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SPOROS: A pipeline to analyze DISE/6mer seed toxicity
Elizabeth T Bartom1,2, Masha Kocherginsky2, Bidur Paudel3
1Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America.
Abstract:
microRNAs (miRNAs) are (18-22nt long) noncoding short (s)RNAs that suppress gene expression by targeting the 3' untranslated region of target mRNAs. This occurs through the seed sequence located in position 2-7/8 of the miRNA guide strand, once it is loaded into the RNA induced silencing complex (RISC). G-rich 6mer seed sequences can kill cells by targeting C-rich 6mer seed matches located in genes that are critical for cell survival. This results in induction of Death Induced by Survival gene Elimination (DISE), through a mechanism we have called 6mer seed toxicity. miRNAs are often quantified in cells by aligning the reads from small (sm)RNA sequencing to the genome. However, the analysis of any smRNA Seq data set for predicted 6mer seed toxicity requires an alternative workflow, solely based on the exact position 2-7 of any short (s)RNA that can enter the RISC. Therefore, we developed SPOROS, a semi-automated pipeline that produces multiple useful outputs to predict and compare 6mer seed toxicity of cellular sRNAs, regardless of their nature, between different samples. We provide two examples to illustrate the capabilities of SPOROS: Example one involves the analysis of RISC-bound sRNAs in a cancer cell line (either wild-type or two mutant lines unable to produce most miRNAs). Example two is based on a publicly available smRNA Seq data set from postmortem brains (either from normal or Alzheimer's patients). Our methods (found at https://github.com/ebartom/SPOROS and at Code Ocean: https://doi.org/10.24433/CO.1732496.v1) are designed to be used to analyze a variety of smRNA Seq data in various normal and disease settings.
Insights
We developed SPOROS, a tool to analyze short (s)RNA sequences for 6mer seed toxicity, a mechanism that can cause cell death. SPOROS predicts toxicity by examining the critical 2-7 positions of sRNAs, regardless of their origin, aiding disease research.
Area of Science:
- Molecular Biology
- Genetics
- Bioinformatics
Background:
- microRNAs (miRNAs) are small noncoding RNAs regulating gene expression via seed sequences.
- Specific G-rich 6mer seed sequences can induce cell death (DISE) by targeting essential genes.
- Standard small (sm)RNA sequencing analysis does not fully capture 6mer seed toxicity mechanisms.
Purpose of the Study:
- To develop a computational pipeline for predicting and comparing 6mer seed toxicity of short (s)RNAs.
- To provide a workflow for analyzing sRNA data independent of miRNA biogenesis.
- To assess 6mer seed toxicity in various biological contexts, including cancer and neurodegenerative diseases.
Main Methods:
- Developed SPOROS, a semi-automated bioinformatics pipeline.
- Focused analysis on the critical 2-7 seed region of sRNAs for RISC loading.
- Applied SPOROS to analyze RISC-bound sRNAs in cancer cell lines and smRNA-Seq data from Alzheimer's patient brains.
Main Results:
- SPOROS successfully predicts and compares 6mer seed toxicity across different samples and sRNA types.
- Demonstrated the pipeline's utility in analyzing cancer cell lines with varying miRNA production.
- Showcased application to publicly available brain smRNA-Seq data, differentiating normal and Alzheimer's samples.
Conclusions:
- SPOROS offers a novel approach to analyze 6mer seed toxicity in diverse smRNA-Seq datasets.
- The pipeline facilitates research into DISE and its role in disease.
- SPOROS is a valuable tool for investigating sRNA function in various normal and pathological conditions.
