An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes

Thiemeyer, Heike; Taher, Leila; Schille, Jan Torben; Packeiser, Eva-Maria; Harder, Lisa K.; Hewicker-Trautwein, Marion; Brenig, Bertram; Schütz, Ekkehard; Beck, Julia; Nolte, Ingo; Murua Escobar, Hugo

doi:10.3390/ijms222111481

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An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes

^1,2,

³,

^1,2

^1,2

¹,

Marion Hewicker-Trautwein

⁴,

⁵

⁶,

⁶,

^1,†

and

Hugo Murua Escobar

^1,2,7,*,†

Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany

Department of Hematology/Oncology/Palliative Care, Rostock University Medical Centre, 18057 Rostock, Germany

Institute of Biomedical Informatics, Graz University of Technology, 8010 Graz, Austria

⁴

Institute of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany

⁵

Institute of Veterinary Medicine, University of Göttingen, 37077 Göttingen, Germany

⁶

Chronix Biomedical GmbH, 37079 Göttingen, Germany

⁷

Comprehensive Cancer Center Mecklenburg-Vorpommern (CCC-MV), Campus Rostock, University of Rostock, 18057 Rostock, Germany

Author to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Academic Editors: Gian Maria Busetto, Alessandro Sciarra, Angelo Porreca, Matteo Ferro and Ettore De Berardinis

Int. J. Mol. Sci. 2021, 22(21), 11481; https://doi.org/10.3390/ijms222111481

Received: 6 September 2021 / Revised: 16 October 2021 / Accepted: 16 October 2021 / Published: 25 October 2021

(This article belongs to the Special Issue Advances in Molecular Research on Prostate Cancer)

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Abstract

Prostate cancer (PCa) in dogs is a highly malignant disease akin to its human counterpart. In contrast to the situation in humans, multi-gene approaches facilitating risk stratification of canine PCa are barely established. The aims of this study were the characterization of the transcriptional landscape of canine PCa and the identification of diagnostic, prognostic and/or therapeutic biomarkers through a multi-step screening approach. RNA-Sequencing of ten malignant tissues and fine-needle aspirations (FNA), and 14 nonmalignant tissues and FNAs was performed to find differentially expressed genes (DEGs) and deregulated pathways. The 4098 observed DEGs were involved in 49 pathways. These 49 pathways could be grouped into five superpathways summarizing the hallmarks of canine PCa: (i) inflammatory response and cytokines; (ii) regulation of the immune system and cell death; (iii) cell surface and PI3K signaling; (iv) cell cycle; and (v) phagosome and autophagy. Among the highly deregulated, moderately to strongly expressed DEGs that were members of one or more superpathways, 169 DEGs were listed in relevant databases and/or the literature and included members of the PCa pathway, oncogenes, prostate-specific genes, and druggable genes. These genes are novel and promising candidate diagnostic, prognostic and/or therapeutic canine PCa biomarkers. View Full-Text

Keywords: canine prostate cancer; RNA-Sequencing; whole transcriptome analysis; candidate biomarker genes; animal model; molecular diagnostics

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MDPI and ACS Style

Thiemeyer, H.; Taher, L.; Schille, J.T.; Packeiser, E.-M.; Harder, L.K.; Hewicker-Trautwein, M.; Brenig, B.; Schütz, E.; Beck, J.; Nolte, I.; Murua Escobar, H. An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes. Int. J. Mol. Sci. 2021, 22, 11481. https://doi.org/10.3390/ijms222111481

AMA Style

Thiemeyer H, Taher L, Schille JT, Packeiser E-M, Harder LK, Hewicker-Trautwein M, Brenig B, Schütz E, Beck J, Nolte I, Murua Escobar H. An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes. International Journal of Molecular Sciences. 2021; 22(21):11481. https://doi.org/10.3390/ijms222111481

Chicago/Turabian Style

Thiemeyer, Heike, Leila Taher, Jan T. Schille, Eva-Maria Packeiser, Lisa K. Harder, Marion Hewicker-Trautwein, Bertram Brenig, Ekkehard Schütz, Julia Beck, Ingo Nolte, and Hugo Murua Escobar. 2021. "An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes" International Journal of Molecular Sciences 22, no. 21: 11481. https://doi.org/10.3390/ijms222111481

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An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes

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