The invasion of cancer cells into the peritumoral, lymph node and perineural system could be detrimental
on cancer patients. In colorectal cancer (CRC) patients, the presence of lymphovascular (LVI) and/or
perineural (PNI) invasion could significantly influence on the survival rates, treatment options and
recurrence tendencies. To date, no study has analyzed the molecular profile of the concomitant existence of
LVI and PNI in CRC. Here, we reanalyzed The Cancer Genome Atlas (TCGA) CRC datasets and focused
on cases where the information regarding LVI and PNI are available (n=176). We performed differential
gene expression, methylation and microRNA analysis by comparing the groups having both or either LVI
and PNI with the control group (LVI negative and PNI negative). Although there was no significant
difference in the methylation and miRNA profiles, we identified a number of differentially expressed genes
(DEGs). The comparison between the LVI+PNI+ and LVI-PNI- groups revealed key DEGs including
SFTA2, PHACTR3, CRABP2, ODZ3, GRP, HAP1, CSDC2, TMEM59L and HDAC9. Meanwhile, in the
LVI-PNI+ vs LVI-PNI- group, some of the DEGs found were PTPRR, EFNA2, FGF20, IGFL4, METRN
and IGFBPL1. We believe that this study could be beneficial and add value to further understand the
complex molecular profiles of CRC.
RNA-seq has become an essential tool in molecular research. Nevertheless, application of RNA-seq was limited by cost and technical difficulties. Illumina has introduced the cost effective and ease to handle Truseq Targeted RNA Sequencing. In this study, we present the requirements and the optimization procedure for this Truseq Targeted RNA sequencing on cell line. Total RNA was recommended as starting materials but it required optimization including additional purification step and adjusting the AMPure beads ratio to eliminate unwanted contaminants. This can be resolved by using PolyA-enriched mRNA as starting material. TREx is a useful assay to evaluate gene expression. Quality library of TREx can be prepared by adding multiple washing steps or changing input sample to mRNA.