1
|
Rossi S, Barresi S, Colafati GS, Genovese S, Tancredi C, Costabile V, Patrizi S, Giovannoni I, Asioli S, Poliani PL, Gardiman MP, Cardoni A, Del Baldo G, Antonelli M, Gianno F, Piccirilli E, Catino G, Martucci L, Quacquarini D, Toni F, Melchionda F, Viscardi E, Zucchelli M, Dal Pos S, Gatti E, Liserre R, Schiavello E, Diomedi-Camassei F, Carai A, Mastronuzzi A, Gessi M, Giannini C, Novelli A, Onetti Muda A, Miele E, Alesi V, Alaggio R. PATZ1-Rearranged Tumors of the Central Nervous System: Characterization of a Pediatric Series of Seven Cases. Mod Pathol 2024; 37:100387. [PMID: 38007157 DOI: 10.1016/j.modpat.2023.100387] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
PATZ1-rearranged sarcomas are well-recognized tumors as part of the family of round cell sarcoma with EWSR1-non-ETS fusions. Whether PATZ1-rearranged central nervous system (CNS) tumors are a distinct tumor type is debatable. We thoroughly characterized a pediatric series of PATZ1-rearranged CNS tumors by chromosome microarray analysis (CMA), DNA methylation analysis, gene expression profiling and, when frozen tissue is available, optical genome mapping (OGM). The series consisted of 7 cases (M:F=1.3:1, 1-17 years, median 12). On MRI, the tumors were supratentorial in close relation to the lateral ventricles (intraventricular or iuxtaventricular), preferentially located in the occipital lobe. Two major histologic groups were identified: one (4 cases) with an overall glial appearance, indicated as "neuroepithelial" (NET) by analogy with the corresponding methylation class (MC); the other (3 cases) with a predominant spindle cell sarcoma morphology, indicated as "sarcomatous" (SM). A single distinct methylation cluster encompassing both groups was identified by multidimensional scaling analysis. Despite the epigenetic homogeneity, unsupervised clustering analysis of gene expression profiles revealed 2 distinct transcriptional subgroups correlating with the histologic phenotypes. Interestingly, genes implicated in epithelial-mesenchymal transition and extracellular matrix composition were enriched in the subgroup associated to the SM phenotype. The combined use of CMA and OGM enabled the identification of chromosome 22 chromothripsis in all cases suitable for the analyses, explaining the physical association of PATZ1 to EWSR1 or MN1. Six patients are currently disease-free (median follow-up 30 months, range 12-92). One patient of the SM group developed spinal metastases at 26 months from diagnosis and is currently receiving multimodal therapy (42 months). Our data suggest that PATZ1-CNS tumors are defined by chromosome 22 chromothripsis as causative of PATZ1 fusion, show peculiar MRI features (eg, relation to lateral ventricles, supratentorial frequently posterior site), and, although epigenetically homogenous, encompass 2 distinct histologic and transcriptional subgroups.
Collapse
Affiliation(s)
- Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Sabina Barresi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giovanna Stefania Colafati
- Imaging Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Neuroscience, Imaging and Clinical Sciences (DNISC), University "Gabriele D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chantal Tancredi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valentino Costabile
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sara Patrizi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Isabella Giovannoni
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sofia Asioli
- Department of Biomedical and Neuromotor Sciences (DIBINEM)-Surgical Pathology Section-Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Pietro Luigi Poliani
- Pathology Unit, San Raffaele Hospital Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Marina Paola Gardiman
- Surgical Pathology and Cytopathology Unit, Department of Medicine, University Hospital of Padua, Padua, Italy
| | - Antonello Cardoni
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giada Del Baldo
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manila Antonelli
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
| | - Francesca Gianno
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Eleonora Piccirilli
- Imaging Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Neuroscience, Imaging and Clinical Sciences (DNISC), University "Gabriele D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Giorgia Catino
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Licia Martucci
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Denise Quacquarini
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesco Toni
- Neuroradiology Unit, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Fraia Melchionda
- SSD Oncoematologia Pediatrica, IRCCS AOU Policlinico S.Orsola, Bologna, Italy
| | - Elisabetta Viscardi
- Department of Pediatrics, Azienda Ospedale-Università di Padova, Padova, Italy
| | - Mino Zucchelli
- Paediatric Neurosurgery, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Sandro Dal Pos
- Department of Radiology, Azienda Ospedale-Università di Padova, Padova, Italy
| | - Enza Gatti
- Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy
| | - Roberto Liserre
- Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy
| | - Elisabetta Schiavello
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Andrea Carai
- Neurosurgery Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marco Gessi
- Neuropathology Unit, Pathology Division, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica S.Cuore, Rome, Italy
| | - Caterina Giannini
- Department of Biomedical and Neuromotor Sciences (DIBINEM)-Surgical Pathology Section-Alma Mater Studiorum - University of Bologna, Bologna, Italy; Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Evelina Miele
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rita Alaggio
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Medico-surgical Sciences and Biotechnologies, Sapienza University, Rome, Italy
| |
Collapse
|
2
|
Alesi V, Genovese S, Lepri FR, Catino G, Loddo S, Orlando V, Di Tommaso S, Morgia A, Martucci L, Di Donato M, Digilio MC, Dallapiccola B, Novelli A, Capolino R. Deep Intronic LINE-1 Insertions in NF1: Expanding the Spectrum of Neurofibromatosis Type 1-Associated Rearrangements. Biomolecules 2023; 13:biom13050725. [PMID: 37238595 DOI: 10.3390/biom13050725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Neurofibromatosis type 1 is an autosomal-dominant condition caused by NF1 gene inactivation. Clinical diagnosis is corroborated by genetic tests on gDNA and cDNA, which are inconclusive in approximately 3-5% of cases. Genomic DNA approaches may overlook splicing-affecting intronic variants and structural rearrangements, especially in regions enriched in repetitive sequences. On the other hand, while cDNA-based methods provide direct information about the effect of a variant on gene transcription, they are hampered by non-sense-mediated mRNA decay and skewed or monoallelic expression. Moreover, analyses on gene transcripts in some patients do not allow tracing back to the causative event, which is crucial for addressing genetic counselling, prenatal monitoring, and developing targeted therapies. We report on a familial NF1, caused by an insertion of a partial LINE-1 element inside intron 15, leading to exon 15 skipping. Only a few cases of LINE-1 insertion have been reported so far, hampering gDNA studies because of their size. Often, they result in exon skipping, and their recognition of cDNA may be difficult. A combined approach, based on Optical Genome Mapping, WGS, and cDNA studies, enabled us to detect the LINE-1 insertion and test its effects. Our results improve knowledge of the NF1 mutational spectrum and highlight the importance of custom-built approaches in undiagnosed patients.
Collapse
Affiliation(s)
- Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Francesca Romana Lepri
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Giorgia Catino
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Sara Loddo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Valeria Orlando
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Silvia Di Tommaso
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Alessandra Morgia
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Licia Martucci
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Maddalena Di Donato
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Maria Cristina Digilio
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Rossella Capolino
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| |
Collapse
|