Validation of novel plasma cell specific transcripts from lrRNAseq data
Multiple myeloma is a cancer of plasma cells which are primarily found in the bone marrow. The overgrowth of plasma cells causes a crowding out of healthy cells which can lead to severe bone lesions, hypercalcemia, and anemia. Several therapies targeting antibodies found on the cell surface of plasma cells currently exist but are not a cure-all for all patients. Historically these cell surface therapy targets were identified and developed using RNA expression obtained through short-read RNA sequencing. With newer technologies emerging, we are now able to identify more isoforms for these cell surface therapies that could result in different folding of these therapeutic targets. The purpose of the research conducted was to determine if we can detect and validate novel isoforms found from long read RNA sequencing (lrRNAseq) data gathered from 34 human multiple myeloma cell lines. To validate novel isoforms, we first synthesized cDNA for each cell line using purified RNA, and then did a quality control check with B2M gene specific primers to validate cDNA synthesis was successful. We then went on to design gene specific primers dependent on our target isoform and resolved the PCR product on a 1% agarose gel. We were able to validate a mono allelic deletion of the TRAF3 gene present in the KMS34 cell line, as well as novel isoform expression present across 34 cell lines within the BCMA gene, and isoform expression in GPRC5D in 33 cell lines. The data from lrRNA sequencing data accurately identified certain novel Isoform events that we were able to successfully validate.
