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Chłopek M, Lasota J, Thompson LDR, Szczepaniak M, Kuźniacka A, Hińcza K, Kubicka K, Kaczorowski M, Newford M, Liu Y, Agaimy A, Biernat W, Durzyńska M, Dziuba I, Hartmann A, Inaguma S, Iżycka-Świeszewska E, Kato H, Kopczyński J, Michal M, Michal M, Pęksa R, Prochorec-Sobieszek M, Starzyńska A, Takahashi S, Wasąg B, Kowalik A, Miettinen M. Alterations in key signaling pathways in sinonasal tract melanoma. A molecular genetics and immunohistochemical study of 90 cases and comprehensive review of the literature. Mod Pathol 2022; 35:1609-1617. [PMID: 35978013 DOI: 10.1038/s41379-022-01122-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 11/09/2022]
Abstract
Sinonasal mucosal melanoma is a rare tumor arising within the nasal cavity, paranasal sinuses, or nasopharynx (sinonasal tract). This study evaluated 90 cases diagnosed in 29 males and 61 females with median age 68 years. Most tumors involved the nasal cavity and had an epithelioid morphology. Spectrum of research techniques used in this analysis includes targeted-DNA and -RNA next-generation sequencing, Sanger sequencing, fluorescence in situ hybridization and immunohistochemistry. Sinonasal melanomas were commonly driven by RAS (38/90, 42%), especially NRAS (n = 36) mutations and rarely (4/90, 4%) displayed BRAF pathogenic variants. BRAF/RAS mutants were more frequent among paranasal sinuses (10/14, 71%) than nasal (26/64, 41%) tumors. BRAF/RAS-wild type tumors occasionally harbored alterations of the key components and regulators of Ras-MAPK signaling pathway: NF1 mutations (1/17, 6%) or NF1 locus deletions (1/25, 4%), SPRED1 (3/25, 12%), PIK3CA (3/50, 6%), PTEN (4/50, 8%) and mTOR (1/50, 2%) mutations. These mutations often occurred in a mutually exclusive manner. In several tumors some of which were NRAS mutants, TP53 was deleted (6/48, 13%) and/or mutated (5/90, 6%). Variable nuclear accumulation of TP53, mirrored by elevated nuclear MDM2 expression was seen in >50% of cases. Furthermore, sinonasal melanomas (n = 7) including RAS/BRAF-wild type tumors (n = 5) harbored alterations of the key components and regulators of canonical WNT-pathway: APC (4/90, 4%), CTNNB1 (3/90, 3%) and AMER1 (1/90, 1%). Both, TERT promoter mutations (5/53, 9%) and fusions (2/40, 5%) were identified. The latter occurred in BRAF/RAS-wild type tumors. No oncogenic fusion gene transcripts previously reported in cutaneous melanomas were detected. Eight tumors including 7 BRAF/RAS-wild type cases expressed ADCK4::NUMBL cis-fusion transcripts. In summary, this study documented mutational activation of NRAS and other key components and regulators of Ras-MAPK signaling pathway such as SPRED1 in a majority of sinonasal melanomas.
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Affiliation(s)
- Małgorzata Chłopek
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | - Jerzy Lasota
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.
| | | | | | - Alina Kuźniacka
- Department of Biology and Genetics, Medical University of Gdańsk, Gdańsk, Poland
| | - Kinga Hińcza
- Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | - Kamila Kubicka
- Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | - Maciej Kaczorowski
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Department of Clinical and Experimental Pathology, Wrocław Medical University, Wrocław, Poland
| | - Michael Newford
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Yalan Liu
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Abbas Agaimy
- Institute of Pathology, University Hospital of Erlangen, Erlangen, Germany
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Monika Durzyńska
- Department of Pathology, The Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Ireneusz Dziuba
- Faculty of Medicine, University of Technology, Katowice, Poland
| | - Arndt Hartmann
- Institute of Pathology, University Hospital of Erlangen, Erlangen, Germany
| | - Shingo Inaguma
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Ewa Iżycka-Świeszewska
- Department of Pathology and Neuropathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Hiroyuki Kato
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Janusz Kopczyński
- Department of Surgical Pathology, Holycross Cancer Center, Kielce, Poland
| | - Michal Michal
- Sikl's Department of Pathology, University Hospital, Charles University in Prague, Medical Faculty in Plzeň, Plzeň, Czech Republic
| | - Michael Michal
- Sikl's Department of Pathology, University Hospital, Charles University in Prague, Medical Faculty in Plzeň, Plzeň, Czech Republic
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Monika Prochorec-Sobieszek
- Department of Pathology, The Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Anna Starzyńska
- Department of Oral Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Bartosz Wasąg
- Department of Biology and Genetics, Medical University of Gdańsk, Gdańsk, Poland
| | - Artur Kowalik
- Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland.,Division of Medical Biology, Institute of Biology Jan Kochanowski University, Kielce, Poland
| | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
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Wu Z, Abdullaev Z, Pratt D, Chung HJ, Skarshaug S, Zgonc V, Perry C, Pack S, Saidkhodjaeva L, Nagaraj S, Tyagi M, Xi L, Raffeld M, Papanicolau-Sengos A, O’Donnell K, Chinquee J, Newford M, Gilbert M, Sahm F, Suwala AK, von Deimling A, Nassiri F, Zadeh G, Ruppin E, Quezado M, Aldape K. PATH-46. DIAGNOSTIC IMPACT OF THE CNS TUMOR METHYLATION PROFILING IN A NEUROPATHOLOGY CONSULT PRACTICE. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.498] [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: 11/14/2022] Open
Abstract
Abstract
DNA methylation profiling coupled with the application of CNS tumor methylation classifier has contributed to precise and accurate diagnostics for a range of tumor types involving the central nervous system. The impact and characteristics of methylation profiling on tumor diagnosis has not been fully assessed in the setting of neuropathology consultation practice. A consecutive series of 1,258 surgical neuropathology samples obtained primarily in a consultation practice were profiled over 2-year period and analyzed using the DKFZ/Heidelberg CNS tumor methylation classifier. Among the 1,045 cases received from outside institutions for consultation, the classifier was able to refine a histologically diagnosed entity (e.g. medulloblastoma) in 13.3% (n = 139) cases. A substantially new diagnosis was able to be rendered in an additional 17.9% (n = 187) cases, many of which could be confirmed using orthogonal methods. A “suggestive” (0.30-0.84) classifier score was found in 23% (242) cases and we found that complementary methods (UMAP, t-SNE and nearest-neighbors) were able to resolve this uncertainty in 118 cases. We found tumor purity significantly associated with varied classifier score (p = 1.53e-11). Computational tumor purity adjustment by deconvolution on a subset of gliomas provided a proof-of-concept to resolve diagnostics in the setting of low tumor purity. Overall, this work directly assesses the benefit of methylation classification in a set of diagnostically challenging CNS tumors, addresses tumor purity diminished methylation signal and provides complementary approaches to address diagnostics in cases of low-confidence classifier scores.
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Affiliation(s)
- Zhichao Wu
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zied Abdullaev
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Drew Pratt
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hye-Jung Chung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Shannon Skarshaug
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Valerie Zgonc
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Candice Perry
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Svetlana Pack
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | | | - Sushma Nagaraj
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Manoj Tyagi
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Liqiang Xi
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Mark Raffeld
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | | | - Kayla O’Donnell
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Joseph Chinquee
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Michael Newford
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Mark Gilbert
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Felix Sahm
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, DKFZ, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Farshad Nassiri
- Department of Surgery, University of Toronto, Toronto, Canada
| | | | - Eytan Ruppin
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Martha Quezado
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Wu Z, Abdullaev Z, Pratt D, Chung HJ, Skarshaug S, Zgonc V, Perry C, Pack S, Saidkhodjaeva L, Nagaraj S, Tyagi M, Gangalapudi V, Valdez K, Turakulov R, Xi L, Raffeld M, Papanicolau-Sengos A, O'Donnell K, Newford M, Gilbert MR, Sahm F, Suwala AK, von Deimling A, Mamatjan Y, Karimi S, Nassiri F, Zadeh G, Ruppin E, Quezado M, Aldape K. Impact of the methylation classifier and ancillary methods on CNS tumor diagnostics. Neuro Oncol 2021; 24:571-581. [PMID: 34555175 DOI: 10.1093/neuonc/noab227] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 12/22/2022] Open
Abstract
BACKGROUND Accurate CNS tumor diagnosis can be challenging, and methylation profiling can serve as an adjunct to classify diagnostically difficult cases. METHODS An integrated diagnostic approach was employed for a consecutive series of 1,258 surgical neuropathology samples obtained primarily in a consultation practice over 2-year period. DNA methylation profiling and classification using the DKFZ/Heidelberg CNS tumor classifier was performed, as well as unsupervised analyses of methylation data. Ancillary testing, where relevant, was performed. RESULTS Among the received cases in consultation, a high confidence methylation classifier score (>0.84) was reached in 66.4% of cases. The classifier impacted the diagnosis in 46.5% of these high-confidence classifier score cases, including a substantially new diagnosis in 26.9% cases. Among the 289 cases received with only a descriptive diagnosis, methylation was able to resolve approximately half (144, 49.8%) with high-confidence scores. Additional methods were able to resolve diagnostic uncertainty in 41.6% of the low-score cases. Tumor purity was significantly associated with classifier score (p = 1.15e-11). Deconvolution demonstrated that suspected GBMs matching as control/inflammatory brain tissue could be resolved into GBM methylation profiles, which provided a proof-of-concept approach to resolve tumor classification in the setting of low tumor purity. CONCLUSIONS This work assesses the impact of a methylation classifier and additional methods in a consultative practice by defining the proportions with concordant vs. change in diagnosis in a set of diagnostically challenging CNS tumors. We address approaches to low-confidence scores and confounding issues of low tumor purity.
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Affiliation(s)
- Zhichao Wu
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Drew Pratt
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hye-Jung Chung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Shannon Skarshaug
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerie Zgonc
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Candice Perry
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Svetlana Pack
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lola Saidkhodjaeva
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sushma Nagaraj
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Manoj Tyagi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Vineela Gangalapudi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kristin Valdez
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rust Turakulov
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Liqiang Xi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark Raffeld
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Antonios Papanicolau-Sengos
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kayla O'Donnell
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Newford
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital of Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
| | - Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, University Hospital of Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital of Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
| | - Yasin Mamatjan
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Shirin Karimi
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Farshad Nassiri
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Gelareh Zadeh
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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