Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human NSCLC samples to predict recurrence-free survival in postoperative nsclc patients

ABSTRACT: Background:; One of the main fields of lung cancer research is identifying patients who are at high risk of post-resection recurrence. Individual recurrence risk evaluation by accurate but simple and reproducible method is needed for the clinical practice. Results:; The log-rank test and further selection by our criteria of assayability generated 87 genes from microarray data with significant level 5%. Of these, by PTQ-PCR, the expression of most significant 18 genes was obtained. Using these gene expression information and clinical parameters, by stepwise variable selection method, the recurrence prediction model, which composed of 6 genes (CALB1, MMP7, SLC1A7, GSTA1, CCL19, IFI44) and pStage and cell differentiation, were developed. Validation into the two independent cohorts showed good results of the proposed model (p=0.0314, 0.0305, respectively). The predicted median recurrence-free survival times for each patient were reflected real ones well. Conclusions:; Our method of individualized recurrence risk prediction is accurate, technically simple and reproducible to be used in clinical practice. Therefore, it would be useful in customizing the lung cancer management strategies. Experiment Overall Design: Methods: Experiment Overall Design: At first, we selected the statistically significant genes from the analysis of time-to-recurrence and censoring information from 138 whole-genome wide microarray data. Then, we further reduced the number of genes which could be reliably reproducible by RTQ-PCR. With these assayable genes and clinical parameters, construction of recurrence prediction model by Cox proportional hazard regression was done. After validation into two independent cohorts (n=59 and n=56), the model was transformed into recurrence prediction for the each patient.

ORGANISM(S): Homo sapiens

SUBMITTER: Jinkook Kim

PROVIDER: E-GEOD-8894 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:When making treatment decisions, oncologists often stratify breast cancers into a low-risk group (ER+, low grade); an intermediate-risk group (ER+, high grade); and a high-risk group that includes Her2+ and triple-negative (ER-/PR-/Her2-) tumors. None of the currently available gene signatures correlates to this clinical classification. We aimed to develop a test that is practical for the oncologists, that offers both molecular characterization of BCs, and improved prediction of prognosis and treatment response. We investigated the molecular basis of such clinical practice by grouping Her2+ and triple-negative breast cancers together during clustering analyses on the genome-wide gene expression profiles of our training cohort, mostly derived from fine needle aspiration biopsies (FNABs) of 149 consecutive evaluable Breast cancers. The analyses consistently divided these tumors into a three-cluster pattern, similar to clinical risk-stratification groups, that was reproducible in published microarray databases (n=2487) annotated with clinical outcomes. The clinicopathologic parameters of each of these three molecular groups were also similar to clinical classification. The low-risk group had good outcomes and benefited from endocrine therapy. Both intermediate- and high-risk groups had poor outcomes and were resistant to endocrine therapy. The latter demonstrated the highest rate of complete pathological response to neoadjuvant chemotherapy; the highest activities in MYC, E2F1, Ras, β-Catenin and IFN-γ pathways; and poor prognosis predicted by 14 independent prognostic signatures. Based on a multivariate analysis, this new gene signature, termed ClinicoMolecular Triad Classification, predicted recurrence and treatment response better than all pathologic parameters and other prognostic signatures. 149 invasive breast cancers from the 172 specimens contained 161 tumors were used in this study. Expression data of the 11 tumors with replicate was separately combined before analysis.

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Transcription profiling of human NSCLC samples to predict recurrence-free survival in postoperative nsclc patients

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