Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair

Amino acid bioavailability impacts mRNA translation in a codon-dependent manner. Here, we report that the anti-cancer MAPK inhibitors (MAPKi) decrease the intracellular concentration of aspartate and glutamate in melanoma cells. This coincides with the accumulation of ribosomes on codons corresponding to these amino acids and triggers the translation-dependent degradation of mRNAs encoding aspartate- and glutamate-rich proteins, involved in DNA metabolism such as DNA replication and repair. Consequently, cells that survive MAPKi degrade aspartate and glutamate likely to generate energy, which simultaneously decreases their requirement for amino acids due to the downregulation of aspartate- and glutamate-rich proteins involved in cell proliferation. Concomitantly, the downregulation of aspartate- and glutamate-rich proteins involved in DNA repair increases DNA damage loads. Thus, DNA repair defects, and therefore mutations, are at least in part a secondary effect of the metabolic adaptation of cells exposed to MAPKi.

Post-transcriptional gene regulation: From mechanisms to RNA chemistry and therapeutics

A better understanding of the RNA biology and chemistry is necessary to then develop new RNA therapeutic strategies. This review is the synthesis of a series of conferences that took place during the 6th international course on post-transcriptional gene regulation at Institut Curie. This year, the course made a special focus on RNA chemistry.

Post-transcriptional checkpoints in autoimmunity

Post-transcriptional regulation is a fundamental process in gene expression that has a role in diverse cellular processes, including immune responses. A core concept underlying post-transcriptional regulation is that protein abundance is not solely determined by transcript abundance. Indeed, transcription and translation are not directly coupled, and intervening steps occur between these processes, including the regulation of mRNA stability, localization and alternative splicing, which can impact protein abundance. These steps are controlled by various post-transcription factors such as RNA-binding proteins and non-coding RNAs, including microRNAs, and aberrant post-transcriptional regulation has been implicated in various pathological conditions. Indeed, studies on the pathogenesis of autoimmune and inflammatory diseases have identified various post-transcription factors as important regulators of immune cell-mediated and target effector cell-mediated pathological conditions. This Review summarizes current knowledge regarding the roles of post-transcriptional checkpoints in autoimmunity, as evidenced by studies in both haematopoietic and non-haematopoietic cells, and discusses the relevance of these findings for developing new anti-inflammatory therapies.

Abstract 2177: Roles of lactate dehydrogenase (LDH) in melanoma: an underestimated prognostic biomarker

Introduction: High LDH activity is associated with a poor prognosis in many cancer types, especially in melanoma where it is the strongest indicator of poor outcome even with the most potent anticancer immunotherapies or targeted therapies. Although high LDH blood activity is often associated with high tumor burden, this is not always the case and there is no definitive demonstration that blood LDH activity is directly derived from tumors cells. Our objectives were 1) to explore the biological impact of LDHA and LDHB independently of their metabolic function 2) to explore the respective prognostic values of the 5 LDH isoforms as well as the relationship between tumor and blood LDH isoforms repartition in melanoma patients.

Material, Patients, Methods: A375 melanoma cells cultured in glucose or galactose (to evaluate glycolytic independent effects) were silenced for LDHA or LDHB expression using si-RNAs. RNAseq analysis of total RNAs and polysomal RNAs was performed to explore the transcriptional and translational impacts of LDHA and LDHB expression. In melanoma patients treated with immunotherapy, the enzymatic activities of each of the 5 LDH isoforms (encoded by LDHA and LDHB) were measured in tumors and blood samples. The prognostic values of the distinct isoforms as well as the correlation between the isoforms distribution in blood and tumors were evaluated.

Results: In vitro, independently of their metabolic effect, both LDHA and LDHB had distinct transcriptional and translational impacts on the control of several key oncogenic pathways (adhesion, survival, proliferation, immunity) with a more important effect of LDHA vs LDHB silencing. In vivo, among 64 melanoma patients including 25% with high LDH, high LDH1 (B4) activity was significantly associated with response and overall survival (OS) whereas high LDH4 (A3B1) was inversely associated with response and OS. LDH1 and LDH4 were associated with survival even among patients with normal LDH levels. For patients with paired (tumor and blood) isoforms analysis, there was no correlation between isoforms repartition suggesting that blood LDH activity is not directly related to tumor LDH. Conclusion: In addition to their metabolic activity, LDH enzymes, particularly LDHA, control several key oncogenic pathways at the transcriptional level but also at the translational level for a set of genes involved in cancer biology. LDH1 and LDH4 isoforms blood levels are differentially correlated with response to immunotherapy and survival. They are more robust prognostic biomarkers than total blood LDH level used in our daily practice. Thus, LDH is much more than just a marker of tumor burden in melanoma and the origins, the significance and the roles of blood LDH isoforms need to be revisited. These results highlight the need to develop anticancer drugs targeting LDH, and especially LDHA.

Citation Format: Laura Soumoy, Virginie Quidville, Lisa Fredeau, Giuseppina Claps, Caroline Pradon, Ludovic Lacroix, Emilie Routier, Djaouida Belkadi, Séverine Roy, Feras Chehade, Stephan Vagner, Caroline Robert. Roles of lactate dehydrogenase (LDH) in melanoma: an underestimated prognostic biomarker [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2177.

Abstract 4282: Total RNA sequencing of frozen biopsies combined to k-mer sequence analysis identify new hallmarks of immune checkpoint therapy response in melanoma

Introduction: Predicting response to immune checkpoint inhibitors (ICI) is key for stratifying patients and identifying factors of resistance. The main recognized ICI response biomarkers in melanoma are T-cell gene expression signatures, PD-L1 expression and tumor clonal mutational burden, all of which are specific of responding tumors but nevertheless not robust enough to guide therapeutic strategies. Biomarkers of progression (eg. TGF-B) are scarce and inconsistent across studies. All current gene expression-based biomarkers of ICT-response are based on formalin-Fixed paraffin-embedded (FFPE) samples, sequenced using RNA capture or polyA+ libraries. This technique is known to incompletely represent RNA populations.

Patients, Material, Methods: Here we introduce the first total RNA-seq dataset from fresh frozen biopsies collected from 80 advanced melanoma patients, prior to treatment with anti PD-1 or combined anti-PD-1/anti-CTA4 therapy. The cohort included 43 responders and 37 non-responders based on RECIST best objective response. To ensure all possible RNA biomarkers are captured, we applied a k-mer based computational protocol that extracts all subsequences of fixed size (31 nt) from the raw RNA-seq reads and performs differential expression statistics on k-mers. This identifies response-specific RNA sequences independently of annotated genes, enabling identification of novel RNAs and RNA isoforms.

Results: In responding patients, this analysis identified a large number of immunoglobulin and HLA mRNA fragments, consistent with an immune-active microenvironment. However, the most remarkable finding was the specific expression in non-responding tumors of centromeric satellite repeats (HSAT-II and ALR elements) and of a set of intergenic loci which independently described the progressor population. Altogether, total RNA-seq biomarkers were found in most non-responding patients, providing the basis for a strong predictor of resistance. This contrasted with results in FFPE/capture seq data that showed few notable k-mers in the progressor group, due to the incomplete RNA sequencing. Our approach revealed a number of other unexpected markers, including a set of circular RNAs in responders and a mutant of the PRAME tumor-specific antigen in progressors. Our main finding is that the combination of frozen sample conservation and total (ribodepleted) RNA sequencing reveals a unique source of non-coding RNAs produced from pervasive transcription of intergenic and repeated regions, likely associated to chromatin derepression, that are not detected by the usual FFPE/capture seq methods.

Conclusion: We argue that these novel RNA sequences will be instrumental in the development of improved ICI-response predictors and a better understanding of resistance to ICI.

Citation Format: Hugues Hermann, Séverine Roy, Sandrine Agoussi, Emilie Routier, Céline Boutros, Djaouida Belkadi, Haoliang Xue, Antoine Lainé, Stephan Vagner, Daniel Gautheret, Caroline Robert. Total RNA sequencing of frozen biopsies combined to k-mer sequence analysis identify new hallmarks of immune checkpoint therapy response in melanoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4282.

At the crossroads of RNA biology, genome integrity and cancer

This article is the synthesis of the scientific presentations that took place during two international courses at Institute Curie, one on post-transcriptional gene regulation and the other on genome instability and human disease, that were joined together in their 2021 edition. This joined course brought together the knowledge on RNA metabolism and the maintenance of genome stability.

A PD-1 /PD-L1 proximity assay as a theranostic marker for PD-1 blockade in patients with metastatic melanoma

PURPOSE

Less than 50% of patients with melanoma respond to anti-PD1, and this treatment can induce severe toxicity. Predictive markers are thus needed to improve the benefit/risk ratio of immune checkpoint inhibitors (ICI). Baseline tumor parameters such as PD-L1 expression, CD8⁺ T cell infiltration, mutational burden and various transcriptomic signatures are associated with response to ICI but their predictive values are not sufficient. Interaction between PD1 and its main ligand, PDL1 appears a valuable target of anti-PD1 therapy. Thus, instead of looking at PD-L1 expression only, we evaluated the predictive value of the proximity between PD1 and its neighboring PD-L1 molecules in terms of response to anti-PD1 therapy.

EXPERIMENTAL DESIGN

PD1/PD-L1 proximity was assessed by proximity ligation assay (PLA) on 137 samples from two cohorts (exploratory n=66 and validation n=71) of samples from melanoma patients treated with anti-PD1+/-anti CTLA4. Additional predictive biomarkers such as PD-L1 expression (MELscore), CD8+ cells density and nanostring RNA signature were also evaluated.

RESULTS

A PD1/PD-L1 PLA model was developed to predict tumor response in an exploratory cohort and further evaluated in an independent validation cohort. This score showed higher predictive ability (AUC=0.85 and 0.79, in the two cohorts respectively) for PD1/PD-L1 PLA as compared to other parameters (AUC from 0.71 to 0.77). Progression free and overall survival were significantly longer in patients with high PLA values (p=0.00019 and p<0.0001 respectively).

CONCLUSION

The proximity between PD-1 and PD-L1, easily assessed by this PLA on one FFPE section, appears as a new biomarker of anti-PD1 efficacy.

BRCA2 promotes DNA-RNA hybrid resolution by DDX5 helicase at DNA breaks to facilitate their repair‡

The BRCA2 tumor suppressor is a DNA double-strand break (DSB) repair factor essential for maintaining genome integrity. BRCA2-deficient cells spontaneously accumulate DNA-RNA hybrids, a known source of genome instability. However, the specific role of BRCA2 on these structures remains poorly understood. Here we identified the DEAD-box RNA helicase DDX5 as a BRCA2-interacting protein. DDX5 associates with DNA-RNA hybrids that form in the vicinity of DSBs, and this association is enhanced by BRCA2. Notably, BRCA2 stimulates the DNA-RNA hybrid-unwinding activity of DDX5 helicase. An impaired BRCA2-DDX5 interaction, as observed in cells expressing the breast cancer variant BRCA2-T207A, reduces the association of DDX5 with DNA-RNA hybrids, decreases the number of RPA foci, and alters the kinetics of appearance of RAD51 foci upon irradiation. Our findings are consistent with DNA-RNA hybrids constituting an impediment for the repair of DSBs by homologous recombination and reveal BRCA2 and DDX5 as active players in their removal.

Evaluation of the efficacy of immunotherapy for non-resectable mucosal melanoma

BACKGROUND

Immune checkpoint inhibitors are now standard-of-care treatments for metastatic cutaneous melanoma. However, for rare sub-groups, such as mucosal melanomas, few published data are available, and with no established therapeutic guidelines. Our objective was to assess the response to anti-CTLA4 and anti-PD1 immunotherapy in patients with mucosal melanomas.

METHODS

We performed a single-center, prospective cohort analysis of patients with non-surgical locally advanced and/or metastatic mucosal melanoma receiving anti-CTLA4 and/or anti-PD1 immunotherapy from 2010 to 2016.

RESULTS

Forty-four patients were enrolled, including 18 (40.9%) with head and neck, 12 (27.3%) with vulvo-vaginal and 14 (31.8%) with ano-rectal primary tumours. Eleven (25%) patients had stage 3 disease, and 11 (25%) had distant metastases. The first-line immunotherapy was ipilimumab in 24 patients and pembrolizumab in 20. The objective response rate (ORR) was 8.2% (one complete response) for ipilimumab and 35% (four complete responses) for pembrolizumab. No significant difference was observed for primary tumour location. The median follow-up was 24 months (range 4-73). The median progression-free survival (PFS) in the first-line ipilimumab and pembrolizumab groups was 3 months [95% confidence interval (CI) 2.5-4.6] and 5 months (95% CI 2.6-33.1), respectively (p = 0.0147).

CONCLUSION

In the patients with unresectable and/or metastatic mucosal melanoma, we found ORR and PFS rates comparable to those in patients with cutaneous melanoma, with no significant differences in the types of mucosal surfaces involved. Anti-PD1 therapy has a more favorable benefit-risk ratio than ipilimumab and should be used preferentially.

A dose escalation phase 1 study of radiotherapy (RT) in combination with anti-cytotoxic-T-lymphocyte-associated antigen 4 (CTLA-4) monoclonal antibody ipilimumab in patients (pts) with metastatic melanoma

9549

Background: Preclinical findings have shown a synergy between RT and anti-CTLA-4 monoclonal antibody in several tumor animal models for both local tumor control and distant effects. Preliminary clinical data suggest that it could be due to an abscopal effect of RT. The Mel-Ipi-Rx phase 1 study aimed to determine the maximum tolerated dose (MTD) and safety profile of RT combined with ipilimumab in pts with metastatic melanoma. Methods: A 3+3 dose escalation design was used with 9, 15, 18 and 24 Gy dose of RT (in 3 fractions) at week 4 combined with 10 mg/kg ipilimumab (every 3 weeks for 4 doses). Pts with evidence of clinical benefit at week 12 were eligible for maintenance ipilimumab at 10 mg/kg every 12 weeks starting at week 24 until severe toxicity or disease progression based on immune-related response criteria (irRC). Results: 19 pts with advanced melanoma received ipilimumab between August 2011 and July 2015. Nine pts received the 4 doses of ipilimumab and 2 pts received maintenance ipilimumab (1 and 2 cycles respectively). All pts received the combined RT at week 4 in 3 fractions. All pts presented at least one AE of any grade. The most common AEs were asthenia, diarrhea, desease-related pain and fever. Grade 3 AEs occurred in 8 pts. They included colitis (n = 3), hepatitis (n = 2), anemia (n = 2), asthenia (n = 1), thyroid disorders (n = 1) and nausea/vomiting (n = 1). Nine pts discontinued the study owing to treatment-related adverse events including colitis (n = 6), hepatitis (n = 2) and DRESS (Drug Rash with Eosinophilia and systemic syndrome) (n = 1). DLT occurred in 2/6 pts in the cohort receiving 15 Gy. No drug-related death occurred. According to irRC, 4 partial responses (ORR: 21%) and 4 stable diseases were observed at week 24. The MTD was 9 Gy dose. One pt out of 12 treated in the 9 Gy cohort presented a DLT (grade 3 colitis). The median progression-free survival [95% CI] was 7.2 months [2.4 – 16.8]. The median overall survival [95% CI] was 14.4 months [7.2 – 20.4]. Conclusions: When combined with ipilimumab at 10 mg/kg, in the present design, the MTD of RT was 9 Gy. This combination appears to be associated with antitumor activity. Clinical trial information: 2010-020317-93.

Abstract B10: Inhibiting eIF4F-mediated adaptive translatome reprogramming is a salvage strategy for targted melanoma therapy

BRAFV600E mutation is observed in ~50% of melanomas. Once melanomas have progressed with acquired resistance to BRAF-targeted therapy, mutational heterogeneity presents a major challenge. While enormous effort has gone into understanding the molecular events in mutational acquired resistance, not much attention has been attributed to what happens during therapy phase when patients still respond to BRAF-targeted treatment. It has been hypothesized that initally drug-tolerant cells without bona fide mutational resistance may survive by cellular adaptations and undergo evolution over time towards acquired genetic mutational resistance. We defined the nature of eIF4F-mediated translatome reprogramming and its role during the early phase of targeted melanoma therapy before acquired mutational resistance developed. To explore the possibility that melanoma cells can develop resistance via drug-tolerant evolution (versus pre-existing mutation), we cultured over 1000 small pools (5000 cells each) of parental A375 cells (BRAFV600E) in the presence of vemurafenib and cobimetinib and monitored the emergence of resistant clones. 99.7% of the wells contained a small number of surviving, drug-tolerant cells after 3 weeks of drug exposure. Strikingly, to further demonstrate adaptive drug-tolerant cells exist as a mechanism of resistance evolution, we established A375 subclones derived from single cells to eliminate possible pre-existing mutational resistant cells. Indeed, in five independent single-cell subclones, no early resistant colonies emerged after 3 weeks of drug treatment. These drug-tolerant cells are transiently resistant to re-exposure of anti-BRAF or anti-MEK treatment, and the cells drifted back to the similar sensitivity compared to parental cells after ~9 days of drug-free culture. These drug-tolerant cells are instead more sensitive to eIF4F inhibition compared to parental cells, indicating that eIF4F plays a central role in reprogramming adaptive translatome of drug-tolerant cells. To study the eIF4F activity at single cell level, we developed a single cell image analysis pipeline by using proximity ligation assay and automatic image analysis. By cell image machine learning, we identified five types of eIF4F localization in a large population of melanoma cells. With the classification model, we classified each single drug-tolerant cell into one of the five localization type. Rather than modifying global translation rate in drug-tolerant cells, we revealed that cell-to-cell heterogeneity of the subcellular localization of eIF4F complex discriminates the parental and drug-tolerant cells. This indicates that differential localized eIF4F might initiate the translation of different subsets of genes in drug-tolerant cells. Particularly, the localization pattern of eIF4F is also dynamic. Consistent with the sensitivity of the drug-tolerant cells, the localization pattern of eIF4F drifted back to the similar distribution of parental cells after ~9 days of drug-free culture. Thus, we delineated a novel level of adaptive regulation of gene expression at translational level during the course of targeted melanoma therapy, which might provide a general mechanism of network rewiring during tumor evolution. This translational controlled network reprogramming is likely to be missed if one looks merely at the genetic alone, we thus stress the need to break the current “glass ceiling” of relying solely on genomic dataset analysis to advance cancer therapies.

Note: This abstract was not presented at the conference.

Citation Format: Shensi Shen, Caroline Robert, Stephan Vagner. Inhibiting eIF4F-mediated adaptive translatome reprogramming is a salvage strategy for targted melanoma therapy. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr B10.

Translational regulation of the mRNA encoding the ubiquitin peptidase USP1 involved in the DNA damage response as a determinant of Cisplatin resistance

Cisplatin (cis-diaminedichloroplatin (II), CDDP) is part of the standard therapy for a number of solid tumors including Non-Small-Cell Lung Cancer (NSCLC). The initial response observed is in most cases only transient and tumors quickly become refractory to the drug. Tumor cell resistance to CDDP relies on multiple mechanisms, some of which still remain unknown. In search for such mechanisms, we examined the impact of CDDP on mRNA translation in a sensitive and in a matched resistant NSCLC cell line. We identified a set of genes whose mRNAs are differentially translated in CDDP resistant vs. sensitive cells. The translation of the mRNA encoding the Ubiquitin-Specific Peptidase 1 (USP1), a Ubiquitin peptidase with important function in multiple DNA repair pathways, is inhibited by CDDP exposure in the sensitive cells, but not in the resistant cells. This lack of down-regulation of USP1 expression at the translational level plays a primary role in CDDP resistance since inhibition of USP1 expression or activity by siRNA or the small molecule inhibitor ML323, respectively is sufficient to re-sensitize resistant cells to CDDP. We involved the USP1 mRNA translation as a major mechanism of CDDP resistance in NSCLC cells and suggest that USP1 could be evaluated as a candidate predictive marker and as a therapeutic target to overcome CDDP resistance. More generally, our results indicate that analysis of gene expression at the level of mRNA translation is a useful approach to identify new determinants of CDDP resistance.

Abstract 758: Loss of USP1 translational control as a targetable cisplatin resistance mechanism in non-small cell lung cancer (NSCLC)

Backgroung :

Cisplatin is part of standard therapy for a number of solid tumors including lung cancer. The initial response to this antineoplastic agent is in most cases only transient and tumors quickly become resistant to the drug. The mechanisms of resistance have been intensively explored, mostly by functional high throughput screening methods or by genomic and transcriptomic approaches. Our aim was to analyze the translational reprogramming following cisplatin treatment in order to identify candidates that mediate cisplatin resistance.

Material and methods:

Here we explored the response of a sensitive and of a matched resistant NSCLC cell line to cisplatin at the level of the nascent proteome by performing polysome profiling. Cellular mRNAs were resolved on a linear sucrose gradient. The heavily translated mRNAs that are associated with ribosome particles (the so-called polysomes) could be isolated and competitively hybridized on a cDNA microarray against the total mRNA fraction. This approach enabled us to identify the mRNAs whose translation is modified upon cisplatin treatment in the resistant cells.

Results :

Amongst the 200 candidate genes identified by this approach, we focused on the Ubiquitin-Specific Peptidase 1 (USP1) gene regulation. We found that while the transcription of the gene remains unaffected in both the sensitive and the resistant cell lines, the translation of USP1 is modulated by cisplatin in the sensitive cells. The immediate response (4h after treatment) results in a decrease of USP1 mRNA translation, followed by a stimulation of the translation at a later time point (16h). Importantly, this translational regulation of USP1 is lost in the resistant cells which instead show a constitutively high translation rate for USP1. Inhibition of cell growth by cisplatin was potentiated when USP 1 expression was suppressed by siRNA. Similarly, ML323, a specific inhibitor of the USP1-UAF1 deubiquitinase complex, dramatically increased cell sensitivity to cisplatin. Thus interfering with USP1 activity in resistant cells by both an siRNA approach and the use of a small molecule inhibitor re-sensitized the resistant cells to cisplatin.

Conclusion:

Our original approach led to the identification of USP1 as a potential determinant of cisplatin resistance of a lung cancer cell line. USP1 protein levels in tumor samples could potentially serve as a predictive marker of the response to cisplatin. We suggest that small molecule inhibitors of USP1 should be tested as cisplatin-sensitizers. The analysis of the ‘nascent proteome’ by polysome profiling could enable the identification of additional candidates mediating cisplatin-resistance.

Citation Format: Carole Helissey, Tony Sourisseau, Hélène Mahieu, Céline Lefebvre, Stephan Vagner, Jean-Charles Soria, Ken Olaussen. Loss of USP1 translational control as a targetable cisplatin resistance mechanism in non-small cell lung cancer (NSCLC). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 758. doi:10.1158/1538-7445.AM2015-758

Abstract A23: eIF4F is a key and targetable convergence nexus of multiple mechanisms of resistance to anti-BRAF and anti-MEK cancer therapies

The V600E mutation in BRAF is the most frequent oncogenic mutation in human cancers, and can be targeted by specific anti-BRAF agents. However, several mechanisms of resistance have been identified, leading to reactivation of the initially blocked MAP-kinase pathway (known as ERK-dependent mechanisms) or reactivation of alternative ones, like the PI3K-AKT-mTOR pathway, or inhibition of the apoptotic cascade (ERK-independent). These pathways converge to regulate the formation of the eIF4F translation initiation complex that binds to the 7-methylguanosine cap at the 5′ end of mRNAs, thereby modulating mRNA translation of specific mRNAs. We addressed the potential role of the eIF4F eukaryotic translation initiation complex in resistance or sensitivity to anti-BRAF and anti-MEK agents in several BRAF mutant cells, xenografts and tumors. Our data demonstrate that the formation of the eIF4F complex is associated with most resistance mechanisms to these targeted therapies, independently of their capacity to reactivate or not the MAP-kinase pathway. Formation of this complex can be explored in tumor samples using a new in situ technology. Inhibitors of the eIF4F complex synergize with anti-BRAF agents and can thus reverse resistance.

Citation Format: Lise Boussemart, Helene Malka-Mahieu, Isabelle Girault, Delphine Allard, Oskar Hemmingson, Nyam Kamsu-Kom, Sandrine Agoussi, Alexander Eggermont, Laurent Desaubry, Caroline Robert, Stephan Vagner. eIF4F is a key and targetable convergence nexus of multiple mechanisms of resistance to anti-BRAF and anti-MEK cancer therapies. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr A23.

Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma

Treatment of BRAF(V600E) mutant melanoma by small molecule drugs that target the BRAF or MEK kinases can be effective, but resistance develops invariably. In contrast, colon cancers that harbour the same BRAF(V600E) mutation are intrinsically resistant to BRAF inhibitors, due to feedback activation of the epidermal growth factor receptor (EGFR). Here we show that 6 out of 16 melanoma tumours analysed acquired EGFR expression after the development of resistance to BRAF or MEK inhibitors. Using a chromatin-regulator-focused short hairpin RNA (shRNA) library, we find that suppression of sex determining region Y-box 10 (SOX10) in melanoma causes activation of TGF-β signalling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-β (PDGFRB), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-β results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-β becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells having varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug, but this is reversed when the drug treatment is discontinued. We find evidence for SOX10 loss and/or activation of TGF-β signalling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Our findings provide a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identify patients with EGFR-positive melanoma as a group that may benefit from re-treatment after a drug holiday.

Vemurafenib cooperates with HPV to promote initiation of cutaneous tumors

Treatment with RAF inhibitors such as vemurafenib causes the development of cutaneous squamous cell carcinomas (cSCC) or keratoacanthomas as a side effect in 18% to 30% of patients. It is known that RAF inhibitors activate the mitogen-activated protein kinase (MAPK) pathway and stimulate growth of RAS-mutated cells, possibly accounting for up to 60% of cSCC or keratoacanthoma lesions with RAS mutations, but other contributing events are obscure. To identify such events, we evaluated tumors from patients treated with vemurafenib for the presence of human papilloma virus (HPV) DNA and identified 13% to be positive. Using a transgenic murine model of HPV-driven cSCC (K14-HPV16 mice), we conducted a functional test to determine whether administration of RAF inhibitors could promote cSCC in HPV-infected tissues. Vemurafenib treatment elevated MAPK markers and increased cSCC incidence from 22% to 70% in this model. Furthermore, 55% of the cSCCs arising in vemurafenib-treated mice exhibited a wild-type Ras genotype, consistent with the frequency observed in human patients. Our results argue that HPV cooperates with vemurafenib to promote tumorigenesis, in either the presence or absence of RAS mutations.

Abstract P3-14-13: eIF4E/4EBP1 axis and response to neoadjuvant trastuzumab-based treatment in HER2+ breast cancer – Results of a multicentre French retrospective cohort

Background

Despite a growing number of studies exploring the underlying mechanisms, resistance to trastuzumab (TTZ) in HER2+ breast cancer (BC) remains elusive and an important issue in clinical practice. Among the proposed mechanisms, involvement of the PI3K/Akt/mTOR pathway is one of the best characterized. In a previous preclinical and clinical study (n = 54) (Bergé Y et al, SABCS 2009 and [1]), we have shown a significant correlation between eIF4E (a downstream effector of the PI3K/Akt/mTOR pathway) expression level as determined by immunohistochemistry (IHC) on initial tumor biopsy and pathological complete response (pCR) in patients with HER2+ BC treated with a neoadjuvant TTZ-containing regimen. The aim of this study was to validate these findings on an independent and larger cohort of HER2+ BC treated in neoadjuvant setting.

Method

In this multicenter (n = 9) study, 274 patients (pts) with HER2+ BC treated were included. All pts received neoadjuvant chemotherapy regimen containing TTZ, consisting mostly of 3-4 cycles of FEC (5FU, Epirubicin, Cyclophosphamid) followed by 3-4 cycles of TTZ–Docetaxel (n = 116). 74 pts received 6 cycles of TTZ–Docetaxel, 18 received 6 cycles of TTZ–Docetaxel-Cyclophosphamid, 12 received 6 cycles of TTZ–Docetaxel-carbolpatine, and the remaining 54 pts received other regimens. Pathological response was assessed according to Sataloff and Chevallier criteria. Unstained slides from the initial tumor biopsy were centrally collected for biomarkers analysis. Expression levels of eIF4E, p-4EBP1 and pS6 were determined by IHC. An immunoreactive score (IRS) combining the percentage of stained tumor cells and staining intensity was assessed by two pathologists.

Results

Median age at diagnosis was 50 years [range 22–84]. Most pts presented with T2 (52.6%), N1 (53.9%) stage, with a median tumor size of 40mm [range 0-150mm] as determined on clinical examination. Tumors were mainly invasive ductal of no special type (93.8%), of histological grade III (50%) and II (45%), ER+ (54.4%). Breast conserving surgery with free margins was achieved in 50.9% of pts. pCR (breast Sataloff TA) was observed in 53% of pts, and in 47.6% when considering both breast and lymph node response. Out of the 274 pts, 257 had sufficient tumor on the initial biopsy for biomarker analysis. Preliminary results showed a median eIF4E IRS of 6 [range 1-12], with 52.1% of cases displaying a low eIF4E expression level (IRS£6). The agreement for inter-observer assessment of eIF4E status was good (k = 0.618, 95% CI [0.523-0.713]). Scoring of p-4EBP1 and pS6 are ongoing and correlations of pCR with eIF4E/4EBP1 axis will be presented.

Conclusion

In this large multicentre retrospective study, the rate of pCR obtained in neoadjuvant setting of HER2+ BC is similar to those described in the literature. Thorough tumor collection allows biomarkers analysis, which has been specifically focused on downstream effectors of the PI3K/Akt/mTOR pathway.

Reference[1] Zindy P, Bergé Y, Allal B et al. Formation of the eIF4F translation-initiation complex determines sensitivity to anticancer drugs targeting the EGFR and HER2 receptors. Cancer Res. 2011;71(12):4068-73.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-14-13.