A preliminary result of three-dimensional microarray technology to gene analysis with endoscopic ultrasound-guided fine-needle aspiration specimens and pancreatic juices.
BACKGROUND
Analysis of gene expression and gene mutation may add information to be different from ordinary pathological tissue diagnosis. Since samples obtained endoscopically are very small, it is desired that more sensitive technology is developed for gene analysis. We investigated whether gene expression and gene mutation analysis by newly developed ultra-sensitive three-dimensional (3D) microarray is possible using small amount samples from endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) specimens and pancreatic juices.


METHODS
Small amount samples from 17 EUS-FNA specimens and 16 pancreatic juices were obtained. After nucleic acid extraction, the samples were amplified with labeling and analyzed by the 3D microarray.


RESULTS
The analyzable rate with the microarray was 46% (6/13) in EUS-FNA specimens of RNAlater storage, and RNA degradations were observed in all the samples of frozen storage. In pancreatic juices, the analyzable rate was 67% (4/6) in frozen storage samples and 20% (2/10) in RNAlater storage. EUS-FNA specimens were classified into cancer and non-cancer by gene expression analysis and K-ras codon 12 mutations were also detected using the 3D microarray.


CONCLUSIONS
Gene analysis from small amount samples obtained endoscopically was possible by newly developed 3D microarray technology. High quality RNA from EUS-FNA samples were obtained and remained in good condition only using RNA stabilizer. In contrast, high quality RNA from pancreatic juice samples were obtained only in frozen storage without RNA stabilizer.
Nonogaki
Koji
K
Department of Gastroenterology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya 4668550, Japan.
Itoh
Akihiro
A
Kawashima
Hiroki
H
Ohno
Eizaburo
E
Ishikawa
Takuya
T
Matsubara
Hiroshi
H
Itoh
Yuya
Y
Nakamura
Yosuke
Y
Nakamura
Masanao
M
Miyahara
Ryoji
R
Ohmiya
Naoki
N
Ishigami
Masatoshi
M
Katano
Yoshiaki
Y
Goto
Hidemi
H
Hirooka
Yoshiki
Y
D000465:Algorithms; D044963:Biopsy, Fine-Needle / Q000379:methods*; D016000:Cluster Analysis; D004247:DNA / Q000378:metabolism; D004252:DNA Mutational Analysis; D004724:Endoscopy / Q000379:methods*; D019160:Endosonography / Q000379:methods*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009696:Nucleic Acids / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010189:Pancreatic Juice / Q000378:metabolism; D010190:Pancreatic Neoplasms / Q000378:metabolism*; D012313:RNA / Q000378:metabolism
D009696:Nucleic Acids; D012313:RNA; D004247:DNA