Reliable gene expression measurements from fine needle aspirates of pancreatic tumors: effect of amplicon length and quality assessment

Suitability of ultrasound-guided fine-needle aspiration biopsy for transcriptome sequencing of the canine prostate

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.

Assessment of fine needle aspiration feasibility and specimen adequacy for molecular diagnostics of benign vocal fold lesions

OBJECTIVES/ HYPOTHESIS

The use of molecular testing is becoming more significant for the diagnosis and classification of disease. The application of fine-needle aspiration (FNA) biopsy as the means of sampling lesions in union with molecular testing could be a powerful combination in laryngology. The objectives of this study were to investigate 1) if FNA was feasible to sample benign vocal fold lesions; 2) if FNA samples provided sufficient RNA quality for molecular analysis; and 3) if gene expression of FNA samples matched paired surgical excised specimens.

STUDY DESIGN

Prospective cross-sectional.

METHODS

Fifteen vocal fold specimens were obtained from adult patients undergoing routine surgical removal for benign vocal fold lesions using FNA and surgical excision. Comparisons were made between FNA and excision biopsies for RNA quality. Correlative analysis was completed for RNA expression of nine genes, including decorin (DCN), connective tissue growth factor (CTGF), vascular endothelial growth factor (VEGF), collagen type VI alpha 3 (COL6A3), superoxide dismutase 1 (SOD1), glutathione S-transferase (GST2), collagen type I alpha 2 (COL1A2), ATP binding cassette (ABC), and procollagen I alpha 1 (COL1A1).

RESULTS

FNA and excision samples demonstrated similar RNA quality (P > 0.05). Per gene expression, four out of nine genes were moderately correlated between the paired samples (P < 0.05).

CONCLUSIONS

FNA of the vocal fold lamina propria is technically feasible to perform. Further improvement in the FNA technology is desirable to optimize RNA quality for reliable gene expression analysis.

Analyzing S100A6 expression in endoscopic ultrasonography-guided fine-needle aspiration specimens: a promising diagnostic method of pancreatic cancer

BACKGROUND AND GOALS

Endoscopic ultrasonography-guided fine-needle aspiration (EUS-FNA) cytology in combination with other tests is necessary to improve diagnostic accuracy. We evaluated the diagnostic utility of S100A6 expression in EUS-FNA tissue samples in pancreatic ductal adenocarcinoma (PDA).

METHODS

RNA was extracted from 36 PDA and 44 nontumor pancreatic tissues obtained during surgery. S100A6 expression was quantified by real-time reverse transcription-polymerase chain reaction, and receiver operating characteristic analysis was performed to determine the cutoff value for PDA. We preoperatively performed EUS-FNA in 52 patients with pancreatic masses, then prospectively evaluated the diagnostic value of S100A6 expression of EUS-FNA samples in pancreatic cancer diagnosis. S100A6 immunohistology was conducted to validate the S100A6 expression data in PDA samples.

RESULTS

Of the 52 EUS-FNA patients with pancreatic masses, RNA was successfully extracted from 44, which comprised 34 pancreatic cancer patients and 10 patients with benign pancreatic diseases. Cytology results were malignant in 23 cases, benign in 9, and atypical or abnormal in 12. The sensitivity, specificity, and accuracy of cytology for diagnosis of pancreatic cancer were 67.65%, 100%, and 75%, respectively. When an S100A6 expression >0.005248 was defined as positive for malignancy, the sensitivity, specificity, and accuracy of S100A6 expression of EUS-FNA for diagnosis of pancreatic cancer were 88.24%, 90.00%, and 88.64%, respectively.

CONCLUSIONS

Quantification of S100A6 expression in EUS-FNA samples had a high sensitivity and specificity for the diagnosis of PDA.

Pancreatic cancer biomarkers and their implication in cancer diagnosis and epidemiology

Pancreatic cancer is the fourth most common cause of cancer-related mortality in the United States. Biomarkers are needed to detect this cancer early during the disease development and for screening populations to identify those who are at risk. In cancer, “biomarker” refers to a substance or process that is indicative of the presence of cancer in the body. A biomarker might be either a molecule secreted by a tumor or it can be a specific response of the body to the presence of cancer. Genetic, epigenetic, proteomic, glycomic, and imaging biomarkers can be used for cancer diagnosis, prognosis, and epidemiology. A number of potential biomarkers have been identified for pancreatic cancer. These markers can be assayed in non-invasively collected biofluids. These biomarkers need analytical and clinical validation so that they can be used for the purpose of screening and diagnosing pancreatic cancer and determining disease prognosis. In this article, the latest developments in pancreatic cancer biomarkers are discussed.