Preoperative profiles of plasma amino acids and derivatives distinguish periampullary cancer and benign disease

Periampullary cancers, including pancreatic ductal adenocarcinoma, ampullary-, cholangio-, and duodenal carcinoma, are frequently diagnosed in an advanced stage and are associated with poor overall survival. They are difficult to differentiate from each other and challenging to distinguish from benign periampullary disease preoperatively. To improve the preoperative diagnostics of periampullary neoplasms, clinical or biological markers are warranted.In this study, 28 blood plasma amino acids and derivatives from preoperative patients with benign (N = 45) and malignant (N = 72) periampullary disease were analyzed by LC-MS/MS.Principal component analysis and consensus clustering both separated the patients with cancer and the patients with benign disease. Glutamic acid had significantly higher plasma expression and 15 other metabolites significantly lower plasma expression in patients with malignant disease compared with patients having benign disease. Phenylalanine was the only metabolite associated with improved overall survival (HR = 0.50, CI 0.30-0.83, P < 0.01).Taken together, plasma metabolite profiles from patients with malignant and benign periampullary disease were significantly different and have the potential to distinguish malignant from benign disease preoperatively.

An integrated omics approach highlights how epigenetic events can explain and predict response to neoadjuvant chemotherapy and bevacizumab in breast cancer

Treatment with the anti-angiogenic drug bevacizumab in addition to chemotherapy has shown efficacy for breast cancer in some clinical trials, but better biomarkers are needed to optimally select patients for treatment. Here, we present an omics approach where DNA methylation profiles are integrated with gene expression and results from proteomic data in breast cancer patients to predict response to therapy and pinpoint response-related epigenetic events. Fresh-frozen tumor biopsies taken before, during, and after treatment from human epidermal growth factor receptor 2 negative non-metastatic patients receiving neoadjuvant chemotherapy with or without bevacizumab were subjected to molecular profiling. Here, we report that DNA methylation at enhancer CpGs related to cell cycle regulation can predict response to chemotherapy and bevacizumab for the estrogen receptor positive subset of patients (AUC = 0.874), and we validated this observation in an independent patient cohort with a similar treatment regimen (AUC = 0.762). Combining the DNA methylation scores with the scores from a previously published protein signature resulted in a slight increase in the prediction performance (AUC = 0.784). We also show that tumors receiving the combination treatment underwent more extensive epigenetic alterations. Finally, we performed an integrative expression-methylation quantitative trait loci analysis on alterations in DNA methylation and gene expression levels, showing that the epigenetic alterations that occur during treatment are different between responders and non-responders and that these differences may be explained by the proliferation-epithelial-to-mesenchymal transition axis through the activity of grainyhead like transcription factor 2. Using tumor purity computed from copy number data, we developed a method for estimating cancer cell-specific methylation to confirm that the association to response reflects DNA methylation in cancer cells. Taken together, these results support the potential for clinical benefit of the addition of bevacizumab to chemotherapy when administered to the correct patients.

Proteome Analysis of Pancreatic Tumors Implicates Extracellular Matrix in Patient Outcome

Pancreatic cancer remains a disease with unmet clinical needs and inadequate diagnostic, prognostic, and predictive biomarkers. In-depth characterization of the disease proteome is limited. This study thus aims to define and describe protein networks underlying pancreatic cancer and identify protein centric subtypes with clinical relevance. Mass spectrometry-based proteomics was used to identify and quantify the proteome in tumor tissue, tumor-adjacent tissue, and patient-derived xenografts (PDX)-derived cell lines from patients with pancreatic cancer, and tissues from patients with chronic pancreatitis. We identified, quantified, and characterized 11,634 proteins from 72 pancreatic tissue samples. Network focused analysis of the proteomics data led to identification of a tumor epithelium-specific module and an extracellular matrix (ECM)-associated module that discriminated pancreatic tumor tissue from both tumor adjacent tissue and pancreatitis tissue. On the basis of the ECM module, we defined an ECM-high and an ECM-low subgroup, where the ECM-high subgroup was associated with poor prognosis (median survival months: 15.3 vs. 22.9 months; log-rank test, P = 0.02). The ECM-high tumors were characterized by elevated epithelial-mesenchymal transition and glycolytic activities, and low oxidative phosphorylation, E2F, and DNA repair pathway activities. This study offers novel insights into the protein network underlying pancreatic cancer opening up for proteome precision medicine development.

Significance

Pancreatic cancer lacks reliable biomarkers for prognostication and treatment of patients. We analyzed the proteome of pancreatic tumors, nonmalignant tissues of the pancreas and PDX-derived cell lines, and identified proteins that discriminate between patients with good and poor survival. The proteomics data also unraveled potential novel drug targets.

Prognostic Significance of the Loss of Heterozygosity of KRAS in Early-Stage Lung Adenocarcinoma

Lung cancer is a common disease with a poor prognosis. Genomic alterations involving the KRAS gene are common in lung carcinomas, although much is unknown about how different mutations, deletions, and expressions influence the disease course. The first approval of a KRAS-directed inhibitor was recently approved by the FDA. Mutations in the KRAS gene have been associated with poor prognosis for lung adenocarcinomas, but implications of the loss of heterozygosity (LOH) of KRAS have not been investigated. In this study, we have assessed the LOH of KRAS in early-stage lung adenocarcinoma by analyzing DNA copy number profiles and have investigated the effect on patient outcome in association with mRNA expression and somatic hotspot mutations. KRAS mutation was present in 36% of cases and was associated with elevated mRNA expression. LOH in KRAS was associated with a favorable prognosis, more prominently in KRAS mutated than in wild-type patients. The presence of both LOH and mutation in KRAS conferred a better prognosis than KRAS mutation alone. For wild-type tumors, no difference in prognosis was observed between patients with and without LOH in KRAS. Our study indicates that LOH in KRAS is an independent prognostic factor that may refine the existing prognostic groups of lung adenocarcinomas.

Reprogrammed transsulfuration promotes basal-like breast tumor progression via realigning cellular cysteine persulfidation

Basal-like breast cancer (BLBC) is the most aggressive subtype of breast tumors with poor prognosis and limited molecular-targeted therapy options. We show that BLBC cells have a high Cys demand and reprogrammed Cys metabolism. Patient-derived BLBC tumors from four different cohorts exhibited elevated expression of the transsulfuration enzyme cystathione β-synthetase (CBS). CBS silencing (shCBS) made BLBC cells less invasive, proliferate slower, more vulnerable to oxidative stress and cystine (CySSCy) deprivation, prone to ferroptosis, and less responsive to HIF1-α activation under hypoxia. shCBS xenograft tumors grew slower than controls and exhibited impaired angiogenesis and larger necrotic areas. Sulfur metabolite profiling suggested that realigned sulfide/persulfide-inducing functions of CBS are important in BLBC tumor progression. Supporting this, the exclusion of serine, a substrate of CBS for producing Cys but not for producing sulfide/persulfide, did not exacerbate CySSCy deprivation-induced ferroptosis in shCBS BLBC cells. Impaired Tyr phosphorylation was detected in shCBS cells and xenografts, likely due to persulfidation-inhibited phosphatase functions. Overexpression of cystathione γ-lyase (CSE), which can also contribute to cellular sulfide/persulfide production, compensated for the loss of CBS activities, and treatment of shCBS xenografts with a CSE inhibitor further blocked tumor growth. Glutathione and protein-Cys levels were not diminished in shCBS cells or xenografts, but levels of Cys persulfidation and the persulfide-catabolizing enzyme ETHE1 were suppressed. Finally, expression of enzymes of the oxidizing Cys catabolism pathway was diminished, but expression of the persulfide-producing CARS2 was elevated in human BLBC tumors. Hence, the persulfide-producing pathways are major targetable determinants of BLBC pathology that could be therapeutically exploited.

Baseline microvessel density predicts response to neoadjuvant bevacizumab treatment of locally advanced breast cancer

A subset of breast cancer patients benefits from preoperative bevacizumab and chemotherapy, but validated predictive biomarkers are lacking. Here, we aimed to evaluate tissue-based angiogenesis markers for potential predictive value regarding response to neoadjuvant bevacizumab treatment in breast cancer. In this randomized 1:1 phase II clinical trial, 132 patients with large or locally advanced HER2-negative tumors received chemotherapy ± bevacizumab. Dual Factor VIII/Ki-67 immunohistochemical staining was performed on core needle biopsies at baseline and week 12. Microvessel density (MVD), proliferative microvessel density (pMVD; Factor VIII/Ki-67 co-expression), glomeruloid microvascular proliferation (GMP), and a gene expression angiogenesis signature score, were studied in relation to pathologic complete response (pCR), clinico-pathologic features and intrinsic molecular subtype. We found that high baseline MVD (by median) significantly predicted pCR in the bevacizumab-arm (odds ratio 4.9, P = 0.012). High pMVD, presence of GMP, and the angiogenesis signature score did not predict pCR, but were associated with basal-like (P ≤ 0.009) and triple negative phenotypes (P ≤ 0.041). pMVD and GMP did also associate with high-grade tumors (P ≤ 0.048). To conclude, high baseline MVD significantly predicted response to bevacizumab treatment. In contrast, pMVD, GMP, and the angiogenesis signature score, did not predict response, but associated with aggressive tumor features, including basal-like and triple-negative phenotypes.

Immune phenotype of tumor microenvironment predicts response to bevacizumab in neoadjuvant treatment of ER-positive breast cancer

Antiangiogenic drugs are potentially a useful supplement to neoadjuvant chemotherapy for a subgroup of patients with human epidermal growth factor receptor 2 (HER2) negative breast cancer, but reliable biomarkers for improved response are lacking. Here, we report on a randomized phase II clinical trial to study the added effect of bevacizumab in neoadjuvant chemotherapy with FEC100 (5-fluorouracil, epirubicin and cyclophosphamide) and taxanes (n = 132 patients). Gene expression from the tumors was obtained before neoadjuvant treatment, and treatment response was evaluated by residual cancer burden (RCB) at time of surgery. Bevacizumab increased the proportion of complete responders (RCB class 0) from 5% to 20% among patients with estrogen receptor (ER) positive tumors (P = .02). Treatment with bevacizumab was associated with improved 8-year disease-free survival (P = .03) among the good responders (RCB class 0 or I). Patients treated with paclitaxel (n = 45) responded better than those treated with docetaxel (n = 21; P = .03). Improved treatment response was associated with higher proliferation rate and an immune phenotype characterized by high presence of classically activated M1 macrophages, activated NK cells and memory activated CD4 T cells. Treatment with bevacizumab increased the number of adverse events, including hemorrhage, hypertension, infection and febrile neutropenia, but despite this, the ECOG status was not affected.

Abstract P3-10-03: Exploiting p53-dependent functional duality of estrogen receptor-beta to repurpose tamoxifen for triple negative breast cancer therapy

Whether estrogen receptor beta (ERβ/ESR2) is a pro- or anti-oncogenic protein in breast cancer has been controversial. ERβ levels are generally high in triple-negative breast cancer (TNBC). Reports including the Cancer Genome Atlas (TCGA) show that about 80% of TNBC express mutant p53 and it is a major driver of these cancers. We tested the hypothesis that WT versus mutant status of p53 will have an important role in determining the duality of ERβ functions. We showed that ERβ directly binds to TP53 in human breast cancer cells. Using glutathione-S-transferase (GST)-pull down and co-imunoprecipitation assays, we have delineated the DNA binding domain (DBD) along with the hinge domain of ERβ and the C-terminal regulatory domain of p53 to be essential for the interaction. The highly sensitive in situ proximity ligation assay (PLA) showed that ERβ is capable of interacting with both wild type (WT) and mutant p53 in breast cancer cells and tumor tissues. ERβ and p53 antibodies validated for specificity were used for all experiments. Combination of proliferation, cell cycle, and apoptosis assays, RNAi technology, quantitative ChIP (qChIP), and real-time PCR (qRT-PCR) showed that ERβ is pro-proliferative in the context of WTp53, whereas it is anti-proliferative in the context of mutant p53 in multiple breast cancer cell lines. The p53-dependent diametrically opposite functions of ERβ were recapitulated in isogenic MDA-MB-231 TNBC cells (generated by CRISPR) that differ only in the presence of WT versus mutant p53. A major gain-of-function of mutant p53 is its ability to bind and inactivate tumor suppressor p73. We show that ERβ binds and sequesters mutant p53 from mutant p53−p73 complex leading to reactivation of p73. Consistent with these observations, immunohistochemistry (IHC) in TNBC patient tumor tissue microarray (TMA) showed that patients with tumors expressing mutant p53 along with high levels of ERβ were of smaller size and lower stage. Complementing these findings, our analysis of the subgroup of the basal-like/TNBC tumors expressing mutant p53 (but not WTp53) in the METABRIC dataset showed that patients with tumors expressing higher levels of ERβ RNA (ESR2) had significantly better breast cancer-specific survival. The finding that ERβ–mutant p53 combination prognosticates survival in TNBC is important as to date there are no effective prognostic markers for TNBC and suggest the potential for using ERβ−mutant p53 combination in stratification of TNBC into therapeutically actionable subgroups.Furthermore, our findings provide a mechanistic explanation for the functional duality of ERβ and the controversy over its pro-versus anti-tumorigenic role.Surprisingly, Tamoxifen (Tam) increased ERβ-mut-p53 interaction in TNBC cells leading to increased transcription of anti-proliferation genes and knockdown experiments showed that the effect on transcription was dependent on both p73 and ERβ. Importantly, when combined with doxorubicin (Adriamycin) Tam decreased several fold the IC50 of doxorubicin resulting in increased apoptosis. The combination was more effective in inhibiting TNBC xenograft tumor growth in vivo compared to either treatment alone. Significant clinical implications of these findings include the potential for treating patients with doxorubicin at much lower dose than what is currently used in the management of TNBC, thereby reducing its major cumulative dose side effects. Importantly, although at present Tam is not indicated for TNBC, our data suggest the possibility for repurposing Tam therapy alone or in combination with chemotherapy to treat TNBC stratified based on ERβ and p53 status. If validated in a clinical trial, our findings could lead to a therapy that is fundamentally better in terms of effectiveness, cost and time needed to reach the TNBC patients.

Citation Format: Gokul M Das, Utpal K Mukhopadhyay, Chetan C Oturkar, Christina Adams, Nadi Wickramasekera, Sanjay Bansal, Rajesh Medisetty, Austin Miller, Wendy M Swetzig, Laxmi Silwal-Pandit, Anne-Lise Borresen-Dale, Creighton J Creighton, Jun Hyoung Park, Santhi D Konduri, Alka Mukhopadhyay, Alexander Caradori, Benny Abraham Kaipparettu. Exploiting p53-dependent functional duality of estrogen receptor-beta to repurpose tamoxifen for triple negative breast cancer therapy [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-10-03.

TP53 Status as a Determinant of Pro- vs Anti-Tumorigenic Effects of Estrogen Receptor-Beta in Breast Cancer

BACKGROUND

Anti-tumorigenic vs pro-tumorigenic roles of estrogen receptor-beta (ESR2) in breast cancer remain unsettled. We investigated the potential of TP53 status to be a determinant of the bi-faceted role of ESR2 and associated therapeutic implications for triple negative breast cancer (TNBC).

METHODS

ESR2-TP53 interaction was analyzed with multiple assays including the in situ proximity ligation assay. Transcriptional effects on TP53-target genes and cell proliferation in response to knocking down or overexpressing ESR2 were determined. Patient survival according to ESR2 expression levels and TP53 mutation status was analyzed in the basal-like TNBC subgroup in the Molecular Taxonomy of Breast Cancer International Consortium (n = 308) and Roswell Park Comprehensive Cancer Center (n = 46) patient cohorts by univariate Cox regression and log-rank test. All statistical tests are two-sided.

RESULTS

ESR2 interaction with wild-type and mutant TP53 caused pro-proliferative and anti-proliferative effects, respectively. Depleting ESR2 in cells expressing wild-type TP53 resulted in increased expression of TP53-target genes CDKN1A (control group mean [SD] = 1 [0.13] vs ESR2 depletion group mean [SD] = 2.08 [0.24], P = .003) and BBC3 (control group mean [SD] = 1 [0.06] vs ESR2 depleted group mean [SD] = 1.92 [0.25], P = .003); however, expression of CDKN1A (control group mean [SD] = 1 [0.21] vs ESR2 depleted group mean [SD] = 0.56 [0.12], P = .02) and BBC3 (control group mean [SD] = 1 [0.03] vs ESR2 depleted group mean [SD] = 0.55 [0.09], P = .008) was decreased in cells expressing mutant TP53. Overexpressing ESR2 had opposite effects. Tamoxifen increased ESR2-mutant TP53 interaction, leading to reactivation of TP73 and apoptosis. High levels of ESR2 expression in mutant TP53-expressing basal-like tumors is associated with better prognosis (Molecular Taxonomy of Breast Cancer International Consortium cohort: log-rank P = .001; hazard ratio = 0.26, 95% confidence interval = 0.08 to 0.84, univariate Cox P = .02).

CONCLUSIONS

TP53 status is a determinant of the functional duality of ESR2. Our study suggests that ESR2-mutant TP53 combination prognosticates survival in TNBC revealing a novel strategy to stratify TNBC for therapeutic intervention potentially by repurposing tamoxifen.

Abstract P6-07-01: A translational and five-year clinical update in patients treated with neoadjuvant chemotherapy randomized to bevacizumab or control in HER2 negative breast cancer

Background: Bevacizumab added to conventional neoadjuvant chemotherapy increase the proportion of patients achieving a pathological complete response (pCR). Identifying patients responding to antiangiogenic therapy have been challenging. The primary objective of this study was to determine the molecular characteristics and treatment induced changes of the primary tumors with reference to treatment response. Clinical outcome measurements according to treatment were exploratory endpoints. Recent updated clinical results, in addition to extended molecular analyses are presented.

Methods: A phase II randomized clinical trial of HER2 negative primary tumors of ≥25 mm (n=132) was conducted, treated with neoadjuvant chemotherapy (4xFEC100 followed by taxane-based therapy) with or without the addition of bevacizumab. Biopsies were obtained at the time of diagnosis, after 12 weeks of treatment, and after 25 weeks at surgery. The response was evaluated using the criteria for determining the residual cancer burden (RCB). We derived a mean immune score per patient by calculating the average score from the 770 genes in the nCounter PanCancer immune panel to detect an association between immune activity and response to antiangiogenic therapy. In addition, the median five-year follow-up for disease recurrence are reported.

Results: The addition of bevacizumab increased the RCB class 0 (pCR) rate in the study population from 12% to 17% and the rate of “good responders” (RCB class 0 and 1) from 24% to 33%, without reaching statistical significance. A pronounced effect of bevacizumab combination therapy was observed in the hormone receptor (HR) positive tumors, were the percentage of patients achieving RCB class 0 increased from 5% to 20% (Fisher's Exact test, p=0.02). More HR positive patients achieved a good response and fewer patients were poor responders (RCB class 3) in the combination treatment arm (Wilcoxon, p=0.035). Previously, our unsupervised analyses demonstrated an enrichment of immune related genes in pretreatment samples from patients responding to combination therapy. A significantly higher mean immune score (p&lt;0.001) was detected among the HR positive patients who received bevacizumab and achieved RCB class 0 after neoadjuvant treatment (n=11, 20%) . Five-year follow-up data revealed a total of 21 events in the study population; 9 relapses in patients treated with combination therapy, and 12 relapses in patients treated with chemotherapy only. DFS was not statistically different between the treatment groups (log rank, p=0.4257). However, among the patients achieving a good response an improved DFS was observed for those treated with combination therapy (1/22 vs. 5/16, log rank, p=0.0254).

Conclusion: Among locally advanced HER2-negative HR positive breast cancer patients, the addition of bevacizumab to neoadjuvant chemotherapy increased the rate of good responders and improved the DFS among these patients. An increased primary tumor immune score may predict good response to neoadjuvant antiangiogenic therapy in HR positive disease. Further studies are needed to validate the use of such immune panels for selection of patients most likely to benefit from antiangiogenic therapy.

Citation Format: Gythfeldt HvdL, Engebråten O, Naume B, Wist E, Borgen E, Lien T, Lindgjærde OC, Garred O, Schlichting E, Silwal-Pandit L, Borresen-Dale AL. A translational and five-year clinical update in patients treated with neoadjuvant chemotherapy randomized to bevacizumab or control in HER2 negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-07-01.

Time series analysis of neoadjuvant chemotherapy and bevacizumab-treated breast carcinomas reveals a systemic shift in genomic aberrations

Background

Chemotherapeutic agents such as anthracyclines and taxanes are commonly used in the neoadjuvant setting. Bevacizumab is an antibody which binds to vascular endothelial growth factor A (VEGFA) and inhibits its receptor interaction, thus obstructing the formation of new blood vessels.

Methods

A phase II randomized clinical trial of 123 patients with Her2-negative breast cancer was conducted, with patients treated with neoadjuvant chemotherapy (fluorouracil (5FU)/epirubicin/cyclophosphamide (FEC) and taxane), with or without bevacizumab. Serial biopsies were obtained at time of diagnosis, after 12 weeks of treatment with FEC ± bevacizumab, and after 25 weeks of treatment with taxane ± bevacizumab. A time course study was designed to investigate the genomic landscape at the three time points when tumor DNA alterations, tumor percentage, genomic instability, and tumor clonality were assessed. Substantial differences were observed with some tumors changing mainly between diagnosis and at 12 weeks, others between 12 and 25 weeks, and still others changing in both time periods.

Results

In both treatment arms, good responders (GR) and non-responders (NR) displayed significant difference in genomic instability index (GII) at time of diagnosis. In the combination arm, copy number alterations at 25 loci at the time of diagnosis were significantly different between the GR and NR. An inverse aberration pattern was also observed between the two extreme response groups at 6p22-p12 for patients in the combination arm. Signs of subclonal reduction were observed, with some aberrations disappearing and others being retained during treatment. Increase in subclonal amplification was observed at 6p21.1, a locus which contains the VEGFA gene for the protein which are targeted by the study drug bevacizumab. Of the 13 pre-treatment samples that had a gain at VEGFA, 12 were responders. Significant decrease of frequency of subclones carrying gains at 17q21.32-q22 was observed at 12 weeks, with the peak occurring at TMEM100, an ALK1 receptor signaling-dependent gene essential for vasculogenesis. This implies that cells bearing amplifications of VEGFA and TMEM100 are particularly sensitive to this treatment regime.

Conclusions

Taken together, these results suggest that heterogeneity and subclonal architecture influence the response to targeted treatment in combination with chemotherapy, with possible implications for clinical decision-making and monitoring of treatment efficacy.

Trial registration

NCT00773695. Registered 15 October 2008

Electronic supplementary material

The online version of this article (10.1186/s13073-018-0601-y) contains supplementary material, which is available to authorized users.

Abstract 3748: p53 status as a determinant of functional duality of estrogen receptor beta in breast cancer: Therapeutic implications

Whether estrogen receptor beta (ERβ) is a pro- or anti-oncogenic protein in breast cancer has been controversial. ERβ levels are high in ERα negative cancers including triple-negative breast cancer (TNBCs). Recent reports including the Cancer Genome Atlas (TCGA) show that about 80% of TNBC express mutant p53 (mut-p53) and it is the most predominant driver in these cancers. We tested the hypothesis that p53 status in breast cancer will have an important role in determining the duality of ERβ functions. We have shown that ERβ directly binds to p53 in human breast cancer cells. Using glutathione-S-transferase (GST)-pull down and co-imunoprecipitation assays, we have delineated the domains of both proteins that are required for the ERβ-p53 interaction. The DNA binding domain (DBD) along with the hinge domain of ERβ and the C-terminal regulatory domain of p53 are essential for the interaction. Using the highly sensitive proximity ligation assay (PLA), we show ERβ-p53 interaction in situ in breast cancer cells expressing either wild type (wt)- or mut-p53. ERβ and p53 antibodies validated for specificity were used. In multiple cell lines, a combination of proliferation and apoptosis assays, RNAi technology, quantitative chromatin immunoprecipitation (qChIP), and quantitative real-time PCR (qRT-PCR) showed that ERβ is pro-proliferative in the context of wt-p53, whereas it is anti-proliferative in the context of mut-p53. The results were recapitulated in isogenic MDA-MB-231 TNBC cells (generated by CRISPR technology) that differ only in the presence of wt-versus mut-p53. ERβ binds and sequesters mut-p53 from mut-p53−p73 complex leading to reactivation of tumor suppressor p73. Consistent with these data, combination of immunohistochemistry (IHC) and PLA in TNBC patient tumor tissue microarray (TMA) showed that patients with tumors expressing wt-p53/ high ERβ had worse prognosis, both in terms of overall survival (OS) and progression-free survival (PFS). On the contrary, tumors expressing mut-p53/ high ERβ were of smaller size and stage. These findings were complemented by data from our analysis of the mut-p53 subgroup of the basal-like tumors in the METABRIC dataset which showed that patients with tumors expressing higher levels of ERβ RNA (ESR2) had better prognosis. Surprisingly, 4-Hyroxy Tamoxifen (Tam) increased ERβ-mut-p53 interaction in TNBC cells and combination of doxorubicin (Adriamycin) and Tam decreased the IC50 of doxorubicin by 10 fold leading to increased apoptosis. These data have significant clinical implications in targeting ERβ and mutant p53 signaling pathways for therapeutic purposes especially in ERα negative cancers such as TNBC. Importantly, although at present Tam is not standard of care for TNBC, our data suggest a possibility for repurposing Tam therapy alone or in combination with chemotherapy to treat TNBC stratified based on p53 status.

Citation Format: Gokul M. Das, Utpal K. Mukhopadhyay, Christina Adams, Nadi Wickramasekera, Rajesh Medisetty, Sanjay Bansal, Laxmi Silwal-Pandit, Anne-Lise Borresen-Dale, Austin Miller, Wendy M. Sweizig, Angela Omilian, Wiam Bshara, Alka Mukhopadhyay. p53 status as a determinant of functional duality of estrogen receptor beta in breast cancer: Therapeutic implications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3748.

Molecular signatures reflecting microenvironmental metabolism and chemotherapy-induced immunogenic cell death in colorectal liver metastases

Background

Metastatic colorectal cancer (CRC) is associated with highly variable clinical outcome and response to therapy. The recently identified consensus molecular subtypes (CMS1-4) have prognostic and therapeutic implications in primary CRC, but whether these subtypes are valid for metastatic disease is unclear. We performed multi-level analyses of resectable CRC liver metastases (CLM) to identify molecular characteristics of metastatic disease and evaluate the clinical relevance.

Methods

In this ancillary study to the Oslo-CoMet trial, CLM and tumor-adjacent liver tissue from 46 patients were analyzed by profiling mutations (targeted sequencing), genome-wide copy number alteration (CNAs), and gene expression.

Results

Somatic mutations and CNAs detected in CLM were similar to reported primary CRC profiles, while CNA profiles of eight metastatic pairs suggested intra-patient divergence. A CMS classifier tool applied to gene expression data, revealed the cohort to be highly enriched for CMS2. Hierarchical clustering of genes with highly variable expression identified two subgroups separated by high or low expression of 55 genes with immune-related and metabolic functions. Importantly, induction of genes and pathways associated with immunogenic cell death (ICD) was identified in metastases exposed to neoadjuvant chemotherapy (NACT).

Conclusions

The uniform classification of CLM by CMS subtyping may indicate that novel class discovery approaches need to be explored to uncover clinically useful stratification of CLM. Detected gene expression signatures support the role of metabolism and chemotherapy in shaping the immune microenvironment of CLM. Furthermore, the results point to rational exploration of immune modulating strategies in CLM, particularly by exploiting NACT-induced ICD.

Abstract 1752: Immune-related gene signatures in colorectal liver metastases: Exposing an opportunity for immune modulating therapy

Colorectal cancer (CRC) is one of the most common cancers and one of the leading causes of cancer death in the Western world. Up to 50% of patients with CRC develop metastatic disease and the liver is the most common site. The recently identified consensus molecular subtypes (CMS1-4) based on analyses of primary CRC have prognostic and therapeutic implications, but it is unclear whether these molecular subtypes are valid for metastatic disease. In this study, characterisation of CRC liver metastases (CLM) was performed at multiple molecular levels to identify characteristics relevant to metastatic disease. Molecular stratification of a defined metastatic CRC cohort may yield results of clinical relevance and novel treatment opportunities.

Surgically resected CLM and tumor-adjacent liver tissue from 46 patients were analysed for the presence of mutations (targeted deep sequencing), genome-wide copy number alterations (CNA), and transcription profiled. Molecular profiles of CLM and tumor-adjacent liver tissues were analyzed and associations with clinicopathological features and outcome were investigated. We found oncogenic mutations in all except one tumor. Both mutation and CNA profiles were similar to profiles reported for primary CRC. A CMS classifier tool applied to gene expression data, revealed the cohort to be highly enriched for CMS2. Unsupervised clustering based on genes with highly variable expression identified a 55-gene cluster that segregated the samples into two subgroups. The segregation pattern was replicated in relevant publicly available data sets, but the clinical significance of this observation is not evident. The 55 genes were associated with lipid metabolic and immune-related functions, revealing a role of the tumor-host microenvironment. The engagement of the immune system was further underlined by analyzing subgroups defined by neoadjuvant chemotherapy (NACT) administration, which revealed altered expression of inflammatory mediators and immune regulatory genes. The majority of treated patients had received Oxaliplatin based chemotherapy.

The uniform classification of CLM by CMS may reflect the patient composition in our cohort, but may also indicate that novel class discovery approaches need to be explored to uncover clinically useful molecular stratification of CLM. Identified immune-related gene expression signatures associated with molecular and clinical features underline the integration and importance of the immune interactome in resectable CLM. Specifically, the transcriptomic snapshot of NACT exposed CLM revealed altered genes associated with immunogenic cell death but also immune suppression. These results point to rational exploration of immune-modulating strategies in CLM in combination with NACT to increase efficacy and broaden treatment opportunities for this patient group.

Citation Format: Vigdis Nygaard, Vegar J. Dagenborg, Olga Østrup, Einar A. Rødland, Veronica Skarpeteig, Laxmi Silwal-Pandit, Krzysztof Grzyb, Audun E. Berstad, Åsmund A. Fretland, Gunhild M. Mælandsmo, Anne-Lise Børresen-Dale, Anne H. Ree, Bjørn Edwin, Kjersti Flatmark. Immune-related gene signatures in colorectal liver metastases: Exposing an opportunity for immune modulating therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1752. doi:10.1158/1538-7445.AM2017-1752

Abstract 2842: Dissecting the transcriptional profiles of metastatic and primary disease across cancer types

Cancer metastasis is the principal cause of death in individuals with cancer; nevertheless, the molecular basis of metastases is poorly understood. Genetic and epigenetic changes in malignant cells and their interaction with the tumor microenvironment are presumably key events in the establishment of metastases. In this study, we pursue to provide insights into potential importance of various fundamental cancer-related pathways in the metastatic process. We have performed a pathway - based analysis on mRNA expression data (Agilent 8X60K array) from colorectal liver metastases (CLM; N = 38 patients, n = 44 metastases), breast lymph-node metastases (BCM; N = n = 43) and melanoma lymph-node metastases (MLM; N = n= 44). For each of the 186 pathways in the KEGG pathway database, each sample is represented as points in a ‘n’ dimensional space according to their gene expression values, where ‘n’ is the number of genes in the pathway. We first calculated centroids for each of the three metastases types (CLM, BCM and MLM) and then calculated the Euclidean distance between centroids to get a measure of how similar or different each cancer type is for that particular pathway. The findings were compared to the corresponding primary cancer types and normal tissue available from TCGA to uncover biological processes specific to metastases. The pathways were functionally classified into genetic information processing, cellular processes, environmental information processing and metabolic pathways as per KEGG database. Across metastases from different cancer types, pathways involved in genetic information processing (e.g. translation, transcription, protein folding and degradation, DNA replication and repair) and metabolic pathways were more similar than the pathways involved in cellular processes (e.g. cell-cycle, apoptosis, adherence junction), and signal transduction pathways (e.g. Notch, MTOR, JAK STAT) responsible for environmental information processing. The genetic information processing pathways were more similar across cancer types also in the primary setting than the pathways involved in cellular and environmental information processing, whereas the metabolic pathways were more similar across cancer types in the metastatic setting compared to the primary setting. Preliminary findings suggest that the basic molecular architecture of the primary tumors is maintained, except for the metabolic pathways, which become more similar in the metastatic setting; and hence may be a common denominator across cancer types during metastatic process.

Citation Format: Laxmi Silwal-Pandit, Vigdis Nygaard, Hege Russnes, Vegar Johansen Dagenborg, Veronica Skarpeteig, Olga Østrup, Silje Nord, Vivi Ann Flørnes, Anne Hansen Ree, Kjersti Flatmark, Anne-Lise Børresen-Dale, Ole Christian Lingjærde, Gunhild Mari Mælandsmo. Dissecting the transcriptional profiles of metastatic and primary disease across cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2842. doi:10.1158/1538-7445.AM2017-2842

Abstract 1813: Bevacizumab potentiates the proteomic response to neoadjuvant chemotherapy in breast cancer patients: Rppa exploration of consecutive tumor samples in the NeoAva randomized phase II trial

Antiangiogenic therapy using bevacizumab has proven effective for a number of cancers; however, in breast cancer there is an unmet need to identify patients that benefit from such treatment. Sampling of tumor biopsies before and during treatment, as well as at the time of surgery enables the assessment of response at multiple molecular levels. At the proteomic level reverse phase protein analysis (RPPA) support expression of numerous cancer associated proteins simultaneously, which can further be used to unravel molecular mechanisms associated with clinical response to bevacizumab treatment.

In this phase II clinical trial, patients with HER2 negative primary tumors of ≥25 mm were treated with neoadjuvant chemotherapy (4 x FEC100 + 12 weeks of taxane-based therapy) and randomized (1:1) to receive bevacizumab or not. Mammography, ultrasound and MR imaging were used for response evaluation, in addition to final pathology assessment. Tumor responses were evaluable in 132 patients; of which 66 received bevacizumab. Ratio of the tumor size at final pathology assessment, and at inclusion was calculated to obtain a continuous scale of response reflecting the percentage of tumor shrinkage in response to therapy. Tumor biopsies were removed before start of treatment, at week 12 at the start of taxane-based tharapy and at the time of surgery. Lysates from each sample was analyzed on reverse phase protein arrays (RPPA) for expression levels of 210 proteins of which 54 were phospho-specific.

The addition of bevacizumab to the chemotherapy do not alter proteomic response from week 0 to 25 to such extent that this patient group cluster naturally together. While the proteomic response from week 0 to 12 in both treatment arms had an overall similar profile regarding up- and down-regulated proteins, the combination treatment (FEC100 + bevacizumab) induced substantially more effect on the regulation of each protein. This suggests that bevacizumab treatment have the capability to potentiate the effects of the anthracyclin based chemotherapy from week 0 to 12. Conversely, from week 12-25 (taxane-based therapy + bevacizumab) this effect was lost or even reversed, possibly due to a de-vascularized and less accessible tumor. An exception to this observation was a few phospho-proteins that do seem to have sustained stronger regulation over the whole treatment period. We are in the process of analyzing in more detail the impact of phosphorylation and thus protein activation states on treatment response.

Deciphering molecular response and activity regulation at the proteomic level is a promising approach and may reveal novel knowledge with potential important clinical relevance.

Citation Format: Mads H. Haugen, Ole Christian Lingjaerde, Marit Krohn, Wei Zhao, Evita M. Lindholm, Laxmi Silwal-Pandit, Elin Borgen, Øystein Garred, Anne Fangberget, Marit M. Holmen, Ellen Schlichting, Helle K. Skjerven, Steinar Lundgren, Erik Wist, Bjørn Naume, Gunhild M. Maelandsmo, Yiling Lu, Anne-Lise Boerresen-Dale, Gordon B. Mills, Olav Engebraaten. Bevacizumab potentiates the proteomic response to neoadjuvant chemotherapy in breast cancer patients: Rppa exploration of consecutive tumor samples in the NeoAva randomized phase II trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1813. doi:10.1158/1538-7445.AM2017-1813

The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer

Purpose: Chemotherapy-induced alterations to gene expression are due to transcriptional reprogramming of tumor cells or subclonal adaptations to treatment. The effect on whole-transcriptome mRNA expression was investigated in a randomized phase II clinical trial to assess the effect of neoadjuvant chemotherapy with the addition of bevacizumab.Experimental Design: Tumor biopsies and whole-transcriptome mRNA profiles were obtained at three fixed time points with 66 patients in each arm. Altogether, 358 specimens from 132 patients were available, representing the transcriptional state before treatment start, at 12 weeks and after treatment (25 weeks). Pathologic complete response (pCR) in breast and axillary nodes was the primary endpoint.Results: pCR was observed in 15 patients (23%) receiving bevacizumab and chemotherapy and 8 patients (12%) receiving only chemotherapy. In the estrogen receptor-positive patients, 11 of 54 (20%) treated with bevacizumab and chemotherapy achieved pCR, while only 3 of 57 (5%) treated with chemotherapy reached pCR. In patients with estrogen receptor-positive tumors treated with combination therapy, an elevated immune activity was associated with good response. Proliferation was reduced after treatment in both treatment arms and most pronounced in the combination therapy arm, where the reduction in proliferation accelerated during treatment. Transcriptional alterations during therapy were subtype specific, and the effect of adding bevacizumab was most evident for luminal-B tumors.Conclusions: Clinical response and gene expression response differed between patients receiving combination therapy and chemotherapy alone. The results may guide identification of patients likely to benefit from antiangiogenic therapy. Clin Cancer Res; 23(16); 4662-70. ©2017 AACR.

Implementing precision cancer medicine in the public health services of Norway: the diagnostic infrastructure and a cost estimate

OBJECTIVE

Through the conduct of an individual-based intervention study, the main purpose of this project was to build and evaluate the required infrastructure that may enable routine practice of precision cancer medicine in the public health services of Norway, including modelling of costs.

METHODS

An eligible patient had end-stage metastatic disease from a solid tumour. Metastatic tissue was analysed by DNA sequencing, using a 50-gene panel and a study-generated pipeline for analysis of sequence data, supplemented with fluorescence in situ hybridisation to cover relevant biomarkers. Cost estimations compared best supportive care, biomarker-agnostic treatment with a molecularly targeted agent and biomarker-based treatment with such a drug. These included costs for medication, outpatient clinic visits, admission from adverse events and the biomarker-based procedures.

RESULTS

The diagnostic procedures, which comprised sampling of metastatic tissue, mutation analysis and data interpretation at the Molecular Tumor Board before integration with clinical data at the Clinical Tumor Board, were completed in median 18 (8-39) days for the 22 study patients. The 23 invasive procedures (12 from liver, 6 from lung, 5 from other sites) caused a single adverse event (pneumothorax). Per patient, 0-5 mutations were detected in metastatic tumours; however, no actionable target case was identified for the current single-agent therapy approach. Based on the cost modelling, the biomarker-based approach was 2.5-fold more costly than best supportive care and 2.5-fold less costly than the biomarker-agnostic option.

CONCLUSIONS

The first project phase established a comprehensive diagnostic infrastructure for precision cancer medicine, which enabled expedite and safe mutation profiling of metastatic tumours and data interpretation at multidisciplinary tumour boards for patients with end-stage cancer. Furthermore, it prepared for protocol amendments, recently approved by the designated authorities for the second study phase, allowing more comprehensive mutation analysis and opportunities to define therapy targets.

Abstract P6-13-01: Proteomic response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Reverse phase protein array (RPPA) results from NeoAva - A randomized phase II study

BACKGROUND: Patients with HER2 negative primary tumors of ≥25 mm were treated with neoadjuvant chemotherapy (4 x FEC100 + 12 weeks of taxane-based therapy) and randomized (1:1) to receive bevacizumab or not. Mammography, ultrasound and MR imaging were used for response evaluation, in addition to the final pathology assessment after surgery.

HYPOTHESIS: RPPA proteomic analyses support identification of molecular mechanisms associated with clinical response to bevacizumab treatment.

METHODS: Tumor responses were evaluable in 132 patients; of which 66 received bevacizumab. Ratio of the tumor size at final pathology assessment, and at inclusion was calculated to obtain a continuous scale of response reflecting the percentage of tumor shrinkage in response to therapy. Tumor material was obtained at screening, 12 weeks into treatment and at surgical removal of tumors at 25 weeks. Lysates from each sample was analyzed on reverse phase protein arrays (RPPA) for expression levels of 210 proteins of which 54 were phospho-specific.

RESULTS: Several proteins were found for which expression prior to treatment reflected a better response on tumor shrinkage in the combination treatment arm (chemotherapy+bevacizumab). The proteomic response from week 0 to 12 in both treatment arms had an overall similar profile regarding up- and down-regulated proteins; however, the combination treatment (FEC100 + bevacizumab) induced a more pronounced effect on regulation of each protein. This might reflect the capability of bevacizumab therapy to potentiate the effects of the anthracyclin based chemotherapy from week 0 to 12. Conversely, from week 12-25 (taxane-based therapy + bevacizumab) this effect was lost or even reversed, except for certain phosphoproteins where potentiation imposed by bevacizumab was sustained throughout the whole treatment period. We are in the process of analyzing the impact of phosphorylation and thus protein activation states on treatment response. Furthermore, tumors with low hormone receptor pathway score demonstrated a better response in the combination treatment (chemotherapy+bevacizumab). Additionally, in these good responders the hormone signaling pathway was significantly upregulated during treatment. Further investigations are conducted to determine if this was due to selective ablation of hormone receptor negative tumor cells, or a re-programming of the molecular phenotype of cells present prior to treatment. The above mentioned results have potentially important clinical relevance and will be further investigated with respect to subtypes and the biological pathways affected by antiangiogenic therapy.

Citation Format: Haugen MH, Lindgjærde OC, Krohn M, Zhao W, Lindholm EM, Silwal-Pandit L, Borgen E, Garred Ø, Fangberget A, Holmen MM, Schlichting E, Skjerven H, Lundgren S, Wist E, Naume B, Mælandsmo GM, Lu Y, Børresen-Dale A-L, Mills GB, Engebråten O. Proteomic response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Reverse phase protein array (RPPA) results from NeoAva - A randomized phase II study [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-13-01.

TP53 Mutations in Breast and Ovarian Cancer

Breast and ovarian cancers are the second and fifth leading causes of cancer deaths among women. Both breast and ovarian cancers are highly heterogeneous and are presented with diverse morphology, natural history, and response to therapy. In recent years, international efforts have led to extensive molecular characterization of both breast and ovarian tumors and identified biologically and clinically relevant subtypes of the diseases based on these molecular features. The role of TP53 in tumor initiation and progression is context dependent, and abrogation of the TP53 pathway seems to be essential for the development of basal-like breast cancers and high-grade serous ovarian cancers. These subtypes of breast and ovarian cancer show several genomic similarities including high frequency of TP53 mutation, which seems to be an early, initiating, and driving alteration in these cancer subtypes.

Abstract 3268: Proteomic response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Reverse phase protein array (RPPA) results from NeoAva - a randomized phase II study

BACKGROUND: In this phase II clinical trial, patients with HER2 negative primary tumors of ≥25 mm were treated with neoadjuvant chemotherapy (4 x FEC100 + 12 weeks of taxane-based therapy) and randomized (1:1) to receive bevacizumab or no bevacizumab. Mammography, ultrasound and MR imaging were used for response evaluation, in addition to final pathology assessment.

HYPOTHESIS: RPPA proteomic analyses support identification of molecular mechanisms associated with clinical response to bevacizumab treatment.

METHODS: Tumor responses were evaluable in 132 patients; of which 66 received bevacizumab. Ratio of the tumor size at final pathology assessment, and at inclusion was calculated to obtain a continuous scale of response reflecting the percentage of tumor shrinkage in response to therapy. Tumor material was obtained at screening, 12 weeks into treatment and at surgical removal of tumors at 25 weeks. Lysates from each sample was analyzed on reverse phase protein arrays (RPPA) for expression levels of 210 proteins of which 54 were phospho-specific. Data from protein analyses was compared to previously generated mRNA expression data.

RESULTS: Several proteins were found for which expression prior to treatment (week 0) reflected a better response on tumor shrinkage in the combination treatment arm (chemotherapy+bevacizumab): E.g. good responders had lower PDGFR-beta expression, and this was also observed at the mRNA level, while this result was not identified in the mono treatment arm (chemotherapy alone) on either level. The proteomic response from week 0 to 12 in both treatment arms had an overall similar profile regarding up- and down-regulated proteins; however, the combination treatment (FEC100 + bevacizumab) induced substantially more effect on regulation of each protein. This might reflect the capability of bevacizumab treatment to potentiate the effects of the anthracyclin based chemotherapy from week 0 to 12. Conversely, from week 12-25 (taxane-based therapy + bevacizumab) this effect was lost or even reversed, and reveals a possible need for further studies investigating changes in protein expression and correlation to response of a given treatment. Of particular interest were proteins that switched direction of regulation between the FEC and taxane-based regimes, however, these effects were not confined to the combination treatment and thus probably not due to the added bevacizumab. We are in the process of analyzing the impact of phosphorylation and thus protein activation states on treatment response. The above mentioned results have potentially important clinical relevance and will be further investigated with respect to subtypes and the biological pathways affected by antiangiogenic therapy.

Citation Format: Mads H. Haugen, Ole Christian Lingjaerde, Marit Krohn, Evita M. Lindholm, Laxmi Silwal-Pandit, Elin Borgen, Øystein Garred, Anne Fangberget, Marit M. Holmen, Ellen Schlichting, Helle Skjerven, Steinar Lundgren, Erik Wist, Bjoern Naume, Gunhild M. Maelandsmo, Yiling Lu, Anne-Lise Boerresen-Dale, Gordon B. Mills, Olav Engebraaten. Proteomic response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Reverse phase protein array (RPPA) results from NeoAva - a randomized phase II study. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3268.

Abstract LB-337: Systemic shift in genomic aberrations in breast carcinomas during neoadjuvant chemotherapy in combination with bevacizumab

A time course study was designed to investigate the dynamics of copy number aberrations in tumor DNA during treatment of breast cancer patients. A phase II randomized clinical trial of Her2 negative breast cancer patients was conducted, with patients being treated with neoadjuvant chemotherapy (FEC and taxane), with or without bevacizumab. Serial biopsies were obtained at time of diagnosis, at 12 weeks after treatment with FEC +/- bevacizumab, and at 25 weeks after treatment with taxane +/- bevacizumab. Tumor DNA alterations and tumor percentage were studied over time, and substantial differences were observed with some tumors changing mainly between diagnosis and 12 weeks (after the FEC cycle), others between 12 and 25 weeks (taxanes), and still others changing in both time periods. In both treatment arms, good responders (GR) and non-responders (NR) displayed significant difference in genomic instability index (GII) at time of diagnosis. In the Combination arm at time of diagnosis, 25 loci harbored copy number alterations, which were significantly different between the GR and NR. An inverse aberration pattern was observed between the two extreme response groups at 6p22-p12 for patients in the Combination arm. In most cases, tumors that retained aberrations at all time points did not decrease in size. Signs of subclonal reduction were observed, with some aberrations disappearing and others being retained during treatment. In both treatment arms an increase in subclonal amplification was observed at 6p21.1, the locus which contains the VEGFA gene targeted by bevacizumab and was associated with good response. Significant decrease of frequency of subclones carrying gains at 17q21.32-q22 was observed at 12 week, with the peak occurring at TMEM100, an ALK1 receptor signaling-dependent gene essential for vasculogenesis. This implies that cells bearing amplifications of TMEM100 are particularly sensitive to the treatment regime. Taken together, these results suggest that heterogeneity and subclonal architecture influence the response to targeted treatment in combination with chemotherapy, with possible implications for clinical decision making and monitoring of treatment efficacy.

Citation Format: Elen K. Møller, Silje Nord, David Wedge, Ole Christian Lngjærde, Laxmi Silwal-Pandit, Hedda vdL Gythfeld, Hans Kristian M. Vollan, Thomas Fleischer, Marit Krohn, Ellen Schlichting, Elin Borgen, Øystein Garred, Marit M. Holmen, Erik Wist, Bjørn Naume, Peter V. Loo, Anne-Lise Børresen-Dale, Olav Engebråten, Vessela Kristensen. Systemic shift in genomic aberrations in breast carcinomas during neoadjuvant chemotherapy in combination with bevacizumab. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-337.

TP53 Mutation Spectrum in Smokers and Never Smoking Lung Cancer Patients

Background:TP53 mutations are among the most common mutations found in lung cancers, identified as an independent prognostic factor in many types of cancers. The purpose of this study was to investigate the frequency and prognostic impact of TP53 mutations in never-smokers and in different histological subtypes of lung cancer.

Methods: We analyzed tumor tissue from 394 non-small cell carcinomas including adenocarcinomas (n = 229), squamous cell carcinomas (n = 112), large cell carcinomas (n = 30), and others (n = 23) for mutations in TP53 by the use of Sanger sequencing (n = 394) and next generation sequencing (n = 100).

Results:TP53 mutations were identified in 47.2% of the samples, with the highest frequency (65%) of mutations among squamous cell carcinomas. Among never-smokers, 36% carried a TP53 mutation, identified as a significant independent negative prognostic factor in this subgroup. For large cell carcinomas, a significantly prolonged progression free survival was found for those carrying a TP53 mutation. In addition, the frequency of frameshift mutations was doubled in squamous cell carcinomas (20.3%) compared to adenocarcinomas (9.1%).

Conclusion:TP53 mutation patterns differ between the histological subgroups of lung cancers, and are also influenced by smoking history. This indicates that the histological subtypes in lung cancer are genetically different, and that smoking-induced TP53 mutations may have a different biological impact than TP53 mutations occurring in never-smokers.

Mutant p53 cooperates with the SWI/SNF chromatin remodeling complex to regulate VEGFR2 in breast cancer cells

In this study, Pfister et al. identified a new mutant p53 target gene, VEGFR2, and demonstrated that mutant p53 stimulates expression of VEGFR2 by cooperating with the SWI/SNF chromatin remodeling complex to superactivate the VEGFR2 gene. They also show that >50% of all mutant p53-regulated gene expression is mediated by SWI/SNF, providing insight into the observation that mutant p53 alters the expression of many genes.

Mutant p53 impacts the expression of numerous genes at the level of transcription to mediate oncogenesis. We identified vascular endothelial growth factor receptor 2 (VEGFR2), the primary functional VEGF receptor that mediates endothelial cell vascularization, as a mutant p53 transcriptional target in multiple breast cancer cell lines. Up-regulation of VEGFR2 mediates the role of mutant p53 in increasing cellular growth in two-dimensional (2D) and three-dimensional (3D) culture conditions. Mutant p53 binds near the VEGFR2 promoter transcriptional start site and plays a role in maintaining an open conformation at that location. Relatedly, mutant p53 interacts with the SWI/SNF complex, which is required for remodeling the VEGFR2 promoter. By both querying individual genes regulated by mutant p53 and performing RNA sequencing, the results indicate that >40% of all mutant p53-regulated gene expression is mediated by SWI/SNF. We surmise that mutant p53 impacts transcription of VEGFR2 as well as myriad other genes by promoter remodeling through interaction with and likely regulation of the SWI/SNF chromatin remodeling complex. Therefore, not only might mutant p53-expressing tumors be susceptible to anti VEGF therapies, impacting SWI/SNF tumor suppressor function in mutant p53 tumors may also have therapeutic potential.

Abstract P4-11-14: Molecular response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Results from NeoAva - a randomized phase II study

The NeoAva study is a phase II clinical trial of patients with HER2 negative primary tumors of ≥25 mm treated with neoadjuvant chemotherapy (4 x FEC100 + 12 weeks of taxane-based therapy) and randomized (1:1) to receive bevacizumab or no bevacizumab. Mammography, ultrasound and MR imaging were used for response evaluation, in addition to final pathology assessment.

Tumor response were evaluable in 131 patients; of which 66 received bevacizumab in addition to chemotherapy. Tumor material was obtained at screening, 12 weeks into treatment and at surgical removal of tumors at 25 weeks. mRNA expression profiling was performed on Agilent 8x60K platform and the tumors were classified into LuminalA, LuminalB, Her2-enriched, Basal and Normal-like subtypes using the PAM50 classifier. Ratio of the tumor size at final pathology assessment, and at inclusion (by radiology assessment) was calculated to obtain a continuous scale of response reflecting the percentage of tumor shrinkage in response to therapy. Genomic Grade Index (GGI scores) based on expression profiles of 97 genes (including cell-cycle and proliferation genes) were calculated.

There were no significant differences in the tumor size, lymph node, hormone receptor status or PAM50 subtypes between the treatment arms. pCR in breast and axilla were obtained in 14 (21.1%) patients in the chemo+bev arm, and in 7 (10.6%) patients in the chemo-only arm. Tumors that obtained pCR were in higher number ER negative and TP53 mutated and exhibited Basal-like phenotype. The overall pCR rates were higher in the ER negative tumors compared to ER positive tumors {39.1% (9 of 23) vs 11.1% (12 of 108)}. However, addition of bevacizumab seemed to improve pCR in the ER positive patient group (9 vs 3) and not in ER negative patient group (5 vs 4).

On evaluating the continuous response variable, ER status, TP53 mutation status and PAM50 subtypes were significantly associated to response (p &lt; 0.001). GGI scores were highly correlated to response (p&lt; 0.001), i. e tumors with higher GGI scores showed better response. Importantly, when the chemo+bev and the chemo-only arms were evaluated separately, although similar trend of associations was observed in both arms, the associations were found to be enhanced in the chemo+bev arm.

Next, we evaluated a shift in PAM50 subtypes across the timepoints. A shift towards a better prognosis group, i.e Luminal A or Normal-like profile was observed in response to therapy. Distribution of Luminal A and Normal-like tumors at week 25, (and not at screening or week 12) was significantly different in the chemo+bev vs chemo-only group (p = 0.026, Fisher’s exact test).

GGI scores regressed across timepoints reflecting the loss of aggressive and proliferating component of the tumors in response to therapy. GGI scores in the chemo+bev group became significantly lower (p &lt; 0.01) already at week 12. This suggests that the removal of the proliferating component of the tumors by chemotherapy is accelerated and improved by addition of bevacizumab.

These results, with potentially important clinical relevance will be further investigated with respect to subtypes and the molecular changes induced by antiangiogenic therapy.

Citation Format: Olav Engebraaten, Laxmi Silwal-Pandit, Marit Krohn, Elen K Møller, Silje Nord, Thomas Fleischer, Hedda von der Lippe Gythfelt, Elin Borgen, Øystein Garred, Anne Fangberget, Marit Muri Holmen, Ellen Schlichting, Helle Skjerven, Steinar Lundgren, Vessela N Kristensen, Ole Christian Lingjaerde, Erik Wist, Bjørn Naume, Anne-Lise Børresen-Dale. Molecular response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Results from NeoAva - a randomized phase II study [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 P4-11-14.

Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53

Lymphocytic infiltration is associated with better prognosis in several epithelial malignancies including breast cancer. The tumor suppressor TP53 is mutated in approximately 30% of breast adenocarcinomas, with varying frequency across molecular subtypes. In this study of 1,420 breast tumors, we tested for interaction between TP53 mutation status and tumor subtype determined by PAM50 and integrative cluster analysis. In integrative cluster 10 (IC10)/basal-like breast cancer, we identify an association between lymphocytic infiltration, determined by an expression score, and retention of wild-type TP53. The expression-derived score agreed with the degree of lymphocytic infiltration assessed by pathologic review, and application of the Nanodissect algorithm was suggestive of this infiltration being primarily of cytotoxic T lymphocytes (CTL). Elevated expression of this CTL signature was associated with longer survival in IC10/Basal-like tumors. These findings identify a new link between the TP53 pathway and the adaptive immune response in estrogen receptor (ER)-negative breast tumors, suggesting a connection between TP53 inactivation and failure of tumor immunosurveillance.

IMPLICATIONS

The association of lymphocytic invasion of ER-negative breast tumors with the retention of wild-type TP53 implies a novel protective connection between TP53 function and tumor immunosurveillance.

TP53 mutation spectrum in breast cancer is subtype specific and has distinct prognostic relevance

PURPOSE

In breast cancer, the TP53 gene is frequently mutated and the mutations have been associated with poor prognosis. The prognostic impact of the different types of TP53 mutations across the different molecular subtypes is still poorly understood. Here, we characterize the spectrum and prognostic significance of TP53 mutations with respect to the PAM50 subtypes and integrative clusters (IC).

EXPERIMENTAL DESIGN

TP53 mutation status was obtained for 1,420 tumor samples from the METABRIC cohort by sequencing all coding exons using the Sanger method.

RESULTS

TP53 mutations were found in 28.3% of the tumors, conferring a worse overall and breast cancer-specific survival [HR = 2.03; 95% confidence interval (CI), 1.65-2.48, P < 0.001], and were also found to be an independent marker of poor prognosis in estrogen receptor-positive cases (HR = 1.86; 95% CI, 1.39-2.49, P < 0.001). The mutation spectrum of TP53 varied between the breast cancer subtypes, and individual alterations showed subtype-specific association. TP53 mutations were associated with increased mortality in patients with luminal B, HER2-enriched, and normal-like tumors, but not in patients with luminal A and basal-like tumors. Similar observations were made in ICs, where mutation associated with poorer outcome in IC1, IC4, and IC5. The combined effect of TP53 mutation, TP53 LOH, and MDM2 amplification on mortality was additive.

CONCLUSION

This study reveals that TP53 mutations have different clinical relevance in molecular subtypes of breast cancer, and suggests diverse roles for TP53 in the biology underlying breast cancer development.

Abstract P4-14-01: A time course study of genomic instability in breast cancer patients receiving neoadjuvant therapy with or without bevacizumab

Tumor heterogeneity is an area of intense research, revealing tumors with high complexity consisting of different subclones and infiltrating cells. Identification of subclones that are resistant to therapy may be critical to improve treatment outcome.

The NeoAva study is a randomized phase II, clinical trial of Her2 negative breast cancer patients treated in a neoadjuvant setting with chemotherapy (FEC and taxane) +/- bevacizumab. Core needle biopsies were obtained at screening and after 12 weeks, and the tumor was surgically removed after 25 weeks. DNA copy number changes in the tumors were analyzed using Affymetrix SNP Array 6.0. Allele specific copy number changes were assessed using the Allele-Specific Copy number Analysis of Tumors (ASCAT) algorithm (Van Loo, Norgard et al., PNAS 2010) and allele-specific Piecewise Constant Fitting (asPCF) algorithms (Nilsen, Liestol et al., BMC Genomics 2012). Measures of genomic instability were obtained through the complex arm-wise aberration index (CAAI) that captures local rearrangements (‘firestorms’) (Russnes, Vollan et al., Sci Transl Med 2010).

Changes in copy number aberrations between the three different time points were observed in almost all tumors. Some tumors showed a decrease in tumor percentage and aberrations after just 12 weeks of treatment, where others showed loss of aberrations only at the time of surgery (25 weeks). Most of the tumors that did retain aberrations at all time points during treatment, did not demonstrate any decrease in tumor size. Other profiles indicated subclonal reduction, where some aberrations are kept throughout treatment and others disappear. Many of the tumors shrinking in size showed fewer whole arm aberrations than before treatment, but retained their focal amplicons. Some of the tumor aberrations seem to disappear after 12 weeks, but to reappear after 25 weeks, but with the addition of novel aberration.

Complex rearrangements were identified in 67% of tumors before treatment. The most frequent ‘firestorms’ were found on 20p, 11q and 8p. Some events were persistent through therapy, but the majority changed. An association between complex tumor genomes and patients having progressive disease/non-responders were observed.

These results show the complex structure of a tumor and suggest that heterogeneity will influence the response to treatment. The subclonal patterns of tumors may be of great importance for clinical decision-making, as well as for monitoring treatment efficacy.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-14-01.

Abstract P4-14-02: Molecular response in breast cancer tumors treated with neoadjuvant chemotherapy with and without bevacizumab: Results from NeoAva - A randomized phase II study

Patients treated with bevacizumab in addition to regular neoadjuvant chemotherapy achieve an increased rate of pathological complete response (pCR). The molecular characteristics of responding and non-responding tumors, including how treatment combinations influence the gene expression profiles and the signaling pathways, may be useful predictors of antiangiogenic response.

The NeoAva study included patients with HER2 negative primary tumors of ≥25 mm that were randomized (1:1) to receive neoadjuvant chemotherapy (4 x FEC100 + 12 weeks of taxane-based therapy) with or without bevacizumab. Mammography, ultrasound and MR imaging were used for response evaluation, in addition to final pathology assessment.

In the first part of the study 74 patients were evaluable for tumor response. The tumor size at time of inclusion was T2, T3 and T4 in 24.3%, 67.6% and 8.1% of the patients, respectively. Lymph node metastases were detected in 56.7% of the patients at inclusion and 82.4% were hormone receptor positive. There were no significant differences in the tumor size, lymph node or hormone receptor status between the treatment arms.

The patients were randomized with bevacizumab + chemotherapy (n = 37) and treatment with chemotherapy alone (n = 37). Of the nine patients who achieved pCR in breast and axilla (12.2%), seven patients received bevacizumab (7/37), while two were treated with chemotherapy alone (2/37). Four of the patients with pCR were hormone receptor negative, of which three received bevacizumab. Of the remaining five hormone receptor positive tumors that achieved complete response, four received bevacizumab.

In the second part of the study we evaluated gene expression signatures by RNA microarray and the time-response of pathways to treatment, using pathway analysis that integrates copy number and gene expression (Paradigm). Biopsies for molecular analyses were collected before therapy, after 12 weeks, and at surgery. Treatment associated gene expression changes to chemotherapy were subtracted, and bevacizumab associated differential expression was observed for 1069 genes. Furthermore, molecular profiling of the tumor tissue was performed at DNA level by copy number analysis (Affymetrix, SNP6.0) and mRNA level by gene expression arrays(Agilent 60K). At the screening time point, we found high proliferation through the activity of cyclin E and B and the transcription factors E2F1 and FOXM1. At 12 weeks, there was a strong increase in predicted p53 signaling, due to increased activity of downstream target genes. The 12 week timepoint was also characterized by an increase of Calmodulin 1, MAPK3, as well as Peroxisome proliferator-activated receptor alpha (PPAR-alpha), and both trends continued to the 25 week time point. At 25 weeks, there were broad increases in ERK1/2, JUN, and FOS signaling. The 25 week timepoint also showed a T-cell response signature that from increased activity of GATA3, IL6/IL6R, IL4, and NFATC1 and NFATC2. These results suggest that there are measurable and strongly significant aberrations in molecular activity during treatment, which may be useful to monitor treatment response.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-14-02.

Abstract P5-17-02: Molecular response in breast cancer tumors treated with neoadjuvant chemotherapy with and without bevacizumab: Results from NeoAva - a randomized phase II study

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Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-17-02.