Biology subjects

Kalogeropoulos, P.

Publications and source records attributed to Kalogeropoulos, P..

2 recordsLinked to original sources

bioRxiv2025

SURFR: genome-free discovery of cancer-unique small RNAs from cohort sequencing data

Small RNAs play numerous roles in cancer biology and function as biomarkers and therapeutic targets. A recently discovered class of small RNAs - the orphan non-coding RNAs (oncRNAs) - are uniquely present in cancer and absent from healthy tissues. Here, we developed a reference-free computational approach that is independent from the human genome and applied it on cohort sequencing data from five cancer types to discover 1211 novel oncRNAs. Most of these new sequences do not map perfectly to the human genome, and hundreds correlate with patient outcomes. Our new oncRNAs include the first bona fide cancer-unique microRNA; oncRNAs predictive of patient survival and a small RNA that is expressed from an evolutionarily ancestral part of the genome that has been lost in most human individuals. In summary, we provide our reference-free computational approach and more than thousand new cancer-unique RNAs as resources to the community.

genomics↗

bioRxiv2022

agoTRIBE detects miRNA-target interactions transcriptome-wide in single cells

MicroRNAs are gene regulatory molecules that play important roles in numerous biological processes including human health. The function of a given microRNA is defined by its selection of target transcripts, yet current state-of-the-art experimental methods to identify microRNA targets are laborious and require millions of cells. We have overcome these limitations by fusing the microRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing for the first time the detection of microRNA targets transcriptome-wide in single cells. Our agoTRIBE method reports functional microRNA targets which are additionally supported by evolutionary sequence conservation. As a proof-of-principle, we study microRNA interactions in single cells, and find substantial differential targeting across the cell cycle. Lastly, agoTRIBE additionally provides transcriptome-wide measurements of RNA abundance and will allow the deconvolution of microRNA targeting in complex samples such as tissues at the single-cell level.

genomics↗