Robert Lindner

A KRAS variant is a biomarker of poor outcome, platinum chemotherapy resistance and a potential target for therapy in ovarian cancer

Germline variants in the 3′ untranslated region (3′UTR) of cancer genes disrupting microRNA (miRNA) regulation have recently been associated with cancer risk. A variant in the 3′UTR of the KRAS oncogene, referred to as the KRAS variant, is associated with both cancer risk and altered tumor biology. Here, we test the hypothesis that the KRAS variant can act as a biomarker of outcome in epithelial ovarian cancer (EOC), and investigate the cause of altered outcome in KRAS variant-positive EOC patients. As this variant seems to be associated with tumor biology, we additionally test the hypothesis that this variant can be directly targeted to impact cell survival. EOC patients with complete clinical data were genotyped for the KRAS variant and analyzed for outcome (n=536), response to neoadjuvant chemotherapy (n=125) and platinum resistance (n=306). Outcome was separately analyzed for women with known BRCA mutations (n=79). Gene expression was analyzed on a subset of tumors with available tissue. Cell lines were used to confirm altered sensitivity to chemotherapy associated with the KRAS variant. Finally, the KRAS variant was directly targeted through small-interfering RNA/miRNA oligonucleotides in cell lines and survival was measured. Postmenopausal EOC patients with the KRAS variant were significantly more likely to die of ovarian cancer by multivariate analysis (hazard ratio=1.67, 95% confidence interval: 1.09–2.57, P=0.019, n=279). Perhaps explaining this finding, EOC patients with the KRAS variant were significantly more likely to be platinum resistant (odds ratio=3.18, confidence interval: 1.31–7.72, P=0.0106, n=291). In addition, direct targeting of the KRAS variant led to a significant reduction in EOC cell growth and survival in vitro. These findings confirm the importance of the KRAS variant in EOC, and indicate that the KRAS variant is a biomarker of poor outcome in EOC likely due to platinum resistance. In addition, this study supports the hypothesis that these tumors have continued dependence on such 3′UTR lesions, and that direct targeting may be a viable future treatment approach.

A comprehensive evaluation of alignment algorithms in the context of RNA-seq.

Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete.

Molecular Phenotypes in Triple Negative Breast Cancer from African American Patients Suggest Targets for Therapy

Triple negative breast cancer (TNBC) is characterized by high proliferation, poor differentiation and a poor prognosis due to high rates of recurrence. Despite lower overall incidence African American (AA) patients suffer from higher breast cancer mortality in part due to the higher proportion of TNBC cases among AA patients compared to European Americans (EA). It was recently shown that the clinical heterogeneity of TNBC is reflected by distinct transcriptional programs with distinct drug response profiles in preclinical models. In this study, gene expression profiling and immunohistochemistry were used to elucidate potential differences between TNBC tumors of EA and AA patients on a molecular level. In a retrospective cohort of 136 TNBC patients, a major transcriptional signature of proliferation was found to be significantly upregulated in samples of AA ethnicity. Furthermore, transcriptional profiles of AA tumors showed differential activation of insulin-like growth factor 1 (IGF1) and a signature of BRCA1 deficiency in this cohort. Using signatures derived from the meta-analysis of TNBC gene expression carried out by Lehmann et al., tumors from AA patients were more likely of basal-like subtypes whereas transcriptional features of many EA samples corresponded to mesenchymal-like or luminal androgen receptor driven subtypes. These results were validated in The Cancer Genome Atlas mRNA and protein expression data, again showing enrichment of a basal-like phenotype in AA tumors and mesenchymal subtypes in EA tumors. In addition, increased expression of VEGF-activated genes together with elevated microvessel area determined by the AQUA method suggest that AA patients exhibit higher tumor vascularization. This study confirms the existence of distinct transcriptional programs in triple negative breast cancer in two separate cohorts and that these programs differ by racial group. Differences in TNBC subtypes and levels of tumor angiogenesis in AA versus EA patients suggest that targeted therapy choices should be considered in the context of race.

A germline mutation in the BRCA1 3’UTR predicts Stage IV breast cancer

BackgroundA germline, variant in the BRCA1 3’UTR (rs8176318) was previously shown to predict breast and ovarian cancer risk in women from high-risk families, as well as increased risk of triple negative breast cancer. Here, we tested the hypothesis that this variant predicts tumor biology, like other 3’UTR mutations in cancer.MethodsThe impact of the BRCA1-3’UTR-variant on BRCA1 gene expression, and altered response to external stimuli was tested in vitro using a luciferase reporter assay. Gene expression was further tested in vivo by immunoflourescence staining on breast tumor tissue, comparing triple negative patient samples with the variant (TG or TT) or non-variant (GG) BRCA1 3’UTR. To determine the significance of the variant on clinically relevant endpoints, a comprehensive collection of West-Irish breast cancer patients were tested for the variant. Finally, an association of the variant with breast screening clinical phenotypes was evaluated using a cohort of women from the High Risk Breast Program at the University of Vermont.ResultsLuciferase reporters with the BRCA1-3’UTR-variant (T allele) displayed significantly lower gene expression, as well as altered response to external hormonal stimuli, compared to the non-variant 3’UTR (G allele) in breast cancer cell lines. This was confirmed clinically by the finding of reduced BRCA1 gene expression in triple negative samples from patients carrying the homozygous TT variant, compared to non-variant patients. The BRCA1-3’UTR-variant (TG or TT) also associated with a modest increased risk for developing breast cancer in the West-Irish cohort (OR = 1.4, 95% CI 1.1-1.8, p = 0.033). More importantly, patients with the BRCA1-3’UTR-variant had a 4-fold increased risk of presenting with Stage IV disease (p = 0.018, OR = 3.37, 95% CI 1.3-11.0). Supporting that this finding is due to tumor biology, and not difficulty screening, obese women with the BRCA1-3’UTR-variant had significantly less dense breasts (p = 0.0398) in the Vermont cohort.ConclusionA variant in the 3’UTR of BRCA1 is functional, leading to decreased BRCA1 expression, modest increased breast cancer risk, and most importantly, presentation with stage IV breast cancer, likely due to aggressive tumor biology.

Abstract P3-04-07: Androgen receptor expression in triple negative breast cancer

Background: Patients with androgen receptor (AR) positive triple-negative breast cancer (TNBC) may derive a significant benefit from anti-androgen therapy. While AR positivity is often defined by protein expression by immunohistochemistry (IHC), the benefit of anti-androgen therapy in patients who have the Luminal Androgen Receptor (LAR) molecular subtype as defined by genomic profiling is unclear. Our aim was to study the clinical, pathologic and molecular profiles of AR+ tumors by IHC in a diverse set of TNBC. Methods: Tissue microarrays from two separate, well-annotated institutional cohorts (Case Western Reserve University, Yale University) of early-stage TNBC were evaluated for AR expression by IHC (clone SP107, Ventana Benchmark Ultra). AR positivity was defined as greater than or equal to 10% staining in tumor nuclei. AR expression was correlated with clinical and pathologic features such as age, race, grade, and stage within and between the two cohorts. Gene expression was analyzed with the DASL assay (Illumina) on RNA extracted from formalin-fixed paraffin-embedded material using the Ambion RecoverAll kit (Applied Biosystems AM1975). Pietenpol TNBC molecular subtypes were calculated using the online TNBC type tool. Co-expression of AR with other hormone-related proteins including gross cystic disease fluid protein-15 (GCDFP-15, clone EP1582Y, Ventana Benchmark Ultra) and GATA transcription factor 3 (GATA3, clone L50-823, Bondmax Leica) were also assessed. Results: Overall, 22% of cases (n=192) were AR+ by IHC. There was no association between AR expression and age, race, grade or stage within or between the two cohorts. Gene expression data was available on 88 tumors with AR staining results and demonstrated that AR positivity by IHC was not exclusive for the TNBC LAR molecular subtype. Three of five (3/5) tumors that were classified and LAR were in fact AR+ by IHC. Tumors that were AR+ by IHC were also identified in the basal-like 2 (BL2), mesenchymal stem-like (MSL), immunomodulatory (IM), and unstable molecular TNBC categories with low frequency. Notably, of cases that were rejected as ER+ by gene expression profiling despite being clinically TNBC, three of five (3/5) were in fact AR+ by IHC. Examination of other hormone-related proteins in a subset of these patients revealed that AR expression was significantly associated with GCDFP-15 expression (p=0.0007) and was borderline significant for GATA3 expression (p=0.068). Conclusions: AR protein expression levels by IHC were similar in two separate institutional archival cohorts of TNBC and did not correlate with age, race, grade or stage. Comparison of AR IHC data with genomic data suggests that the AR+ phenotype is not unique to LAR subtype of TNBC by gene expression profiling. AR protein expression may be seen in clinically TNBC patients who have a more luminal subtype as evidenced by co-expression of GCDFP-15 and GATA3. Our results suggest that AR staining by IHC may be necessary to capture all patients who may benefit from anti-androgen therapy. Citation Format: Hannah Gilmore, Vinay Varadan, Nicole Williams, Cheryl L Thompson, Stephanie Kim, Peter Hsu, Kristy Miskimen, Aditi Palkar, Shaveta Vinayak, Robert Lindner, Lyndsay Harris. Androgen receptor expression in triple negative breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P3-04-07.

Differing long term trends for two common amphibian species (Bufo bufo and Rana temporaria) in alpine landscapes of Salzburg, Austria

This study focuses on the population trends of two widespread European anuran species: the common toad (Bufo bufo) and the common frog (Rana temporaria). The basis of this study is data gathered over two decades of amphibian fencing alongside roads in the Austrian state of Salzburg. Different statistical approaches were used to analyse the data. Overall average increase or decrease of each species was estimated by calculating a simple average locality index. In addition the statistical software TRIM was used to verify these trends as well as to categorize the data based on the geographic location of each migration site. The results show differing overall trends for the two species: the common toad being stable and the common frog showing a substantial decline over the last two decades. Further analyses based on geographic categorization reveal the strongest decrease in the alpine range of the species. Drainage and agricultural intensification are still ongoing problems within alpine areas, not only in Salzburg. Particularly in respect to micro-climate and the availability of spawning places these changes appear to have a greater impact on the habitats of the common frog than the common toad. Therefore we consider habitat destruction to be the main potential reason behind this dramatic decline. We also conclude that the substantial loss of biomass of a widespread species such as the common frog must have a severe, and often overlooked, ecological impact.

Abstract P6-04-04: Hypoxia Is Associated with Somatic Loss of BRCA1 Protein and Pathway Activity in Triple Negative Breast Cancer

Background: Triple negative breast cancer (TNBC) has loss of BRCA1 activity either through germline mutation, epigenetic modification or negative transcriptional regulators. Yale investigators have demonstrated that tumor hypoxia leads to loss of critical DNA repair activities, including BRCA1, RAD-51 and γ-H2AX (Bindra RS, et al. Cancer Res 2005;65(24): 11597-604). This study was designed to explore the relationship of BRCA1 loss and hypoxia using Carbonic Anhydrase IX (CA-IX), a downstream target of hypoxia-induced factor 1a (HIF-1a), an accepted surrogate biomarker for tumor hypoxia, in TNBC. Methods: Two cohorts of breast tumors from Yale archival materials were studied. The first consisted of 660, unselected breast tumors, the second a cohort of 130 TNBC, both with long term clinical followup. Automated Quantitative Analysis (AQUA) was used to detect the intensity of BRCA1 and CAIX within specific subcellular compartments. CA-IX antibody M75 was provided by the J Zavada lab (1:10000), BRCA1 monoclonal antibody M110 (Ab-1) was purchased from Calbiochem (1:1000). The 130 TNBC cohort was also subjected to whole genome expression analysis. In brief, tissue core biopsies from tumor blocks were subjected to nucleic acid extraction using RecoverAll Total Nucleic Acid Isolation kit (Applied Biosystems) and 600ng total RNA were processed by the Keck Microarray Facility for the Illumina DASL platform. Statistical analysis of gene expression data was carried out in Bioconductor/R software. A set of relevant signatures was selected by enrichment analysis of modules identified by principal component analysis. Signature scores were computed as Pearson correlation between the signature vector of gene contributions and each sample9s expression profile for these genes. Results: In the cohort of 660 specimens, 22 were found to have high CA-IX expression score (above cut-off value of 10). Cut-off was based on known positive cell lines and corresponding AQUA scores, as well as visual confirmation of positivity. A negative correlation (Rho=-0.6, p=0.0165) of BRCA1 nuclear protein with CA-IX level was found and this data was reproducible on a duplicate array. Of note, 14 out of 22 hypoxic breast tumors were from triple negative breast cancers (TNBC) (p=0.0034). In the triple negative cohort, CAIX staining was positive in 20 % of cases (n=15/75) and in these samples it was associated with the 2002 van ‘t Veer BRCA1 mutant signature (Rho=0.51). Positive CAIX staining was also associated with worse outcome (p=0.046) as was CAIX mRNA expression (p=0.02). Conclusions: In human breast tumors BRCA1 nuclear expression is negatively correlated with tumor hypoxia, measured by CAIX. A subset of TNBC has higher levels of hypoxia and BRCA1 signatures. This data suggests that CAIX may be a useful biomarker for BRCA1 loss, and possibly for response to PARP inhibitor therapy. This will be evaluated in our recently completed trial of BSI-201+Irinotecan. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-04-04.