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 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.

Age at cancer onset in germline TP53 mutation carriers: association with polymorphisms in predicted G-quadruplex structures

Germline TP53 mutations predispose to multiple cancers defining Li-Fraumeni/Li-Fraumeni-like syndrome (LFS/LFL), a disease with large individual disparities in cancer profiles and age of onset. G-quadruplexes (G4s) are secondary structural motifs occurring in guanine tracks, with regulatory effects on DNA and RNA. We analyzed 85 polymorphisms within or near five predicted G4s in TP53 in search of modifiers of penetrance of LFS/LFL in Brazilian cancer families with (n = 35) or without (n = 110) TP53 mutations. Statistical analyses stratified on family structure showed that cancer tended to occur ~15 years later in mutation carriers who also carried the variant alleles of two polymorphisms within predicted G4-forming regions, rs17878362 (TP53 PIN3, 16 bp duplication in intron 3; P = 0.082) and rs17880560 (6 bp duplication in 3' flanking region; P = 0.067). Haplotype analysis showed that this inverse association was driven by the polymorphic status of the remaining wild-type (WT) haplotype in mutation carriers: in carriers with a WT haplotype containing at least one variant allele of rs17878362 or rs17880560, cancer occurred ~15 years later than in carriers with other WT haplotypes (P = 0.019). No effect on age of cancer onset was observed in subjects without a TP53 mutation. The G4 in intron 3 has been shown to regulate alternative p53 messenger RNA splicing, whereas the biological roles of predicted G4s in the 3' flanking region remain to be elucidated. In conclusion, this study demonstrates that G4 polymorphisms in haplotypes of the WT TP53 allele have an impact on LFS/LFL penetrance in germline TP53 mutation carriers.

Abstract 3120: Functional characterization of ERCC1 isoforms in NSCLC

Background: ERCC1 is a DNA repair protein whose expression is a prognostic and predictive biomarker of chemotherapy effect in NSCLC. Five alternative transcripts of the ERCC1 gene have been described or hypothesized to exist (isoforms 201 to 205). Nevertheless, little is known about the function and relative expression of these isoforms. We explored 3 main questions: a- Which ERCC1 isoforms are detected by clinically validated antibodies? b- Which isoforms are expressed in lung cancer cell lines and patient samples? c- Which isoforms are functional for removal of cisplatin DNA-adducts and potentially relevant as predictors of cisplatin resistance? Methods: To determine the specificity of anti-ERCC1 antibodies, a screening of isoform specific peptide sequences was achieved using a peptide array (Epitope Mapping CelluSpots™). The expression of ERCC1 isoforms was evaluated in 20 lung cancer cell lines and in 123 NSCLC patients by qRT-PCR. We established a functional DNA repair assay by monitoring the accumulation of cisplatin adducts over time with a specific antibody RC-18 (courtesy of Juergen Thomale, Germany). To investigate isoforms functionality, we created stable ERCC1 attenuated A549 cells with Zinc Finger Nucleases technology (Sigma). Using lentiviral constructs we rescued ERCC1 isoforms expression. Results: The 2 monoclonal antibodies, clone 8F1 and 3H11 recognize a conserved region shared by all isoforms of ERCC1 protein, and so, are unable to distinguish the different isoforms. The 5 isoforms were all detected at mRNA level, both in cancer cell lines and in patient tissues. Interestingly, a significant increase in isoform 201 expression was observed in all tumor tissues compared to normal counterparts. We obtained 7 A549 clones harboring a 85-95% decrease in ERCC1 expression. In these cells we observed a 7-fold increase in IC50 of cisplatin accompanied by a significant decrease in the rate of nucleotide excision repair (NER). We are currently exploring isoform function by analyzing DNA repair efficiency in the different stable cell lines. Conclusions: Alternative roles for ERCC1 beyond NER are currently emerging. Our 7 A549 clones, with stable and strong ERCC1 attenuation, provide a very promising tool to analyse all functions of ERCC1. Since most antibodies used to test ERCC1 positivity in patients do not distinguish the different isoforms, it is urgent to characterize their function further, particularly the role of isoform 201 overexpression in NSCLC tumors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3120. doi:1538-7445.AM2012-3120

Molecular Characteristics of ERCC1-Negative versus ERCC1-Positive Tumors in Resected NSCLC

PURPOSE

Excision repair cross-complementation group 1 (ERCC1) is a protein involved in repair of DNA platinum adducts and stalled DNA replication forks. We and others have previously shown the influence of ERCC1 expression upon survival rates and benefit of cisplatin-based chemotherapy in patients with resected non-small-cell lung cancer (NSCLC). However, little is known about the molecular characteristics of ERCC1-positive and ERCC1-negative tumors.

EXPERIMENTAL DESIGN

We took advantage of a cohort of 91 patients with resected NSCLC, for which we had matched frozen and paraffin-embedded samples to explore the comparative molecular portraits of ERCC1-positive and ERCC1-negative tumors of NSCLC. We carried out a global molecular analysis including assessment of ERCC1 expression levels by using both immunohistochemistry (IHC) and quantitative reverse transcriptase PCR (qRT-PCR), genomic instability, global gene and miRNA expression, and sequencing of selected key genes involved in lung carcinogenesis.

RESULTS

ERCC1 protein and mRNA expression were significantly correlated. However, we observed several cases with clear discrepancies. We noted that ERCC1-negative tumors had a higher rate of genomic abnormalities versus ERCC1-positive tumors. ERCC1-positive tumors seemed to share a common DNA damage response (DDR) phenotype with the overexpression of seven genes linked to DDR. The miRNA expression analysis identified miR-375 as significantly underexpressed in ERCC1-positive tumors.

CONCLUSIONS

Our data show inconsistencies in ERCC1 expression between IHC and qRT-PCR readouts. Furthermore, ERCC1 status is not linked to specific mutational patterns or frequencies. Finally, ERCC1-negative tumors have a high rate of genomic aberrations that could consequently influence prognosis in patients with resected NSCLC.

Abstract 1623: The spliceosome as a new therapeutic target for anticancer treatment

Background: Bioinformatics analyses of pathways that are differentially expressed between malignant and benign lesions could allow discovering new therapeutic targets. In the present study, we identified spliceosome assembly components as candidate target for cancer treatment. The spliceosome, an intracellular ribonucleoprotein complex, is involved in eukaryotic pre-mRNA processing by splicing out intronic nucleic acids.

Experimental procedures: Pathway analyses were done on exon and gene expression arrays datasets. Differential gene expression between malignant and benign lesions was applied to four public datasets. Small nuclear ribonucleoprotein E (SNRPE) downregulation was achieved by short interfering RNA technology in SKBr-3 and MDA-MB-231 human breast cancer cells. Functional effects of siRNA-induced knockdown of SNRPE expression on cell viability, cell cycle distribution and apoptosis were respectively determined using WST-1 assay, FACS analysis and annexin-V/7-AAD double-staining assay. Autophagy was investigated by electron microscopy (EM). We also evaluated alternative RNA splicing at the exon level using SpliceArray microarray.

Results: Pathway analyses with BioCarta database identified spliceosome assembly component (SAC) as the most differentially expressed pathway between breast malignant and benign lesions (permutation p=0.002). The differential expression of SAC was confirmed in four different public dataset on breast, ovarian, lung and skin cancers. Based on these data we investigated whether SNRPE, a component of spliceosome, could be a candidate target. Knockdown of SNRPE protein expression resulted in a high inhibition of SKBr-3 (70%) and MDA-MB-231 (48%) cell proliferation as compared to non-targeting siRNA-transfected cells. Splice array analyses suggested a deregulation of alternative splicing, together with a dramatic reduction of mTOR transcripts. mTOR downregulation, together with a decrease in phosphorylation of downstream protein in the mTOR pathway (i.e 4E-BP1) was confirmed by western blot analyses. We then investigated the mechanisms of cell death. siRNA-mediatd SNRPE knockdown was not found to induce typical apoptosis as annexin-V-positive cells were not detected. However, the presence of numerous vesicular organelle of autophagy revealed by EM is strongly amplified in SNRPE-transfected cells. This observed deregulation of the mTOR pathway in SNRPE-depleted cells might in part explain the induction of autophagy following SNRPE silencing.

Conclusion : Our data report that specific inactivation of SNRPE protein expression induces mTOR downregulation and autophagy in cancer cell lines, suggesting that the spliceosome could represent a new potential target that may open new perspectives in cancer therapy. Molecular mechanisms that lead to mTOR dowregulation by SNRPE extinction are being investigated.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1623. doi:10.1158/1538-7445.AM2011-1623

Occult infection of peripheral B cells by hepatitis C variants which have low translational efficiency in cultured hepatocytes

BACKGROUND

Plasma hepatitis C virus (HCV) originates from hepatocytes. However, in certain subjects, B cells may harbour both plasma strains and occult HCV strains tha t are not detected in the plasma. The internal ribosome entry site (IRES) of these latter strains is mutated, suggesting that the efficiency of viral translation could drive the cellular tropism of HCV.

AIMS

To determine if the translational efficiency of IRES variants in cultured hepatocytes or B cells is correlated with their cellular tropism in vivo.

METHODS

The efficiency of IRES of 10 B cell-specific variants and nine plasma variants, isolated from six patients with compartmentalised variants in B cells, was estimated by bicistronic dual luciferase expression in hepatocyte cell types (Huh7), in primary cultured human hepatocytes (PCHs) and in two B cell lines (Raji and Daudi).

RESULTS

For each of the six subjects, the plasma IRESes were significantly and repeatedly more efficient than B cell IRESes in Huh7 (1.7+/-0.3 vs 0.7+/-0.2; p<0.01) and PCH cells. In B cell lines, B cell and plasma IRES had similar low efficiencies (0.8+/-0.1 vs 0.9+/-0.1; NS). For three subjects, two IRES variants from the same compartment could be analysed, and had the same efficiency in each cell type. Silencing the lupus antigen, a known IRES trans-acting factor, inhibited plasma IRES variants to a greater extent than B cell-specific IRESes.

CONCLUSIONS

B cells can harbour occult variants that have a poor translational efficiency in hepatocytes, strongly suggesting their extra-hepatic origin and raising the hypothesis that competition between HCV variants with different IRESes is driven at a translational level in hepatic, as well as in extra-hepatic, sites.

Alternative splicing and breast cancer

Alternative splicing is a key molecular event in the gene expression process. It allows for the synthesis of different products from the same gene, and consequently increases the complexity of the proteome encoded by a limited number of genes. Although alterations of alternative splicing are among the myriad of alterations present in tumor cells, increasing evidence indicates that cancer-associated splicing variants play an important role in tumor initiation and progression. Therefore, alternative splicing studies are opening new avenues of research in basic and translational molecular oncology.

Abstract 2049: Post transcriptional regulation of RhoB expression

Rho GTPases contribute to most steps of cancer initiation and progression, including the acquisition of unlimited proliferation potential, survival, tissue invasion and the establishment of metastases. By contrast to RhoA and RhoC, RhoB has been proposed to act as a tumor suppressor as it is activated in response to various stresses including UV exposure, and since it has been reported to inhibit tumor growth, cell migration and invasion. Unlike RhoA and RhoC, RhoB is often down regulated in human tumour tissues including lung and head and neck cancer and its expression is inversely correlated with tumor aggressiveness. However, the epigenetic regulation of RhoB expression in cancer cells remains to be elucidated. Since several recent works demonstrate that post-transcriptional deregulation of gene expression is involved in carcinogenesis, we have investigated the post-transcriptional regulation of RhoB expression. The RhoB 3’ untranslated region is well conserved between species and has numerous putative binding sites for post-transcriptional regulators such as mRNA binding proteins and microRNAs. By using luciferase assays and polysome analysis, we have found that the translation of the RhoB mRNA is regulated upon UV exposure. One specific miRNA, miR-19b whose expression is regulated by UV, directly targets the RhoB mRNA to control RhoB expression and UV-induced apoptosis. Interestingly, other post-transcriptionnal regulators involved in RhoB expression, such as the mRNA binding proteins HuR and TiaR were also indentified by functional assays using RNA interference strategy. Immunohistochemical analysis on a cohort of human lung tissues ranging from normal to invasive carcinoma are underway to detect a possible correlation between the expression of these proteins and RhoB downregulation in tumor.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2049.

Exon-based clustering of murine breast tumor transcriptomes reveals alternative exons whose expression is associated with metastasis

In the field of bioinformatics, exon profiling is a developing area of disease-associated transcriptome analysis. In this study, we performed a microarray-based transcriptome analysis at the single exon level in mouse 4T1 primary mammary tumors with different metastatic capabilities. A novel bioinformatics platform was developed that identified 679 genes with differentially expressed exons in 4T1 tumors, many of which were involved in cell morphology and movement. Of 152 alternative exons tested by reverse transcription-PCR, 97 were validated as differentially expressed in primary tumors with different metastatic capability. This analysis revealed candidate progression genes, hinting at variations in protein functions by alternate exon usage. In a parallel effort, we developed a novel exon-based clustering analysis and identified alternative exons in tumor transcriptomes that were associated with dissemination of primary tumor cells to sites of pulmonary metastasis. This analysis also revealed that the splicing events identified by comparing primary tumors were not aberrant events. Lastly, we found that a subset of differentially spliced variant transcripts identified in the murine model was associated with poor prognosis in a large clinical cohort of patients with breast cancer. Our findings illustrate the utility of exon profiling to define novel theranostic markers for study in cancer progression and metastasis.

Influence of EIF4E and HER2 Protein Expression on the Response to Neoadjuvant Chemotherapy and Trastuzumab in Breast Cancer

Background:Resistance to trastuzumab (TTZ) is still poorly understood. Many proteins implicated in signaling pathways of breast cancer cells have so far been studied as potential markers of TTZ resistance in preclinical models.Method:63 consecutive patients were treated for HER2 + breast cancer with a neoadjuvant chemotherapy regimen containing TTZ between December 2003 and July 2008. This regimen was mostly 4 cycles of FEC 100 (5FU, Epirubicin and Cyclophosphamide) followed by 4 cycles of TTZ – Docetaxel 100mg/m².Immunohistochemistry (IHC) was used to analyse, in the initial biopsy, the expression of HER family receptors (EGFR, HER3, HER4 and HER2), PTEN, cMyc and p27. We also analyzed the expression of two proteins (eIF4E and 4EBP1) involved in translational control of mRNAs. 4EBP1 is a small protein that represses the initiation of protein translation through its association with eIF4E, the mRNA cap-binding subunit of the eIF4F complex. mTOR-dependent phosphorylation of 4E-BP1 decreases the affinity of the protein for eIF4E, which facilitates the formation of eIF4F complex. Furthermore, the expression of eIF4E is elevated in many cancers.We analysed the pathologic response rate (pRR) after chemotherapy + TTZ, and we established correlations between the expression of these markers and pRR.Results:Among the 63 patients, 54 had a valuable pre-chemotherapy biopsy.For those 54 patients, median age was 48 years (range [21;80]), median tumor size was 50 mm clinically (range [20;120]), and 26 mm by ultrasound (range [10;80]). Respectively 63%, 57% and 52% were estrogen receptor (ER) negative, progesterone receptor (PR) negative and ER/PR negative. Histology type was ductal infiltrant carcinoma for 91% of patients. Respectively 28% and 72% were grade SBR (EE) II and III.A pathologic complete response (pCR) (Sataloff TA) was observed on 63% of patients, 28% had a partial response but superior to 50% (Sataloff TB) and 9% had a poor or absent pathologic response (Sataloff TC and TD).This pCR was not statistically linked to any initial clinical characteristics (age, grade, hormonal status and tumoral size).pCR was strongly correlated with weak eIf4E and with percentage of HER2 strong-stained cells (respectively p=0,0114 et 0,0056). 93% of tumors with an eIF4E IRS &lt;7 (n=13/14) had a pCR, and only 5% (1/19) with an incomplete pRR had an eIF4E IRS &lt;7. Moreover, 78% (25/32) of tumors with 100% of tumoral cells harboring a strong intensity of HER2 had a pCR versus 41% (9/22) of tumors with less than 100% of cells expressing HER2 with a strong staining.Conclusion:Our study shows a strong correlation between eIF4E expression or HER2 expression and pRR in patients with HER2 + breast treated with a neoadjuvant TTZ-containing regimen. IHC of eIF4E might be a powerful test to predict sensitivity to TTZ.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2043.

Post-transcriptional control of gene expression through subcellular relocalization of mRNA binding proteins

Eukaryotic cells have developed multiple mechanisms to respond to different physiological cues, such as cellular stress, which allow the cells to adapt themselves to their new environment. The regulation of post-transcriptional gene expression is an important component of the cellular stress response and is mediated by mRNA binding proteins (mRBPs). Recently, several studies have shown that regulated subcellular localization of mRBPs upon diverse stimuli (such as cellular stress) provides an additional level of regulation for gene expression.

Characterization of a short isoform of human Tgs1 hypermethylase associating with small nucleolar ribonucleoprotein core proteins and produced by limited proteolytic processing

Tgs1 is the hypermethylase responsible for m(3)G cap formation of U small nuclear RNAs (U snRNAs) and small nucleolar RNAs (snoRNAs). In vertebrates, hypermethylation of snRNAs occurs in the cytoplasm, whereas this process takes place in the nucleus for snoRNAs. Accordingly, the hypermethylase is found in both compartments with a diffuse localization in the cytoplasm and a concentration in Cajal bodies in the nucleoplasm. In this study, we report that the Tgs1 hypermethylase exists as two species, a full-length cytoplasmic isoform and a shorter nuclear isoform of 65-70 kDa. The short isoform exhibits methyltransferase activity and associates with components of box C/D and H/ACA snoRNPs, pointing to a role of this isoform in hypermethylation of snoRNAs. We also show that production of the short Tgs1 isoform is inhibited by MG132, suggesting that it results from proteasomal limited processing of the full-length Tgs1 protein. Together, our results suggest that proteasome maturation constitutes a mechanism regulating Tgs1 function by generating Tgs1 species with different substrate specificities, subcellular localizations, and functions.

Testosterone regulates FGF-2 expression during testis maturation by an IRES-dependent translational mechanism

Spermatogenesis is a complex process involving cell proliferation, differentiation, and apoptosis. Fibroblast growth factor 2 (FGF-2) is involved in testicular function, but its role in spermatogenesis has not been fully documented. The control of FGF-2 expression particularly occurs at the translational level, by an internal ribosome entry site (IRES)-dependent mechanism driving the use of alternative initiation codons. To study IRES activity regulation in vivo, we have developed transgenic mice expressing a bicistronic construct coding for two luciferase genes. Here, we show that the FGF-2 IRES is age-dependently activated in mouse testis, whereas EMCV and c-myc IRESs are not. Real-time PCR confirms that this regulation is translational. By using immunohistological techniques, we demonstrate that FGF-2 IRES stimulation occurs in adult, but not in immature, type-A spermatogonias. This is correlated with activation of endogenous FGF-2 expression in spermatogonia; whereas FGF-2 mRNA transcription is known to decrease in adult testis. Interestingly, the FGF-2 IRES activation is triggered by testosterone and is partially inhibited by siRNA directed against the androgen receptor. Two-dimensional analysis of proteins bound to the FGF-2 mRNA 5'UTR after UV cross-linking reveals that testosterone treatment correlates with the binding of several proteins. These data suggest a paracrine loop where IRES-dependent FGF-2 expression, stimulated by Sertoli cells in response to testosterone produced by Leydig cells, would in turn activate Leydig function and testosterone production. In addition, nuclear FGF-2 isoforms could be involved in an intracrine function of FGF-2 in the start of spermatogenesis, mitosis, or meiosis initiation. This report demonstrates that mRNA translation regulation by an IRES-dependent mechanism participates in a physiological process.

Chemical-Based Translational Induction of Luciferase Expression: An Efficient Tool for in Vivo Screening of Protein Farnesylation Inhibitors

We describe the development of a cell system for in vivo screening of inhibitors of the mevalonate pathway. To this aim, we have constructed a bicistronic mRNA, transcribed from a constitutive cytomegalovirus promoter, containing the Renilla reniformis luciferase RNA open reading frame sequence as first cistron and the Firefly luciferase RNA sequence as a second cistron. The intercistronic space is made of the R17 binding sequence of the bacteriophage R17 protein. A chimeric protein able to bind to a specific sequence in the hairpin and to induce internal ribosome entry in the RNA switches on translation of the second cistron. This chimeric protein is made up of the bacteriophage RNA binding domain (R17) fused to the ribosome recruitment core of the eIF-4G1 eukaryotic translation initiation factor and to the CAAX box of H-Ras addressing the protein to the plasma membrane where it is not efficient. Internal ribosome entry upstream of the Firefly cistron is therefore under the dependence of the mevalonate pathway inhibitors. Indeed, products that are able to inhibit protein farnesylation rescue the cytoplasmic location of the R17-eIF-4G-CAAX protein, which once more becomes a translation factor for the expression of the second cistron. To exemplify the system, the present work checks the ability of various antiestrogens to interfere with the mevalonate pathway. It seems that pure antiestrogen, able to selectively bind the estrogen receptor, is unable to switch on the second Firefly cistron although selective antiestrogen-binding-site ligands are able to do so.

Irresistible IRES. Attracting the translation machinery to internal ribosome entry sites

Studies on the control of eukaryotic translation initiation by a cap-independent recruitment of the 40S ribosomal subunit to internal messenger RNA sequences called internal ribosome entry sites (IRESs) have shown that these sequence elements are present in a growing list of viral and cellular RNAs. Here we discuss their prevalence, mechanisms whereby they may function and their uses in regulating gene expression.

The carboxyl terminus of vertebrate poly(A) polymerase interacts with U2AF 65 to couple 3'-end processing and splicing

Although it has been established that the processing factors involved in pre-mRNA splicing and 3'-end formation can influence each other positively, the molecular basis of this coupling interaction was not known. Stimulation of pre-mRNA splicing by an adjacent cis-linked cleavage and polyadenylation site in HeLa cell nuclear extract is shown to occur at an early step in splicing, the binding of U2AF 65 to the pyrimidine tract of the intron 3' splice site. The carboxyl terminus of poly(A) polymerase (PAP) previously has been implicated indirectly in the coupling process. We demonstrate that a fusion protein containing the 20 carboxy-terminal amino acids of PAP, when tethered downstream of an intron, increases splicing efficiency and, like the entire 3'-end formation machinery, stimulates U2AF 65 binding to the intron. The carboxy-terminal domain of PAP makes a direct and specific interaction with residues 17-47 of U2AF 65, implicating this interaction in the coupling of splicing and 3'-end formation.

Position-dependent inhibition of the cleavage step of pre-mRNA 3'-end processing by U1 snRNP

The 3' ends of most eukaryotic pre-mRNAs are generated by 3' endonucleolytic cleavage and subsequent polyadenylation. 3'-end formation can be influenced positively or negatively by various factors. In particular, U1 snRNP acts as an inhibitor when bound to a 5' splice site located either upstream of the 3'-end formation signals of bovine papilloma virus (BPV) late transcripts or downstream of the 3'-end processing signals in the 5' LTR of the HIV-1 provirus. Previous work showed that in BPV it is not the first step, 3' cleavage, that is affected by U1 snRNP, but rather the second step, polyadenylation, that is inhibited. Since in HIV-1 the biological requirement is to produce transcripts that read through the 5' LTR cleavage site rather than being cleaved there, this mechanism seemed unlikely to apply. The obvious difference between the two examples was the relative orientation of the 3'-end formation signals and the U1 snRNP-binding site. In vitro assays were therefore used to assess the effect of U1 snRNP bound at various locations relative to a cleavage/polyadenylation site on the 3' cleavage reaction. U1 snRNP was found to inhibit cleavage when bound to a 5' splice site downstream of the cleavage/polyadenylation site, as in the HIV-1 LTR. U1 snRNP binding at this location was shown not to affect the recruitment of multiple cleavage/polyadenylation factors to the cleavage substrate, indicating that inhibition is unlikely to be due to steric hindrance. Interactions between U1A, U1 70K, and poly(A) polymerase, which mediate the effect of U1 snRNP on polyadenylation of other pre-mRNAs, were shown not to be required for cleavage inhibition. Therefore, U1 snRNP bound to a 5' splice site can inhibit cleavage and polyadenylation in two mechanistically different ways depending on whether the 5' splice site is located upstream or downstream of the cleavage site.

A new 34-kilodalton isoform of human fibroblast growth factor 2 is cap dependently synthesized by using a non-AUG start codon and behaves as a survival factor

Four isoforms of human fibroblast growth factor 2 (FGF-2) result from alternative initiations of translation at three CUG start codons and one AUG start codon. Here we characterize a new 34-kDa FGF-2 isoform whose expression is initiated at a fifth initiation codon. This 34-kDa FGF-2 was identified in HeLa cells by using an N-terminal directed antibody. Its initiation codon was identified by site-directed mutagenesis as being a CUG codon located at 86 nucleotides (nt) from the FGF-2 mRNA 5' end. Both in vitro translation and COS-7 cell transfection using bicistronic RNAs demonstrated that the 34-kDa FGF-2 was exclusively expressed in a cap-dependent manner. This contrasted with the expression of the other FGF-2 isoforms of 18, 22, 22.5, and 24 kDa, which is controlled by an internal ribosome entry site (IRES). Strikingly, expression of the other FGF-2 isoforms became partly cap dependent in vitro in the presence of the 5,823-nt-long 3' untranslated region of FGF-2 mRNA. Thus, the FGF-2 mRNA can be translated both by cap-dependent and IRES-driven mechanisms, the balance between these two mechanisms modulating the ratio of the different FGF-2 isoforms. The function of the new FGF-2 was also investigated. We found that the 34-kDa FGF-2, in contrast to the other isoforms, permitted NIH 3T3 cell survival in low-serum conditions. A new arginine-rich nuclear localization sequence (NLS) in the N-terminal region of the 34-kDa FGF-2 was characterized and found to be similar to the NLS of human immunodeficiency virus type 1 Rev protein. These data suggest that the function of the 34-kDa FGF-2 is mediated by nuclear targets.

Alternative translation of the proto-oncogene c-myc by an internal ribosome entry site

The human proto-oncogene c-myc encodes two proteins, c-Myc1 and c-Myc2, from two initiation codons, CUG and AUG, respectively. It is also transcribed from four alternative promoters (P0, P1, P2, and P3), giving rise to different RNA 5'-leader sequences, the long sizes of which suggest that they must be inefficiently translated by the classical ribosome scanning mechanism. Here we have examined the influence of three c-myc mRNA 5'-leaders on the translation of chimeric myc-CAT mRNAs. We observed that in the reticulocyte rabbit lysate, these 5'-leaders lead to cap-independent translation initiation. To determine whether this kind of initiation resulted from the presence of an internal ribosome entry site (IRES), COS-7 cells were transfected with bicistronic vectors containing the different c-myc 5'-leaders in the intercistronic region. An IRES was identified, requiring elements located within the P2 leader, between nucleotides -363 and -94 upstream from the CUG start codon. This is the first demonstration of the existence of IRES-dependent translation for a proto-oncogene. This IRES could be a translation enhancer, allowing activation of c-myc expression under the control of trans-acting factors and in response to specific cell stimuli.

Involvement of the carboxyl terminus of vertebrate poly(A) polymerase in U1A autoregulation and in the coupling of splicing and polyadenylation

Interactions required for inhibition of poly(A) polymerase (PAP) by the U1 snRNP-specific U1A protein, a reaction whose function is to autoregulate U1A protein production, are examined. PAP inhibition requires a substrate RNA to which at least two molecules of U1A protein can bind tightly, but we demonstrate that the secondary structure of the RNA is not highly constrained. A mutational analysis reveals that the carboxy-terminal 20 amino acids of PAP are essential for its inhibition by the U1A-RNA complex. Remarkably, transfer of these amino acids to yeast PAP, which is otherwise not affected by U1A protein, is sufficient to confer U1A-mediated inhibition onto the yeast enzyme. A glutathione S-transferase fusion protein containing only these 20 PAP residues can interact in vitro with an RNA-U1A protein complex containing two U1A molecules, but not with one containing a single U1A protein, explaining the requirement for two U1A-binding sites on the autoregulatory RNA element. A mutational analysis of the U1A protein demonstrates that amino acids 103-119 are required for PAP inhibition. A monomeric synthetic peptide consisting of the conserved U1A amino acids from this region has no detectable effect on PAP activity. However, the same U1A peptide, when conjugated to BSA, inhibits vertebrate PAP. In addition to this activity, the U1A peptide-BSA conjugate specifically uncouples splicing and 3'-end formation in vitro without affecting uncoupled splicing or 3'-end cleavage efficiencies. This suggests that the carboxy-terminal region of PAP with which it interacts is involved not only in U1A autoregulation but also in the coupling of splicing and 3'-end formation.

Translation of CUG- but not AUG-initiated forms of human fibroblast growth factor 2 is activated in transformed and stressed cells

Four isoforms of the human fibroblast growth factor 2 (FGF-2), with different intracellular localizations and distinct effects on cell phenotype, result from alternative initiations of translation at three CUG and one AUG start codons. We showed here by Western immunoblotting and immunoprecipitation that the CUG-initiated forms of FGF-2 were synthesized in transformed cells, whereas "normal" cells almost exclusively produced the AUG-initiated form. CUG-initiated FGF-2 was induced in primary skin fibroblasts in response to heat shock and oxidative stress. In transformed cells and in stressed fibroblasts, CUG expression was dependent on cis-elements within the 5' region of FGF-2 mRNA and was not correlated to mRNA level, indicating a translational regulation. UV cross-linking experiments revealed that CUG expression was linked to the binding of several cellular proteins to FGF-2 mRNA 5' region. Since translation of FGF-2 mRNA was previously shown to occur by internal ribosome entry, a nonclassical mechanism already described for picornaviruses, the cross-linking patterns of FGF-2 and picornavirus mRNAs were compared. Comigration of several proteins, including a p60, was observed. However, this p60 was shown to be different from the p57/PTB internal entry factor, suggesting a specificity towards FGF-2 mRNA. We report here a process of translational activation of the FGF-2 CUG-initiated forms in direct relation with trans-acting factors specific to transformed and stressed cells. These data favor a critical role of CUG-initiated FGF-2 in cell transformation and in the stress response.

Relief of ornithine decarboxylase messenger RNA translational repression induced by alternative splicing of its 5' untranslated region

The ornithine decarboxylase enzyme (ODC) is the key regulator of polyamine synthesis and is a member of the cellular proto-oncogene family. Its expression becomes constitutively activated by carcinogens, viruses, and oncogenes. ODC mRNA has a long 5' untranslated region that could be important in the regulation of enzyme levels by affecting translation. To test this hypothesis, we have determined the role of this region on the constitutive ODC hyperexpression measured in AR4-2J cells, an azaserine-induced, tumor-derived pancreatic acinar cell line. Construction of expression vectors in which ODC 5' leader sequence was placed flanking the chloramphenicol acetyltransferase reporter gene allowed us to identify three AR4-2J specific, different alternatively spliced ODC 5' leaders. The 5' ends of exons 2 and 3 were lengthened by 17 and 13 bases, respectively. Translation performed in a cell-free system as well as in COS7 transient transfection experiments demonstrated that AR4-2J isoforms induce a strong increase in the rate of translation. These results provide evidence that alternative splicing observed in tumoral cells, coupled with translation regulation, relieves the translation repression mediated by the long and structured 5' untranslated region of the ODC proto-oncogene.

Alternative translation initiation of the Moloney murine leukemia virus mRNA controlled by internal ribosome entry involving the p57/PTB splicing factor

Moloney murine leukemia virus (Mo-MuLV) genomic mRNA codes for two gag precursors by alternative initiations of translation. An AUG codon governs the synthesis of the retroviral capsid proteins precursor, whereas a CUG codon directs the synthesis of a glycosylated cell surface antigen, the gross cell surface antigen. Control of the relative synthesis of the two precursors is crucial for MuLV infectivity and pathology. Furthermore, the MuLV mRNA leader sequence is very long and should inhibit translation according to the classical scanning model. This suggests a different translation initiation mechanism allowing gag efficient expression. We demonstrate, by using bicistronic vectors expressed in COS-7 cells, that the Mo-MuLV mRNA leader drives translation initiation by internal ribosome entry. We have localized the internal ribosome entry site (IRES) between the two initiation codons. This 126 nucleotide long IRES implies an oligopyrimidine tract located 45 nucleotides upstream of AUG codon. UV cross-linking and affinity chromatography experiments show that the PTB/p57 splicing factor specifically interacts with this oligopyrimidine tract. The MuLV IRES controls alternative translation initiation by activating the capsid protein precursor expression. This gag translational enhancer could exist in other retroviruses.

Alternative translation of human fibroblast growth factor 2 mRNA occurs by internal entry of ribosomes

Alternative initiations of translation of the human fibroblast growth factor 2 (FGF-2) mRNA, at three CUG start codons and one AUG start codon, result in the synthesis of four isoforms of FGF-2. This process has important consequences on the fate of FGF-2: the CUG-initiated products are nuclear and their constitutive expression is able to induce cell immortalization, whereas the AUG-initiated product, mostly cytoplasmic, can generate cell transformation. Thus, the different isoforms probably have distinct targets in the cell. We show here that translation initiation of the FGF-2 mRNA breaks the rule of the cap-dependent ribosome scanning mechanism. First, translation of the FGF-2 mRNA was shown to be cap independent in vitro. This cap-independent translation required a sequence located between nucleotides (nt) 192 and 256 from the 5' end of the 318-nt-long 5' untranslated region. Second, expression of bicistronic vectors in COS-7 cells indicated that the FGF-2 mRNA is translated through a process of internal ribosome entry mediated by the mRNA leader sequence. By introducing additional AUG codons into the RNA leader sequence, we localized an internal ribosome entry site to between nt 154 and 318 of the 5' untranslated region, just upstream of the first CUG. The presence of an internal ribosome entry site in the FGF-2 mRNA suggests that the process of internal translation initiation, by controlling the expression of a growth factor, could have a crucial role in the control of cell proliferation and differentiation.