scholarly journals The Lung Adenocarcinoma Microenvironment Mining and Its Prognostic Merit

2020 ◽  
Vol 19 ◽  
pp. 153303382097754
Author(s):  
Rongchang Zhao ◽  
Dan Ding ◽  
Wenyan Yu ◽  
Chunrong Zhu ◽  
Yan Ding

Background: As a common pathological type of lung cancer, lung adenocarcinoma (LUAD) is mainly treated by surgery, chemotherapy, targeted therapy and radiotherapy. Although a relatively mature treatment system has been established, there are few studies on the microenvironment of LUAD. Material and Methods: The immune and stromal scores of patients from the LUAD cohort in the TCGA database were obtained by using ESTIMATE. The relationship of immune and stromal scores with the clinicopathological characteristics and overall survival of LUAD patients was assessed by R. GO, KEGG and Cox regression analyses were employed to analyze intersecting genes and to identify reliable prognostic markers. The identified genes were also analyzed in the GEPIA database to assess their correlations with survival, and these relationships were verified with the Kaplan-Meier Plotter database. Results: The immune score was related to the survival time and tumor topography of LUAD patients. There was a significant correlation between stromal score and tumor metastasis. Through multivariate analysis, stage (HR = 1.640, 95% CI = 1.019-2.642, P = 0.042) and risk score (HR = 1.036, 95% CI = 1.026-1.046, P < 0.001). The genes (ARHGAP15, BTLA, CASS4, CLECL1, FAM129C, STAP1, TESPA1, and S100P) showed credible prognostic value in LUAD patients in TCGA through GEPIA database online analysis and verification in the Kaplan-Meier plotter database. Conclusions: In the microenvironment of lung adenocarcinoma, the differentially expressed genes screened by immune score and stromal score have certain value in evaluating the survival/prognosis of patients, as well as the invasion and progression of tumors.

2018 ◽  
Vol 38 (6) ◽  
Author(s):  
Ji-sheng Jing ◽  
Hongbo Li ◽  
Shun-cai Wang ◽  
Jiu-ming Ma ◽  
La-qing Yu ◽  
...  

N-myc downstream-regulated gene 3 (NDRG3), an important member of the NDRG family, is involved in cell proliferation, differentiation, and other biological processes. The present study analyzed NDRG3 expression in hepatocellular carcinoma (HCC) and explored the relationship between expression of NDRG3 in HCC patients and their clinicopathological characteristics. We performed quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) analysis and immunohistochemistry (IHC) analyses on HCC tissues to elucidate NDRG3 expression characteristics in HCC patients. Kaplan–Meier survival curve and Cox regression analyses were used to evaluate the prognoses of 102 patients with HCC. The results revealed that compared with non-tumor tissues, HCC tissues showed significantly higher NDRG3 expression. In addition, our analyses showed that NDRG3 expression was statistically associated with tumor size (P=0.048) and pathological grade (P=0.001). Survival analysis and Kaplan–Meier curves revealed that NDRG3 expression is an independent prognostic indicator for disease-free survival (P=0.002) and overall survival (P=0.005) in HCC patients. The data indicate that NDRG3 expression may be considered as a oncogenic biomarker and a novel predictor for HCC prognosis.


2021 ◽  
Vol 12 ◽  
Author(s):  
Fei Peng ◽  
Si Lei ◽  
Quan Zhang ◽  
Yanjun Zhong ◽  
Shangjie Wu

BackgroundCigarette smoking has been proven to be a risk factor in the development of many diseases. However, it remains controversial with respect to the relationship of smoking with COVID-19. The purpose of this study was to explore the role of smoking in COVID-19.MethodsA total of 622 patients with COVID-19 in China were enrolled in the study. Corresponding clinical and laboratory data were collected and analyzed. Meanwhile, Kaplan-Meier curve and Cox regression analysis were employed to analyze the association of smoking with survival in patients with COVID-19.ResultsSmoking was statistically significant comparing non-survivors and survivors of patients with COVID-19 (P = 0.007). Males had higher proportion of smoking than females (91.9% vs. 8.1%, P &lt; 0.001). Compared with the non-smoker, there was significant statistical difference in the incidence of cerebrovascular disease in smoking patients with COVID-19 (9.7% vs. 3.4%, P = 0.017). White blood cell count (6.3 vs. 5.4; P = 0.037), hemoglobin level (139.0 vs. 127.0; P &lt; 0.001), and creatinine level (77.3 vs. 61.0; P &lt; 0.001) were significantly increased in COVID-19 patients who smoked. Moreover, smoking patients showed a worse survival compared with non-smoking patients (Log Rank P = 0.045). After adjustment for age, gender and underlying diseases, patients with smoking still had higher risk of mortality than that of non-smoking patients (hazard ratio[HR] 1.897, 95% confidence interval [CI]1.058–3.402, P = 0.032).ConclusionSmoking was thought to be a risk factor in predicting the prognosis of COVID-19 and smoking patients might have a higher risk of mortality than that of the non-smoking patients.


2021 ◽  
Vol 8 ◽  
Author(s):  
Chenfang Wu ◽  
Guyi Wang ◽  
Quan Zhang ◽  
Bo Yu ◽  
Jianlei Lv ◽  
...  

Aim: The aim of the study was to describe the clinical characteristics of patients with or without respiratory alkalosis, and analyze the relationship of respiratory alkalosis and the outcome of adult coronavirus disease 2019 (COVID-19) patients.Methods: Clinical and laboratory data of adult COVID-19 patients in a single center in China, were retrospectively collected and analyzed. The Kaplan-Meier (KM) curve and cox regression were adopted to analyze the association between respiratory alkalosis and prognosis of COVID-19 patients.Results: Of 230 adult COVID-19 patients, 66 patients (28.7%) had respiratory alkalosis on admission. Of 66 patients, the median age was 53 years old (range, 21–84 years), and 43 (65.2%) were female. Compared with those without respiratory alkalosis, patients with respiratory alkalosis were significantly older (P = 0.002), had a higher proportion of female (P = 0.004), and showed higher ratios of underlying diseases including hypertension (P = 0.023) and cardiovascular disease (P = 0.028). Moreover, they demonstrated higher proportion of severe events (P = 0.001). Patients with respiratory alkalosis had a higher possibility of developing severe events compared with those without respiratory alkalosis (Log Rank P = 0.001). After adjusting for gender, age, and comorbidities, patients with respiratory alkalosis still showed significantly elevated risks of developing to severe cases (HR 2.445, 95% CI 1.307–4.571, P = 0.005) using cox regression analyses.Conclusions: Respiratory alkalosis as a common acid—base disorder in COVID-19 patients, was associated with a higher risk of developing severe event.


BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Weishuang Ma ◽  
Jiaming Liang ◽  
Junjian Mo ◽  
Siyuan Zhang ◽  
Ningdong Hu ◽  
...  

Abstract Background Lung adenocarcinoma (LUAD) is the most prevalent non-small cell lung cancer (NSCLC). Patients with LUAD have a poor 5-year survival rate. The use of immune checkpoint inhibitors (ICIs) for the treatment of LUAD has been on the rise in the past decade. This study explored the prognostic role of butyrophilin-like 9 (BTNL9) in LUAD. Methods Gene expression profile of buytrophilins (BTNs) was determined using the GEPIA database. The effect of BTNL9 on the survival of LUAD patients was assessed using Kaplan-Meier plotter and OncoLnc. Correlation between BTNL9 expression and tumor-infiltrating immune cells (TILs) was explored using TIMER and GEPIA databases. Further, the relationship between BTNL9 expression and drug response was evaluated using CARE. Besides, construction and evaluation of nomogram based on BTNL9 expression and TNM stage. Results BTNL9 expression was downregulated in LUAD and was associated with a poor probability of 1, 3, 5-years overall survival (OS). In addition, BTNL9 expression was regulated at epigenetic and post-transcriptional modification levels. Moreover, BTNL9 expression was significantly positively correlated with ImmuneScore and ESTIMATEScore. Furthermore, BTNL9 expression was positively associated with infiltration levels of B cells, CD4+ T cells, and macrophages. Kaplan-Meier analysis showed that BTNL9 expression in B cells and dendritic cells (DCs) was significantly associated with OS. BTNL9 expression was significantly positively correlated with CARE scores. Conclusions These findings show that BTNL9 is a potential prognostic biomarker for LUAD. Low BTNL9 expression levels associated with low infiltration levels of naïve B cells, and DCs in the tumor microenvironment are unfavorable for OS in LUAD patients.


2020 ◽  
Author(s):  
Pengbo Deng ◽  
Rongrong Zhou ◽  
Jinghui Zhang ◽  
Jian An ◽  
Liming Cao

Abstract Background: Available evidence indicates that kinetochore-localized astrin/SPAG5-binding protein (KNSTRN) is an oncogene in skin carcinoma. This study aimed to evaluate the prognostic value of KNSTRN in lung adenocarcinoma (LUAD) underlying the Cancer Genome Atlas (TCGA) database. Methods: The relationship between clinicopathological features and KNSTRN was analyzed with the Wilcoxon signed-rank test and logistic regression. The clinicopathological characteristics associated with overall survival (OS) were evaluated using Cox regression and the Kaplan–Meier method. Gene ontology (GO) analysis, gene set enrichment analysis (GSEA), and single-sample GSEA (ssGSEA) were performed using TCGA data.Results: The KNSTRN expression level was found to be significantly higher in LUAD tissue than in normal lung tissue. Also, it correlated significantly with advanced clinicopathological characteristics. The Kaplan–Meier survival curve revealed a significant relationship of high expression of KNSTRN with poor OS in patients with LUAD. The multivariate Cox regression hazard model demonstrated the KNSTRN expression level as an independent prognostic factor for patients with LUAD. GO and GSEA analyses indicated the involvement of KNSTRN in cell cycle checkpoints, DNA replication, and G2-M checkpoint M phase. Based on ssGSEA analysis, KNSTRN had a positive relationship with Th2 cells and CD56dim natural killer cells. The KNSTRN expression levels in several types of immune cells were significantly different.Conclusion: The findings suggested that the increased expression level of KNSTRN was significantly associated with the progression of LUAD and could also serve as a novel prognostic biomarker for patients with LUAD.


2021 ◽  
Author(s):  
hu panyi ◽  
Yongwei Zhang ◽  
yeben qian

Abstract Background: Objective to evaluate the predictive value of preoperative fibrinogen and systemic inflammatory response index (F-SIRI) in the prognosis of patients with hepatocellular carcinoma after radical hepatectomy. Methods: the clinical data of 298 patients with hepatocellular carcinoma who underwent surgery and confirmed by postoperative pathology in our hospital from January 2015 to December 2017 were retrospectively analyzed. The F-SIRI score was calculated according to FIB and SIRI data of peripheral blood. The relationship between F-SIRI score and clinicopathological characteristics was analyzed. The survival analysis was performed by Kaplan Meier method, Cox regression analysis was used to analyze the prognostic factors. Results: preoperative F-SIRI score was correlated with tumor diameter, FIB and SIRI (P<0.05), but not with age, gender, TNM stage and other clinical features (P>0.05). There were significant differences in the 5-year DFS rate and OS rate among patients with different preoperative F-SIRI scores(P<0.05); Cox regression analysis showed that preoperative tumor diameter, alpha fetoprotein level and F-SIRI score were independent predictors of DFS in patients with HCC (P< 0.05), while preoperative tumor diameter, ALB and F-SIRI score as independent predictors of OS (P<0.05). Conclusion: preoperative F-SIRI is an independent prognostic factor in patients with HCC after radical hepatectomy, with poor prognosis in patients with high level of F-SIRI.


2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Yang-Jie Wu ◽  
Ai-Tao Nai ◽  
Gui-Cheng He ◽  
Fei Xiao ◽  
Zhi-Min Li ◽  
...  

Abstract Background Dihydropyrimidinase like 2 (DPYSL2) has been linked to tumor metastasis. However, the function of DPSY2L in lung adenocarcinoma (LUAD) is yet to be explored. Methods Herein, we assessed DPYSL2 expression in various tumor types via online databases such as Oncomine and Tumor Immune Estimation Resource (TIMER). Further, we verified the low protein and mRNA expressions of DPYSL2 in LUAD via the ULCAN, The TCGA and GEPIA databases. We applied the ROC curve to examine the role of DPYSL2 in diagnosis. The prognostic significance of DPYSL2 was established through the Kaplan–Meier plotter and the Cox analyses (univariate and multivariate). TIMER was used to explore DPYSL2 expression and its connection to immune infiltrated cells. Through Gene Set Enrichment Analysis, the possible mechanism of DPYSL2 in LUAD was investigated. Results In this study, database analysis revealed lower DPYSL2 expression in LUAD than in normal tissues. The ROC curve suggested that expression of DPYSL2 had high diagnostic efficiency in LUAD. The DPYSL2 expression had an association with the survival time of LUAD patients in the Kaplan–Meier plotter and the Cox analyses. The results from TIMER depicted a markedly positive correlation of DPYSL2 expression with immune cells infiltrated in LUAD, such as macrophages, dendritic cells, CD4+ T cells, and neutrophils. Additionally, many gene markers for the immune system had similar positive correlations in the TIMER analysis. In Gene Set Enrichment Analysis, six immune-related signaling pathways were associated with DPYSL2. Conclusions In summary, DPYSL2 is a novel biomarker with diagnostic and prognostic potential for LUAD as well as an immunotherapy target. Highlights Expression of DPYSL2 was considerably lower in LUAD than in normal tissues. Investigation of multiple databases showed a high diagnostic value of DPYSL2 in LUAD. DPYSL2 can independently predict the LUAD outcomes. Immune-related mechanisms may be potential ways for DPYSL2 to play a role in LUAD.


2019 ◽  
Vol 8 (6) ◽  
pp. 661-671 ◽  
Author(s):  
Shuang Ye ◽  
Yuanyuan Xu ◽  
Jiehao Li ◽  
Shuhui Zheng ◽  
Peng Sun ◽  
...  

The role of G protein-coupled estrogen receptor 1 (GPER) signaling, including promotion of Ezrin phosphorylation (which could be activated by estrogen), has not yet been clearly identified in triple-negative breast cancer (TNBC). This study aimed to evaluate the prognostic value of GPER and Ezrin in TNBC patients. Clinicopathologic features including age, menopausal status, tumor size, nuclear grade, lymph node metastasis, AJCC TNM stage, and ER, PR and HER-2 expression were evaluated from 249 TNBC cases. Immunohistochemical staining of GPER and Ezrin was performed on TNBC pathological sections. Kaplan–Meier analyses, as well as logistic regressive and Cox regression model tests were applied to evaluate the prognostic significance between different subgroups. Compared to the GPER-low group, the GPER-high group exhibited higher TNM staging (P = 0.021), more death (P < 0.001), relapse (P < 0.001) and distant events (P < 0.001). Kaplan–Meier analysis showed that GPER-high patients had a decreased OS (P < 0.001), PFS (P < 0.001), LRFS (P < 0.001) and DDFS (P < 0.001) than GPER-low patients. However, these differences in prognosis were not statistically significant in post-menopausal patients (OS, P = 0.8617; PFS, P = 0.1905; LRFS, P = 0.4378; DDFS, P = 0.2538). There was a significant positive correlation between GPER and Ezrin expression level (R = 0.508, P < 0.001) and the effect of Ezrin on survival prognosis corresponded with GPER. Moreover, a multivariable analysis confirmed that GPER and Ezrin level were both significantly associated with poor DDFS (HR: 0.346, 95% CI 0.182–0.658, P = 0.001; HR: 0.320, 95% CI 0.162–0.631, P = 0.001). Thus, overexpression of GPER and Ezrin may contribute to aggressive behavior and indicate unfavorable prognosis in TNBC; this may correspond to an individual’s estrogen levels.


2020 ◽  
Author(s):  
Guorong Yang ◽  
Shu Tang ◽  
Jie Zhang ◽  
Ling Qin

Abstract Purpose: TRAF3IP3 is involved in the maturation of immune cells, the development of immune tissues and the immune response of the body. TRAF3IP3 is shown to expressed in a variety of malignant tumor cell lines. Down-regulated expression of TRAF3IP3 in malignant melanoma can inhibit tumor growth. However, the role of TRAF3IP3 in glioma is still unknown. In this study, we aimed to study the relationship between TRAF3IP3 and glioma based on TCGA data.Method: We used the Wilcoxon rank sum test to compare the expression of TRAF3IP3 in glioma and normal tissues. Subsequently, Kruskal-Wallis test, Wilcoxon rank sum test, and logistics regression were used to evaluate the relationship between TRAF3IP3 and clinicopathological parameters of glioma patients. GSEA was used to verify the key signal pathways involved in TRAF3IP3. We used the ssGSEA method to analyze the relationship between the expression level of TRAF3IP3 and the immune infiltration in the glioma tumor microenvironment. Finally, we used Kaplan-Meier and COX regression to evaluate the prognostic value of TRAF3IP3.Results: TRAF3IP3 transcription level was highly expressed in gliomas(P<0.001). And the high expression of TRAF3IP3 and WHO grade(OR=3.57(2.42-5.34), P<0.001), IDH status (OR=4.79(3.40-6.83), P<0.001), 1P /19q codeletion (OR=0.07(0.04-0.11), P<0.001), EGFR status (OR=2.77(1.65-4.81), P<0.001), histological type (OR=3.64(2.48-5.43), P<0.001), age (OR=1.64(1.13-2.41), P=0.01), and primary therapy outcome (OR=2.29(1.47-3.61), P<0.001) were significantly correlated. GSEA showed that six signaling pathways were significantly enriched in the TRAF3IP3 high expression phenotype group, including JAK STAT signaling pathway, interferon-γ signaling pathway, apoptosis, P53 signaling pathway, PD-1 signaling pathway, and CTLA4 signaling pathway. ssGSEA showed that the expression of TRAF3IP3 was significantly positively correlated with the infiltration of Macrophages, Th17 cells, etc. Multivariate COX regression showed that TRAF3IP3 was an independent prognostic factor for glioma OS (HR=2.169(1.301-3.615), P=0.003). Kaplan-Meier analysis showed that high expression of TRAF3IP3 was associated with worse PFS(HR=2.39(1.39-3.01), P<0.001), DFS(HR=3.02(2.27-4.01), P<0.001) and OS(HR=2.87(2.20-3.75), P<0.001).Conclusion: TRAF3IP3 may play an important role in the occurrence and development of glioma, and may be a potential biomarker for the diagnosis and prognosis of glioma.


2020 ◽  
Vol 9 (11) ◽  
pp. 3693
Author(s):  
Ching-Fu Weng ◽  
Chi-Jung Huang ◽  
Mei-Hsuan Wu ◽  
Henry Hsin-Chung Lee ◽  
Thai-Yen Ling

Introduction: Coxsackievirus/adenovirus receptors (CARs) and desmoglein-2 (DSG2) are similar molecules to adenovirus-based vectors in the cell membrane. They have been found to be associated with lung epithelial cell tumorigenesis and can be useful markers in predicting survival outcome in lung adenocarcinoma (LUAD). Methods: A gene ontology enrichment analysis disclosed that DSG2 was highly correlated with CAR. Survival analysis was then performed on 262 samples from the Cancer Genome Atlas, forming “Stage 1A” or “Stage 1B”. We therefore analyzed a tissue microarray (TMA) comprised of 108 lung samples and an immunohistochemical assay. Computer counting software was used to calculate the H-score of the immune intensity. Cox regression and Kaplan–Meier analyses were used to determine the prognostic value. Results: CAR and DSG2 genes are highly co-expressed in early stage LUAD and associated with significantly poorer survival (p = 0.0046). TMA also showed that CAR/DSG2 expressions were altered in lung cancer tissue. CAR in the TMA was correlated with proliferation, apoptosis, and epithelial–mesenchymal transition (EMT), while DSG2 was associated with proliferation only. The Kaplan–Meier survival analysis revealed that CAR, DSG2, or a co-expression of CAR/DSG2 was associated with poorer overall survival. Conclusions: The co-expression of CAR/DSG2 predicted a worse overall survival in LUAD. CAR combined with DSG2 expression can predict prognosis.


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