Quantification and localization of oncogenic receptor tyrosine kinase variant transcripts using molecular inversion probes

Abstract Oncogenic membrane receptor tyrosine kinases such as MET and EGFR, or auto-active variants thereof, are important targets for cancer precision therapy. Targeted inhibition of these oncogenic receptors however invariably leads to resistance, resulting from acquisition of resistance-inducing...

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Autores principales:	Corina N. A. M. van den Heuvel, Arvid I. Das, Tessa de Bitter, Femke Simmer, Thomas Wurdinger, Miguel Angel Molina-Vila, William P. J. Leenders
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a96e3530439a41b7b9df6a5ba6233936
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spelling	oai:doaj.org-article:a96e3530439a41b7b9df6a5ba62339362021-12-02T15:09:09ZQuantification and localization of oncogenic receptor tyrosine kinase variant transcripts using molecular inversion probes10.1038/s41598-018-25328-52045-2322https://doaj.org/article/a96e3530439a41b7b9df6a5ba62339362018-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-25328-5https://doaj.org/toc/2045-2322Abstract Oncogenic membrane receptor tyrosine kinases such as MET and EGFR, or auto-active variants thereof, are important targets for cancer precision therapy. Targeted inhibition of these oncogenic receptors however invariably leads to resistance, resulting from acquisition of resistance-inducing mutations or from selective outgrowth of a priori resistant tumour cells. Most applied molecular protocols cannot distinguish between intracellular and intercellular heterogeneity of oncogene (variant) expression, which may lead to misinterpretation of the molecular make-up of a cancer and suboptimal application of targeted therapies. We here combined two related techniques to allow semiquantitative and localized in situ detection of specific transcript splice variants using single molecule molecular inversion probe (smMIP)-based next generation sequencing and padlock probe-based rolling circle amplification, respectively. We show highly specific padlock probe-based multiplex detection of MET, METΔ7-8 and METΔ14 transcripts, lacking exons 7–8 and exon 14 respectively, and of EGFR and the auto-active EGFRvIII, lacking exons 2–7. The combination of quantitative transcript variant detection with smMIPs and transcript localization using padlock probes can be used for detection of oncogenic transcripts on the single-cell level, allowing study of tumour heterogeneity. Visualization of tumour heterogeneity can shed light on the biology underlying drug resistance and potentially improve targeted therapeutics.Corina N. A. M. van den HeuvelArvid I. DasTessa de BitterFemke SimmerThomas WurdingerMiguel Angel Molina-VilaWilliam P. J. LeendersNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-12 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Corina N. A. M. van den Heuvel Arvid I. Das Tessa de Bitter Femke Simmer Thomas Wurdinger Miguel Angel Molina-Vila William P. J. Leenders Quantification and localization of oncogenic receptor tyrosine kinase variant transcripts using molecular inversion probes
description	Abstract Oncogenic membrane receptor tyrosine kinases such as MET and EGFR, or auto-active variants thereof, are important targets for cancer precision therapy. Targeted inhibition of these oncogenic receptors however invariably leads to resistance, resulting from acquisition of resistance-inducing mutations or from selective outgrowth of a priori resistant tumour cells. Most applied molecular protocols cannot distinguish between intracellular and intercellular heterogeneity of oncogene (variant) expression, which may lead to misinterpretation of the molecular make-up of a cancer and suboptimal application of targeted therapies. We here combined two related techniques to allow semiquantitative and localized in situ detection of specific transcript splice variants using single molecule molecular inversion probe (smMIP)-based next generation sequencing and padlock probe-based rolling circle amplification, respectively. We show highly specific padlock probe-based multiplex detection of MET, METΔ7-8 and METΔ14 transcripts, lacking exons 7–8 and exon 14 respectively, and of EGFR and the auto-active EGFRvIII, lacking exons 2–7. The combination of quantitative transcript variant detection with smMIPs and transcript localization using padlock probes can be used for detection of oncogenic transcripts on the single-cell level, allowing study of tumour heterogeneity. Visualization of tumour heterogeneity can shed light on the biology underlying drug resistance and potentially improve targeted therapeutics.
format	article
author	Corina N. A. M. van den Heuvel Arvid I. Das Tessa de Bitter Femke Simmer Thomas Wurdinger Miguel Angel Molina-Vila William P. J. Leenders
author_facet	Corina N. A. M. van den Heuvel Arvid I. Das Tessa de Bitter Femke Simmer Thomas Wurdinger Miguel Angel Molina-Vila William P. J. Leenders
author_sort	Corina N. A. M. van den Heuvel
title	Quantification and localization of oncogenic receptor tyrosine kinase variant transcripts using molecular inversion probes
title_short	Quantification and localization of oncogenic receptor tyrosine kinase variant transcripts using molecular inversion probes
title_full	Quantification and localization of oncogenic receptor tyrosine kinase variant transcripts using molecular inversion probes
title_fullStr	Quantification and localization of oncogenic receptor tyrosine kinase variant transcripts using molecular inversion probes
title_full_unstemmed	Quantification and localization of oncogenic receptor tyrosine kinase variant transcripts using molecular inversion probes
title_sort	quantification and localization of oncogenic receptor tyrosine kinase variant transcripts using molecular inversion probes
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/a96e3530439a41b7b9df6a5ba6233936
work_keys_str_mv	AT corinanamvandenheuvel quantificationandlocalizationofoncogenicreceptortyrosinekinasevarianttranscriptsusingmolecularinversionprobes AT arvididas quantificationandlocalizationofoncogenicreceptortyrosinekinasevarianttranscriptsusingmolecularinversionprobes AT tessadebitter quantificationandlocalizationofoncogenicreceptortyrosinekinasevarianttranscriptsusingmolecularinversionprobes AT femkesimmer quantificationandlocalizationofoncogenicreceptortyrosinekinasevarianttranscriptsusingmolecularinversionprobes AT thomaswurdinger quantificationandlocalizationofoncogenicreceptortyrosinekinasevarianttranscriptsusingmolecularinversionprobes AT miguelangelmolinavila quantificationandlocalizationofoncogenicreceptortyrosinekinasevarianttranscriptsusingmolecularinversionprobes AT williampjleenders quantificationandlocalizationofoncogenicreceptortyrosinekinasevarianttranscriptsusingmolecularinversionprobes
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Quantification and localization of oncogenic receptor tyrosine kinase variant transcripts using molecular inversion probes

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