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Zeng N, Jian Z, Xu J, Peng T, Hong G, Xiao F. Identification of qualitative characteristics of immunosuppression in sepsis based on immune-related genes and immune infiltration features. Heliyon 2024; 10:e29007. [PMID: 38628767 PMCID: PMC11019180 DOI: 10.1016/j.heliyon.2024.e29007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
Objective Sepsis is linked to high morbidity and mortality rates. Consequently, early diagnosis is crucial for proper treatment, reducing hospitalization, and mortality rates. Additionally, over one-fifth of sepsis patients still face a risk of death. Hence, early diagnosis, and effective treatment play pivotal roles in enhancing the prognosis of patients with sepsis. Method The study analyzed whole blood data obtained from patients with sepsis and control samples sourced from three datasets (GSE57065, GSE69528, and GSE28750). Commonly dysregulated immune-related genes (IRGs) among these three datasets were identified. The differential characteristics of these common IRGs in the sepsis and control samples were assessed using the REO-based algorithm. Based on these differential characteristics, samples from eight Gene Expression Omnibus (GEO) databases (GSE57065, GSE69528, GSE28750, GSE65682, GSE69063, GSE95233, GSE131761, and GSE154918), along with three ArrayExpress databases (E-MTAB-4421, E-MTAB-4451, and E-MTAB-7581), were categorized and scored. The effectiveness of these differential characteristics in distinguishing sepsis samples from control samples was evaluated using the AUC value derived from the receiver operating characteristic curve (ROC) curve. Furthermore, the expression of IRGs was validated in peripheral blood samples obtained from patients with sepsis through qRT-PCR. Results Among the three training datasets, a total of 84 common dysregulated immune-related genes (IRGs) were identified. Utilizing a within-sample relative expression ordering (REOs)-based algorithm to analyze these common IRGs, differential characteristics were observed in three reverse stable pairs (ELANE-RORA, IL18RAP-CD247, and IL1R1-CD28). In the eight GEO datasets, the expression of ELANE, IL18RAP, and IL1R1 demonstrated significant upregulation, while RORA, CD247, and CD28 expression exhibited notable downregulation during sepsis. These three pairs of immune-related marker genes displayed accuracies of 95.89% and 97.99% in distinguishing sepsis samples among the eight GEO datasets and the three independent ArrayExpress datasets, respectively. The area under the receiver operating characteristic curve ranged from 0.81 to 1.0. Additionally, among these three immune-related marker gene pairs, mRNA expression levels of ELANE and IL1R1 were upregulated, whereas the levels of CD247 and CD28 mRNA were downregulated in blood samples from patients with sepsis compared to normal controls. Conclusion These three immune-related marker gene pairs exhibit high predictive performance for blood samples from patients with sepsis. They hold potential as valuable auxiliary clinical blood screening tools for sepsis.
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Affiliation(s)
- Ni Zeng
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Zaijin Jian
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Junmei Xu
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Tian Peng
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Guiping Hong
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Feng Xiao
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
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2
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Wang L, Fu D, Weng S, Xu H, Liu L, Guo C, Ren Y, Liu Z, Han X. Genome-scale CRISPR-Cas9 screening stratifies pancreatic cancer with distinct outcomes and immunotherapeutic efficacy. Cell Signal 2023; 110:110811. [PMID: 37468054 DOI: 10.1016/j.cellsig.2023.110811] [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: 04/05/2023] [Revised: 07/02/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
Pancreatic cancer (PC) was featured by dramatic heterogeneity and dismal outcomes. An ideal classification strategy capable of achieving risk stratification and individualized treatment is urgently needed to significantly improve prognosis. In this study, using the 105 prognostic cancer essential genes identified by genome-scale CRISPR-Cas9 screening and univariate Cox analysis, we established and verified three heterogeneous subtypes via non-negative matrix factorization (NMF) and nearest template prediction (NTP) algorithms in the TCGA-PAAD cohort (176 samples) and four multi-center cohorts (233 samples), respectively. Among them, C1 with the worst prognosis was enriched in immune-related pathways, possessed superior infiltration abundance of immune cells and immune checkpoint molecules expression, and might be most sensitive to immunotherapy. C3, owing a moderate prognosis, might be featured by proliferative biological function, and despite its highest immunogenicity, the defects in antigen processing and presentation ability coupled with barren immune environment render it ineffective for immunotherapy, while it had potential sensitivity to paclitaxel and methotrexate. Besides, C2 harbored the best prognosis and was characterized by metabolism-related functions. These results could deepen our understanding of PC molecular heterogeneity and provide a trustworthy reference for prognostic stratification management and precision medicine in clinical practice.
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Affiliation(s)
- Libo Wang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Deshuang Fu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China; Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China.
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3
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Su Y, Qi R, Li L, Wang X, Li S, Zhao X, Hou R, Ma W, Liu D, Zheng J, Shi M. An immune-related gene prognostic risk index for pancreatic adenocarcinoma. Front Immunol 2022; 13:945878. [PMID: 35958614 PMCID: PMC9360334 DOI: 10.3389/fimmu.2022.945878] [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: 05/17/2022] [Accepted: 07/04/2022] [Indexed: 11/19/2022] Open
Abstract
Objective Our goal is to construct an immune-related gene prognostic risk index (IRGPRI) for pancreatic adenocarcinoma (PAAD), and to clarify the immune and molecular features in IRGPRI-defined PAAD subgroups and the benefit of immune checkpoint inhibitors (ICIs) therapy. Method Through differential gene expression analysis, weighted gene co-expression network analysis (WGCNA), and univariate Cox regression analysis, 16 immune-related hub genes were identified using the Cancer Genome Atlas (TCGA) PAAD dataset (n = 182) and immune gene set. From these genes, we constructed an IRGPRI with the Cox regression method and the IRGPRI was verified based on the Gene Expression Omnibus (GEO) dataset (n = 45). Then, we analyzed the immune and molecular features and the benefit of ICI therapy in IRGPRI-defined subgroups. Results Five genes, including S100A16, CD40, VCAM1, TNFRSF4 and TRAF1 were used to construct IRGPRI. As with the results of the GEO cohort, the overall survival (OS) was more favorable in low IRGPRI patients versus high IRGPRI patients. The composite results pointed out that low IRGPRI was associated with immune response-related pathways, high level of CTLA4, low KRAS and TP53 mutation rate, more infiltration of activated memory CD4+ T cells, CD8+ T cells, and more benefits from ICIs therapy. In comparison, high IRGPRI was associated with cancer-related pathways, low expression of CTLA4, high KRAS and TP53 mutation rate, more infiltration of M2 macrophages, and less benefit from ICIs therapies. Conclusion This IRGPRI is an encouraging biomarker to define the prognosis, immune and molecular features, and benefits from ICIs treatments in PAAD.
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Affiliation(s)
- Yang Su
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Ruoshan Qi
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Lanying Li
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Xu Wang
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Sijin Li
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Xuan Zhao
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Rui Hou
- College of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Wen Ma
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Dan Liu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Ming Shi, ; Junnian Zheng, ; Dan Liu,
| | - Junnian Zheng
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Ming Shi, ; Junnian Zheng, ; Dan Liu,
| | - Ming Shi
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Ming Shi, ; Junnian Zheng, ; Dan Liu,
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4
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A Novel Immune-Related Prognostic Signature Predicting Survival in Patients with Pancreatic Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2022:8909631. [PMID: 35342420 PMCID: PMC8956421 DOI: 10.1155/2022/8909631] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/03/2021] [Accepted: 02/16/2022] [Indexed: 12/13/2022]
Abstract
Pancreatic adenocarcinoma (PAAD) carries the lowest survival rate of all major organ cancers, which is of dismal prognosis and high mortality rate. Thus, the present study attempted to identify a few novel prognostic biomarkers and establish an immune-related prognostic signature which could predict the prognosis of PAAD. Four prognostic immune-related genes (IRGs) including S100A6, S100A10, S100A16, and SDC1 were screened by differentially expressed gene (DEG) identification and weighted gene coexpression network analysis (WGCNA). Subsequent analysis proved the high expression of these IRGs in PAAD tissues, suggested by TCGA-PAAD data, merged microarray-acquired dataset (MMD), GEPIA, and Oncomine webtool. By using MMD and TCGA-PAAD data, S100A6 (MMD: AUC = 0.897; TCGA: AUC = 0.843), S100A10 (MMD: AUC = 0.880; TCGA: AUC = 0.780), S100A16 (MMD: AUC = 0.878; TCGA: AUC = 0.838), and SDC1 (MMD: AUC = 0.885; TCGA: AUC = 0.812) exhibited excellent diagnostic efficiency for PAAD. By conducting connectivity map (CMap) analysis, we concluded that three molecule drugs (sulpiride, famotidine, and nalidixic acid) might have worked in the treatment of PAAD. Then, an immune-related prognostic index was constructed, which was validated as an independent prognostic factor for PAAD patients (P=0.004). We further constructed a nomogram by using this immune-related signature and age, the prognostic value of which was validated by using concordance index (C-index = 0.780) and area under curve (AUC = 0.909). Moreover, the immune-related prognostic signature was associated with response to anti-PD-1/L1 immunotherapy. To sum up, four IRGs were screened out and verified to be novel immune-related prognostic biomarkers in PAAD. Besides, sulpiride, famotidine, and nalidixic acid might be potential choices in the treatment of PAAD. An immune-related signature was established to show great potential for prognosis prediction for PAAD, independently, which might guide more effective immunotherapy strategies. A nomogram is further established by using this immune-related prognostic index, which might contribute to more effective prognosis prediction in PAAD patients.
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5
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Lu J, Chen R, Ou Y, Jiang Q, Wang L, Liu G, Liu Y, Yang B, Zhou Z, Zuo L, Chen Z. Characterization of immune-related genes andimmune infiltration features for early diagnosis, prognosis and recognition of immunosuppression in sepsis. Int Immunopharmacol 2022; 107:108650. [PMID: 35272172 DOI: 10.1016/j.intimp.2022.108650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/23/2022] [Accepted: 02/20/2022] [Indexed: 12/29/2022]
Abstract
Among the body systems, the immune system plays a fundamental role in the pathophysiology of sepsis. The effects of immunogenomic and immune cell infiltration in sepsis were still not been systematically understood. Based on modified Lasso penalized regression and RF, 8 DEIRGs (ADM, CX3CR1, DEFA4, HLA-DPA1, MAPK14, ORM1, RETN, and SLPI) were combined to construct an IRG classifier. In the discovery cohort, IRG classifier exhibited superior diagnostic efficacy and performed better in predicting mortality than clinical characteristics or MARS/SRS endotypes. Encouragingly, similar results were observed in the ArrayExpress databases. The use of hydrocortisone in IRG high-risk subgroup was associated with increased risk of mortality. In IRG low-risk phenotypes, NK cells, T helper cells, and infiltrating lymphocyte (IL) are significantly richer, while T cells regulatory (Tregs) and myeloid-derived suppressor cells (MDSC) are more abundant in IRG high-risk phenotypes. IRG score were significantly negatively correlated with Cytokine cytokine receptor interaction (CCR) and human leukocyte antigen (HLA). Between the IRG subgroups, the expression levels of several cytokines (IL-10, IFNG, TNF) were significantly different, and IRG score was significantly positively correlated with ratio of IL-10/TNF. Results of qRT-PCR validated that higher expression level of ADM, DEFA4, MAPK14, ORM1, RETN, and SLPI as well as lower expression level of CX3CR1 and HLA-DPA1 in sepsis samples compared to control sample. A diagnostic and prognostic model, namely IRG classifier, was established based on 8 IRGs that is closely correlated with responses to hydrocortisone and immunosuppression status and might facilitate personalized counseling for specific therapy.
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Affiliation(s)
- Jianhai Lu
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, Guangdong Province, PR China
| | - Rui Chen
- Department of Medical Intensive Care Unit, General Hospital of Southern Theater Command, PLA, Guangzhou 510010, Guangdong Province, PR China
| | - Yangpeng Ou
- Department of Oncology, Huizhou Third People's Hospital, Guangzhou Medical University, Huizhou, 516000, Guangdong Province, PR China
| | - Qianhua Jiang
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, Guangdong Province, PR China
| | - Liping Wang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan Province, PR China
| | - Genglong Liu
- Department of Pathology, The Third Affiliated Hospital of Guangdong Medical University (Longjiang Hospital of Shunde District), Foshan 528318, Guangdong Province, PR China
| | - Yayun Liu
- Department of Endocrinology, GuiYang Huaxi District People's Hospital. Guiyang 550025, Guizhou Province, PR China
| | - Ben Yang
- Department of Burn Surgery, Huizhou Municipal Central Hospital, Huizhou 516000, Guangdong Province, PR China
| | - Zhujiang Zhou
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, Guangdong Province, PR China
| | - Liuer Zuo
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, Guangdong Province, PR China.
| | - Zhen Chen
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, Guangdong Province, PR China.
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6
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Huang L, Ye T, Wang J, Gu X, Ma R, Sheng L, Ma B. Identification of Survival-Associated Hub Genes in Pancreatic Adenocarcinoma Based on WGCNA. Front Genet 2022; 12:814798. [PMID: 35047023 PMCID: PMC8762281 DOI: 10.3389/fgene.2021.814798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
Pancreatic adenocarcinoma is one of the leading causes of cancer-related death worldwide. Since little clinical symptoms were shown in the early period of pancreatic adenocarcinoma, most patients were found to carry metastases when diagnosis. The lack of effective diagnosis biomarkers and therapeutic targets makes pancreatic adenocarcinoma difficult to screen and cure. The fundamental problem is we know very little about the regulatory mechanisms during carcinogenesis. Here, we employed weighted gene co-expression network analysis (WGCNA) to build gene interaction network using expression profile of pancreatic adenocarcinoma from The Cancer Genome Atlas (TCGA). STRING was used for the construction and visualization of biological networks. A total of 22 modules were detected in the network, among which yellow and pink modules showed the most significant associations with pancreatic adenocarcinoma. Dozens of new genes including PKMYT1, WDHD1, ASF1B, and RAD18 were identified. Further survival analysis yielded their valuable effects on the diagnosis and treatment of pancreatic adenocarcinoma. Our study pioneered network-based algorithm in the application of tumor etiology and discovered several promising regulators for pancreatic adenocarcinoma detection and therapy.
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Affiliation(s)
- Liya Huang
- Department of Gastroenterology, The General Hospital of NingXia Medical University, Yinchuan, China
| | - Ting Ye
- Department of Gastroenterology, The General Hospital of NingXia Medical University, Yinchuan, China
| | - Jingjing Wang
- Department of Gastroenterology, The General Hospital of NingXia Medical University, Yinchuan, China
| | - Xiaojing Gu
- Department of Gastroenterology, The General Hospital of NingXia Medical University, Yinchuan, China
| | - Ruiting Ma
- Department of Gastroenterology, The General Hospital of NingXia Medical University, Yinchuan, China
| | - Lulu Sheng
- Department of Emergency Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Binwu Ma
- Department of Neurology, The General Hospital of NingXia Medical University, Yinchuan, China
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7
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Xiao Z, Li J, Yu Q, Zhou T, Duan J, Yang Z, Liu C, Xu F. An Inflammatory Response Related Gene Signature Associated with Survival Outcome and Gemcitabine Response in Patients with Pancreatic Ductal Adenocarcinoma. Front Pharmacol 2022; 12:778294. [PMID: 35002712 PMCID: PMC8733666 DOI: 10.3389/fphar.2021.778294] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive tumors with an extremely low 5-year survival rate. Accumulating evidence has unveiled that inflammatory response promotes tumor progression, enhances angiogenesis, and causes local immunosuppression. Herein, we aim to develop an inflammatory related prognostic signature, and found it could be used to predict gemcitabine response in PDAC. Methods: PDAC cohorts with mRNA expression profiles and clinical information were systematically collected from the four public databases. An inflammatory response related genes (IRRGs) prognostic signature was constructed by LASSO regression analysis. Kaplan–Meier survival analysis, receiver operating characteristic analysis, principal component analysis, and univariate and multivariate Cox analyses were carried out to evaluate effectiveness, and reliability of the signature. The correlation between gemcitabine response and risk score was evaluated in the TCGA-PAAD cohort. The GDSC database, pRRophetic algorithm, and connectivity map analysis were used to predict gemcitabine sensitivity and identify potential drugs for the treatment of PDAC. Finally, we analyzed differences in frequencies of gene mutations, infiltration of immune cells, as well as biological functions between different subgroups divided by the prognostic signature. Results: We established a seven IRRGs (ADM, DCBLD2, EREG, ITGA5, MIF, TREM1, and BTG2) signature which divided the PDAC patients into low- and high-risk groups. Prognostic value of the signature was validated in 11 PDAC cohorts consisting of 1337 PDAC patients from 6 countries. A nomogram that integrated the IRRGs signature and clinicopathologic factors of PDAC patients was constructed. The risk score showed positive correlation with gemcitabine resistance. Two drugs (BMS-536924 and dasatinib) might have potential therapeutic implications in high-risk PDAC patients. We found that the high-risk group had higher frequencies of KRAS, TP53, and CDKN2A mutations, increased infiltration of macrophages M0, neutrophils, and macrophages M2 cells, as well as upregulated hypoxia and glycolysis pathways, while the low-risk group had increased infiltration of CD8+ T, naïve B, and plasma and macrophages M1 cells. Conclusion: We constructed and validated an IRRGs signature that could be used to predict the prognosis and gemcitabine response of patients with PDAC, as well as two drugs (BMS-536924 and dasatinib) may contribute to PDAC treatment.
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Affiliation(s)
- Zhijun Xiao
- Department of Pharmacy, Shanghai University of Medicine and Health Sciences Affiliated Sixth People's Hospital South Campus, Shanghai, China
| | - Jinyin Li
- Department of Pharmacy, Xuhui Central Hospital of Shanghai, Shanghai, China
| | - Qian Yu
- Division of Interventional Radiology, University of Chicago, Chicago, IL, United States
| | - Ting Zhou
- Department of Pharmacy, Shanghai University of Medicine and Health Sciences Affiliated Sixth People's Hospital South Campus, Shanghai, China
| | - Jingjing Duan
- Department of Pharmacy, Shanghai University of Medicine and Health Sciences Affiliated Sixth People's Hospital South Campus, Shanghai, China
| | - Zhen Yang
- Department of Central Laboratory, Shanghai University of Medicine and Health Sciences Affiliated Sixth People's Hospital South Campus, Shanghai, China
| | - Cuicui Liu
- Department of Clinical Laboratory, Shanghai University of Medicine and Health Sciences Affiliated Sixth People's Hospital South Campus, Shanghai, China
| | - Feng Xu
- Department of Pharmacy, Shanghai University of Medicine and Health Sciences Affiliated Sixth People's Hospital South Campus, Shanghai, China.,Department of Pharmacy, Fengxian Hospital, Southern Medical University, Shanghai, China
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8
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Gao Y, Liu J, Cai B, Chen Q, Wang G, Lu Z, Jiang K, Miao Y. Development of epithelial-mesenchymal transition-related lncRNA signature for predicting survival and immune microenvironment in pancreatic cancerwithexperiment validation. Bioengineered 2021; 12:10553-10567. [PMID: 34854360 PMCID: PMC8809919 DOI: 10.1080/21655979.2021.2000197] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) have crucial function in epithelial–mesenchymal transition (EMT) in pancreatic cancer. It is necessary to comprehensively analyze the potential role of EMT-related lncRNA in pancreatic cancer. In the present study, genomic data of pancreatic cancer from the TCGA database were downloaded and we found 368 EMT-related lncRNAs. According to the expression characteristics of prognostic-related lncRNAs, all samples could be divided into two clusters with different clinical outcomes and different tumor microenvironments. Moreover, an eleven EMT-related lncRNAs signature was established and verified. Patients with pancreatic cancer in the high-risk group had a shorter overall survival than those in the low-risk group and the signature could act as an independent prognostic factor. Further analysis suggested that the EMT-related lncRNAs might affect the prognosis of patients through immune mechanisms. All findings indicated that the signature and eleven lncRNAs might serve as potential prognostic biomarkers and therapeutic targets in the treatment of pancreatic cancer.
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Affiliation(s)
- Yong Gao
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Baobao Cai
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Qun Chen
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Guangfu Wang
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Zipeng Lu
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Kuirong Jiang
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yi Miao
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China.,Pancreas Center, the Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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9
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Zou W, Li L, Wang Z, Jiang N, Wang F, Hu M, Liu R. Up-regulation of S100P predicts the poor long-term survival and construction of prognostic signature for survival and immunotherapy in patients with pancreatic cancer. Bioengineered 2021; 12:9006-9020. [PMID: 34654352 PMCID: PMC8806945 DOI: 10.1080/21655979.2021.1992331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Pancreatic cancer is associated with a high mortality rate, and the prognosis is positively related to immune status. In this study, we constructed a prognostic signature from survival- and immune-related genes (IRGs) to guide treatment and assess prognosis of patients with pancreatic cancer. The transcriptomic data were obtained from The Cancer Genome Atlas (TCGA) database, and IRGs were extracted from the ImmPort database. Univariate and LASSO regression analysis were used to obtain survival-related IRGs. Finally, the prognostic signature was constructed using multivariate regression analysis. The laboratory experiments were conducted to verify the key IRG expression. Immune cells infiltration was analyzed using the CIBERSORT algorithm and TIMER database. Prognostic signature containing four IRGs (ADA2, TLR1, PTPN6, S100P) was constructed with good predictive performance; in particular, S100P played a significant role in the immune microenvironment, and tumorigenesis of pancreatic cancer. Moreover, we found that CD8+ T cell and activated CD4+ memory T cell tumor infiltration was lower in the high-risk group, while high-risk score correlated positively with higher tumor mutational burden, and the higher half inhibitory centration 50 of chemotherapeutic agents Docetaxel and Sunitinib. In summary, this study identified and constructed an immune-related prognostic signature that can predict overall survival, besides suggests that S100P was a novel immune-related biomarker. We hope that this signature will aid the identification of new biomarkers for the individualized immunotherapy of pancreatic cancer.
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Affiliation(s)
- Wenbo Zou
- Medical School of Chinese PLA, Beijing, China.,Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
| | - Lincheng Li
- Medical School of Chinese PLA, Beijing, China.,Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
| | - Zizheng Wang
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
| | - Nan Jiang
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
| | - Fei Wang
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
| | - Minggen Hu
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
| | - Rong Liu
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
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