Exploring disease and infection through the lens of alternative splicing and spatial transcriptomics

Alternative splicing is a fundamental mechanism that amplifies proteomic diversity by selectively combining exons to produce varied mRNA isoforms from a single gene. Beyond generating functional proteins, this process can yield nonproductive transcripts, potentially degraded or serving undiscovered roles. Emerging evidence suggests that infection and disease significantly alter splicing patterns, yet this area remains underexplored. Most publicly available gene expression datasets rely on short-read sequencing, which overlooks splicing complexity. Recent advances in long-read RNA sequencing and spatial transcriptomics now enable detailed investigation of splicing dynamics and their spatial context within tissues. These technologies offer a transformative lens to study how splicing modulates cellular responses during infection and disease, paving the way for deeper insights into these critical biological processes.This Research Topic seeks to address the underexplored impact of infection and disease on alternative splicing, particularly within host immune system cells, and to evaluate whether these changes influence immune function. A key challenge is the limited integration of splicing-aware analyses in current research, hindering a comprehensive understanding of disease responses. By leveraging recent advances in long-read RNA sequencing, we aim to uncover splicing variations at unprecedented resolution. Additionally, incorporating spatial transcriptomics will illuminate how splicing alterations correlate with immune cell distribution and tissue architecture during infection or disease states, such as inflammation or tumorigenesis. The ultimate objective is to expand the scope of splicing-aware research, fostering novel perspectives on immune regulation and disease pathology, and potentially identifying new therapeutic targets informed by these cutting-edge technologies.This Research Topic welcomes manuscripts that investigate host gene splicing in the context of infection and disease, with a focus on immune system responses. We encourage submissions that utilize long-read RNA sequencing or spatial transcriptomics to explore how splicing isoforms and immune cell distributions are influenced by proximity to infected cells, tumors, or inflammatory microenvironments. Specific themes include splicing regulation in immune cells, spatial mapping of splice variants, and their functional implications in disease progression or host defense. We are interested in original research, reviews, and methodology papers that advance the application of these technologies. Contributions must align with the journal’s scope, and Frontiers reserves the right to redirect out-of-scope manuscripts to appropriate sections or journals during peer review. Topic editors: Daniel Ramos Ram, Malika Aid, Michael R Ladomery Source: https://www.frontiersin.org/research-topics/70716/exploring-disease-and-infection-through-the-lens-of-alternative-splicing-and-spatial-transcriptomics