TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma

MicroRNAs (miRNAs) are small 21–22 nt RNAs that act to regulate the expression of mRNA target genes through direct binding to mRNA targets. While miRNAs typically dominate small RNA (sRNA) transcriptomes, many other classes are present including tRNAs, snoRNAs, snRNAs, Y-RNAs, piRNAs, and siRNAs. Interactions between processing machinery and targeting networks of these various sRNA classes remains unclear, largely because these sRNAs are typically analyzed separately. Here, we present TEsmall, a tool that allows for the simultaneous processing and analysis of sRNAs from each annotated class in a single integrated workflow. The pipeline begins with raw fastq reads and proceeds all the way to producing count tables formatted for differential expression analysis. Several interactive charts are also produced to look at overall distributions in length and annotation classes. We next applied the TEsmall pipeline to sRNA libraries generated from melanoma cells responding to targeted inhibitors of the MAPK pathway. Targeted oncogene inhibitors have emerged as way to tailor cancer therapies to the particular mutations present in a given tumor. While these targeted strategies are typically effective for short intervals, the emergence of resistance is extremely common, limiting the effectiveness of single-agent therapeutics and driving the need for a better understanding of resistance mechanisms. Using TEsmall, we identified several microRNAs and other sRNA classes that are enriched in inhibitor resistant melanoma cells in multiple melanoma cell lines and may be able to serve as markers of resistant populations more generally.