scholarly journals Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity

2007 ◽  
Vol 104 (18) ◽  
pp. 7564-7569 ◽  
Author(s):  
Lao H. Saal ◽  
Peter Johansson ◽  
Karolina Holm ◽  
Sofia K. Gruvberger-Saal ◽  
Qing-Bai She ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Signature ◽  
Pi3k Pathway ◽  
Negative Regulator ◽  
Mrna Levels ◽  
Pathway Activity ◽  
Pten Loss ◽  
Expression Signature ◽  
Cancer Management ◽  
Pathway Activation

Pathway-specific therapy is the future of cancer management. The oncogenic phosphatidylinositol 3-kinase (PI3K) pathway is frequently activated in solid tumors; however, currently, no reliable test for PI3K pathway activation exists for human tumors. Taking advantage of the observation that loss of PTEN, the negative regulator of PI3K, results in robust activation of this pathway, we developed and validated a microarray gene expression signature for immunohistochemistry (IHC)-detectable PTEN loss in breast cancer (BC). The most significant signature gene was PTEN itself, indicating that PTEN mRNA levels are the primary determinant of PTEN protein levels in BC. Some PTEN IHC-positive BCs exhibited the signature of PTEN loss, which was associated to moderately reduced PTEN mRNA levels cooperating with specific types of PIK3CA mutations and/or amplification of HER2. This demonstrates that the signature is more sensitive than PTEN IHC for identifying tumors with pathway activation. In independent data sets of breast, prostate, and bladder carcinoma, prediction of pathway activity by the signature correlated significantly to poor patient outcome. Stathmin, encoded by the signature gene STMN1, was an accurate IHC marker of the signature and had prognostic significance in BC. Stathmin was also pathway-pharmacodynamic in vitro and in vivo. Thus, the signature or its components such as stathmin may be clinically useful tests for stratification of patients for anti-PI3K pathway therapy and monitoring therapeutic efficacy. This study indicates that aberrant PI3K pathway signaling is strongly associated with metastasis and poor survival across carcinoma types, highlighting the enormous potential impact on patient survival that pathway inhibition could achieve.

A blood-based gene expression signature of early-stage non-small cell lung cancer.

2012 ◽  
Vol 30 (30_suppl) ◽  
pp. 69-69
Author(s):  
Melissa Rotunno ◽  
Nan Hu ◽  
Hua Su ◽  
Chaoyu Wang ◽  
Pier Alberto Bertazzi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Predictive Accuracy ◽  
Early Stage ◽  
Single Gene ◽  
Gene Expression Signature ◽  
Mrna Levels ◽  
Healthy Controls ◽  
Expression Signature ◽  
Qrt Pcr

69 Background: Accurate blood-based biomarker for early cancer detection could be an easier and more convenient screening option than monitoring the target organ via tissue or imaging. We recently identified and validated eight genetic biomarkers of early-stage lung adenocarcinoma detectable in both peripheral whole blood (PWB) and lung tissue of smokers. Since biomarkers distinguishing benign disease versus lung malignancy across all cell types are needed in the diagnostic clinical setting, it is important to test the identified biomarkers in other lung cancer histologies, particularly in squamous cell carcinoma (SQCC), the second most common lung cancer histology after adenocarcinoma (AD). Methods: Using Real-Time Quantitative PCR (qRT-PCR), we measured mRNA levels for the eight candidate genes in PWB of 48 randomly sampled stage I SQCC cases, in addition to previously analyzed 82 AD cases and 130 age, sex, and smoking frequency matched healthy controls from the Environment And Genetics in Lung cancer Etiology (EAGLE) case-control study. The qRT-PCR data were analyzed using the 2-ΔΔCtmethod to compare SQCC cases with controls. The area under the receiver operating characteristic curve (AUC) was computed to assess the predictive accuracy of the candidate biomarkers in SQCC separately, and in SQCC and AD together. Results: Expression of TGFBR3, RUNX3, TRGC2, TRGV9, TARP, and TSTA3 genes, significantly differentiated SQCC cases versus controls, while ACP1 and VCAN gene expression did not. The eight genes combined discriminated patients with lung cancer from healthy controls with similarly high accuracy in SQCC and overall (AUC = 0.80 ± 0.1). RUNX3 showed the highest single gene accuracy for SQCC (AUC = 0.78). Conclusions: We showed that the previously identified gene expression signature of early-stage lung AD also differentiated early stage SQCC from healthy controls and demonstrated its sensitivity and specificity as a potential diagnostic lung cancer biomarker. Since lung cancer is the most common cause of cancer mortality worldwide and current smokers are at very high risk, our smoking-specific findings, if confirmed and translated into screening approaches, have the potential to impact public health.

Prognostic and predictive effects of a gene expression signature for NRF2 pathway activation in lung squamous cell carcinoma (SqCC).

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 7517-7517
Author(s):  
David W. Cescon ◽  
Desmond She ◽  
ChangQi Zhu ◽  
Shingo Sakashita ◽  
Melania Pintilie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adjuvant Chemotherapy ◽  
Gene Expression Signature ◽  
Phase Iii ◽  
Nrf2 Pathway ◽  
Expression Signature ◽  
Prognostic Effect ◽  
Pathway Activation ◽  
Somatic Alterations ◽  
Mutational Activation

7517 Background: Genomic profiling of SqCC in TCGA identified somatic alterations that activate the NRF2 transcriptional program – a master regulator of the oxidative stress response – in ~35% of tumors (NFE2L2 mutations/amplifications, KEAP1 or CUL3 mutations/deletions). This pathway has been implicated in resistance to chemotherapy. To evaluate the clinical significance of this molecular subset, we developed a gene expression classifier and tested this signature as a predictor of adjuvant chemotherapy benefit with cisplatin/vinorelbine (cis/vin) in a subset of SqCC patients with microarray data from the NCIC JBR.10 Phase III clinical trial. Methods: Logistic regression (LR) and SAM analysis were independently applied to 104 TCGA SqCC cases that had both microarray gene expression and mutation data to identify genes associated with NRF2 pathway mutational status. Overlapping genes were used to define the signature, which was then tested in 3 independent SqCC datasets (62 JBR.10; 54 UHN; 129 UM) to evaluate the prognostic and predictive values of putative NRF2 pathway activation. Results: 29 genes comprising the signature were identified by overlap between LR (291 genes) and SAM (45 genes). The signature consistently separated SqCC into 2 groups in all datasets, corresponding to putatively activated and wild type (WT) NRF2 pathway tumors. No prognostic effect of the activated signature was observed in independent datasets (UHN HR 0.86, 95%CI 0.28 – 2.67; UM HR 1.43, 95%CI 0.82 – 2.48). Similarly, in JBR10, no prognostic effect was observed in the observation arm (n=24, HR 0.66, 95%CI 0.13 – 3.29). A trend toward improved survival with adjuvant chemotherapy was observed in patients with the WT signature (HR 0.34, 95%CI 0.08 – 1.78, p=0.13), but not in patients with the activated signature (HR 1.16, 95%CI 0.19 – 6.97, p=0.87; interaction p=0.18). Conclusions: A gene expression signature based on mutational activation of the NRF2 pathway may be predictive of benefit from adjuvant cis/vin in SqCC. Patients with NRF2 pathway activating somatic alterations may have reduced benefit from this therapy. Validation of this potentially "actionable" finding in additional datasets is necessary.

Molecular Effects of Rituximab on CLL Cells In Vivo: Rapid Increase in Serum Interferon gamma, Induction of a Distinct Tumor Cell Gene Expression Signature and Loss of CD20 Expression.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2048-2048
Author(s):  
Adrian Wiestner ◽  
Elinor Lee ◽  
Berengere Vire ◽  
Federica Gibellini ◽  
Ndegwa Njuguna ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tumor Cells ◽  
Dominant Role ◽  
Tumor Biology ◽  
Gene Expression Signature ◽  
Leukemic Cells ◽  
Mrna Levels ◽  
Expression Signature ◽  
Protein Levels

Abstract Proposed mechanisms on how the monoclonal anti-CD20 antibody rituximab (R) depletes B-cells include antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity. In vitro studies have suggested that R induced pro-apoptotic signals contribute to clinical efficacy and may sensitize cells to chemotherapy. To investigate the effect of R on tumor biology in vivo, we analyzed the molecular changes in leukemic cells of 12 previously untreated CLL patients during the first R (375mg/m2) infusion. The median reduction of circulating tumor cells within 24h was 50% (range 0–67%). We first determined whether R affects gene expression in CLL cells obtained before and at 6h and 24h after the start of R. Cells were purified by CD19+ selection and gene expression was measured on Affymetrix HU133A 2.0 arrays. A one-way ANOVA test with a stringent cutoff (false discovery rate of <20%) identified 69 genes whose expression increased >50% at 6h compared to pre treatment, and 31 genes whose expression decreased by >30%. Most of the up-regulated genes are known to be regulated by interferon (IFN) and include the pro-apoptotic genes IRF1, STAT1, FAS and OAS2. Of 12 cytokines assayed in the serum, we found that only IFNy, IL–6, IL–8, IL–10, and TNFa were induced by R with a peak at 2h. Consistent with a dominant role of IFNy on gene expression in the CLL cells, STAT1, a direct and essential mediator of IFNy signaling, was activated in circulating leukemic cells in vivo. In addition, when comparing the response between patients, IFNy serum protein levels correlated strongly with the intensity of the gene expression changes in the tumor cells (r=0.83, p=0.008). We could not detect any IFNy mRNA in CLL cells and conclude that the IFNy is most likely released by NK cells activated through FcyRIII signaling. Considering the long half-life of R, we were surprised to see that both cytokine serum levels and gene expression changes almost completely subsided by 24h. Intriguingly, among the few genes that were down-regulated by treatment, the gene encoding CD20 was the most strongly and consistently affected showing a 50% decrease in expression at 24h. We also assessed CD20 protein levels by Western blotting. Total CD20 levels were markedly decreased already at 6h and by 24h almost all CD20 had been lost. The more rapid and more pronounced decrease of CD20 protein as opposed to mRNA levels is consistent with a process previously described as shaving, during which R bound CD20 is pulled of the cell surface (Kennedy AD, J Immunol. 2004). Despite the absence of a clinical cytokine release syndrome, we observed basically identical changes in serum cytokines and gene expression with subsequent infusions in 2 patients analyzed. In summary, R induced a characteristic gene expression signature in CLL cells that is dominated by IFN response genes, many of which have well characterized pro-apoptotic functions. Thus, our data suggest that signaling for apoptosis is not so much a direct effect of R, but due to a complex immune response to the R coated CLL cells. Modified treatment schedules capable of delivering sustained pro-apoptotic signals hold promise for improved efficacy of R and should be explored.

Correlation of PIK3CA mutation-associated gene expression signature (PIK3CA-GS) with deactivation of the PI3K pathway and with prognosis within the luminal-B ER+ breast cancers

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 533-533
Author(s):  
S. Loi ◽  
B. Haibe-Kains ◽  
F. Lallemand ◽  
L. Pusztai ◽  
A. Bardelli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Outcome ◽  
Expression Profiles ◽  
Pik3ca Mutation ◽  
Gene Expression Signature ◽  
Pi3k Pathway ◽  
Mutation Status ◽  
Luminal B ◽  
Pik3ca Mutations ◽  
Expression Signature

533 Background: The phosphathidylinositol-3-kinase (PI3K) signaling pathway is frequently deregulated in tumor biology and is an attractive target for cancer therapy. Our aim was to characterize the molecular and clinical outcome effects of PIK3CA mutations in breast cancer (BC). Methods: We analyzed 173 BC samples for PIK3CA mutations. Corresponding gene expression profiles were used to understand its effects on the PI3K pathway. We validated a PIK3CA-GS in 2 independent BC cohorts (n = 183) with known PIK3CA mutation status and evaluated its correlation with clinical outcome in 1748 BC samples stratified by treatment and subtype. Results: 26% of BCs had a PIK3CA mutation. Tumors with PIK3CA mutation demonstrated a distinct gene expression signature (p = 0.03 after 1000 perm). In 2 datasets it could discriminate PIK3CA mutation carriers from wild-type (ROC 0.68, 0.71, p = 0.001for both). However, the PIK3CA-GS was correlated with deactivation of the PI3K pathway probably through a negative feedback loop. This observation was supported by: 1) the PIK3CA-GS was significantly correlated with gene expression changes induced by PI3K inhibitors (Connectivity Map, Gene set enrichment analyses) and 2) the PIK3CA-GS was anti-correlated with a GS of PTEN loss (R = -0.3; Saal et al, 2007). Higher levels of the PIK3CA signature were observed in HER-2+ and estrogen receptor positive (ER+), luminal BC subtypes. Whilst there was no association with mutation status alone and prognosis, increasing expression of the PIK3CA-GS (suggesting deactivation) was significantly associated with better clinical outcome in both untreated (p = 0.04) and particularly ER+, luminal-B, tamoxifen only-treated (p = 0.004) BC. Multivariate analysis (HR: 0.4; 95%CI: 0.3–0.7; p = 0.002) confirmed that the PI3KCA-GS provided independent prognostic information. Conclusions: Paradoxically, the PIK3CA-GS correlates with inhibition of the PI3K pathway in ER+ BC and identifies a subgroup of luminal B BCs with a favorable outcome. The PIK3CA-GS may be a better indicator of PI3K pathway dysfunction than mutation status, potentially indicating patients who may benefit from combined endocrine therapy and PI3K inhibition. No significant financial relationships to disclose.

Generation of a prognostic cancer stem-like gene expression signature in men undergoing radical prostatectomy for localized prostate cancer.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 4563-4563
Author(s):  
Adrian Stuart Fairey ◽  
Dongyun Yang ◽  
Susan G. Groshen ◽  
David I. Quinn ◽  
Philip Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Radical Prostatectomy ◽  
Wnt Signaling Pathway ◽  
Gene Expression Signature ◽  
Disease Recurrence ◽  
Localized Prostate Cancer ◽  
Mrna Levels ◽  
Expression Signature

4563 Background: Novel biomarkers are needed to predict recurrence after radical prostatectomy for localized prostate cancer. Recent data suggest that cancer stem-like cells (CSC) are present in prostate tumors, and the CSC phenotype has been associated with an aggressive cancer phenotype. We investigated whether tumor mRNA levels of genes typically expressed by CSC are associated with disease recurrence. Methods: Clinically annotated prostatectomy specimens (FFPE) were used for this nested case-control study. Samples represented men who underwent radical prostatectomy and either experienced a recurrence (PSA or clinical; n=152) or no recurrence (controls; n=124) with minimum 5-year follow-up. Men were excluded if they received neoadjuvant hormone therapy. Cases and controls were frequency matched based on D’Amico risk group. Laser capture microdissection with mRNA extraction and quantitative RT-PCR were used to quantify the expression of 12 candidate CSC-associated genes (ALDH1A1, Axin2, Bmi1, CD133, CD44a, CTNNB1/β-catenin, ITGA2/integrin α2, NANOG, Nkx3-1, Notch1, OCT 4, TACSTD2/Trop2). Univariable and multivariable analyses were conducted to measure associations with recurrence. Results: mRNA data were evaluable for 241 of 276 patients. Univariate Wilcoxon analysis showed that 4 genes (Axin2, p<0.001; CD44a, p=0.036; OCT 4, p=0.017; TACSTD2, p=0.008) were expressed at low levels in tumors of patients whose disease recurred. Recursive partitioning analysis identified 3 genes significantly predictive of disease recurrence (Axin2, NANOG, CTNNB1), with cutpoints yielding odds ratios (OR) of 8.5 (Axin2low/NANOGhigh; n=94, 95%CI 3.7-19.2) and 5.1 (Axin2low/NANOGvery high/CTNNB1low; n=26, 95%CI 1.7-14.8). Conclusions: We identified a novel CSC-associated 3 gene expression signature with the potential to predict recurrence after radical prostatectomy. Axin2 is known to interact with CTNNB1/β-catenin in the Wnt signaling pathway, which in turn has been shown to regulate expression of NANOG, a key protein that mediates pluripotency. In vitro experiments and an independent cohort validation study are planned based on these novel findings.

A gene expression signature of MEK pathway activation to predict survival in triple-negative breast cancer.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 1024-1024 ◽  
Author(s):  
Justin M. Balko ◽  
Melinda Sanders ◽  
Maria Gabriela Kuba ◽  
Joseph A. Pinto ◽  
Franco F. Doimi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Signaling Pathway ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Molecular Subtype ◽  
Gene Expression Signature ◽  
Expression Signature ◽  
Node Status ◽  
Pathway Activation

1024 Background: Tumor cell proliferation measured by Ki67 in the surgically removed tumor after neoadjuvant chemotherapy (NAC) has been shown to predict patient outcome in breast cancer. It is unclear from these studies if breast cancer subtype may account in part for the predictive ability of Ki67. Thus, we tested whether Ki67 score in the surgically-resected residual tumor (RT) after NAC predicted outcome in a cohort of triple negative breast cancer (TNBC). Gene expression profiling was performed to identify molecular subtype and test the association with gene modules indicative of signaling pathway activation. Methods: Ki67 was scored in the RT of 89 patients with stage II-III TNBC (ER/PR/HER2 negative by IHC at diagnosis) that had been treated with NAC. Expression levels for 450 genes were quantified by Nanostring. Ki67, node and menopause status, age, therapy type (± taxanes), molecular subtype, and gene expression scores were tested for association to RFS and OS using univariate and multivariate CoxPH models. Results: Ki67 score in the post-NAC RT demonstrated a wide range (1.5-77.7%; median: 36.2%). Twenty seven % of RTs were 3+ HER2 by IHC. Molecular subtype in the RT was as follows: 64% Basal-like; 20% HER2-enriched; 6% LumA; 6% LumB; 4% Normal-like. In univariate analyses to respectively predict RFS and OS, node status (p=0.005 and p=0.02), number of nodes (p=0.003 and p<0.001), and the score of a gene expression module of MEK pathway activation (p=0.04 and p=0.01,) were significant. Basal-like subtype approached significance for RFS (p=0.1) and OS (p=0.05). In multivariate analyses, node status (p=0.002 for RFS and p<0.001 for OS) and MEK pathway activation score (p=0.04 and p=0.01) were significant predictors. Conclusions: Ki67 in the RT after NAC was not predictive of outcome in a cohort of TNBC. However, a gene expression signature of activated MEK was negatively associated with outcome. These data are consistent with the reported preclinical activity of MEK inhibitors against basal-like breast cancer cells and a possible role of this signaling pathway in chemotherapy resistance. They also support deep sequencing studies to identify genetic alterations in the RAS/MEK/MAPK pathway in TNBC.

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