Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research

Abstract Cancer research requires models closely resembling the tumor in the patient. Human tissue cultures can overcome interspecies limitations of animal models or the loss of tissue architecture in in vitro models. However, analysis of tissue slices is often limited to histology. Here, we demonst...

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Autores principales:	Susann Haehnel, Kristin Reiche, Dennis Loeffler, Andreas Horn, Conny Blumert, Sven-Holger Puppel, Nicole Kaiser, Felicitas Rapp, Michael Rade, Friedemann Horn, Juergen Meixensberger, Ingo Bechmann, Frank Gaunitz, Karsten Winter
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/806433dc29524087a1454b735a1e3e16
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spelling	oai:doaj.org-article:806433dc29524087a1454b735a1e3e162021-12-02T13:57:00ZDeep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research10.1038/s41598-019-56509-52045-2322https://doaj.org/article/806433dc29524087a1454b735a1e3e162019-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-56509-5https://doaj.org/toc/2045-2322Abstract Cancer research requires models closely resembling the tumor in the patient. Human tissue cultures can overcome interspecies limitations of animal models or the loss of tissue architecture in in vitro models. However, analysis of tissue slices is often limited to histology. Here, we demonstrate that slices are also suitable for whole transcriptome sequencing and present a method for automated histochemistry of whole slices. Tumor and peritumoral tissue from a patient with glioblastoma was processed to slice cultures, which were treated with standard therapy including temozolomide and X-irradiation. Then, RNA sequencing and automated histochemistry were performed. RNA sequencing was successfully accomplished with a sequencing depth of 243 to 368 x 106 reads per sample. Comparing tumor and peritumoral tissue, we identified 1888 genes significantly downregulated and 2382 genes upregulated in tumor. Treatment significantly downregulated 2017 genes, whereas 1399 genes were upregulated. Pathway analysis revealed changes in the expression profile of treated glioblastoma tissue pointing towards downregulated proliferation. This was confirmed by automated analysis of whole tissue slices stained for Ki67. In conclusion, we demonstrate that RNA sequencing of tissue slices is possible and that histochemical analysis of whole tissue slices can be automated which increases the usability of this preclinical model.Susann HaehnelKristin ReicheDennis LoefflerAndreas HornConny BlumertSven-Holger PuppelNicole KaiserFelicitas RappMichael RadeFriedemann HornJuergen MeixensbergerIngo BechmannFrank GaunitzKarsten WinterNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-15 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Susann Haehnel Kristin Reiche Dennis Loeffler Andreas Horn Conny Blumert Sven-Holger Puppel Nicole Kaiser Felicitas Rapp Michael Rade Friedemann Horn Juergen Meixensberger Ingo Bechmann Frank Gaunitz Karsten Winter Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research
description	Abstract Cancer research requires models closely resembling the tumor in the patient. Human tissue cultures can overcome interspecies limitations of animal models or the loss of tissue architecture in in vitro models. However, analysis of tissue slices is often limited to histology. Here, we demonstrate that slices are also suitable for whole transcriptome sequencing and present a method for automated histochemistry of whole slices. Tumor and peritumoral tissue from a patient with glioblastoma was processed to slice cultures, which were treated with standard therapy including temozolomide and X-irradiation. Then, RNA sequencing and automated histochemistry were performed. RNA sequencing was successfully accomplished with a sequencing depth of 243 to 368 x 106 reads per sample. Comparing tumor and peritumoral tissue, we identified 1888 genes significantly downregulated and 2382 genes upregulated in tumor. Treatment significantly downregulated 2017 genes, whereas 1399 genes were upregulated. Pathway analysis revealed changes in the expression profile of treated glioblastoma tissue pointing towards downregulated proliferation. This was confirmed by automated analysis of whole tissue slices stained for Ki67. In conclusion, we demonstrate that RNA sequencing of tissue slices is possible and that histochemical analysis of whole tissue slices can be automated which increases the usability of this preclinical model.
format	article
author	Susann Haehnel Kristin Reiche Dennis Loeffler Andreas Horn Conny Blumert Sven-Holger Puppel Nicole Kaiser Felicitas Rapp Michael Rade Friedemann Horn Juergen Meixensberger Ingo Bechmann Frank Gaunitz Karsten Winter
author_facet	Susann Haehnel Kristin Reiche Dennis Loeffler Andreas Horn Conny Blumert Sven-Holger Puppel Nicole Kaiser Felicitas Rapp Michael Rade Friedemann Horn Juergen Meixensberger Ingo Bechmann Frank Gaunitz Karsten Winter
author_sort	Susann Haehnel
title	Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research
title_short	Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research
title_full	Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research
title_fullStr	Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research
title_full_unstemmed	Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research
title_sort	deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/806433dc29524087a1454b735a1e3e16
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Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research

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