A Pirna As A Biomarker For the Her2 Status in Breast Cancer

Background and aim: breast cancer is the most common malignancy and second leading cause of cancer death among women. several studies have discussed the crucial role of non-coding rnas in carcinogenesis. piwi-interacting rnas (pirnas) are a novel class of small non-coding rnas with a length of 26 to 30 nt that are important mediators of various cellular processes including proliferation, apoptosis, and, invasion. based on the provided evidence, pirnas might serve as valuable biomarkers for breast cancer diagnosis. in this study, we identify the differential expression of a very novel pirna located within the her2 gene in breast cancer tissues compared to normal tissues.methods: a high-throughput transcriptome sequencing (rna-seq) analysis was performed on the gse39162 and gse68085 datasets, which includes tumor, tumor-adjacent, and normal breast tissues. raw mirseq data was obtained from the arrayexpress database (https://www.ebi.ac.uk/arrayexpress/browse.html). the sra file was downloaded and converted to fastq format. the reads were aligned to grch38 using bowtie1. differential expression of the candidate pirna was gauged using limma package through r software and expression was stated in cpm (count per million).results: the expression of the pirna was significantly up-regulated in cancer tissues compared to normal and adjacent tumor tissues with a p-value of 0.002 and 0.04, respectively. no significant difference was observed between adjacent tumor and normal tissues. log2 cpm showed a clear increased number of reads in tumor samples compared to normals.conclusion: although molecular biomarkers make great improvements in cancer diagnosis, it still has been a critical challenge. biomarkers can be used to diagnose cancer, distinguish different types of a particular cancer or to select the right therapy. one of the key steps to find a potential biomarker is to recognize differentially expressed genes and rna-seq is one of the main strategies. amplification of the erbb2/her2 gene leads to overexpression of candidate pirna, due to its location within the erbb2/her2 gene. therefore this pirna could be a potent oncogene and a great indicator of her2 status and an important clinical marker. in summary, this pirna has a clear differential expression pattern in normal and cancer tissues and it might be useful to distinguish normal and cancerous breast tissues.