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A signature for immune response correlates with HCV treatment outcome in Caucasian subjects.

ABSTRACT: This data article contains Supplementary material for a published research article describing a whole-blood proteomic signature that predicts treatment outcome for subjects infected with hepatitis C virus (HCV) [1]. The proteomic signature is derived from whole-blood samples from subjects infected with HCV. The article includes detailed experimental and computational methods used in the analysis. The article also includes tables of demographic and other information about the subjects. Finally, the article includes several figures and tables showing detailed results of the analyses (e.g. lists of identified proteins and coefficients/ROC curves for the regression models).

SUBMITTER: Hare BJ

PROVIDER: S-EPMC4510051 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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A signature for immune response correlates with HCV treatment outcome in Caucasian subjects.

Hare Brian J BJ Haseltine Eric E Fleming Mark M Chelsky Daniel D McIntosh Laura L Allard Rene R Botfield Martyn M

Data in brief 20150211

This data article contains Supplementary material for a published research article describing a whole-blood proteomic signature that predicts treatment outcome for subjects infected with hepatitis C virus (HCV) [1]. The proteomic signature is derived from whole-blood samples from subjects infected with HCV. The article includes detailed experimental and computational methods used in the analysis. The article also includes tables of demographic and other information about the subjects. Finally, t ...[more]

PMID: 26217718

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Project description:Immune checkpoint inhibitors (ICIs) represent a new therapeutic standard for an increasing number of tumor entities. Nevertheless, individual response and outcome to ICI is very heterogeneous, and the identification of the ideal ICI candidate has remained one of the major issues. Sarcopenia and the progressive loss of muscle mass and strength, as well as muscular fat deposition, have been established as negative prognostic factors for a variety of diseases, but their role in the context of ICI therapy is not fully understood. Here, we have evaluated skeletal muscle composition as a novel prognostic marker in patients undergoing ICI therapy for solid malignancies. We analyzed patients with metastasized cancers receiving ICI therapy according to the recommendation of the specific tumor board. Routine CT scans before treatment initialization and during ICI therapy were used to assess the skeletal muscle index (L3SMI) as well as the mean skeletal muscle attenuation (MMA) in n = 88 patients receiving ICI therapy. While baseline L3SMI and MMA values were unsuitable for predicting the individual response and outcome to ICI therapy, longitudinal changes of the L3SMI and MMA (∆L3SMI, ∆MMA) during ICI therapy turned out to be a relevant marker of therapy response and overall survival. Patients who responded to ICI therapy at three months had a significantly higher ∆L3SMI compared to non-responders (-3.20 mm2/cm vs. 1.73 mm2/cm, p = 0.002). Moreover, overall survival (OS) was significantly lower in patients who had a strongly decreasing ∆L3SMI (<-6.18 mm2/cm) or a strongly decreasing ∆MMA (<-0.4 mm2/cm) during the first three month of ICI therapy. Median OS was only 127 days in patients with a ∆L3SMI of below -6.18 mm2/cm, compared to 547 days in patients with only mildly decreasing or even increasing ∆L3SMI values (p < 0.001). Both progressive sarcopenia and an increasing skeletal muscle fat deposition are associated with poor response and outcome to ICI therapy, which might help to guide treatment decisions during ICI therapy.

Project description:BackgroundHepatitis C Virus (HCV) infection is a global health burden particularly in Egypt, where HCV genotype 4a (GT-4a) predominates. The prevention and control of HCV infection will remain a challenge until the development of an effective vaccine that protects against different genotypes. Several HCV GT-1-based vaccines are in different stages of clinical trials, but antigenic differences could make protection against other genotypes problematic. In this regard, data comparing the cell-mediated immune (CMI) response to different HCV genotypes are limited. We aimed to ex vivo investigate whether GT-1-based vaccine may protect against HCV GT-4 infections. This was carried out on samples collected from genotype 4 infected/exposed subjects.Methods/principal findingsThe CMI responses of 35 subjects; infected with HCV GT-4/or who had spontaneously-resolved the infection and 10 healthy control subjects; to two sets of seven HCV overlapping 15-mer peptide pools derived from both genotypes; and covering most of the viral proteins; were evaluated. This was carried out using an interferon gamma (IFN?) enzyme-linked immunospot (ELISpot) assay. Peripheral blood mononuclear cells (PBMC) from 17 subjects (48%) responded to at least one peptide pool derived from GT-1b/GT-4a with 13 subjects responding to peptide pools from both genotypes. A strong correlation was found in the responses to both genotypes (r?=?0.82, p<0.001; 95% confidence interval?=?0.562-0.933). The average IFN? total spot forming cells (SFC)/10(6) PBMC (±SE) from the responding subjects for GT-1b and GT-4a was 216±56 and 199±55, respectively (p?=?0.833). Also, there were no significant differences between those who cleared their HCV infection or who remained HCV-RNA positive (p?=?0.8).Conclusion/significanceOur data suggest that an effective GT-1b vaccine could protect from GT-4a infection. These data could help in HCV rationale vaccine design and efficacy studies and further our understanding of HCV cross protection against different genotypes.

Project description:BackgroundGlioma is the most frequent brain malignancy presenting very poor prognosis and high recurrence rate. Focal adhesion complexes play pivotal roles in cell migration and act as hubs of several signaling pathways.MethodsWe used bioinformatic databases (CGGA, TCGA, and GEO) and identified a focal adhesion-related differential gene expression (FADG) signature by uniCox and LASSO regression analysis. We calculated the risk score of every patient using the regression coefficient value and expression of each gene. Survival analysis, receiver operating characteristic curve (ROC), principal component analysis (PCA), and stratified analysis were used to validate the FADG signature. Then, we conducted GSEA to identify the signaling pathways related to the FADG signature. Correlation analysis of risk scores between the immune checkpoint was performed. In addition, the correlation of risk scores and genes related with DNA repair was performed. CIBERSORT and ssGSEA were used to explore the tumor microenvironment (TME). A nomogram that involved our FADG signature was also constructed.ResultsIn total, 1,726 (528 patients diagnosed with WHO II, 591 WHO III, and 603 WHO IV) cases and 23 normal samples were included in our study. We identified 29 prognosis-related genes in the LASSO analysis and constructed an eight FADG signature. The results from the survival analysis, stratified analysis, ROC curve, and univariate and multivariate regression analysis revealed that the prognosis of the high-risk group was significantly worse than the low-risk group. Correlation analysis between risk score and genes that related with DNA repair showed that the risk score was positively related with BRCA1, BRCA2, RAD51, TGFB1, and TP53. Besides, we found that the signature could predict the prognosis of patients who received radiation therapy. SsGSEA indicated that the high-risk score was positively correlated with the ESTIMATE, immune, and stromal scores but negatively correlated with tumor purity. Notably, patients in the high-risk group had a high infiltration of immunocytes. The correlation analysis revealed that the risk score was positively correlated with B7-H3, CTLA4, LAG3, PD-L1, and TIM3 but inversely correlated with PD-1.ConclusionThe FADG signature we constructed could provide a sensitive prognostic model for patients with glioma and contribute to improve immunotherapy management guidelines.

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A signature for immune response correlates with HCV treatment outcome in Caucasian subjects.

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A signature for immune response correlates with HCV treatment outcome in Caucasian subjects.

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