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Status |
Public on Oct 08, 2019 |
Title |
Comparative transcriptomic characterisation of canine prostate fine-needle-aspiration and tissue samples - from sampling to sequencing |
Organism |
Canis lupus familiaris |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Ultrasound-guided fine-needle aspiration (US-FNA) biopsy is a widely used minimally invasive sampling procedure for cytological diagnosis. This study investigates the feasibility of using US-FNA samples for both cytological diagnosis and whole transcriptome RNA-sequencing analysis (RNA-Seq), with the ultimate aim of improving canine prostate cancer management. The feasibility of the US-FNA procedure was evaluated intra vitam on 43 dogs. Additionally, aspirates from 31 euthanised dogs were collected for standardising the procedure. Each aspirate was separated into two subsamples: for cytology and RNA extraction. Additional prostate tissue samples served as control for RNA quantity and quality evaluation, and differential expression analysis. The US-FNA sampling procedure was feasible in 95% of dogs. RNA isolation of US-FNA samples was successfully performed using phenol-chloroform extraction. The extracted RNA of 56% of a subset of US-FNA samples met the quality requirements for RNA-seq. Expression analysis revealed that only 153 genes were exclusively differentially expressed between non-malignant US-FNAs and tissues. Moreover, only 36 differentially expressed genes were associated with the US-FNA sampling technique and unrelated to the diagnosis. Furthermore, the gene expression profiles clearly distinguished between non-malignant and malignant samples. This proves US-FNA to be useful for molecular profiling.
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Overall design |
Fine-needle aspirates of the canine prostate: non-malignant (n=5) and malignant (n=2); canine prostate tissues: non-malignant (n=9) and malignant (n=9). Aspirates and tissue samples of the canine prostate were used for RNA-sequencing. Non-malignant prostate tissue samples were used as control. Differentially expressed genes were used for evaluation of similarities and differences in aspirates and canine prostate tissues.
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Contributor(s) |
Taher L, Escobar HM, Nolte I, Thiemeyer H, Schille JT, Beck J, Schütz E, Brenig B, Hewicker-Trautwein M, Mischke R, Hungerbuehler SO, Harder L, Kielbowicz Z |
Citation(s) |
31519932, 34768937 |
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Submission date |
Nov 26, 2018 |
Last update date |
Feb 08, 2022 |
Contact name |
Leila Taher |
Organization name |
Graz University of Technology
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Street address |
Stremayrgasse 16/I
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City |
Graz |
ZIP/Postal code |
8010 |
Country |
Austria |
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Platforms (1) |
GPL21400 |
Illumina NextSeq 500 (Canis lupus familiaris) |
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Samples (25)
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Relations |
BioProject |
PRJNA506907 |
SRA |
SRP170673 |
Supplementary file |
Size |
Download |
File type/resource |
GSE122916_RAW.tar |
2.8 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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