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De Martino M, Pellecchia S, Esposito F, Liotti F, Credendino SC, Prevete N, Decaussin-Petrucci M, Chieffi P, De Vita G, Melillo RM, Fusco A, Pallante P. The lncRNA RMST is drastically downregulated in anaplastic thyroid carcinomas where exerts a tumor suppressor activity impairing epithelial-mesenchymal transition and stemness. Cell Death Discov 2023; 9:216. [PMID: 37393309 DOI: 10.1038/s41420-023-01514-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023] Open
Abstract
Thyroid cancer is the most prevalent endocrine malignancy and comprises a wide range of lesions subdivided into differentiated (DTC) and undifferentiated thyroid cancer (UTC), mainly represented by the anaplastic thyroid carcinoma (ATC). This is one of the most lethal malignancies in humankind leading invariably to patient death in few months. Then, a better comprehension of the mechanisms underlying the development of ATC is required to set up new therapeutic approaches. Long non-coding RNAs (lncRNAs) are transcripts over 200 nucleotides in length that do not code for proteins. They show a strong regulatory function at both transcriptional and post-transcriptional level and are emerging as key players in regulating developmental processes. Their aberrant expression has been linked to several biological processes, including cancer, making them potential diagnostic and prognostic markers. We have recently analyzed the lncRNA expression profile in ATC through a microarray technique and have identified rhabdomyosarcoma 2-associated transcript (RMST) as one of the most downregulated lncRNA in ATC. RMST has been reported to be deregulated in a series of human cancers, to play an anti-oncogenic role in triple-negative breast cancer, and to modulate neurogenesis by interacting with SOX2. Therefore, these findings prompted us to investigate the role of RMST in ATC development. In this study we show that RMST levels are strongly decreased in ATC, but only slightly in DTC, indicating that the loss of this lncRNA could be related to the loss of the differentiation and high aggressiveness. We also report a concomitant increase of SOX2 levels in the same subset of ATC, that inversely correlated with RMST levels, further supporting the RMST/SOX2 relationship. Finally, functional studies demonstrate that the restoration of RMST in ATC cells reduces cell growth, migration and the stemness properties of ATC stem cells. In conclusion, these findings support a critical role of RMST downregulation in ATC development.
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Affiliation(s)
- Marco De Martino
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale (IEOS) "G. Salvatore", Consiglio Nazionale delle Ricerche (CNR), Via Pansini 5, 80131, Napoli, Italy
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138, Napoli, Italy
| | - Simona Pellecchia
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale (IEOS) "G. Salvatore", Consiglio Nazionale delle Ricerche (CNR), Via Pansini 5, 80131, Napoli, Italy
| | - Francesco Esposito
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale (IEOS) "G. Salvatore", Consiglio Nazionale delle Ricerche (CNR), Via Pansini 5, 80131, Napoli, Italy
| | - Federica Liotti
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale (IEOS) "G. Salvatore", Consiglio Nazionale delle Ricerche (CNR), Via Pansini 5, 80131, Napoli, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli "Federico II", Via Pansini 5, 80131, Napoli, Italy
| | - Sara Carmela Credendino
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale (IEOS) "G. Salvatore", Consiglio Nazionale delle Ricerche (CNR), Via Pansini 5, 80131, Napoli, Italy
| | - Nella Prevete
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale (IEOS) "G. Salvatore", Consiglio Nazionale delle Ricerche (CNR), Via Pansini 5, 80131, Napoli, Italy
- Dipartimento di Scienze Mediche Traslazionali (DiSMeT), Università degli Studi di Napoli "Federico II", Via Pansini 5, 80131, Napoli, Italy
| | - Myriam Decaussin-Petrucci
- Service d'Anatomie et Cytologie Pathologiques, Centre de Biologie Sud, Groupement Hospitalier Lyon Sud, Universite Lyon 1, 69495, Pierre Bénite, France
| | - Paolo Chieffi
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138, Napoli, Italy
| | - Gabriella De Vita
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli "Federico II", Via Pansini 5, 80131, Napoli, Italy
| | - Rosa Marina Melillo
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale (IEOS) "G. Salvatore", Consiglio Nazionale delle Ricerche (CNR), Via Pansini 5, 80131, Napoli, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli "Federico II", Via Pansini 5, 80131, Napoli, Italy
| | - Alfredo Fusco
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale (IEOS) "G. Salvatore", Consiglio Nazionale delle Ricerche (CNR), Via Pansini 5, 80131, Napoli, Italy.
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli "Federico II", Via Pansini 5, 80131, Napoli, Italy.
- Instituto Nacional de Cancer, 37908, Laboratorio de Carcinogênese Molecular, Rua Andre Cavalcanti 37, Centro, 20231-050, Rio de Janeiro, Brazil.
| | - Pierlorenzo Pallante
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale (IEOS) "G. Salvatore", Consiglio Nazionale delle Ricerche (CNR), Via Pansini 5, 80131, Napoli, Italy.
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Parra-Rincón E, Velandia-Huerto CA, Gittenberger A, Fallmann J, Gatter T, Brown FD, Stadler PF, Bermúdez-Santana CI. The Genome of the "Sea Vomit" Didemnum vexillum. Life (Basel) 2021; 11:1377. [PMID: 34947908 PMCID: PMC8704543 DOI: 10.3390/life11121377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/25/2022] Open
Abstract
Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt Didemnum vexillum, commonly known as "sea vomit", is a colonial tunicate considered an invasive species with substantial ecological and economical risk. We report the assembly of the D. vexillum genome using a hybrid approach that combines 28.5 Gb Illumina and 12.35 Gb of PacBio data. The new hybrid scaffolded assembly has a total size of 517.55 Mb that increases contig length about eightfold compared to previous, Illumina-only assembly. As a consequence of an unusually high genetic diversity of the colonies and the moderate length of the PacBio reads, presumably caused by the unusually acidic milieu of the tunic, the assembly is highly fragmented (L50 = 25,284, N50 = 6539). It is sufficient, however, for comprehensive annotations of both protein-coding genes and non-coding RNAs. Despite its shortcomings, the draft assembly of the "sea vomit" genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians.
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Affiliation(s)
- Ernesto Parra-Rincón
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, Colombia; (E.P.-R.); (P.F.S.)
| | - Cristian A. Velandia-Huerto
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
| | - Adriaan Gittenberger
- GiMaRIS, Rijksstraatweg 75, 2171 AK Sassenheim, The Netherlands;
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
| | - Thomas Gatter
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
| | - Federico D. Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Tr. 14 no. 101, São Paulo 05508-090, Brazil;
- Centro de Biologia Marinha, Universidade de São Paulo, Rod. Manuel Hypólito do Rego km. 131.5, São Sebastião 11612-109, Brazil
| | - Peter F. Stadler
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, Colombia; (E.P.-R.); (P.F.S.)
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
- Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
- Santa Fe Institute, Santa Fe, NM 87506, USA
| | - Clara I. Bermúdez-Santana
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, Colombia; (E.P.-R.); (P.F.S.)
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Di Gregorio A. The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to vertebrates. Curr Top Dev Biol 2020; 139:325-374. [PMID: 32450965 DOI: 10.1016/bs.ctdb.2020.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The notochord is a structure required for support and patterning of all chordate embryos, from sea squirts to humans. An increasing amount of information on notochord development and on the molecular strategies that ensure its proper morphogenesis has been gleaned through studies in the sea squirt Ciona. This invertebrate chordate offers a fortunate combination of experimental advantages, ranging from translucent, fast-developing embryos to a compact genome and impressive biomolecular resources. These assets have enabled the rapid identification of numerous notochord genes and cis-regulatory regions, and provide a rather unique opportunity to reconstruct the gene regulatory network that controls the formation of this developmental and evolutionary chordate landmark. This chapter summarizes the morphogenetic milestones that punctuate notochord formation in Ciona, their molecular effectors, and the current knowledge of the gene regulatory network that ensures the accurate spatial and temporal orchestration of these processes.
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Affiliation(s)
- Anna Di Gregorio
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, NY, United States.
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