Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion.

ABSTRACT: The use of long-read direct RNA sequencing (DRS) and PCR cDNA sequencing (PCS) in clinical oncology remains limited, with no direct comparison between the two methods. We used DRS and PCS to study clear cell renal cell carcinoma (ccRCC), focusing on new transcript and gene discovery. Twelve primary ccRCC archival tumors, six from patients who went on to relapse, were analyzed. Results were validated in an independent cohort of 20 patients by qRT-PCR and compared to DRS analysis of RCC4 cells. In archival clinical samples and due to the long-term storage, the average read length was lower (400-500 nt) than that achieved through DRS of RCC4 cells (>1100 nt). Still, deconvolution analysis showed a loss of immune infiltrate in primary tumors of patients who relapse as reported by others. Diffe

SUBMITTER: Lee J 

PROVIDER: S-EPMC11610457 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature