scholarly journals IMUP and GPRC5A: Two Newly Identified Risk Score Indicators in Pancreatic Ductal Adenocarcinoma

Author(s):  
Rong Wei ◽  
Zixin Zeng ◽  
Ningning Shen ◽  
Ziyue Wang ◽  
Honghong Shen ◽  
...  

Abstract Background Pancreatic cancer has been a threateningly lethal malignant tumor worldwide. Despite the promising survival improvement in other cancer types attributing to the fast development of molecular precise medicine, the current treatment situation of pancreatic cancer is still woefully challenging since its limited response to neither traditional radiotherapy and chemotherapy nor emerging immunotherapy. The study is to explore potential responsible genes during the development of pancreatic cancer, thus identifying promising gene indicators and probable drug targets. Methods Different bioinformatic analysis were used to interpret the genetic events in pancreatic cancer development. Firstly, based on multiple cDNA microarray profiles from Gene Expression Omnibus (GEO) database, the genes with differently mRNA expression in cancer comparing to normal pancreatic tissues were identified, followed by being grouped based on the difference level. Then, GO and KEGG were performed to separately interpret the multiple groups of genes, and further Kaplan-Meier survival and Cox Regression analysis assisted us to scale down the candidate genes and select the potential key genes. Further, the basic physicochemical properties, the association with immune cells infiltration, mutation or other types variations besides expression gap in pancreatic cancer comparing to normal tissues of the selected key genes were analyzed. Moreover, the aberrant changed expression of key genes was validated by immunohistochemistry (IHC) experiment using local hospital tissue microarray samples and the clinical significance was explored based on TCGA clinical data. Results Firstly, a total of 22491 genes were identified to express differently in cancer comparing to normal pancreatic tissues based on 5 cDNA expression profiles, and the difference of 487/22491 genes was over 8-fold, and 55/487 genes were shared in multi profiles. Moreover, after genes interpretation which showed the >8-fold genes were mainly related to extracellular matrix structural constituent regulation, Kaplan-Meier survival and Cox-regression analysis were performed continually, and the result indicated that of the 55 extracellular locating genes, GPRC5A and IMUP were the only two independent prognostic indicators of pancreatic cancer. Further, detailed information of IMUP and GPRC5A were analyzed including their physicochemical properties, their expression and variation ratio and their association with immune cells infiltration in cancer, as well as the probable signaling pathways of genes regulation on pancreatic cancer development. Lastly, local IHC experiment performed on PAAD tissue array which was produced with 64 local hospital patients samples confirmed that GPRC5A and IMUP were abnormally up-regulated in pancreatic cancer, which directly associated with worse patients both overall (OS) and recurrence free survival (RFS). Conclusions Using multiple bioinformatic analysis as well as local hospital samples validation, we revealed that GPRC5A and IMUP expression were abnormally up-regulated in pancreatic cancer which associated statistical significantly with patients survival, and the genes’ biological features and clinical significance were also explored. However, more detailed experiments and clinical trials are obligatory to support their further potential drug-target role in clinical medical treatment.

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Rong Wei ◽  
Guoye Qi ◽  
Zixin Zeng ◽  
Ningning Shen ◽  
Ziyue Wang ◽  
...  

Abstract Background Pancreatic cancer has been a threateningly lethal malignant tumor worldwide. Despite the promising survival improvement in other cancer types attributing to the fast development of molecular precise medicine, the current treatment situation of pancreatic cancer is still woefully challenging since its limited response to neither traditional radiotherapy and chemotherapy nor emerging immunotherapy. The study is to explore potential responsible genes during the development of pancreatic cancer, thus identifying promising gene indicators and probable drug targets. Methods Different bioinformatic analysis were used to interpret the genetic events in pancreatic cancer development. Firstly, based on multiple cDNA microarray profiles from Gene Expression Omnibus (GEO) database, the genes with differently mRNA expression in cancer comparing to normal pancreatic tissues were identified, followed by being grouped based on the difference level. Then, GO and KEGG were performed to separately interpret the multiple groups of genes, and further Kaplan–Meier survival and Cox Regression analysis assisted us to scale down the candidate genes and select the potential key genes. Further, the basic physicochemical properties, the association with immune cells infiltration, mutation or other types variations besides expression gap in pancreatic cancer comparing to normal tissues of the selected key genes were analyzed. Moreover, the aberrant changed expression of key genes was validated by immunohistochemistry (IHC) experiment using local hospital tissue microarray samples and the clinical significance was explored based on TCGA clinical data. Results Firstly, a total of 22,491 genes were identified to express differently in cancer comparing to normal pancreatic tissues based on 5 cDNA expression profiles, and the difference of 487/22491 genes was over eightfold, and 55/487 genes were shared in multi profiles. Moreover, after genes interpretation which showed the > eightfold genes were mainly related to extracellular matrix structural constituent regulation, Kaplan–Meier survival and Cox-regression analysis were performed continually, and the result indicated that of the 55 extracellular locating genes, GPRC5A and IMUP were the only two independent prognostic indicators of pancreatic cancer. Further, detailed information of IMUP and GPRC5A were analyzed including their physicochemical properties, their expression and variation ratio and their association with immune cells infiltration in cancer, as well as the probable signaling pathways of genes regulation on pancreatic cancer development. Lastly, local IHC experiment performed on PAAD tissue array which was produced with 62 local hospital patients samples confirmed that GPRC5A and IMUP were abnormally up-regulated in pancreatic cancer, which directly associated with worse patients both overall (OS) and recurrence free survival (RFS). Conclusions Using multiple bioinformatic analysis as well as local hospital samples validation, we revealed that GPRC5A and IMUP expression were abnormally up-regulated in pancreatic cancer which associated statistical significantly with patients survival, and the genes’ biological features and clinical significance were also explored. However, more detailed experiments and clinical trials are obligatory to support their further potential drug-target role in clinical medical treatment.


2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Pengfeng Xie ◽  
Shichao Wu ◽  
Lijuan Guo ◽  
Jun Ren ◽  
Kaizhi Cai ◽  
...  

Background. The advance of new treatment strategies for more effective management of oral cancer requires identification of novel biological targets. Therefore, the purpose of this study is to identify novel biomarkers associated with oral tumorigenesis and prognostic signature by comparing gene expression profile of oral squamous cell carcinomas (OSCCs). Methods. Four datasets including GSE25099, GSE30784, GSE37991, and GSE41613 were collected from Gene Expression Omnibus (GEO) database. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Cox model analysis, identification of key genes, and Kaplan-Meier analysis were also performed. The xCell was utilized to analyze the infiltration levels of immune cells. Results. A total of 235 differentially expressed genes (DEGs) were found to be dysregulated in OSCC. These genes were mainly enriched in ECM receptor interaction and focal adhesion. Cox regression analysis identified 10 genes considered as key genes. Kaplan-Meier analysis showed that low expression of SERPINE1 (also known as PAI-1), high expression of CD1C, and C-X3-C motif chemokine receptor 1 (CX3CR1) were associated with well prognostic status in OSCC patients. In addition, we constructed a 3-immune-cell signature (myeloid dendritic cell, T cell CD4+ central memory, and common myeloid progenitor) that may be used to predict the survival status of OSCC patients. Conclusion. Three key genes and 3-immune-cell signature were potential biomarkers for the prognosis of OSCC, and they may serve as potential targets for the treatment of OSCC patients.


2021 ◽  
Author(s):  
Andras Szabo ◽  
Krisztina Toth ◽  
Adam Nagy ◽  
Dominika Domokos ◽  
Nikoletta Czobor ◽  
...  

Abstract Background: In recent decades, previous studies have noted the importance of frailty, which is a frequently used term in perioperative risk evaluations. Psychological and socioeconomical domains were investigated as part of frailty syndrome. The aim of this study was to assess the importance of these factors in mortality after vascular surgery.Methods: In our prospective, observational study (ClinicalTrials.gov Identifier: NCT02224222), we examined 164 patients who underwent elective vascular surgery between 2014 and 2017. At the outpatient anaesthesiology clinic, patients completed a questionnaire about cognitive functions, depression and anxiety, social support and self-reported quality of life were assessed using a comprehensive frailty index, in addition to medical variables. Propensity score matching was performed to analyse the difference between patients and controls in a nationwide population cohort. The primary outcome was 4 year mortality. The Kaplan-Meier method and Cox regression analysis were used for statistical analyses.Results: The patients’ mean age was 67.05 years (SD: 9.49 years). Mini-Mental State Examination scores of less than 27 points were recorded for 41 patients. Overall mortality rates were 22.4% and 47.6% in the control and cognitive impairment groups, respectively (p=0.013). In the univariate Cox regression analysis, cognitive impairment measured using age- and education-adjusted MMSE scores increased the risk of mortality (AHR: 2.842, 95% CI: 1.389-5.815, p=0.004).Conclusion: Even mild cognitive dysfunction measured preoperatively using the MMSE represents a potentially important risk factor for mortality after vascular surgery.


2020 ◽  
Author(s):  
Rong Wei ◽  
Ziyue Wang ◽  
Yaping Zhang ◽  
Bin Wang ◽  
Ningning Shen ◽  
...  

Abstract Background Lung cancer has been the leading cause of tumor related death, and 80%~85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the treatment is still challenging. The study is to identify credible responsible genes during the development of NSCLC using bioinformatic analysis, developing new prognostic biomarkers and potential gene targets to the disease. Methods Firstly, three genes expression profiles GSE44077, GSE18842 and GSE33532 were picked from Gene Expression Omnibus (GEO) to analyze the genes with different expression level (GDEs) between NSCLC and normal lung samples, and the cellular location, molecular function and the biology pathways the GDEs enriched in were analyzed. Then, gene function modules of GDEs were explored based on the protein-protein interaction network (PPI), and the top module which contains most genes was identified, followed by containing genes annotation and survival analysis. Moreover, multivariate cox regression analysis was performed in addition to the Kaplan meier survival to narrow down the key genes scale. Further, the clinical pathological features of the picked key genes were explored using TCGA data. Results Three GEO profiles shared a total of 664 GDEs, including 232 up-regulated and 432 down-regulated genes. Based on the GDEs PPI network, the top function module containing a total of 69 genes was identified, and 31 of 69 genes were mitotic cell cycle regulation related. And survival analysis of the 31 genes revealed that 17/31 genes statistical significantly related to NSCLC overall survival, including 4 spindle assembly checkpoints, namely NDC80, BUB1B, MAD2L1 and AURKA. Further, multivariate cox regression analysis identified NDC80 and MAD2L1 as independent prognostic indicators in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) respectively. Interestingly, pearson correlation analysis indicated strong connection between the four genes NDC80, BUB1B, MAD2L1 and AURKA, and their clinical pathological features were addressed. Conclusions Using bioinformatic analysis of GEO combined with TCGA data, we revealed two independent prognostic indicators in LUAD and LUSC respectively and analyzed their clinical features. However, more detailed experiments and clinical trials are needed to verify their drug targets role in clinical medical use.


2017 ◽  
Vol 11 ◽  
pp. 117955491772804 ◽  
Author(s):  
Mridula Krishnan ◽  
Aabra Ahmed ◽  
Ryan W Walters ◽  
Peter T Silberstein

Background: Adjuvant therapy after curative resection is associated with survival benefit in stage III pancreatic cancer. We analyzed the factors affecting the outcome of adjuvant therapy in stage III pancreatic cancer and compared overall survival with different modalities of adjuvant treatment. Methods: This is a retrospective study of patients with stage III pancreatic cancer listed in the National Cancer Database (NCDB) who were diagnosed between 2004 and 2012. Patients were stratified based on adjuvant therapy they received. Unadjusted Kaplan-Meier and multivariable Cox regression analysis were performed. Results: We analyzed a cohort included 1731 patients who were recipients of adjuvant therapy for stage III pancreatic cancer within the limits of our database. Patients who received adjuvant chemoradiation had the longest postdiagnosis survival time, followed by patients who received adjuvant chemotherapy, and finally patients who received no adjuvant therapy. On multivariate analysis, advancing age and patients with Medicaid had worse survival, whereas Spanish origin and lower Charlson comorbidity score had better survival. Conclusions: Our study is the largest trial using the NCDB addressing the effects of adjuvant therapy specifically in stage III pancreatic cancer. Within the limits of our study, survival benefit with adjuvant therapy was more apparent with longer duration from date of diagnosis.


Diagnostics ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2252
Author(s):  
Sihang Cheng ◽  
Zhengyu Jin ◽  
Huadan Xue

In this paper, we assess changes in CT texture of metastatic liver lesions after treatment with chemotherapy in patients with pancreatic cancer and determine if texture parameters correlate with measured time to progression (TTP). This retrospective study included 110 patients with pancreatic cancer with liver metastasis, and mean, entropy, kurtosis, skewness, mean of positive pixels, and standard deviation (SD) values were extracted during texture analysis. Response assessment was also obtained by using RECIST 1.1, Choi and modified Choi criteria, respectively. The correlation of texture parameters and existing assessment criteria with TTP were evaluated using Kaplan-Meier and Cox regression analyses in the training cohort. Kaplan-Meier curves of the proportion of patients without disease progression were significantly different for several texture parameters, and were better than those for RECIST 1.1-, Choi-, and modified Choi-defined response (p < 0.05 vs. p = 0.398, p = 0.142, and p = 0.536, respectively). Cox regression analysis showed that percentage change in SD was an independent predictor of TTP (p = 0.016) and confirmed in the validation cohort (p = 0.019). In conclusion, CT texture parameters have the potential to become predictive imaging biomarkers for response evaluation in pancreatic cancer with liver metastasis.


2020 ◽  
Author(s):  
Andras Szabo ◽  
Krisztina Toth ◽  
Adam Nagy ◽  
Dominika Domokos ◽  
Nikoletta Czobor ◽  
...  

Abstract Background: In recent decades, previous studies have noted the importance of frailty, which is a frequently used term in perioperative risk evaluations. Psychological and socioeconomical domains were investigated as part of frailty syndrome. The aim of this study was to assess the importance of these factors in mortality after vascular surgery.Methods: In our prospective, observational study (ClinicalTrials.gov Identifier: NCT02224222), we examined 164 patients who underwent elective vascular surgery between 2014 and 2017. At the outpatient anaesthesiology clinic, patients completed a questionnaire about cognitive functions, depression and anxiety, social support and self-reported quality of life were assessed using a comprehensive frailty index, in addition to medical variables. Propensity score matching was performed to analyse the difference between patients and controls in a nationwide population cohort. The primary outcome was 4 year mortality. The Kaplan-Meier method and Cox regression analysis were used for statistical analyses.Results: The patients’ mean age was 67.05 years (SD: 9.49 years). Mini-Mental State Examination scores of less than 27 points were recorded for 41 patients. Overall mortality rates were 22.4% and 47.6% in the control and cognitive impairment groups, respectively (p=0.013). In the univariate Cox regression analysis, cognitive impairment measured using age- and education-adjusted MMSE scores increased the risk of mortality (AHR: 2.842, 95% CI: 1.389-5.815, p=0.004).Conclusion: Even mild cognitive dysfunction measured preoperatively using the MMSE represents a potentially important risk factor for mortality after vascular surgery.


2021 ◽  
Author(s):  
Caiqin Gan ◽  
Mengting Li ◽  
Ganjing Peng ◽  
Wenjie Li ◽  
Haizhou Wang ◽  
...  

Abstract Background: Immune cells and stromal cells in the tumor microenvironment (TME) play a vital role in the initiation and progression of colorectal cancer (CRC). The study aimed to screen valuable prognostic biomarkers in CRC based on stromal and immune scores.Method: We used the ESTIMATE algorithm to calculate the immune and stromal scores of CRC samples in TCGA. Then the CRC samples were divided into high and low score groups based on the median value of the immune and stromal scores. Differentially expressed genes (DEGs) associated with immune score and stromal score were screened. WGCNA and univariate COX regression analysis were performed to further identify key prognostic genes. The prognostic value of key genes was validated based on The Gene Expression Profiling Interactive Analysis (GEPIA) and GSE17536 dataset.TIMER and CIBERSORT algorithms were applied to analyze the correlations among key genes and tumor-infiltrating immune cells. Several pairs of colon cancer tissue were used to be proven.Result: 1314 upregulated and 4 downregulated genes associated with immune score and stromal score were identified, which were significantly enriched in immune-related biological processes and pathways. Among these DEGs, SPOCK1 and POSTN were identified as key prognostic genes. High expression of SPCOK1 and POSTN was associated with advanced clinical stage, T stage, N stage, and poor prognosis of CRC. The results from CIBERSORT and TIMER revealed that SPOCK1 and POSTN were associated with tumor-infiltrating immune cells, especially macrophages and neutrophils. Meanwhile, in several pairs of human colorectal tissue samples, SPOK1 and POSTN were found to be significantly overexpressed in colorectal tissue compared with para-cancer tissue, and macrophage surface markers CD68 (co-expressed by M1 and M2 macrophages) and CD206 (M2-specific macrophage expression) were also overexpressed in cancer tissue. Besides, SPOCK1 and POSTN expression were positively correlated with the expression of immune checkpoints.Conclusion: Collectively, our results indicate that SPOCK1 and POSTN may be novel prognostic biomarkers in CRC and correlate with immune infiltrates.


2021 ◽  
Author(s):  
Shaomei Tang ◽  
Xiaoliang Huang ◽  
Haixing Jiang ◽  
Shanyu Qin

Abstract Background: Pancreatic adenocarcinoma (PAAD) is an extremely malignant cancer. Immunotherapy is a promising avenue for elevating survival time of PAAD patients.Methods: The RNA sequencing and clinical data of PAAD were downloaded from the TCGA database. The ssGSEA method and weighted gene co-expression network analysis were used to calculate the relative abundance of tumor-infiltrated immune cells and identified the immune cells closely related module. Least absolute shrinkage and selection operator (LASSO) and Cox regression analysis were used to construct a prognostic model. MCPcounter and EPIC were also applied to assess the immune cell components using gene expression profile.Results: The B cells closely related module was identified and five genes including ARID5A, CLEC2B, MICAL1, MZB1 and RAPGEF1 were ultimately selected to establish the prognostic signature for calculating risk scores of PAAD patients. Kaplan-Meier curves presented a worse survival in the high-risk patients (p<0.05) and the area under the Receiver operating characteristic (ROC) curve of risk score for 1-year and 3-year survival were 0.78 and 0.80 based on the training set. Also, similar results were verified in the validated and combined sets. Interestingly, low-risk group presented significantly elevated immune, stroma scores and proportion of B cells and associations between these five genes and B cells were identified by using multiple methods including ssGSEA, MCPcounter and EPIC. Conclusions: This is the first attempt to study a B cells related prognostic signature, which is instrumental in exploration of novel prognostic biomarkers in PAAD.


2020 ◽  
Author(s):  
Rong Wei ◽  
Ziyue Wang ◽  
Yaping Zhang ◽  
Bin Wang ◽  
Ningning Shen ◽  
...  

Abstract Background Lung cancer has been the leading cause of tumor related death, and 80%~85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the treatment is still challenging. The study is to identify credible responsible genes during the development of NSCLC using bioinformatic analysis, developing new prognostic biomarkers and potential gene targets to the disease. Methods Firstly, three genes expression profiles GSE44077, GSE18842 and GSE33532 were picked from Gene Expression Omnibus (GEO) to analyze the genes with different expression level (GDEs) between NSCLC and normal lung samples, and the cellular location, molecular function and the biology pathways the GDEs enriched in were analyzed. Then, gene function modules of GDEs were explored based on the protein-protein interaction network (PPI), and the top module which contains most genes was identified, followed by containing genes annotation and survival analysis. Moreover, multivariate cox regression analysis was performed in addition to the Kaplan meier survival to narrow down the key genes scale. Further, the clinical pathological features of the picked key genes were explored using TCGA data. Results Three GEO profiles shared a total of 664 GDEs, including 232 up-regulated and 432 down-regulated genes. Based on the GDEs PPI network, the top function module containing a total of 69 genes was identified, and 31 of 69 genes were mitotic cell cycle regulation related. And survival analysis of the 31 genes revealed that 17/31 genes statistical significantly related to NSCLC overall survival, including 4 spindle assembly checkpoints, namely NDC80, BUB1B, MAD2L1 and AURKA. Further, multivariate cox regression analysis identified NDC80 and MAD2L1 as independent prognostic indicators in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) respectively. Interestingly, pearson correlation analysis indicated strong connection between the four genes NDC80, BUB1B, MAD2L1 and AURKA, and their clinical pathological features were addressed. Conclusions Using bioinformatic analysis of GEO combined with TCGA data, we revealed two independent prognostic indicators in LUAD and LUSC respectively and analyzed their clinical features. However, more detailed experiments and clinical trials are needed to verify their drug targets role in clinical medical use.


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