1
|
Vibert R, Cyrta J, Girard E, Vacher S, Dupain C, Antonio S, Wong J, Baulande S, De Sousa JMF, Vincent-Salomon A, Masliah-Planchon J, Girard N, Le Tourneau C, Kamal M, Bièche I. Molecular characterisation of tumours of the lacrimal apparatus. Histopathology 2023; 83:925-935. [PMID: 37706251 DOI: 10.1111/his.15040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/02/2023] [Accepted: 08/19/2023] [Indexed: 09/15/2023]
Abstract
AIMS Malignant tumours of the lacrimal apparatus are rare and frequently show a poor prognosis, with no clear therapeutic standards. Characterisation of the genetic landscape of these rare tumours is sparse, and therefore therapeutics generally follow those of their common salivary gland counterparts. To further clarify the pathophysiology and discover potential therapeutic targets, we investigated the genetic landscape of eight tumours of the lacrimal apparatus. METHODS AND RESULTS DNA and RNA sequencing were performed to identify genetic mutations and gene fusions. Immunohistochemistry, fluorescence in-situ hybridisation and reverse transcription-polymerase chain reaction followed by Sanger sequencing were performed to confirm the identified molecular alterations. Genetic alterations were detected in six tumours. Among five adenoid cystic carcinomas (ACC), four had confirmed alterations of MYB or MYBL1 genes, including a MYB::NFIB fusion, a MYBL1::NFIB fusion, a MYB amplification and a novel NFIB::THSD7B fusion. Mutations in genes encoding epigenetic modifiers, as well as NOTCH1, FGFR2 and ATM mutations, were also identified in ACCs. A carcinoma ex pleomorphic adenoma showed TP53 and CIC mutations and an amplification of ERBB2. A transitional cell carcinoma was associated with HPV16 infection. No genetic alteration was found for one adenocarcinoma, not otherwise specified. CONCLUSIONS Our study highlights the variety of molecular alterations associated with lacrimal system tumours and emphasises the importance of molecular testing in these tumours, which can reveal potentially targetable mutations. Our results also reinforce the hypothesis of a common physiopathology of all ACCs, regardless of their primary location.
Collapse
Affiliation(s)
- Roseline Vibert
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Joanna Cyrta
- Department of Pathology, Institut Curie, PSL Research University, Paris, France
| | - Elodie Girard
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Sophie Vacher
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Célia Dupain
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Samantha Antonio
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Jennifer Wong
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) NGS Platform, Institut Curie, Paris, France
| | | | | | - Julien Masliah-Planchon
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Nicolas Girard
- Thorax Institute Curie Montsouris, Institut Curie, Paris, France
- UVSQ, Paris Saclay University, Versailles, France
| | | | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Ivan Bièche
- Pharmacogenomics Unit, Department of Genetics, Institut Curie, PSL Research University, Paris, France
- Faculty of Pharmaceutical and Biological Sciences, INSERM U1016, Université de Paris Cité, Paris, France
| |
Collapse
|
2
|
Caro H, Dollin S, Biton A, Brancotte B, Desvillechabrol D, Dufresne Y, Li B, Kornobis E, Lemoine F, Maillet N, Perrin A, Traut N, Néron B, Cokelaer T. BioConvert: a comprehensive format converter for life sciences. NAR Genom Bioinform 2023; 5:lqad074. [PMID: 37608802 PMCID: PMC10440784 DOI: 10.1093/nargab/lqad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/18/2023] [Accepted: 08/15/2023] [Indexed: 08/24/2023] Open
Abstract
Bioinformatics is a field known for the numerous standards and formats that have been developed over the years. This plethora of formats, sometimes complementary, and often redundant, poses many challenges to bioinformatics data analysts. They constantly need to find the best tool to convert their data into the suitable format, which is often a complex, technical and time consuming task. Moreover, these small yet important tasks are often difficult to make reproducible. To overcome these difficulties, we initiated BioConvert, a collaborative project to facilitate the conversion of life science data from one format to another. BioConvert aggregates existing software within a single framework and complemented them with original code when needed. It provides a common interface to make the user experience more streamlined instead of having to learn tens of them. Currently, BioConvert supports about 50 formats and 100 direct conversions in areas such as alignment, sequencing, phylogeny, and variant calling. In addition to being useful for end-users, BioConvert can also be utilized by developers as a universal benchmarking framework for evaluating and comparing numerous conversion tools. Additionally, we provide a web server implementing an online user-friendly interface to BioConvert, hence allowing direct use for the community.
Collapse
Affiliation(s)
- Hugo Caro
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France
| | - Sulyvan Dollin
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Anne Biton
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Bryan Brancotte
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Dimitri Desvillechabrol
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Yoann Dufresne
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, G5 Sequence Bioinformatics, Paris, France
| | - Blaise Li
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Etienne Kornobis
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Nicolas Maillet
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Amandine Perrin
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Nicolas Traut
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et Théorique, F-75015 Paris, France
| | - Bertrand Néron
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| |
Collapse
|