Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level.

Abstract

It is widely accepted that N6-methyladenosine (m6A) exhibits significant intercellular specificity, which poses challenges for its detection using existing m6A quantitative methods. In this study, we introduced Single-cell m6A Analysis (Scm6A), a machine learning-based approach for single-cell m6A quantification. Scm6A leverages input features derived from the expression levels of m6A trans regulators and cis sequence features, and offers remarkable prediction efficiency and reliability. To further validate the robustness and precision of Scm6A, we first applied Scm6A to single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) and calculated the m6A levels in CD4+ and CD8+ T cells. We also applied a winscore-based m6A calculation method to conduct N6-methyladenosine sequencing (m6A-seq) analysis on CD4+ and CD8+ T cells isolated through magnetic-activated cell sorting (MACS) from the same samples. Notably, the m6A levels calculated by Scm6A exhibited a significant positive correlation with those quantified through m6A-seq in different cells isolated by MACS, providing compelling evidence for Scm6A's reliability. Additionally, we performed single-cell-level m6A analysis on lung cancer tissues as well as blood samples from patients with coronavirus disease 2019 (COVID-19), and demonstrated the landscape and regulatory mechanisms of m6A in different T cell subtypes from these diseases. In summary, Scm6A is a novel, dependable, and accurate method for single-cell m6A detection and has broad applications in the realm of m6A-related research.