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Liu R, Chu W, Liu X, Hong J, Wang H. Establishment of Golgi apparatus-related genes signature to predict the prognosis and immunotherapy response in gastric cancer patients. Medicine (Baltimore) 2024; 103:e37439. [PMID: 38489711 PMCID: PMC10939665 DOI: 10.1097/md.0000000000037439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/17/2024] Open
Abstract
The Golgi apparatus plays a crucial role in intracellular protein transportation, processing, and sorting. Dysfunctions of the Golgi apparatus have been implicated in tumorigenesis and drug resistance. This study aimed to investigate the prognostic and treatment response assessment value of Golgi apparatus-related gene (GARGs) features in gastric cancer patients. Transcriptome data and clinical information of gastric cancer patients were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. Cox regression analysis was employed to assess the prognostic significance of GARGs and construct risk features. The immune landscape, drug sensitivity, immune therapy response, gene expression patterns, and somatic mutation characteristics were analyzed between different risk groups. A nomogram model for predicting gastric cancer prognosis was developed and evaluated. Among 1643 GARGs examined, 365 showed significant associations with gastric cancer prognosis. Five independent prognostic GARGs (NGF, ABCG1, CHAC1, GBA2, PCSK7) were selected to construct risk features for gastric cancer patients. These risk features effectively stratified patients into high-risk and low-risk groups, with the former exhibiting worse prognosis than the latter. Patients in the high-risk group displayed higher levels of immune cell infiltration, while the expression levels of NGF, CHAC1, GBA2, PCSK7 were significantly correlated with immune cell infiltration. Notably, the low-risk group exhibited higher sensitivity to epothilone.B, metformin, and tipifarnib compared to the high-risk group. Moreover, patients in the low-risk group demonstrated greater responsiveness to immune therapy than those in the high-risk group. In terms of biological processes and KEGG pathways related to immunity regulation, significant suppression was observed in the high-risk group compared to the low-risk group; meanwhile cell cycle pathways exhibited significant activation in the high-risk group. Furthermore, the low-risk group exhibited a higher tumor mutation burden compared to the high-risk group. The risk features derived from GARGs, in conjunction with age, were identified as independent risk factors for gastric cancer. The nomogram incorporating these factors demonstrated improved performance in predicting gastric cancer prognosis. Our study established risk features derived from GARGs that hold potential clinical utility in prognostic assessment and immune therapy response evaluation of gastric cancer patients.
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Affiliation(s)
- Rui Liu
- Department of Gastrointestinal Surgery, Hangzhou Third Peopleâs Hospital, Hangzhou, Zhejiang, China
| | - Weiwei Chu
- Department of Gastrointestinal Surgery, Hangzhou Third Peopleâs Hospital, Hangzhou, Zhejiang, China
| | - Xiaojin Liu
- Department of Gastrointestinal Surgery, Hangzhou Third Peopleâs Hospital, Hangzhou, Zhejiang, China
| | - Jie Hong
- Department of Gastrointestinal Surgery, Hangzhou Third Peopleâs Hospital, Hangzhou, Zhejiang, China
| | - Haiming Wang
- Department of Gastrointestinal Surgery, Hangzhou Third Peopleâs Hospital, Hangzhou, Zhejiang, China
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Chung CJ, Hermes BM, Gupta Y, Ibrahim S, Belheouane M, Baines JF. Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling. Anim Microbiome 2023; 5:31. [PMID: 37264412 DOI: 10.1186/s42523-023-00250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Mammalian lungs comprise a complex microbial ecosystem that interacts with host physiology. Previous research demonstrates that the environment significantly contributes to bacterial community structure in the upper and lower respiratory tract. However, the influence of host genetics on the makeup of lung microbiota remains ambiguous, largely due to technical difficulties related to sampling, as well as challenges inherent to investigating low biomass communities. Thus, innovative approaches are warranted to clarify host-microbe interactions in the mammalian lung. RESULTS Here, we aimed to characterize host genomic regions associated with lung bacterial traits in an advanced intercross mouse line (AIL). By performing quantitative microbial profiling (QMP) using the highly precise method of droplet digital PCR (ddPCR), we refined 16S rRNA gene amplicon-based traits to identify and map candidate lung-resident taxa using a QTL mapping approach. In addition, the two abundant core taxa Lactobacillus and Pelomonas were chosen for independent microbial phenotyping using genus-specific primers. In total, this revealed seven significant loci involving eight bacterial traits. The narrow confidence intervals afforded by the AIL population allowed us to identify several promising candidate genes related to immune and inflammatory responses, cell apoptosis, DNA repair, and lung functioning and disease susceptibility. Interestingly, one genomic region associated with Lactobacillus abundance contains the well-known anti-inflammatory cytokine Il10, which we confirmed through the analysis of Il10 knockout mice. CONCLUSIONS Our study provides the first evidence for a role of host genetic variation contributing to variation in the lung microbiota. This was in large part made possible through the careful curation of 16S rRNA gene amplicon data and the incorporation of a QMP-based methods. This approach to evaluating the low biomass lung environment opens new avenues for advancing lung microbiome research using animal models.
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Affiliation(s)
- C J Chung
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - B M Hermes
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - Y Gupta
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - S Ibrahim
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Meriem Belheouane
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
- Research Center Borstel, Evolution of the Resistome, Leibniz Lung Center, Parkallee 1-40, 23845, Borstel, Germany.
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
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AczĂ©l T, Benczik B, Ăgg B, KörtĂ©si T, UrbĂĄn P, Bauer W, Gyenesei A, Tuka B, Tajti J, Ferdinandy P, VĂ©csei L, Bölcskei K, Kun J, Helyes Z. Disease- and headache-specific microRNA signatures and their predicted mRNA targets in peripheral blood mononuclear cells in migraineurs: role of inflammatory signalling and oxidative stress. J Headache Pain 2022; 23:113. [PMID: 36050647 PMCID: PMC9438144 DOI: 10.1186/s10194-022-01478-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Migraine is a primary headache with genetic susceptibility, but the pathophysiological mechanisms are poorly understood, and it remains an unmet medical need. Earlier we demonstrated significant differences in the transcriptome of migraineurs' PBMCs (peripheral blood mononuclear cells), suggesting the role of neuroinflammation and mitochondrial dysfunctions. Post-transcriptional gene expression is regulated by miRNA (microRNA), a group of short non-coding RNAs that are emerging biomarkers, drug targets, or drugs. MiRNAs are emerging biomarkers and therapeutics; however, little is known about the miRNA transcriptome in migraine, and a systematic comparative analysis has not been performed so far in migraine patients. METHODS We determined miRNA expression of migraineurs' PBMC during (ictal) and between (interictal) headaches compared to age- and sex-matched healthy volunteers. Small RNAÂ sequencing was performed from the PBMC, and mRNA targets of miRNAs were predicted using a network theoretical approach by miRNAtarget.comâą. Predicted miRNA targets were investigated by Gene Ontology enrichment analysis and validated by comparing network metrics to differentially expressed mRNA data. RESULTS In the interictal PBMC samples 31 miRNAs were differentially expressed (DE) in comparison to healthy controls, including hsa-miR-5189-3p, hsa-miR-96-5p, hsa-miR-3613-5p, hsa-miR-99a-3p, hsa-miR-542-3p. During headache attacks, the top DE miRNAs as compared to the self-control samples in the interictal phase were hsa-miR-3202, hsa-miR-7855-5p, hsa-miR-6770-3p, hsa-miR-1538, and hsa-miR-409-5p. MiRNA-mRNA target prediction and pathway analysis indicated several mRNAs related to immune and inflammatory responses (toll-like receptor and cytokine receptor signalling), neuroinflammation and oxidative stress, also confirmed by mRNA transcriptomics. CONCLUSIONS We provide here the first evidence for disease- and headache-specific miRNA signatures in the PBMC of migraineurs, which might help to identify novel targets for both prophylaxis and attack therapy.
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Affiliation(s)
- Timea Aczél
- Department of Pharmacology and Pharmacotherapy, Medical School & SzentĂĄgothai Research Centre, Molecular Pharmacology Research Group, Centre for Neuroscience, University of PĂ©cs, PĂ©cs, Hungary
| | - Bettina Benczik
- Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary.,Pharmahungary Group, Szeged, Hungary
| | - Bence Ăgg
- Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary.,Pharmahungary Group, Szeged, Hungary
| | - Tamås Körtési
- MTA-SZTE Neuroscience Research Group, University of Szeged, Szeged, Hungary.,Faculty of Health Sciences and Social Studies, University of Szeged, Szeged, Hungary
| | - PĂ©ter UrbĂĄn
- SzentĂĄgothai Research Centre, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, University of PĂ©cs, PĂ©cs, Hungary
| | - Witold Bauer
- SzentĂĄgothai Research Centre, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, University of PĂ©cs, PĂ©cs, Hungary
| | - Attila Gyenesei
- SzentĂĄgothai Research Centre, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, University of PĂ©cs, PĂ©cs, Hungary
| | - Bernadett Tuka
- MTA-SZTE Neuroscience Research Group, University of Szeged, Szeged, Hungary.,Faculty of Health Sciences and Social Studies, University of Szeged, Szeged, Hungary
| | - JĂĄnos Tajti
- Department of Neurology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - PĂ©ter Ferdinandy
- Cardiometabolic and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary.,Pharmahungary Group, Szeged, Hungary
| | - LĂĄszlĂł VĂ©csei
- MTA-SZTE Neuroscience Research Group, University of Szeged, Szeged, Hungary.,Department of Neurology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - Kata Bölcskei
- Department of Pharmacology and Pharmacotherapy, Medical School & SzentĂĄgothai Research Centre, Molecular Pharmacology Research Group, Centre for Neuroscience, University of PĂ©cs, PĂ©cs, Hungary
| | - JĂłzsef Kun
- Department of Pharmacology and Pharmacotherapy, Medical School & SzentĂĄgothai Research Centre, Molecular Pharmacology Research Group, Centre for Neuroscience, University of PĂ©cs, PĂ©cs, Hungary.,SzentĂĄgothai Research Centre, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, University of PĂ©cs, PĂ©cs, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School & SzentĂĄgothai Research Centre, Molecular Pharmacology Research Group, Centre for Neuroscience, University of PĂ©cs, PĂ©cs, Hungary. .,PharmInVivo Ltd., PĂ©cs, Hungary. .,Department of Pharmacology and Pharmacotherapy, University of PĂ©cs Medical School, Szigeti Ășt 12, 7624, PĂ©cs, Hungary.
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Zheng T, Song Z, Qiang J, Tao Y, Zhu H, Ma J, Xu P. Transport Stress Induces Skin Innate Immunity Response in Hybrid Yellow Catfish ( Tachysurus fulvidracoâ Ă P. vachelliiâ) Through TLR/NLR Signaling Pathways and Regulation of Mucus Secretion. Front Immunol 2021; 12:740359. [PMID: 34712228 PMCID: PMC8545808 DOI: 10.3389/fimmu.2021.740359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022] Open
Abstract
The transport of live fish is a necessary step for commercial production. The skin of teleost fish is the first non-specific immune barrier against exogenous stimuli, and it plays an important protective role under transport stress. Thus, the aim of this study was to explore the skin responses to transport stress in hybrid yellow catfish (Tachysurus fulvidracoâ Ă Pseudobagrus vachelliiâ) through transcriptome and biochemical analyses. Water samples were collected during a simulated transport treatment. Biochemical indexes and/or gene expression in blood, skin, and mucus in fish in control groups and transport-stress groups (0 h, 2 h, 4 h, 8 h, 16 h) were assayed. The levels of total ammonia-nitrogen and nitrite-nitrogen in the water increased with increasing transport time. Comparison of skin transcriptomes between the control group and the group subjected to 16 h of transport revealed 1547 differentially expressed genes (868 up-regulated and 679 down-regulated). The results of the transcriptome analysis were validated by analyses of the expression levels of selected genes by qRT-PCR. The results indicated that the toll-like receptors and nod-like receptors signaling pathways mediate the skin's immune response to transport stress: tlr9, mfn2, and ikbke were significantly up-regulated and nfkbia and map3k7cl were significantly down-regulated under transport stress. With increasing transport time, lysozyme activity and the immunoglobulin M content in skin mucus first increased and then decreased. The number of mucous cells peaked at 8 h of transport stress, and then decreased. The mucus cells changed from types II and IV to types I, II, III, and IV. The amounts of red and white blood cells and the levels of hemoglobin and hematocrit first increased and then decreased during 16 h of transport stress. Together, the results showed that the skin responds to transport stress by activating the immune signaling pathway and regulating mucus secretion. These findings have important biological significance for selecting strains that tolerate transport, as well as economic significance for optimizing the transport conditions for scaleless fish.
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Affiliation(s)
- Tao Zheng
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Zhuo Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jun Qiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China.,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Yifan Tao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Haojun Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Junlei Ma
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China.,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
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Niu L, Guo W, Song X, Song X, Xie L. Tumor-educated leukocytes mRNA as a diagnostic biomarker for non-small cell lung cancer. Thorac Cancer 2021; 12:737-745. [PMID: 33474835 PMCID: PMC7952788 DOI: 10.1111/1759-7714.13833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/24/2020] [Accepted: 12/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background This study aimed to investigate the diagnostic and prognostic role of tumorâeducated leukocytes (TELs) mRNA in Chinese patients with nonâsmall cell lung cancer (NSCLC). Methods The TELs collected underwent total RNA isolation. RNAâsequencing (RNAâseq) technology was used to analyze the transcriptome of the TELs. The mRNA expression levels of differential genes were analyzed by RTâqPCR. Statistical analyses were performed using Prism and SPSS by MannâWhitney nonparametric test, KruskalâWallis test and oneâway ANOVA. Results We used RNAâseq technology to screen 95 differential genes (DEGs) from seven NSCLC and four controls, wherein 15 genes were upregulated, and 80 were downregulated. Of these, four genes were selected for further analysis, wherein one was upregulated (GPX1) and three were downregulated (BCL9L, MAP3K7CL, PCSK7). RTâqPCR was performed in 431 samples (237 NSCLC, 194 healthy donors). The fourâgene panel showed significant differences (pâ<â0.001) in the expression levels between NSCLC and healthy samples. ROC curves of the panel revealed an AUC of 0.803, with a sensitivity of 73.8% and specificity of 75.3%. GPX1, BCL9L and PCSK7 genes distinguished earlyâstage NSCLC patients from healthy group (p <â0.05). When the three genes were combined to diagnose earlyâstage NSCLC, the diagnostic efficacy was 0.772, sensitivity was 73.7%, and specificity was 72.2%. In addition, the downregulated gene BCL9L was associated with chemotherapeutic effect. Conclusions The present study provided a systematic description of gene expression profiling in the TELs. It is worth noting that these four genes may be potential candidate genes for NSCLC diagnostic biomarkers and provide a basis for further biological and functional studies.
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Affiliation(s)
- Limin Niu
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Wei Guo
- Ultrasound Diagnosis Department, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xingguo Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xianrang Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Li Xie
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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