Understanding the role of rRNA modifications in colorectal cancer | LC26

Abstract
Beyond genetic mutations, post-transcriptional gene regulation through ribosomal RNA (rRNA) modifications represents a critical yet underexplored mechanism of tumor adaptation. These modifications, guided by small nucleolar RNAs (snoRNAs), generate specialized ribosomes that reprogram translation to support cancer fitness. While dysregulated snoRNA expression impacts cancer fitness, their mechanistic contributions remain poorly understood. By profiling snoRNA expression downstream of an oncogenic mutation and in human colorectal cancer (CRC) samples, we found SNORA9 elevated in both, suggesting oncogenic potential. We demonstrated its critical role in CRC fitness, as SNORA9 knockout reduced tumor growth by approximately 75% in vivo. Notably, SNORA9 guides three pseudouridylations at the ribosomal decoding center, positioning it to directly influence translational control. To interrogate the rRNA epitranscriptome, we used Oxford Nanopore Technologies direct RNA sequencing of rRNA from CRC cell lines with and without SNORA9. Using Dorado modification-aware basecalling and Modkit analysis, we confirmed that SNORA9 knockout abolishes its target pseudouridylations while leaving other modifications intact. By integrating direct RNA sequencing with ribosome profiling, we found that loss of SNORA9 reduces translation efficiency of specific metabolic transcripts, including lipid metabolism and amino acid starvation response factors. These transcripts are enriched for upstream open reading frames (uORFs), regulatory elements upstream of the coding sequence that restrict downstream translation. Under stress conditions, ribosomes must bypass uORFs to engage the coding sequence and translate proteins required for adaptation. In SNORA9 knockout cells, ribosomes accumulate at uORFs and fail to efficiently engage the coding sequence, indicating that SNORA9-guided rRNA modifications promote stress-induced uORF bypass and adaptation in CRC.

Biography
Macey Slota is a doctoral researcher at the University of California, San Francisco, studying post-transcriptional gene regulation in colorectal cancer. Her work focuses on how small nucleolar RNA-guided ribosomal RNA modifications reprogram translation to support tumor growth and metabolic adaptation. Using Oxford Nanopore direct RNA sequencing alongside molecular and cellular approaches, she investigates how specialized ribosomes alter translational output in cancer, integrating epitranscriptomics, ribosome biology, and functional genomics.