{"doi":"10.1167/iovs.66.9.53","title":"LIRTS Viewer: A Web-Based Resource to View the Transcriptional Response of Lens Epithelial Cells to Injury","abstract":"Purpose: Residual lens epithelial cells (LECs) respond to injury after cataract surgery, leading to posterior capsular opacification (PCO). Transcriptomic profiling of lens capsule-associated cells (CACs) post-cataract surgery (PCS) revealed that LECs quickly alter their transcriptome, producing numerous pro-inflammatory cytokines within a few hours PCS. In contrast, the significant activation of TGFβ signaling and fibrotic extracellular matrix deposition related to PCO only begins 1 to 3 days later. However, the global changes in gene expression in CACs, following the establishment of robust TGFβ signaling, remain unknown. Methods: Lens fiber cells were removed from wild-type mice, and CACs were isolated at 0, 72, or 120 hours PCS to perform bulk RNA sequencing (RNA-seq) to obtain estimates of RNA abundance. These data were combined with existing RNA-seq datasets to create a web-based visualization resource to explore the expression dynamics of most protein coding genes in CACs. Results: At 72 hours PCS, CACs differentially express genes consistent with a surge in proliferation and changes in actin filament organization while also robustly expressing fibrotic marker genes by 120 hours PCS. We developed a data visualization resource, the Lens Injury Response Time Series (LIRTS) Viewer, which integrates all data to gather valuable insights from gene expression in CACs over the first 5 days PCS. Conclusions: The LIRTS Viewer is useful for generating hypotheses related to PCO pathogenesis, as it reveals CAC gene expression dynamics, gene correlations, and biological pathways during the first 5 days following lens injury in an in vivo cataract surgery model.","journal":"Investigative Ophthalmology & Visual Science","year":2025,"id":539756,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9085,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":356349,"name":"Adam Faranda","orcid":"0000-0001-6993-8361","position":1,"is_corresponding":false},{"id":719556,"name":"Mahbubul H. Shihan","orcid":"0000-0001-5190-389X","position":2,"is_corresponding":false},{"id":550966,"name":"Yan Wang","orcid":"0000-0003-0671-7312","position":3,"is_corresponding":false},{"id":356350,"name":"Melinda K. Duncan","orcid":"0000-0003-1570-322X","position":4,"is_corresponding":false},{"id":1427685,"name":"Suhotro Gorai","orcid":null,"position":0,"is_corresponding":true}],"reference_count":71,"raw_metadata":null,"created_at":"2026-07-19T02:52:34.520788Z","pmid":"40679332","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}