1
|
Bencivenga D, Stampone E, Vastante A, Barahmeh M, Della Ragione F, Borriello A. An Unanticipated Modulation of Cyclin-Dependent Kinase Inhibitors: The Role of Long Non-Coding RNAs. Cells 2022; 11:cells11081346. [PMID: 35456025 PMCID: PMC9028986 DOI: 10.3390/cells11081346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022] Open
Abstract
It is now definitively established that a large part of the human genome is transcribed. However, only a scarce percentage of the transcriptome (about 1.2%) consists of RNAs that are translated into proteins, while the large majority of transcripts include a variety of RNA families with different dimensions and functions. Within this heterogeneous RNA world, a significant fraction consists of sequences with a length of more than 200 bases that form the so-called long non-coding RNA family. The functions of long non-coding RNAs range from the regulation of gene transcription to the changes in DNA topology and nucleosome modification and structural organization, to paraspeckle formation and cellular organelles maturation. This review is focused on the role of long non-coding RNAs as regulators of cyclin-dependent kinase inhibitors’ (CDKIs) levels and activities. Cyclin-dependent kinases are enzymes necessary for the tuned progression of the cell division cycle. The control of their activity takes place at various levels. Among these, interaction with CDKIs is a vital mechanism. Through CDKI modulation, long non-coding RNAs implement control over cellular physiology and are associated with numerous pathologies. However, although there are robust data in the literature, the role of long non-coding RNAs in the modulation of CDKIs appears to still be underestimated, as well as their importance in cell proliferation control.
Collapse
|
4
|
Barnes DJ, Hookway E, Athanasou N, Kashima T, Oppermann U, Hughes S, Swan D, Lueerssen D, Anson J, Hassan AB. A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report. BMC Cancer 2016; 16:629. [PMID: 27519597 PMCID: PMC4983003 DOI: 10.1186/s12885-016-2669-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 08/02/2016] [Indexed: 12/19/2022] Open
Abstract
Background Melanotic neuroectodermal tumor of infancy (MNTI) is exceptionally rare and occurs predominantly in the head and neck (92.8 % cases). The patient reported here is only the eighth case of MNTI presenting in an extremity, and the first reported in the fibula. Case presentation A 2-month-old female presented with a mass arising in the fibula. Exhaustive genomic, transcriptomic, epigenetic and pathological characterization was performed on the excised primary tumor and a derived cell line. Whole-exome analysis of genomic DNA from both the tumor and blood indicated no somatic, non-synonymous coding mutations within the tumor, but a heterozygous, unique germline, loss of function mutation in CDKN2A (p16INK4A, D74A). SNP-array CGH on DNA samples revealed the tumor to be euploid, with no detectable gene copy number variants. Multiple chromosomal translocations were identified by RNA-Seq, and fusion genes included RPLP1-C19MC, potentially deregulating the C19MC cluster, an imprinted locus containing microRNA genes reactivated by gene fusion in embryonal tumors with multilayered rosettes. Since the presumed cell of origin of MNTI is from the neural crest, we also compared gene expression with a dataset from human neural crest cells and identified 185 genes with significantly different expression. Consistent with the melanotic phenotype of the tumor, elevated expression of tyrosinase was observed. Other highly expressed genes encoded muscle proteins and modulators of the extracellular matrix. A derived MNTI cell line was sensitive to inhibitors of lysine demethylase, but not to compounds targeting other epigenetic regulators. Conclusions In the absence of somatic copy number variations or mutations, the fully transformed phenotype of the MNTI may have arisen in infancy because of the combined effects of a germline CDKN2A mutation, tumor promoting somatic fusion genes and epigenetic deregulation. Very little is known about the etiology of MNTI and this report advances knowledge of these rare tumors by providing the first comprehensive genomic, transcriptomic and epigenetic characterization of a case. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2669-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- David J Barnes
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK
| | - Edward Hookway
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK
| | - Nick Athanasou
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK
| | - Takeshi Kashima
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK
| | - Udo Oppermann
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK
| | - Simon Hughes
- Oxford Gene Technology Ltd, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK
| | - Daniel Swan
- Oxford Gene Technology Ltd, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK
| | - Dietrich Lueerssen
- Oxford Gene Technology Ltd, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK
| | - John Anson
- Oxford Gene Technology Ltd, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK
| | - A Bassim Hassan
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK. .,Tumour Growth Group, Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
| |
Collapse
|
6
|
Avril MF, Bahadoran P, Cabaret O, Caron O, de la Fouchardière A, Demenais F, Desjardins L, Frébourg T, Hammel P, Leccia MT, Lesueur F, Mahé E, Martin L, Maubec E, Remenieras A, Richard S, Robert C, Soufir N, Stoppa-Lyonnet D, Thomas L, Vabres P, Bressac-de Paillerets B. [Recommendations for genetic testing and management of individuals genetically at-risk of cutaneous melanoma]. Ann Dermatol Venereol 2014; 142:26-36. [PMID: 25600792 DOI: 10.1016/j.annder.2014.09.606] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 07/08/2014] [Accepted: 09/01/2014] [Indexed: 11/19/2022]
Abstract
Cutaneous melanoma is a multifactorial disease resulting from both environmental and genetic factors. Five susceptibility genes have been identified over the past years, comprising high-risk susceptibility genes (CDKN2A, CDK4, and BAP1 genes) and intermediate-risk susceptibility genes (MITF, and MC1R genes). The aim of this expert consensus was to define clinical contexts justifying genetic analyses, to describe the conduct of these analyses, and to propose surveillance recommendations. Given the regulatory constraints, it is recommended that dermatologists work in tandem with a geneticist. Genetic analysis may be prescribed when at least two episodes of histologically proven invasive cutaneous melanoma have been diagnosed before the age of 75 years in two 1st or 2nd degree relatives or in the same individual. The occurrence in the same individual or in a relative of invasive cutaneous melanoma with ocular melanoma, pancreatic cancer, renal cancer, mesothelioma or a central nervous system tumour are also indications for genetic testing. Management is based upon properly managed photoprotection and dermatological monitoring according to genetic status. Finally, depending on the mutated gene and the familial history, associated tumour risks require specific management (e.g. ocular melanoma, pancreatic cancer). Due to the rapid progress in genetics, these recommendations will need to be updated regularly.
Collapse
Affiliation(s)
- M-F Avril
- Service de dermatologie, groupe hospitalier Cochin-Saint-Vincent-de-Paul, AP-HP, pavillon Tarnier, 89, rue d'Assas, 75006 Paris, France
| | - P Bahadoran
- Inserm U895, service de dermatologie, hôpital Archet 2, CHU, 151, route Saint-Antoine-Ginestiere, BP 79, 06200 Nice cedex 3, France
| | - O Cabaret
- Service de génétique, département de biologie et pathologie médicales, Gustave-Roussy, 114, rue Édouard-Vaillant, 94805 Villejuif cedex, France
| | - O Caron
- Consultation d'oncogénétique, Gustave-Roussy, 114, rue Édouard-Vaillant, 94805 Villejuif, France
| | - A de la Fouchardière
- Département de biopathologie, centre Léon-Bérard, 28, rue Laennec, 69008 Lyon, France
| | - F Demenais
- Inserm, UMR946, variabilité génétique et maladies humaines, fondation Jean-Dausset, CEPH, 27, rue Juliette-Dodu, 75010 Paris, France
| | - L Desjardins
- Service d'ophtalmologie, institut Curie, 26, rue d'Ulm, 75231 Paris cedex 05, France
| | - T Frébourg
- Inserm U1079, service de génétique, CHU de Rouen, IRIB, faculté de médecine et de pharmacie, 22, boulevard Gambetta, 76183 Rouen cedex, France
| | - P Hammel
- Service de gastro-entérologie-pancréatologie, hôpital Beaujon, AP-HP, 100, boulevard du Général-Leclerc, 92118 Clichy cedex, France
| | - M-T Leccia
- Service de dermatologie, CHU Michallon, BP 217, 38043 Grenoble cedex 9, France
| | - F Lesueur
- Inserm U900, équipe épidémiologie génétique des cancers, institut Curie, 26, rue d'Ulm, 75248 Paris cedex 05, France
| | - E Mahé
- Service de dermatologie, centre hospitalier Victor-Dupouy, 69, rue du Lieutenant-Colonel-Prud'hon, 95107 Argenteuil cedex, France
| | - L Martin
- Service de dermatologie, CHU d'Angers, université d'Angers, 4, rue Larrey, 49933 Angers cedex 9, France
| | - E Maubec
- Inserm, UMR946, variabilité génétique et maladies humaines, fondation Jean-Dausset, CEPH, 27, rue Juliette-Dodu, 75010 Paris, France; Service de dermatologie, hôpital Bichat, AP-HP, 46, rue Henri-Huchard, 75018 Paris, France
| | - A Remenieras
- Département d'oncologie génétique, institut Paoli-Calmettes, 232, boulevard Saint-Marguerite, 13273 Marseille cedex 9, France
| | - S Richard
- Service d'urologie, hôpital Bicêtre, Centre expert national cancers rares INCa PREDIR, 78, rue du Général-Leclerc, 94275 Le Kremlin-Bicêtre cedex, France
| | - C Robert
- Service de dermatologie, Gustave-Roussy, 114, rue Édouard-Vaillant, 94805 Villejuif, France
| | - N Soufir
- Inserm U976, laboratoire de génétique moléculaire, unité fonctionnelle de génétique, hôpital Xavier-Bichat-Claude-Bernard, AP-HP, Paris 7 université, 75018 Paris, France
| | - D Stoppa-Lyonnet
- Inserm U830, service de génétique, département de biologie des tumeurs, institut Curie, 26, rue d'Ulm, 75231 Paris cedex 05, France
| | - L Thomas
- Service de dermatologie, centre hospitalier Lyon Sud, université Lyon 1, 165, chemin du Grand-Revoyet, 69495 Pierre-Bénite cedex, France
| | - P Vabres
- Service de dermatologie, CHU de Dijon, BP 77908, 21079 Dijon cedex, France
| | - B Bressac-de Paillerets
- Service de génétique, département de biologie et pathologie médicales, Gustave-Roussy, 114, rue Édouard-Vaillant, 94805 Villejuif cedex, France.
| |
Collapse
|