Our research axes

SR proteins are critical regulators of constitutive and alternative pre-mRNA splicing. We previously demonstrated that SR proteins (namely SRSF1, SRSF2, SRSF6) are up-regulated in NSCLCs and neuroendocrine lung tumors as compared to normal lung tissues (Edmond et al., 2011; Gout et al., 2012). These data supported a role of SR proteins in lung tumor progression. Up to now, the molecular mechanisms by which these proteins contribute to lung tumorigenesis remain largely unknown. We recently obtained results demonstrating that SRSF2 overexpression promotes replication/transcription-dependent DNA double strand breaks and regulates DNA repair to allow survival of NSCLC cell lines. More and more studies have now reported a link between RNA binding proteins and DNA Damage signaling to control genomic stability. Genomic instability increases tumor mutation rate and promotes tumor progression. In addition, recent studies have proposed that genomic instability also contributes to tumor escape from therapies by increasing mutations. In this axis, we want to better understand the role of SR proteins in the DNA damage response related to therapeutic resilience in NSCLC treated with targeted therapies (such as EGFR-TKI) in link with genomic instability. In this setting, we want to investigate the contribution of SR proteins to error-prone versus non-error-prone DNA repair processes. To answer our objectives, we are currently developing cellular tools derived from various NSCLC cell lines in which SR proteins will be either knocked-down or overexpressed. The consequences of SR proteins modulation in the response/escape of NSCLC to targeted therapies will be assessed.

In eukaryotes, constitutive and alternative RNA splicing is a key process that controls gene expression and regulates proteome diversity. These recent years, high throughput transcriptomic analyses have led to the identification of thousands splice variants that are aberrantly expressed in cancers, and that allow to distinguish between tumors and normal tissues, tumor types or clinical stage. Although the functional consequences of most of these cancer-associated aberrant splice variants remain unknown, RNA splicing alterations have been shown to contribute to all the hallmarks of cancer. Beside its role in promoting tumor initiation and/or maintenance, deregulated RNA splicing contributes to drug resistance (either primary or secondary). However, this is still an emerging field with only a few examples being described up to now, notably in the context of acquired resistance. Some studies highly support the idea that spliceosome inhibitors could be promising molecular target drugs used alone or in combination with conventional/targeted therapies. However, the molecular mechanisms sustaining their effects remain to be elucidated.

In patients with non-small cell lung carcinomas (NSCLC) with no targetable activating mutations, chemotherapy based on platinum salts (cisplatin, carboplatin) remains one of the cornerstones of treatment in association or not with immunotherapies. However, even in the 30% of responders, treatment efficacy remains limited by the recurrent appearance of resistance. We have shown that some inhibitors of the splicing machinery induce the death of lung cancer cells with acquired resistance to chemotherapy (platinum salts). Using classical and analytical approaches in 2D and 3D culture as well as global RNA sequencing analyses, our objectives are to understand the molecular mechanisms (involving or not splicing modifications of targeted genes) involved in the anti-cancer response induced by splicing machinery inhibitors and to identify new combinatory therapeutic strategies. The most promising therapeutic associations will be validated in patient-derived xenografts (PDX) which response to platinum salts is known (Coll D. Decaudin, Institut Curie).

EGFR tyrosine kinase inhibitors (EGFR-TKI) have revolutionized the natural history of patients with metastatic lung cancer by extending progression-free survival compared to conventional chemotherapy. However, despite a high response rate, resistance to EGFR-TKI is an inevitable phenomenon occurring after 9 to 20 months of treatment despite the development of different generations of EGFR-TKIs. The molecular characterization of tumors having progressed under EGFR-TKI is therefore a crucial issue for adapting the therapeutic strategy in order to prolong patient survival. Recent studies show that RNA splicing alterations may play a role in resistance to targeted cancer therapies. To test the contribution of RNA splicing reprogramming to the development of acquired resistance to EGFR-TKI in NSCLC, we have generated or obtained by collaboration (A.Maraver, Montpellier) lung tumor cell lines with acquired resistance to 1st, 2nd or 3rd generation EGFR-TKIs. Using RNA sequencing techniques and bioinformatics analysis (coll. D.Auboeuf, ENS, Lyon) we have demonstrated distinct splicing profiles between sensitive parental cells and resistant cells. We have shown that the accumulation of the β isoform of ATG16-L1 in resistant cells inhibits autophagy and thereby prevents the induction of apoptosis in response to treatment with 1st and 2nd generation TKIs (Hatat AS et al Mol. Oncol. 2022). More recently we have identified another splice variant whose accumulation could be a resistance mechanism common to all generations of EGFR-TKIs by inhibiting the apoptosis induced by these drugs. We use 2D and 3D cell culture models and mouse xenografts (Coll. D.Decaudin, Curie, Paris) to study the molecular mechanisms involved in this resistance and identify new therapeutic strategies. We are also developing the RNA BaseScope technology to study the expression of this splice variant in paired tumor biopsies (before/after treatment) from lung cancer patients treated with EGFR TKIs.

Circular RNAs (circRNAs) belong to a new category of mostly non-coding RNAs. Due to their circularity, circRNAs are more stable than linear RNAs because they are less subject to degradation by RNAses. In recent years, their role in the initiation and progression of cancers as well as in the response to treatments has emerged, but the molecular mechanisms involved remain largely unknown. Importantly, at the clinical level, circRNAs also appear to be promising biomarkers for the diagnosis and prognosis of cancers due to the possibility of detecting them in liquid biopsies, in particular via their ability to be secreted into exosomes.In patients with non-small cell lung carcinomas (NSCLC) with no targetable activating mutations, chemotherapy based on platinum salts (cisplatin, carboplatin) remains one of the cornerstones of treatment in combination or not with immunotherapies. However, even in the 30% of responder patients, the efficacy of the treatment remains limited by the recurrent appearance of resistance. We have developed different cellular models of lung tumor with secondary resistance to platinum salts and have identified by a RNA sequencing approach different circRNAs that are overexpressed in resistant cells compared to sensitive cells. We combine 2D and 3D culture approaches to (1) characterize the molecular mechanisms by which identified circRNAs contribute to chemotherapy resistance; (2) study the impact of these circRNAs expressed by tumor cells on cells of the tumor microenvironment using fibroblasts and macrophages as study models. We have developed the digital droplet PCR (ddPCR) technique to quantify the expression of these circRNAs in exosomes purified from plasmas of patients who have been treated with platinum salts and for whom the clinical response is known. This will allow us to test the potential of these circRNAs as predictive biomarkers of treatment response.