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Uveal melanoma (UM), the most common primary intraocular tumor in adults, has been extensively characterized by omics technologies during the last 5 years. Despite the discovery of gene signatures, the molecular actors driving the cancer aggressiveness are not fully understood and UM is still associated to a dismal overall survival at metastatic stage. Here, we showed that microRNA-16 (miR-16) is involved in uveal melanoma by an unexpected mechanism. By defining the miR-16-interactome, we revealed that miR-16 mainly interacts via non-canonical base-pairing to a subset of RNAs, promoting their expression levels (sponge RNAs). Consequently, the canonical miR-16 activity, involved in the RNA decay of oncogenes such as cyclin D1 and D3, is impaired. This miR-16 non-canonical base-pairing to sponge RNAs can explain both the derepression of miR-16 targets and the promotion of oncogenes expression observed for patients with poor overall survival in two cohorts. miR-16 activity assessment using our sponge-signature discriminates the patient’s overall survival as efficiently as the current method based on copy number variations and driver mutations detection. To conclude, miRNA loss of function due to miRNA sequestration seems to promote cancer burden by two combined events – “loss of brake and an acceleration”. Our results highlight the oncogenic role of the non-canonical base-pairing between miRNAs/mRNAs in uveal melanoma.

Most genetic alterations that drive melanoma development and resistance to targeted therapy have been uncovered. In contrast, and despite their increasingly recognized contribution, little is known about the non‐genetic mechanisms that drive these processes. Here, we performed in vivo gain‐of‐function CRISPR screens and identified SMAD3, BIRC3, and SLC9A5 as key actors of BRAFi resistance. We show that their expression levels increase during acquisition of BRAFi resistance and remain high in persister cells and during relapse. The upregulation of the SMAD3 transcriptional activity (SMAD3‐signature) promotes a mesenchymal‐like phenotype and BRAFi resistance by acting as an upstream transcriptional regulator of potent BRAFi‐resistance genes such as EGFR and AXL. This SMAD3‐signature predicts resistance to both current melanoma therapies in different cohorts. Critically, chemical inhibition of SMAD3 may constitute amenable target for melanoma since it efficiently abrogates persister cells survival. Interestingly, decrease of SMAD3 activity can also be reached by inhibiting the Aryl hydrocarbon Receptor (AhR), another druggable transcription factor governing SMAD3 expression level. Our work highlights novel drug vulnerabilities that can be exploited to develop long‐lasting antimelanoma therapies., Using a CRISPR activation screening, we identified genes involved in BRAF inhibitor (BRAFi) resistance in cutaneous melanoma. Their upregulation promoted tumour growth of therapy‐naïve melanoma cells and BRAFi‐resistance. Inhibition of these genes (not mutated) may be useful for therapy.

Most genetic alterations that drive melanoma development and resistance to targeted therapy have been uncovered. In contrast, and despite their increasingly recognized contribution, little is known about the non-genetic mechanisms that drive these processes. Here, we performed in vivo gain-of-function CRISPR screens and identified SMAD3, BIRC3 and SLC9A5 as key actors of BRAFi-resistance and these genes promote the tumor growth capability of persister cells. We show that their expression levels increase during acquisition of BRAFi-resistance, and remain high in persister cells and during relapse. The upregulation of the SMAD3 transcriptional activity (SMAD3-signature) promotes a mesenchymal-like phenotype and BRAFi-resistance by acting as an upstream transcriptional regulator of potent BRAFi-resistance genes such as EGFR and AXL. This SMAD3-signature predicts resistance to both current melanoma therapies in different cohorts. Critically, chemical inhibition of SMAD3 may constitute amenable target for melanoma since it efficiently abrogates persister cells survival. Interestingly, decrease of SMAD3 activity can also be reached by inhibiting the aryl hydrocarbon receptor (AhR), another druggable transcription factor governing SMAD3 expression level. Our work expands our understanding of the biology of persister cells and highlight novel drug vulnerabilities that can be exploited to develop long-lasting antimelanoma therapies.

International audience; Antisense oligonucleotides (ASOs) represent a new and highly promising class of drugs for personalized medicine. In the last decade, major chemical developments and improvements of the backbone structure of ASOs have transformed them into true approved and commercialized drugs. ASOs target both DNA and RNA, including pre-mRNA, mRNA, and ncRDA, based on sequence complementary. They are designed to be specific for each identified molecular and genetic alteration to restore a normal, physiological situation. Thus, the characterization of the underpinning mechanisms and alterations that sustain pathology is critical for accurate ASO-design. ASOs can be used to cure both rare and common diseases, such as orphan genetic alterations and cancer. Through pioneering examples, this review shows the versatility of the mechanisms of action that provide ASOs with the potential capacity to achieve custom treatment, revolutionizing personalized medicine. This article is categorized under RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions

Introduction La plupart des melanomes sont porteurs d’un grand nombre de mutations, parmi lesquelles il n’est pas aise de distinguer les mutations passageres des mutations oncogeniques pilotes. Pour mettre en evidence de nouvelles mutations oncogeniques ciblables dans les melanomes, nous avons propose la realisation d’un mini-exome a des patients jeunes atteints de melanome en cas de contexte evocateur de predisposition familiale aux cancers quand les recherches prealables de mutations germinales d’oncogenes classiques s’etaient revelees negatives. Materiel et methodes Un mini-exome incluant 4816 genes a ete realise sur ADN germinal. Les tests cellulaires fonctionnels de perte de fonction ont ete realises par transfection de siRNA et/ou de plasmides mutes ou sauvages de KAT6B sur lignees cellulaires. L’expression des genes regules par KAT6B (BRM, Bax et p21) a ete mesuree par RTqPCR. Observations Chez une patiente de 23 ans avec un melanome ayant de multiples antecedents familiaux de cancers cote maternel, les recherches oncogenetiques classiques etaient negatives. L’exome medical a identifie une mutation heterozygote jamais decrite T931 M du gene KAT6B, codant pour l’histone 3 lysine acetyl transferase, mutation tres fortement pathogene selon les algorithmes predictifs. Parmi 7 apparentes, 4/7 etaient porteurs de cette mutation, chacun d’eux ayant eu au moins un cancer. Les 3/7 autres apparentes n’etaient pas porteurs et n’ont pas d’antecedent de cancer a ce jour. Resultats Lors des tests fonctionnels, l’extinction de KAT6B conduit a une diminution l’expression du gene suppresseur de tumeur BRM. En presence d’un stress genotoxique (UV), les cellules transfectees avec le plasmide mute KAT6B T931 M presentent un defaut d’induction d’expression de Bax et de p21 dont l’expression augmente classiquement de maniere p53-dependante, en reponse a l’acetylation de la lysine 120 de p53 sous UV. Discussion La proteine KAT6B acetyle les lysines 4, 9, 14, 23 de l’histone H3 ainsi que la lysine 120 de p53. Elle joue un role important dans l’epigenetique des cancers et l’activation de la voie des MAPK. La threonine 931 se situe dans l’helice alpha 5 du domaine catalytique acetyltransferase, dont la sequence est commune a toutes les proteines de la famille histone-acetyltransferase MYST. Cet acide amine est hautement conserve entre les especes. D’apres l’homologie de sequence entre KAT6B/KAT6A, la mutation T931 M pourrait alterer l’interaction de la threonine 931 avec la valine 909 du domaine de liaison a l’acetylCoA de KAT6B et causer un defaut d’acetylation de l’histone H3 ou de p53. Cela modifierait la transcription des genes dont l’expression depend de l’histone H3 et favoriserait ainsi l’oncogenese. Conclusion Au total, ces donnees suggerent que KAT6B est un bon candidat pour expliquer la survenue de cancers precoces dans cette famille et pourrait ouvrir la voie vers de nouvelles therapies ciblees.