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Malapelle U, Pepe F, Pisapia P, Altimari A, Bellevicine C, Brunnström H, Bruno R, Büttner R, Cirnes L, De Andrea CE, de Biase D, Dumur CI, Ericson Lindquist K, Fontanini G, Gautiero E, Gentien D, Hofman P, Hofman V, Iaccarino A, Lozano MD, Mayo-de-Las-Casas C, Merkelbach-Bruse S, Pagni F, Roman R, Schmitt FC, Siemanowski J, Roy-Chowdhuri S, Tallini G, Tresserra F, Vander Borght S, Vielh P, Vigliar E, Vita GAC, Weynand B, Rosell R, Molina Vila MA, Troncone G. Reference standards for gene fusion molecular assays on cytological samples: an international validation study. J Clin Pathol 2023; 76:47-52. [PMID: 34429353 DOI: 10.1136/jclinpath-2021-207825] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 07/17/2021] [Accepted: 08/06/2021] [Indexed: 02/05/2023]
Abstract
AIMS Gene fusions assays are key for personalised treatments of advanced human cancers. Their implementation on cytological material requires a preliminary validation that may make use of cell line slides mimicking cytological samples. In this international multi-institutional study, gene fusion reference standards were developed and validated. METHODS Cell lines harbouring EML4(13)-ALK(20) and SLC34A2(4)-ROS1(32) gene fusions were adopted to prepare reference standards. Eight laboratories (five adopting amplicon-based and three hybridisation-based platforms) received, at different dilution points two sets of slides (slide A 50.0%, slide B 25.0%, slide C 12.5% and slide D wild type) stained by Papanicolaou (Pap) and May Grunwald Giemsa (MGG). Analysis was carried out on a total of 64 slides. RESULTS Four (50.0%) out of eight laboratories reported results on all slides and dilution points. While 12 (37.5%) out of 32 MGG slides were inadequate, 27 (84.4%) out of 32 Pap slides produced libraries adequate for variant calling. The laboratories using hybridisation-based platforms showed the highest rate of inadequate results (13/24 slides, 54.2%). Conversely, only 10.0% (4/40 slides) of inadequate results were reported by laboratories adopting amplicon-based platforms. CONCLUSIONS Reference standards in cytological format yield better results when Pap staining and processed by amplicon-based assays. Further investigation is required to optimise these standards for MGG stained cells and for hybridisation-based approaches.
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Affiliation(s)
| | - Francesco Pepe
- Public Health, University of Naples Federico II, Naples, Italy
| | | | - Annalisa Altimari
- Molecular Pathology, University of Bologna Hospital of Bologna Sant'Orsola-Malpighi Polyclinic, Bologna, Italy
| | | | - Hans Brunnström
- Clinical Sciences Lund, Division of Pathology, Lund University, Lund, Sweden
| | - Rossella Bruno
- Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | | | | | | | - Dario de Biase
- Pharmacy and Biotechnology (FaBiT), Molecular Pathology Laboratory, University of Bologna, Bologna, Italy
| | | | | | - Gabriella Fontanini
- Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | | | - David Gentien
- Translational Research Department, Genomics Platform, Curie Institute Hospital Group, Paris, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, University Hospital Centre Nice Pasteur Hospital, Nice, France
| | - Veronique Hofman
- Laboratory of Clinical and Experimental Pathology, University Hospital Centre Nice Pasteur Hospital, Nice, France
| | | | | | | | | | - Fabio Pagni
- Medicine and Surgery, San Gerardo Hospital, Monza, Italy
| | - Ruth Roman
- Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | | | - Sinchita Roy-Chowdhuri
- Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Giovanni Tallini
- Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Sara Vander Borght
- Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Philippe Vielh
- Pathology, Medipath and American Hospital of Paris, Paris, France
| | - Elena Vigliar
- Public Health, University of Naples Federico II, Naples, Italy
| | | | - Birgit Weynand
- Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Rafael Rosell
- Oncology, Hospital Municipal de Badalona, Barcelona, Spain
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Conconi D, Redaelli S, Lissoni AA, Cilibrasi C, Perego P, Gautiero E, Sala E, Paderno M, Dalprà L, Landoni F, Lavitrano M, Roversi G, Bentivegna A. Genomic and Epigenomic Profile of Uterine Smooth Muscle Tumors of Uncertain Malignant Potential (STUMPs) Revealed Similarities and Differences with Leiomyomas and Leiomyosarcomas. Int J Mol Sci 2021; 22:ijms22041580. [PMID: 33557274 PMCID: PMC7914585 DOI: 10.3390/ijms22041580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 01/20/2023] Open
Abstract
Uterine smooth muscle tumors of uncertain malignant potential (STUMPs) represent a heterogeneous group of tumors that cannot be histologically diagnosed as unequivocally benign or malignant. For this reason, many authors are working to obtain a better definition of diagnostic and prognostic criteria. In this work, we analyzed the genomic and epigenomic profile of uterine smooth muscle tumors (USMTs) in order to find similarities and differences between STUMPs, leiomyosarcomas (LMSs) and leiomyomas (LMs), and possibly identify prognostic factors in this group of tumors. Array-CGH data on 23 USMTs demonstrated the presence of a more similar genomic profile between STUMPs and LMSs. Some genes, such as PRKDC and PUM2, with a potential prognostic value, were never previously associated with STUMP. The methylation data appears to be very promising, especially with regards to the divergent profile found in the sample that relapsed, characterized by an overall CGI hypomethylation. Finally, the Gene Ontology analysis highlighted some cancer genes that could play a pivotal role in the unexpected aggressive behavior that can be found in some of these tumors. These genes could prove to be prognostic markers in the future.
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Affiliation(s)
- Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
- Correspondence: (D.C.); (A.B.); Tel.: +39-0264488133 (A.B.)
| | - Serena Redaelli
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
| | - Andrea Alberto Lissoni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
- Clinic of Obstetrics and Gynecology, San Gerardo Hospital, 20900 Monza, Italy
| | - Chiara Cilibrasi
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RH, UK;
| | - Patrizia Perego
- Division of Pathology, San Gerardo Hospital, 20900 Monza, Italy;
| | - Eugenio Gautiero
- Medical Genetics Laboratory, San Gerardo Hospital, 20900 Monza, Italy; (E.G.); (E.S.)
| | - Elena Sala
- Medical Genetics Laboratory, San Gerardo Hospital, 20900 Monza, Italy; (E.G.); (E.S.)
| | - Mariachiara Paderno
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
- Clinic of Obstetrics and Gynecology, San Gerardo Hospital, 20900 Monza, Italy
| | - Leda Dalprà
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
| | - Fabio Landoni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
- Clinic of Obstetrics and Gynecology, San Gerardo Hospital, 20900 Monza, Italy
| | - Marialuisa Lavitrano
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
| | - Gaia Roversi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
- Medical Genetics Laboratory, San Gerardo Hospital, 20900 Monza, Italy; (E.G.); (E.S.)
| | - Angela Bentivegna
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (S.R.); (A.A.L.); (M.P.); (L.D.); (F.L.); (M.L.); (G.R.)
- Correspondence: (D.C.); (A.B.); Tel.: +39-0264488133 (A.B.)
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