Abstract 5865: The composition of the human ribosome varies significantly in different normal and malignant tissues
Authors: Panda Anshuman , Yadav Anupama , Yeerna Huwate , Singh Amartya , Biehl Michael , Lux Markus , Schulz Alexander , Klecha Tyler , Doniach Sebastian , Khiabanian Hossein , Ganesan Shridar , Tamayo Pablo , Bhanot Gyan 
Published: September 2020

Background: In all organisms, the ribosome performs the unique and essential function of translating mRNA into protein. Since deletion of any ribosomal protein (RP) is embryonic lethal in complex eukaryotes, the ribosome is believed to be structurally uniform throughout the organism, with all RPs essential for cell viability.

Results: We tested the structural homogeneity of RP use in ribosomes for normal and cancer tissues and cell lines using RP mRNA, ribosome profiling, and protein data. Analysis of RP mRNA data from 11,688 normal samples for 53 human tissues from 714 subjects and 10,363 tumor samples for 33 human cancers, normalized by total RP mRNA level per sample, showed that both normal (non-diseased) and tumor samples cluster by tissue type in humans. Matrix factorization showed that at least 3 RP mRNA signatures are necessary to describe normal blood and brain tissues, and a minimum of 16 RP mRNA signatures are necessary to describe data from 53 different normal tissues. A pan-cancer analysis of copy number variation (CNV) in 10,845 tumor samples for 33 human cancers showed that loss of one or both copies of RP genes was prevalent in every cancer type. Furthermore, there was no association between the number of double-deleted RP genes in tumors and patient survival, showing that RP loss does not reduce tumor fitness. CRISPR-Cas9 deletion of RP genes shows that many RPs are not essential in many cell lines. In several cancers, multiple RP-subtypes exist, with significant survival and genomic differences among them. These RP-subtypes often map to known molecular subtypes, and various RP genes are often deleted in one or both subtypes. This suggests that when genomic landscapes are modified in tumors, genes coding RPs are often lost, but these losses do not affect tumor viability. Analysis of mRNA data and ribosome profiling data of RP genes for cells and tissues from human, mouse and rat showed that these are highly correlated, showing that transcripts encoding ribosomal proteins are being translated into ribosomal proteins at rates proportional to their mRNA levels. Consistently, both mRNA data and ribosome profiling data of RP genes, normalized by total level per sample, showed tissue specific and development-stage specific clusters. Finally, analysis of RP protein levels in human adult and fetal tissues, standardized per sample, showed both development-stage and tissue specificity, showing that there is both tissue and development-stage specific heterogeneity of RP protein usage.

Conclusions: These results suggest that there are multiple ribosome types in complex eukaryotes, with different RP composition which are regulated in a tissue and development-stage specific manner by some novel, yet unknown mechanism.

Citation Format: Anshuman Panda, Anupama Yadav, Huwate Yeerna, Amartya Singh, Michael Biehl, Markus Lux, Alexander Schulz, Tyler Klecha, Sebastian Doniach, Hossein Khiabanian, Shridar Ganesan, Pablo Tamayo, Gyan Bhanot. The composition of the human ribosome varies significantly in different normal and malignant tissues [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5865.