Abstract 6317: Molecular subtyping in prostate cancer associate with outcomes to abiraterone and ipatasertib treatment from the phase III IPATential150 trial

Prostate cancer is a heterogeneous disease and genomic subtyping offers an opportunity to better understand underlying disease biology. Here, we performed transcriptional profiling by RNA-Seq (n=582) and targeted genomic sequencing by FoundationONE CDx (n=743) from prostate cancer tumor specimens in the phase III IPATential150 trial of first-line ipatasertib (Ipat) plus abiraterone (Abi) in metastatic castration-resistant prostate cancer (N=1101). Unsupervised transcriptomic analysis of the 582 samples with RNA-Seq with Nonnegative Matrix Factorization (NMF) reveals four consensus subtypes. This includes an immune/cell cycle-high, an AR signature/cell cycle-high, a stroma program-enriched, and an ERG fusion-enriched subtype. Subgroups of patients with immune/cell cycle-high and AR signature/cell cycle-high tumors had the shortest radiographic progression-free survival (rPFS) and were characterized by high MYC and cell cycle-related gene signatures. Patients with AR signature/cell cycle-high tumors showed the greatest increase in rPFS with Ipat + Abi vs. Placebo (Pbo) + Abi (HR = 0.58).

Cluster n Enriched processes Median rPFS (Pbo + Abi) (months, 95% CI) Median rPFS (Ipat + Abi) (months, 95% CI) HR (95% CI) NMF1 84 Immune processes, metabolism, cell cycle 10.3 (8.3 - 12.7) 13.9 (10.9 - 16.4) 0.77 (0.47 - 1.28) NMF2 165 Androgen response signature, cell cycle, MYC signature 11.9 (8.8 - 16.5) 20.9 (16.4 - NA) 0.58 (0.38 - 0.90) NMF3 156 Fibroblast, Wnt, Notch, Hedgehog, TGFb 20.0 (16.4 - NA) 22.3 (15.6 - 24.9) 0.96 (0.59 - 1.56) NMF4 177 ERG fusion 18.4 (13.8 - 23.8) 24.7 (16.2 - NA) 0.78 (0.50 - 1.20)

Citation Format: Zhen Shi, Malgorzata Nowicka, Johann de Bono, Kim N. Chi, Christopher Sweeney, Cora N. Sternberg, David Olmos, Sergio Bracarda, Christophe Massard, Nobuaki Matsubara, Josep Garcia, Geng Chen, Matthew Wongchenko, Shahneen K. Sandhu. Molecular subtyping in prostate cancer associate with outcomes to abiraterone and ipatasertib treatment from the phase III IPATential150 trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6317.

PI3K/AKT pathway biomarkers analysis from the phase III IPATential150 trial of ipatasertib plus abiraterone in metastatic castration-resistant prostate cancer

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Background: In IPATential150 (NCT03072238), ipatasertib (ipat) + abiraterone (abi) as first-line treatment for metastatic castration-resistant prostate cancer (mCRPC) significantly reduced the risk for disease worsening or death vs placebo (pbo) + abi in patients (pts) with tumors with PTEN loss by immunohistochemistry (IHC; HR, 0.77 [95% CI: 0.61, 0.98]; P = 0.0335) but not in the intention-to-treat population (de Bono, ESMO 2020). In patients with PTEN loss tumors by IHC, median radiographic progression-free survival (rPFS) was 16.5 mo (95% CI: 13.9, 17.0) with pbo + abi and 18.5 mo (95% CI: 16.3, 22.1) with ipat + abi. Here, we present exploratory analyses evaluating putative biomarker associations with rPFS. Methods: Before randomization, tumor samples ( > 90% archival) were tested for PTEN loss by VENTANA PTEN (SP218) IHC assay (N = 1101). PTEN loss was pre-defined as ≥ 50% of tumor cells with no specific cytoplasmic IHC staining. Exploratory analysis evaluated different IHC staining cutoffs. Tumor genomic alterations were profiled with next-generation sequencing (NGS) using the Foundation Medicine FoundationOne CDx NGS assay (Shi, ASGO-GU 2020; n = 743 evaluable by NGS, of which n = 518 were PTEN evaluable). rPFS was determined by the investigator. Results: Consistent benefit with the combination arm vs pbo + abi was observed when PTEN loss by IHC was defined more stringently (rPFS at ≥ 60% tumor cells with PTEN loss: HR, 0.72 [95% CI, 0.56, 0.92]; ≥ 70%: HR, 0.72 [95% CI, 0.56, 0.93]; ≥ 80%: HR, 0.71 [95% CI, 0.54, 0.92]; ≥ 90%: HR, 0.72 [95% CI, 0.53, 0.97]; 100%: HR, 0.65 [95% CI, 0.39, 1.08]). In contrast, ipat + abi was not associated with improved rPFS in pts with PTEN intact by IHC tumors ( < 50% no staining; stratified HR, 0.91 [95% CI: 0.72, 1.16]); the median rPFS was 19.1 mo (95% CI: 16.4, 21.9) with pbo + abi and 19.7 mo (95% CI: 16.4, 26.3) with ipat + abi. By NGS assessment, pts with tumors with PTEN loss and with genomic alterations in PIK3CA/AKT1/PTEN had a larger magnitude of rPFS benefit with ipat + abi than pts with no detectable alterations (Table). Conclusions: Analyses of more-stringent biomarkers associated with activation of the PI3K/AKT pathway further support ipat + abi as a treatment option for first-line mCRPC with PI3K/AKT pathway alterations, a mCRPC subtype with a worse prognosis. Clinical trial information: NCT03072238. [Table: see text]

Tumour gene expression signature in primary melanoma predicts long-term outcomes

Adjuvant systemic therapies are now routinely used following resection of stage III melanoma, however accurate prognostic information is needed to better stratify patients. We use differential expression analyses of primary tumours from 204 RNA-sequenced melanomas within a large adjuvant trial, identifying a 121 metastasis-associated gene signature. This signature strongly associated with progression-free (HR = 1.63, p = 5.24 × 10-5) and overall survival (HR = 1.61, p = 1.67 × 10-4), was validated in 175 regional lymph nodes metastasis as well as two externally ascertained datasets. The machine learning classification models trained using the signature genes performed significantly better in predicting metastases than models trained with clinical covariates (pAUROC = 7.03 × 10-4), or published prognostic signatures (pAUROC < 0.05). The signature score negatively correlated with measures of immune cell infiltration (ρ = -0.75, p < 2.2 × 10-16), with a higher score representing reduced lymphocyte infiltration and a higher 5-year risk of death in stage II melanoma. Our expression signature identifies melanoma patients at higher risk of metastases and warrants further evaluation in adjuvant clinical trials.

Abstract PD14-03: Molecular mechanism of ipatasertib (IPAT) and its combination with atezolizumab (atezo) in patients (pts) with locally advanced/metastatic triple-negative breast cancer (aTNBC)

Background: Phase 3 trials (IMpassion130, KEYNOTE-355) have shown improved efficacy with the addition of immune checkpoint modulators to chemotherapy in PD-L1 +ve aTNBC. However, unmet need remains in the ~60% of pts with aTNBC who have PD-L1 -ve tumors. Preliminary data from a multicenter phase 1b study (NCT03800836) evaluating the safety and efficacy of the oral AKT inhibitor IPAT + atezo + paclitaxel/nab-paclitaxel showed promising antitumor activity (73% confirmed objective response rate) irrespective of PD-L1 status [Schmid, AACR 2019], suggesting a potential role for the triplet independent of PD-L1 status. We report on-treatment changes in the tumor microenvironment in Cohort 2.

Methods: In Cohort 2, pts with aTNBC and ≤2 prior lines of chemotherapy for aTNBC received oral IPAT 400 mg on d1-28 of cycle 1 (35-d cycle) and on d1-21 of subsequent cycles (28-d cycles). IV atezo 840 mg was given on d8 & 22 of cycle 1 and on d1 & 15 of subsequent cycles. Biopsies were collected before treatment administration during cycle 1 on d1 (C1D1) & d8 (C1D8), and on d15 of cycle 2 (C2D15). PD-L1 (VENTANA SP142 immune cell ≥1%) and CD8 expression was assessed by immunohistochemistry (IHC); % immune infiltrate was measured by H&E staining. Changes in gene expression were assessed by RNA-Seq. Gene set enrichment analysis was used to study molecular pathway activation (enrichment score [ES] &gt;0 to 1) or inhibition (ES -1 to &lt;0).

Results: In Cohort 2, 11 pts had PD-L1 -ve tumors at baseline and are included in the analyses below, 2 had PD-L1 +ve tumors and 3 were unevaluable for PD-L1. IHC analysis of serial biopsies from pts with PD-L1 -ve tumors showed a statistically significant increase in immune infiltrates (mean % infiltrates C1D8/C1D1=1.44; p=0.042) and a trend toward increased CD8 protein expression (mean CD8 % staining C1D8/C1D1=1.75; Kruskal-Wallis p=0.16) at the tumor center during the first week of single-agent IPAT compared with the baseline biopsy. An increase in PD-L1 expression (mean PD-L1 % infiltrating immune cells C2D15/C1D1=4.33; Kruskal-Wallis p=0.044) was seen during IPAT + atezo combination treatment. No significant changes in immune infiltrates or CD8 expression were observed after initiating atezo versus IPAT alone. As expected, MTORC1 activity decreased (ES=-0.43; p&lt;0.005) in response to IPAT. IPAT (± atezo) enhanced key immunogenic pathways, including antigen processing and presentation (ES=0.49; p&lt;0.005), allograft rejection (ES=0.47; p&lt;0.0001), inflammatory response (ES=0.34; p&lt;0.05), and NK cell activation (ES=0.66; p&lt;0.05). In addition, IPAT + atezo enhanced TCR signaling (ES=0.52; p&lt;0.0005) and interferon gamma response (ES=0.30; p&lt;0.05). IPAT treatment was associated with decreased expression of gene sets predicting pathway upregulation, including E2F signaling, G2M checkpoint, and MYC activity. IPAT was also associated with apoptotic pathway enrichment. Using a syngeneic melanoma mouse model, we validated clinical findings and identified additional molecular changes after treatment with IPAT and/or anti-PD-L1. To date, 3 enrolled pts achieved a partial response and 6 had stable disease. Clinical and preclinical studies are ongoing to explore associations between treatment-driven molecular changes and clinical response.

Conclusion: Inhibition of AKT signaling may remodel the microenvironment of PD-L1 -ve tumors by increasing immune infiltration, priming immune pathways, promoting tumor cell apoptosis, and inhibiting oncogenic cell proliferative pathways. To our knowledge, these are the first reports evaluating molecular changes during AKT-targeted therapy for aTNBC in the context of immunotherapy irrespective of PD-L1 status. IPAT warrants further investigation combined with atezo as treatment for PD-L1 -ve aTNBC.

Citation Format: Peter Schmid, Delphine Loirat, Peter Savas, Enrique Espinosa, Valentina Boni, Antoine Italiano, Shane White, Victor Laliman, Geraldine Strasser, Kui Lin, Karen Cheng, Aruna Mani, Matthew Wongchenko, Marie-Paule Sablin, Kalpit Shah. Molecular mechanism of ipatasertib (IPAT) and its combination with atezolizumab (atezo) in patients (pts) with locally advanced/metastatic triple-negative breast cancer (aTNBC) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD14-03.

Abstract LB-274: Primary tumor gene expression signature predicts long-term outcomes in primary melanoma: A prospective multicenter study

Purpose: Adjuvant therapies prolong survival in patients with stage III melanoma. However, biomarkers are needed to stratify patients with primary melanoma at highest risk for metastases which could help minimize exposure to potentially irreversible toxicities and allow for rational clinical trial designs in the adjuvant setting.

Methods: We analyzed data from 194 RNA-sequenced primary cutaneous melanomas from patients with stage IIB-IIIC disease recruited to the multicenter AVAST-M phase III randomized trial. By undertaking covariate-corrected differential expression between patients experiencing distant metastasis (n=89) versus no-metastases (n=105), we identified metastasis-associated genes of which 121 were externally validated and made up our predictive signature, “Cam_121”. Several machine learning classification models were trained using nested leave-one-out cross validation (LOOCV) to test the signature's capacity to predict metastases. Univariate and multivariate Cox proportional hazard regression survival analyses were performed. The signatures' predictive accuracy was further externally validated in an independent population-controlled cohort study measuring melanoma-specific survival (Leeds Melanoma Cohort, n=687).

Results: The signature distinguished patients with distant recurrence from those without across multiple machine learning models (sensitivity=0.64, specificity=0.79, accuracy=0.72, kappa=0.43) and performed significantly better than any of the models trained with the clinical covariates alone (pAccuracy =4.92x10-3), as well as those trained with predictive signatures selected from two published datasets (Decision-Dx MelanomaTM and Leeds Melanoma Cohort 150 genes). The signature also correlated with progression-free survival (PFS), overall survival (OS) and melanoma-specific survival (MSS) while retaining its predictive accuracy following multivariate correction (PFS: HR=0.49 (0.35-0.69), p=2.8x10-5, OS: HR=0.6 (0.42-0.86), p=0.005 and MSS: HR=0.57, p=8x10-5). Importantly, we found that the median signature expression score positively correlated with measures of immune cell infiltration, with a lower score representing a poorer tumor lymphocytic infiltration and worse long-term prognosis.

Conclusions: We have identified Cam_121 a primary melanoma expression signature that outperforms currently available predictive signatures. The signature confirms (using unbiased approaches) the central prognostic importance of immune cell infiltration in long-term patient outcomes and could help identify primary melanoma patients at highest risk of metastases and poor survival who might benefit most from adjuvant therapies.

Citation Format: Manik Garg, Dominique-Laurent Courturier, Nuno A. Fonseca, Matthew Wongchenko, Yibing Yan, Jeremie Nsengimana, Tim Bishop, Julia Newton-Bishop, Mark Middleton, Pippa Corrie, David J. Adams, Alvis Brazma, Roy Rabbie. Primary tumor gene expression signature predicts long-term outcomes in primary melanoma: A prospective multicenter study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-274.

FAIRLANE, a double-blind placebo-controlled randomized phase II trial of neoadjuvant ipatasertib plus paclitaxel for early triple-negative breast cancer

BACKGROUND

This hypothesis-generating trial evaluated neoadjuvant ipatasertib-paclitaxel for early triple-negative breast cancer (TNBC).

PATIENTS AND METHODS

In this randomized phase II trial, patients with early TNBC (T ≥ 1.5 cm, N0-2) were randomized 1 : 1 to receive weekly paclitaxel 80 mg/m2 with ipatasertib 400 mg or placebo (days 1-21 every 28 days) for 12 weeks before surgery. Co-primary end points were pathologic complete response (pCR) rate (ypT0/TisN0) in the intention-to-treat (ITT) and immunohistochemistry phosphatase and tensin homolog (PTEN)-low populations. Secondary end points included pCR rate in patients with PIK3CA/AKT1/PTEN-altered tumors and pre-surgery response rates by magnetic resonance imaging (MRI).

RESULTS

pCR rates with ipatasertib versus placebo were 17% versus 13%, respectively, in the ITT population (N = 151), 16% versus 13% in the immunohistochemistry PTEN-low population (N = 35), and 18% versus 12% in the PIK3CA/AKT1/PTEN-altered subgroup (N = 62). Rates of overall and complete response (CR) by MRI favored ipatasertib in all three populations (CR rate 39% versus 9% in the PIK3CA/AKT1/PTEN-altered subgroup). Ipatasertib was associated with more grade ≥3 adverse events (32% versus 16% with placebo), especially diarrhea (17% versus 1%). Higher cycle 1 day 8 (C1D8) immune score was significantly associated with better response only in placebo-treated patients. All ipatasertib-treated patients with low immune scores and a CR had PIK3CA/AKT1/PTEN-altered tumors.

CONCLUSIONS

Adding ipatasertib to 12 weeks of paclitaxel for early TNBC did not clinically or statistically significantly increase pCR rate, although overall response rate by MRI was numerically higher with ipatasertib. The antitumor effect of ipatasertib was most pronounced in biomarker-selected patients. Safety was consistent with prior experience of ipatasertib-paclitaxel. A T-cell-rich environment at C1D8 had a stronger association with improved outcomes in paclitaxel-treated patients than seen for baseline tumor-infiltrating lymphocytes. This dependency may be overcome with the addition of AKT inhibition, especially in patients with PIK3CA/AKT1/PTEN-altered tumors.

CLINICALTRIALS.GOV

NCT02301988.

Circulating tumor DNA (ctDNA) dynamics associate with treatment response and radiological progression-free survival (rPFS): Analyses from a randomized phase II trial in metastatic castration-resistant prostate cancer (mCRPC)

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Background: ctDNA can inform on prognosis, treatment response and survival. We evaluated ctDNA in serial plasma samples from patients enrolled in A.MARTIN (NCT01485861), a randomized phase II study of abiraterone with or without ipatasertib in patients with mCRPC. Methods: Blood was collected in cell-free DNA Streck tubes from 216 patients at 3 time points; baseline, C3D1 and end of treatment. Cell-free DNA (cfDNA) was extracted from plasma using a Circulating DNA Kit (Qiagen) on a QIASymphony machine (Qiagen). 25ng of extracted cfDNA was used in library preparation, constructed with a custom designed, 58 gene, QIAseq Targeted DNA panel (Qiagen) enriched for PI3K/AR pathway genes. Samples were sequenced to mean depth of 3394x on a NextSeq500 machine. Unless otherwise noted, all analyses combine patients across the 3 study arms, and reported p-values are unadjusted. Results: Baseline (BL) ctDNA positivity correlated with radiological progression-free survival (rPFS; HR: 1.8 [95% CI 1.3-2.6], p < 0.01); this association with rPFS was maintained in a multivariate cox model with > 5 baseline clinical variables (HR: 1.6 [95% CI 1.1-2.4]; p = 0.011). Patients with a C3D1 reduction in ctDNA had superior rPFS compared to patients with a C3D1 increase in ctDNA (HR: 2 [95% CI 1.3-3.2], p < 0.01). The rate of ctDNA clearance at C3D1 was higher in the Ipatasertib 400mg arm compared to placebo (56.3% versus 24.4%, p < 0.01). We find that changes in ctDNA associated with best confirmed overall response (p = 0.024); CR patients had the greatest reduction in ctDNA (mean of -23.4%), followed by PR (-16.3%), then SD (-4.1%), and lastly PD patients (-1.3%). Changes in ctDNA levels correlated with SLD changes (rs = 0.289, p = 0.05), and also PSA changes (rs = 0.33, p < 0.01). Changes in ctDNA were associated with rPFS in a multivariate cox analysis that included PSA change (p < 0.01), as well as in a separate multivariate analysis that included SLD change (p < 0.01). Lastly, we explored CNVs and observed emerging resistance mutations in progression samples, including alterations in TP53, AR, FOXA, PTEN, and PI3K/AKT pathway genes. Conclusions: ctDNA analyses may help (i) identify poorer prognosis disease at baseline, (ii) inform on treatment response (CR/PR/SD/PD) and radiological progression free survival (rPFS) in on-treatment (C3D1) samples, and (iii) can elucidate emerging resistance mechanisms at disease progression. Clinical trial information: NCT01485861 .

Biomarker analysis of the phase III IPATential150 trial of first-line ipatasertib (Ipat) plus abiraterone (Abi) in metastatic castration-resistant prostate cancer (mCRPC)

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Background: IPATential150 is a randomized trial comparing Ipat + Abi vs placebo + Abi in patients (pts) with 1L mCRPC (NCT03072238). We evaluated the potential associations between PTEN loss, genomic alterations, and country of enrollment (East Asian [EAS] vs non-EAS). Methods: Before randomization, tumor samples (archival > 90%) were centrally tested for PTEN loss by VENTANA PTEN (SP218) immunohistochemistry (IHC) assay (N = 1101). Tumor genetic alterations were profiled by Foundation Medicine FoundationOne CDx (F1CDx) NGS assay (n = 735). Results: Of 1101 pts enrolled, 521 (47%) had PTEN loss by IHC. An overall 76% agreement was observed between PTEN IHC and F1CDx. TMPRSS2 fusion, alterations in TP53 and PTEN were most frequent (28%-32%). Alterations in PIK3CA, SPOP, APC, MYC, RAD21, and genes involved in DNA damage repair, including BRCA2, CDK12, ATM, had a 5%-8% prevalence. PTEN loss (IHC) tended to co-occur with genetic alterations in TP53 and TMPRSS2. The prevalence of PTEN loss in EAS vs non-EAS pts was 35% vs 50% by IHC and 15% vs 31% by F1CDx. Alterations in CDK12, BRCA2, SPOP, and MYC were more prevalent in EAS pts, whereas alterations in TMPRSS2, PTEN, and TP53 were more prevalent in non-EAS pts. Conclusions: This analysis reveals molecular heterogeneity in prostate cancer and association between potentially actionable targets. It also suggests that EAS pts with mCRPC have a genetic profile that may be at least quantitatively different from non-EAS pts. Clinical trial information: NCT03072238. [Table: see text]

bcGST-an interactive bias-correction method to identify over-represented gene-sets in boutique arrays

MOTIVATION

Gene annotation and pathway databases such as Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes are important tools in Gene-Set Test (GST) that describe gene biological functions and associated pathways. GST aims to establish an association relationship between a gene-set of interest and an annotation. Importantly, GST tests for over-representation of genes in an annotation term. One implicit assumption of GST is that the gene expression platform captures the complete or a very large proportion of the genome. However, this assumption is neither satisfied for the increasingly popular boutique array nor the custom designed gene expression profiling platform. Specifically, conventional GST is no longer appropriate due to the gene-set selection bias induced during the construction of these platforms.

RESULTS

We propose bcGST, a bias-corrected GST by introducing bias-correction terms in the contingency table needed for calculating the Fisher's Exact Test. The adjustment method works by estimating the proportion of genes captured on the array with respect to the genome in order to assist filtration of annotation terms that would otherwise be falsely included or excluded. We illustrate the practicality of bcGST and its stability through multiple differential gene expression analyses in melanoma and the Cancer Genome Atlas cancer studies.

AVAILABILITY AND IMPLEMENTATION

The bcGST method is made available as a Shiny web application at http://shiny.maths.usyd.edu.au/bcGST/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Extended 5-Year Follow-up Results of a Phase Ib Study (BRIM7) of Vemurafenib and Cobimetinib in BRAF-Mutant Melanoma

PURPOSE

To report the 5-year overall survival (OS) landmark and the long-term safety profile of vemurafenib plus cobimetinib (BRAF plus MEK inhibition, respectively) in the BRIM7 study.

PATIENTS AND METHODS

This phase Ib, dose-finding, and expansion study evaluated combination treatment with vemurafenib and cobimetinib in two cohorts of patients with advanced BRAF ^V600-mutated melanoma: patients who were BRAF inhibitor (BRAFi)-naïve (n = 63) or patients who had progressed on prior treatment with BRAFi monotherapy [vemurafenib monotherapy-progressive disease (PD); n = 66]. Patients in the dose-escalation phase received vemurafenib at 720 or 960 mg twice daily in combination with cobimetinib at 60, 80, or 100 mg/d for 14 days on/14 days off, 21 days on/7 days off, or continuously. Two regimens were selected for expansion: vemurafenib (720 and 960 mg twice daily) and cobimetinib (60 mg/d 21/7).

RESULTS

Median OS was 31.8 months [95% confidence interval (CI), 24.5-not estimable] in the BRAFi-naïve cohort. The landmark OS rate plateaued at 39.2% at years 4 and 5 of follow-up. In the vemurafenib monotherapy-PD cohort, the median OS was 8.5 months (95% CI, 6.7-11.1), and the landmark OS rate plateaued at 14.0% from 3 years of follow-up. No increase was observed in the frequency and severity of adverse events with long-term follow-up. No new toxicities were detected, and there was no increase in the frequency of symptomatic MEK inhibitor class-effect adverse events.

CONCLUSIONS

A subset of patients with advanced BRAF ^V600-mutated melanoma treated with a combination regimen of vemurafenib and cobimetinib achieve favorable long-term outcomes.

Impact of depth of response on survival in patients treated with cobimetinib ± vemurafenib: pooled analysis of BRIM-2, BRIM-3, BRIM-7 and coBRIM

BACKGROUND

This pooled analysis investigated the prognostic value of depth of response in two cohorts of patients with BRAF^V600-mutated metastatic melanoma treated with vemurafenib or cobimetinib plus vemurafenib.

METHODS

The data were pooled from BRIM-2, BRIM-3, BRIM-7 and coBRIM. Association of depth of response with survival was estimated by Cox proportional hazards regression, adjusted for clinically relevant covariates. Depth of response was analysed in previously identified prognostic subgroups based on disease characteristics and gene signatures.

RESULTS

Greater tumour reduction and longer time to maximal response were significantly associated with longer progression-free survival (PFS) and overall survival (OS) when evaluated as continuous variables. Patients with the deepest responses had long-lasting survival outcomes (median PFS: 14 months; OS: 32 months with vemurafenib; not estimable with cobimetinib plus vemurafenib). Cobimetinib plus vemurafenib improved depth of response versus vemurafenib monotherapy regardless of other prognostic factors, including gene signatures.

CONCLUSIONS

Greater depth of response was associated with improved survival, supporting its utility as a measure of treatment efficacy in melanoma and further evaluation of its incorporation into existing prognostic models. Cobimetinib plus vemurafenib improved outcomes across quartiles of response regardless of prognostic factors or gene signatures and provided durable survival benefits in patients with deep responses.

The cancer cell proteome and transcriptome predicts sensitivity to targeted and cytotoxic drugs

This study shows that the proteomic and transcriptomic states of cancer cells are more predictive of drug sensitivity than genomic markers for most drugs, both within and across tumor types.

Tumors of different molecular subtypes can show strongly deviating responses to drug treatment, making stratification of patients based on molecular markers an important part of cancer therapy. Pharmacogenomic studies have led to the discovery of selected genomic markers (e.g., BRAF^V600E), whereas transcriptomic and proteomic markers so far have been largely absent in clinical use, thus constituting a potentially valuable resource for further substratification of patients. To systematically assess the explanatory power of different -omics data types, we assembled a panel of 49 melanoma cell lines, including genomic, transcriptomic, proteomic, and pharmacological data, showing that drug sensitivity models trained on transcriptomic or proteomic data outperform genomic-based models for most drugs. These results were confirmed in eight additional tumor types using published datasets. Furthermore, we show that drug sensitivity models can be transferred between tumor types, although after correcting for training sample size, transferred models perform worse than within-tumor–type predictions. Our results suggest that transcriptomic/proteomic signals may be alternative biomarker candidates for the stratification of patients without known genomic markers.

Phase II COLET study: Atezolizumab (A) + cobimetinib (C) + paclitaxel (P)/nab-paclitaxel (nP) as first-line (1L) treatment (tx) for patients (pts) with locally advanced or metastatic triple-negative breast cancer (mTNBC)

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Background: COLET showed that the addition of C (MEK1/2 inhibitor) to P resulted in an increased ORR (38%; Brufsky, SABCS 2017); IMpassion130 demonstrated clinical benefit with the combination of PD-L1 inhibitor A and nP as 1L tx for pts with mTNBC (Schmid, N Engl J Med, 2018). We investigated the efficacy and safety of A + C + P/nP in pts with mTNBC, as this combination may target multiple cancer immune escape mechanisms simultaneously. Methods: In the multi-stage, multi-cohort Phase II COLET study, pts with histologically confirmed mTNBC were randomized 1:1 to receive 1L tx with A 840 mg IV (d1, d15) + C 60 mg qd (d3-d23) + P 80 mg/m2 IV (d1, d8, d15; cohort 2) or + nP 100 mg/m2 (d1, d8, d15; cohort 3) in 28-day cycles until progression or toxicity. The primary endpoint (EP) was confirmed ORR per investigator-assessed RECIST 1.1. Additional EPs were DOR, PFS, OS, safety and exploratory efficacy by PD-L1 status. Results: As of 10 Aug 2018 (6.5-mo median follow-up), 63 and 62 pts were evaluable for efficacy and safety, respectively. In cohorts 2 and 3, 21 pts (66%) and 20 pts (65%) had received neo/adjuvant taxane tx, 9 pts (28%) and 6 pts (19%) had a disease-free interval of ≤12 mo, respectively. All pts had ≥1 AE; 69% and 70% had Gr 3-5 AEs and 47% and 43% had serious AEs in cohorts 2 and 3, respectively. Efficacy data for all pts and by PD-L1 expression on tumor-infiltrating immune cells (IC ≥1%; PD-L1+) are summarized in the Table. Conclusions: ORRs were similar between the A + C + P arm and A + C + nP arm. Numerically higher ORR and PFS were observed in pts with PD-L1+ disease. The combination’s safety profile was consistent with the known individual safety profiles, and A did not increase toxicity. Clinical trial information: NCT02322814. [Table: see text]

Phase Ib study of the MEK inhibitor cobimetinib (GDC-0973) in combination with the PI3K inhibitor pictilisib (GDC-0941) in patients with advanced solid tumors

Purpose We investigated the combination of the MEK inhibitor, cobimetinib, and the pan-PI3K inhibitor, pictilisib, in an open-label, phase Ib study. Experimental Design Patients with advanced solid tumors were enrolled in 3 dose escalation schedules: (1) both agents once-daily for 21-days-on 7-days-off ("21/7"); (2) intermittent cobimetinib and 21/7 pictilisib ("intermittent"); or (3) both agents once-daily for 7-days-on 7-days-off ("7/7"). Starting doses for the 21/7, intermittent, and 7/7 schedules were 20/80, 100/130, and 40/130 mg of cobimetinib/pictilisib, respectively. Nine indication-specific expansion cohorts interrogated the recommended phase II dose and schedule. Results Of 178 enrollees (dose escalation: n = 98), 177 patients were dosed. The maximum tolerated doses for cobimetinib/pictilisib (mg) were 40/100, 125/180, and not reached, for the 21/7, intermittent, and 7/7 schedules, respectively. Six dose-limiting toxicities included grade 3 (G3) elevated lipase, G4 elevated creatine phosphokinase, and G3 events including fatigue concurrent with a serious adverse event (SAE) of diarrhea, decreased appetite, and SAEs of hypersensitivity and dehydration. Common drug-related adverse events included nausea, fatigue, vomiting, decreased appetite, dysgeusia, rash, and stomatitis. Pharmacokinetic parameters of the drugs used in combination were unaltered compared to monotherapy exposures. Confirmed partial responses were observed in patients with BRAF-mutant melanoma (n = 1) and KRAS-mutant endometrioid adenocarcinoma (n = 1). Eighteen patients remained on study ≥6 months. Biomarker data established successful blockade of MAP kinase (MAPK) and PI3K pathways. The metabolic response rate documented by FDG-PET was similar to that observed with cobimetinib monotherapy. Conclusions Cobimetinib and pictilisib combination therapy in patients with solid tumors had limited tolerability and efficacy.

Distinct Molecular Profiles and Immunotherapy Treatment Outcomes of V600E and V600K BRAF-Mutant Melanoma

PURPOSE

BRAF V600E and V600K melanomas have distinct clinicopathologic features, and V600K appear to be less responsive to BRAFi±MEKi. We investigated mechanisms for this and explored whether genotype affects response to immunotherapy.

EXPERIMENTAL DESIGN

Pretreatment formalin-fixed paraffin-embedded tumors from patients treated with BRAFi±MEKi underwent gene expression profiling and DNA sequencing. Molecular results were validated using The Cancer Genome Atlas (TCGA) data. An independent cohort of V600E/K patients treated with anti-PD-1 immunotherapy was examined.

RESULTS

Baseline tissue and clinical outcome with BRAFi±MEKi were studied in 93 patients (78 V600E, 15 V600K). V600K patients had numerically less tumor regression (median, -31% vs. -52%, P = 0.154) and shorter progression-free survival (PFS; median, 5.7 vs. 7.1 months, P = 0.15) compared with V600E. V600K melanomas had lower expression of the ERK pathway feedback regulator dual-specificity phosphatase 6, confirmed with TCGA data (116 V600E, 17 V600K). Pathway analysis showed V600K had lower expression of ERK and higher expression of PI3K-AKT genes than V600E. Higher mutational load was observed in V600K, with a higher proportion of mutations in PIK3R1 and tumor-suppressor genes. In patients treated with anti-PD-1, V600K (n = 19) had superior outcomes than V600E (n = 84), including response rate (53% vs. 29%, P = 0.059), PFS (median, 19 vs. 2.7 months, P = 0.049), and overall survival (20.4 vs. 11.7 months, P = 0.081).

CONCLUSIONS

BRAF V600K melanomas appear to benefit less from BRAFi±MEKi than V600E, potentially due to less reliance on ERK pathway activation and greater use of alternative pathways. In contrast, these melanomas have higher mutational load and respond better to immunotherapy.

Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy

Cancer immunotherapies provide survival benefits in responding patients, but many patients fail to respond. Identifying the biology of treatment response and resistance are a priority to optimize drug selection and improve patient outcomes. We performed transcriptomic and immune profiling on 158 tumor biopsies from melanoma patients treated with anti-PD-1 monotherapy (n = 63) or combined anti-PD-1 and anti-CTLA-4 (n = 57). These data identified activated T cell signatures and T cell populations in responders to both treatments. Further mass cytometry analysis identified an EOMES⁺CD69⁺CD45RO⁺ effector memory T cell phenotype that was significantly more abundant in responders to combined immunotherapy compared with non-responders (n = 18). The gene expression profile of this population was associated with longer progression-free survival in patients treated with single agent and greater tumor shrinkage in both treatments.

Abstract CT041: Primary results from FAIRLANE (NCT02301988), a double-blind placebo (PBO)-controlled randomized phase II trial of neoadjuvant ipatasertib (IPAT) + paclitaxel (PAC) for early triple-negative breast cancer (eTNBC)

Purpose: This hypothesis-generating trial evaluated neoadjuvant IPAT + PAC for eTNBC.

Methods: Patients (pts) with eTNBC, T ≥1.5 cm and N0-2 were randomized 1:1 to receive 12 wks of weekly PAC 80 mg/m² + either IPAT 400 mg or PBO d1-21 q28d before surgery. Investigators chose adjuvant therapy. Stratification factors were PTEN status (Targos IHC), nodal status and tumor size. Co-primary endpoints were pathologic complete response (pCR) rate (ypT0/TisN0) in the intent-to-treat (ITT) and PTEN-low (Ventana IHC) populations. Secondary endpoints included pCR rate in pts with PIK3CA/AKT1/PTEN-altered tumors (NGS; Foundation Medicine), pre-surgery clinical response rates by MRI and safety.

Results: From Feb 2015 to Mar 2017, 151 pts were randomized. Most had T1/2 (87%) N0 (65%) tumors. At the final analysis (9 Nov 2017), 132 pts (87%) had completed surgery. In all 3 populations, rates of pCR, overall clinical response and complete response (CR) by MRI favored IPAT (Table). IPAT was associated with more grade ≥3 AEs (32% vs 16% with PBO), especially diarrhea (17% vs 1%). AEs leading to IPAT/PBO discontinuation (9% vs 3%) or dose reduction (16% vs 1%) or PAC interruption (20% vs 12%) were more common with IPAT but median PAC dose intensity was 100% (IQR 100-100%) in both arms. Incidences of neuropathy (57% vs 61%) and neutropenia (14% vs 13%) were similar with IPAT vs PBO.

Conclusions: Adding IPAT to PAC for eTNBC showed a small non-significant increase in pCR rate. The anti-tumor effect of IPAT was most pronounced in biomarker-selected pts: CR rates were 32% vs 6% in pts with PTEN-low tumors and 39% vs 9% in PIK3CA/AKT1/PTEN-altered tumors. Safety was consistent with prior IPAT + PAC experience. Similar to LOTUS in metastatic TNBC, FAIRLANE results support further evaluation of IPAT + PAC in pts with PIK3CA/AKT1/PTEN-altered tumors. A comprehensive translational research program is ongoing.

TableEndpointITTPTEN-low (by IHC)PIK3CA/AKT1/PTEN-altered (by NGS)IPAT + PACPBO + PACIPAT + PACPBO + PACIPAT + PACPBO + PACpCR rate (ypT0/TisN0)13/76 (17.1%)10/75 (13.3%)3/19 (15.8%)2/16 (12.5%)5/28 (17.9%)4/34 (11.8%)Difference (95% CI)3.8% (-9.0 to 16.5)3.3% (-25.5 to 32.1)6.1% (-15.0 to 27.2)Overall clinical response ratea by MRI51/76 (67.1%)42/75 (56.0%)14/19 (73.7%)8/16 (50.0%)19/28 (67.9%)18/34 (52.9%)Difference (95% CI)11.1% (-5.6 to 27.9)23.7% (-13.6 to 60.9)14.9% (-12.4% to 42.3%)CR rateb by MRI21/76 (27.6%)10/75 (13.3%)6/19 (31.6%)1/16 (6.3%)11/28 (39.3%)3/34 (8.8%)aUnconfirmed complete or partial response. bUnconfirmed complete response.

Citation Format: Mafalda Oliveira, Cristina Saura, Isabel Calvo, Jay Andersen, José Luis Passos Coelho, Miguel Gil Gil, Begoña Bermejo, Debra A. Patt, Eva Ciruelos, Stina M. Singel, Daniel J. Maslyar, Matthew Wongchenko, Wai Y. Chan, Amy V. Kapp, Lorena de la Peña, José Baselga, Steven J. Isakoff. Primary results from FAIRLANE (NCT02301988), a double-blind placebo (PBO)-controlled randomized phase II trial of neoadjuvant ipatasertib (IPAT) + paclitaxel (PAC) for early triple-negative breast cancer (eTNBC) [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 CT041.

Abstract 2582: A novel PI3K/Akt-pathway activation biomarker using comprehensive genomic profiling (CGP) for clinical trial assay

Introduction Patients with PI3K/Akt-pathway activation may be sensitive to selective Akt-inhibitors that are currently under development. We have developed a novel next-generation sequencing (NGS)-based composite biomarker assay that identifies patients with PI3K/Akt-pathway activated tumors by identifying activating PIK3CA and AKT1 alterations, and inactivating alterations in PTEN. This assay was analytically validated, and applied to triple-negative breast cancer (TNBC) patients in the LOTUS trial (NCT02162719), a placebo-controlled phase II clinical trial to assess the safety and efficacy of adding ipatasertib to paclitaxel treatment in patients with metastatic TNBC (Kim et al., 2017).

Methods DNA extracted from FFPE tumor tissue underwent whole-genome shotgun library construction and hybridization-based capture, followed by sequencing using Illumina HiSeq 4000. Sequence data were processed using a proprietary analysis pipeline designed to detect base substitutions, indels, copy number alterations, genomic rearrangements, microsatellite instability, and tumor mutational burden. The assay further evaluated the PI3K/Akt-pathway activation biomarker status that consists of six features: 1-2) AKT1 and PIK3CA activating mutations, 3) PTEN homozygous deletion, 4) PTEN heterozygous deletion (HE), 5) PTEN dominant negative mutations, and 6) bi-allelically inactivated (BI) PTEN mutations defined as mutation plus loss of heterozygosity (LOH). We evaluated the limit of detection (LoD) and the precision of the biomarker for two novel genomic features: HE and BI, with the other four features previously validated.

Results Analytical validation of novel biomarker features: The LoD of detecting PTEN HE and BI was determined to be 30%, the lowest tumor content at which the features can be detected at 90% probability. In the precision study, 100% (81/81) agreement was achieved across different replicates within the same sequencer run and across different sequencer runs for biomarker positive samples, demonstrating high reproducibility in calling PTEN HE and BI.

Conclusions We developed and analytically validated an NGS-based assay that identifies complex and novel genomic alterations (heterozygous deletion and bi-allelic inactivation) in PTEN that is part of a composite PI3K/Akt-pathway activation biomarker. This assay identified patients that appeared to derive greater benefit in the Phase II LOTUS study as compared to using PTEN IHC to only identify patients with PTEN protein loss (Kim et al., 2017). This assay could be generalized to identify other biomarkers with similar types of genetic alterations. It also demonstrates that NGS-based CGP can broaden the intent to treat population to be more specifically related to the mechanism of action of a drug, while also being more selective to patients with potential to respond.

Citation Format: Yuting He, Matthew Wongchenko, Joel Skoletsky, Christine Burns, Yali Li, Paula Maness, Doris Kim, Doron Lipson, Philip Stephens, Vincent Miller, Jeffrey Ross, Steven Gendreau, James Sun. A novel PI3K/Akt-pathway activation biomarker using comprehensive genomic profiling (CGP) for clinical trial assay [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 2582.

A transcriptional MAPK Pathway Activity Score (MPAS) is a clinically relevant biomarker in multiple cancer types

KRAS- and BRAF-mutant tumors are often dependent on MAPK signaling for proliferation and survival and thus sensitive to MAPK pathway inhibitors. However, clinical studies have shown that MEK inhibitors are not uniformly effective in these cancers indicating that mutational status of these oncogenes does not accurately capture MAPK pathway activity. A number of transcripts are regulated by this pathway and are recurrently identified in genome-based MAPK transcriptional signatures. To test whether the transcriptional output of only 10 of these targets could quantify MAPK pathway activity with potential predictive or prognostic clinical utility, we created a MAPK Pathway Activity Score (MPAS) derived from aggregated gene expression. In vitro, MPAS predicted sensitivity to MAPK inhibitors in multiple cell lines, comparable to or better than larger genome-based statistical models. Bridging in vitro studies and clinical samples, median MPAS from a given tumor type correlated with cobimetinib (MEK inhibitor) sensitivity of cancer cell lines originating from the same tissue type. Retrospective analyses of clinical datasets showed that MPAS was associated with the sensitivity of melanomas to vemurafenib (HR: 0.596) and negatively prognostic of overall or progression-free survival in both adjuvant and metastatic CRC (HR: 1.5 and 1.4), adrenal cancer (HR: 1.7), and HER2+ breast cancer (HR: 1.6). MPAS thus demonstrates potential clinical utility that warrants further exploration.

Association of body-mass index and outcomes in patients with metastatic melanoma treated with targeted therapy, immunotherapy, or chemotherapy: a retrospective, multicohort analysis

BACKGROUND

Obesity has been linked to increased mortality in several cancer types; however, the relation between obesity and survival outcomes in metastatic melanoma is unknown. The aim of this study was to examine the association between body-mass index (BMI) and progression-free survival or overall survival in patients with metastatic melanoma who received targeted therapy, immunotherapy, or chemotherapy.

METHODS

This retrospective study analysed independent cohorts of patients with metastatic melanoma assigned to treatment with targeted therapy, immunotherapy, or chemotherapy in randomised clinical trials and one retrospective study of patients treated with immunotherapy. Patients were classified according to BMI, following the WHO definitions, as underweight, normal, overweight, or obese. Patients without BMI and underweight patients were excluded. The primary outcomes were the associations between BMI and progression-free survival or overall survival, stratified by treatment type and sex. We did multivariable analyses in the independent cohorts, and combined adjusted hazard ratios in a mixed-effects meta-analysis to provide a precise estimate of the association between BMI and survival outcomes; heterogeneity was assessed with meta-regression analyses. Analyses were done on the predefined intention-to-treat population in the randomised controlled trials and on all patients included in the retrospective study.

FINDINGS

The six cohorts consisted of a total of 2046 patients with metastatic melanoma treated with targeted therapy, immunotherapy, or chemotherapy between Aug 8, 2006, and Jan 15, 2016. 1918 patients were included in the analysis. Two cohorts containing patients from randomised controlled trials treated with targeted therapy (dabrafenib plus trametinib [n=599] and vemurafenib plus cobimetinib [n=240]), two cohorts containing patients treated with immunotherapy (one randomised controlled trial of ipilimumab plus dacarbazine [n=207] and a retrospective cohort treated with pembrolizumab, nivolumab, or atezolizumab [n=331]), and two cohorts containing patients treated with chemotherapy (two randomised controlled trials of dacarbazine [n=320 and n=221]) were classified according to BMI as normal (694 [36%] patients), overweight (711 [37%]), or obese (513 [27%]). In the pooled analysis, obesity, compared with normal BMI, was associated with improved survival in patients with metastatic melanoma (average adjusted hazard ratio [HR] 0·77 [95% CI 0·66-0·90] for progression-free survival and 0·74 [0·58-0·95] for overall survival). The survival benefit associated with obesity was restricted to patients treated with targeted therapy (HR 0·72 [0·57-0·91] for progression-free survival and 0·60 [0·45-0·79] for overall survival) and immunotherapy (HR 0·75 [0·56-1·00] and 0·64 [0·47-0·86]). No associations were observed with chemotherapy (HR 0·87 [0·65-1·17, p_interaction=0·61] for progression-free survival and 1·03 [0·80-1·34, p_interaction=0·01] for overall survival). The association of BMI with overall survival for patients treated with targeted and immune therapies differed by sex, with inverse associations in men (HR 0·53 [0·40-0·70]), but no associations observed in women (HR 0·85 [0·61-1·18, p_interaction=0·03]).

INTERPRETATION

Our results suggest that in patients with metastatic melanoma, obesity is associated with improved progression-free survival and overall survival compared with those outcomes in patients with normal BMI, and that this association is mainly seen in male patients treated with targeted or immune therapy. These results have implications for the design of future clinical trials for patients with metastatic melanoma and the magnitude of the benefit found supports further investigation of the underlying mechanism of these associations.

FUNDING

ASCO/CCF Young Investigator Award, ASCO/CCF Career Development Award, MD Anderson Cancer Center (MDACC) Melanoma Moonshot Program, MDACC Melanoma SPORE, and the Dr Miriam and Sheldon G Adelson Medical Research Foundation.

A phase Ib study of safety and clinical activity of atezolizumab (A) and cobimetinib (C) in patients (pts) with metastatic colorectal cancer (mCRC)

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Background: The majority of pts with mCRC have microsatellite stable (MSS) tumors with minimal response to PD-L1/PD-1 blockade. MEK inhibition upregulates tumor major histocompatibility complex-I expression, promotes intratumoral T-cell accumulation and improves anti–PD-L1 responses (Ebert, Immunity. 2016), supporting clinical evaluation of combined anti–PD-L1 (A) plus MEKi (C) in pts with mCRC. Methods: Pts with chemotherapy-refractory or locally advanced mCRC were evaluated. A was administered IV q2w at 800 mg. C was dosed PO daily at 20 to 60 mg during dose escalation and 60 mg during dose expansion (14/14 or 21/7 d on/off schedule). Primary endpoints were safety and tolerability. Investigator-assessed ORR and PFS by RECIST v1.1 and OS were secondary endpoints. Microsatellite instability (MSI) status was locally reported and centrally confirmed by NGS-based scoring. Results: As of May 10, 2017, 84 pts (57 KRASmt, 25 KRASwt, 2 unknown) were enrolled and evaluable. 66 pts had received 5+ prior therapies; 38 had known MSI status at baseline (MSS [n = 29], MSI-low [n = 8], MSI-H [n = 1]). A + C combination was tolerable. Treatment-related Gr 1-2 and Gr 3-4 AEs occurred at 60% and 37%, respectively. The most frequent related Gr 3-4 AEs were increased blood CPK, rash, diarrhea and fatigue (5% each). No treatment-related Gr 5 AEs occurred. 13% and 24% of pts experienced AEs leading to A and C withdrawal, respectively. Median follow-up was 14.3 mo (range, 0.5-29.8). Confirmed PR was observed in 7 pts (8%; locally reported MSS [n = 3], MSI-low [n = 1], MSI unknown [n = 3]). Median DOR was 14.8 mo (95% CI: 6.0, NE); DCR (PR + SD) was 31%. Median PFS was 1.9 mo (95% CI: 1.8, 2.3); median OS was 10.0 mo (95% CI: 6.2, 14.1). The 6-mo and 1-y OS rates were 65% (95% CI: 54, 76) and 46% (95% CI: 34, 58), respectively. Molecular determinants and immune biomarkers of response will be presented. Conclusions: A + C demonstrated a tolerable safety profile and improvements in OS vs those reported with SOC in heavily pretreated pts with mCRC. Objective responses observed in pts with MSS/MSI-low mCRC were durable, suggesting benefit of this novel combination in a pt population refractory to immune therapies. Clinical trial information: NCT01988896.

Repression of Stress-Induced LINE-1 Expression Protects Cancer Cell Subpopulations from Lethal Drug Exposure

Maintenance of phenotypic heterogeneity within cell populations is an evolutionarily conserved mechanism that underlies population survival upon stressful exposures. We show that the genomes of a cancer cell subpopulation that survives treatment with otherwise lethal drugs, the drug-tolerant persisters (DTPs), exhibit a repressed chromatin state characterized by increased methylation of histone H3 lysines 9 and 27 (H3K9 and H3K27). We also show that survival of DTPs is, in part, maintained by regulators of H3K9me3-mediated heterochromatin formation and that the observed increase in H3K9me3 in DTPs is most prominent over long interspersed repeat element 1 (LINE-1). Disruption of the repressive chromatin over LINE-1 elements in DTPs results in DTP ablation, which is partially rescued by reducing LINE-1 expression or function.

LOTUS (NCT02162719): A double-blind placebo (PBO)-controlled randomized phase II trial of first-line ipatasertib (IPAT) + paclitaxel (P) for metastatic triple-negative breast cancer (TNBC)

1009

Background: The oral Akt inhibitor IPAT is being evaluated in cancers with a high prevalence of PI3K/Akt pathway activation, including TNBC. Methods: Eligible patients (pts) had measurable inoperable locally advanced/metastatic TNBC previously untreated with systemic therapy. Pts were stratified by prior (neo)adjuvant therapy, chemotherapy-free interval and tumor PTEN status, and randomized 1:1 to P 80 mg/m2 (d1, 8 & 15) with either IPAT 400 mg or PBO (d1–21) q28d until progression or unacceptable toxicity. Co-primary endpoints were progression-free survival (PFS) in the ITT population and pts with PTEN-low tumors by IHC. Secondary endpoints included objective response rate (ORR), duration of response (DoR) and overall survival in the ITT and IHC PTEN-low populations, efficacy in pts with PIK3CA/AKT1/PTEN-altered tumors by next-generation sequencing (NGS), and safety. Results: Baseline characteristics were generally balanced between arms. Efficacy is shown below. The most common grade ≥3 AEs (grouped terms) were diarrhea (23% IPAT+P vs 0% PBO+P; no grade 4 or colitis in either arm), neutropenia (18% vs 8%), asthenia (5% vs 6%), peripheral neuropathy (5% vs 5%) and pneumonia (5% vs 0%). More pts receiving IPAT+P than PBO+P had an AE leading to dose reduction of IPAT/PBO (21% vs 6%) or P (38% vs 11%) but median cumulative dose intensity was similar (IPAT/PBO: 99% vs 100%; P: 100% vs 100%). AEs led to IPAT/PBO discontinuation in 13% vs 11% of pts, respectively; 2 pts (3%) discontinued IPAT for grade 3 diarrhea. Conclusions: Adding IPAT to P for TNBC modestly improved PFS in the ITT pts. The effect was more pronounced in the prespecified subgroup with PIK3CA/AKT1/PTEN alterations, warranting further evaluation of IPAT in these pts. AEs were manageable. Clinical trial information: NCT02162719. [Table: see text]

Distinct gene expression, mutational profile and clinical outcomes of V600E and V600K/R BRAF-mutant metastatic melanoma (MM)

9541

Background: BRAF V600E and V600K/R mm have distinct clinicopathologic features suggesting different etiology. V600K/R mm appears less responsive to MAPK inhibitors (MAPKi) compared to V600E MM. We investigated potential mechanisms for this by comparing the gene expression and mutation profiles of these two melanoma subgroups. Methods: BRAF V600 mutant mm patients (pts) treated with MAPKi (BRAFi +/- MEKi) between July/2009 and July/2013 were selected. Demographics, clinicopathologic features and clinical outcomes were examined. Pre-treatment FFPE tumors underwent RNA expression profiling (795-gene nanostring panel) and DNA sequencing (239 gene NGS panel). Molecular results were validated using an independent cohort from the The Cancer Genome Atlas (TCGA). Results: 95 mm pts were included (78 V600E, 17 V600K/R), with median (med) follow-up of 18.4 months (mo). 74 (78%) had BRAFi, 21 (22%) had BRAF/MEKi. At MAPKi start, there were no differences between subgroups regarding age, gender, ECOG, AJCC stage or LDH level. V600K/R pts had a trend to less tumour regression by RECIST (med 30% vs 51%, p = 0.08) and shorter PFS (med 5.1 vs 7.1mo, p = 0.08) than V600E, with no difference in OS (20.8mo vs 17.9mo, p = 0.64). V600K/R had lower expression of the MAPK-pathway feedback regulator DUSP6 and glycosyltransferase GCNT1, compared to V600E (p < 0.05). Analysis of TCGA data (122 V600E, 21 V600K/R) confirmed these findings. There was a trend toward higher mutational load in V600K/R than V600E, confirmed with TCGA data (p < 0.05). V600K/R had a higher proportion of mutations in PIK3CA and several tumour suppressor genes (FBXW7, NF2, RB1 and SMAD4), with only FBXW7 confirmed using TCGA data. Conclusions: V600K/R mm has inferior response and shorter survival with MAPKi than V600E, potentially due to less reliance on MAPK pathway activation (lower DUSP6 expression) and greater use of alternative drivers of oncogenesis (higher mutational load, particularly in tumor suppressor genes). Further analyses will be performed, including comparison of MAPK and additional pathway signalling in cell models. Response to immunotherapy will also be examined.

Abstract OT2-01-02: COLET: A multistage, phase 2 study evaluating the safety and efficacy of a doublet regimen of cobimetinib (C) in combination with paclitaxel (P) or triplet regimens of C in combination with atezolizumab (atezo) plus either P or nab-paclitaxel (nab-P) in metastatic triple-negative breast cancer (TNBC)

Preclinical data suggest that upregulation of the MAPK pathway confers resistance to taxane chemotherapy. Mutations and gene amplifications in the MAPK pathway are present in many TNBC tumors and may contribute to taxane resistance. Preliminary data from an initial safety run-in stage of the COLET study (ClinicalTrials.gov ID, NCT02322814; EudraCT number, 2014-002230-32) suggest improvement of clinical outcomes when MEK inhibition is combined with taxane chemotherapy. Additionally, in preclinical models, MEK inhibition was shown to enhance anti–PD-L1 activity. The monoclonal antibody PD-L1 inhibitor atezo has shown promising activity in combination with nab-P in metastatic TNBC. Accordingly, the COLET protocol was amended to include the evaluation of triplet regimens combining atezo with MEK inhibition and taxane chemotherapy[SL1] . COLET is evaluating the safety and efficacy of various combinations of C as first-line treatment for metastatic or locally advanced TNBC. Key eligibility criteria include measurable disease per Response Evaluation Criteria in Solid Tumors, version 1.1 (RECIST v1.1) and left ventricular ejection fraction &gt; institutional lower limit of normal or &gt;50%. Neoadjuvant or adjuvant therapy is allowed if completed &gt;6 months prior to study entry. COLET has 3 cohorts: I, II, and III. Cohort I has 2 stages: an initial safety run-in stage (n∼12) followed by an expansion stage (n∼90) of 1:1 randomization to C + P or placebo (PBO) + P. Patients received P 80 mg/m2 on days 1, 8, and 15 and C/PBO 60 mg/day on days 3-23 of each 28-day cycle. In the expansion stage of Cohort I, randomization is stratified by prior neoadjuvant/adjuvant taxane therapy and disease-free interval from last chemotherapy dose. Cohorts II and III will evaluate the safety and efficacy of adding atezo to C + P or nab-P, respectively. Each cohort has a safety run-in stage (n∼15) and an expansion stage (additional n∼15); each will receive atezo 840 mg on days 1 and 15 and C 60 mg/day on days 3-23 of every 28-day cycle. Cohort II will receive P 80 mg/m2 and Cohort III will receive intravenous nab-P 100 mg/m2 on days 1, 8, and 15. Patients will receive treatment until disease progression or toxicity. The primary efficacy end point is investigator-assessed progression-free survival (PFS) for the expansion stage (Cohort I), and the primary PFS analysis will be performed when 60 PFS events occur across the 2 arms. This provides 77% power to detect a hazard ratio of 0.5 at a two-sided significance level of 0.05. For Cohorts II and III, the primary efficacy end point is overall response rate per RECIST v1.1; secondary end points include duration of response, PFS, and overall survival. Recruitment into the safety run-in stage of Cohort I is complete. Accrual into the randomization stage of Cohort I and the initial safety run-in stage of Cohorts II and III are ongoing. Patients from sites across North America, Europe, and the Asia-Pacific region will be enrolled.

Citation Format: Miles D, Kim S-B, McNally V, Simmons B, Wongchenko M, Xu N, Brufsky A. COLET: A multistage, phase 2 study evaluating the safety and efficacy of a doublet regimen of cobimetinib (C) in combination with paclitaxel (P) or triplet regimens of C in combination with atezolizumab (atezo) plus either P or nab-paclitaxel (nab-P) in metastatic triple-negative breast cancer (TNBC) [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 OT2-01-02.

Abstract P4-22-22: Cobimetinib (C) combined with paclitaxel (P) as a first-line treatment in patients (pts) with advanced triple-negative breast cancer (COLET study): Updated clinical and biomarker results

Resistance to standard taxane-based chemotherapy is common in triple-negative breast cancer (TNBC). Mutations and gene amplifications in the MAPK pathway that upregulate MAPK signaling are present in many TNBC tumors. Upregulation of the MAPK signaling pathway can result in degradation of the pro-apoptotic protein BIM and upregulation of anti-apoptotic proteins, including BCL-2, BCL-XL, and MCL-1, thus promoting cell survival and desensitizing tumor cells to the pro-apoptotic effects of taxane chemotherapy. Updated data on clinical safety and efficacy are presented along with biomarker data evaluating the effects of treatment on induction of apoptosis.The COLET study (ClinicalTrials.gov ID, NCT02322814; EudraCT number, 2014-002230-32) consisted of a safety run-in (n∼12) followed by a blinded 1:1 randomized expansion stage (n∼90) to C + P or placebo (PBO) + P. The safety stage is complete and the randomized stage is enrolling pts. Two additional cohorts investigating the effect of adding atezolizumab will be recruiting and are out of scope of this submission. Pts in cohort I were treated with P 80 mg/m2 on days 1, 8, and 15 and C/PBO 60 mg/day on days 3–23 of each 28-day cycle until disease progression or unacceptable toxicity. Gene expression and apoptotic index were measured by RNA-Seq and TUNEL staining, respectively, to assess the biologic activity of C + P.Sixteen women (median age, 55.5 years) were enrolled in the safety run-in stage. At data snapshot (April 22, 2016), all 16 pts had received ≥1 dose of study treatment. Median time on treatment was 116 days (range, 7-336) for C and 84 days (range, 0-351) for P. Fifteen (94%) pts had ≥1 adverse event (AE); 5 (31%) pts had grade 1/2 AEs and 10 (63%) pts had grade 3 AEs (Table). No pts experienced grade 4–5 AEs. Among the 16 safety run-in patients, responses to date include partial response (PR; n = 8 [50.0%]), stable disease (SD, n = 4 [25.0%]), and progressive disease (n = 2 [12.5%]), as well as 2 pts with no post-baseline tumor assessment. Six pts maintained a PR at ∼20 weeks and three maintained a PR at ≥40 weeks. To date, matched pre- and on-treatment biopsies were evaluable for 2 pts, 1 with a PR and 1 with SD. In the patient who attained a PR, increased expression of pro-apoptosis genes, including BIM, was observed; but this was not seen in the patient experiencing SD. The PR patient also had an increase in apoptotic index. Updated biomarker data will be reported.This is the first study to evaluate C + P in TNBC. The safety profile of C + P is consistent with that of known safety profiles. Efficacy and safety will be further evaluated in the ongoing randomized stage.

Most common (any grade ≥20%) AEsTreatment-emergent AEs, n (%)C + P (safety run-in stage), N = 16 All gradesGrade 3Diarrhea10 (63)1 (6)Rash8 (50)0Nausea7 (44)0Alopecia5 (31)0Blood CPK level increase5 (31)1 (6)Stomatitis4 (25)2 (13)Asthenia4 (25)1 (6)Constipation4 (25)0Dyspnea4 (25)0Edema peripheral4 (25)0Pyrexia4 (25)0Vomiting4 (25)0AEs, adverse events; C, cobimetinib; CPK, creatinine phosphokinase; P, paclitaxel.

Citation Format: Brufsky A, Kim S-B, Velu T, García-Saenz JA, Tan-Chiu E, Sohn JH, Dirix L, Borms MV, Liu M-C, Moezi MM, Kozloff MF, Sparano JA, Xu N, Wongchenko M, Simmons B, McNally V, Miles D. Cobimetinib (C) combined with paclitaxel (P) as a first-line treatment in patients (pts) with advanced triple-negative breast cancer (COLET study): Updated clinical and biomarker results [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 P4-22-22.

Melanoma and immunotherapy bridge 2015 : Naples, Italy. 1-5 December 2015

MELANOMA BRIDGE 2015

KEYNOTE SPEAKER PRESENTATIONS

Molecular and immuno-advances

K1 Immunologic and metabolic consequences of PI3K/AKT/mTOR activation in melanoma

Vashisht G. Y. Nanda, Weiyi Peng, Patrick Hwu, Michael A. Davies

K2 Non-mutational adaptive changes in melanoma cells exposed to BRAF and MEK inhibitors help the establishment of drug resistance

Gennaro Ciliberto, Luigi Fattore, Debora Malpicci, Luigi Aurisicchio, Paolo Antonio Ascierto, Carlo M. Croce, Rita Mancini

K3 Tumor-intrinsic beta-catenin signaling mediates tumor-immune avoidance

Stefani Spranger, Thomas F. Gajewski

K4 Intracellular tumor antigens as a source of targets of antibody-based immunotherapy of melanoma

Yangyang Wang, Soldano Ferrone

Combination therapies

K5 Harnessing radiotherapy to improve responses to immunotherapy in cancer

Claire Vanpouille-Box, Erik Wennerberg, Karsten A. Pilones, Silvia C. Formenti, Sandra Demaria

K6 Creating a T cell-inflamed tumor microenvironment overcomes resistance to checkpoint blockade

Haidong Tang, Yang Wang, Yang-Xin Fu

K7 Biomarkers for treatment decisions?

Reinhard Dummer

K8 Combining oncolytic therapies in the era of checkpoint inhibitors

Igor Puzanov

K9 Immune checkpoint blockade for melanoma: should we combine or sequence ipilimumab and PD-1 antibody therapy?

Michael A. Postow

News in immunotherapy

K10 An update on adjuvant and neoadjuvant therapy for melanom

Ahmad Tarhini

K11 Targeting multiple inhibitory receptors in melanoma

Joe-Marc Chauvin, Ornella Pagliano, Julien Fourcade, Zhaojun Sun, Hong Wang, Cindy Sanders, John M. Kirkwood, Tseng-hui Timothy Chen, Mark Maurer, Alan J. Korman, Hassane M. Zarour

K12 Improving adoptive immune therapy using genetically engineered T cells

David F. Stroncek

Tumor microenvironment and biomarkers

K13 Myeloid cells and tumor exosomes: a crosstalk for assessing immunosuppression?

Veronica Huber, Licia Rivoltini

K14 Update on the SITC biomarker taskforce: progress and challenges

Magdalena Thurin

World-wide immunoscore task force: an update

K15 The immunoscore in colorectal cancer highlights the importance of digital scoring systems in surgical pathology

Tilman Rau, Alessandro Lugli

K16 The immunoscore: toward an integrated immunomonitoring from the diagnosis to the follow up of cancer’s patients

Franck Pagès

Economic sustainability of melanoma treatments: regulatory, health technology assessment and market access issues

K17 Nivolumab, the regulatory experience in immunotherapy

Jorge Camarero, Arantxa Sancho

K18 Evidence to optimize access for immunotherapies

Claudio Jommi

ORAL PRESENTATIONS

Molecular and immuno-advances

O1 Ipilimumab treatment results in CD4 T cell activation that is concomitant with a reduction in Tregs and MDSCs

Yago Pico de Coaña, Maria Wolodarski, Yuya Yoshimoto, Giusy Gentilcore, Isabel Poschke, Giuseppe V. Masucci, Johan Hansson, Rolf Kiessling

O2 Evaluation of prognostic and therapeutic potential of COX-2 and PD-L1 in primary and metastatic melanoma

Giosuè Scognamiglio, Francesco Sabbatino, Federica Zito Marino, Anna Maria Anniciello, Monica Cantile, Margherita Cerrone, Stefania Scala, Crescenzo D’alterio, Angela Ianaro, Giuseppe Cirino, Paolo Antonio Ascierto, Giuseppina Liguori, Gerardo Botti

O3 Vemurafenib in patients with BRAFV600 mutation–positive metastatic melanoma: final overall survival results of the BRIM-3 study

Paul B. Chapman, Caroline Robert, James Larkin, John B. Haanen, Antoni Ribas, David Hogg, Omid Hamid, Paolo Antonio Ascierto, Alessandro Testori, Paul Lorigan, Reinhard Dummer, Jeffrey A. Sosman, Keith T. Flaherty, Huibin Yue, Shelley Coleman, Ivor Caro, Axel Hauschild, Grant A. McArthur

O4 Updated survival, response and safety data in a phase 1 dose-finding study (CA209-004) of concurrent nivolumab (NIVO) and ipilimumab (IPI) in advanced melanoma

Mario Sznol, Margaret K. Callahan, Harriet Kluger, Michael A. Postow, RuthAnn Gordan, Neil H. Segal, Naiyer A. Rizvi, Alexander Lesokhin, Michael B. Atkins, John M. Kirkwood, Matthew M. Burke, Amanda Ralabate, Angel Rivera, Stephanie A. Kronenberg, Blessing Agunwamba, Mary Ruisi, Christine Horak, Joel Jiang, Jedd Wolchok

Combination therapies

O5 Efficacy and correlative biomarker analysis of the coBRIM study comparing cobimetinib (COBI) + vemurafenib (VEM) vs placebo (PBO) + VEM in advanced BRAF-mutated melanoma patients (pts)

Paolo A. Ascierto, Grant A. McArthur, James Larkin, Gabriella Liszkay, Michele Maio, Mario Mandalà, Lev Demidov, Daniil Stoyakovskiy, Luc Thomas, Luis de la Cruz-Merino, Victoria Atkinson, Caroline Dutriaux, Claus Garbe, Matthew Wongchenko, Ilsung Chang, Daniel O. Koralek, Isabelle Rooney, Yibing Yan, Antoni Ribas, Brigitte Dréno

O6 Preliminary clinical safety, tolerability and activity results from a Phase Ib study of atezolizumab (anti-PDL1) combined with vemurafenib in BRAFV600-mutant metastatic melanoma

Ryan Sullivan, Omid Hamid, Manish Patel, Stephen Hodi, Rodabe Amaria, Peter Boasberg, Jeffrey Wallin, Xian He, Edward Cha, Nicole Richie, Marcus Ballinger, Patrick Hwu

O7 Preliminary safety and efficacy data from a phase 1/2 study of epacadostat (INCB024360) in combination with pembrolizumab in patients with advanced/metastatic melanoma

Thomas F. Gajewski, Omid Hamid, David C. Smith, Todd M. Bauer, Jeffrey S. Wasser, Jason J. Luke, Ani S. Balmanoukian, David R. Kaufman, Yufan Zhao, Janet Maleski, Lance Leopold, Tara C. Gangadhar

O8 Primary analysis of MASTERKEY-265 phase 1b study of talimogene laherparepvec (T-VEC) and pembrolizumab (pembro) for unresectable stage IIIB-IV melanoma

Reinhard Dummer, Georgina V. Long, Antoni Ribas, Igor Puzanov, Olivier Michielin, Ari VanderWalde, Robert H.I. Andtbacka, Jonathan Cebon, Eugenio Fernandez, Josep Malvehy, Anthony J. Olszanski, Thomas F. Gajewski, John M. Kirkwood, Christine Gause, Lisa Chen, David R. Kaufman, Jeffrey Chou, F. Stephen Hodi

News in immunotherapy

O9 Two-year survival and safety update in patients (pts) with treatment-naïve advanced melanoma (MEL) receiving nivolumab (NIVO) or dacarbazine (DTIC) in CheckMate 066

Victoria Atkinson, Paolo A. Ascierto, Georgina V. Long, Benjamin Brady, Caroline Dutriaux, Michele Maio, Laurent Mortier, Jessica C. Hassel, Piotr Rutkowski, Catriona McNeil, Ewa Kalinka-Warzocha, Celeste Lebbé, Lars Ny, Matias Chacon, Paola Queirolo, Carmen Loquai, Parneet Cheema, Alfonso Berrocal, Karmele Mujika Eizmendi, Luis De La Cruz-Merino, Gil Bar-Sela, Christine Horak, Joel Jiang, Helene Hardy, Caroline Robert

O10 Efficacy and safety of nivolumab (NIVO) in patients (pts) with advanced melanoma (MEL) who were treated beyond progression in CheckMate 066/067

Georgina V. Long, Jeffrey S. Weber, James Larkin, Victoria Atkinson, Jean-Jacques Grob, Reinhard Dummer, Caroline Robert, Ivan Marquez-Rodas, Catriona McNeil, Henrik Schmidt, Karen Briscoe, Jean-François Baurain, F. Stephen Hodi, Jedd D. Wolchok

Tumor microenvironment and biomarkers

O11 New biomarkers for response/resistance to BRAF inhibitor therapy in metastatic melanoma

Rosamaria Pinto, Simona De Summa, Vito Michele Garrisi, Sabino Strippoli, Amalia Azzariti, Gabriella Guida, Michele Guida, Stefania Tommasi

O12 Chemokine receptor patterns in lymphocytes mirror metastatic spreading in melanoma and response to ipilimumab

Nicolas Jacquelot, David Enot, Caroline Flament, Jonathan M. Pitt, Nadège Vimond, Carolin Blattner, Takahiro Yamazaki, Maria-Paula Roberti, Marie Vetizou, Romain Daillere, Vichnou Poirier-Colame, Michaëla Semeraro, Anne Caignard, Craig L Slingluff Jr, Federica Sallusto, Sylvie Rusakiewicz, Benjamin Weide, Aurélien Marabelle, Holbrook Kohrt, Stéphane Dalle, Andréa Cavalcanti, Guido Kroemer, Anna Maria Di Giacomo, Michaele Maio, Phillip Wong, Jianda Yuan, Jedd Wolchok, Viktor Umansky, Alexander Eggermont, Laurence Zitvogel

O13 Serum levels of PD1- and CD28-positive exosomes before Ipilimumab correlate with therapeutic response in metastatic melanoma patients

Passarelli Anna, Tucci Marco, Stucci Stefania, Mannavola Francesco, Capone Mariaelena, Madonna Gabriele, Ascierto Paolo Antonio, Silvestris Franco

O14 Immunological prognostic factors in stage III melanomas

María Paula Roberti, Nicolas Jacquelot, David P Enot, Sylvie Rusakiewicz, Michaela Semeraro, Sarah Jégou, Camila Flores, Lieping Chen, Byoung S. Kwon, Ana Carrizossa Anderson, Caroline Robert, Christophe Borg, Benjamin Weide, François Aubin, Stéphane Dalle, Michele Maio, Jedd D. Wolchok, Holbrook Kohrt, Maha Ayyoub, Guido Kroemer, Aurélien Marabelle, Andréa Cavalcanti, Alexander Eggermont, Laurence Zitvogel

POSTER PRESENTATIONS

Molecular and immuno-advances

P1 Human melanoma cells resistant to B-RAF and MEK inhibition exhibit mesenchymal-like features

Anna Lisa De Presbiteris, Fabiola Gilda Cordaro, Rosa Camerlingo, Federica Fratangelo, Nicola Mozzillo, Giuseppe Pirozzi, Eduardo J. Patriarca, Paolo A. Ascierto, Emilia Caputo

P2 Anti-proliferative and pro-apoptotic effect of ABT888 on melanoma cell lines and its potential role in the treatment of melanoma resistant to B-RAF inhibitors

Federica Fratangelo, Rosa Camerlingo, Emilia Caputo, Maria Letizia Motti, Rosaria Falcone, Roberta Miceli, Mariaelena Capone, Gabriele Madonna, Domenico Mallardo, Maria Vincenza Carriero, Giuseppe Pirozzi and Paolo Antonio Ascierto

P3 Involvement of the L-cysteine/CSE/H2S pathway in human melanoma progression

Elisabetta Panza, Paola De Cicco, Chiara Armogida, Giuseppe Ercolano, Rosa Camerlingo, Giuseppe Pirozzi, Giosuè Scognamiglio, Gerardo Botti, Giuseppe Cirino, Angela Ianaro

P4 Cancer stem cell antigen revealing pattern of antibody variable region genes were defined by immunoglobulin repertoire analysis in patients with malignant melanoma

Beatrix Kotlan, Gabriella Liszkay, Miri Blank, Timea Balatoni, Judit Olasz, Emil Farkas, Andras Szollar, Akos Savolt, Maria Godeny, Orsolya Csuka, Szabolcs Horvath, Klara Eles, Yehuda Shoenfeld and Miklos Kasler

P5 Upregulation of Neuregulin-1 expression is a hallmark of adaptive response to BRAF/MEK inhibitors in melanoma

Debora Malpicci, Luigi Fattore, Susan Costantini, Francesca Capone, Paolo Antonio Ascierto, Rita Mancini, Gennaro Ciliberto

P6 HuR positively regulates migration of HTB63 melanoma cells

Farnaz Moradi, Pontus Berglund, Karin Leandersson, Rickard Linnskog, Tommy Andersson, Chandra Prakash Prasad

P7 Prolyl 4- (C-P4H) hydroxylases have opposing effects in malignant melanoma: implication in prognosis and therapy

Cristiana Lo Nigro, Laura Lattanzio, Hexiao Wang, Charlotte Proby, Nelofer Syed, Marcella Occelli, Carolina Cauchi, Marco Merlano, Catherine Harwood, Alastair Thompson, Tim Crook

P8 Urokinase receptor antagonists: novel agents for the treatment of melanoma

Maria Letizia Motti, Katia Bifulco, Vincenzo Ingangi, Michele Minopoli, Concetta Ragone, Federica Fratangelo, Antonello Pessi, Gennaro Ciliberto, Paolo Antonio Ascierto, Maria Vincenza Carriero

P9 Exosomes released by melanoma cell lines enhance chemotaxis of primary tumor cells

Francesco Mannavola, Stella D’Oronzo, Claudia Felici, Marco Tucci, Antonio Doronzo, Franco Silvestris

P10 New insights in mitochondrial metabolic reprogramming in melanoma

Anna Ferretta, Gabriella Guida, Stefania Guida, Imma Maida, Tiziana Cocco, Sabino Strippoli, Stefania Tommasi, Amalia Azzariti, Michele Guida

P11 Lenalidomide restrains the proliferation in melanoma cells through a negative regulation of their cell cycle

Stella D’Oronzo, Anna Passarelli, Claudia Felici, Marco Tucci, Davide Quaresmini, Franco Silvestris

Combination therapies

P12 Chemoimmunotherapy elicits polyfunctional anti-tumor CD8 + T cells depending on the activation of an AKT pathway sustained by ICOS

Ornella Franzese, Belinda Palermo, Cosmo Di Donna, Isabella Sperduti, MariaLaura Foddai, Helena Stabile, Angela Gismondi, Angela Santoni, Paola Nisticò

P13 Favourable toxicity profile of combined BRAF and MEK inhibitors in metastatic melanoma patients

Andrea P. Sponghini, Francesca Platini, Elena Marra, David Rondonotti, Oscar Alabiso, Maria T. Fierro, Paola Savoia, Florian Stratica, Pietro Quaglino

P14 Electrothermal bipolar vessel sealing system dissection reduces seroma output or time to drain removal following axillary and ilio-inguinal node dissection in melanoma patients: a pilot study

Di Monta Gianluca, Caracò Corrado, Di Marzo Massimiliano, Marone Ugo, Di Cecilia Maria Luisa, Mozzillo Nicola

News in immunotherapy

P15 Clinical and immunological response to ipilimumab in a metastatic melanoma patient with HIV infection

Francesco Sabbatino, Celeste Fusciello1, Antonio Marra, Rosario Guarrasi, Carlo Baldi, Rosa Russo, Di Giulio Giovanni, Vincenzo Faiola, Pio Zeppa, Stefano Pepe

P16 Immunotherapy and hypophysitis: a case report

Elisabetta Gambale, Consiglia Carella, Alessandra Di Paolo, Michele De Tursi

Tumor microenvironment and biomarkers

P17 New immuno- histochemical markers for the differential diagnosis of atypical melanocytic lesions with uncertain malignant potential

Laura Marra, Giosuè Scognamiglio, Monica Cantile, Margherita Cerrone, Fara De Murtas, Valeria Sorrentino, Anna Maria Anniciello, Gerardo Botti

P18 Utility of simultaneous measurement of three serum tumor markers in melanoma patients

Angela Sandru, Silviu Voinea, Eugenia Panaitescu, Madalina Bolovan, Adina Stanciu, Sabin Cinca

P19 The significance of various cut-off levels of melanoma inhibitory activity in evaluation of cutaneous melanoma patients

Angela Sandru, Silviu Voinea, Eugenia Panaitescu, Madalina Bolovan, Adina Stanciu, Sabin Cinca

P20 The long noncoding RNA HOTAIR is associated to metastatic progression of melanoma and it can be identified in the blood of patients with advanced disease

Chiara Botti, Giosuè Scognamiglio, Laura Marra, Gabriella Aquino, Rosaria Falcone, Annamaria Anniciello, Paolo Antonio Ascierto, Gerardo Botti, Monica Cantile

Other

P21 The effect of Sentinel Lymph Node Biopsy in melanoma mortality: timing of dissection

Cristina Fortes, Simona Mastroeni, Alessio Caggiati, Francesca Passarelli, Alba Zappalà, Maria Capuano, Riccardo Bono, Maurizio Nudo, Claudia Marino, Paola Michelozzi

P22 Epidemiological survey on related psychopathology in melanoma

Valeria De Biasio, Vincenzo C. Battarra

IMMUNOTHERAPY BRIDGE

KEYNOTE SPEAKER PRESENTATIONS

Immunotherapy beyond melanoma

K19 Predictor of response to radiation and immunotherapy

Silvia Formenti

K20 Response and resistance to PD-1 pathway blockade: clues from the tumor microenvironment

Maria Libera Ascierto, Tracee L. McMiller, Alan E. Berger, Ludmila Danilova, Robert A. Anders, George J. Netto, Haiying Xu, Theresa S. Pritchard, Jinshui Fan, Chris Cheadle, Leslie Cope, Charles G. Drake, Drew M. Pardoll, Janis M. Taube and Suzanne L. Topalian

K21 Combination immunotherapy with autologous stem cell transplantation, protein immunization, and PBMC reinfusion in myeloma patients

Sacha Gnjatic, Sarah Nataraj, Naoko Imai, Adeeb Rahman, Achim A. Jungbluth, Linda Pan, Ralph Venhaus, Andrew Park, Frédéric F. Lehmann, Nikoletta Lendvai, Adam D. Cohen, and Hearn J. Cho

K22 Anti-cancer immunity despite T cell “exhaustion”

Speiser Daniel

Immunotherapy in oncology (I-O): data from clinical trial

K23 The Checkpoint Inhibitors for the Treatment of Metastatic Non-small Cell Lung Cancer (NSCLC)

Vera Hirsh

Abstract PR03: CD8+ T-cell distribution and immunomodulator expression in BRAF-mutant melanoma affect the response to BRAF inhibitor and chemotherapy

Although intense effort has been made in studying immune cell dynamics in tumors after treatment with targeted therapies and to recharacterize tumor stages based on their immune cell components, less is known about how baseline immune cell characteristics in tumors affect response to approved therapies. Here we describe baseline expression of immune regulators and CD8+ T-cell distribution in BRAF-mutated metastatic melanoma and their relationship with progression-free survival (PFS) on vemurafenib and chemotherapy. To our knowledge, we are the first to describe the baseline characteristics of tumor-infiltrating lymphocytes and their impact on outcomes in a large randomized, controlled trial in melanoma.

Archival or baseline samples were collected from patients in 2 clinical trials (BRIM2 and BRIM3) and analyzed. A total of 252 RNA samples were prepared from formalin-fixed, paraffin-embedded (FFPE) tissue samples and profiled for expression using a panel of 96 immune genes on the Fluidigm platform (Fluidigm Corp). Additionally, for 277 patients from the BRIM3 trial, CD8+ T cells were detected by immunohistochemistry (IHC) and quantified using Definiens (Definiens AG). Patients were defined as high or low expressers based on a median cutoff, and hazard ratios (HRs) were determined by cox proportional hazards modeling of PFS. HRs refer to the comparison of high and low expressing groups, where an HR&lt;1 is indicative of a better outcome for the high-expressing group.

A discovery (BRIM2) – validation (BRIM3) scheme was applied to assess the prognostic value of the expression of immune-related genes. Samples from the BRIM3 dacarbazine and vemurafenib arms were compared to assess the predictive value of the markers on the treatment effect of vemurafenib. Of the genes tested, 26 met our discovery criteria in the BRIM2 trial and 2, IL7 and IL12A, were validated in BRIM3. In the vemurafenib arm of BRIM3, patients with high expression of IL7 had improved PFS compared with patients with low IL7, with an HR of 0.63 (95% confidence interval [CI]: 0.41-0.97; P=0.03); high expression of IL12A had an HR of 0.58 (0.38-0.88; P=0.01). Neither gene was associated with PFS in the dacarbazine-treated arm; however, high and low expressers of both genes benefited from vemurafenib treatment.

Because immune contexture is known to be associated with outcomes, slides were stained for CD8+ T-cell content in 3 marker areas: center, peripheral, and invasive margin. In the dacarbazine arm, increased PFS was seen in patients with higher CD8+ T-cell content in the tumor center or periphery, with HRs of 0.58 (0.43-0.94; P=0.02) and 0.39 (0.25-0.59; P&lt;0.01), respectively. CD8+ T-cell content did not show a significant effect in vemurafenib-treated patients, and all groups benefited from vemurafenib treatment.

Based on these characterizations, tumor immune cell components seem to play important but varying roles in response to dacarbazine or vemurafenib treatment in BRAF-mutant melanoma.

This abstract is also being presented as Poster B22.

Citation Format: Matthew Wongchenko, Christina Rabe, Jeffrey Sosman, Grant McArthur, Yuanyuan Xiao, Houston Gilbert, Luc Andries, Mark Kockx, Hartmut Koeppen, Priti Hegde, Lukas Amler, Yibing Yan, Antoni Ribas. CD8+ T-cell distribution and immunomodulator expression in BRAF-mutant melanoma affect the response to BRAF inhibitor and chemotherapy. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Melanoma: From Biology to Therapy; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(14 Suppl):Abstract nr PR03.

Amphiregulin and PTEN evoke a multimodal mechanism of acquired resistance to PI3K inhibition

Phosphoinositide-3 kinase (PI3K) signaling pathway alterations occur broadly in cancer and PI3K is a promising therapeutic target. Here, we investigated acquired resistance to GDC-0941, a PI3K inhibitor in clinical trials. Colorectal cancer (CRC) cells made to be resistant to GDC-0941 were discovered to secrete amphiregulin, which resulted in increased EGFR/MAPK signaling. Moreover, prolonged PI3K pathway inhibition in cultured cells over a period of months led to a secondary loss of PTEN in 40% of the CRC lines with acquired resistance to PI3K inhibition. In the absence of PI3K inhibitor, these PTEN-null PI3K inhibitor-resistant clones had elevated PI3K pathway signaling and decreased sensitivity to MAPK pathway inhibitors. Importantly, PTEN loss was not able to induce resistance to PI3K inhibitors in the absence of amphiregulin, indicating a multimodal mechanism of acquired resistance. The combination of PI3K and MAPK pathway inhibitors overcame acquired resistance in vitro and in vivo.

Evaluation and clinical analyses of downstream targets of the Akt inhibitor GDC-0068

PURPOSE

The oncogenic PI3K/Akt/mTOR pathway is an attractive therapeutic target in cancer. However, it is unknown whether the pathway blockade required for tumor growth inhibition is clinically achievable. Therefore, we conducted pharmacodynamic studies with GDC-0068, an ATP competitive, selective Akt1/2/3 inhibitor, in preclinical models and in patients treated with this compound.

EXPERIMENTAL DESIGN

We used a reverse phase protein array (RPPA) platform to identify a biomarker set indicative of Akt inhibition in cell lines and human-tumor xenografts, and correlated the degree of pathway inhibition with antitumor activity. Akt pathway activity was measured using this biomarker set in pre- and post-dose tumor biopsies from patients treated with GDC-0068 in the dose escalation clinical trial.

RESULTS

The set of biomarkers of Akt inhibition is composed of 10 phosphoproteins, including Akt and PRAS40, and is modulated in a dose-dependent fashion, both in vitro and in vivo. In human-tumor xenografts, this dose dependency significantly correlated with tumor growth inhibition. Tumor biopsies from patients treated with GDC-0068 at clinically achievable doses attained a degree of biomarker inhibition that correlated with tumor growth inhibition in preclinical models. In these clinical samples, compensatory feedback activation of ERK and HER3 was observed, consistent with preclinical observations.

CONCLUSION

This study identified a set of biomarkers of Akt inhibition that can be used in the clinical setting to assess target engagement. Here, it was used to show that robust Akt inhibition in tumors from patients treated with GDC-0068 is achievable, supporting the clinical development of this compound in defined patient populations.

Abstract 3395: BCR-Abl independent, Abl-TKI-therapy-resistant CML cells show enhanced sensitivity to GDC0941

Introduction: Chronic Myeloid leukemia (CML) is driven by the BCR-ABL oncogene and is initially treated with ABL tyrosine-kinase inhibitors (ABL-TKI), such as Imatinib or Dasatinib. Despite strong initial responses to these drugs, many patients acquire resistance over time through acquisition of BCR-ABL mutations such as T315I, compound BCR-ABL mutations or through BCR-ABL-independent mechanisms. Even though the next generation pan-ABL inhibitor, Ponatinib, targets all know resistant ABL mutations, some patients don't benefit from Ponatinib and in these cases resistance to TKI therapy may be due to BCR-ABL-independent mechanisms. We analyzed the mechanism of ABL-TKI-dual-resistant CML cells independent of new BCR-ABL mutations and tested the sensitivity of these resistant cells to the PI3K inhibitor, GDC-0941 and/or the MEK inhibitor GDC-0973.

Methods: We created ABL-TKI-dual-resistant cells and clones through prolonged treatment of K562 and KCL22 cells with Imatinib and then Dasatinib. The cells and clones were tested for sensitivity to Imatinib, Dasatinib, Ponatinib, GDC-0941 and GDC-0973. Whole genome copy number scan (Oncoscan) and targeted deep sequencing using GAII were used to identify BCR-ABL mutations and newly acquired somatic gene alterations. Phosphoproteomic analysis of cell lysates by Reverse Phase Protein Arrays was used to profile cell signaling pathway status associated with resistance and sensitivity to these drugs.

Results: The K562 ABL-TKI-dual-resistant cells were insensitive to all three ABL-TKIs including Ponatinib suggesting that resistance was mediated by a BCR-ABL-independent mechanism. Unexpectedly, the resistant cells and clones became more sensitive to GDC-0941 but not GDC-0973 compared to the parental cells. These resistant cells and clones had acquired new somatic mutations in p53, BRCA2, PTEN, RB, SMARCA4 and PBRM1, but not in BCR-ABL. Phosphoprotein profiling showed low phosphorylation of the BCR-ABL substrates c-ABL, SHC and FAK indicative of BCR-ABL-independent mechanisms of resistance. Activity of the PI3K/AKT and MEK/ERK pathways varied across the resistant clones. However, high levels of the AKT substrate, FOXO-1 directly correlated with Dasatinib resistance and with GDC-0941 sensitivity. Sensitivity to GDC-0941 also correlated with modulation of phospho-FOXO-1. Our data suggest that GDC-0941 may be a therapeutic candidate for CML patients who progress on TKI therapy through BCR-ABL-independent mechanisms of resistance.

Citation Format: Marie Wagle, Matthew Wongchenko, Shan Lu, Yinghui Guan, Yulei Wang, Mark Lackner, Garret Hampton, Yibing Yan. BCR-Abl independent, Abl-TKI-therapy-resistant CML cells show enhanced sensitivity to GDC0941. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3395. doi:10.1158/1538-7445.AM2013-3395