Transcriptional effects of copy number alterations in a large set of human cancers

Copy number alterations (CNAs) can promote tumor progression by altering gene expression levels. Due to transcriptional adaptive mechanisms, however, CNAs do not always translate proportionally into altered expression levels. By reanalyzing >34,000 gene expression profiles, we reveal the degree of transcriptional adaptation to CNAs in a genome-wide fashion, which strongly associate with distinct biological processes. We then develop a platform-independent method-transcriptional adaptation to CNA profiling (TACNA profiling)-that extracts the transcriptional effects of CNAs from gene expression profiles without requiring paired CNA profiles. By applying TACNA profiling to >28,000 patient-derived tumor samples we define the landscape of transcriptional effects of CNAs. The utility of this landscape is demonstrated by the identification of four genes that are predicted to be involved in tumor immune evasion when transcriptionally affected by CNAs. In conclusion, we provide a novel tool to gain insight into how CNAs drive tumor behavior via altered expression levels

Considering the biology of late recurrences in selecting patients for extended endocrine therapy in breast cancer

Extended endocrine therapy can reduce recurrences occurring more than 5 years after diagnosis (late recurrences) in estrogen receptor (ER)-positive breast cancer. Given the side effects of endocrine therapy, optimal patient selection for extended treatment is crucial. Enhanced understanding of late recurrence biology could optimize patient selection in this setting. We therefore summarized the current knowledge of late recurrence biology, clinical trials on extended endocrine therapy, and tools for predicting late recurrence and benefit from treatment extension. Extending 5 years of tamoxifen therapy with 5 years of tamoxifen or an aromatase inhibitor (AI) reduces late recurrence risk by 2-5%, but results of extending AI-based therapy are inconsistent. Although several clinicopathological parameters and multigene assays are prognostic for late recurrence, selection tools predicting benefit from extended endocrine therapy are sparse. Therefore, we additionally performed a pooled analysis using 2231 mRNA profiles of patients with ER-positive/human epidermal growth factor receptor 2 negative breast cancer. Gene Set Enrichment Analysis was applied on genes ranked according to their association with early and late recurrence risk. Higher expression of estrogen-responsive genes was associated with a high recurrence risk beyond 5 years after diagnosis when patients had received no systemic therapy. Although 5 years of endocrine therapy reduced this risk, this effect disappeared after treatment cessation. This suggests that late recurrences of tumors with high expression of estrogen-responsive genes are likely ER-driven. Long-term intervention in this pathway by means of extended endocrine therapy might reduce late recurrences in patients with tumors showing high expression of estrogen-responsive genes

Functional genomic mRNA profiling of a large cancer data base demonstrates mesothelin overexpression in a broad range of tumor types

The membrane bound glycoprotein mesothelin (MSLN) is a highly specific tumor marker, which is currently exploited as target for drugs. There are only limited data available on MSLN expression by human tumors. Therefore we determined overexpression of MSLN across different tumor types with Functional Genomic mRNA (FGM) profiling of a large cancer database. Results were compared with data in articles reporting immunohistochemical (IHC) MSLN tumor expression. FGM profiling is a technique that allows prediction of biologically relevant overexpression of proteins from a robust data set of mRNA microarrays. This technique was used in a database comprising 19,746 tumors to identify for 41 tumor types the percentage of samples with an overexpression of MSLN compared to a normal background. A literature search was performed to compare the FGM profiling data with studies reporting IHC MSLN tumor expression. FGM profiling showed MSLN overexpression in gastrointestinal (12-36%) and gynecological tumors (20-66%), non-small cell lung cancer (21%) and synovial sarcomas (30%). The overexpression found in thyroid cancers (5%) and renal cell cancers (10%) was not yet reported with IHC analyses. We observed that MSLN amplification rate within esophageal cancer depends on the histotype (31% for adenocarcinomas versus 3% for squamous-cell carcinomas). Subset analysis in breast cancer showed MSLN amplification rates of 28% in triple-negative breast cancer (TNBC) and 33% in basal-like breast cancer. Further subtype analysis of TNBCs showed the highest amplification rate (42%) in the basal-like 1 subtype and the lowest amplification rate (9%) in the luminal androgen receptor subtype

Cyclin E expression is associated with high levels of replication stress in triple-negative breast cancer

Replication stress entails the improper progression of DNA replication. In cancer cells, including breast cancer cells, an important cause of replication stress is oncogene activation. Importantly, tumors with high levels of replication stress may have different clinical behavior, and high levels of replication stress appear to be a vulnerability of cancer cells, which may be therapeutically targeted by novel molecularly targeted agents. Unfortunately, data on replication stress is largely based on experimental models. Further investigation of replication stress in clinical samples is required to optimally implement novel therapeutics. To uncover the relation between oncogene expression, replication stress, and clinical features of breast cancer subgroups, we immunohistochemically analyzed the expression of a panel of oncogenes (Cyclin E, c-Myc, and Cdc25A,) and markers of replication stress (phospho-Ser33-RPA32 and γ-H2AX) in breast tumor tissues prior to treatment (n = 384). Triple-negative breast cancers (TNBCs) exhibited the highest levels of phospho-Ser33-RPA32 (P < 0.001 for all tests) and γ-H2AX (P < 0.05 for all tests). Moreover, expression levels of Cyclin E (P < 0.001 for all tests) and c-Myc (P < 0.001 for all tests) were highest in TNBCs. Expression of Cyclin E positively correlated with phospho-RPA32 (Spearman correlation r = 0.37, P < 0.001) and γ-H2AX (Spearman correlation r = 0.63, P < 0.001). Combined, these data indicate that, among breast cancers, replication stress is predominantly observed in TNBCs, and is associated with expression levels of Cyclin E. These results indicate that Cyclin E overexpression may be used as a biomarker for patient selection in the clinical evaluation of drugs that target the DNA replication stress response

Duct-to-duct reconstruction in liver transplantation for primary sclerosing cholangitis is associated with fewer biliary complications in comparison with hepaticojejunostomy

There is no consensus on the preferred type of biliary reconstruction for patients undergoing orthotopic liver transplantation (OLT) for primary sclerosing cholangitis (PSC). The aim of this study was to compare long-term outcomes after OLT for PSC using either duct-to-duct anastomosis or Roux-en-Y hepaticojejunostomy for biliary reconstruction. In a consecutive series of 98 adult patients undergoing OLT for PSC, 45 underwent duct-to-duct reconstruction, and 53 underwent Roux-en-Y biliary reconstruction. The median follow-up was 8.2 years (interquartile range = 3.9-14.5 years). The outcomes of the 2 groups were compared. There were no significant differences in patient demographics or general surgical variables between the groups. The overall patient and graft survival rates were similar for the 2 groups. The incidence of biliary strictures and biliary leakage within the first year after transplantation did not differ between the 2 groups. However, significantly more patients in the Roux-en-Y group suffered at least 1 episode of cholangitis within the first year (9% in the duct-to-duct group versus 25% in the Roux-en-Y group, P = 0.04). In addition, Roux-en-Y reconstruction was associated with a significantly higher rate of late-onset (>1 year after transplantation) nonanastomotic biliary strictures (NAS) in comparison with duct-to-duct reconstruction (24% versus 7% at 5 years and 30% versus 7% at 10 years, P = 0.01). In conclusion, duct-to-duct biliary reconstruction in patients with PSC is associated with lower rates of posttransplant cholangitis and late-onset NAS in comparison with Roux-en-Y hepaticojejunostomy. If technically and anatomically feasible, duct-to-duct anastomosis can be performed safely in patients undergoing OLT for PSC. Liver Transpl 20:457-463, 2014. (c) 2014 AASLD

Relevance of Tumor-Infiltrating Immune Cell Composition and Functionality for Disease Outcome in Breast Cancer

Background: Not all breast cancer patients benefit from neoadjuvant or adjuvant therapy, resulting in considerable undertreatment or overtreatment. New insights into the role of tumor-infiltrating immune cells suggest that their composition, as well as their functionality, might serve as a biomarker to enable optimal patient selection for current systemic therapies and upcoming treatment options such as immunotherapy. Methods: We performed several complementary unbiased in silico analyses on gene expression profiles of 7270 unrelated tumor samples of nonmetastatic breast cancer patients with known clinical follow-up. CIBERSORT was used to estimate the fraction of 22 immune cell types to study their relations with pathological complete response (pCR), disease-free survival (DFS), and overall survival (OS). In addition, we used four previously reported immune gene signatures and a CD8+ T-cell exhaustion signature to assess their relationships with breast cancer outcome. Multivariable binary logistic regression and multivariable Cox regression were used to assess the association of immune cell-type fractions and immune signatures with pCR and DFS/OS, respectively. Results: Increased fraction of regulatory T-cells in human epidermal growth factor receptor 2 (HER2)-positive tumors was associated with a lower pCR rate (odds ratio [OR] = 0.15, 95% confidence interval [CI] = 0.03 to 0.69), as well as shorter DFS (hazard ratio [HR] = 3.13, 95% CI = 1.23 to 7.98) and OS (HR = 7.69, 95% CI = 3.43 to 17.23). A higher fraction of M0 macrophages in estrogen receptor (ER)-positive tumors was associated with worse DFS (HR = 1.66, 95% CI = 1.18 to 2.33) and, in ER-positive/HER2-negative tumors, with worse OS (HR = 1.71, 95% CI = 1.12 to 2.61). Increased fractions of gamma delta T-cells in all breast cancer patients related to a higher pCR rate (OR = 1.55, 95% CI = 1.01 to 2.38), prolonged DFS (HR = 0.68, 95% CI = 0.48 to 0.98), and, in HER2-positive tumors, with prolonged OS (HR = 0.27, 95% CI = 0.10 to 0.73). A higher fraction of activated mast cells was associated with worse DFS (HR = 5.85, 95% CI = 2.20 to 15.54) and OS (HR = 5.33, 95% CI = 2.04 to 13.91) in HER2-positive tumors. The composition of relevant immune cell types frequently differed per breast cancer subtype. Furthermore, a high CD8+ T-cell exhaustion signature score was associated with shortened DFS in patients with ER-positive tumors regardless of HER2 status (HR = 1.80, 95% CI = 1.07 to 3.04). Conclusions: The main hypothesis generated in our unbiased in silico approach is that a multitude of immune cells are related to treatment response and outcome in breast cancer

Consideration of breast cancer subtype in targeting the androgen receptor

The androgen receptor (AR) is a drug target in breast cancer, and AR-targeted therapies have induced tumor responses in breast cancer patients. In this review, we summarized the role of AR in breast cancer based on preclinical and clinical data. Response to AR-targeted therapies in unselected breast cancer populations is relatively low. Pre-clinical and clinical data show that AR antagonists might have a role in estrogen receptor (ER)-negative/AR-positive tumors. The prognostic value of AR for patients remains uncertain due to the use of various antibodies and cut-off values for immunohistochemical assessment. To get more insight into the role of AR in breast cancer, we additionally performed a retrospective pooled analysis to determine the prognostic value of the AR using mRNA profiles of 7270 primary breast tumors. Our analysis shows that a higher AR mRNA level is associated with improved disease outcome in patients with ER-positive/human epidermal growth factor receptor 2 (HER2)-negative tumors, but with worse disease outcome in HER2-positive subgroups. In conclusion, next to AR expression, incorporation of additional tumor characteristics will potentially make AR targeting a more valuable therapeutic strategy in breast cancer. (C) 2019 The Authors. Published by Elsevier Inc