Analyse des microARNs sous-exprimés dans le cancer papillaire thyroïdien :caractérisation fonctionnelle et implication diagnostique

Notre travail s’inscrit dans un projet de recherche dont l’objectif global est de mieux caractériser les modifications moléculaires impliquées dans les cancers thyroïdiens et de déterminer des signatures diagnostiques et pronostiques mais également des cibles moléculaires potentielles pour améliorer leur traitement. Le cancer papillaire thyroïdien (PTC) est le plus fréquent des cancers endocriniens, avec une incidence qui augmente en continu depuis des décennies. Il est de bon pronostic mais peut présenter des récidives et des métastases distantes et lymphatiques qui diminuent les chances de survie des patients. Les nodules thyroïdiens sont fréquents mais seulement 5% sont cancéreux. Cependant, jusqu’à 30% des ponctions de nodules thyroïdiens ne donnent pas de certitude sur le diagnostic. Cela conduit à des opérations qui se révèlent à postériori inutiles chez un nombre conséquent de patients. Les microARNs sont une famille de petits ARNs simple brin (18 à 24 nucléotides) très conservés dans l’évolution et qui régulent de façon négative l’expression génique.Ils agissent de façon post-transcriptionnelle en empêchant la traduction d’ARNm cibles et/ou en provoquant leur dégradation. Cette famille d’ARNs joue un rôle dans de nombreux processus physiologiques et pathologiques dont la tumorigenèse. Les microARNs ont montré leur implication dans la tumorigenèse thyroïdienne et leur potentielle utilité dans des signatures diagnostiques des cancers thyroïdiens. Néanmoins, aucune étude n’avait encore analysé le transcriptome global des microARNs dans les PTC et leurs métastases ganglionnaires lymphatiques. Dans un premier temps, nous avons montré que la sous-expression de microARNs dans les PTC et dans leurs métastases ganglionnaires lymphatiques est un phénomène tout aussi présent que la surexpression de microARNs qui était déjà connue. De plus, ces microARNs sous-exprimés montrent une expression différentielle entre des tumeurs de sous-types histopathologiques différents et ils montrent une diminution accrue de leur expression dans les tumeurs décrites comme agressives, ce qui semble principalement associé au taux de mutation BRAF V600E, qui est plus élevé dans les tumeurs agressives. Ensuite, nous avons caractérisé in vitro la fonction cellulaire de 3 microARNs très conservés dans l’évolution des espèces, fortement sous-exprimés dans les PTC par rapport aux tissus normaux adjacents mais également sous-exprimés dans les métastases ganglionnaires par rapport aux tumeurs primaires de PTC :miR-7-5p, miR-204-5p et miR-204-3p. Nous avons montré que ces microARNs ont un rôle de suppresseur de tumeur dans les thyrocytes. Le miR-7-5p inhibe la prolifération cellulaire, le miR-204-5p inhibe l’invasion et la migration cellulaires et le miR-204-3p inhibe l’invasion dans des lignées cellulaires thyroïdiennes humaines (TPC-1 et HTori). Le croisement de nos données avec celles de la littérature nous a montré que la diminution de l’expression de nos microARNs d’intérêt semble s’exercer principalement via une réduction de leur transcription suite à des délétions génomiques ou via l’action répressive de facteurs de transcription. Nos données indiquent que ces microARNs pourraient être utilisés comme agents thérapeutiques pour le traitement des PTC. Enfin, nous avons montré que les microARNs sous-exprimés dans les PTC sont d’aussi bons, voire de meilleurs marqueurs moléculaires diagnostiques que les microARNs surexprimés dans ces mêmes tumeurs. En analysant, dans des ponctions nodulaires, l’expression de 5 microARNs surexprimés et 9 microARNs sous-exprimés dans les PTC par rapport aux tissus normaux,nous avons déterminé 2 listes de microARNs qui maximalisent l’efficacité d’une prédiction du statut histopathologique (bénin ou malin) du nodule. Nos données suggèrent que le niveau d’expression du miR-7-5p combiné à ceux d’autres microARNs sur et sous-exprimés pourraient être utilisés dans un futur test diagnostique des nodules malins.Doctorat en Sciences biomédicales et pharmaceutiques (Médecine)info:eu-repo/semantics/nonPublishe

MiR-7-5p inhibits thyroid cell proliferation by targeting the EGFR/MAPK and IRS2/PI3K signaling pathways

The aberrant expression of miRNAs is often correlated to tumor development. MiR-7-5p is a recently discovered downregulated miRNA in thyroid papillary carcinoma (PTC). The goal of this project was to characterize its functional role in thyroid tumorigenesis and to identify the targeted modulated pathways. MiR-7-5p overexpression following transfection in TPC1 and HT-ori3 cells decreased proliferation of the two thyroid cell lines. Analysis of global transcriptome modifications showed that miR-7-5p inhibits thyroid cell proliferation by modulating the MAPK and PI3K signaling pathways which are both necessary for normal thyroid proliferation and play central roles in PTC tumorigenesis. Several effectors of these pathways are indeed targets of miR-7-5p, among which EGFR and IRS2, two upstream activators. We confirmed the upregulation of IRS2 and EGFR in human PTC and showed the existence of a negative correlation between the decreased expression of miR-7-5p and the increased expression of IRS2 or EGFR. Our results thus support a tumor-suppressor activity of miR-7-5p. The decreased expression of miR-7-5p during PTC tumorigenesis might give the cells a proliferative advantage and delivery of miR-7-5p may represent an innovative approach for therapy.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

2-iodohexadecanal Inhibits thyroid cell growth in part through the induction of let-7f microRNA

It is well known that pituitary TSH exerts the major task in the regulation of thyroid function. However, this gland is capable of certain degree of autonomy, independently of TSH control. Iodine plays an important role in thyroid physiology and biochemistry. The thyroid is capable of producing different iodolipids such as 2-iodohexadecanal (2-IHDA). It was shown that this iodolipid mimic some of the inhibitory effects of excess iodide on several thyroid parameters. Objectives: To identify the miRNAs regulated by 2-IHDA in rat thyroid cells and likely characterize their role in thyroid cell proliferation and function. Results: FRTL-5 cells were grown in the presence of TSH and treated with 2-IHDA. Among the miRNAs up-regulated by 2-IHDA we focused on miR-let-7f and miR-138. When we transfected the miRNAs, miR-let-7f but not miR-138 overexpression inhibited proliferation of FRTL 5 cells, while miR-let-7f inhibition restored cell growth in 2-IHDA treated cultures. Analysis of cell cycle by flow cytometric DNA analysis revealed that miR-let-7f inhibition reduced the percentage of 2-IHDA treated cells in G1 phase and an increased of the percentage of cells in S phase was observed upon anti-let-7f transfection. The expresion of Cyclin D1 and Cyclin D3 were reduced after the transfection of miR-let-7f and miR-138, respectively. In in vivo studies we observed that miR-let-7f and miR-138 were up regulated by 2-IHDA during goiter involution. Conclusion: These results suggest that the inhibitory effects of 2-IHDA on FRTL-5 thyroid cell proliferation are mediated in part through the induction of let-7f microRNA.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Revisiting the transcriptional analysis of primary tumours and associated nodal metastases with enhanced biological and statistical controls: application to thyroid cancer.

Transcriptome profiling has helped characterise nodal spread. The interpretation of these data, however, is not without ambiguities.C. Maenhaut and V. Detours contributed equallyinfo:eu-repo/semantics/publishe

FUS:CREM-rearranged malignant epithelioid neoplasm mimicking neuroendocrine neoplasm of unknown primary

SCOPUS: no.jinfo:eu-repo/semantics/publishe

New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer

Background: Papillary Thyroid Cancer (PTC) is the most prevalent type of endocrine cancer. Its incidence has rapidly increased in recent decades but little is known regarding its complete microRNA transcriptome (miRNome). In addition, there is a need for molecular biomarkers allowing improved PTC diagnosis. Methods: We performed small RNA deep-sequencing of 3 PTC, their matching normal tissues and lymph node metastases (LNM). We designed a new bioinformatics framework to handle each aspect of the miRNome: whole expression profiles, isomiRs distribution, non-templated additions distributions, RNA-editing or mutation. Results were validated experimentally by qRT-PCR on normal samples, tumors and LNM from 14 independent patients and in silico using the dataset from The Cancer Genome Atlas (small RNA deepsequencing of 59 normal samples, 495 PTC, and 8 LNM). Results: We performed small RNA deep-sequencing of 3 PTC, their matching normal tissues and lymph node metastases (LNM). We designed a new bioinformatics framework to handle each aspect of the miRNome: whole expression profiles, isomiRs distribution, non-templated additions distributions, RNA-editing or mutation. Results were validated experimentally by qRT-PCR on normal samples, tumors and LNM from 14 independent patients and in silico using the dataset from The Cancer Genome Atlas (small RNA deep-sequencing of 59 normal samples, 495 PTC, and 8 LNM). We confirmed already described up-regulations of microRNAs in PTC, such as miR-146b-5p or miR-222-3p, but we also identified down-regulated microRNAs, such as miR-7-5p or miR-30c-2-3p. We showed that these down-regulations are linked to the tumorigenesis process of thyrocytes. We selected the 14 most down-regulated microRNAs in PTC and we showed that they are potential biomarkers of PTC samples. Nevertheless, they can distinguish histological classical variants and follicular variants of PTC in the TCGA dataset. In addition, 12 of the 14 down-regulated microRNAs are significantly less expressed in aggressive PTC compared to non-aggressive PTC. We showed that the associated aggressive expression profile is mainly due to the presence of the BRAF V600E mutation. In general, primary tumors and LNM presented similar microRNA expression profiles but specific variations like the down-regulation of miR-7-2-3p and miR-30c-2-3p in LNM were observed. Investigations of the 5p-to-3p arm expression ratios, non-templated additions or isomiRs distributions revealed no major implication in PTC tumorigenesis process or LNM appearance. Conclusions: Our results showed that down-regulated microRNAs can be used as new potential common biomarkers of PTC and to distinguish main subtypes of PTC. MicroRNA expressions can be linked to the development of LNM of PTC. The bioinformatics framework that we have developed can be used as a starting point for the global analysis of any microRNA deep-sequencing data in an unbiased way.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

miRNA expression and function in thyroid carcinomas: A comparative and critical analysis and a model for other cancers

As in many cancer types, miRNA expression profiles and functions have become an important field of research on non-medullary thyroid carcinomas, the most common endocrine cancers. This could lead to the establishment of new diagnostic tests and new cancer therapies. However, different studies showed important variations in their research strategies and results. In addition, the action of miRNAs is poorly considered as a whole because of the use of underlying dogmatic truncated concepts. These lead to discrepancies and limits rarely considered. Recently, this field has been enlarged by new miRNA functional and expression studies. Moreover, studies using next generation sequencing give a new view of general miRNA differential expression profiles of papillary thyroid carcinoma. We analyzed in detail this literature from both physiological and differential expression points of view. Based on explicit examples, we reviewed the progresses but also the discrepancies and limits trying to provide a critical approach of where this literature may lead. We also provide recommendations for future studies. The conclusions of this systematic analysis could be extended to other cancer types.SCOPUS: re.jHydrainfo:eu-repo/semantics/publishe

MiRNA expression may account for chronic but not for acute regulation of mRNA expression in human thyroid tumor models

Background: For thyroid tumorigenesis, two main human in vitro models are available: primary cultures of human thyrocytes treated with TSH or EGF/serum as models for autonomous adenomas (AA) or papillary thyroid carcinomas (PTC) respectively, and human thyroid tumor derived cell lines. Previous works of our group have assessed properties of those models, with a special emphasis on mRNA regulations. It is often assumed that miRNA may be one of the primary events inducing these mRNA regulations.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

miRNA expression in anaplastic thyroid carcinomas.

Anaplastic thyroid carcinoma (ATC) is the most lethal form of thyroid neoplasia and represents an end stage of thyroid tumor progression. No effective treatment exists so far. In this study, we analyzed the miRNA expression profiles of 11 ATC by microarrays and their relationship with the mRNA expression profiles of the same 11 ATC samples. ATC show distinct miRNA expression profiles compared to other less aggressive thyroid tumor types. ATC show 18 commonly deregulated miRNA compared to normal thyroid tissue (17 downregulated and 1 upregulated miRNA). First, the analysis of a combined approach of the mRNA gene expression and of the bioinformatically predicted mRNA targets of the deregulated miRNA suggested a role for these regulations in the epithelial to mesenchymal transition (EMT) process in ATC. Second, the direct interaction between one of the upregulated mRNA target, the LOX gene which is an EMT key player, and a downregulated miRNA, the miR-29a, was experimentally validated by a luciferase assay in HEK cell. Third, we confirmed that the ATC tissue is composed of about 50% of tumor associated macrophages (TAM) and suggested, by taking into account our data and published data, their most likely direct or paracrine intercommunication between them and the thyroid tumor cells, amplifying the tumor aggressiveness. Finally, we demonstrated by in situ hybridization a specific thyrocyte localization of 3 of the deregulated miRNA: let-7g, miR-29a and miR-30e and we pointed out the importance of identifying the cell type localization before drawing any conclusion on the physiopathological role of a given gene.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Transcriptional output, cell types densities and normalization in spatial transcriptomics

C. Maenhaut and V. Detours contributed equallyinfo:eu-repo/semantics/publishe