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Liu S, Wen H, Li F, Xue X, Sun X, Li F, Hu R, Xi H, Boccellato F, Meyer TF, Mi Y, Zheng P. Revealing the pathogenesis of gastric intestinal metaplasia based on the mucosoid air-liquid interface. J Transl Med 2024; 22:468. [PMID: 38760813 PMCID: PMC11101349 DOI: 10.1186/s12967-024-05276-7] [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: 02/22/2024] [Accepted: 05/04/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Gastric intestinal metaplasia (GIM) is an essential precancerous lesion. Although the reversal of GIM is challenging, it potentially brings a state-to-art strategy for gastric cancer therapeutics (GC). The lack of the appropriate in vitro model limits studies of GIM pathogenesis, which is the issue this work aims to address for further studies. METHOD The air-liquid interface (ALI) model was adopted for the long-term culture of GIM cells in the present work. This study conducted Immunofluorescence (IF), quantitative real-time polymerase chain reaction (qRT-PCR), transcriptomic sequencing, and mucoproteomic sequencing (MS) techniques to identify the pathways for differential expressed genes (DEGs) enrichment among different groups, furthermore, to verify novel biomarkers of GIM cells. RESULT Our study suggests that GIM-ALI model is analog to the innate GIM cells, which thus can be used for mucus collection and drug screening. We found genes MUC17, CDA, TRIM15, TBX3, FLVCR2, ONECUT2, ACY3, NMUR2, and MAL2 were highly expressed in GIM cells, while GLDN, SLC5A5, MAL, and MALAT1 showed down-regulated, which can be used as potential biomarkers for GIM cells. In parallel, these genes that highly expressed in GIM samples were mainly involved in cancer-related pathways, such as the MAPK signal pathway and oxidative phosphorylation signal pathway. CONCLUSION The ALI model is validated for the first time for the in vitro study of GIM. GIM-ALI model is a novel in vitro model that can mimic the tissue micro-environment in GIM patients and further provide an avenue for studying the characteristics of GIM mucus. Our study identified new markers of GIM as well as pathways associated with GIM, which provides outstanding insight for exploring GIM pathogenesis and potentially other related conditions.
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Affiliation(s)
- Simeng Liu
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117, Berlin, Germany
| | - Huijuan Wen
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
| | - Fazhan Li
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
| | - Xia Xue
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
| | - Xiangdong Sun
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
| | - Fuhao Li
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
| | - Ruoyu Hu
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 453000, China
| | - Huayuan Xi
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 453000, China
| | - Francesco Boccellato
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117, Berlin, Germany
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, 11743, UK
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117, Berlin, Germany
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrecht University of Kiel and University Hospital Schleswig-Holstein - Campus Kiel, Rosalind-Franklin- Straße 12, 24105, Kiel, Germany
| | - Yang Mi
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China.
| | - Pengyuan Zheng
- Henan Key Laboratory of Helicobacter pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, No. 3, Kangfuqian Street, Erqi District, Zhengzhou, Henan, 450002, China.
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 453000, China.
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Wang S, Wang R, Hu D, Zhang C, Cao P, Huang J. Machine learning reveals diverse cell death patterns in lung adenocarcinoma prognosis and therapy. NPJ Precis Oncol 2024; 8:49. [PMID: 38409471 PMCID: PMC10897292 DOI: 10.1038/s41698-024-00538-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Cancer cell growth, metastasis, and drug resistance pose significant challenges in the management of lung adenocarcinoma (LUAD). However, there is a deficiency in optimal predictive models capable of accurately forecasting patient prognoses and guiding the selection of targeted treatments. Programmed cell death (PCD) pathways play a pivotal role in the development and progression of various cancers, offering potential as prognostic indicators and drug sensitivity markers for LUAD patients. The development and validation of predictive models were conducted by integrating 13 PCD patterns with comprehensive analysis of bulk RNA, single-cell RNA transcriptomics, and pertinent clinicopathological details derived from TCGA-LUAD and six GEO datasets. Utilizing the machine learning algorithms, we identified ten critical differentially expressed genes associated with PCD in LUAD, namely CHEK2, KRT18, RRM2, GAPDH, MMP1, CHRNA5, TMPRSS4, ITGB4, CD79A, and CTLA4. Subsequently, we conducted a programmed cell death index (PCDI) based on these genes across the aforementioned cohorts and integrated this index with relevant clinical features to develop several prognostic nomograms. Furthermore, we observed a significant correlation between the PCDI and immune features in LUAD, including immune cell infiltration and the expression of immune checkpoint molecules. Additionally, we found that patients with a high PCDI score may exhibit resistance to immunotherapy and standard adjuvant chemotherapy regimens; however, they may benefit from other FDA-supported drugs such as docetaxel and dasatinib. In conclusion, the PCDI holds potential as a prognostic signature and can facilitate personalized treatment for LUAD patients.
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Affiliation(s)
- Shun Wang
- Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200031, China
| | - Ruohuang Wang
- Department of Otolaryngology, the Second Affiliated Hospital of the Naval Military Medical University (Shanghai Changzheng Hospital), Shanghai, 200003, China
| | - Dingtao Hu
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, 200433, China
| | - Caoxu Zhang
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Peng Cao
- Department of Interventional Pulmonology, Anhui Chest Hospital, Hefei, Anhui, 230022, China
| | - Jie Huang
- Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200031, China.
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3
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Li L, Lin M, Luo J, Sun H, Zhang Z, Lin D, Chen L, Feng S, Lin X, Zhou R, Song J. Loss of keratin 23 enhances growth inhibitory effect of melatonin in gastric cancer. Mol Med Rep 2024; 29:22. [PMID: 38099343 PMCID: PMC10784722 DOI: 10.3892/mmr.2023.13145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
To investigate the effect of keratin 23 (KRT23) on the anticancer activity of melatonin (MLT) against gastric cancer (GC) cells, microarray analysis was applied to screen differentially expressed genes in AGS GC cells following MLT treatment. Western blotting was used to detect the expression of KRT23 in GC cells and normal gastric epithelial cell line GES‑1. KRT23 knockout was achieved by CRISPR/Cas9. Assays of cell viability, colony formation, cell cycle, electric cell‑substrate impedance sensing and western blotting were conducted to reveal the biological functions of KRT23‑knockout cells without or with MLT treatment. Genes downregulated by MLT were enriched in purine metabolism, pyrimidine metabolism, genetic information processing and cell cycle pathway. Expression levels of KRT23 were downregulated by MLT treatment. Expression levels of KRT23 in AGS and SNU‑216 GC cell lines were significantly higher compared with normal gastric epithelial cell line GES‑1. KRT23 knockout led to reduced phosphorylation of ERK1/2 and p38, arrest of the cell cycle and inhibition of GC cell proliferation. Moreover, KRT23 knockout further enhanced the inhibitory activity of MLT on the tumor cell proliferation by inhibiting the phosphorylation of p38/ERK. KRT23 knockout contributes to the antitumor effects of MLT in GC via suppressing p38/ERK phosphorylation. In the future, KRT23 might be a potential prognostic biomarker and a novel molecular target for GC.
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Affiliation(s)
- Li Li
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian 350108, P.R. China
- Department of Cell Biology and Genetics, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China
| | - Meifang Lin
- Department of Pathology, Affiliated Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Jianhua Luo
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian 350108, P.R. China
| | - Huaqin Sun
- Center of Translational Hematology, Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Zhiguang Zhang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian 350108, P.R. China
- Department of Cell Biology and Genetics, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China
| | - Dacen Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian 350108, P.R. China
| | - Lushan Chen
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Sisi Feng
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian 350108, P.R. China
| | - Xiuping Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian 350108, P.R. China
| | - Ruixiang Zhou
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian 350108, P.R. China
- Department of Histology and Embryology, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China
| | - Jun Song
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian 350108, P.R. China
- Department of Cell Biology and Genetics, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China
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Wu B, Gao X, Hu M, Hu J, Lan T, Xue T, Xu W, Zhu C, Yuan Y, Zheng J, Qin T, Xin P, Li Y, Gong L, Feng C, He S, Liu H, Li H, Wang Q, Ma Z, Qiu Q, Wang K. Distinct and shared endothermic strategies in the heat producing tissues of tuna and other teleosts. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2629-2645. [PMID: 37273070 DOI: 10.1007/s11427-022-2312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/28/2023] [Indexed: 06/06/2023]
Abstract
Although most fishes are ectothermic, some, including tuna and billfish, achieve endothermy through specialized heat producing tissues that are modified muscles. How these heat producing tissues evolved, and whether they share convergent molecular mechanisms, remain unresolved. Here, we generated a high-quality genome from the mackerel tuna (Euthynnus affinis) and investigated the heat producing tissues of this fish by single-nucleus and bulk RNA sequencing. Compared with other teleosts, tuna-specific genetic variation is strongly associated with muscle differentiation. Single-nucleus RNA-seq revealed a high proportion of specific slow skeletal muscle cell subtypes in the heat producing tissues of tuna. Marker genes of this cell subtype are associated with the relative sliding of actin and myosin, suggesting that tuna endothermy is mainly based on shivering thermogenesis. In contrast, cross-species transcriptome analysis indicated that endothermy in billfish relies mainly on non-shivering thermogenesis. Nevertheless, the heat producing tissues of the different species do share some tissue-specific genes, including vascular-related and mitochondrial genes. Overall, although tunas and billfishes differ in their thermogenic strategies, they share similar expression patterns in some respects, highlighting the complexity of convergent evolution.
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Affiliation(s)
- Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xueli Gao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Mingling Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Jing Hu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150006, China
| | - Tingfeng Xue
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Jiangmin Zheng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Tao Qin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Peidong Xin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Ye Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Chenguang Feng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150006, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenhua Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
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Habib R, Fahim S, Wahid M, Ainuddin J. Optimisation of a Method for the Differentiation of Human Umbilical Cord-derived Mesenchymal Stem Cells Toward Renal Epithelial-like Cells. Altern Lab Anim 2023; 51:363-375. [PMID: 37831588 DOI: 10.1177/02611929231207774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Human umbilical cord-derived mesenchymal stem cells (hucMSCs) can differentiate into multiple cell lineages, but few methods have been developed to generate kidney lineage cells. Due to their human origin, pluripotent nature and immunomodulatory properties, these stem cells are attractive candidates for clinical applications such as the repair or regeneration of damaged organs. This study evaluated the renal differentiation potential of hucMSCs, when exposed for 10 days to optimised concentrations of retinoic acid, activin-A and bone morphogenetic protein-7 (BMP-7) in various combinations, with and without the priming of the cells with a Wnt signalling pathway activator (CHIR99021). The hucMSCs were isolated and characterised according to surface marker expression (CD73, CD90, CD44, CD146 and CD8) and tri-lineage differentiation potential. The expression of key marker genes (OSR1, TBXT, HOXA13, SIX2, PAX2, KRT18 and ZO1) was examined by qRT-PCR. Specific marker protein expression (E-cadherin, cytokeratin-8 and cytokeratin-19) was analysed by immunocytochemistry. CHIR99021-primed cells treated with the retinoic acid, activin-A and BMP-7 cocktail showed epithelial cell-like differentiation - i.e. distinct phenotypic changes, as well as upregulated gene and protein expression, were observed that were consistent with an epithelial cell phenotype. Thus, our results showed that hucMSCs can efficiently differentiate into renal epithelial-like cells. This work may help in the development of focused therapeutic strategies, in which lineage-defined human stem cells can be used for renal regeneration.
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Affiliation(s)
- Rakhshinda Habib
- Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences (Ojha campus), Karachi, Pakistan
| | - Shumaila Fahim
- Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences (Ojha campus), Karachi, Pakistan
| | - Mohsin Wahid
- Department of Pathology, Dow International Medical College, Dow University of Health Sciences (Ojha campus), Karachi, Pakistan
| | - Jahanara Ainuddin
- Department of Gynaecology and Obstetrics, Dow University Hospital, Karachi, Pakistan
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Arslan S, Şahin NÖ, Bayyurt B, Berkan Ö, Yılmaz MB, Aşam M, Ayaz F. Role of lncRNAs in Remodeling of the Coronary Artery Plaques in Patients with Atherosclerosis. Mol Diagn Ther 2023; 27:601-610. [PMID: 37347334 DOI: 10.1007/s40291-023-00659-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2023] [Indexed: 06/23/2023]
Abstract
INTRODUCTION Cardiovascular diseases (CVDs) are the leading cause of death worldwide according to World Health Organization (WHO) data. Atherosclerosis is considered as a chronic inflammatory disease that develops in response to damage to the vascular intima-media layer in most cases. In recent years, epigenetic events have emerged as important players in the development and progression of CVDs. Since noncoding RNA (ncRNAs) are important regulators in the organization of the pathophysiological processes of the cardiovascular system, they have the potential to be used as therapeutic targets, diagnostic and prognostic biomarkers. In this study long noncoding RNA (lncRNA) and mRNA gene expression were compared between coronary atherosclerotic plaques (CAP) and the internal mammary artery (IMA) which has the same genetic makeup and is exposed to the same environmental stress conditions with CAP in the same individual. METHODS lncRNA and mRNA gene expressions were determined using the microarray in the samples. Microarray results were validated by RT-qPCR. Differentially expressed genes (DEGs; lncRNAs and mRNAs) were determined by GeneSpring (Ver 3.0) [p values < 0.05 and fold change (FC) > 2]. DAVID bioinformatics program was used for Gene Ontology (GO) annotation and enrichment analyses of statistically significant genes between CAP and IMA tissue. RESULTS AND CONCLUSIONS In our study, 345 DEGs were found to be statistically significant (p < 0.05; FC > 2) between CAP and IMA. Of these, 65 were lncRNA and 280 were mRNA. Thirty-three lncRNAs were upregulated, while 32 lncRNAs were downregulated. Some of the important mRNAs are SPP1, CYP4B1, CHRDL1, MYOC, and ALKAL2, while some of the lncRNAs are LOC105377123, LINC01857, DIO3OS, LOC101928134, and KCNA3 between CAP and IMA tissue. We also identified genes that correlated with statistically significant lncRNAs. The results of this study are expected to be an important source of data in the development of new genetically based drugs to prevent atherosclerotic plaque. In addition, the data obtained may contribute to the explanation of the epigenetic mechanisms that play a role in the pathological basis of the process that protects the IMA from atherosclerosis.
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Affiliation(s)
- Serdal Arslan
- Department of Medical Biology, Faculty of Medicine, Mersin University, 33343, Mersin, Turkey.
| | - Nil Özbilum Şahin
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, 58140, Sivas, Turkey
| | - Burcu Bayyurt
- Department of Medical Biology, Faculty of Medicine, Sivas Cumhuriyet University, 58140, Sivas, Turkey
| | - Öcal Berkan
- Department of Cardiovascular Surgery, Cigli Regional Training Hospital, Izmir, Turkey
| | - Mehmet Birhan Yılmaz
- Department of Cardiology, Faculty of Medicine, Dokuz Eylul University, 35340, Izmir, Turkey
| | - Mehmet Aşam
- Department of Cardiovascular Surgery, SBU Van Training and Research Hospital, 65300, Edremit, Van, Turkey
| | - Furkan Ayaz
- Mersin University Biotechnology Research and Application Center, Mersin University, 33343, Mersin, Turkey.
- Department of Biotechnology, Faculty of Arts and Science, Mersin University, 33343, Mersin, Turkey.
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Li JS, Chen X, Luo A, Chen D. TFRC-RNA interactions show the regulation of gene expression and alternative splicing associated with IgAN in human renal tubule mesangial cells. Front Genet 2023; 14:1176118. [PMID: 37547464 PMCID: PMC10397801 DOI: 10.3389/fgene.2023.1176118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction: IgA nephropathy (IgAN) is the most common primary glomerular disease (PGD) which could progress to renal failure and is characterized by aberrant IgA immune complex deposition. Transferrin receptor1 (TFRC), an IgA receptor, is a potential RNA binding protein (RBP) which regulates expression of genes positively associated with the cell cycle and proliferation and is involved in IgAN. Molecular mechanisms by which TFRC affects IgAN development remain unclear. Methods: In this study, TFRC was overexpressed in human renal tubular mesangial cells (HRMCs) and RNA-sequencing (RNA-seq) and improved RNA immunoprecipitation sequencing (iRIP-seq) were performed. The aim was to identify potential RNA targets of TFRC at transcriptional and alternative splicing (AS) levels. Results: TFRC-regulated AS genes were enriched in mRNA splicing and DNA repair, consistent with global changes due to TFRC overexpression (TFRC-OE). Expression of TFRC-regulated genes potentially associated with IgAN, including CENPH, FOXM1, KIFC1, TOP2A, FABP4, ID1, KIF20A, ATF3, H19, IRF7, and H1-2, and with AS, CYGB, MCM7 and HNRNPH1, were investigated by RT-qPCR and iRIP-seq data analyzed to identify TFRC-bound RNA targets. RCC1 and RPPH1 were found to be TFRC-bound RNA targets involved in cell proliferation. Discussion: In conclusion, molecular TFRC targets were identified in HRMCs and TFRC found to regulate gene transcription and AS. TFRC is considered to have potential as a clinical therapeutic target.
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Affiliation(s)
- Jian-Si Li
- Department of Nephrology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiao Chen
- Heilongjiang Provincial Hospital Affiliated to Harbin Institute of Technology, Harbin, China
| | - Ailing Luo
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, China
| | - Dong Chen
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, China
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Cui J, Ma Q, Zhang C, Li Y, Liu J, Xie K, Luo E, Zhai M, Tang C. Keratin 18 Depletion as a Possible Mechanism for the Induction of Apoptosis and Ferroptosis in the Rat Hippocampus After Hypobaric Hypoxia. Neuroscience 2023; 513:64-75. [PMID: 36395917 DOI: 10.1016/j.neuroscience.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Memory impairment is one of the neuropsychological effects of hypobaric hypoxia (HH), which can be associated with programmed cell death, such as apoptosis and ferroptosis. Emerging evidence indicates crosstalk between apoptosis and ferroptosis, while the crosstalk between HH-induced apoptosis and ferroptosis in the hippocampus has not been clarified. Here, microarray profiles were extracted to analyze the differentially expressed genes with and without HH exposure, and keratin 18 (Krt18) was found to be a potential gene related to both apoptosis and ferroptosis. Then, we conducted morphological observations that showed that apoptosis and ferroptosis coexisted in the rat hippocampus after HH exposure. Combined with the real-time q-PCR analysis, the mRNA expression of Krt18 decreased significantly after HH exposure for 1 day and 3 days, and Mapk10 (JNK3) was upregulated at the corresponding time points. After exposure for 7 days, Krt18 and JNK3 showed no significant change. In conclusion, Krt18 may regulate apoptosis and ferroptosis simultaneously, possibly via the JNK signaling pathway, which might provide a potential central target for apoptosis and ferroptosis in hippocampal injury after HH exposure.
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Affiliation(s)
- Jinxiu Cui
- Department of Military Medical Equipment and Metrology, School of Military Biomedical Engineering, Fourth Military Medical University, 710032 Xi'an, Shaanxi, PR China
| | - Qianqian Ma
- Department of Military Medical Equipment and Metrology, School of Military Biomedical Engineering, Fourth Military Medical University, 710032 Xi'an, Shaanxi, PR China; The College of Life Sciences, Northwest University, 710069 Xi'an, Shaanxi, PR China
| | - Chenxu Zhang
- Department of Military Medical Equipment and Metrology, School of Military Biomedical Engineering, Fourth Military Medical University, 710032 Xi'an, Shaanxi, PR China
| | - Yuanzhe Li
- Department of Military Medical Equipment and Metrology, School of Military Biomedical Engineering, Fourth Military Medical University, 710032 Xi'an, Shaanxi, PR China
| | - Juan Liu
- Department of Military Medical Equipment and Metrology, School of Military Biomedical Engineering, Fourth Military Medical University, 710032 Xi'an, Shaanxi, PR China
| | - Kangning Xie
- Department of Military Medical Equipment and Metrology, School of Military Biomedical Engineering, Fourth Military Medical University, 710032 Xi'an, Shaanxi, PR China
| | - Erping Luo
- Department of Military Medical Equipment and Metrology, School of Military Biomedical Engineering, Fourth Military Medical University, 710032 Xi'an, Shaanxi, PR China
| | - Mingming Zhai
- Department of Military Medical Equipment and Metrology, School of Military Biomedical Engineering, Fourth Military Medical University, 710032 Xi'an, Shaanxi, PR China.
| | - Chi Tang
- Department of Military Medical Equipment and Metrology, School of Military Biomedical Engineering, Fourth Military Medical University, 710032 Xi'an, Shaanxi, PR China; Shaanxi Provincial Key Laboratory of Bioelectromagnetic Detection and Intelligent Perception, School of Military Biomedical Engineering, Fourth Military Medical University, 710032 Xi'an, Shaanxi, PR China.
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Wang Y, Li J, Hao P, Li J, Han R, Lin J, Li X. Integrated Whole-Exome and Transcriptome Sequencing Indicated Dysregulation of Cholesterol Metabolism in Eyelid Sebaceous Gland Carcinoma. Transl Vis Sci Technol 2023; 12:4. [PMID: 36735267 PMCID: PMC9907373 DOI: 10.1167/tvst.12.2.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Purpose To identify the molecular background of eyelid sebaceous gland carcinomas (SCs), we conducted the integrated whole-exome sequencing and transcriptome sequencing for eyelid SCs in this study. Methods The genetic alterations were studied by whole-exome sequencing, and the messenger RNA expression was studied using Oxford Nanopore Technologies (ONT) in five paired fresh eyelid SC tissues and adjacent normal tissues. Integrated analysis of exome and transcriptomic information was conducted for filtering candidate driver genes. Protein-protein interaction (PPI) network of filtered candidate genes was analyzed by STRING. The protein expression was verified by immunohistochemistry in 29 eyelid SCs and 17 compared normal sebaceous gland tissues. Results The average numbers of pathogenic somatic single-nucleotide variants (SNVs) and indels in eyelid SCs were 75 and 28, respectively. Tumor protein p53 (TP53), zinc finger protein 750 (ZNF750), filaggrin 2 (FLG2), valosin-containing protein (VCP), and zinc finger protein 717 (ZNF717) were recurrent mutated genes. A mean of 844 differentially expressed genes (DEGs) were upregulated, and 1401 DEGs were downregulated in SC samples. The intersection of DEG-based pathways and mutation-based pathways was mainly involved in microbial infection and inflammation, immunodeficiency, cancer, lipid metabolism, and the other pathways. The intersection of DEGs and mutated genes consisted of 55 genes, of which 15 genes formed a PPI network with 4 clusters. The PPI cluster composed of scavenger receptor class B member 1 (SCARB1), peroxisome proliferator-activated receptor γ (PPARG), peroxisome proliferator-activated receptor γ coactivator 1α (PPARGC1A) was involved in cholesterol metabolism. The expression of SCARB1 protein was found to be increased, whereas that of PPARG protein was decreased in eyelid SCs compared to that in the normal sebaceous glands. Conclusions Increased SCARB1 and decreased PPARG indicated that dysregulation of cholesterol metabolism might be involved in carcinogenesis of eyelid SCs. Translational Relevance The malfunction in cholesterol metabolism might advance our knowledge of the carcinogenesis of eyelid SCs.
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Affiliation(s)
- Yuchuan Wang
- Tianjin Eye Hospital, Tianjin Key lab of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin, China,Nankai University Affiliated Eye Hospital, Tianjin, China,Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Jun Li
- Tianjin Eye Hospital, Tianjin Key lab of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin, China,Nankai University Affiliated Eye Hospital, Tianjin, China,Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Peng Hao
- Tianjin Eye Hospital, Tianjin Key lab of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin, China,Nankai University Affiliated Eye Hospital, Tianjin, China,Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Jing Li
- Tianjin Eye Hospital, Tianjin Key lab of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin, China,Nankai University Affiliated Eye Hospital, Tianjin, China,Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Ruifang Han
- Tianjin Eye Hospital, Tianjin Key lab of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin, China,Nankai University Affiliated Eye Hospital, Tianjin, China,Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Jinyong Lin
- Tianjin Eye Hospital, Tianjin Key lab of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin, China,Nankai University Affiliated Eye Hospital, Tianjin, China,Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Xuan Li
- Tianjin Eye Hospital, Tianjin Key lab of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin, China,Nankai University Affiliated Eye Hospital, Tianjin, China,Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
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Mykhaliuk VV, Havryliak VV, Salyha YT. The Role of Cytokeratins in Ensuring the Basic Cellular Functions and in Dignosis of Disorders. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722060093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Barrett's Metaplasia Progression towards Esophageal Adenocarcinoma: An Attempt to Select a Panel of Molecular Sensors and to Reflect Clinical Alterations by Experimental Models. Int J Mol Sci 2022; 23:ijms23063312. [PMID: 35328735 PMCID: PMC8955539 DOI: 10.3390/ijms23063312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/06/2023] Open
Abstract
The molecular processes that predispose the development of Barrett’s esophagus (BE) towards esophageal adenocarcinoma (EAC) induced by gastrointestinal reflux disease (GERD) are still under investigation. In this study, based on a scientific literature screening and an analysis of clinical datasets, we selected a panel of 20 genes covering BE- and EAC-specific molecular markers (FZD5, IFNGR1, IL1A, IL1B, IL1R1, IL1RN, KRT4, KRT8, KRT15, KRT18, NFKBIL1, PTGS1, PTGS2, SOCS3, SOX4, SOX9, SOX15, TIMP1, TMEM2, TNFRSF10B). Furthermore, we aimed to reflect these alterations within an experimental and translational in vitro model of BE to EAC progression. We performed a comparison between expression profiles in GSE clinical databases with an in vitro model of GERD involving a BE cell line (BAR-T) and EAC cell lines (OE33 and OE19). Molecular responses of cells treated with acidified bile mixture (BM) at concentration of 100 and 250 μM for 30 min per day were evaluated. We also determined a basal mRNA expression within untreated, wild type cell lines on subsequent stages of BE and EAC development. We observed that an appropriately optimized in vitro model based on the combination of BAR-T, OE33 and OE19 cell lines reflects in 65% and more the clinical molecular alterations observed during BE and EAC development. We also confirmed previous observations that exposure to BM (GERD in vitro) activated carcinogenesis in non-dysplastic cells, inducing molecular alternations in the advanced stages of BE. We conclude that it is possible to induce, to a high extent, the molecular profile observed clinically within appropriately and carefully optimized experimental models, triggering EAC development. This experimental scheme and molecular marker panel might be implemented in further research, e.g., aiming to develop and evaluate novel compounds and prodrugs targeting GERD as well as BE and EAC prevention and treatment.
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