Abstract B114: Next generation whole genome transcriptome SOLiD sequencing analysis of pancreatic ductal adenocarcinoma in LSL-KrasG12D/+ mice
Authors: Janakiram Naveena B. , Mohammed Altaf , Brewer Misty F. , Gillaspy Allison , Lightfoot Stan , Steele Vernon E. , Rao Chinthalapally V. 
Published: January 2014

Pancreatic cancer carries the most dismal prognosis of all solid tumors. It is the fourth leading cause of cancer death in the U.S. During the last three decades, the genetic alterations underlying pancreatic cancer have been well characterized. The identification and characterization of these cancer-related genes have increased our understanding of the genetic basis of pancreatic cancer development; but, unfortunately, this knowledge has not translated into better clinical practice since survival of patients with this disease has not improved significantly over the past two decades. Hence, to identify new targets that are differentially expressed in pancreatic cancer and that can be exploited for chemoprevention, coordinated screening efforts are necessary not only at the DNA level, but also at the RNA and protein levels. In this study, we used a strategy of genome-wide screening via next-generation sequencing with oligonucleotide ligation and detection (SOLiD) to analyze the whole transcriptome expression in pancreatic tumors (PT) from LSL-KrasG12D/+ mice in comparison to normal pancreas from wild type mice. Biomarker selection and real time PCR validation of novel genes was performed and ontology of key target genes was analyzed. Mapped reads data were analyzed using the Geospiza software package. Our results show ∼44,175,598 effective exon/intron reads in cancerous tissue vs. ∼30,220,306 in noncancerous pancreatic tissue. We have observed ∼12,202 differentially expressed genes using t-test with Benjamini and Hochberg correction in pancreatic tumors compared to wild type pancreas. Among them ∼12,008 genes were found to be up-regulated in PT. The first 32 genes (Cldn18, Serpinb5, Rik (2210407C18), Rik (1110032A04), sdcbp2, Fst, Sftpd, S100A8, Aspa, Cfi, Adam28, Rbp1, Cdh17, Dkk3, Krt20, Mcpt1, Ltf, Col8a1, Plac8, Il18r1, Mcpt2, Prap1, Exp1, P2ry10, AA467197, 110785, Flrt3, Gabrp, Nt5e, Gcnt3, Anxa8, Cyp2c65), were found to be altered by more than 100-fold, variations that might have potential roles during tumor development. Out of these 32 genes, Rik, sdcbp2, S100A8, Rbp1, Krt20, Ltf, Plac8, Il18r1, Mcpt2, Prap1, Exp1, AA467197, Anxa8, and Cyp2c65 were identified to have a lower splice index value, indicating more splicing of these mRNAs and differential splicing between tumor and normal. Most of the novel and previously reported genes having the highest Z scores (e.g., BMP-1, Notch-2, Adam 9, 10, 12, 17; Akap 7, 8, 12, 13; Akirin 2, 5-LOX, Axin 2, Cyclin A2, B1, D2, E2, F, H, K, L2, Y; FGF1, FGFr1, FGFr2; jak 1, 2, 3; Interleukin 6ra, 7, 15, 16, 18; chemokine receptor 1, 5, 8; Jak 1, 2 and 3) are known to be involved in cellular and metabolic processes. Among down-regulated genes, those associated with movement and establishment of cell/cellular entity (e.g., aquaporin 12, EGF, INS2, syncollin 2) were the most altered in pancreatic tumors according to Z-score, followed by genes affecting metabolic and cellular processes. The functional significance of the novel genes identified in this study for development of PT is being more fully explored. In summary, the whole genome transcriptome analysis has led to discovery of many altered key mRNAs in PT. These newly identified molecular changes may be useful as potential targets for PT detection and possibly for development of chemopreventive regimens. {Supported by NCI-CN-N01- 53300}.

Citation Format: Naveena B. Janakiram, Altaf Mohammed, Misty F. Brewer, Allison Gillaspy, Stan Lightfoot, Vernon E. Steele, Chinthalapally V. Rao. Next-generation whole-genome transcriptome SOLiD sequencing analysis of pancreatic ductal adenocarcinoma in LSL-KrasG12D/+ mice. [abstract]. In: Proceedings of the Eleventh Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2012 Oct 16-19; Anaheim, CA. Philadelphia (PA): AACR; Cancer Prev Res 2012;5(11 Suppl):Abstract nr B114.