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Mastrosimini MG, Mafficini A, Tondulli L, Milella M, Piccoli P, Mattiolo P, Fassan M, Hong SM, Scarpa A, Luchini C. Recurrent gastric amphicrine tumor with neuroendocrine and pancreatic acinar cell differentiation and somatic MEN1 inactivation arisen during immunotherapy. Virchows Arch 2023; 483:415-419. [PMID: 37581694 DOI: 10.1007/s00428-023-03624-4] [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: 01/14/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 08/16/2023]
Abstract
Amphicrine neoplasms (ANs) are poorly understood epithelial malignancies composed of cells with co-existing exocrine-neuroendocrine features. Here, we report a recurrent mucin-producing gastric amphicrine tumor co-expressing neuroendocrine (chromogranin-A, synaptophysin, and CD56) and pancreatic acinar cell (BCL10 and trypsin) markers, arisen in a 64-year-old woman during adjuvant immunotherapy for melanoma. Ki-67 was < 2%. The gastric background context was atrophic gastritis. Next-generation sequencing showed MEN1 mutation (p.P71fs*42) coupled with loss of heterozygosity. The key lessons were as follows: (1) gastric ANs can show the co-existence of exocrine mucin-producing elements with neuroendocrine and pancreatic acinar differentiation; (2) they may represent a new entity arising in the context of atrophic gastritis and during immunotherapy; (3) they should be considered in the diagnostic workup of gastric neuroendocrine tumors; and (4) their molecular profile can show striking similarities with well-differentiated neuroendocrine tumors. These findings may be of help to improve the knowledge and the biological taxonomy of ANs.
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Affiliation(s)
- Maria G Mastrosimini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
- ARC-Net Research Center, University of Verona, Verona, Italy
| | - Luca Tondulli
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Paola Piccoli
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Matteo Fassan
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, and Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
- ARC-Net Research Center, University of Verona, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy.
- ARC-Net Research Center, University of Verona, Verona, Italy.
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Simbolo M, Silvestris N, Malleo G, Mafficini A, Maggino L, Cocomazzi A, Veghini L, Mombello A, Pezzini F, Sereni E, Martelli FM, Gkountakos A, Ciaparrone C, Piredda ML, Ingravallo G, Paolino G, Nappo F, Rapposelli IG, Frassinetti L, Saragoni L, Lonardi S, Pea A, Paiella S, Fassan M, Brunetti O, Cingarlini S, Salvia R, Milella M, Corbo V, Lawlor RT, Scarpa A, Luchini C. Clinical and Genomic Characterization of Pancreatic Ductal Adenocarcinoma with Signet-Ring/Poorly Cohesive Cells. Mod Pathol 2023; 36:100251. [PMID: 37355152 DOI: 10.1016/j.modpat.2023.100251] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/12/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023]
Abstract
Signet-ring cell (SRC)/poorly cohesive cell carcinoma is an aggressive variant of pancreatic ductal adenocarcinoma (PDAC). This study aimed to clarify its clinicopathologic and molecular profiles based on a multi-institutional cohort of 20 cases. The molecular profiles were investigated using DNA and RNA sequencing. The clinicopathologic parameters and molecular alterations were analyzed based on survival indices and using a validation/comparative cohort of 480 conventional PDAC patients. The primary findings were as follows: (1) clinicopathologic features: SRC carcinomas are highly aggressive neoplasms with poor prognosis, and the lungs are elective metastatic sites; (2) survival analysis: a higher SRC component was indicative of poorer prognosis. In particular, the most clinically significant threshold of SRC was 80%, showing statistically significant differences in both disease-specific and disease-free survival; (3) genomic profiles: SRC carcinomas are similar to conventional PDAC with the most common alterations affecting the classic PDAC drivers KRAS (70% of cases), TP53 (55%), SMAD4 (25%), and CDKN2A (20%). EGFR alterations, RET::CCDC6 fusion gene, and microsatellite instability (3 different cases, 1 alteration per case) represent novel targets for precision oncology. The occurrence of SMAD4 mutations was associated with poorer prognosis; (4) pancreatic SRC carcinomas are genetically different from gastric SRC carcinomas: CDH1, the classic driver gene of gastric SRC carcinoma, is not altered in pancreatic SRC carcinoma; (5) transcriptome analysis: the cases clustered into 2 groups, one classical/exocrine-like, and the other squamous-like; and (6) SRC carcinoma-derived organoids can be successfully generated, and their cultures preserve the histologic and molecular features of parental SRC carcinoma. Although pancreatic SRC carcinoma shares similarities with conventional PDAC regarding the most important genetic drivers, it also exhibits important differences. A personalized approach for patients with this tumor type should consider the clinical relevance of histologic determination of the SRC component and the presence of potentially actionable molecular targets.
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Affiliation(s)
- Michele Simbolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina, Italy
| | - Giuseppe Malleo
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Laura Maggino
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | | | - Lisa Veghini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Mombello
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Francesco Pezzini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Elisabetta Sereni
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Filippo M Martelli
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | | | - Chiara Ciaparrone
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Maria L Piredda
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Giuseppe Ingravallo
- Department of Emergency and Transplantation, Pathology Section, University of Bari Medical School, Bari, Italy
| | - Gaetano Paolino
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Floriana Nappo
- Medical Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | | | - Luca Saragoni
- Department of Pathological Anatomy, AUSL Romagna, Morgagni-Pierantoni Hospital, Forlì, Italy
| | - Sara Lonardi
- Medical Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Antonio Pea
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Salvatore Paiella
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Matteo Fassan
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, and Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Oronzo Brunetti
- IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, Vari, Italy
| | - Sara Cingarlini
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Vincenzo Corbo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Rita T Lawlor
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy.
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Danzi F, Pacchiana R, Mafficini A, Scupoli MT, Scarpa A, Donadelli M, Fiore A. To metabolomics and beyond: a technological portfolio to investigate cancer metabolism. Signal Transduct Target Ther 2023; 8:137. [PMID: 36949046 PMCID: PMC10033890 DOI: 10.1038/s41392-023-01380-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [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: 11/15/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/24/2023] Open
Abstract
Tumour cells have exquisite flexibility in reprogramming their metabolism in order to support tumour initiation, progression, metastasis and resistance to therapies. These reprogrammed activities include a complete rewiring of the bioenergetic, biosynthetic and redox status to sustain the increased energetic demand of the cells. Over the last decades, the cancer metabolism field has seen an explosion of new biochemical technologies giving more tools than ever before to navigate this complexity. Within a cell or a tissue, the metabolites constitute the direct signature of the molecular phenotype and thus their profiling has concrete clinical applications in oncology. Metabolomics and fluxomics, are key technological approaches that mainly revolutionized the field enabling researchers to have both a qualitative and mechanistic model of the biochemical activities in cancer. Furthermore, the upgrade from bulk to single-cell analysis technologies provided unprecedented opportunity to investigate cancer biology at cellular resolution allowing an in depth quantitative analysis of complex and heterogenous diseases. More recently, the advent of functional genomic screening allowed the identification of molecular pathways, cellular processes, biomarkers and novel therapeutic targets that in concert with other technologies allow patient stratification and identification of new treatment regimens. This review is intended to be a guide for researchers to cancer metabolism, highlighting current and emerging technologies, emphasizing advantages, disadvantages and applications with the potential of leading the development of innovative anti-cancer therapies.
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Affiliation(s)
- Federica Danzi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Raffaella Pacchiana
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maria T Scupoli
- Department of Neurosciences, Biomedicine and Movement Sciences, Biology and Genetics Section, University of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy.
| | - Alessandra Fiore
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
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Luchini C, Mattiolo P, Basturk O, Mafficini A, Ozcan K, Lawlor RT, Hong SM, Brosens LA, Marchegiani G, Pea A, Manfrin E, Sciacca G, Zampieri F, Polati R, De Robertis R, Milella M, D'Onofrio M, Malleo G, Salvia R, Adsay V, Scarpa A. Acinar Cystic Transformation of the Pancreas: Histomorphology and Molecular Analysis to Unravel its Heterogeneous Nature. Am J Surg Pathol 2023; 47:379-386. [PMID: 36649476 DOI: 10.1097/pas.0000000000002017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Acinar cystic transformation (ACT) of the pancreas, previously called acinar cell cystadenoma, is a poorly understood and rare entity among pancreatic cystic lesions. This study aims to clarify its real nature. This research cohort included 25 patients with pancreatic ACT, representing the largest series in the literature. We describe their clinicopathological features and molecular profile using next-generation sequencing. ACT arose more often in women (F/M≃2:1), in the body-tail region, with a mean size of ~4 cm. At the latest follow-up, all patients were alive and disease free. Histologically, a typical acinar epithelium lined all cysts, intermingled with ductal-like epithelium in 11/25 (44%) cases. All the cases lacked any evidence of malignancy. Three ACT showed peculiar features: 1 showed an extensive and diffuse microcystic pattern, and the other 2 harbored foci of low-grade pancreatic intraepithelial neoplasia (PanIN) in the ductal-like epithelium. Next-generation sequencing revealed the presence of 2 pathogenic/likely pathogenic mutations in 2 different cases, 1 with ductal-like epithelium and 1 with PanIN, and affecting KRAS (c.34G>C, p.G12R) and SMO (c.1685G>A, p.R562Q) genes, respectively. The other case with PanIN was not available for sequencing. Overall, our findings support that ACT is a benign entity, potentially arising from heterogeneous conditions/background, including: (1) acinar microcysts, (2) malformations, (3) obstructive/inflammatory setting, (4) genetic predisposition, (5) possible neoplastic origin. Although all indications are that ACT is benign, the potential occurrence of driver mutations suggests discussing a potential role of long-term surveillance for these patients.
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Affiliation(s)
- Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, Verona, Italy
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology
| | - Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, NY
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, Verona, Italy
| | - Kerem Ozcan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, NY
| | - Rita T Lawlor
- Department of Diagnostics and Public Health, Section of Pathology
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, Verona, Italy
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Lodewijk A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht, and Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Antonio Pea
- Department of Surgery, The Pancreas Institute
| | - Erminia Manfrin
- Department of Diagnostics and Public Health, Section of Pathology
| | - Giuseppe Sciacca
- Department of Diagnostics and Public Health, Section of Pathology
| | | | - Rita Polati
- Department of Diagnostics and Public Health, Section of Pathology
| | | | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Mirko D'Onofrio
- Department of Diagnostics and Public Health, Section of Radiology
| | | | | | - Volkan Adsay
- Department of Pathology, Koç University Hospital and Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, Verona, Italy
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5
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Pedrazzani C, Conti C, Di Vittori A, Turri G, Bernardoni L, Mafficini A, Luchini C, Gabbrielli A, Scarpa A, Guglielmi A. Video technical notes for approaching a unique case of Juvenile Polyposis with massive gastric ingrowth. Asian J Surg 2023; 46:924-925. [PMID: 35918225 DOI: 10.1016/j.asjsur.2022.07.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/15/2022] [Indexed: 02/08/2023] Open
Affiliation(s)
- Corrado Pedrazzani
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University of Verona, Verona, Italy.
| | - Cristian Conti
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University of Verona, Verona, Italy
| | - Angelo Di Vittori
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University of Verona, Verona, Italy
| | - Giulia Turri
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University of Verona, Verona, Italy
| | - Laura Bernardoni
- Digestive Endoscopy Unit, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134, Verona, Italy
| | - Armando Gabbrielli
- Digestive Endoscopy Unit, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134, Verona, Italy
| | - Alfredo Guglielmi
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University of Verona, Verona, Italy
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, 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George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu 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KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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Barresi V, Simbolo M, Ciaparrone C, Pedron S, Mafficini A, Scarpa A. pRB immunostaining in the differential diagnosis between pleomorphic xanthoastrocytoma and glioblastoma with giant cells. Histopathology 2022; 81:661-669. [PMID: 35945679 PMCID: PMC9804328 DOI: 10.1111/his.14768] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 01/05/2023]
Abstract
AIMS Pleomorphic xanthoastrocytoma (PXA) is a rare circumscribed glioma, characterized by frequent BRAF p. V600E mutation, and classified as grade 2 or 3. Owing to overlapping clinical-pathological features, the histological distinction from glioblastoma (GBM) with giant cells (GCs) is challenging. Based on the high frequency of TP53 and RB1 alterations in the latter, this study aimed to assess the value of BRAF, p53, and pRB immunostainings in the differential diagnosis. METHODS AND RESULTS In 37 GBMs with ≥30% GCs and in eight PXAs, we assessed the alterations of 409 cancer-related genes and immunostainings for BRAF, p53, and pRB. GBMs with GCs were TP53-mutated in 30 cases, RB1-altered in 11, and BRAF-mutated in none. PXAs were BRAF-mutated in six cases, TP53-mutated in three, and RB1-altered in none. pRb immunostaining was lost in 25 GBMs (11 RB1-altered and 14 RB1-unaltered), retained in all PXAs and six GBMs, and inconclusive in six GBMs. pRb loss had 100% specificity and 80.6% sensitivity for GBM with GCs. P53 immunostaining was observed in 22 TP53-mutated GBMs and in one TP53-mutated PXA. It showed 87.5% specificity and 60% sensitivity to identify GBM with GCs. BRAF immunostaining corresponded to BRAF mutation status and it had 100% specificity and 75% sensitivity for detecting PXA. CONCLUSION This study shows for the first time that loss of pRB immunostaining is sensitive and specific for distinguishing GBM with GCs from PXA in routine practice. Thus, it could complement an immunohistochemical panel that includes BRAF and p53 immunostainings for the differential diagnosis.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public HealthUniversity of VeronaVeronaItaly
| | - Michele Simbolo
- Department of Diagnostics and Public HealthUniversity of VeronaVeronaItaly
| | - Chiara Ciaparrone
- Department of Diagnostics and Public HealthUniversity of VeronaVeronaItaly
| | - Serena Pedron
- Department of Diagnostics and Public HealthUniversity of VeronaVeronaItaly
| | - Andrea Mafficini
- Department of Diagnostics and Public HealthUniversity of VeronaVeronaItaly
| | - Aldo Scarpa
- Department of Diagnostics and Public HealthUniversity of VeronaVeronaItaly,ARC‐NET Research CentreUniversity and Hospital Trust of VeronaVeronaItaly
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9
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Barresi V, Lawlor RT, Mafficini A, Gilioli E, Scarpa A. Metastatic grade 1 meningioma lacking genetic abnormalities commonly associated with bad prognosis. Pathol Res Pract 2022; 238:154089. [PMID: 36067609 DOI: 10.1016/j.prp.2022.154089] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022]
Abstract
AIMS Meningioma metastasis is a rare event, observed primarily in World Health Organization (WHO) grade 3 tumors, although it has also been reported in WHO grade 1 meningiomas. This study aims at clarifying whether the metastasis of a WHO grade 1 meningioma was associated with genetic abnormalities commonly found in cases that are more aggressive. METHODS Using next generation sequencing of a panel of 174 genes, we analyzed the genetic alterations of a WHO grade 1 skull-base meningioma and its paired lung metastases detected 22 years after craniotomy. RESULTS Similar to the primary tumor, lung metastases did not show mitoses or histological signs of malignancy. Consistent with their origin from intracranial tumor, they harbored the same genetic alterations as this one. These consisted of the pathogenic mutation p. E17K of AKT1 and variants of unknown significance in NOTCH1 (p. P2133T), SERPINB8 (p. H359Y) and SMARCA4 (p. P277S). CONCLUSIONS The E17K AKT1 mutation is frequently found in skull base meningiomas and without prognostic significance. Our findings suggest that metastasis of grade 1 meningiomas is independent of genetic alterations (CDKN2A homozygous deletion, pTERT mutation, or 1p, 9p, 14q and 18q loss of heterozygosity) commonly found in more aggressive tumors.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy.
| | - Rita T Lawlor
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy; ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Eliana Gilioli
- Department of Pathology and Diagnostics, Unit of Anatomic Pathology, Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy; ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
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10
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Riva S, Luchini C, Zacchi F, Mafficini A, Borghesani M, Mongillo M, Scaglione I, Manduca S, Lucin E, Moscarda V, Pafumi S, Leta L, Dodi A, Reni A, Messineo L, Chiamulera C, Urso E, Scarpa A, Lawlor R, Milella M. 1683P Implementing next generation sequencing (NGS)/molecular tumor board (MTB)-based precision oncology practice: One-year experience at the Verona University Hospital. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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11
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Gkountakos A, Mafficini A, Lou E, Malleo G, Salvia R, Calicchia M, Silvestris N, Racila E, Amin K, Veronese N, Brunetti O, Antonini P, Ingravallo G, Mattiolo P, Saponaro C, Nappo F, Simbolo M, Bariani E, Lonardi S, Fassan M, Milella M, Lawlor RT, Scarpa A, Luchini C. Genomic characterization of undifferentiated sarcomatoid carcinoma of the pancreas. Hum Pathol 2022; 128:124-133. [PMID: 35850360 DOI: 10.1016/j.humpath.2022.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022]
Abstract
Undifferentiated sarcomatoid carcinoma (USC) of the pancreas is a rare but especially aggressive variant of pancreatic ductal adenocarcinoma (PDAC), composed of at least 80% of sarcomatoid cells. This study aimed to elucidate its clinicopathological and molecular features. The study cohort included 10 patients with pancreatic USC. Clinicopathological parameters were determined for each patient. The molecular profile was investigated using next-generation sequencing (NGS). Histologically, all tumors were hypercellular neoplasms with spindle-shaped or sarcomatoid cells. All patients showed vascular and perineural invasion. Most patients had a poor prognosis. NGS showed important similarities with conventional PDAC, including frequent alterations in the classic PDAC drivers, KRAS (100% of cases), TP53 (90%), and CDKN2A (60%). There were also some important distinctions from conventional PDAC: 1) SMAD4, a typical PDAC driver gene, was mutated in only one case (10%); 2) Another distinctive molecular feature was the recurrent KRAS amplification (30% of cases), which is very rare in conventional PDAC. It has been previously reported in another subtype of pancreatic undifferentiated carcinoma, the rhabdoid variant, and may be a key event leading to the acquisition of an undifferentiated phenotype in a subgroup of cases; 3) Lastly, in two different cases, we detected two potentially actionable targets, not belonging to the typical PDAC molecular landscape, such as MCL1 amplification and POLQ mutation. Our study sheds light on this rare tumor type, which shows aggressive biological behavior and few druggable alterations. The most distinctive molecular features of pancreatic USC are the paucity of SMAD4 alterations and recurrent KRAS amplification.
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Affiliation(s)
| | - Andrea Mafficini
- ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy; Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Emil Lou
- Division of Hematology, Oncology and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Giuseppe Malleo
- Department of General and Pancreatic Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Roberto Salvia
- Department of General and Pancreatic Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Martina Calicchia
- ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina, Italy
| | - Emilian Racila
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Khalid Amin
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Nicola Veronese
- Department of Internal Medicine and Geriatrics, University of Palermo, Palermo, Italy
| | - Oronzo Brunetti
- Medical Oncology Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Pietro Antonini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Giuseppe Ingravallo
- ,Department of Emergency and Organ Transplantation, Section of Pathology, University of Bari, Bari, Italy
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Concetta Saponaro
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Floriana Nappo
- Medical Oncology 1, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Michele Simbolo
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena Bariani
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Sara Lonardi
- Medical Oncology 3, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Matteo Fassan
- Department of Medicine, Surgical Pathology Unit, University of Padua; Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Rita T Lawlor
- ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy; Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Claudio Luchini
- ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy; Department of Diagnostics and Public Health, University of Verona, Verona, Italy.
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12
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Mattiolo P, Mafficini A, Lawlor RT, Marchegiani G, Malleo G, Pea A, Salvia R, Piccoli P, Sciammarella C, Santonicco N, Parisi A, Silvestris N, Milella M, Adsay V, Scarpa A, Luchini C. "Pure" hepatoid tumors of the pancreas harboring CTNNB1 somatic mutations: a new entity among solid pseudopapillary neoplasms. Virchows Arch 2022; 481:41-47. [PMID: 35359182 PMCID: PMC9226109 DOI: 10.1007/s00428-022-03317-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/04/2022] [Accepted: 03/26/2022] [Indexed: 02/06/2023]
Abstract
Hepatoid tumors (HTs) represent a rare group of neoplasms that are histologically similar to hepatocellular carcinoma but arise outside the liver. The current World Health Organization classification recognizes the hepatoid morphology of pancreatic tumors only as a possible variant of pancreatic ductal adenocarcinoma (PDAC). Here, we describe two cases of "pure" HT of the pancreas showing common features and characterized by indolent biological behavior. These tumors were roundish nodules with pushing borders, hyaline globules, and pure hepatoid histology; they were diffusely positive for β-catenin and LEF1 on immunohistochemistry. At next-generation sequencing, both neoplasms harbored only one pathogenic somatic mutation that affected the CTNNB1 gene at exon 3 and showed a loss of heterozygosity on chromosomes 18 and 21. By integrating macroscopic and microscopic features, along with their molecular profiles, we advocate that such tumors represent a distinct entity from PDAC and should be considered a new variant of solid pseudopapillary neoplasms. The recognition of this new neoplastic category may have immediate implications not only for tumor taxonomy but also for clinical practice.
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Affiliation(s)
- Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Rita T Lawlor
- ARC-Net Research Center for Applied Research On Cancer, University of Verona, 37134, Verona, Italy
| | - Giovanni Marchegiani
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134, Verona, Italy
| | - Giuseppe Malleo
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134, Verona, Italy
| | - Antonio Pea
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134, Verona, Italy
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134, Verona, Italy
| | - Paola Piccoli
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Concetta Sciammarella
- ARC-Net Research Center for Applied Research On Cancer, University of Verona, 37134, Verona, Italy
| | - Nicola Santonicco
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Alice Parisi
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, 98125, Messina, Italy
| | - Michele Milella
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, 37134, Verona, Italy
| | - Volkan Adsay
- Department of Pathology, Koç University Hospital and Koç University Research Center for Translational Medicine (KUTTAM), 34010, Istanbul, Turkey
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
- ARC-Net Research Center for Applied Research On Cancer, University of Verona, 37134, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy.
- ARC-Net Research Center for Applied Research On Cancer, University of Verona, 37134, Verona, Italy.
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13
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Luchini C, Mafficini A, Chatterjee D, Piredda ML, Sciammarella C, Navale P, Malleo G, Mattiolo P, Marchegiani G, Pea A, Salvia R, Brosens LA, Paolino G, Mastrosimini MG, Silvestris N, Milella M, Cheng L, Adsay VN, Lawlor RT, Scarpa A. Histo-molecular characterization of pancreatic cancer with microsatellite instability: intra-tumor heterogeneity, B2M inactivation, and the importance of metastatic sites. Virchows Arch 2022; 480:1261-1268. [PMID: 34613461 DOI: 10.1007/s00428-021-03205-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 07/13/2021] [Revised: 08/28/2021] [Accepted: 09/10/2021] [Indexed: 12/11/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) with microsatellite instability (MSI)/defective mismatch repair (dMMR) is the only subtype of pancreatic cancer with potential response to immunotherapy. Here, we report the histo-molecular characterization of MSI/dMMR PDAC with immunohistochemistry, MSI-based PCR, and next-generation sequencing. Five paradigmatic cases have been identified. The main results include the first report in pancreatic cancer of MSI/dMMR intra-tumor heterogeneity, the presence of microsatellite-stable metastases from MSI/dMMR primary and recurrent B2M gene inactivation, which may confer resistance to immunotherapy. In addition to the classic PDAC drivers, ARID1A was the most common mutated gene in the cohort. Intra-tumor heterogeneity, B2M inactivation, and metastatic sites should be carefully considered in MSI/dMMR PDAC, which should also be investigated in routine diagnostic practice with specific molecular analysis. The chromatin remodeler ARID1A represents another potential driver gene in this context.
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Affiliation(s)
- Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy.
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Deyali Chatterjee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria L Piredda
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | | | - Pooja Navale
- Department of Pathology and Immunology, Washington University, St. Louis, MO, USA
| | - Giuseppe Malleo
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Giovanni Marchegiani
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Antonio Pea
- IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, and Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Lodewijk A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gaetano Paolino
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Maria G Mastrosimini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy
| | - Nicola Silvestris
- IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, and Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Volkan N Adsay
- Department of Pathology, Koç University Hospitals, Istanbul, Turkey
| | - Rita T Lawlor
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona, Italy.
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy.
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14
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Luchini C, Pantanowitz L, Adsay V, Asa SL, Antonini P, Girolami I, Veronese N, Nottegar A, Cingarlini S, Landoni L, Brosens LA, Verschuur AV, Mattiolo P, Pea A, Mafficini A, Milella M, Niazi MK, Gurcan MN, Eccher A, Cree IA, Scarpa A. Ki-67 assessment of pancreatic neuroendocrine neoplasms: Systematic review and meta-analysis of manual vs. digital pathology scoring. Mod Pathol 2022; 35:712-720. [PMID: 35249100 PMCID: PMC9174054 DOI: 10.1038/s41379-022-01055-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 12/18/2022]
Abstract
Ki-67 assessment is a key step in the diagnosis of neuroendocrine neoplasms (NENs) from all anatomic locations. Several challenges exist related to quantifying the Ki-67 proliferation index due to lack of method standardization and inter-reader variability. The application of digital pathology coupled with machine learning has been shown to be highly accurate and reproducible for the evaluation of Ki-67 in NENs. We systematically reviewed all published studies on the subject of Ki-67 assessment in pancreatic NENs (PanNENs) employing digital image analysis (DIA). The most common advantages of DIA were improvement in the standardization and reliability of Ki-67 evaluation, as well as its speed and practicality, compared to the current gold standard approach of manual counts from captured images, which is cumbersome and time consuming. The main limitations were attributed to higher costs, lack of widespread availability (as of yet), operator qualification and training issues (if it is not done by pathologists), and most importantly, the drawback of image algorithms counting contaminating non-neoplastic cells and other signals like hemosiderin. However, solutions are rapidly developing for all of these challenging issues. A comparative meta-analysis for DIA versus manual counting shows very high concordance (global coefficient of concordance: 0.94, 95% CI: 0.83-0.98) between these two modalities. These findings support the widespread adoption of validated DIA methods for Ki-67 assessment in PanNENs, provided that measures are in place to ensure counting of only tumor cells either by software modifications or education of non-pathologist operators, as well as selection of standard regions of interest for analysis. NENs, being cellular and monotonous neoplasms, are naturally more amenable to Ki-67 assessment. However, lessons of this review may be applicable to other neoplasms where proliferation activity has become an integral part of theranostic evaluation including breast, brain, and hematolymphoid neoplasms.
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Affiliation(s)
- Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy.
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy.
| | - Liron Pantanowitz
- Department of Pathology & Clinical Labs, University of Michigan, Ann Arbor, MI, USA
| | - Volkan Adsay
- Department of Pathology, Koç University Hospital and Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Sylvia L Asa
- University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH, USA
| | - Pietro Antonini
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Ilaria Girolami
- Division of Pathology, San Maurizio Central Hospital, Bolzano, Italy
| | - Nicola Veronese
- Department of Internal Medicine and Geriatrics, University of Palermo, Palermo, Italy
| | - Alessia Nottegar
- Pathology Unit, Azienda Ospedaliera Universitaria Integrata (AOUI), Verona, Italy
| | - Sara Cingarlini
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Lodewijk A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anna V Verschuur
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Antonio Pea
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Muhammad K Niazi
- Center for Biomedical Informatics, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Metin N Gurcan
- Center for Biomedical Informatics, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Albino Eccher
- Pathology Unit, Azienda Ospedaliera Universitaria Integrata (AOUI), Verona, Italy
| | - Ian A Cree
- International Agency for Research on Cancer, IARC, Lyon, France
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy.
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy.
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15
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Hackeng WM, Brosens LAA, Kim JY, O'Sullivan R, Sung YN, Liu TC, Cao D, Heayn M, Brosnan-Cashman J, An S, Morsink FHM, Heidsma CM, Valk GD, Vriens MR, Nieveen van Dijkum E, Offerhaus GJA, Dreijerink KMA, Zeh H, Zureikat AH, Hogg M, Lee K, Geller D, Marsh JW, Paniccia A, Ongchin M, Pingpank JF, Bahary N, Aijazi M, Brand R, Chennat J, Das R, Fasanella KE, Khalid A, McGrath K, Sarkaria S, Singh H, Slivka A, Nalesnik M, Han X, Nikiforova MN, Lawlor RT, Mafficini A, Rusev B, Corbo V, Luchini C, Bersani S, Pea A, Cingarlini S, Landoni L, Salvia R, Milione M, Milella M, Scarpa A, Hong SM, Heaphy CM, Singhi AD. Non-functional pancreatic neuroendocrine tumours: ATRX/DAXX and alternative lengthening of telomeres (ALT) are prognostically independent from ARX/PDX1 expression and tumour size. Gut 2022; 71:961-973. [PMID: 33849943 PMCID: PMC8511349 DOI: 10.1136/gutjnl-2020-322595] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/16/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Recent studies have found aristaless-related homeobox gene (ARX)/pancreatic and duodenal homeobox 1 (PDX1), alpha-thalassemia/mental retardation X-linked (ATRX)/death domain-associated protein (DAXX) and alternative lengthening of telomeres (ALT) to be promising prognostic biomarkers for non-functional pancreatic neuroendocrine tumours (NF-PanNETs). However, they have not been comprehensively evaluated, especially among small NF-PanNETs (≤2.0 cm). Moreover, their status in neuroendocrine tumours (NETs) from other sites remains unknown. DESIGN An international cohort of 1322 NETs was evaluated by immunolabelling for ARX/PDX1 and ATRX/DAXX, and telomere-specific fluorescence in situ hybridisation for ALT. This cohort included 561 primary NF-PanNETs, 107 NF-PanNET metastases and 654 primary, non-pancreatic non-functional NETs and NET metastases. The results were correlated with numerous clinicopathological features including relapse-free survival (RFS). RESULTS ATRX/DAXX loss and ALT were associated with several adverse prognostic findings and distant metastasis/recurrence (p<0.001). The 5-year RFS rates for patients with ATRX/DAXX-negative and ALT-positive NF-PanNETs were 40% and 42% as compared with 85% and 86% for wild-type NF-PanNETs (p<0.001 and p<0.001). Shorter 5-year RFS rates for ≤2.0 cm NF-PanNETs patients were also seen with ATRX/DAXX loss (65% vs 92%, p=0.003) and ALT (60% vs 93%, p<0.001). By multivariate analysis, ATRX/DAXX and ALT status were independent prognostic factors for RFS. Conversely, classifying NF-PanNETs by ARX/PDX1 expression did not independently correlate with RFS. Except for 4% of pulmonary carcinoids, ATRX/DAXX loss and ALT were only identified in primary (25% and 29%) and NF-PanNET metastases (62% and 71%). CONCLUSIONS ATRX/DAXX and ALT should be considered in the prognostic evaluation of NF-PanNETs including ≤2.0 cm tumours, and are highly specific for pancreatic origin among NET metastases of unknown primary.
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Affiliation(s)
- Wenzel M Hackeng
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lodewijk A A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joo Young Kim
- Department of Pathology, Nowon Eulji Medical Center, Eulji University, Seoul, Republic of Korea
| | - Roderick O'Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - You-Na Sung
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St, Louis, MO, USA
| | - Dengfeng Cao
- Department of Pathology and Immunology, Washington University School of Medicine, St, Louis, MO, USA
| | - Michelle Heayn
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Soyeon An
- Department of Pathology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Folkert H M Morsink
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Charlotte M Heidsma
- Department of Surgery, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Gerlof D Valk
- Department of Endocrinology and Internal Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Menno R Vriens
- Department of Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - G Johan A Offerhaus
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Koen M A Dreijerink
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Endocrinology and Internal Medicine, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Herbert Zeh
- Department of Clinical Sciences, Surgery, University of Texas Southwestern, Dallas, TX, USA
| | - Amer H Zureikat
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Melissa Hogg
- Department of Surgery, NorthShore University Health System, Evanston, IL, USA
| | - Kenneth Lee
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - David Geller
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - J Wallis Marsh
- Department of Surgery, West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Alessandro Paniccia
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Melanie Ongchin
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - James F Pingpank
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Nathan Bahary
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Muaz Aijazi
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Randall Brand
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jennifer Chennat
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Rohit Das
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kenneth E Fasanella
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Asif Khalid
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kevin McGrath
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Savreet Sarkaria
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Harkirat Singh
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Adam Slivka
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Michael Nalesnik
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Xiaoli Han
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Marina N Nikiforova
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Rita Teresa Lawlor
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Boris Rusev
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Vincenzo Corbo
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
| | - Samantha Bersani
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Antonio Pea
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Sara Cingarlini
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Roberto Salvia
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Milione
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Michele Milella
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Christopher M Heaphy
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Aatur D Singhi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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16
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Barresi V, Mafficini A, Calicchia M, Piredda ML, Musumeci A, Ghimenton C, Scarpa A. Recurrent oligodendroglioma with changed 1p/19q status. Neuropathology 2022; 42:160-166. [PMID: 35144313 PMCID: PMC9546156 DOI: 10.1111/neup.12789] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022]
Abstract
We report a case of oligodendroglioma that had consistent histopathological features as well as a distinct change in 1p/19q status in the second recurrence, after temozolomide chemotherapy and radiotherapy. The first tumor recurrence had oligodendroglial morphology, IDH1 R132H and TERT promoter mutations, and 1p/19q codeletion detected by fluorescent in situ hybridization (FISH). Copy number analysis, assessed by next‐generation sequencing, confirmed 1p/19q codeletion, and disclosed loss of heterozygosity (LOH) of chromosomes 4 and 9 and chromosome 11 gain. The second recurrence featured not only oligodendroglial morphology but also the appearance of admixed multinucleated giant cells or neoplastic cells having oval nuclei and mitoses and showing microvascular proliferation; it maintained IDH1 R132H and TERT promoter mutations, acquired TP53 mutation, and showed 19q LOH, but disomic 1p, detected by FISH. Copy number analysis depicted LOH of chromosomes 3p, 13, and 19q, 1p partial deletion (1p chr1p34.2‐p11), and gain of chromosomes 2p25.3‐p24.1, 8q12.2‐q24.3, and 11q13.3‐q25. B‐allele frequency analysis of polymorphic sites disclosed copy‐neutral LOH at 1p36.33‐p34.2, supporting the initial deletion of 1p, followed by reduplication of 1p36.33‐p34.2 alone. These findings suggest that the two tumor recurrences might have originated from an initial neoplastic clone, featuring 1p/19q codeletion and IDH1 and TERT promoter mutations, and have independently acquired other copy number alterations. The reduplication of chromosome 1p might be the result of temozolomide treatment, and gave rise to false negative 1p deletion detected by FISH. The possibility of 1p copy‐neutral LOH should be considered in recurrent oligodendrogliomas with altered 1p/19q status detected by FISH.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy.,ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Martina Calicchia
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Maria Liliana Piredda
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Angelo Musumeci
- Department of Neurosciences, Unit of Neurosurgery, Hospital Trust of Verona, Verona, Italy
| | - Claudio Ghimenton
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy.,ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
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17
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Simbolo M, Centonze G, Ali G, Garzone G, Taormina S, Sabella G, Ciaparrone C, Mafficini A, Grillo F, Mangogna A, Volante M, Mastracci L, Fontanini G, Pilotto S, Bria E, Infante M, Capella C, Rolli L, Pastorino U, Milella M, Milione M, Scarpa A. Integrative molecular analysis of combined small-cell lung carcinomas identifies major subtypes with different therapeutic opportunities. ESMO Open 2022; 7:100308. [PMID: 34952268 PMCID: PMC8695295 DOI: 10.1016/j.esmoop.2021.100308] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Combined small-cell lung cancer (C-SCLC) is composed of SCLC admixed with a non-small-cell cancer component. They currently receive the same treatment as SCLC. The recent evidence that SCLC may belong to either of two lineages, neuroendocrine (NE) or non-NE, with different vulnerability to specific cell death pathways such as ferroptosis, opens new therapeutic opportunities also for C-SCLC. MATERIALS AND METHODS Thirteen C-SCLCs, including five with adenocarcinoma (CoADC), five with large-cell neuroendocrine carcinoma (CoLCNEC) and three with squamous cell carcinoma (CoSQC) components, were assessed for alterations in 409 genes and transcriptomic profiling of 20 815 genes. RESULTS All 13 cases harbored TP53 (12 cases) and/or RB1 (7 cases) inactivation, which was accompanied by mutated KRAS in 4 and PTEN in 3 cases. Potentially targetable alterations included two KRAS G12C, two PIK3CA and one EGFR mutations. Comparison of C-SCLC transcriptomes with those of 57 pure histology lung cancers (17 ADCs, 20 SQCs, 11 LCNECs, 9 SCLCs) showed that CoLCNEC and CoADC constituted a standalone group of NE tumors, while CoSQC transcriptional setup was overlapping that of pure SQC. Using transcriptional signatures of NE versus non-NE SCLC as classifier, CoLCNEC was clearly NE while CoSQC was strongly non-NE and CoADC exhibited a heterogeneous phenotype. Similarly, using ferroptosis sensitivity/resistance markers, CoSQC was classified as sensitive (as expected for non-NE), CoLCNEC as resistant (as expected for NE) and CoADC showed a heterogeneous pattern. CONCLUSIONS These data support routine molecular profiling of C-SCLC to search for targetable driver alterations and to precisely classify them according to therapeutically relevant subgroups (e.g. NE versus non-NE).
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Affiliation(s)
- M Simbolo
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - G Centonze
- Pathology Unit 1, Pathology and Laboratory Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - G Ali
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - G Garzone
- Pathology Unit 1, Pathology and Laboratory Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - S Taormina
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - G Sabella
- Pathology Unit 1, Pathology and Laboratory Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy; School of Pathology, University of Milan, Milan, Italy
| | - C Ciaparrone
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - A Mafficini
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy; ARC-Net Research Centre for Applied Research on Cancer, University of Verona, Verona, Italy
| | - F Grillo
- Department of Surgical and Diagnostic Sciences (DISC), University of Genova and IRCCS S. Martino-IST University Hospital, Genoa, Italy
| | - A Mangogna
- Institute for Maternal and Child Health, IRCCS Burlo Garofalo, Trieste, Italy
| | - M Volante
- Department of Oncology, University of Turin at San Luigi Hospital, Orbassano, Torino, Italy
| | - L Mastracci
- Department of Surgical and Diagnostic Sciences (DISC), University of Genova and IRCCS S. Martino-IST University Hospital, Genoa, Italy
| | - G Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - S Pilotto
- Section of Oncology, Department of Medicine, University of Verona, Verona, Italy
| | - E Bria
- Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - M Infante
- Thoracic Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - C Capella
- Unit of Pathology, Department of Medicine and Surgery and Research Centre for the Study of Hereditary and Familial tumors, University of Insubria, Varese, Italy
| | - L Rolli
- Thoracic Surgery Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - U Pastorino
- Thoracic Surgery Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - M Milella
- Section of Oncology, Department of Medicine, University of Verona, Verona, Italy
| | - M Milione
- Pathology Unit 1, Pathology and Laboratory Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
| | - A Scarpa
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy; ARC-Net Research Centre for Applied Research on Cancer, University of Verona, Verona, Italy
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18
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Sciammarella C, Bencivenga M, Mafficini A, Piredda ML, Tsvetkova V, Paolino G, Mastrosimini MG, Hetoja S, de Manzoni G, Mattiolo P, Borga C, Fassan M, Scarpa A, Luchini C, Lawlor RT. Molecular Analysis of an Intestinal Neuroendocrine/Non-neuroendocrine Neoplasm (MiNEN) Reveals MLH1 Methylation-driven Microsatellite Instability and a Monoclonal Origin: Diagnostic and Clinical Implications. Appl Immunohistochem Mol Morphol 2022; 30:145-152. [PMID: 34483242 DOI: 10.1097/pai.0000000000000969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/04/2021] [Indexed: 01/13/2023]
Abstract
Mixed neuroendocrine/non-neuroendocrine neoplasms (MiNEN) are rare mixed epithelial neoplasms in which a neuroendocrine component is combined with a non-neuroendocrine component. Here, we provide the clinical, pathologic, and molecular report of a 73-year-old-man presenting with an intestinal MiNEN. The lesion was composed of a well-differentiated G3 neuroendocrine tumor and a colloid adenocarcinoma. The molecular characterization was performed using a multigene next-generation sequencing panel. The neoplasm displayed microsatellite instability due to MLH1 promoter methylation. The extended molecular profile documented the same mutations affecting ARID1A, ASXL1, BLM, and RNF43 genes in both components, indicating a monoclonal origin of the tumor. Regarding component-specific gene mutations, BRCA2 was specifically altered in the neuroendocrine area. It may represent a new actionable target for precision oncology in MiNEN, but the lack of its alteration in the colloid component calls for further considerations on intratumor heterogeneity. The most important finding with potential immediate implications regards the presence of microsatellite instability: it indicates that this molecular alteration should become part of the diagnostic algorithm for these rare neoplasms.
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Affiliation(s)
| | - Maria Bencivenga
- Unit of General and Upper GI Surgery, University of Verona, Verona
| | - Andrea Mafficini
- ARC-Net Research Center
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona
| | | | - Vassilena Tsvetkova
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona
| | - Gaetano Paolino
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona
| | - Maria G Mastrosimini
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona
| | - Selma Hetoja
- Unit of General and Upper GI Surgery, University of Verona, Verona
| | | | - Paola Mattiolo
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona
| | - Chiara Borga
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Matteo Fassan
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Aldo Scarpa
- ARC-Net Research Center
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona
| | - Claudio Luchini
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona
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19
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Mattiolo P, Kryklyva V, Brosens LA, Mafficini A, Lawlor RT, Milella M, Scarpa A, Corbo V, Luchini C. Refining targeted therapeutic approaches in pancreatic cancer: from histology and molecular pathology to the clinic. Expert Opin Ther Targets 2021; 26:1-4. [DOI: 10.1080/14728222.2022.2021397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Valentyna Kryklyva
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lodewijk A. Brosens
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Rita T. Lawlor
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Vincenzo Corbo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
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20
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Barresi V, Simbolo M, Mafficini A, Martini M, Calicchia M, Piredda ML, Ciaparrone C, Bonizzato G, Ammendola S, Caffo M, Pinna G, Sala F, Lawlor RT, Ghimenton C, Scarpa A. IDH-wild type glioblastomas featuring at least 30% giant cells are characterized by frequent RB1 and NF1 alterations and hypermutation. Acta Neuropathol Commun 2021; 9:200. [PMID: 34952640 PMCID: PMC8709962 DOI: 10.1186/s40478-021-01304-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/08/2021] [Indexed: 01/07/2023] Open
Abstract
Giant cell glioblastoma (GC-GBM) is a rare variant of IDH-wt GBM histologically characterized by the presence of numerous multinucleated giant cells and molecularly considered a hybrid between IDH-wt and IDH-mutant GBM. The lack of an objective definition, specifying the percentage of giant cells required for this diagnosis, may account for the absence of a definite molecular profile of this variant. This study aimed to clarify the molecular landscape of GC-GBM, exploring the mutations and copy number variations of 458 cancer-related genes, tumor mutational burden (TMB), and microsatellite instability (MSI) in 39 GBMs dichotomized into having 30-49% (15 cases) or ≥ 50% (24 cases) GCs. The type and prevalence of the genetic alterations in this series was not associated with the GCs content (< 50% or ≥ 50%). Most cases (82% and 51.2%) had impairment in TP53/MDM2 and PTEN/PI3K pathways, but a high proportion also featured TERT promoter mutations (61.5%) and RB1 (25.6%) or NF1 (25.6%) alterations. EGFR amplification was detected in 18% cases in association with a shorter overall survival (P = 0.004). Sixteen (41%) cases had a TMB > 10 mut/Mb, including two (5%) that harbored MSI and one with a POLE mutation. The frequency of RB1 and NF1 alterations and TMB counts were significantly higher compared to 567 IDH wild type (P < 0.0001; P = 0.0003; P < 0.0001) and 26 IDH-mutant (P < 0.0001; P = 0.0227; P < 0.0001) GBMs in the TCGA PanCancer Atlas cohort. These findings demonstrate that the molecular landscape of GBMs with at least 30% giant cells is dominated by the impairment of TP53/MDM2 and PTEN/PI3K pathways, and additionally characterized by frequent RB1 alterations and hypermutation and by EGFR amplification in more aggressive cases. The high frequency of hypermutated cases suggests that GC-GBMs might be candidates for immune check-point inhibitors clinical trials.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Michele Simbolo
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Maurizio Martini
- Unit of Anatomic Pathology, Catholic University of Sacred Hearth, Rome, Italy
| | - Martina Calicchia
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Maria Liliana Piredda
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Chiara Ciaparrone
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Giada Bonizzato
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Serena Ammendola
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Maria Caffo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Neurosurgery, University of Messina, Messina, Italy
| | - Giampietro Pinna
- Department of Neurosciences, Unit of Neurosurgery, Hospital Trust of Verona, Verona, Italy
| | - Francesco Sala
- Department of Neurosciences, Biomedicines and Movement Sciences, Institute of Neurosurgery, University of Verona, Verona, Italy
| | - Rita Teresa Lawlor
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Ghimenton
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
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21
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Simbolo M, Bersani S, Vicentini C, Taormina SV, Ciaparrone C, Bagante F, Rusev B, Centonze G, Montresor M, Brunelli M, Pedron S, Mafficini A, Paolino G, Mattiolo P, Conci S, Milione M, Guglielmi A, Ruzzenente A, Scarpa A, Luchini C. Molecular characterization of extrahepatic cholangiocarcinoma: perihilar and distal tumors display divergent genomic and transcriptomic profiles. Expert Opin Ther Targets 2021; 25:1095-1105. [PMID: 34873971 DOI: 10.1080/14728222.2021.2013801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Extrahepatic cholangiocarcinoma (ECC) is classified into two subtypes based on anatomic origin: distal extrahepatic (DECC) and perihilar (PHCC) cholangiocarcinoma. This study aimed to shed light on its genomic and transcriptomic profiles. RESEARCH DESIGN AND METHODS The genomic alterations of 99 ECC (47 PHCC and 52 DECC) were investigated by next-generation sequencing of 96 genes. A subgroup of cases, representative of each subtype, was further investigated using transcriptomic analysis. Bioinformatics tools were applied for clustering and pathway analysis and defining the immune composition of the tumor microenvironment. RESULTS PHCC had more frequent KRAS mutations (p = 0.0047), whereas TP53 mutations were more common in DECC (p = 0.006). Potentially actionable alterations included high-tumor mutational burden and/or microsatellite instability (7.1%), PI3KCA mutations (8.1%), and MYC (10.1%) and ERBB2 amplification (5.1%). The transcriptomic profiles showed the presence of three distinct clusters, which followed the anatomic origin and differed in immune microenvironment. DECC appeared to contain two distinct tumor subgroups, one enriched for druggable alterations and one lacking actionable opportunities. CONCLUSIONS This study provides new insights into the molecular landscape and the actionable alterations of ECC. Our findings represent a step toward improved ECC molecular taxonomy and therapeutic strategies for precision oncology.
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Affiliation(s)
- Michele Simbolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Samantha Bersani
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Caterina Vicentini
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Sergio V Taormina
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Chiara Ciaparrone
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Fabio Bagante
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Borislav Rusev
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.,ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Giovanni Centonze
- Pathology Unit, Foundation IRCCS, Istituto Nazionale Tumori, Milano, Italy
| | - Marina Montresor
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Matteo Brunelli
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Serena Pedron
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.,ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Gaetano Paolino
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Simone Conci
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Milione
- Pathology Unit, Foundation IRCCS, Istituto Nazionale Tumori, Milano, Italy
| | - Alfredo Guglielmi
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Ruzzenente
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.,ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.,ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
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22
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Alors-Perez E, Blázquez-Encinas R, Alcalá S, Viyuela-García C, Pedraza-Arevalo S, Herrero-Aguayo V, Jiménez-Vacas JM, Mafficini A, Sánchez-Frías ME, Cano MT, Abollo-Jiménez F, Marín-Sanz JA, Cabezas-Sainz P, Lawlor RT, Luchini C, Sánchez L, Sánchez-Hidalgo JM, Ventura S, Martin-Hijano L, Gahete MD, Scarpa A, Arjona-Sánchez Á, Ibáñez-Costa A, Sainz B, Luque RM, Castaño JP. Dysregulated splicing factor SF3B1 unveils a dual therapeutic vulnerability to target pancreatic cancer cells and cancer stem cells with an anti-splicing drug. J Exp Clin Cancer Res 2021; 40:382. [PMID: 34857016 PMCID: PMC8638119 DOI: 10.1186/s13046-021-02153-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/23/2021] [Indexed: 12/13/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, requiring novel treatments to target both cancer cells and cancer stem cells (CSCs). Altered splicing is emerging as both a novel cancer hallmark and an attractive therapeutic target. The core splicing factor SF3B1 is heavily altered in cancer and can be inhibited by Pladienolide-B, but its actionability in PDAC is unknown. We explored the presence and role of SF3B1 in PDAC and interrogated its potential as an actionable target. Methods SF3B1 was analyzed in PDAC tissues, an RNA-seq dataset, and publicly available databases, examining associations with splicing alterations and key features/genes. Functional assays in PDAC cell lines and PDX-derived CSCs served to test Pladienolide-B treatment effects in vitro, and in vivo in zebrafish and mice. Results SF3B1 was overexpressed in human PDAC and associated with tumor grade and lymph-node involvement. SF3B1 levels closely associated with distinct splicing event profiles and expression of key PDAC players (KRAS, TP53). In PDAC cells, Pladienolide-B increased apoptosis and decreased multiple tumor-related features, including cell proliferation, migration, and colony/sphere formation, altering AKT and JNK signaling, and favoring proapoptotic splicing variants (BCL-XS/BCL-XL, KRASa/KRAS, Δ133TP53/TP53). Importantly, Pladienolide-B similarly impaired CSCs, reducing their stemness capacity and increasing their sensitivity to chemotherapy. Pladienolide-B also reduced PDAC/CSCs xenograft tumor growth in vivo in zebrafish and in mice. Conclusion SF3B1 overexpression represents a therapeutic vulnerability in PDAC, as altered splicing can be targeted with Pladienolide-B both in cancer cells and CSCs, paving the way for novel therapies for this lethal cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02153-9.
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Affiliation(s)
- Emilia Alors-Perez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Cordoba, Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Avenida Menéndez Pidal s/n, Edificio IMIBIC, 14004, Córdoba, Spain
| | - Ricardo Blázquez-Encinas
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Cordoba, Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Avenida Menéndez Pidal s/n, Edificio IMIBIC, 14004, Córdoba, Spain
| | - Sonia Alcalá
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols (IIBM), CSIC-UAM, Madrid, Spain.,Department of Cancer Biology, Chronic Diseases and Cancer Area 3-Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Cristina Viyuela-García
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,Surgery Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Sergio Pedraza-Arevalo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Cordoba, Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Avenida Menéndez Pidal s/n, Edificio IMIBIC, 14004, Córdoba, Spain
| | - Vicente Herrero-Aguayo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Cordoba, Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Avenida Menéndez Pidal s/n, Edificio IMIBIC, 14004, Córdoba, Spain
| | - Juan M Jiménez-Vacas
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Cordoba, Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Avenida Menéndez Pidal s/n, Edificio IMIBIC, 14004, Córdoba, Spain
| | - Andrea Mafficini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Marina E Sánchez-Frías
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,Pathology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - María T Cano
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,Medical Oncology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Fernando Abollo-Jiménez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Department of Computer Sciences, University of Cordoba, Córdoba, Spain
| | - Juan A Marín-Sanz
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Department of Computer Sciences, University of Cordoba, Córdoba, Spain
| | - Pablo Cabezas-Sainz
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Lugo, Spain
| | - Rita T Lawlor
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Luchini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Laura Sánchez
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Lugo, Spain
| | - Juan M Sánchez-Hidalgo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,Surgery Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Sebastián Ventura
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Department of Computer Sciences, University of Cordoba, Córdoba, Spain
| | - Laura Martin-Hijano
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols (IIBM), CSIC-UAM, Madrid, Spain.,Department of Cancer Biology, Chronic Diseases and Cancer Area 3-Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Manuel D Gahete
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Cordoba, Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Avenida Menéndez Pidal s/n, Edificio IMIBIC, 14004, Córdoba, Spain
| | - Aldo Scarpa
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Álvaro Arjona-Sánchez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,Surgery Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Cordoba, Córdoba, Spain.,Reina Sofia University Hospital, Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Avenida Menéndez Pidal s/n, Edificio IMIBIC, 14004, Córdoba, Spain
| | - Bruno Sainz
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols (IIBM), CSIC-UAM, Madrid, Spain. .,Centro de Investigación Biomédica en Red, Área Cáncer, CIBERONC, ISCIII, Madrid, Spain.
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain. .,Department of Cell Biology, Physiology, and Immunology, University of Cordoba, Córdoba, Spain. .,Reina Sofia University Hospital, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Avenida Menéndez Pidal s/n, Edificio IMIBIC, 14004, Córdoba, Spain.
| | - Justo P Castaño
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba, Spain. .,Department of Cell Biology, Physiology, and Immunology, University of Cordoba, Córdoba, Spain. .,Reina Sofia University Hospital, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Avenida Menéndez Pidal s/n, Edificio IMIBIC, 14004, Córdoba, Spain.
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23
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Young K, Lawlor RT, Ragulan C, Patil Y, Mafficini A, Bersani S, Antonello D, Mansfield D, Cingarlini S, Landoni L, Pea A, Luchini C, Piredda L, Kannan N, Nyamundanda G, Morganstein D, Chau I, Wiedenmann B, Milella M, Melcher A, Cunningham D, Starling N, Scarpa A, Sadanandam A. Immune landscape, evolution, hypoxia-mediated viral mimicry pathways and therapeutic potential in molecular subtypes of pancreatic neuroendocrine tumours. Gut 2021; 70:1904-1913. [PMID: 32883872 PMCID: PMC8458094 DOI: 10.1136/gutjnl-2020-321016] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE A comprehensive analysis of the immune landscape of pancreatic neuroendocrine tumours (PanNETs) was performed according to clinicopathological parameters and previously defined molecular subtypes to identify potential therapeutic vulnerabilities in this disease. DESIGN Differential expression analysis of 600 immune-related genes was performed on 207 PanNET samples, comprising a training cohort (n=72) and two validation cohorts (n=135) from multiple transcriptome profiling platforms. Different immune-related and subtype-related phenotypes, cell types and pathways were investigated using different in silico methods and were further validated using spatial multiplex immunofluorescence. RESULTS The study identified an immune signature of 132 genes segregating PanNETs (n=207) according to four previously defined molecular subtypes: metastasis-like primary (MLP)-1 and MLP-2, insulinoma-like and intermediate. The MLP-1 subtype (26%-31% samples across three cohorts) was strongly associated with elevated levels of immune-related genes, poor prognosis and a cascade of tumour evolutionary events: larger hypoxic and necroptotic tumours leading to increased damage-associated molecular patterns (viral mimicry), stimulator of interferon gene pathway, T cell-inflamed genes, immune checkpoint targets, and T cell-mediated and M1 macrophage-mediated immune escape mechanisms. Multiplex spatial profiling validated significantly increased macrophages in the MLP-1 subtype. CONCLUSION This study provides novel data on the immune microenvironment of PanNETs and identifies MLP-1 subtype as an immune-high phenotype featuring a broad and robust activation of immune-related genes. This study, with further refinement, paves the way for future precision immunotherapy studies in PanNETs to potentially select a subset of MLP-1 patients who may be more likely to respond.
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Affiliation(s)
- Kate Young
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Department of Medicine, Royal Marsden Hospital, London and Surrey, UK
| | - Rita T Lawlor
- ARC-Net Research Centre, University of Verona, Verona, Italy
| | - Chanthirika Ragulan
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Centre for Molecular Pathology, Royal Marsden Hospital, London, UK
| | - Yatish Patil
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Andrea Mafficini
- ARC-Net Research Centre, University of Verona, Verona, Italy
- Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
| | - Samantha Bersani
- ARC-Net Research Centre, University of Verona, Verona, Italy
- Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
| | - Davide Antonello
- General and Pancreatic Surgery Department, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - David Mansfield
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, UK
| | - Sara Cingarlini
- Department of Medicine, Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- General and Pancreatic Surgery Department, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Antonio Pea
- General and Pancreatic Surgery Department, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Luchini
- ARC-Net Research Centre, University of Verona, Verona, Italy
- Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
| | - Liliana Piredda
- ARC-Net Research Centre, University of Verona, Verona, Italy
| | - Nagarajan Kannan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Gift Nyamundanda
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | | | - Ian Chau
- Department of Medicine, Royal Marsden Hospital, London and Surrey, UK
| | - Bertram Wiedenmann
- Institut für Pathologie, Charite, Campus Virchow-Klinikum, University Medicine, Berlin, Germany
| | - Michele Milella
- Department of Medicine, Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Alan Melcher
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, UK
| | - David Cunningham
- Department of Medicine, Royal Marsden Hospital, London and Surrey, UK
| | - Naureen Starling
- Department of Medicine, Royal Marsden Hospital, London and Surrey, UK
| | - Aldo Scarpa
- ARC-Net Research Centre, University of Verona, Verona, Italy
- Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
| | - Anguraj Sadanandam
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Centre for Molecular Pathology, Royal Marsden Hospital, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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24
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Lawlor RT, Mafficini A, Sciammarella C, Cantù C, Rusev BC, Piredda ML, Antonello D, Grimaldi S, Bonizzato G, Sperandio N, Marchegiani G, Malleo G, Pea A, Salvia R, Mombello A, Mazzoleni G, Nottegar A, Hanspeter E, Riva G, Tomezzoli A, Bencivenga M, de Manzoni G, Pedron S, Paolino G, Mattiolo P, Brosens LA, Silvestris N, Fassan M, Cooke SL, Beer PA, Milella M, Adsay VN, Cheng L, Scarpa A, Luchini C. Genomic characterization of hepatoid tumors: context matters. Hum Pathol 2021; 118:30-41. [PMID: 34562502 DOI: 10.1016/j.humpath.2021.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022]
Abstract
Hepatoid tumors (HT) are rare neoplasms morphologically resembling hepatocellular carcinoma, which arise in several organs other than the liver. A comprehensive molecular profile of this group of neoplasms is still lacking. Genomic characterization of 19 HTs from different organs (three colon HTs, four esophagogastric HTs, four biliary HTs, six genitourinary HTs, two lung HTs) was performed using a multigene next-generation sequencing panel. NGS unraveled a composite molecular profile of HT. Their genetic alterations were clearly clustered by tumor site: (i) colorectal HT displayed microsatellite instability, high tumor mutational burden, mutations in ARID1A/B genes and NCOA4-RET gene fusion (2/3 cases); (ii) gastric HT had TP53 mutations (2/4); (iii) biliary HT displayed loss of CDKN2A (3/4) and loss of chromosome 18 (2/4); (iv) genital HT showed gain of chromosome 12 (3/6); (v) lung HT had STK11 somatic mutations (2/2). The only commonly mutated gene occurring in HT of different sites was TP53 (8/19 cases: colon 2, esophagogastric 2, biliary 2, genital 1, lungs 1). This study shows that most genetic alterations of HT were clustered by site, indicating that context matters. The novel potential targets for HT precision oncology are also clustered based on the anatomic origin. This study shed light on the biology of these rare cancers and may have important consequences for treatment decisions and clinical trial selection for HT patients.
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Affiliation(s)
- Rita T Lawlor
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Andrea Mafficini
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Concetta Sciammarella
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Cinzia Cantù
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Borislav C Rusev
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Maria L Piredda
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Davide Antonello
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Sonia Grimaldi
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Giada Bonizzato
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Nicola Sperandio
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Giovanni Marchegiani
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Giuseppe Malleo
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Antonio Pea
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Aldo Mombello
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Guido Mazzoleni
- Department of Pathology, Central Hospital of Bolzano, 39100 Bolzano, Italy
| | - Alessia Nottegar
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Esther Hanspeter
- Department of Pathology, Central Hospital of Bolzano, 39100 Bolzano, Italy
| | - Giulio Riva
- Department of Diagnostics, Pathology Unit, San Bortolo Hospital, 36100 Vicenza, Italy
| | - Anna Tomezzoli
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Maria Bencivenga
- Unit of General and Upper GI Surgery, University of Verona, 37134 Verona, Italy
| | - Giovanni de Manzoni
- Unit of General and Upper GI Surgery, University of Verona, 37134 Verona, Italy
| | - Serena Pedron
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Gaetano Paolino
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Lodewijk A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Department of Pathology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Nicola Silvestris
- IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, and Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", 70121 Bari, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), University of Padua, 35121 Padua, Italy
| | - Susanna L Cooke
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, G61 1QH Glasgow, UK
| | - Philip A Beer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, G61 1QH Glasgow, UK; Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Cambridge, UK
| | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Volkan N Adsay
- Department of Pathology, Koç University Hospital and Koç University Research Center for Translational Medicine (KUTTAM), 34010 Istanbul, Turkey
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | - Aldo Scarpa
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy.
| | - Claudio Luchini
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy.
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Lawlor RT, Mattiolo P, Mafficini A, Hong SM, Piredda ML, Taormina SV, Malleo G, Marchegiani G, Pea A, Salvia R, Kryklyva V, Shin JI, Brosens LA, Milella M, Scarpa A, Luchini C. Tumor Mutational Burden as a Potential Biomarker for Immunotherapy in Pancreatic Cancer: Systematic Review and Still-Open Questions. Cancers (Basel) 2021; 13:cancers13133119. [PMID: 34206554 PMCID: PMC8269341 DOI: 10.3390/cancers13133119] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Tumor mutational burden (TMB) represents the number of mutations per megabase (muts/Mb) harbored by tumor cells in a given neoplasm, and can be determined with next-generation sequencing. High values are an indicator of potential response to immunotherapy. With this systematic review, we assessed its role in pancreatic ductal adenocarcinoma (PDAC). Our main findings can be summarized as: (i) high-TMB can be found in about 1% of PDAC; (ii) it is associated with mucinous/colloid and medullary histology; (iii) high-TMB PDAC frequently harbor other actionable alterations, with microsatellite instability as the most common; (iv) immunotherapy has shown promising results in high-TMB PDAC. Abstract Tumor mutational burden (TMB) is a numeric index that expresses the number of mutations per megabase (muts/Mb) harbored by tumor cells in a neoplasm. TMB can be determined using different approaches based on next-generation sequencing. In the case of high values, it indicates a potential response to immunotherapy. In this systematic review, we assessed the potential predictive role of high-TMB in pancreatic ductal adenocarcinoma (PDAC), as well as the histo-molecular features of high-TMB PDAC. High-TMB appeared as a rare but not-negligible molecular feature in PDAC, being present in about 1.1% of cases. This genetic condition was closely associated with mucinous/colloid and medullary histology (p < 0.01). PDAC with high-TMB frequently harbored other actionable alterations, with microsatellite instability/defective mismatch repair as the most common. Immunotherapy has shown promising results in high-TMB PDAC, but the sample size of high-TMB PDAC treated so far is quite small. This study highlights interesting peculiarities of PDAC harboring high-TMB and may represent a reliable starting point for the assessment of TMB in the clinical management of patients affected by pancreatic cancer.
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Affiliation(s)
- Rita T. Lawlor
- ARC-Net Research Center, University and Hospital Trust of Verona, 37134 Verona, Italy; (R.T.L.); (A.M.); (M.L.P.); (S.V.T.)
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy;
| | - Andrea Mafficini
- ARC-Net Research Center, University and Hospital Trust of Verona, 37134 Verona, Italy; (R.T.L.); (A.M.); (M.L.P.); (S.V.T.)
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy;
| | - Seung-Mo Hong
- Asan Medical Center, Department of Pathology, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Maria L. Piredda
- ARC-Net Research Center, University and Hospital Trust of Verona, 37134 Verona, Italy; (R.T.L.); (A.M.); (M.L.P.); (S.V.T.)
| | - Sergio V. Taormina
- ARC-Net Research Center, University and Hospital Trust of Verona, 37134 Verona, Italy; (R.T.L.); (A.M.); (M.L.P.); (S.V.T.)
| | - Giuseppe Malleo
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy; (G.M.); (G.M.); (A.P.); (R.S.)
| | - Giovanni Marchegiani
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy; (G.M.); (G.M.); (A.P.); (R.S.)
| | - Antonio Pea
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy; (G.M.); (G.M.); (A.P.); (R.S.)
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy; (G.M.); (G.M.); (A.P.); (R.S.)
| | - Valentyna Kryklyva
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (V.K.); (L.A.B.)
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul 120-752, Korea;
| | - Lodewijk A. Brosens
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (V.K.); (L.A.B.)
- Department of Pathology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, 37134 Verona, Italy;
| | - Aldo Scarpa
- ARC-Net Research Center, University and Hospital Trust of Verona, 37134 Verona, Italy; (R.T.L.); (A.M.); (M.L.P.); (S.V.T.)
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy;
- Correspondence: (A.S.); (C.L.); Tel.: +39-045-812-7458 (A.S.); +39-045-812-4835 (C.L.)
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy;
- Correspondence: (A.S.); (C.L.); Tel.: +39-045-812-7458 (A.S.); +39-045-812-4835 (C.L.)
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26
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Piredda ML, Ammendola S, Sciammarella C, Turri G, Bagante F, Fassan M, Mafficini A, Mombello A, Cataldi S, Paolino G, Mattiolo P, Florena AM, Genna M, Fior F, Cheng L, Lawlor RT, Scarpa A, Pedrazzani C, Luchini C. Colorectal cancer with microsatellite instability: Right-sided location and signet ring cell histology are associated with nodal metastases, and extranodal extension influences disease-free survival. Pathol Res Pract 2021; 224:153519. [PMID: 34119815 DOI: 10.1016/j.prp.2021.153519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 02/08/2023]
Abstract
Colorectal cancer (CRC) with microsatellite instability (MSI) accounts for 15-18 % of all CRCs and represents the category with the best prognosis. This study aimed at determining any possible clinical/pathological features associated with a higher risk of nodal metastasization in MSI-CRC, and at defining any possible prognostic moderators in this setting. All surgically resected CRCs of the last 20 years (mono-institutional series) with a PCR-based diagnosis of MSI, with and without nodal metastasis, have been retrieved for histological review, which was performed following WHO guidelines. Furthermore, the most important prognostic moderators have been investigated with a survival analysis. The study of 33 cases of MSI-CRCs with nodal metastasis highlighted a high fidelity of histology maintenance between primary tumors and matched nodal metastases. At survival analysis, the strongest prognostic variable in MSI-CRCs with nodal metastasis was the extranodal extension (multivariate analysis, HR: 14.4, 95 %CI: 1.46-140.9, p = 0.022). Furthermore, through a comparison between nodal positive (33 cases) and nodal negative (71 cases) MSI-CRCs, right-sided location (p < 0.0001), pT4 stage (p = 0.0004) and signet-ring histology (p = 0.0089) emerged as parameters more commonly associated with nodal metastasization. These findings shed new light on the biology of MSI-CRC and can be of help for the prognostic stratification of MSI-CRC patients.
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Affiliation(s)
- Maria L Piredda
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Serena Ammendola
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | | | - Giulia Turri
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University of Verona, Verona, Italy
| | - Fabio Bagante
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University of Verona, Verona, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
| | - Andrea Mafficini
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Mombello
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Simone Cataldi
- Department of Sciences for Promotion of Health and Mother and Child Care, Anatomic Pathology, University of Palermo, Palermo, Italy
| | - Gaetano Paolino
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Ada M Florena
- Department of Sciences for Promotion of Health and Mother and Child Care, Anatomic Pathology, University of Palermo, Palermo, Italy
| | - Michele Genna
- Department of General Surgery, Unit of General and Obesity Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Francesca Fior
- Department of General Surgery, Unit of General and Obesity Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rita T Lawlor
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Corrado Pedrazzani
- Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, Unit of General and Hepatobiliary Surgery, University of Verona, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.
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27
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Simbolo M, Bilotta M, Mafficini A, Luchini C, Furlan D, Inzani F, Petrone G, Bonvissuto D, La Rosa S, Schinzari G, Bianchi A, Rossi E, Menghi R, Giuliante F, Boccia S, Scarpa A, Rindi G. Gene Expression Profiling of Pancreas Neuroendocrine Tumors with Different Ki67-Based Grades. Cancers (Basel) 2021; 13:cancers13092054. [PMID: 33922803 PMCID: PMC8122987 DOI: 10.3390/cancers13092054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Ki67-based grading is a major prognostic parameter for pancreatic neuroendocrine tumors. Gene expression profiles of these tumors have been explored, yet their relationship with Ki67-based tumor grade has only been superficially investigated. To fill this gap, we analyzed differentially expressed genes across 29 cases of different grades. Our data provided the first proof that the switch from lower to higher grades is associated with a profound change in the transcriptome. The comparison of multiple samples from the same patients, including primaries and metastasis, showed that the major determinant of difference was tumor grade, irrespective of the anatomic location or patient of origin. These data call for further investigation of this association and of the role of Ki67 in affecting chromosomal stability in neuroendocrine tumors of different grades, which may clarify the basis of tumor progression and provide clues on how to interfere with it. Abstract Pancreatic neuroendocrine tumors (PanNETs) display variable aggressive behavior. A major predictor of survival is tumor grade based on the Ki67 proliferation index. As information on transcriptomic profiles of PanNETs with different tumor grades is limited, we investigated 29 PanNETs (17 G1, 7 G2, 5 G3) for their expression profiles, mutations in 16 PanNET relevant genes and LINE-1 DNA methylation profiles. A total of 3050 genes were differentially expressed between tumors with different grades (p < 0.05): 1279 in G3 vs. G2; 2757 in G3 vs. G1; and 203 in G2 vs. G1. Mutational analysis showed 57 alterations in 11 genes, the most frequent being MEN1 (18/29), DAXX (7/29), ATRX (6/29) and MUTYH (5/29). The presence and type of mutations did not correlate with the specific expression profiles associated with different grades. LINE-1 showed significantly lower methylation in G2/G3 versus G1 tumors (p = 0.007). The expression profiles of matched primaries and metastasis (nodal, hepatic and colorectal wall) of three cases confirmed the role of Ki67 in defining specific expression profiles, which clustered according to tumor grades, independently from anatomic location or patient of origin. Such data call for future exploration of the role of Ki67 in tumor progression, given its involvement in chromosomal stability.
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Affiliation(s)
- Michele Simbolo
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (M.S.); (A.M.); (C.L.)
- ENETS Center of Excellence of Verona, 37134 Verona, Italy
| | - Mirna Bilotta
- Section of Anatomic Pathology, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00100 Roma, Italy; (M.B.); (G.R.)
- Anatomic Pathology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy; (F.I.); (G.P.); (A.B.); (R.M.); (F.G.)
- ENETS Center of Excellence of Roma, 00100 Roma, Italy;
| | - Andrea Mafficini
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (M.S.); (A.M.); (C.L.)
- ENETS Center of Excellence of Verona, 37134 Verona, Italy
- ARC-NET Applied Research on Cancer Centre, University of Verona, 37134 Verona, Italy
| | - Claudio Luchini
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (M.S.); (A.M.); (C.L.)
- ENETS Center of Excellence of Verona, 37134 Verona, Italy
| | - Daniela Furlan
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (D.F.); (S.L.R.)
| | - Frediano Inzani
- Anatomic Pathology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy; (F.I.); (G.P.); (A.B.); (R.M.); (F.G.)
- ENETS Center of Excellence of Roma, 00100 Roma, Italy;
| | - Gianluigi Petrone
- Anatomic Pathology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy; (F.I.); (G.P.); (A.B.); (R.M.); (F.G.)
- ENETS Center of Excellence of Roma, 00100 Roma, Italy;
| | - Davide Bonvissuto
- Section of Human Anatomy, Department of Neurosciences, Università Cattolica del Sacro Cuore, 00100 Roma, Italy;
| | - Stefano La Rosa
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (D.F.); (S.L.R.)
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, 1001 Lausanne, Switzerland
| | - Giovanni Schinzari
- ENETS Center of Excellence of Roma, 00100 Roma, Italy;
- Department of Oncology, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy;
| | - Antonio Bianchi
- Anatomic Pathology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy; (F.I.); (G.P.); (A.B.); (R.M.); (F.G.)
- Pituitary Unit, Department of Endocrinology and Diabetes, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy
| | - Ernesto Rossi
- Department of Oncology, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy;
| | - Roberta Menghi
- Anatomic Pathology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy; (F.I.); (G.P.); (A.B.); (R.M.); (F.G.)
- Digestive Surgery Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy
| | - Felice Giuliante
- Anatomic Pathology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy; (F.I.); (G.P.); (A.B.); (R.M.); (F.G.)
- Hepatobiliary Surgery Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy
| | - Stefania Boccia
- Section of Hygiene, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00100 Roma, Italy;
| | - Aldo Scarpa
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (M.S.); (A.M.); (C.L.)
- ENETS Center of Excellence of Verona, 37134 Verona, Italy
- ARC-NET Applied Research on Cancer Centre, University of Verona, 37134 Verona, Italy
- Correspondence:
| | - Guido Rindi
- Section of Anatomic Pathology, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00100 Roma, Italy; (M.B.); (G.R.)
- Anatomic Pathology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00100 Roma, Italy; (F.I.); (G.P.); (A.B.); (R.M.); (F.G.)
- ENETS Center of Excellence of Roma, 00100 Roma, Italy;
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Mafficini A, Lawlor RT, Ghimenton C, Antonello D, Cantù C, Paolino G, Nottegar A, Piredda ML, Salvia R, Milella M, Dei Tos AP, Fassan M, Scarpa A, Luchini C. Solid Pseudopapillary Neoplasm of the Pancreas and Abdominal Desmoid Tumor in a Patient Carrying Two Different BRCA2 Germline Mutations: New Horizons from Tumor Molecular Profiling. Genes (Basel) 2021; 12:genes12040481. [PMID: 33810291 PMCID: PMC8065547 DOI: 10.3390/genes12040481] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 02/08/2023] Open
Abstract
This case report describes the history of a 41 year-old woman with a solid pseudopapillary neoplasm (SPN) of the pancreas and a metachronous abdominal desmoid tumor (DT) that occurred two years after the SPN surgical resection. At next-generation sequencing of 174 cancer-related genes, both neoplasms harbored a CTNNB1 somatic mutation which was different in each tumor. Moreover, two BRCA2 pathogenic mutations were found in both tumors, confirmed as germline by the sequencing of normal tissue. The BRCA2 mutations were c.631G>A, resulting in the amino-acid change p.V211I, and c.7008-2A>T, causing a splice acceptor site loss. However, as the two neoplasms showed neither loss of heterozygosity nor somatic mutation in the second BRCA2 allele, they cannot be considered as BRCA-dependent tumors. Nevertheless, this study highlights the important opportunities opened by extensive tumor molecular profiling. In this particular case, it permitted the detection of BRCA2-germline mutations, essential for addressing the necessary BRCA-related genetic counseling, surveillance, and screening for the patient and her family.
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Affiliation(s)
- Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy; (A.M.); (R.T.L.); (C.C.); (A.N.); (A.S.)
| | - Rita T. Lawlor
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy; (A.M.); (R.T.L.); (C.C.); (A.N.); (A.S.)
| | - Claudio Ghimenton
- ARC-Net Research Centre, University and Hospital Trust of Verona, 37134 Verona, Italy; (C.G.); (G.P.); (M.L.P.)
| | - Davide Antonello
- Department of Surgery, The Pancreas Institute, University of Verona, 37134 Verona, Italy; (D.A.); (R.S.)
| | - Cinzia Cantù
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy; (A.M.); (R.T.L.); (C.C.); (A.N.); (A.S.)
| | - Gaetano Paolino
- ARC-Net Research Centre, University and Hospital Trust of Verona, 37134 Verona, Italy; (C.G.); (G.P.); (M.L.P.)
| | - Alessia Nottegar
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy; (A.M.); (R.T.L.); (C.C.); (A.N.); (A.S.)
| | - Maria L. Piredda
- ARC-Net Research Centre, University and Hospital Trust of Verona, 37134 Verona, Italy; (C.G.); (G.P.); (M.L.P.)
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University of Verona, 37134 Verona, Italy; (D.A.); (R.S.)
| | - Michele Milella
- Department of Medicine, Section of Medical Oncology, University of Verona, 37134 Verona, Italy;
| | - Angelo P. Dei Tos
- Department of Medicine (DIMED), Section of Pathological Anatomy, University of Padua, 35121 Padua, Italy; (A.P.D.T.); (M.F.)
| | - Matteo Fassan
- Department of Medicine (DIMED), Section of Pathological Anatomy, University of Padua, 35121 Padua, Italy; (A.P.D.T.); (M.F.)
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy; (A.M.); (R.T.L.); (C.C.); (A.N.); (A.S.)
- ARC-Net Research Centre, University and Hospital Trust of Verona, 37134 Verona, Italy; (C.G.); (G.P.); (M.L.P.)
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy; (A.M.); (R.T.L.); (C.C.); (A.N.); (A.S.)
- Correspondence: ; Tel.: +39-045-8127548
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29
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Lakis V, Lawlor RT, Newell F, Patch AM, Mafficini A, Sadanandam A, Koufariotis LT, Johnston RL, Leonard C, Wood S, Rusev B, Corbo V, Luchini C, Cingarlini S, Landoni L, Salvia R, Milella M, Chang D, Bailey P, Jamieson NB, Duthie F, Gingras MC, Muzny DM, Wheeler DA, Gibbs RA, Milione M, Pederzoli P, Samra JS, Gill AJ, Johns AL, Pearson JV, Biankin AV, Grimmond SM, Waddell N, Nones K, Scarpa A. DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association. Commun Biol 2021; 4:155. [PMID: 33536587 PMCID: PMC7859232 DOI: 10.1038/s42003-020-01469-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Here we report the DNA methylation profile of 84 sporadic pancreatic neuroendocrine tumors (PanNETs) with associated clinical and genomic information. We identified three subgroups of PanNETs, termed T1, T2 and T3, with distinct patterns of methylation. The T1 subgroup was enriched for functional tumors and ATRX, DAXX and MEN1 wild-type genotypes. The T2 subgroup contained tumors with mutations in ATRX, DAXX and MEN1 and recurrent patterns of chromosomal losses in half of the genome with no association between regions with recurrent loss and methylation levels. T2 tumors were larger and had lower methylation in the MGMT gene body, which showed positive correlation with gene expression. The T3 subgroup harboured mutations in MEN1 with recurrent loss of chromosome 11, was enriched for grade G1 tumors and showed histological parameters associated with better prognosis. Our results suggest a role for methylation in both driving tumorigenesis and potentially stratifying prognosis in PanNETs.
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Affiliation(s)
- Vanessa Lakis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Rita T Lawlor
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Andrea Mafficini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - Lambros T Koufariotis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Rebecca L Johnston
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Borislav Rusev
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Vincenzo Corbo
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Claudio Luchini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Sara Cingarlini
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Roberto Salvia
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Milella
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - David Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Academic Unit of Surgery, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 OSF, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Department of General Surgery, University of Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Baden-Württemberg, Germany
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Academic Unit of Surgery, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 OSF, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
| | - Fraser Duthie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Department of Pathology, Queen Elizabeth University Hospital, Greater Glasgow & Clyde NHS, Glasgow, G51 4TF, UK
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
- Michael E. DeBakey Department of Surgery and The Elkins Pancreas Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030-3411, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Massimo Milione
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | | | | | - Anthony J Gill
- University of Sydney, Sydney, New South Wales, 2006, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, New South Wales, 2010, Australia
| | - Amber L Johns
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, New South Wales, 2010, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, Victoria, 3000, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia.
| | - Aldo Scarpa
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy.
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy.
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy.
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Gkountakos A, Pilotto S, Mafficini A, Vicentini C, Simbolo M, Milella M, Tortora G, Scarpa A, Bria E, Corbo V. Unmasking the impact of Rictor in cancer: novel insights of mTORC2 complex. Carcinogenesis 2019; 39:971-980. [PMID: 29955840 DOI: 10.1093/carcin/bgy086] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/16/2018] [Accepted: 06/26/2018] [Indexed: 12/15/2022] Open
Abstract
Genomic alterations affecting components of the mechanistic target of rapamycin (mTOR) pathway are found rather frequently in cancers, suggesting that aberrant pathway activity is implicated in oncogenesis of different tumor types. mTOR functions as the core catalytic kinase of two distinct complexes, mTOR complex 1 (mTORC1) and 2 (mTORC2), which control numerous vital cellular processes. There is growing evidence indicating that Rictor, an essential subunit of the mTORC2 complex, is inappropriately overexpressed across numerous cancer types and this is associated with poor survival. To date, the candidate mechanisms responsible for aberrant Rictor expression described in cancer are two: (i) gene amplification and (ii) epigenetic regulation, mainly by microRNAs. Moreover, different mTOR-independent Rictor-containing complexes with oncogenic role have been documented, revealing alternative routes of Rictor-driven tumorigenesis, but simultaneously, paving the way for identifying novel biomarkers and therapeutic targets. Here, we review the main preclinical and clinical data regarding the role of Rictor in carcinogenesis and metastatic behavior as well as the potentiality of its alteration as a target.
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Affiliation(s)
- Anastasios Gkountakos
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Sara Pilotto
- Medical Oncology Section, Department of Medicine, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Andrea Mafficini
- ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy
| | - Caterina Vicentini
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy.,ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy
| | - Michele Simbolo
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Michele Milella
- Medical Oncology 1, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giampaolo Tortora
- Medical Oncology Section, Department of Medicine, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Aldo Scarpa
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy.,ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy
| | - Emilio Bria
- Medical Oncology, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Vincenzo Corbo
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy.,ARC-NET Applied Research on Cancer Center, University of Verona, Verona, Italy
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Vicentini C, Mafficini A, Simbolo M, Fassan M, Delfino P, Lawlor RT, Rusev B, Scarpa A, Corbo V. Comparative Lesions Analysis Through a Targeted Sequencing Approach. J Vis Exp 2019. [PMID: 31762465 DOI: 10.3791/59844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Assessing intra-tumoral heterogeneity (ITH) is of paramount importance to anticipate failure of targeted therapies and design accordingly effective anti-tumor strategies. Although concerns are frequently raised due to differences in sample processing and depth of coverage, next-generation sequencing of solid tumors have unraveled a highly variable degree of ITH across tumor types. Capturing the genetic relatedness between primary and metastatic lesions through the identification of clonal and subclonal populations is critical to the design of therapies for advance-stage diseases. Here, we report a method for comparative lesions analysis that allows for the identification of clonal and subclonal populations among different specimens from the same patient. The experimental approach described here integrates three well-established approaches: histological analysis, high-coverage multi-lesion sequencing, and immunophenotypic analyses. In order to minimize the effects on the detection of subclonal events by inappropriate sample processing, we subjected tissues to careful pathological examination and neoplastic cell enrichment. Quality controlled DNA from neoplastic lesions and normal tissues was then subjected to high coverage sequencing, targeting the coding regions of 409 relevant cancer genes. While only looking at a limited genomic space, our approach enables evaluating the extent of heterogeneity among somatic alterations (single-nucleotide mutations and copy-number variations) in distinct lesions from a given patient. Through comparative analysis of sequencing data, we were able to distinguish clonal vs. subclonal alterations. The majority of ITH is often ascribed to passenger mutations; therefore, we also used immunohistochemistry to predict functional consequences of mutations. While this protocol has been applied to a specific tumor type, we anticipate that the methodology described here is broadly applicable to other solid tumor types.
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Affiliation(s)
| | - Andrea Mafficini
- ARC-Net Research Centre, University and Hospital Trust of Verona
| | - Michele Simbolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology and Cytopathology Unit, University of Padua
| | - Pietro Delfino
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona
| | | | - Borislav Rusev
- ARC-Net Research Centre, University and Hospital Trust of Verona
| | - Aldo Scarpa
- ARC-Net Research Centre, University and Hospital Trust of Verona; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona
| | - Vincenzo Corbo
- ARC-Net Research Centre, University and Hospital Trust of Verona; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona;
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Pilotto S, Vita E, Sperduti I, Noia VPD, Grizzi G, D’Argento E, Simbolo M, Vicentini C, Caliò A, Mafficini A, Carbognin L, Corbo V, Gkountakos A, Santo A, Brunelli M, Martini M, Scarpa A, Milella M, Tortora G, Bria E. Exploring resistance to nivolumab [NIV] applying an Immune Genomic Signature (IGS) in advanced pretreated NSCLC [PRINCiPe study]. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz260.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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34
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Pilotto S, Di Noia V, Sperduti I, Grizzi G, D'Argento E, Simbolo M, Vicentini C, Caliò A, Mafficini A, Carbognin L, Corbo V, Gkountakos A, Vita E, Santo A, Brunelli M, Martini M, Scarpa A, Milella M, Tortora G, Bria E. P2.04-51 A 6-Gene Immune Genomic Signature (IGS) Predicts Resistance to Nivolumab [NIV] in Advanced Pretreated NSCLC: Results of PRINCiPe Trial. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Mafficini A, Cantù C, Antonello D, Simbolo M, Piredda L, Lever V, Rusev B, Pecori S, Milella M, Lawlor R, Scarpa A. Validation of a tumour mutational burden workflow on routine histological samples of colorectal cancer and assessment of a cohort with synchronous hepatic metastases. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Simbolo M, Barbi S, Fassan M, Mafficini A, Ali G, Vicentini C, Sperandio N, Corbo V, Rusev B, Mastracci L, Grillo F, Pilotto S, Pelosi G, Pelliccioni S, Lawlor RT, Tortora G, Fontanini G, Volante M, Scarpa A, Bria E. Gene Expression Profiling of Lung Atypical Carcinoids and Large Cell Neuroendocrine Carcinomas Identifies Three Transcriptomic Subtypes with Specific Genomic Alterations. J Thorac Oncol 2019; 14:1651-1661. [PMID: 31085341 DOI: 10.1016/j.jtho.2019.05.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/25/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
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Barresi V, Simbolo M, Mafficini A, Piredda ML, Caffo M, Cardali SM, Germanò A, Cingarlini S, Ghimenton C, Scarpa A. Ultra-Mutation in IDH Wild-Type Glioblastomas of Patients Younger than 55 Years is Associated with Defective Mismatch Repair, Microsatellite Instability, and Giant Cell Enrichment. Cancers (Basel) 2019; 11:cancers11091279. [PMID: 31480372 PMCID: PMC6770353 DOI: 10.3390/cancers11091279] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 12/16/2022] Open
Abstract
Background: Glioblastomas (GBMs) are classified into isocitrate dehydrogenase (IDH) mutants and IDH wild-types (IDH-wt). This study aimed at identifying the mutational assets of IDH-wt GBMs in patients aged 18–54 years for which limited data are available. Methods: Sixteen IDH-wt GBMs from adults < 55 years old were explored for mutations, copy number variations, tumour mutational load (TML), and mutational spectrum by a 409 genes TML panel. Results: Eight (50%) IDH-wt GBMs were hypermutated (TML > 9 mutations/Mb) and two (12.5%) were ultra-mutated (TML > 100 mutations/Mb). One ultra-mutated GBM had microsatellite instability (MSI), a somatic MSH6 mutation, and a germline POLE mutation. The other ultra-mutated GBMs had MSI and two somatic mutations in MSH2. Both ultra-mutated GBMs featured at least 25% giant cells. The overall survival of eight patients with hypermutated GBMs was significantly longer than that of patients with non-hypermutated GBMs (p = 0.04). Conclusions: We identified a hyper-mutated subgroup among IDH-wt GBMs in adults < 55 years that had improved prognosis. Two cases were ultra-mutated and characterized by the presence of at least 25% giant cells, MMR mutations, and MSI. Since high TML has been associated with response to immune checkpoint inhibition in paediatric gliomas, the identification of a subtype of ultra-mutated IDH-wt GBM may have implications for immunotherapy.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy.
| | - Michele Simbolo
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Andrea Mafficini
- ARC-Net Research Centre, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Maria Liliana Piredda
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Maria Caffo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Neurosurgery, University of Messina, 98125 Messina, Italy
| | - Salvatore Massimiliano Cardali
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Neurosurgery, University of Messina, 98125 Messina, Italy
| | - Antonino Germanò
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Neurosurgery, University of Messina, 98125 Messina, Italy
| | - Sara Cingarlini
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust Verona, 37134 Verona, Italy
| | - Claudio Ghimenton
- Department of Pathology and Diagnostics, Section of Pathology, Hospital Trust Verona, 37134 Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
- ARC-Net Research Centre, University and Hospital Trust of Verona, 37134 Verona, Italy
- Department of Pathology and Diagnostics, Section of Pathology, Hospital Trust Verona, 37134 Verona, Italy
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38
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Simbolo M, Mafficini A, Vicentini C, Ruzzenente A, Rusev B, Brunelli M, Pedron S, Bertuzzo F, Barbi S, Fassan M, Corbo V, Bagante F, Turri G, Luchini C, Lawlor R, Guglielmi A, Bassi C, Scarpa A. Perihilar and distal extrahepatic cholangiocarcinomas show different genetic profiles but share MYC copy gain and TP53 mutation as independent poor prognostic markers. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz155.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Gastroenteropancreatic (GEP) neuroendocrine neoplasms (NENs) are heterogeneous regarding site of origin, biological behavior, and malignant potential. There has been a rapid increase in data publication during the last 10 years, mainly driven by high-throughput studies on pancreatic and small intestinal neuroendocrine tumors (NETs). This review summarizes the present knowledge on genetic and epigenetic alterations. We integrated the available information from each compartment to give a pathway-based overview. This provided a summary of the critical alterations sustaining neoplastic cells. It also highlighted similarities and differences across anatomical locations and points that need further investigation. GEP-NENs include well-differentiated NETs and poorly differentiated neuroendocrine carcinomas (NECs). NENs are graded as G1, G2, or G3 based on mitotic count and/or Ki-67 labeling index, NECs are G3 by definition. The distinction between NETs and NECs is also linked to their genetic background, as TP53 and RB1 inactivation in NECs set them apart from NETs. A large number of genetic and epigenetic alterations have been reported. Recurrent changes have been traced back to a reduced number of core pathways, including DNA damage repair, cell cycle regulation, and phosphatidylinositol 3-kinase/mammalian target of rapamycin signaling. In pancreatic tumors, chromatin remodeling/histone methylation and telomere alteration are also affected. However, also owing to the paucity of disease models, further research is necessary to fully integrate and functionalize data on deregulated pathways to recapitulate the large heterogeneity of behaviors displayed by these tumors. This is expected to impact diagnostics, prognostic stratification, and planning of personalized therapy.
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Affiliation(s)
- Andrea Mafficini
- ARC-Net Center for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Center for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
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40
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Amato E, Mafficini A, Hirabayashi K, Lawlor RT, Fassan M, Vicentini C, Barbi S, Delfino P, Sikora K, Rusev B, Simbolo M, Esposito I, Antonello D, Pea A, Sereni E, Ballotta M, Maggino L, Marchegiani G, Ohike N, Wood LD, Salvia R, Klöppel G, Zamboni G, Scarpa A, Corbo V. Molecular alterations associated with metastases of solid pseudopapillary neoplasms of the pancreas. J Pathol 2018; 247:123-134. [PMID: 30306561 PMCID: PMC6588017 DOI: 10.1002/path.5180] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 09/13/2018] [Accepted: 10/04/2018] [Indexed: 12/13/2022]
Abstract
Solid pseudopapillary neoplasms (SPN) of the pancreas are rare, low‐grade malignant neoplasms that metastasise to the liver or peritoneum in 10–15% of cases. They almost invariably present somatic activating mutations of CTNNB1. No comprehensive molecular characterisation of metastatic disease has been conducted to date. We performed whole‐exome sequencing and copy‐number variation (CNV) analysis of 10 primary SPN and comparative sequencing of five matched primary/metastatic tumour specimens by high‐coverage targeted sequencing of 409 genes. In addition to CTNNB1‐activating mutations, we found inactivating mutations of epigenetic regulators (KDM6A, TET1, BAP1) associated with metastatic disease. Most of these alterations were shared between primary and metastatic lesions, suggesting that they occurred before dissemination. Differently from mutations, the majority of CNVs were not shared among lesions from the same patients and affected genes involved in metabolic and pro‐proliferative pathways. Immunostaining of 27 SPNs showed that loss or reduction of KDM6A and BAP1 expression was significantly enriched in metastatic SPNs. Consistent with an increased transcriptional response to hypoxia in pancreatic adenocarcinomas bearing KDM6A inactivation, we showed that mutation or reduced KDM6A expression in SPNs is associated with increased expression of the HIF1α‐regulated protein GLUT1 at both primary and metastatic sites. Our results suggest that BAP1 and KDM6A function is a barrier to the development of metastasis in a subset of SPNs, which might open novel avenues for the treatment of this disease. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Eliana Amato
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Kenichi Hirabayashi
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.,Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Rita T Lawlor
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Matteo Fassan
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Caterina Vicentini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Stefano Barbi
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Pietro Delfino
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Katarzyna Sikora
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Borislav Rusev
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Simbolo
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Irene Esposito
- Institute of Pathology, Heinrich-Heine-University and University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Davide Antonello
- Department of Surgery, General Surgery B, University of Verona, Verona, Italy
| | - Antonio Pea
- Department of Surgery, General Surgery B, University of Verona, Verona, Italy
| | - Elisabetta Sereni
- Department of Surgery, General Surgery B, University of Verona, Verona, Italy
| | - Maria Ballotta
- Section of Anatomic Pathology, Azienda Ospedaliera Rovigo, Rovigo, Italy
| | - Laura Maggino
- Department of Surgery, General Surgery B, University of Verona, Verona, Italy
| | | | - Nobuyuki Ohike
- Department of Pathology and Laboratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Japan
| | - Laura D Wood
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Roberto Salvia
- Department of Surgery, General Surgery B, University of Verona, Verona, Italy
| | - Günter Klöppel
- Department of Pathology, Technical University Munich, Munich, Germany
| | - Giuseppe Zamboni
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.,Division of Pathology, Sacro Cuore-Don Calabria Hospital, Negrar, Italy
| | - Aldo Scarpa
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Vincenzo Corbo
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
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Pilotto S, Grizzi G, Sperduti I, Simbolo M, Vicentini C, Caliò A, Caccese M, Mafficini A, Carbognin L, Corbo V, Gkountakos A, Santo A, Infante M, Brunelli M, Scarpa A, Tortora G, Bria E. P2.04-12 A Genomic Signature [JAK2, JAK3, PIAS4, PTPN2, STAT3, IFNAR2] Predicts Baseline Resistance to Nivolumab in Advanced NSCLC. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gkountakos A, Pilotto S, Simbolo M, Vicentini C, Mafficini A, del Curatolo A, Scarpa A, Tortora G, Corbo V, Bria E. Potential role of RICTOR copy number gain (CNG) as a key biomarker of mTOR activity: A comprehensive preclinical analysis in squamous cell lung cancer (SQLC) models. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy303.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Pilotto S, Grizzi G, Sperduti I, Simbolo M, Vicentini C, Caliò A, Caccese M, Mafficini A, Carbognin L, Corbo V, Gkountakos A, Santo A, Infante M, Brunelli M, Scarpa A, Tortora G, Bria E. Preliminary results of PRINCiPe (predictors of resistance to immunotherapy with nivolumab [NIV]) study in advanced pretreated non-small cell lung cancer (APNSCLC), investigating the role of an immune genomic signature (IGS) including JAK2, JAK3, PIAS4, PTPN2, STAT3, IFNAR2 alterations. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy292.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Simbolo M, Vicentini C, Mafficini A, Fassan M, Pedron S, Corbo V, Mastracci L, Rusev B, Pedrazzani C, Landoni L, Grillo F, Cingarlini S, Rindi G, Luchini C, Scarpa A, Lawlor RT. Mutational and copy number asset of primary sporadic neuroendocrine tumors of the small intestine. Virchows Arch 2018; 473:709-717. [PMID: 30219970 PMCID: PMC6267237 DOI: 10.1007/s00428-018-2450-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/06/2018] [Accepted: 08/27/2018] [Indexed: 01/25/2023]
Abstract
Small intestine neuroendocrine tumors (SI-NETs) represent the most common histotype among small intestine neoplasms, and metastatic disease is usually present at diagnosis. A retrospective series of 52 sporadic primary surgically resected SI-NETs, which were metastatic at diagnosis, was analyzed by high-coverage target sequencing (HCTS) for the mutational status of 57 genes and copy number status of 40 genes selected from recently published genome sequencing data. Seven genes were found to be recurrently mutated: CDKN1B (9.6%), APC and CDKN2C (each 7.7%), BRAF, KRAS, PIK3CA, and TP53 (each 3.8%). Copy number analysis showed frequent allelic loss of 4 genes located on chromosome 18 (BCL2, CDH19, DCC, and SMAD4) in 23/52 (44.2%) and losses on chromosomes 11 (38%) and 16 (15%). Other recurrent copy number variations were gains for genes located on chromosomes 4 (31%), 5 (27%), 14 (36%), and 20 (20%). Univariate survival analysis showed that SRC gene copy number gains were associated with a poorer prognosis (p = 0.047). Recurrent copy number variations are important events in SI-NET and SRC may represent a novel prognostic biomarker for this tumor type.
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Affiliation(s)
- Michele Simbolo
- ARC-Net Research Centre, University and Hospital Trust of Verona, Policlinico GB Rossi, Piazzale L.A. Scuro, 10, Piastra Odontoiatrica (II floor), Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Caterina Vicentini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Policlinico GB Rossi, Piazzale L.A. Scuro, 10, Piastra Odontoiatrica (II floor), Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Policlinico GB Rossi, Piazzale L.A. Scuro, 10, Piastra Odontoiatrica (II floor), Verona, Italy
| | - Matteo Fassan
- ARC-Net Research Centre, University and Hospital Trust of Verona, Policlinico GB Rossi, Piazzale L.A. Scuro, 10, Piastra Odontoiatrica (II floor), Verona, Italy.,Department of Medicine (DIMED), Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
| | - Serena Pedron
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Vincenzo Corbo
- ARC-Net Research Centre, University and Hospital Trust of Verona, Policlinico GB Rossi, Piazzale L.A. Scuro, 10, Piastra Odontoiatrica (II floor), Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Mastracci
- Department of Surgical and Diagnostic Sciences (DISC), University of Genoa and IRCCS S. Martino-IST University Hospital, Genoa, Italy
| | - Borislav Rusev
- ARC-Net Research Centre, University and Hospital Trust of Verona, Policlinico GB Rossi, Piazzale L.A. Scuro, 10, Piastra Odontoiatrica (II floor), Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Corrado Pedrazzani
- Department of Surgery, General and Hepatobiliary Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- Department of Surgery and Oncology, Unit of Surgery B, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Federica Grillo
- Department of Surgical and Diagnostic Sciences (DISC), University of Genoa and IRCCS S. Martino-IST University Hospital, Genoa, Italy
| | - Sara Cingarlini
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Guido Rindi
- Intitute of Pathology, Università Cattolica-IRCCS Fondazione Policlinico A. Gemelli, Rome, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Research Centre, University and Hospital Trust of Verona, Policlinico GB Rossi, Piazzale L.A. Scuro, 10, Piastra Odontoiatrica (II floor), Verona, Italy. .,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.
| | - Rita T Lawlor
- ARC-Net Research Centre, University and Hospital Trust of Verona, Policlinico GB Rossi, Piazzale L.A. Scuro, 10, Piastra Odontoiatrica (II floor), Verona, Italy.,Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
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45
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Vaughn CP, Costa JL, Feilotter HE, Petraroli R, Bagai V, Rachiglio AM, Marino FZ, Tops B, Kurth HM, Sakai K, Mafficini A, Bastien RRL, Reiman A, Le Corre D, Boag A, Crocker S, Bihl M, Hirschmann A, Scarpa A, Machado JC, Blons H, Sheils O, Bramlett K, Ligtenberg MJL, Cree IA, Normanno N, Nishio K, Laurent-Puig P. Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study. BMC Cancer 2018; 18:828. [PMID: 30115026 PMCID: PMC6097211 DOI: 10.1186/s12885-018-4736-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 08/09/2018] [Indexed: 12/30/2022] Open
Abstract
Background Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material. Methods We describe here a multi-institutional study using the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples. Results Reproducibility between laboratories using diluted fusion-positive cell lines was 100%. A cohort of lung clinical research samples from different origins (tissue biopsies, tissue resections, lymph nodes and pleural fluid samples) were used to evaluate the panel. We observed 97% concordance for ALK (28/30 positive; 71/70 negative samples), 95% for ROS1 (3/4 positive; 19/18 negative samples), and 93% for RET (2/1 positive; 13/14 negative samples) between the AmpliSeq assay and other methodologies. Conclusion This methodology enables simultaneous detection of multiple ALK, ROS1, RET, and NTRK1 gene fusion transcripts in a single panel, enhanced by an integrated analysis solution. The assay performs well on limited amounts of input RNA (10 ng) and offers an integrated single assay solution for detection of actionable fusions in lung adenocarcinoma, with potential savings in both cost and turn-around-time compared to the combination of all four assays by other methods. Electronic supplementary material The online version of this article (10.1186/s12885-018-4736-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cecily P Vaughn
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - José Luis Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal. .,Medical Faculty of the University of Porto, Porto, Portugal.
| | - Harriet E Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | | | | | - Anna Maria Rachiglio
- Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Federica Zito Marino
- Pathology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Bastiaan Tops
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Henriette M Kurth
- Viollier AG, Department of Genetics/Molecular Biology, Basel, Switzerland
| | - Kazuko Sakai
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka, Japan
| | - Andrea Mafficini
- ARC-NET: Centre for Applied Research on Cancer, Department of Pathology and Diagnostic, University and Hospital Trust of Verona, Verona, Italy
| | - Roy R L Bastien
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Anne Reiman
- Centre for Sport, Exercise and Life Sciences, Coventry University, Coventry, UK
| | - Delphine Le Corre
- University Paris Descartes, Paris, France.,Biology Department, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou Hospital, Paris, France
| | - Alexander Boag
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Susan Crocker
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Michel Bihl
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Aldo Scarpa
- ARC-NET: Centre for Applied Research on Cancer, Department of Pathology and Diagnostic, University and Hospital Trust of Verona, Verona, Italy
| | - José Carlos Machado
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Medical Faculty of the University of Porto, Porto, Portugal
| | - Hélène Blons
- University Paris Descartes, Paris, France.,Biology Department, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou Hospital, Paris, France
| | - Orla Sheils
- Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Dublin, Ireland
| | | | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ian A Cree
- Department of Pathology, University Hospitals Coventry and Warwickshire, Walsgrave, Coventry, UK
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Kazuto Nishio
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka, Japan
| | - Pierre Laurent-Puig
- University Paris Descartes, Paris, France.,Biology Department, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou Hospital, Paris, France
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46
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Luchini C, Cros J, Pea A, Pilati C, Veronese N, Rusev B, Capelli P, Mafficini A, Nottegar A, Brosens LAA, Noë M, Offerhaus GJA, Chianchiano P, Riva G, Piccoli P, Parolini C, Malleo G, Lawlor RT, Corbo V, Sperandio N, Barbareschi M, Fassan M, Cheng L, Wood LD, Scarpa A. PD-1, PD-L1, and CD163 in pancreatic undifferentiated carcinoma with osteoclast-like giant cells: expression patterns and clinical implications. Hum Pathol 2018; 81:157-165. [PMID: 30031096 DOI: 10.1016/j.humpath.2018.07.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 02/07/2023]
Abstract
Undifferentiated carcinoma with osteoclast-like giant cells (UCOGC), a variant of pancreatic ductal adenocarcinoma (PDAC), has a striking genetic similarity to PDAC but a significantly improved overall survival. We hypothesize that this difference could be due to the immune response to the tumor, and as such, we investigated the expression of PD-1, PD-L1, and CD163 in a series of UCOGC. To this aim, 27 pancreatic UCOGCs (11 pure and 16 PDAC-associated), 5 extrapancreatic tumors with osteoclast-like giant cells and 10 pancreatic anaplastic carcinomas were immunostained using antibodies against PD-1, PD-L1, and CD163. In pancreatic UCOGCs, PD-L1 was expressed in neoplastic cells of 17 (63%) of 27 cases, more often in cases with an associated PDAC (P = .04). Expression of PD-L1 was associated with poor prognosis, confirmed by multivariate analysis: patients with PD-L1-positive UCOGCs had a risk of all-cause mortality that was 3 times higher than did patients with PD-L1-negative UCOGCs (hazard ratio, 3.397; 95% confidence interval, 1.023-18.375; P = .034). PD-L1 expression on tumor cells was also associated with aberrant P53 expression (P = .035). PD-1 was expressed on rare lymphocytes in 12 UCOGCs (44.4%), mainly located at the tumor periphery. CD163 was expressed on histiocytes, with a diffuse and strong staining pattern in all UCOGCs. Extrapancreatic tumors with osteoclast-like giant cells showed very similar staining patterns for the same proteins. Anaplastic carcinomas have some similarities to UCOGCs, but PD-L1 has no prognostic roles. Our results may have important implications for immunotherapeutic strategies in UCOGCs; these tumors may also represent a model for future therapeutic approaches against PDAC.
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Affiliation(s)
- Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy
| | - Jerome Cros
- Department of Pathology, Beaujon Hospital, 92110 Clichy, France; Paris-Diderot School of Medicine, Inflammation Research Center, 75013 Paris, France
| | - Antonio Pea
- Department of Surgery, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Camilla Pilati
- Personalized Medicine, Pharmacogenomics, Therapeutic Optimization, Paris-Descartes University, 75006 Paris, France
| | - Nicola Veronese
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis," 70013, Castellana Grotte, Bari, Italy
| | - Borislav Rusev
- ARC-Net Research Center, University of Verona, 37134 Verona, Italy
| | - Paola Capelli
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy
| | - Andrea Mafficini
- ARC-Net Research Center, University of Verona, 37134 Verona, Italy
| | - Alessia Nottegar
- Department of Surgery, Section of Pathology, San Bortolo Hospital, 36100 Vicenza, Italy
| | - Lodewijk A A Brosens
- Department of Pathology, University Medical Center Utrecht, 3508 Utrecht, The Netherlands; Department of Pathology, Radboud University Medical Center, 6500, HB, Nijmegen, The Netherlands
| | - Michaël Noë
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21211, USA
| | - G Johan A Offerhaus
- Department of Pathology, University Medical Center Utrecht, 3508 Utrecht, The Netherlands
| | - Peter Chianchiano
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21211, USA
| | - Giulio Riva
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy
| | - Paola Piccoli
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy
| | - Claudia Parolini
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy
| | - Giuseppe Malleo
- Department of Surgery, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Rita T Lawlor
- ARC-Net Research Center, University of Verona, 37134 Verona, Italy
| | - Vincenzo Corbo
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy
| | - Nicola Sperandio
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy
| | | | - Matteo Fassan
- ARC-Net Research Center, University of Verona, 37134 Verona, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Laura D Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21211, USA; Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21211, USA.
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy; ARC-Net Research Center, University of Verona, 37134 Verona, Italy.
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47
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Affiliation(s)
- Aldo Scarpa
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy,Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
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48
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Abstract
Neuroendocrine tumours (NETs) may arise throughout the body and are a highly heterogeneous, relatively rare class of neoplasms difficult to study also for the lack of disease models. Despite this, knowledge on their molecular alterations has expanded in the latest years, also building from genetic syndromes causing their onset. Pancreatic NETs (PanNETs) have been among the most studied, and research so far has outlined a series of recurring features, as inactivation of MEN1, VHL, TSC1/2 genes and hyperactivation of the PI3K/mTOR pathway. Next-generation sequencing has added new information by showing the key role of alternative lengthening of telomeres, driven in a fraction of PanNETs by inactivation of ATRX/DAXX. Despite this accumulation of knowledge, single studies often relied on few cases or were limited to the DNA, RNA, protein or epigenetic level with lack of integrative analysis. The International Cancer Genome Consortium aimed at removing these barriers through a strict process of data and samples collection, to produce whole-genome integrated analyses for many tumour types. The results of this effort on PanNETs have been recently published and, while confirming previous observations provide a first snapshot of how heterogeneous is the combination of genetic alterations that drive this tumour type, yet converging into four pathways whose alteration has been enriched by newly discovered mechanisms. While calling for further integration of genetic and epigenetic analyses, these data allow to reconcile previous findings in a defined frame and may provide clinical research with markers for patients stratification and to guide targeted therapy decisions.
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Affiliation(s)
- Andrea Mafficini
- ARC-Net Centre for Applied Research on CancerUniversity and Hospital Trust of Verona, Verona, Italy
- Department of Diagnostics and Public HealthSection of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Centre for Applied Research on CancerUniversity and Hospital Trust of Verona, Verona, Italy
- Department of Diagnostics and Public HealthSection of Pathology, University and Hospital Trust of Verona, Verona, Italy
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49
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Pelosi G, Bianchi F, Dama E, Simbolo M, Mafficini A, Sonzogni A, Pilotto S, Harari S, Papotti M, Volante M, Fontanini G, Mastracci L, Albini A, Bria E, Calabrese F, Scarpa A. Most high-grade neuroendocrine tumours of the lung are likely to secondarily develop from pre-existing carcinoids: innovative findings skipping the current pathogenesis paradigm. Virchows Arch 2018; 472:567-577. [PMID: 29388013 DOI: 10.1007/s00428-018-2307-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/30/2017] [Accepted: 01/21/2018] [Indexed: 12/16/2022]
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50
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Trombetta D, Graziano P, Scarpa A, Sparaneo A, Rossi G, Rossi A, Di Maio M, Antonello D, Mafficini A, Fabrizio FP, Manzorra MC, Balsamo T, Centra F, Simbolo M, Pantalone A, Notarangelo M, Parente P, Lucia Dimitri MC, Bonfitto A, Fiordelisi F, Storlazzi CT, L'Abbate A, Taurchini M, Maiello E, Fazio VM, Muscarella LA. Frequent NRG1 fusions in Caucasian pulmonary mucinous adenocarcinoma predicted by Phospho-ErbB3 expression. Oncotarget 2018. [PMID: 29515761 PMCID: PMC5839392 DOI: 10.18632/oncotarget.23800] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
NRG1 fusions were recently reported as a new molecular feature of Invasive Mucinous Adenocarcinoma (IMA) of the lung. The NRG1 chimeric ligand acts as a strong inductor of phosphorylation and tyrosine kinase activity of the ErbB2/ErbB3 heterodimer, thus enhancing the PI3K–AKT/MAPK pathways. The NRG1 fusions were widely investigated in Asian IMA cohorts, whereas just anecdotal information are available about the occurrence of NRG1 fusions in IMA Caucasian population. Here we firstly explored a large Caucasian cohort of 51 IMAs and 34 non-IMA cases for the occurrence of NRG1 rearrangements by fluorescent in situ hybridization (FISH) and RNA target sequencing. FISH results were correlated to the immunohistochemical expression of phosphorylated-ErbB3 (pErbB3) receptor and the mutational status of KRAS, EGFR and ALK genes. The NRG1 rearrangements were detected in 31% IMAs and 3% non-IMAs and the CD74-NRG1 fusion transcript variant was characterized in 4 NRG1-positive IMAs. Moreover, pErbB3 expression was found to be strictly associated to the mucinous pattern (p = 0.012, Chi-square test) and all IMA cases showing aberrant expression of pErbB3 demonstrated NRG1 rearrangements. No significant correlation between NRG1 rearrangements and EGFR, KRAS or ALK mutations respectively, was observed. We report for the first time that NRG1 fusions are driver alterations clearly associated with mucinous lung adenocarcinoma subtype of Caucasian patients and not exclusive of Asiatic population. pErbB3 immunostaining may represent a strong predictor of NRG1 fusions, pointing out the detection of pErbB3 by IHC as a rapid and effective pre-screening method to select the NRG1-positive patients.
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Affiliation(s)
- Domenico Trombetta
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Paolo Graziano
- Unit of Pathology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Aldo Scarpa
- ARC-NET Research Centre and Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Angelo Sparaneo
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Giulio Rossi
- Division of Anatomic Pathology, Regional Hospital Umberto Parini, Aosta, Italy
| | - Antonio Rossi
- Oncology Department, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Massimo Di Maio
- Department of Oncology, University of Turin, A. O. Ordine Mauriziano, Torino, Italy
| | - Davide Antonello
- ARC-NET Research Centre and Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- ARC-NET Research Centre and Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Federico Pio Fabrizio
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Maria Carmina Manzorra
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Teresa Balsamo
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Flavia Centra
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Michele Simbolo
- ARC-NET Research Centre and Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Angela Pantalone
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Michela Notarangelo
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Paola Parente
- Unit of Pathology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | | | - Antonio Bonfitto
- Unit of Pathology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Fabiola Fiordelisi
- Unit of Pathology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | | | - Alberto L'Abbate
- Department of Biology, University of Bari "A. Moro", Bari, Italy
| | - Marco Taurchini
- Unit of Thoracic-Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Evaristo Maiello
- Oncology Department, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Vito Michele Fazio
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Foggia, Italy
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