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Wang Y, Lih TM, Lee JW, Ohtsuka T, Hozaka Y, Mino-Kenudson M, Adsay NV, Luchini C, Scarpa A, Maker AV, Kim GE, Paulino J, Chen L, Jiao L, Sun Z, Goodman D, Pflüger MJ, Roberts NJ, Matthaei H, Wood LD, Furukawa T, Zhang H, Hruban RH. Multi-omic profiling of intraductal papillary neoplasms of the pancreas reveals distinct expression patterns and potential markers of progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602385. [PMID: 39005476 PMCID: PMC11245086 DOI: 10.1101/2024.07.07.602385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In order to advance our understanding of precancers in the pancreas, 69 pancreatic intraductal papillary neoplasms (IPNs), including 64 intraductal papillary mucinous neoplasms (IPMNs) and 5 intraductal oncocytic papillary neoplasms (IOPNs), 32 pancreatic cyst fluid samples, 104 invasive pancreatic ductal adenocarcinomas (PDACs), 43 normal adjacent tissues (NATs), and 76 macro-dissected normal pancreatic ducts (NDs) were analyzed by mass spectrometry. A total of 10,246 proteins and 22,284 glycopeptides were identified in all tissue samples, and 756 proteins with more than 1.5-fold increase in abundance in IPMNs relative to NDs were identified, 45% of which were also identified in cyst fluids. The over-expression of selected proteins was validated by immunolabeling. Proteins and glycoproteins overexpressed in IPMNs included those involved in glycan biosynthesis and the immune system. In addition, multiomics clustering identified two subtypes of IPMNs. This study provides a foundation for understanding tumor progression and targets for earlier detection and therapies. Significance This multilevel characterization of intraductal papillary neoplasms of the pancreas provides a foundation for understanding the changes in protein and glycoprotein expression during the progression from normal duct to intraductal papillary neoplasm, and to invasive pancreatic carcinoma, providing a foundation for informed approaches to earlier detection and treatment.
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Liu J, Zhang Y, Wu J, Liu X, Li L, Zhang J. LncRNA FOXD2-AS1 promotes the growth, invasion and migration of OSCC cells by regulating the MiR-185-5p/PLOD1/Akt/mTOR pathway. Cancer Genet 2024; 284-285:48-57. [PMID: 38729078 DOI: 10.1016/j.cancergen.2024.05.001] [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: 03/20/2024] [Revised: 05/05/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
Although lncRNAs are recognized to contribute to the development of oral squamous-cell carcinoma (OSCC), their exact function in invasion and cell migration is not clear. In this research, we explored the molecular and cellular mechanisms of FOXD2-AS1 in OSCC. Prognostic and bioinformatics analyses were used to test for the differential expression of FOXD2-AS1-PLOD1. Following FOXD2-AS1 suppression or overexpression, changes in cell viability were measured using the CCK-8 test; changes in cell migration and invasion abilities were measured using the migration and the Transwell assay. The expression of associated genes and proteins was found using Western blot and RT-qPCR. Analysis of luciferase reporter genes was done to look for regulatory connections between various molecules. The FOXD2-AS1-PLOD1 pair, which was highly expressed in OSCC, was analyzed and experimentally verified to be closely related to the prognosis of OSCC, and a nomogram model and correction curve were constructed. The inhibition of FOXD2-AS1 resulted in the reduction of cell activity, migration, invasion ability and changes in genes related to invasion and migration. In vivo validation showed that inhibition of FOXD2-AS1 expression slowed tumor growth, and related proteins changed accordingly. The experiments verified that FOXD2-AS1 negatively regulated miR-185-5 p and that miR-185-5 p negatively regulated PLOD1. In addition, it was found that the expression of PLOD1, p-Akt and p-mTOR proteins in OSCC cells was reduced by the inhibition of FOXD2-AS1, and FOXD2-AS1 and PLOD1 were closely related to the Akt/mTOR pathway. Increased expression of FOXD2-AS1 promotes OSCC growth, invasion and migration, which is important in part by targeting miR-185-5 p/PLOD1/Akt/mTOR pathway activity.
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Affiliation(s)
- Jian Liu
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, Hebei, PR China
| | - Yong Zhang
- Department of Stomatology, Hebei General Hospital, Shijiazhuang 050011, Hebei, PR China
| | - Jingjing Wu
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, Hebei, PR China
| | - Xin Liu
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, Hebei, PR China
| | - Lifang Li
- Department of Stomatology, Hebei Provincial Hospital of Chinese Medicine, Shijiazhuang 050011, Hebei, PR China
| | - Jinhong Zhang
- Department of Stomatology, The First Hospital of Hebei Medical University, Shijiazhuang 050011, Hebei, PR China.
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Zang L, Zhang B, Zhou Y, Zhang F, Tian X, Tian Z, Chen D, Miao Q. Machine learning algorithm integrates bulk and single-cell transcriptome sequencing to reveal immune-related personalized therapy prediction features for pancreatic cancer. Aging (Albany NY) 2023; 15:14109-14140. [PMID: 38095640 PMCID: PMC10756117 DOI: 10.18632/aging.205293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/03/2023] [Indexed: 12/21/2023]
Abstract
Pancreatic cancer (PC) is a digestive malignancy with worse overall survival. Tumor immune environment (TIME) alters the progression and proliferation of various solid tumors. Hence, we aimed to detect the TIME-related classifier to facilitate the personalized treatment of PC. Based on the 1612 immune-related genes (IRGs), we classified patients into Immune_rich and Immune_desert subgroups via consensus clustering. Patients in distinct subtypes exhibited a difference in sensitivity to immune checkpoint blockers (ICB). Next, the immune-related signature (IRS) model was established based on 8 IRGs (SYT12, TNNT1, TRIM46, SMPD3, ANLN, AFF3, CXCL9 and RP1L1) and validated its predictive efficiency in multiple cohorts. RT-qPCR experiments demonstrated the differential expression of 8 IRGs between tumor and normal cell lines. Patients who gained lower IRS score tended to be more sensitive to chemotherapy and immunotherapy, and obtained better overall survival compared to those with higher IRS scores. Moreover, scRNA-seq analysis revealed that fibroblast and ductal cells might affect malignant tumor cells via MIF-(CD74+CD44) and SPP1-CD44 axis. Eventually, we identified eight therapeutic targets and one agent for IRS high patients. Our study screened out the specific regulation pattern of TIME in PC, and shed light on the precise treatment of PC.
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Affiliation(s)
- Longjun Zang
- Department of General Surgery, Taiyuan Central Hospital, Taiyuan 030009, Shanxi, P.R. China
| | - Baoming Zhang
- Department of General Surgery, Taiyuan Central Hospital, Taiyuan 030009, Shanxi, P.R. China
| | - Yanling Zhou
- University of Shanghai for Science and Technology, Shanghai 200093, P.R. China
| | - Fusheng Zhang
- Department of General Surgery, Peking University First Hospital, Beijing 100034, P.R. China
| | - Xiaodong Tian
- Department of General Surgery, Peking University First Hospital, Beijing 100034, P.R. China
| | - Zhongming Tian
- Department of General Surgery, Taiyuan Central Hospital, Taiyuan 030009, Shanxi, P.R. China
| | - Dongjie Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200025, P.R. China
| | - Qingwang Miao
- Department of General Surgery, Taiyuan Central Hospital, Taiyuan 030009, Shanxi, P.R. China
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Cao ZR, Zheng WX, Jiang YX, Chai H, Gong JH, Zhao MJ, Yan P, Liu YY, Liu XY, Huang ZT, Yang H, Peng DD, Zong KZ, Wu ZJ. miR-449a ameliorates acute rejection after liver transplantation via targeting procollagen-lysine1,2-oxoglutarate5-dioxygenase 1 in macrophages. Am J Transplant 2023; 23:336-352. [PMID: 36695693 DOI: 10.1016/j.ajt.2022.12.009] [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: 05/17/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 01/13/2023]
Abstract
Acute rejection (AR) is an important factor that leads to poor prognosis after liver transplantation (LT). Macrophage M1-polarization is an important mechanism in AR development. MicroRNAs play vital roles in disease regulation; however, their effects on macrophages and AR remain unclear. In this study, rat models of AR were established following LT, and macrophages and peripheral blood mononuclear cells were isolated from rats and humans, respectively. We found miR-449a expression to be significantly reduced in macrophages and peripheral blood mononuclear cells. Overexpression of miR-449a not only inhibited the M1-polarization of macrophages in vitro but also improved the AR of transplant in vivo. The mechanism involved inhibiting the noncanonical nuclear factor-kappaB (NF-κB) pathway. We identified procollagen-lysine1,2-oxoglutarate5-dioxygenase 1 (PLOD1) as a target gene of miR-449a, which could reverse miR-449a's inhibition of macrophage M1-polarization, amelioration of AR, and inhibition of the NF-κB pathway. Overall, miR-449a inhibited the NF-κB pathway in macrophages through PLOD1 and also inhibited the M1-polarization of macrophages, thus attenuating AR after LT. In conclusion, miR-449a and PLOD1 may be new targets for the prevention and mitigation of AR.
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Affiliation(s)
- Zhen-Rui Cao
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Wei-Xiong Zheng
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Yu-Xin Jiang
- Department of Dermatology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Hao Chai
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Jun-Hua Gong
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Min-Jie Zhao
- Department of Hepatobiliary Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Ping Yan
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Yan-Yao Liu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Xiao-Ya Liu
- Department of Oncology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Zuo-Tian Huang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Hang Yang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Da-Di Peng
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Ke-Zhen Zong
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
| | - Zhong-Jun Wu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.
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Yang Z, Zhou L, Si T, Chen S, Liu C, Ng KK, Wang Z, Chen Z, Qiu C, Liu G, Wang Q, Zhou X, Zhang L, Yao Z, He S, Yang M, Zhou Z. Lysyl hydroxylase LH1 promotes confined migration and metastasis of cancer cells by stabilizing Septin2 to enhance actin network. Mol Cancer 2023; 22:21. [PMID: 36721170 PMCID: PMC9887875 DOI: 10.1186/s12943-023-01727-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/22/2023] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Excessive extracellular matrix deposition and increased stiffness are typical features of solid tumors such as hepatocellular carcinoma (HCC) and pancreatic ductal adenocarcinoma (PDAC). These conditions create confined spaces for tumor cell migration and metastasis. The regulatory mechanism of confined migration remains unclear. METHODS LC-MS was applied to determine the differentially expressed proteins between HCC tissues and corresponding adjacent tissue. Collective migration and single cell migration microfluidic devices with 6 μm-high confined channels were designed and fabricated to mimic the in vivo confined space. 3D invasion assay was created by Matrigel and Collagen I mixture treat to adherent cells. 3D spheroid formation under various stiffness environment was developed by different substitution percentage GelMA. Immunoprecipitation was performed to pull down the LH1-binding proteins, which were identified by LC-MS. Immunofluorescent staining, FRET, RT-PCR, Western blotting, FRAP, CCK-8, transwell cell migration, wound healing, orthotopic liver injection mouse model and in vivo imaging were used to evaluate the target expression and cellular phenotype. RESULTS Lysyl hydroxylase 1 (LH1) promoted the confined migration of cancer cells at both collective and single cell levels. In addition, LH1 enhanced cell invasion in a 3D biomimetic model and spheroid formation in stiffer environments. High LH1 expression correlated with poor prognosis of both HCC and PDAC patients, while it also promoted in vivo metastasis. Mechanistically, LH1 bound and stabilized Septin2 (SEPT2) to enhance actin polymerization, depending on the hydroxylase domain. Finally, the subpopulation with high expression of both LH1 and SEPT2 had the poorest prognosis. CONCLUSIONS LH1 promotes the confined migration and metastasis of cancer cells by stabilizing SEPT2 and thus facilitating actin polymerization.
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Affiliation(s)
- Zihan Yang
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People’s Republic of China ,grid.35030.350000 0004 1792 6846Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong China
| | - Li Zhou
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People’s Republic of China ,grid.412461.40000 0004 9334 6536Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tongxu Si
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People’s Republic of China ,grid.35030.350000 0004 1792 6846Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong China
| | - Siyuan Chen
- grid.412461.40000 0004 9334 6536Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chengxi Liu
- grid.16890.360000 0004 1764 6123State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Kelvin Kaki Ng
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People’s Republic of China ,grid.35030.350000 0004 1792 6846Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong China
| | - Zesheng Wang
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People’s Republic of China ,grid.35030.350000 0004 1792 6846Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong China
| | - Zhiji Chen
- grid.412461.40000 0004 9334 6536Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chan Qiu
- grid.412461.40000 0004 9334 6536Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guopan Liu
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People’s Republic of China ,grid.35030.350000 0004 1792 6846Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong China
| | - Qingliang Wang
- grid.412461.40000 0004 9334 6536Department of Pathology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoyu Zhou
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People’s Republic of China ,grid.35030.350000 0004 1792 6846Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong China
| | - Liang Zhang
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People’s Republic of China ,grid.35030.350000 0004 1792 6846Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong China
| | - Zhongping Yao
- grid.16890.360000 0004 1764 6123State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Song He
- grid.412461.40000 0004 9334 6536Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mengsu Yang
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People’s Republic of China ,grid.35030.350000 0004 1792 6846Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong China
| | - Zhihang Zhou
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People’s Republic of China ,grid.412461.40000 0004 9334 6536Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Chen R, Jiang M, Hu B, Fu B, Sun T. Comprehensive Analysis of the Expression, Prognosis, and Biological Significance of PLOD Family in Bladder Cancer. Int J Gen Med 2023; 16:707-722. [PMID: 36872941 PMCID: PMC9975538 DOI: 10.2147/ijgm.s399875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Background Large numbers of studies have identified that procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD) family members play important roles in tumorigenesis and tumor progression in various cancers. However, the expression pattern, clinical value and function of PLOD family have yet to be analyzed systematically and comprehensively in bladder urothelial carcinoma (BLCA). Methods We investigated the transcriptional levels, genetic alteration, biological function, immune cell infiltration, data on survival of PLODs in patients with BLCA based on UALCAN, the Cancer Genome Atlas (TCGA) database, Gene Expression Profiling Interactive Analysis (GEPIA), TIMER, STRING, cBioPortal and GSCALite databases. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed in R software using the Cluster Profiler Bioconductor package. Protein-protein interaction (PPI) network was established by STRING and visualized by using R version (3.6.3) software. Survival analysis was performed using the packages "survminer". Results The mRNA and protein expression patterns of PLOD family members were noticeably increased in BLC compared with normal tissue. The mRNA expression levels of PLOD1-2 genes were significantly correlated with histological subtypes and PLOD1 was significantly correlated with pathological stage. Furthermore, the high expression levels of PLOD1-2 were remarkably associated with poor overall survival (OS) in BLCA patients, meanwhile high expression levels of PLOD1 and PLOD3 were markedly associated with poor progression-free interval (PFI). In co-expression gene analysis, 50 genes were primarily associated with the differentially expressed PLODs in BLCA. Functional enrichment analysis revealed that protein hydroxylation, collagen fibril organization, and lysine degradation were key biological functions of PLODs in BLCA. Moreover, PLOD family genes were identified as being associated with the activities of tumor-infiltrating immune cells and closely associated with immune responses in BLCA. Conclusion PLOD family members might serve as potential therapeutic targets and prognostic markers for BLCA patients' survival.
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Affiliation(s)
- Ru Chen
- Department of Urology, the First Affiliated Hospital of Nanchang University, Nanchang City, People's Republic of China.,Department of Urology, the First Hospital of Putian City, Putian City, People's Republic of China
| | - Ming Jiang
- Department of Urology, the First Affiliated Hospital of Nanchang University, Nanchang City, People's Republic of China
| | - Bing Hu
- Department of Urology, the First Affiliated Hospital of Nanchang University, Nanchang City, People's Republic of China
| | - Bin Fu
- Department of Urology, the First Affiliated Hospital of Nanchang University, Nanchang City, People's Republic of China
| | - Ting Sun
- Department of Urology, the First Affiliated Hospital of Nanchang University, Nanchang City, People's Republic of China
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Prognostic Model and Immune Infiltration of Ferroptosis Subcluster-Related Modular Genes in Gastric Cancer. JOURNAL OF ONCOLOGY 2022; 2022:5813522. [PMID: 36276279 PMCID: PMC9584706 DOI: 10.1155/2022/5813522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/28/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022]
Abstract
Background Gastric cancer (GC) is one of the gastrointestinal tumors with the highest mortality rate. The number of GC patients is still high. As a way of iron-dependent programmed cell death, ferroptosis activates lipid peroxidation and accumulates large reactive oxygen species. The role of ferroptosis in GC prognosis was underrepresented. The objective was to investigate the role of ferroptosis-related genes (FRGs) in the prognosis and development of GC. Methods Datasets of GC patients were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database that include clinical information and RNA seq data. Through nonnegative matrix factorization (NMF) clustering, we identified and unsupervised cluster analysis of the expression matrix of FRGs. And we constructed the co-expression network between genes and clinical characteristics by consensus weighted gene co-expression network analysis (WGCNA). The prognostic model was constructed by univariate and multivariate regression analysis. The potential mechanisms of development and prognosis in GC were explored by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene ontology (GO), tumor immune microenvironment (TIME), and tumor mutation burden (TMB). Results Two molecular subclusters with different expression patterns of FRGs were identified, which have significantly different survival states. Ferroptosis subcluster-related modular genes were identified by WGCNA. Based on 8 ferroptosis subcluster-related modular genes (collagen triple helix repeat containing 1 (CTHRC1), podoplanin (PDPN), procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 (PLOD2), glutamine-fructose-6-phosphate transaminase 2 (GFPT2), ATP-binding cassette subfamily A member 1 (ABCA1), G protein-coupled receptor 176 (GPR176), serpin family E member 1 (SERPINE1), dual specificity phosphatase 1 (DUSP1)) and clinicopathological features, a nomogram was constructed and validated for their predictive efficiency on GC prognosis. Through receiver operating characteristic (ROC) analysis, the results showed that the area under the curve (AUC) of 1-, 3-, and 5-year survival were 0.721, 0.747, and 0.803, respectively, indicating that the risk-scoring model we constructed had good prognosis efficacy in GC. The degree of immune infiltration in high-risk group was largely higher than low-risk group. It indicated that the immune cells have a good response in high-risk group of GC. The TMB of high-risk group was higher, which could generate more mutations and was more conducive to the body's resistance to the development of cancer. Conclusion The risk-scoring model based on 8 ferroptosis subcluster-related modular genes has shown outstanding advantages in predicting patient prognosis. The interaction of ferroptosis in GC development may provide new insights into exploring molecular mechanisms and targeted therapies for GC patients.
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8
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Gong S, Schopow N, Duan Y, Wu C, Kallendrusch S, Osterhoff G. PLOD Family: A Novel Biomarker for Prognosis and Personalized Treatment in Soft Tissue Sarcoma. Genes (Basel) 2022; 13:genes13050787. [PMID: 35627171 PMCID: PMC9141206 DOI: 10.3390/genes13050787] [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: 03/25/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Despite various treatment attempts, the heterogenous group of soft tissue sarcomata (STS) with more than 100 subtypes still shows poor outcomes. Therefore, effective biomarkers for prognosis prediction and personalized treatment are of high importance. The Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase (PLOD) gene family, which is related to multiple cancer entities, consists of three members which encode important enzymes for the formation of connective tissue. The relation to STS, however, has not yet been explored. In this study, data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases were used to analyze the role of PLOD1–3 in STS. It was found that an overexpression of PLOD family members correlates with poor prognosis, which might be due to an increased infiltration of immune-related cells in the tumor microenvironment. In STS, the expression of PLOD genes could be a novel biomarker for prognosis and a personalized, more aggressive treatment in these patients.
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Affiliation(s)
- Siming Gong
- Institute of Anatomy, University of Leipzig, Liebigstraße 13, 04103 Leipzig, Germany; (S.G.); (N.S.); (S.K.)
| | - Nikolas Schopow
- Institute of Anatomy, University of Leipzig, Liebigstraße 13, 04103 Leipzig, Germany; (S.G.); (N.S.); (S.K.)
- Sarcoma Center, Department for Orthopedics, Trauma Surgery and Reconstructive Surgery, University Hospital Leipzig, Liebigstraße 20, 04103 Leipzig, Germany;
| | - Yingjuan Duan
- Faculty of Chemistry and Mineralogy, University of Leipzig, Johannisallee 29, 04103 Leipzig, Germany;
| | - Changwu Wu
- Institute of Anatomy, University of Leipzig, Liebigstraße 13, 04103 Leipzig, Germany; (S.G.); (N.S.); (S.K.)
- Correspondence: or
| | - Sonja Kallendrusch
- Institute of Anatomy, University of Leipzig, Liebigstraße 13, 04103 Leipzig, Germany; (S.G.); (N.S.); (S.K.)
- Department of Medicine, Health and Medical University Potsdam, Olympischer Weg 1, 14471 Potsdam, Germany
| | - Georg Osterhoff
- Sarcoma Center, Department for Orthopedics, Trauma Surgery and Reconstructive Surgery, University Hospital Leipzig, Liebigstraße 20, 04103 Leipzig, Germany;
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