Homologous recombination (HR) repair deficiency predisposes to cancer development, but also sensitizes cancer cells to DNA damage-inducing therapeutics. Here we identify an HR defect (HRD) gene signature that can be used to functionally assess HR repair status without interrogating individual genetic alterations in cells. By using this HRD gene signature as a functional network analysis tool, w...

Purpose There is a need for adjuvant/neo-adjuvant treatment strategies to prevent metastatic relapse in soft tissue sarcoma (STS). Tumor hypoxia is associated with a high-risk of metastasis and is potentially targetable. This study aimed to derive and validate a hypoxia mRNA signature for STS for future biomarker-driven trials of hypoxia targeted therapy. Materials and Methods RNA sequencing ...

Gliomas are the most common and aggressive primary tumors in adults. The current approaches, such as histological classification and molecular genetics, have limitation in prediction of individual therapeutic outcomes due to heterogeneity within the tumor groups. Recent studies have proposed several gene signatures to predict glioma's prognosis. However, most of the gene expression profiling st...

BACKGROUND Lung cancer remains the leading cause of cancer-related deaths worldwide. The recurrence rate ranges from 35-50% among early stage non-small cell lung cancer patients. To date, there is no fully-validated and clinically applied prognostic gene signature for personalized treatment. METHODOLOGY/PRINCIPAL FINDINGS From genome-wide mRNA expression profiles generated on 256 lung adenoca...

Soft tissue sarcomas are rare and aggressive tumors arising from connective tissues. Adjuvant radiotherapy is a commonly used treatment approach for the majority of sarcomas. We attempted to identify a gene signature that can predict radiosensitive patients who are most likely to have a better treatment response from radiotherapy, compared with disease progression. Using the publicly available ...

BACKGROUND Renal cancers account for more than 3% of all adult malignancies and cause more than 23,400 deaths per year in China alone. The four most common types of kidney tumours include clear cell, papillary, chromophobe and benign oncocytoma. These histological subtypes vary in their clinical course and prognosis, and different clinical strategies have been developed for their management. So...

INTRODUCTION Gene expression profiling has been extensively used to predict outcome in breast cancer patients. We have previously reported on biological hypothesis-driven analysis of gene expression profiling data and we wished to extend this approach through the combinations of various gene signatures to improve the prediction of outcome in breast cancer. METHODS We have used gene expression...

Background. Many gene-expression signatures exist for describing the biological state of profiled tumors. Principal Component Analysis (PCA) can be used to summarize a gene signature into a single score. Our hypothesis is that gene signatures can be validated when applied to new datasets, using inherent properties of PCA. Results. This validation is based on four key concepts. Coherence: elemen...

Collective cell migration is a key feature of transition ductal carcinoma in situ (DCIS) to invasive (IDC) among many other cancers, yet the microenvironmental factors and underlying mechanisms that trigger collective remain poorly understood. Here, we investigated two factors, tumor-intrinsic hypoxia tumor-secreted (secretome), as triggers using three-dimensional (3D) discrete-sized microtumor...

PURPOSE We hypothesize that a gene expression profile characteristic for inflammatory breast cancer (IBC), an aggressive form of breast cancer associated with rapid cancer dissemination and poor survival, might be related to tumor aggressiveness in non-IBC (nIBC). EXPERIMENTAL DESIGN RNA from 17 IBC samples and 40 nIBC samples was hybridized onto Affymetrix chips. A gene signature predictive ...