Abstract A46: Tissue biology is shaped by noncoding RNAs that depend on gender, population, and race
Authors: Rigoutsos Isidore , Telonis Aristeidis , Loher Phillipe , Londin Eric 
Published: May 2016

Transcriptome profiling using next generation sequencing has revealed the existence of many RNA species that do not code for proteins and are differentially abundant between normal and tumor. Despite great advances in elucidating their roles in the cell, the vast majority of these non-coding RNAs (ncRNAs) remain to be functionalized. Through several recent studies, we found that the populations of transcriptional products from many human ncRNA loci are far more dynamic than currently believed. Specifically, we have discovered that the human genome loci that harbor microRNAs (mIRNAs) and transfer RNAs (tRNAs) respectively produce a multitude of constitutive, previously unsuspected transcripts that differ between normal and tumor and whose composition and abundance depend on several variables that include a patient's gender, population, and race. Such patient attributes will thus need to be considered explicitly in studies of post-transcriptional regulatory programs in cancer.

The conventional view holds that miRNA precursors produce at most one consequential mature miRNA from each arm of the precursor hairpin. In the public repositories, each of the known genomic miRNA loci is represented by at most two such sequences, one per arm. We refer to this representative product of a hairpin arm as the arm's “archetype” miRNA. The increasing numbers of transcriptomic datasets have uncovered a different reality wherein each miRNA precursor arm produces multiple isoforms (the “isomiRs”) of the archetype miRNA. These isomiRs enter the RNA interference pathway just like the archetype miRNA sequences and have sequence-dependent downstream regulatory effects. By analyzing transcriptomic data from the 1,000 Genome Project (1KG) and from The Cancer Genome Atlas (TCGA), we found that the production of isomIRs from a miRNA locus is marshaled and depends on a person's gender, population, and race. IsomiR production from a miRNA locus also depends on the tissue under consideration and on disease type/subtype. Moreover, co-expressed isomiRs from the same miRNA locus are generally not well-correlated. Lastly, in a cancer model cell line, we over-expressed isoforms of a miRNA with race-depended abundance in TCGA data: we found that these isoforms had targetomes that had little overlap even though they originated from the same miRNA locus.

tRNAs have long been considered to serve as adaptor molecules with well-defined roles in the translation of messenger RNA (mRNA) into amino acid sequences. In recent years, this view is starting to change. Key to the renewed attention to tRNAs has been the discovery of tRNA fragments (tRFs), which are produced in parallel to the mature tRNAs that are used in translation. Increasing numbers of reports have been linking tRFs to cell growth, cell proliferation, response to DNA damage, translation initiation, response to stress, etc. and have shown that some tRFs are loaded on Argonaute and thus enter the RNAi pathway. Our analyses of data from the 1KG and the TCGA projects have revealed that nuclear and mitochondrial tRNAs produce a multitude of tRFs with variable, yet quantized, lengths. We found that, in complete analogy to isomiRs, the tRFs are constitutive in nature, exhibit composition and abundance that differ across tissues and between normal and tumor samples, and depend on a person's gender, population, and race. We also discovered a novel and very rich category of tRFs, the internal-tRFs or i-tRFs: i-tRFs have variable quantized lengths, and variable starting and ending points that are wholly contained within the span of the mature tRNA. Of note, i-tRFs contribute much of the difference that we observe across the gender, population, race, tissue, and disease subtype boundaries. Lastly, using fragment-specific approaches, we were able to validate several i-tRFs in clinical samples and in model cell lines.

Citation Format: Isidore Rigoutsos, Aristeidis Telonis, Phillipe Loher, Eric Londin. Tissue biology is shaped by noncoding RNAs that depend on gender, population, and race. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A46.