5-gene signature enhances prediction of patient survival in PDAC.

<p>(A) ROC curve demonstrating predictive power of pancreatic survival signature in the Pancreatic ICGC (left), GSE57495 (middle), and GSE71729 (right) datasets. (B) Kaplan-Meier plot demonstrating predictive power of pancreatic survival signature in Pancreatic ICGC (left), GSE57495 (middle), and GSE71729 (right) datasets.</p

Pancreatic cancer survival analysis defines a signature that predicts outcome

<div><p>Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in the US. Despite multiple large-scale genetic sequencing studies, identification of predictors of patient survival remains challenging. We performed a comprehensive assessment and integrative analysis of large-scale gene expression datasets, across multiple platforms, to enable discovery of a prognostic gene signature for patient survival in pancreatic cancer. PDAC RNA-Sequencing data from The Cancer Genome Atlas was stratified into Survival+ (>2-year survival) and Survival–(<1-year survival) cohorts (n = 47). Comparisons of RNA expression profiles between survival groups and normal pancreatic tissue expression data from the Gene Expression Omnibus generated an initial PDAC specific prognostic differential expression gene list. The candidate prognostic gene list was then trained on the Australian pancreatic cancer dataset from the ICGC database (n = 103), using iterative sampling based algorithms, to derive a gene signature predictive of patient survival. The gene signature was validated in 2 independent patient cohorts and against existing PDAC subtype classifications. We identified 707 candidate prognostic genes exhibiting differential expression in tumor versus normal tissue. A substantial fraction of these genes was also found to be differentially methylated between survival groups. From the candidate gene list, a 5-gene signature (<i>ADM</i>, <i>ASPM</i>, <i>DCBLD2</i>, <i>E2F7</i>, and <i>KRT6A</i>) was identified. Our signature demonstrated significant power to predict patient survival in two distinct patient cohorts and was independent of AJCC TNM staging. Cross-validation of our gene signature reported a better ROC AUC (≥ 0.8) when compared to existing PDAC survival signatures. Furthermore, validation of our signature through immunohistochemical analysis of patient tumor tissue and existing gene expression subtyping data in PDAC, demonstrated a correlation to the presence of vascular invasion and the aggressive squamous tumor subtype. Assessment of these genes in patient biopsies could help further inform risk-stratification and treatment decisions in pancreatic cancer.</p></div

5-gene signature captures histological and molecular features of aggressive PDAC.

<p>(A) Box plots showing composite H-score from immunohistochemistry staining of human PDAC samples for ADM, KRT6a, ASPM, DCBLD2, and E2F7 with samples grouped based on AJCC stage, differentiation status, and presence of vascular invasion on histology. N = 10 human PDAC tumor samples. (B) Signature score boxplot versus GSE71729 and (C) GSE57495. *p = 0.01381 and ns = non-significant based on t-test. **p = 4.6 x 10⁻⁸ and ***p = 7.1 x 10⁻⁷ based on Anova analysis.</p

Survival based gene expression gene analysis in PDAC.

<p>Flow diagram depicting analysis pipeline to identify 707 differentially expressed genes (DEG) between Survival- and Survival+ groups with subsequent analysis to determine a survival signature.</p

5-Gene pancreatic cancer survival signature.

<p>5-Gene pancreatic cancer survival signature.</p

Interactome of E2f1 and E2f3 in Rb family deficient liver cancer

Endogenous E2f1 and E2f3 were pulled-down from Rb family deficient liver cancer derived cell lines (in parallel, an anti HA pull-down was performed as a negative control). The resulting fractions were loaded on a polyacrylamide gel and different bands were excised to be run on a Mass Spectrometer. The experiment was performed independently three times and the associated file is one of the three replicates

Enrichment of Targetable Mutations in the Relapsed Neuroblastoma Genome - Fig 1

<p><b>Study cohort overview</b> A) Tabulation of Children’s Oncology Group (COG) risk classification and treatment time points of biopsy for 151 samples. (Intermed. = intermediate risk group) B) Number of samples taken at each treatment time point for nine patients with serial biopsies. (HR = high risk, IR = intermediate risk, LR = low risk at time of biopsy; further information in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006501#pgen.1006501.s003" target="_blank">S2 Table</a>) C) Tabulation of all variants identified (VUS: variants of unknown significance) D) Total number of variants identified per sample, stratified by COG risk group. Inset shows a similar calculation for suspected driver variants only. Heavy line represents the median of the data. “n” indicates the number of patients in each risk group. E) Total number of variants in each sample. Each bar represents an individual sample; color corresponds to risk group (red = high, blue = intermediate, green = low).</p

Genetic variants from a single patient at different treatment time points.

<p>Each biopsy was at a different anatomic site. Red denotes suspected driver variants; gray denotes variants of unknown significance. Letter preceding tumor location indicates primary (P) or metastatic (M) site. Number in parentheses indicates inferred allelic fraction for mutation calls, or inferred copy number for amplification or deletion calls. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006501#pgen.1006501.s003" target="_blank">S2 Table</a> for additional details. Note that this patient was treated with crizotinib following the 5^th relapse.</p

Calcium-activated chloride channel ANO1 promotes breast cancer progression by activating EGFR and CAMK signaling

The calcium-activated chloride channel anoctamin 1 (ANO1) is located within the 11q13 amplicon, one of the most frequently amplified chromosomal regions in human cancer, but its functional role in tumorigenesis has remained unclear. The 11q13 region is amplified in ¯15% of breast cancers. Whether ANO1 is amplified in breast tumors, the extent to which gene amplification contributes to ANO1 overexpression, and whether overexpression of ANO1 is important for tumor maintenance have remained unknown. We have found that ANO1 is amplified and highly expressed in breast cancer cell lines and primary tumors. Amplification of ANO1 correlatedwith disease grade and poor prognosis. Knockdown of ANO1 in ANO1-amplified breast cancer cell lines and other cancers bearing 11q13 amplification inhibited proliferation, induced apoptosis, and reduced tumorgrowth inestablishedcancer xenografts.Moreover,ANO1chloride channel activity was important for cell viability. Mechanistically, ANO1 knockdown or pharmacological inhibition of its chloride-channel activity reduced EGF receptor (EGFR) and calmodulin-dependent protein kinase II (CAMKII) signaling, which subsequently attenuated AKT, v-src sarcoma viral oncogene homolog (SRC), and extracellular signal-regulated kinase (ERK) activation in vitro and in vivo. Our results highlight the involvement of the ANO1 chloride channel in tumor progression and provide insights into oncogenic signaling in human cancerswith 11q13 amplification, thereby establishing ANO1 as a promising target for therapy in these highly prevalent tumor types

Additional file 1 of Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours

Additional file 1. Supplementary figures for the manuscript