RT Journal
A1 Karakulak, Tülay
A1 Zajac, Natalia
A1 Bolck, Hella Anna
A1 Bratus-Neuenschwander, Anna
A1 Zhang, Qin
A1 Qi, Weihong
A1 Basu, Debleena
A1 Oltra, Tamara Carrasco
A1 Rehrauer, Hubert
A1 von Mering, Christian
A1 Moch, 
Holger
A1 Kahraman, Abdullah
T1 Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids
JF Genome Research 
JO Genome Research 
YR 2025 
FD April 01 
VO 35 
IS 4 
SP 698 
OP 711 
DO 10.1101/gr.279345.124 
UL http://genome.cshlp.org/content/35/4/698.abstract 
AB Splicing is often dysregulated in cancer, leading to alterations in the expression of canonical and alternatively spliced isoforms. We used the multiplexed arrays sequencing (MAS-seq) protocol of PacBio to sequence full-length transcripts in patient-derived organoid (PDO) cells of clear cell renal cell carcinoma (ccRCC). The sequencing revealed a heterogeneous dysregulation of splicing across 2599 single ccRCC cells. The majority of novel transcripts could be removed with stringent filtering criteria. The remaining 31,531 transcripts (36.6% of the 86,182 detected transcripts on average) were previously uncharacterized. In contrast to known transcripts, many of the novel transcripts have cell-specific expression. Novel transcripts common to ccRCC cells belong to genes involved in ccRCC-related pathways, such as hypoxia and oxidative phosphorylation. A novel transcript of the ccRCC-related gene nicotinamide N-methyltransferase is validated using PCR. Moreover, >50% of novel transcripts possess a predicted complete protein-coding open reading frame. An analysis of the most dominant transcript-switching events between ccRCC and non-ccRCC cells shows many switching events that are cell- and sample-specific, underscoring the heterogeneity of alternative splicing events in ccRCC. Overall, our study elucidates the intricate transcriptomic architecture of ccRCC, underlying its aggressive phenotype and providing insights into its molecular complexity.