Identification of Fusion Genes and Targets for Genetically Matched Therapies in a Large Cohort of Salivary Gland Cancer Patients
Introduction: Salivary gland cancer (SGC) is a rare cancer for which systemic treatment options are limited. Therefore, it is important to characterize its genetic landscape in search for actionable aberrations, such as NTRK gene fusions. This research aimed to identify these actionable aberrations...
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| Veröffentlicht in: | Cancers 2022-08, Vol.14 (17), p.4156 |
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| creator | Lassche, Gerben van Helvert, Sjoerd Eijkelenboom, Astrid Tjan, Martijn J. H. Jansen, Erik A. M. van Cleef, Patricia H. J. Verhaegh, Gerald W. Kamping, Eveline J. Grünberg, Katrien van Engen-van Grunsven, Adriana C. H. Ligtenberg, Marjolijn J. L. van Herpen, Carla M. L. |
| description | Introduction: Salivary gland cancer (SGC) is a rare cancer for which systemic treatment options are limited. Therefore, it is important to characterize its genetic landscape in search for actionable aberrations, such as NTRK gene fusions. This research aimed to identify these actionable aberrations by combining NGS-based analysis of RNA (gene fusions) and DNA (single and multiple nucleotide variants, copy number variants, microsatellite instability and tumor mutational burden) in a large cohort of SGC patients. Methods: RNA and DNA were extracted from archival tissue of 121 patients with various SGC subtypes. Gene fusion analysis was performed using a customized RNA-based targeted NGS panel. DNA was sequenced using a targeted NGS panel encompassing 523 cancer-related genes. Cross-validation of NGS-based NTRK fusion detection and pan-TRK immunohistochemistry (IHC) was performed. Results: Fusion transcripts were detected in 50% of the cases and included both known (MYB-NFIB, MYBL1-NFIB, CRTC1-MAML2) and previously unknown fusions (including transcripts involving RET, BRAF or RAD51B). Only one NTRK fusion transcript was detected, in a secretory carcinoma case. Pan-TRK IHC (clone EPR17341) was false positive in 74% of cases. The proportion of patients with targets for genetically matched therapies differed among subtypes (salivary duct carcinoma: 82%, adenoid cystic carcinoma 28%, mucoepidermoid carcinoma 50%, acinic cell carcinoma 33%). Actionable aberrations were most often located in PIK3CA (n = 18, 15%), ERBB2 (n = 15, 12%), HRAS and NOTCH1 (both n = 9, 7%). Conclusions: Actionable genetic aberrations were seen in 53.7% of all SGC cases on the RNA and DNA level, with varying percentages between subtypes. |
| doi_str_mv | 10.3390/cancers14174156 |
| format | Article |
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H. ; Jansen, Erik A. M. ; van Cleef, Patricia H. J. ; Verhaegh, Gerald W. ; Kamping, Eveline J. ; Grünberg, Katrien ; van Engen-van Grunsven, Adriana C. H. ; Ligtenberg, Marjolijn J. L. ; van Herpen, Carla M. L.</creator><creatorcontrib>Lassche, Gerben ; van Helvert, Sjoerd ; Eijkelenboom, Astrid ; Tjan, Martijn J. H. ; Jansen, Erik A. M. ; van Cleef, Patricia H. J. ; Verhaegh, Gerald W. ; Kamping, Eveline J. ; Grünberg, Katrien ; van Engen-van Grunsven, Adriana C. H. ; Ligtenberg, Marjolijn J. L. ; van Herpen, Carla M. L.</creatorcontrib><description>Introduction: Salivary gland cancer (SGC) is a rare cancer for which systemic treatment options are limited. Therefore, it is important to characterize its genetic landscape in search for actionable aberrations, such as NTRK gene fusions. This research aimed to identify these actionable aberrations by combining NGS-based analysis of RNA (gene fusions) and DNA (single and multiple nucleotide variants, copy number variants, microsatellite instability and tumor mutational burden) in a large cohort of SGC patients. Methods: RNA and DNA were extracted from archival tissue of 121 patients with various SGC subtypes. Gene fusion analysis was performed using a customized RNA-based targeted NGS panel. DNA was sequenced using a targeted NGS panel encompassing 523 cancer-related genes. Cross-validation of NGS-based NTRK fusion detection and pan-TRK immunohistochemistry (IHC) was performed. Results: Fusion transcripts were detected in 50% of the cases and included both known (MYB-NFIB, MYBL1-NFIB, CRTC1-MAML2) and previously unknown fusions (including transcripts involving RET, BRAF or RAD51B). Only one NTRK fusion transcript was detected, in a secretory carcinoma case. Pan-TRK IHC (clone EPR17341) was false positive in 74% of cases. The proportion of patients with targets for genetically matched therapies differed among subtypes (salivary duct carcinoma: 82%, adenoid cystic carcinoma 28%, mucoepidermoid carcinoma 50%, acinic cell carcinoma 33%). Actionable aberrations were most often located in PIK3CA (n = 18, 15%), ERBB2 (n = 15, 12%), HRAS and NOTCH1 (both n = 9, 7%). Conclusions: Actionable genetic aberrations were seen in 53.7% of all SGC cases on the RNA and DNA level, with varying percentages between subtypes.</description><identifier>ISSN: 2072-6694</identifier><identifier>EISSN: 2072-6694</identifier><identifier>DOI: 10.3390/cancers14174156</identifier><identifier>PMID: 36077692</identifier><language>eng</language><publisher>Basel: MDPI AG</publisher><subject>Adenoid ; Archives & records ; Cancer ; Care and treatment ; Copy number ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; ErbB-2 protein ; Exocrine glands ; Fusion protein ; Genes ; Genetic aspects ; Genomes ; Hybridization ; Immunohistochemistry ; Medical research ; Methods ; Microsatellite instability ; Molecular diagnostic techniques ; Mutation ; Next-generation sequencing ; Notch1 protein ; Nucleotide sequence ; Oncology ; Otolaryngology ; Patients ; Response rates ; Ribonucleic acid ; RNA ; Salivary gland ; Salivary gland tumors ; Tumors</subject><ispartof>Cancers, 2022-08, Vol.14 (17), p.4156</ispartof><rights>COPYRIGHT 2022 MDPI AG</rights><rights>2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 by the authors. 2022</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c426t-8161761b1e25989b9658f86f1667af5882dd5ebeabfe5e6b28341ada21174f03</citedby><cites>FETCH-LOGICAL-c426t-8161761b1e25989b9658f86f1667af5882dd5ebeabfe5e6b28341ada21174f03</cites><orcidid>0000-0002-4935-6206 ; 0000-0002-4958-9819 ; 0000-0003-0227-2280 ; 0000-0003-1290-1474</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9454424/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9454424/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids></links><search><creatorcontrib>Lassche, Gerben</creatorcontrib><creatorcontrib>van Helvert, Sjoerd</creatorcontrib><creatorcontrib>Eijkelenboom, Astrid</creatorcontrib><creatorcontrib>Tjan, Martijn J. H.</creatorcontrib><creatorcontrib>Jansen, Erik A. M.</creatorcontrib><creatorcontrib>van Cleef, Patricia H. J.</creatorcontrib><creatorcontrib>Verhaegh, Gerald W.</creatorcontrib><creatorcontrib>Kamping, Eveline J.</creatorcontrib><creatorcontrib>Grünberg, Katrien</creatorcontrib><creatorcontrib>van Engen-van Grunsven, Adriana C. H.</creatorcontrib><creatorcontrib>Ligtenberg, Marjolijn J. L.</creatorcontrib><creatorcontrib>van Herpen, Carla M. L.</creatorcontrib><title>Identification of Fusion Genes and Targets for Genetically Matched Therapies in a Large Cohort of Salivary Gland Cancer Patients</title><title>Cancers</title><description>Introduction: Salivary gland cancer (SGC) is a rare cancer for which systemic treatment options are limited. Therefore, it is important to characterize its genetic landscape in search for actionable aberrations, such as NTRK gene fusions. This research aimed to identify these actionable aberrations by combining NGS-based analysis of RNA (gene fusions) and DNA (single and multiple nucleotide variants, copy number variants, microsatellite instability and tumor mutational burden) in a large cohort of SGC patients. Methods: RNA and DNA were extracted from archival tissue of 121 patients with various SGC subtypes. Gene fusion analysis was performed using a customized RNA-based targeted NGS panel. DNA was sequenced using a targeted NGS panel encompassing 523 cancer-related genes. Cross-validation of NGS-based NTRK fusion detection and pan-TRK immunohistochemistry (IHC) was performed. Results: Fusion transcripts were detected in 50% of the cases and included both known (MYB-NFIB, MYBL1-NFIB, CRTC1-MAML2) and previously unknown fusions (including transcripts involving RET, BRAF or RAD51B). Only one NTRK fusion transcript was detected, in a secretory carcinoma case. Pan-TRK IHC (clone EPR17341) was false positive in 74% of cases. The proportion of patients with targets for genetically matched therapies differed among subtypes (salivary duct carcinoma: 82%, adenoid cystic carcinoma 28%, mucoepidermoid carcinoma 50%, acinic cell carcinoma 33%). Actionable aberrations were most often located in PIK3CA (n = 18, 15%), ERBB2 (n = 15, 12%), HRAS and NOTCH1 (both n = 9, 7%). Conclusions: Actionable genetic aberrations were seen in 53.7% of all SGC cases on the RNA and DNA level, with varying percentages between subtypes.</description><subject>Adenoid</subject><subject>Archives & records</subject><subject>Cancer</subject><subject>Care and treatment</subject><subject>Copy number</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>ErbB-2 protein</subject><subject>Exocrine glands</subject><subject>Fusion protein</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Hybridization</subject><subject>Immunohistochemistry</subject><subject>Medical research</subject><subject>Methods</subject><subject>Microsatellite instability</subject><subject>Molecular diagnostic techniques</subject><subject>Mutation</subject><subject>Next-generation sequencing</subject><subject>Notch1 protein</subject><subject>Nucleotide sequence</subject><subject>Oncology</subject><subject>Otolaryngology</subject><subject>Patients</subject><subject>Response rates</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Salivary gland</subject><subject>Salivary gland tumors</subject><subject>Tumors</subject><issn>2072-6694</issn><issn>2072-6694</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNpdks1r3DAQxUVoaUKac6-CXHrZxvq2L4WwNJvAlgS6dyHLo10Fr7WV7EBu-dM7TkLTRhcNmh_vvRFDyBdWfROiqS68GzzkwiQzkil9RE54ZfhC60Z--Kc-Jmel3Fd4hGBGm0_kWOjKGN3wE_J008EwxhC9G2MaaAr0aipztYIBCnVDRzcub2EsNKT8_Doi3PeP9Kcb_Q6wv4PsDhHpOFBH1zNOl2mX8jjr_XJ9fHD5ka76WW35nJreoR86l8_kY3B9gbPX-5Rsrn5slteL9e3qZnm5XnjJ9biomcbsrGXAVVM3baNVHWodmNbGBVXXvOsUtODaAAp0y2shmescZ_g5oRKn5PuL7GFq99B5tM6ut4cc9xjNJhft_50h7uw2PdhGKim5RIGvrwI5_Z6gjHYfi4ceZ4I0FcsN47XSojKInr9D79OUB5xuphhXQnDxRm1dDzYOIaGvn0XtpZEKSZRC6uKF8jmVkiH8jcwqO2-BfbcF4g-0OKTK</recordid><startdate>20220827</startdate><enddate>20220827</enddate><creator>Lassche, Gerben</creator><creator>van Helvert, Sjoerd</creator><creator>Eijkelenboom, Astrid</creator><creator>Tjan, Martijn J. 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H. ; Jansen, Erik A. M. ; van Cleef, Patricia H. J. ; Verhaegh, Gerald W. ; Kamping, Eveline J. ; Grünberg, Katrien ; van Engen-van Grunsven, Adriana C. H. ; Ligtenberg, Marjolijn J. L. ; van Herpen, Carla M. 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H.</au><au>Jansen, Erik A. M.</au><au>van Cleef, Patricia H. J.</au><au>Verhaegh, Gerald W.</au><au>Kamping, Eveline J.</au><au>Grünberg, Katrien</au><au>van Engen-van Grunsven, Adriana C. H.</au><au>Ligtenberg, Marjolijn J. L.</au><au>van Herpen, Carla M. L.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of Fusion Genes and Targets for Genetically Matched Therapies in a Large Cohort of Salivary Gland Cancer Patients</atitle><jtitle>Cancers</jtitle><date>2022-08-27</date><risdate>2022</risdate><volume>14</volume><issue>17</issue><spage>4156</spage><pages>4156-</pages><issn>2072-6694</issn><eissn>2072-6694</eissn><abstract>Introduction: Salivary gland cancer (SGC) is a rare cancer for which systemic treatment options are limited. Therefore, it is important to characterize its genetic landscape in search for actionable aberrations, such as NTRK gene fusions. This research aimed to identify these actionable aberrations by combining NGS-based analysis of RNA (gene fusions) and DNA (single and multiple nucleotide variants, copy number variants, microsatellite instability and tumor mutational burden) in a large cohort of SGC patients. Methods: RNA and DNA were extracted from archival tissue of 121 patients with various SGC subtypes. Gene fusion analysis was performed using a customized RNA-based targeted NGS panel. DNA was sequenced using a targeted NGS panel encompassing 523 cancer-related genes. Cross-validation of NGS-based NTRK fusion detection and pan-TRK immunohistochemistry (IHC) was performed. Results: Fusion transcripts were detected in 50% of the cases and included both known (MYB-NFIB, MYBL1-NFIB, CRTC1-MAML2) and previously unknown fusions (including transcripts involving RET, BRAF or RAD51B). Only one NTRK fusion transcript was detected, in a secretory carcinoma case. Pan-TRK IHC (clone EPR17341) was false positive in 74% of cases. The proportion of patients with targets for genetically matched therapies differed among subtypes (salivary duct carcinoma: 82%, adenoid cystic carcinoma 28%, mucoepidermoid carcinoma 50%, acinic cell carcinoma 33%). Actionable aberrations were most often located in PIK3CA (n = 18, 15%), ERBB2 (n = 15, 12%), HRAS and NOTCH1 (both n = 9, 7%). Conclusions: Actionable genetic aberrations were seen in 53.7% of all SGC cases on the RNA and DNA level, with varying percentages between subtypes.</abstract><cop>Basel</cop><pub>MDPI AG</pub><pmid>36077692</pmid><doi>10.3390/cancers14174156</doi><orcidid>https://orcid.org/0000-0002-4935-6206</orcidid><orcidid>https://orcid.org/0000-0002-4958-9819</orcidid><orcidid>https://orcid.org/0000-0003-0227-2280</orcidid><orcidid>https://orcid.org/0000-0003-1290-1474</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MDPI - Multidisciplinary Digital Publishing Institute; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access |
| subjects | Adenoid Archives & records Cancer Care and treatment Copy number Deoxyribonucleic acid DNA DNA sequencing ErbB-2 protein Exocrine glands Fusion protein Genes Genetic aspects Genomes Hybridization Immunohistochemistry Medical research Methods Microsatellite instability Molecular diagnostic techniques Mutation Next-generation sequencing Notch1 protein Nucleotide sequence Oncology Otolaryngology Patients Response rates Ribonucleic acid RNA Salivary gland Salivary gland tumors Tumors |
| title | Identification of Fusion Genes and Targets for Genetically Matched Therapies in a Large Cohort of Salivary Gland Cancer Patients |
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