reflect a poor understanding of the key gene inter-activities and/or pathway associations underlying these disease processes. Improved understanding is critical for early differential recognition of sepsis and SIRS and to improve patient management and clinical outcomes. Judicious selection of gene biomarkers suitable for development of diagnostic tests/testing could make differentiation of sepsis and SIRS feasible. Here we describe a methodologic framework for the identification and validation of biomarkers in SIRS, sepsis and septic shock patients, using a 2-tier gene screening, artificial neural network (ANN) data mining technique, using previously published gene expression datasets. Eight key hub markers have been identified which may delineate distinct, core disease processes and which show potential for informing underlying immunological and pathological processes and thus patient stratification and treatment. These do not show sufficient fold change differences between the different disease states to be useful as primary diagnostic biomarkers, but are instrumental in identifying candidate pathways and other associated biomarkers for further exploration.
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Affiliation(s)
- Dong Ling Tong
- Artificial Intelligence Laboratory, Faculty of Engineering and Computing, First City University College, Petaling Jaya, Malaysia.,School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Karen E Kempsell
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Tamas Szakmany
- Department of Anaesthesia Intensive Care and Pain Medicine, Division of Population Medicine, Cardiff University, Cardiff, United Kingdom
| | - Graham Ball
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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20
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Iori S, Rovere GD, Ezzat L, Smits M, Ferraresso SS, Babbucci M, Marin MG, Masiero L, Fabrello J, Garro E, Carraro L, Cardazzo B, Patarnello T, Matozzo V, Bargelloni L, Milan M. The effects of glyphosate and AMPA on the mediterranean mussel Mytilus galloprovincialis and its microbiota. ENVIRONMENTAL RESEARCH 2020; 182:108984. [PMID: 31830695 DOI: 10.1016/j.envres.2019.108984] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/29/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
Glyphosate, the most widely used herbicide worldwide, targets the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme in the shikimate pathway found in plants and some microorganisms. While the potential for glyphosate to induce a broad range of biological effects in exposed organisms has been demonstrated, the global molecular mechanisms of toxicity and potential effects in bacterial symbionts remain unclear, in particular for ecologically important marine species such as bivalve molluscs. Here, the effects of glyphosate (GLY), its degradation product aminomethylphosphonic acid (AMPA), and a mixture of both (MIX) on the mussel M. galloprovincialis were assessed in a controlled experiment. For the first time, next generation sequencing (RNA-seq and 16S rRNA amplicon sequencing) was used to evaluate such effects at the molecular level in both the host and its respective microbiota. The results suggest that the variable capacity of bacterial species to proliferate in the presence of these compounds and the impairment of host physiological homeostasis due to AMPA and GLY toxicity may cause significant perturbations to the digestive gland microbiota, as well as elicit the spread of potential opportunistic pathogens such as Vibrio spp.. The consequent host-immune system activation identified at the molecular and cellular level could be aimed at controlling changes occurring in the composition of symbiotic microbial communities. Overall, our data raise further concerns about the potential adverse effects of glyphosate and AMPA in marine species, suggesting that both the effects of direct toxicity and the ensuing changes occurring in the host-microbial community must be taken into consideration to determine the overall ecotoxicological hazard of these compounds.
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Affiliation(s)
- S Iori
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - L Ezzat
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, CA, 93106, Santa Barbara, United States
| | - M Smits
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - S S Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - M Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - M G Marin
- Department of Biology, University of Padova, Via Basssi 58/B, 35131, Padova, Italy
| | - L Masiero
- Department of Biology, University of Padova, Via Basssi 58/B, 35131, Padova, Italy
| | - J Fabrello
- Department of Biology, University of Padova, Via Basssi 58/B, 35131, Padova, Italy
| | - E Garro
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - L Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - B Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - V Matozzo
- Department of Biology, University of Padova, Via Basssi 58/B, 35131, Padova, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - M Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy.
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21
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Paim AC, Cummins NW, Natesampillai S, Garcia-Rivera E, Kogan N, Neogi U, Sönnerborg A, Sperk M, Bren GD, Deeks S, Polley E, Badley AD. HIV elite control is associated with reduced TRAILshort expression. AIDS 2019; 33:1757-1763. [PMID: 31149947 PMCID: PMC6873462 DOI: 10.1097/qad.0000000000002279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) dependent apoptosis has been implicated in CD4 T-cell death and immunologic control of HIV-1 infection. We have described a splice variant called TRAILshort, which is a dominant negative ligand that antagonizes TRAIL-induced cell death in the context of HIV-1 infection. HIV-1 elite controllers naturally control viral replication for largely unknown reasons. Since enhanced death of infected cells might be responsible, as might occur in situations of low (or inhibited) TRAILshort, we tested whether there was an association between elite controller status and reduced levels of TRAILshort expression. DESIGN Cohort study comparing TRAILshort and full length TRAIL expression between HIV-1 elite controllers and viremic progressors from two independent populations. METHODS TRAILshort and TRAIL gene expression in peripheral blood mononuclear cells (PBMCs) was determined by RNA-seq. TRAILshort and TRAIL protein expression in plasma was determined by antibody bead array and proximity extension assay respectively. RESULTS HIV-1 elite controllers expressed less TRAILshort transcripts in PBMCs (P = 0.002) and less TRAILshort protein in plasma (P < 0.001) than viremic progressors. CONCLUSION Reduced TRAILshort expression in PBMCs and plasma is associated with HIV-1 elite controller status.
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Affiliation(s)
- Ana C Paim
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota
| | - Nathan W Cummins
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota
| | | | | | | | - Ujjwal Neogi
- Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Maike Sperk
- Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Gary D Bren
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota
| | - Steve Deeks
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, California
| | - Eric Polley
- Division of Biomedical Statistics and Informatics
| | - Andrew D Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
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22
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Song Y, Pan Y, Liu J. The relevance between the immune response-related gene module and clinical traits in head and neck squamous cell carcinoma. Cancer Manag Res 2019; 11:7455-7472. [PMID: 31496804 PMCID: PMC6689548 DOI: 10.2147/cmar.s201177] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 07/17/2019] [Indexed: 02/05/2023] Open
Abstract
Purpose Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer in the world, accounting for more than 90% of head and neck malignant tumors. However, its molecular mechanism is largely unknown. To help elucidate the potential mechanism of HNSCC tumorigenesis, we investigated the gene interaction patterns associated with tumorigenesis. Methods Weighted gene co-expression network analysis (WGCNA) can help us to predict the intrinsic relationship or correlation between gene expression. Additionally, we further explored the combination of clinical information and module construction. Results Sixteen modules were constructed, among which the key module most closely associated with clinical information was identified. By analyzing the genes in this module, we found that the latter may be related to the immune response, inflammatory response and formation of the tumor microenvironment. Sixteen hub genes were identified-ARHGAP9, SASH3, CORO1A, ITGAL, PPP1R16B, TBC1D10C, IL10RA, ITK, AKNA, PRKCB, TRAF3IP3, GIMAP4, CCR7, P2RY8, GIMAP7, and SP140. We further validated these genes at the transcriptional and translation levels. Conclusion The innovative use of a weighted network to analyze HNSCC samples provides new insights into the molecular mechanism and prognosis of HNSCC. Additionally, the hub genes we identified can be used as biomarkers and therapeutic targets of HNSCC, laying the foundation for the accurate diagnosis and treatment of HNSCC in clinical and research in the future.
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Affiliation(s)
- Yidan Song
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Yihua Pan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jun Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, People's Republic of China
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Ilan-Ber T, Ilan Y. The role of microtubules in the immune system and as potential targets for gut-based immunotherapy. Mol Immunol 2019; 111:73-82. [DOI: 10.1016/j.molimm.2019.04.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/11/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022]
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Rey-Campos M, Moreira R, Valenzuela-Muñoz V, Gallardo-Escárate C, Novoa B, Figueras A. High individual variability in the transcriptomic response of Mediterranean mussels to Vibrio reveals the involvement of myticins in tissue injury. Sci Rep 2019; 9:3569. [PMID: 30837561 PMCID: PMC6401078 DOI: 10.1038/s41598-019-39870-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022] Open
Abstract
Mediterranean mussels (Mytilus galloprovincialis) are sessile filter feeders that live in close contact with numerous marine microorganisms. As all invertebrates, they lack an adaptive immune response and how these animals are able to respond to a bacterial infection and discriminate it from their normal microbiome is difficult to understand. In this work, we conducted Illumina sequencing of the transcriptome of individual mussels before and after being infected with Vibrio splendidus. The control mussels were injected with filtered seawater. We demonstrate that a great variability exists among individual transcriptomes and that each animal showed an exclusive repertoire of genes not shared with other individuals. The regulated genes in both the control and infected mussels were also analyzed and, unexpectedly, the sampling before the injection was considered a stress stimulus strong enough to trigger and modulate the response in hemocytes, promoting cell migration and proliferation. We found a clear response against the injection of filtered seawater, suggesting a reaction against a tissue injury in which the myticins, the most expressed antimicrobial peptides in mussel, appeared significantly up regulated. Functional experiments with flow cytometry confirmed the transcriptomic results since a significant alteration of hemocyte structures and a decrease in the number of hemocytes positive for myticin C were found only after a Vibrio infection and not observed when mussels were bled before, generating a tissue injury. Therefore, we report the involvement of myticins in the response to a danger signal such as a simple injection in the adductor muscle.
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Affiliation(s)
- Magalí Rey-Campos
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain
| | - Rebeca Moreira
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain
| | - Valentina Valenzuela-Muñoz
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile
| | - Beatriz Novoa
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain
| | - Antonio Figueras
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain.
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Chen X, Xu Y, Cheng Z, Su H, Liu X, Xu D, Kapron C, Liu J. Low-dose cadmium activates the JNK signaling pathway in human renal podocytes. Int J Mol Med 2018; 41:2359-2365. [PMID: 29393374 DOI: 10.3892/ijmm.2018.3445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 01/24/2018] [Indexed: 11/05/2022] Open
Abstract
Cadmium (Cd) is an environmental toxin. Our previous study demonstrated that low‑dose Cd damages the integrity of the glomerular filtration barrier (GFB); however, the underlying mechanisms are poorly understood. Podocytes are a major component of the GFB, which regulate the passage of proteins. The present study aimed to investigate the effects of low‑dose Cd on human renal podocytes (HRPs). HRPs were treated with Cd and activation of the c-Jun N-terminal kinase (JNK) pathway was examined by western blot analysis. Proliferation, viability and apoptosis of HRPs were evaluated by MTT assay, trypan blue exclusion assay and flow cytometry, respectively. The properties of HRPs were validated by immunofluorescence staining and Phalloidin‑labeling. The results indicated that 4 µM Cd may activate the JNK pathway, and increase the protein expression levels of c‑Jun and c‑Fos. However, proliferation, viability, apoptosis and alignment of the F‑actin cytoskeleton in HRPs were not significantly affected by Cd treatment, with or without SP600125 pretreatment. In addition, the expression levels of CD2‑associated protein and synaptopodin, which are differentiation markers of HRPs, remained unchanged following Cd treatment. These results indicated that low‑dose Cd activates the JNK pathway but does not significantly affect HRP function.
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Affiliation(s)
- Xiaocui Chen
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Yinghua Xu
- School of Graduate Studies, Taishan Medical College, Tai'an, Shandong 271000, P.R. China
| | - Zuowang Cheng
- School of Graduate Studies, Taishan Medical College, Tai'an, Shandong 271000, P.R. China
| | - Hong Su
- Department of Nephrology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Xiu Liu
- Department of Cardiography, Binzhou Medical University Affiliated Hospital, Binzhou, Shandong 256600, P.R. China
| | - Dongmei Xu
- Department of Nephrology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Carolyn Kapron
- Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Ju Liu
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
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Ho CH, Tsai SF. Functional and biochemical characterization of a T cell-associated anti-apoptotic protein, GIMAP6. J Biol Chem 2017; 292:9305-9319. [PMID: 28381553 DOI: 10.1074/jbc.m116.768689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 03/31/2017] [Indexed: 11/06/2022] Open
Abstract
GTPases of immunity-associated proteins (GIMAPs) are expressed in lymphocytes and regulate survival/death signaling and cell development within the immune system. We found that human GIMAP6 is expressed primarily in T cell lines. By sorting human peripheral blood mononuclear cells and performing quantitative RT-PCR, GIMAP6 was found to be expressed in CD3+ cells. In Jurkat cells that had been knocked down for GIMAP6, treatment with hydrogen peroxide, FasL, or okadaic acid significantly increased cell death/apoptosis. Exogenous expression of GMAP6 protected Huh-7 cells from apoptosis, suggesting that GIMAP6 is an anti-apoptotic protein. Furthermore, knockdown of GIMAP6 not only rendered Jurkat cells sensitive to apoptosis but also accelerated T cell activation under phorbol 12-myristate 13-acetate/ionomycin treatment conditions. Using this experimental system, we also observed a down-regulation of p65 phosphorylation (Ser-536) in GIMAP6 knockdown cells, indicating that GIMAP6 might display anti-apoptotic function through NF-κB activation. The conclusion from the study on cultured T cells was corroborated by the analysis of primary CD3+ T cells, showing that specific knockdown of GIMAP6 led to enhancement of phorbol 12-myristate 13-acetate/ionomycin-mediated activation signals. To characterize the biochemical properties of GIMAP6, we purified the recombinant GIMAP6 to homogeneity and revealed that GIMAP6 had ATPase as well as GTPase activity. We further demonstrated that the hydrolysis activity of GIMAP6 was not essential for its anti-apoptotic function in Huh-7 cells. Combining the expression data, biochemical properties, and cellular features, we conclude that GIMAP6 plays a role in modulating immune function and that it does this by controlling cell death and the activation of T cells.
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Affiliation(s)
- Ching-Huang Ho
- From the Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan and
| | - Shih-Feng Tsai
- From the Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan and .,the Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan
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27
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Identification of sperm mRNA biomarkers associated with testis injury during preclinical testing of pharmaceutical compounds. Toxicol Appl Pharmacol 2017; 320:1-7. [PMID: 28167222 DOI: 10.1016/j.taap.2017.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 01/03/2017] [Accepted: 02/03/2017] [Indexed: 12/30/2022]
Abstract
The human testis is sensitive to toxicant-induced injury but current methods for detecting adverse effects are limited, insensitive and unreliable. Animal studies use sensitive histopathological endpoints to assess toxicity, but require testicular tissue that is not available during human clinical trials. More sensitive and reliable molecular biomarkers of testicular injury are needed to better monitor testicular toxicity in both clinical and preclinical. Adult male Wistar Han rats were exposed for 4weeks to compounds previously associated with testicular injury, including cisplatin (0, 0.2, 0.3, or 0.4mg/kg/day), BI665915 (0, 20, 70, 100mg/kg/d), BI665636 (0, 20, 100mg/kg/d) or BI163538 (0, 70, 150, 300mg/kg/d) to evaluate reproductive toxicity and assess changes in sperm mRNA levels. None of the compounds resulted in any significant changes in body, testis or epididymis weights, nor were there decreases in testicular homogenization resistant spermatid head counts. Histopathological evaluation found that only BI665915 treatment caused any testicular effects, including minor germ cell loss and disorganization of the seminiferous tubule epithelium, and an increase in the number of retained spermatid heads. A custom PCR-array panel was used to assess induced changes in sperm mRNA. BI665915 treatment resulted in a significant increase in clusterin (Clu) levels and decreases in GTPase, IMAP family member 4 (Gimap4), prostaglandin D2 synthase (Ptgds) and transmembrane protein with EGF like and two follistatin like domains 1 (Tmeff1) levels. Correlation analysis between transcript levels and quantitative histopathological endpoints found a modest association between Clu with retained spermatid heads. These results demonstrate that sperm mRNA levels are sensitive molecular indicators of testicular injury that can potentially be translated into a clinical setting.
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28
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Chen X, Li J, Cheng Z, Xu Y, Wang X, Li X, Xu D, Kapron CM, Liu J. Low Dose Cadmium Inhibits Proliferation of Human Renal Mesangial Cells via Activation of the JNK Pathway. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13100990. [PMID: 27739415 PMCID: PMC5086729 DOI: 10.3390/ijerph13100990] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/29/2016] [Indexed: 12/15/2022]
Abstract
Cadmium (Cd) is a heavy metal and environmental pollutant. The kidney is the principal target organ of Cd exposure. Previously, we found that low concentration of Cd damages the integrity of the glomerular filtration barrier. However, little is known about the effects of Cd on renal mesangial cells, which provide structural support for the glomerular capillary loops and regulate intraglomerular blood flow. In this study, human renal mesangial cells (HRMCs) were cultured in the presence of serum and treated with 4 μM Cd. We found that Cd activates the c-Jun N-terminal kinase (JNK) pathway, and increases the protein levels of c-Jun and c-Fos. Cd treatment also induces a decrease in proliferation and an increase in apoptosis of HRMCs, but only the decrease in HRMC proliferation was reversed by pretreatment with SP600125, an inhibitor of the JNK pathway. In addition, Cd does not change the expression of α-smooth muscle actin and platelet-derived growth factor receptor-β, the markers of mesangial cells, or the alignment of the filamentous actin (F-actin) cytoskeleton of HRMCs. Our data indicate that the JNK pathway mediates the inhibitory effects of Cd on HRMC proliferation.
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Affiliation(s)
- Xiaocui Chen
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, 16766 Jingshi Road, Jinan 250014, China.
| | - Jing Li
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | | | - Yinghua Xu
- Taishan Medical College, Taian 271000, China.
| | - Xia Wang
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, 16766 Jingshi Road, Jinan 250014, China.
| | - Xiaorui Li
- Taishan Medical College, Taian 271000, China.
| | - Dongmei Xu
- Department of Nephrology, Shandong Provincial Qianfoshan Hospital, Shandong University, 16766 Jingshi Road, Jinan 250014, China.
| | - Carolyn M Kapron
- Department of Biology, Trent University, Peterborough, ON K9L0G2, Canada.
| | - Ju Liu
- Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, 16766 Jingshi Road, Jinan 250014, China.
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29
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Varadan V, Gilmore H, Miskimen KLS, Tuck D, Parsai S, Awadallah A, Krop IE, Winer EP, Bossuyt V, Somlo G, Abu-Khalaf MM, Fenton MA, Sikov W, Harris LN. Immune Signatures Following Single Dose Trastuzumab Predict Pathologic Response to PreoperativeTrastuzumab and Chemotherapy in HER2-Positive Early Breast Cancer. Clin Cancer Res 2016; 22:3249-59. [PMID: 26842237 PMCID: PMC5439498 DOI: 10.1158/1078-0432.ccr-15-2021] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/20/2016] [Indexed: 12/25/2022]
Abstract
PURPOSE Recent data suggest that intrinsic subtype and immune cell infiltration may predict response to trastuzumab-based therapy. We studied the interaction between these factors, changes in immune signatures following brief exposure to trastuzumab, and achievement of pathologic complete response (pCR) to subsequent preoperative trastuzumab and chemotherapy in HER2-positive breast cancer. EXPERIMENTAL DESIGN In patients enrolled on two multicenter trials (03-311 and 211B), tumor core biopsies were obtained at baseline and after brief exposure to single-agent trastuzumab or nab-paclitaxel. Gene expression profiles were assessed to assign PAM50 subtypes, measure immune cell activation, and were correlated with response. RESULTS The pCR rate was significantly higher in HER2-enriched tumors in the Discovery, 03-311 (36%, P = 0.043) dataset, as compared with other subtypes, which validated in 211B (50%, P = 0.048). Significant increases in a signature of immune cell admixture (Immune Index) were observed only following brief exposure to trastuzumab in HER2-enriched tumors (Discovery/03-311, P = 0.05; Validation/211B, P = 0.02). Increased Immune Index was predictive of response after brief exposure (03-311, P = 0.03; 211B, P = 0.04), but not at baseline, in addition to increased expression of a CD4(+) follicular helper T-cell signature (03-311, P = 0.05; 211B, P = 0.04). Brief exposure to trastuzumab significantly increased gene expression of the T-cell marker PD-1 in HER2-enriched tumors (Discovery/03-311, P = 0.045) and PD-1 positivity by IHC (Validation/211B, P = 0.035). CONCLUSIONS Correlations between pCR rates, increases in Immune Index and markers of T-cell activity following brief exposure to trastuzumab in HER2-enriched tumors provide novel insights into the interaction between tumor biology, antitumor immunity, and response to treatment, and suggest potential clinically useful biomarkers in HER2(+) breast cancers. Clin Cancer Res; 22(13); 3249-59. ©2016 AACR.
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Affiliation(s)
- Vinay Varadan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio.
| | - Hannah Gilmore
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Kristy L S Miskimen
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | | | - Shikha Parsai
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Amad Awadallah
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Ian E Krop
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Eric P Winer
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Veerle Bossuyt
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - George Somlo
- City of Hope National Medical Center, Duarte, California
| | - Maysa M Abu-Khalaf
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Mary Anne Fenton
- Lifespan Comprehensive Cancer Center, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - William Sikov
- Women and Infants Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Lyndsay N Harris
- Case Western Reserve University School of Medicine, Cleveland, Ohio.
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Heller S, Cable C, Penrose H, Makboul R, Biswas D, Cabe M, Crawford SE, Savkovic SD. Intestinal inflammation requires FOXO3 and prostaglandin E2-dependent lipogenesis and elevated lipid droplets. Am J Physiol Gastrointest Liver Physiol 2016; 310:G844-54. [PMID: 26968210 PMCID: PMC4895869 DOI: 10.1152/ajpgi.00407.2015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/07/2016] [Indexed: 01/31/2023]
Abstract
Intestinal inflammation has been recently characterized by the dysregulation of lipids as metabolic and energy sources, revealing a novel feature of its pathophysiology. Because intracellular lipids, stored in dynamic lipid droplets (LDs), provide energy for cellular needs, we investigated whether they play a role in intestinal inflammation. In the inflamed intestine of mice, elevated LDs were found in colonic and infiltrating immune cells as shown by staining for the LD coat protein PLIN2 and for lipids with BODIPY. In colonic cells, TNF stimulated LD increases by receptor signaling rely on phosphatidylinositol 3-kinase activation. Downstream, TNF triggered a negative regulatory loop between LDs and the transcription factor FOXO3. This was shown in the colon of Foxo3-deficient mice, where elevation in PLIN2 and lipids were further facilitated by inflammation and were more prominent relative to wild-type, whereas, in colonic cells, inhibition of lipogenesis blocked the TNF-mediated loss of FOXO3. Furthermore, blockade of PGE2 synthesis abrogated TNF-stimulated increases in LDs and FOXO3 inactivation. We found in colonic tissue of Foxo3-deficient mice higher levels of cyclooxygenase-2, a mediator of prostaglandin E2 (PGE2) synthesis, supporting involvement of PGE2 in the LD-FOXO3 regulatory loop. Ultimately, TNF-stimulated lipogenesis leading to elevated LDs facilitated NF-κB-mediated increases in IL-8 protein, which is associated with the surface of LDs found in the lumina of the endoplasmic reticulum and Golgi apparatus. This novel immunometabolic mechanism of colonic inflammation involving elevated LDs could provide opportunities for new treatment options.
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Affiliation(s)
- Sandra Heller
- 1Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, Louisiana;
| | - Chloe Cable
- 1Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, Louisiana;
| | - Harrison Penrose
- 1Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, Louisiana;
| | - Rania Makboul
- 1Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, Louisiana; ,3Pathology Department, Assiut University, Assiut, Egypt
| | - Debjani Biswas
- 1Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, Louisiana;
| | - Maleen Cabe
- 1Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, Louisiana;
| | - Susan E. Crawford
- 2Department of Pathology, St. Louis University, St Louis, Missouri; and
| | - Suzana D. Savkovic
- 1Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, Louisiana;
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Chen XL, Serrano D, Mayhue M, Hoebe K, Ilangumaran S, Ramanathan S. GIMAP5 Deficiency Is Associated with Increased AKT Activity in T Lymphocytes. PLoS One 2015; 10:e0139019. [PMID: 26440416 PMCID: PMC4595448 DOI: 10.1371/journal.pone.0139019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/07/2015] [Indexed: 01/05/2023] Open
Abstract
Long-term survival of T lymphocytes in quiescent state is essential to maintain their cell numbers in secondary lymphoid organs. In mice and in rats, the loss of functional GTPase of the immune associated nucleotide binding protein 5 (GIMAP5) causes peripheral T lymphopenia due to spontaneous death of T cells. The underlying mechanism responsible for the disruption of quiescence in Gimap5 deficient T cells remains largely unknown. In this study, we show that loss of functional Gimap5 results in increased basal activation of mammalian target of rapamycin (mTOR), independent of protein phosphatase 2A (PP2A) or AMP-activated protein kinase (AMPK). Our results suggest that the constitutive activation of the phosphoinositide 3-kinase (PI3K) pathway may be one of the consequences of the absence of functional GIMAP5.
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Affiliation(s)
- Xi-Lin Chen
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Daniel Serrano
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Marian Mayhue
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Kasper Hoebe
- Department of Pediatrics, Division of Cellular and Molecular Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, United States of America
| | - Subburaj Ilangumaran
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
- Centre de Recherche Clinique, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Sheela Ramanathan
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
- Centre de Recherche Clinique, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
- * E-mail:
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Heinonen MT, Laine AP, Söderhäll C, Gruzieva O, Rautio S, Melén E, Pershagen G, Lähdesmäki HJ, Knip M, Ilonen J, Henttinen TA, Kere J, Lahesmaa R. GIMAP GTPase family genes: potential modifiers in autoimmune diabetes, asthma, and allergy. THE JOURNAL OF IMMUNOLOGY 2015; 194:5885-94. [PMID: 25964488 DOI: 10.4049/jimmunol.1500016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/30/2015] [Indexed: 12/31/2022]
Abstract
GTPase of the immunity-associated protein (GIMAP) family members are differentially regulated during human Th cell differentiation and have been previously connected to immune-mediated disorders in animal studies. GIMAP4 is believed to contribute to the Th cell subtype-driven immunological balance via its role in T cell survival. GIMAP5 has a key role in BB-DR rat and NOD mouse lymphopenia. To elucidate GIMAP4 and GIMAP5 function and role in human immunity, we conducted a study combining genetic association in different immunological diseases and complementing functional analyses. Single nucleotide polymorphisms tagging the GIMAP haplotype variation were genotyped in Finnish type 1 diabetes (T1D) families and in a prospective Swedish asthma and allergic sensitization birth cohort. Initially, GIMAP5 rs6965571 was associated with risk for asthma and allergic sensitization (odds ratio [OR] 3.74, p = 0.00072, and OR 2.70, p = 0.0063, respectively) and protection from T1D (OR 0.64, p = 0.0058); GIMAP4 rs13222905 was associated with asthma (OR 1.28, p = 0.035) and allergic sensitization (OR 1.27, p = 0.0068). However, after false discovery rate correction for multiple testing, only the associations of GIMAP4 with allergic sensitization and GIMAP5 with asthma remained significant. In addition, transcription factor binding sites surrounding the associated loci were predicted. A gene-gene interaction in the T1D data were observed between the IL2RA rs2104286 and GIMAP4 rs9640279 (OR 1.52, p = 0.0064) and indicated between INS rs689 and GIMAP5 rs2286899. The follow-up functional analyses revealed lower IL-2RA expression upon GIMAP4 knockdown and an effect of GIMAP5 rs2286899 genotype on protein expression. Thus, the potential role of GIMAP4 and GIMAP5 as modifiers of immune-mediated diseases cannot be discarded.
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Affiliation(s)
- Mirkka T Heinonen
- Turku Centre of Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Department of Biology, University of Turku, 20014 Turku, Finland; Turku Doctoral Programme of Molecular Medicine, University of Turku, 20520 Turku Finland
| | - Antti-Pekka Laine
- Immunogenetics Laboratory, University of Turku, 20520 Turku, Finland
| | - Cilla Söderhäll
- Department of Bioscience and Nutrition and Center for Innovative Medicine, Karolinska Institutet, 141 83 Huddinge, Stockholm, Sweden
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Sini Rautio
- Department of Information and Computer Science, Aalto University, 02150 Espoo, Finland
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden; Karolinska University Hospital, Astrid Lindgren Children's Hospital, 171 76 Solna, Stockholm, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Harri J Lähdesmäki
- Turku Centre of Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland; Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland; Folkhälsan Research Institute, 00290 Helsinki, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, 20520 Turku, Finland; Department of Clinical Microbiology, University of Eastern Finland, 70211 Kuopio, Finland; and
| | | | - Juha Kere
- Department of Bioscience and Nutrition and Center for Innovative Medicine, Karolinska Institutet, 141 83 Huddinge, Stockholm, Sweden; Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
| | - Riitta Lahesmaa
- Turku Centre of Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland;
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Quantitative changes in Gimap3 and Gimap5 expression modify mitochondrial DNA segregation in mice. Genetics 2015; 200:221-35. [PMID: 25808953 DOI: 10.1534/genetics.115.175596] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/20/2015] [Indexed: 01/22/2023] Open
Abstract
Mammalian mitochondrial DNA (mtDNA) is a high-copy maternally inherited genome essential for aerobic energy metabolism. Mutations in mtDNA can lead to heteroplasmy, the co-occurence of two different mtDNA variants in the same cell, which can segregate in a tissue-specific manner affecting the onset and severity of mitochondrial dysfunction. To investigate mechanisms regulating mtDNA segregation we use a heteroplasmic mouse model with two polymorphic neutral mtDNA haplotypes (NZB and BALB) that displays tissue-specific and age-dependent selection for mtDNA haplotypes. In the hematopoietic compartment there is selection for the BALB mtDNA haplotype, a phenotype that can be modified by allelic variants of Gimap3. Gimap3 is a tail-anchored member of the GTPase of the immunity-associated protein (Gimap) family of protein scaffolds important for leukocyte development and survival. Here we show how the expression of two murine Gimap3 alleles from Mus musculus domesticus and M. m. castaneus differentially affect mtDNA segregation. The castaneus allele has incorporated a uORF (upstream open reading frame) in-frame with the Gimap3 mRNA that impairs translation and imparts a negative effect on the steady-state protein abundance. We found that quantitative changes in the expression of Gimap3 and the paralogue Gimap5, which encodes a lysosomal protein, affect mtDNA segregation in the mouse hematopoietic tissues. We also show that Gimap3 localizes to the endoplasmic reticulum and not mitochondria as previously reported. Collectively these data show that the abundance of protein scaffolds on the endoplasmic reticulum and lysosomes are important to the segregation of the mitochondrial genome in the mouse hematopoietic compartment.
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