scholarly journals TYRO Protein Tyrosine Kinase-binding Protein Predicts Favorable Overall Survival in Osteosarcoma and Correlates With Antitumor Immunity

Author(s):  
Hai-ru Xu ◽  
Jun-jie Chen ◽  
Jin-ming Shen ◽  
Wei-hang Ding ◽  
Jie Chen

Abstract Objective: To explore the prognostic significance and underlying mechanism of TYRO protein tyrosine kinase-binding protein (TYROBP) in osteosarcoma. Methods: Firstly, the expression of TYROBP was analyzed using the t-test. The Kaplan-Meier plotter analysis and a receiver operating characteristic (ROC) curve were performed to evaluate the influence of TYROBP on overall survival (OS). Further, Cox regression analysis was conducted to predict the independent prognostic factors for OS of osteosarcoma patients, and a nomogram was constructed. Then, the relationship between TYROBP and clinicopathological characteristics was determined using statistical methods. Enrichment analyses were conducted to evaluate the biological functions of TYROBP. Finally, ESTIMATE algorithm was used to assess the association of TYROBP with immune cell infiltration. Results: TYROBP was significantly increased in osteosarcoma (all P <0.001). However, the high expression of TYROBP was related to better OS of osteosarcoma patients. Cox regression analysis showed that TYROBP was an independent prognostic factor for predicting OS (P =0.005), especially in patients with male sex, age <18 years, metastasis, and tumor site leg/foot (all P <0.05). Besides, TYROBP mRNA expression was significantly associated with tumor site (P <0.01) but had no remarkable relationship with age, gender, and metastasis status (all P>0.05). Functional annotation and GSEA revealed that TYROBP was mainly involved in immune-related pathways. Importantly, TYROBP positively correlated with immune scores (P <0.001, r=0.87). Conclusions: TYROBP served as an independent prognostic biomarker for OS in osteosarcoma. High TYROBP expression might prolong the survival of osteosarcoma patients mainly through promoting antitumor immunity.

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chunlei Wu ◽  
Quanteng Hu ◽  
Dehua Ma

AbstractLung adenocarcinoma (LUAD) is the main pathological subtype of Non-small cell lung cancer. We downloaded the gene expression profile and immune-related gene set from the TCGA and ImmPort database, respectively, to establish immune-related gene pairs (IRGPs). Then, IRGPs were subjected to univariate Cox regression analysis, LASSO regression analysis, and multivariable Cox regression analysis to screen and develop an IRGPs signature. The receiver operating characteristic curve (ROC) was applied for evaluating the predicting accuracy of this signature by calculating the area under ROC (AUC) and data from the GEO set was used to validate this signature. The relationship of 22 tumor-infiltrating immune cells (TIICs) to the immune risk score was also investigated. An IRGPs signature with 8 IRGPs was constructed. The AUC for 1- and 3-year overall survival in the TCGA set was 0.867 and 0.870, respectively. Similar results were observed in the AUCs of GEO set 1, 2 and 3 (GEO set 1 [1-year: 0.819; 3-year: 0.803]; GEO set 2 [1-year: 0.834; 3-year: 0.870]; GEO set 3 [1-year: 0.955; 3-year: 0.827]). Survival analysis demonstrated high-risk LUAD patients exhibited poorer prognosis. The multivariable Cox regression indicated that the risk score was an independent prognostic factor. The immune risk score was highly associated with several TIICs (Plasma cells, memory B cells, resting memory CD4 T cells, and activated NK cells). We developed a novel IRGPs signature for predicting 1- and 3- year overall survival in LUAD, which would be helpful for prognosis assessment of LUAD.


2021 ◽  
Vol 12 ◽  
Author(s):  
Shaojie Chen ◽  
Feifei Huang ◽  
Shangxiang Chen ◽  
Yinting Chen ◽  
Jiajia Li ◽  
...  

ObjectiveGrowing evidence has highlighted that the immune and stromal cells that infiltrate in pancreatic cancer microenvironment significantly influence tumor progression. However, reliable microenvironment-related prognostic gene signatures are yet to be established. The present study aimed to elucidate tumor microenvironment-related prognostic genes in pancreatic cancer.MethodsWe applied the ESTIMATE algorithm to categorize patients with pancreatic cancer from TCGA dataset into high and low immune/stromal score groups and determined their differentially expressed genes. Then, univariate and LASSO Cox regression was performed to identify overall survival-related differentially expressed genes (DEGs). And multivariate Cox regression analysis was used to screen independent prognostic genes and construct a risk score model. Finally, the performance of the risk score model was evaluated by Kaplan-Meier curve, time-dependent receiver operating characteristic and Harrell’s concordance index.ResultsThe overall survival analysis demonstrated that high immune/stromal score groups were closely associated with poor prognosis. The multivariate Cox regression analysis indicated that the signatures of four genes, including TRPC7, CXCL10, CUX2, and COL2A1, were independent prognostic factors. Subsequently, the risk prediction model constructed by those genes was superior to AJCC staging as evaluated by time-dependent receiver operating characteristic and Harrell’s concordance index, and both KRAS and TP53 mutations were closely associated with high risk scores. In addition, CXCL10 was predominantly expressed by tumor associated macrophages and its receptor CXCR3 was highly expressed in T cells at the single-cell level.ConclusionsThis study comprehensively investigated the tumor microenvironment and verified immune/stromal-related biomarkers for pancreatic cancer.


2021 ◽  
Vol 20 ◽  
pp. 153303382110414
Author(s):  
Xiaoyong Li ◽  
Jiaqong Lin ◽  
Yuguo pan ◽  
Peng Cui ◽  
Jintang Xia

Background: Liver progenitor cells (LPCs) play significant roles in the development and progression of hepatocellular carcinoma (HCC). However, no studies on the value of LPC-related genes for evaluating HCC prognosis exist. We developed a gene signature of LPC-related genes for prognostication in HCC. Methods: To identify LPC-related genes, we analyzed mRNA expression arrays from a dataset (GSE57812 & GSE 37071) containing LPCs, mature hepatocytes, and embryonic stem cell samples. HCC RNA-Seq data from The Cancer Genome Atlas (TCGA) were used to explore the differentially expressed genes (DEGs) related to prognosis through DEG analysis and univariate Cox regression analysis. Lasso and multivariate Cox regression analyses were performed to construct the LPC-related gene prognostic model in the TCGA training dataset. This model was validated in the TCGA testing set and an external dataset (International Cancer Genome Consortium [ICGC] dataset). Finally, we investigated the relationship between this prognostic model with tumor-node-metastasis stage, tumor grade, and vascular invasion of HCC. Results: Overall, 1770 genes were identified as LPC-related genes, of which 92 genes were identified as DEGs in HCC tissues compared with normal tissues. Furthermore, we randomly assigned patients from the TCGA dataset to the training and testing cohorts. Twenty-six DEGs correlated with overall survival (OS) in the univariate Cox regression analysis. Lasso and multivariate Cox regression analyses were performed in the TCGA training set, and a 3-gene signature was constructed to stratify patients into 2 risk groups: high-risk and low-risk. Patients in the high-risk group had significantly lower OS than those in the low-risk group. Receiver operating characteristic curve analysis confirmed the signature's predictive capacity. Moreover, the risk score was confirmed to be an independent predictor for patients with HCC. Conclusion: We demonstrated that the LPC-related gene signature can be used for prognostication in HCC. Thus, targeting LPCs may serve as a therapeutic alternative for HCC.


2021 ◽  
Author(s):  
Chao Zhang ◽  
Haixiao Wu ◽  
Guijun Xu ◽  
Wenjuan Ma ◽  
Lisha Qi ◽  
...  

Abstract Background: Osteosarcoma is the most common primary malignant bone tumor. The current study was conducted to describe the general condition of patients with primary osteosarcoma in a single cancer center in Tianjin, China and to investigate the associated factors in osteosarcoma patients with lung metastasis. Methods: From February 2009 to October 2020, patients from Tianjin Medical University Cancer Institute and Hospital, China were retrospectively analyzed. The Kaplan–Meier method was used to evaluate the overall survival of osteosarcoma patients. Prognostic factors of patients with osteosarcoma were identified by the Cox proportional hazard regression analysis. Risk factor of lung metastasis in osteosarcoma were investigated by the logistic regression model. Results: A total of 203 patients were involved and 150 patients were successfully followed up for survival status. The 5-year survival rate of osteo-sarcoma patients was 70.0%. Surgery, bone and lung metastasis were the significant prognostic factors in multivariable Cox regression analysis. Twenty-one (10.3%) patients showed lung metastasis at the diagnosis of osteosarcoma and 67 (33%) lung metastases during the later course. T3 stage (OR=11.415, 95%CI 1.362-95.677, P=0.025) and synchronous bone metastasis (OR=6.437, 95%CI 1.69-24.51, P=0.006) were risk factors of synchronous lung metastasis occurrence. Good necrosis (≥90%, OR=0.097, 95%CI 0.028-0.332, P=0.000) and elevated Ki-67 (≥50%, OR=4.529, 95%CI 1.241-16.524, P=0.022) were proved to be significantly associated with metachronous lung metastasis occurrence. Conclusion: The overall survival, prognostic factors and risk factors for lung metastasis in this single center provided insight about osteosarcoma management.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 4241-4241
Author(s):  
Kendra L. Sweet ◽  
Robert M. Crescentini ◽  
Jennifer L. Cultrera ◽  
Jeffrey E Lancet ◽  
Rami S. Komrokji

Abstract 4241 Background: Acute lymphocytic leukemia (ALL) incidence is approximately 4000 cases per year in the USA. Several standard induction regimens are used upfront for the treatment of ALL. The HyperCVAD regimen is currently a widely used upfront treatment option for adult ALL patients based on pioneer work at MD Anderson Cancer Center (MDACC). Here we present our experience with the HyperCVAD regimen treating ALL at Moffitt Cancer Center (MCC), representing the largest cohort treated with this regimen outside MDACC. Methods: Patients who were diagnosed and treated at MCC with ALL were identified through the MCC Total Cancer Care database. Individual charts were reviewed. All patients treated with the HyperCVAD regimen frontline were included in this analysis. The HyperCVAD regimen was administered as originally described at MDACC. Philadelphia positive patients were treated with addition of tyrosine kinase inhibitors (TKI) (imatinib or dasatinib). Descriptive data are reported, t-test was used to compare continuous variables, chi square test for categorical variables, Kaplan Meier curves were used for overall survival (OS). Log rank test was used to compare survival times between groups. Cox regression analysis was used for multivariable analysis. All analyses were conducted using SPSS version 19.0 Results: Between 1/1/2002 and 6/30/2011, 100 ALL patients were treated with HyperCVAD at MCC. The median age was 45 years (range 18–83), 26 were above age of 60 years and 26 were below age of 30 years. Sixty three percent were male and 37% were female. Sixty five percent were white, 6% were African America, 7% were Hispanic and 22% were described as other. B-Cell ALL accounted for 83% of patients, while the other 17% had T-Cell origin. Of the 100 patients, 23% of patients were Philadelphia chromosome positive, while 72% were negative, and in 5% karyotype was unknown. Splenomegaly was present at diagnosis in 18% of patients, while 17% presented with lymphadenopathy. Twenty-three percent of patients presented with a WBC of 50,000 or greater. CNS disease was noted in 9% of patients at diagnosis. Seventy-six percent achieved a complete response (CR), while 12% had refractory disease. Response to frontline was not documented in 12% of patients. The median overall survival was 27 months (95% CI 15.6–38.3). In univariable analysis, no difference in outcome was observed based on gender, race, Philadelphia chromosome positivity, B or T-cell origin, presence of lymphadenopathy, splenomegaly, WBC >50,000 or CNS disease at presentation. Age was a significant prognostic factor. The median OS for patients <60 years old was 34 months (95% CI 20.8–47.), and 16 months for patients >60 years old (95% CI 6.9–25.1) (p= 0.006) (figure-1) The median OS was higher in patients who achieved CR with frontline chemotherapy. OS was 34 months (95% CI 22.5–45.4) compared to 13 months in patients who did not achieve CR after frontline (95% CI 7.3–18.7) (p=< 0.005). Thirty-eight patients proceeded to allogeneic SCT. The median OS was 40 months in patients who proceeded to allogeneic SCT compared with 16 months in patients who did not (p=0.002). In Cox regression analysis, achieving CR with frontline induction, and allogeneic SCT were statistically significant independent variables for OS for adult patients with ALL. The odds ratio was 3.4 in patients achieving CR with frontline therapy, and 3.1 in patients who underwent allogeneic SCT. Conclusion: To our knowledge, this cohort represents the largest group of ALL patients treated outside MDACC with HyperCVAD based regimens, with similar overall results in the setting of tertiary centers. Achievement of CR after frontline therapy, and undergoing allogeneic SCT were statistically significant prognostic indicators. The outcome of elderly patients (age >60) was inferior. In the elderly population there were lower rates of CR and less number of patients proceeded to allogeneic SCT. The outcome in Philadelphia chromosome positive ALL has improved with the introduction of TKI’s and allogeneic SCT. Disclosures: No relevant conflicts of interest to declare.


2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 18211-18211
Author(s):  
S. R. Bella ◽  
M. E. Richardet ◽  
P. Gomez Storniolo ◽  
P. Celiz ◽  
A. Lingua ◽  
...  

18211 Background: Prognostic factors identified in advanced non small cell lung cancer are: age, gender, PS, h. SWOG univariable analysis in patients with chemotheraphy; confirmed these factors and show a relationship between the hemoglobin level and the overall survival; in addition the metastasic site number and cisplatin- based chemotheraphy (7). To analyse and compare the hemoglobin level before cisplatin- based chemotheraphy with survival in patients with advanced non- small cell lung cancer. Methods: Retrospective study conducted at the IONC of the 179 clinical record were analized, over a 5 year period. The collected data were: age, gender, PS, histologic type, stage, chemotheraphy cycles number, smooke history, number and metastasic site. We analyzed median and overal survival using Kaplan Meier, and the anemia as a prognostic implication factor with univariable and multivariable Cox regression analysis. Istologic type and TNM (1–6). Results: The mean age was 59 (40–79); 146 (81.5%) male and 33 (18.5%) women; histological types found were squamous cell carcinomas in 66 (37%), and adenocarcinoma in 113 (63%); stage IIIB in 61 (34%) and IV in 118 (66%). 147 (82%) were smokers and 32 (18%) were never smokers. All the patients had PS 0–1. Median overall survival time was 11.53 months and 13.88 months in the haemoglobin level < or > 11 gr/ 100 ml, respectively. (p=0.3). In univariable Cox regression analysis, smoking rates and chemotheraphy cycles number were predictors of survival (p=0.05 y p=0.018, respectively). Hemoglobine (p=0.55). In multivariable Cox regression analysis, only the number of cycles was predictor of survival (p=0.026). Hemoglobine (p=0.34). Conclusions: In our experience, a greater survival tendency was observed in patients with advanced non- small cell lung cancer who presented levels of Hemoglobine greater than 11 gr/dl, previous to cisplatin- based chemotherapy without statistical significance. [Table: see text]


2012 ◽  
Vol 30 (34_suppl) ◽  
pp. 39-39
Author(s):  
Christopher G. Lis ◽  
Maurie Markman ◽  
Mark Rodeghier ◽  
Digant Gupta

39 Background: Prostate cancer is the second leading cause of cancer death among U.S. men. While self-reported quality of life has been shown to be prognostic of survival, there has been limited exploration of whether a patient’s assessment of the overall quality-of-care received might influence survival in prostate cancer. We evaluated the relationship between patient-reported experience with service quality and overall survival in prostate cancer. Methods: 832 returning prostate cancer patients treated at Cancer Treatment Centers of America between July 2007 and December 2010. Overall patient experience (“considering everything, how satisfied are you with your overall experience?”) was measured on a 7-point Likert scale ranging from “completely dissatisfied” to “completely satisfied”. It was dichotomized into 2 categories: top box response (7) versus all others (1-6). Cox regression was used to evaluate the association between patient experience and survival. Results: 560 patients were newly diagnosed while 272 had been previously treated. Majority of patients (n=570, 68.5%) had stage II disease at diagnosis. The mean age was 63.6 years. By the time of this analysis, 93 (11.2%) patients had expired. 710 (85.3%) patients were “completely satisfied” with the service quality they received while 122 (14.7%) patients were not. Median overall survival was 47.9 months. On univariate Cox regression analysis, “completely satisfied” patients had a significantly lower risk of mortality compared to those not “completely satisfied” (HR=0.48; 95% CI: 0.30-0.78; p=0.003). On multivariate Cox regression analysis controlling for stage at diagnosis, treatment history and age, “completely satisfied” patients demonstrated significantly lower mortality (HR=0.50; 95% CI: 0.29-0.87; p=0.01) compared to those not “completely satisfied”. Conclusions: Patient experience with service quality was an independent predictor of survival in prostate cancer. Based on this provocative observation, it is reasonable to suggest that further exploration of a possible meaningful relationship between patient perceptions of the care they have received and outcome in prostate cancer is indicated.


2021 ◽  
Author(s):  
Liusheng Wu ◽  
Xiaoqiang Li ◽  
Jixian Liu ◽  
Da Wu ◽  
Dingwang Wu ◽  
...  

Abstract Objective: Autophagy-related LncRNA genes play a vital role in the development of esophageal adenocarcinoma.Our study try to construct a prognostic model of autophagy-related LncRNA esophageal adenocarcinoma, and use this model to calculate patients with esophageal adenocarcinoma. The survival risk value of esophageal adenocarcinoma can be used to evaluate its survival prognosis. At the same time, to explore the sites of potential targeted therapy genes to provide valuable guidance for the clinical diagnosis and treatment of esophageal adenocarcinoma.Methods: Our study have downloaded 261 samples of LncRNA-related transcription and clinical data of 87 patients with esophageal adenocarcinoma from the TCGA database, and 307 autophagy-related gene data from www.autuphagy.com. We applied R software (Version 4.0.2) for data analysis, merged the transcriptome LncRNA genes, autophagy-related genes and clinical data, and screened autophagy LncRNA genes related to the prognosis of esophageal adenocarcinoma. We also performed KEGG and GO enrichment analysis and GSEA enrichment analysis in these LncRNA genes to analysis the risk characteristics and bioinformatics functions of signal transduction pathways. Univariate and multivariate Cox regression analysis were used to determine the correlation between autophagy-related LncRNA and independent risk factors. The establishment of ROC curve facilitates the evaluation of the feasibility of predicting prognostic models, and further studies the correlation between autophagy-related LncRNA and the clinical characteristics of patients with esophageal adenocarcinoma. Finally, we also used survival analysis, risk analysis and independent prognostic analysis to verify the prognosis model of esophageal adenocarcinoma.Results: We screened and identified 22 autophagic LncRNA genes that are highly correlated with the overall survival (OS) of patients with esophageal adenocarcinoma. The area under the ROC curve(AUC=0.941)and the calibration curve have a good lineup, which has statistical analysis value. In addition, univariate and multivariate Cox regression analysis showed that the autophagy LncRNA feature of this esophageal adenocarcinoma is an independent predictor of esophageal adenocarcinoma.Conclusion: These LncRNA screened and identified may participate in the regulation of cellular autophagy pathways, and at the same time affect the tumor development and prognosis of patients with esophageal adenocarcinoma. These results indicate that risk signature and nomogram are important indicators related to the prognosis of patients with esophageal adenocarcinoma.


2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Yang Li ◽  
Rongrong Sun ◽  
Rui Li ◽  
Yonggang Chen ◽  
He Du

Evidence is increasingly indicating that circular RNAs (circRNAs) are closely involved in tumorigenesis and cancer progression. However, the function and application of circRNAs in lung adenocarcinoma (LUAD) are still unknown. In this study, we constructed a circRNA-associated competitive endogenous RNA (ceRNA) network to investigate the regulatory mechanism of LUAD procession and further constructed a prognostic signature to predict overall survival for LUAD patients. Differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed mRNAs (DEmRNAs) were selected to construct the ceRNA network. Based on the TargetScan prediction tool and Pearson correlation coefficient, we constructed a circRNA-associated ceRNA network including 11 DEcircRNAs, 8 DEmiRNAs, and 49 DEmRNAs. GO and KEGG enrichment indicated that the ceRNA network might be involved in the regulation of GTPase activity and endothelial cell differentiation. After removing the discrete points, a PPI network containing 12 DEmRNAs was constructed. Univariate Cox regression analysis showed that three DEmRNAs were significantly associated with overall survival. Therefore, we constructed a three-gene prognostic signature for LUAD patients using the LASSO method in the TCGA-LUAD training cohort. By applying the signature, patients could be categorized into the high-risk or low-risk subgroups with significant survival differences (HR: 1.62, 95% CI: 1.12-2.35, log-rank p = 0.009 ). The prognostic performance was confirmed in an independent GEO cohort (GSE42127, HR: 2.59, 95% CI: 1.32-5.10, log-rank p = 0.004 ). Multivariate Cox regression analysis proved that the three-gene signature was an independent prognostic factor. Combining the three-gene signature with clinical characters, a nomogram was constructed. The primary and external verification C -indexes were 0.717 and 0.716, respectively. The calibration curves for the probability of 3- and 5-year OS showed significant agreement between nomogram predictions and actual observations. Our findings provided a deeper understanding of the circRNA-associated ceRNA regulatory mechanism in LUAD pathogenesis and further constructed a useful prognostic signature to guide personalized treatment of LUAD patients.


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