GSE167858
miRNAs signature as potential biomarkers for cervical precancerous lesions in Human Papillomavirus Positive women
Cervical cancer ranks as the first in cancer mortality among women of low-middle income countries, where 80% of the 570,000 cases and 311,000 worldwide deaths estimated for 2018 occurred (Ferlay et al. 2018  ). Persistent infections with high-risk HPV (hrHPV) genotypes can lead to high-grade cervical intraepithelial (CIN) grade 2 (CIN2) or higher, (CIN2+), if untreated, a high percentage of these lesions may progress to cancer. Despite its high sensitivity, the hrHPV test has low specificity to detect CIN2+ lesions given that a high percentage of women (80 %) infected with hrHPV genotypes will resolve the infection spontaneously. microRNAs (miRNAs) are small non-coding RNAs and their differential expression patterns seen to be associated with cervical intraepithelial lesions. Our work aimed to identify miRNAs differentially expressed in CIN2+ respect with <CIN1 and to evaluate their potential use as biomarkers to distinguish low- from high-grade lesions within hrHPV positive women. For our discovery set we used  small RNA sequencing (miRNA-seq) to compare the miRNA expression patterns in 20 Formalin-Fixed Paraffin-Embedded (FFPE) tissues from hrHPV-positive women from Medellin, Colombia presenting low- (n=10) and high-grade lesions (n=10). Top five miRNAs presenting high fold change and low coefficient of variation were  used validated by RT-PCR in our validation set composed 210 age-matched independent hrHPV-positive FFPE tissues, and  an in-silico approach was used to understand the function of the differentially expressed miRNAs in the context of HPV infection. Overall design: We did smallRNA-seq in 20 preneoplastic cervical lesion and non lesion tissue samples from women hr-HPV positive (10 high-grade cervical lesion and 10 low grade cervical lesion). RNA was extracted, qualified by Agilent 2100, quanitfied by qubit. Librarires were prepared using the QIAseq miRNA Library Kit from Qiagen and sequenced at 1 x 75bp (2,5M reads/sample) Case samples =  high-grade cervical lesion samples Control samples = low-grade cervical lesion or no lesion samples