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Host gene expression signatures of H1N1, H3N2, HRV, RSV virus infection in adults

ABSTRACT: Consider the problem of designing a panel of complex biomarkers to predict a patient's health or disease state when one can pair his or her current test sample, called a target sample, with the patient's previously acquired healthy sample, called a reference sample. As contrasted to a population averaged reference, this reference sample is individualized. Automated predictor algorithms that compare and contrast the paired samples to each other could result in a new generation of test panels that compare to a person's healthy reference to enhance predictive accuracy. This study develops such an individualized predictor and illustrates the added value of including the healthy reference for design of predictive gene expression panels. The objective is to predict each subject's state of infection, e.g., neither exposed nor infected, exposed but not infected, pre-acute phase of infection, acute phase of infection, post-acute phase of infection. Using gene microarray data collected in a large-scale serially sampled respiratory virus challenge study, we quantify the diagnostic advantage of pairing a person's baseline reference with his or her target sample.

ORGANISM(S): Homo sapiens

PROVIDER: GSE73072 | GEO | 2016/06/22

SECONDARY ACCESSION(S): PRJNA296033

REPOSITORIES: GEO

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Project description:Background/Aims: Recurrence-free survival (RFS) following curative resection of hepatocellular carcinoma (HCC) in subjects with hepatitis C virus (HCV) infection is highly variable. Traditional clinico-pathological endpoints are recognized as weak predictors of RFS. It has been suggested that gene expression profiling of HCC and nontumoral liver tissue may improve prediction of RFS, aid in understanding of the underlying liver disease, and guide individualized therapy. The goal of this study was to create a gene expression predictor of HCC recurrence in subjects with HCV. Methods: Frozen samples of the tumors and nontumoral liver were obtained from 47 subjects with HCV-associated HCC. Additional nontumoral liver samples were obtained from HCV-free subjects with metastatic liver tumors. Gene expression profiling data was used to determine the molecular signature of HCV-associated HCC and to develop a predictor of RFS. Results: The molecular profile of the HCV-associated HCC confirmed central roles for MYC and TGF-beta1 in liver tumor development. Gene expression in tumors was found to have poor predictive power with regards to RFS, but analysis of nontumoral tissues yielded a strong predictor for RFS in late-recurring (>1 year) subjects. Importantly, nontumoral tissue-derived gene expression predictor of RFS was highly significant in both univariable and multivariable Cox proportional hazard model analyses. Conclusions: Microarray analysis of the nontumoral tissues from subjects with HCV-associated HCC delivers novel molecular signatures of RFS, especially among the late-recurrence subjects. The gene expression signature of the predictor gives important insights into the pathobiology of HCC recurrence and used in design of the individualized therapy. 43 tumor (JT) and 44 non-tumor (JNT) liver tissues surgically resected from patients with HCV-associated hepatocellular carcinoma; 8 non-tumor liver tissues (control samples, JC) surgically resected from HCV- or HBV-free patients with metastatic liver tumor. Inter-batch normalization was carried out using Distance Weighted Discrimination procedure. The supplementary file 'GSE17856_Readme.txt' contains a description of the replicates used for normalization. The 'GSE17856_US14702406_2514850*' files are the raw data files for the replicates.

Project description:For Samples GSM601017-28: The aim of this study was to use expression profiling to define transcriptional patterns and regulatory pathways that characterize the host liver response to E. multilocularis infection in the experimental model of secondary infection, to compare gene expression in this model to those described in the model of "primary infection", and to follow the changes in gene expression and in the expression of a cell proliferation marker over time during the complete chronic phase of E.multilocularis infection, following early and middle stages. For Samples GSM601029-40: The aim of this study was to use expression profiling to define transcriptional patterns and regulatory pathways that characterize the host liver response to E. multilocularis infection in the experimental model of secondary infection, to compare gene expression in this model to those described in the model of "primary infection", and to follow the changes in gene expression and in the expression of a cell proliferation marker over time during the complete chronic phase of E.multilocularis infection, following its middle and late stages. For Samples GSM601017-28: The anterior liver tissue sample of control mice group and alveolar echinococcosis mice group were obtained at each time point(1 month and 3 month). Biological replicates is 3. Then, total RNA from anterior liver of both groups were used as test sample, which labelled cy5 fluorescein, and the pool RNA of healthy BALB/c mice anterior liver was used as reference sample, which labelled cy3 fluorescein, and then hybridized to 32K Mouse Genome Array Genechips, representing about 25000 characterized murine genes. For Samples GSM601029-40: The anterior liver tissue sample of control mice group and alveolar echinococcosis mice group were obtained at each time point(2 month and 6 month). Biological replicates is 3. Then, total RNA from anterior liver of both groups were used as test sample, which labelled cy5 fluorescein, and the pool RNA of healthy BALB/c mice anterior liver was used as reference sample, which labelled cy3 fluorescein, and then hybridized to 36K Mouse Genome Array Genechips, representing about 25000 characterized murine genes.

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Host gene expression signatures of H1N1, H3N2, HRV, RSV virus infection in adults

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