Single-cell alternative polyadenylation analysis reveals mechanistic insights of COVID-19-associated neurological and psychiatric effects
Qun Chen, Ying Gu, Shuai Liu, Xingyu Li, Ruizhi Xu, Ruixi Ye, Jingjing Yang, Wanshan Ning
Abstract
COVID-19 is associated with increased risks of neurological and psychiatric sequelae. Alternative polyadenylation (APA) is ubiquitous in human genes, resulting in mRNA diversity, and has been validated to play a pivotal regulatory role in the onset and progression of a variety of diseases, including viral infections. Here, we analyzed the APA usage across different cell types in frontal cortex cells from non-viral control group and COVID-19 patients, and identified functionally related APA events in COVID-19.
Introduction
Brain and peripheral nerve tissues express a larger proportion of the genome than any other tissue, providing a broad transcriptomic repertoire [1]. This broad expression profile, together with extensive post-transcriptional regulation-including alternative splicing, alternative transcription initiation, and alternative polyadenylation (APA)-underlies the exceptionally high mRNA diversity observed in the nervous system [2].
Materials and methods
Data pre-processing and snRNA-seq quality control
The dataset is publicly available in the GEO repository (accession number GSE159812), generated using the 3’ tag-based single-cell RNA sequencing protocol (10x Genomics v3) [12]. A total of 15 frontal cortex samples were selected from individuals in the COVID-19 and non-viral control groups. Donor information, including age, sex, group, and number of nuclei, is summarized in Supplementary Table 10.5 in S10 Table, with complete metadata available in the original publication.
Results
Global APA levels in neural cells
The PAS were annotated using the latest genome annotation, with 27.9% located in 3’ UTRs, and the remainder distributed across other genomic regions (i.e., 5’ UTR, coding sequence (CDS), and intron) (Fig 1A). Although 3’ UTR PAS are not the majority, they are of particular biological interest because APA events in this region can alter mRNA stability, localization, and translational efficiency by modulating regulatory elements such as microRNA target sites and RNA-binding protein motifs.
Discussion
There is growing evidence that SARS-CoV-2 infection causes neurological deficits in a large proportion of infected patients [6,42,43]. Several studies have reported psychiatric symptoms in patients with COVID-19, and a growing body of research suggests that brain disorders may persist after recovery from primary infection [44,45]. Though it has been reported that the gene expression level changes after infections [46,47], the changes in APA level have not been reported in the brain tissue after infection. We selected an appropriate analytical approach and identified significant changes in global APA levels (Fig 2).
Acknowledgments
The authors would like to thank professor Baofa Sun for his support during the research process.
Citation: Chen Q, Gu Y, Liu S, Li X, Xu R, Ye R, et al. (2025) Single-cell alternative polyadenylation analysis reveals mechanistic insights of COVID-19-associated neurological and psychiatric effects. PLoS One 20(12): e0324689. https://doi.org/10.1371/journal.pone.0324689
Editor: Milad Khorasani, Neyshabur University of Medical Sciences, IRAN, ISLAMIC REPUBLIC OF
Received: April 30, 2025; Accepted: November 22, 2025; Published: December 26, 2025
Copyright: © 2025 Chen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: The publicly available datasets used in this study can be found in GSE159812 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159812). The data supporting the results in this study are available within the paper and its Supplementary Information. All source datasets are archived at https://www.jianguoyun.com/p/DcmMT-cQq8KtDBi_sI8GIAA. All source codes for the data analysis or figure creation are available at https://github.com/yinggu94/APA.
Funding: This work was supported by the National Key Research and Development Program of China (2022YFC2704300 and 2021ZD0201300), the National Natural Science Foundation of China (32400532), the Fujian Provincial Health Technology Project (2024GGB18), the Natural Science Foundation of Fujian Province, China (Grant No.2025J08313), the Fujian Science and Technology Program Guiding Project (2025D022), the China Postdoctoral Science Foundation (2021M701337 and 2022T150242), and the Project of Xiamen Cell Therapy Research Center, Xiamen, Fujian, China (3502Z20214001). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
