Beyond miRNAs: exploratory profiling of PIWI-interacting RNAs and small nucleolar RNAs in non-small cell lung cancer-related malignant pleural effusions

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Background: Small RNAs in pleural fluid (PF) are increasingly being explored as potential sources of biological insight in malignant pleural effusion (MPE). While several microRNAs (miRNAs) have been explored, the presence and potential diagnostic relevance of other small RNA species in PF, including PIWI-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and transfer RNAs (tRNAs), remain largely unknown. The aim of the study was to determine the detection of piRNAs, snoRNAs, and tRNAs and whether differential expression analysis between BPE and MPE yields potentially biologically relevant information. Methods: In this exploratory pilot study, PF samples from eight patients [four with benign pleural effusions (BPEs) due to heart failure and four with MPE, including two non-small cell lung cancer (NSCLC) and two colorectal cancer (CRC) cases] underwent small extracellular vesicle (sEV) isolation and small RNA sequencing. Reads were mapped to dedicated reference databases, and differential expression was assessed using the Limma-Voom approach with false discovery rate correction by RNA class. Target prediction and pathway enrichment analyses were performed using specialized RNA repositories and gprofiler2. Results: Multiple classes of small RNAs, including miRNAs, piRNAs, snoRNAs, and tRNAs, were detected in sEVs isolated from all PF samples. After correction for multiple testing, statistically significant differences were observed only between BPE and NSCLC-derived MPE. Five miRNAs (miR-200c-3p, miR-1269a, miR-1246, miR-4455 and miR-141-3p), three piRNAs (piR-33165, piR-32165 and piR-33057) and one snoRNA (SNORA21) were significantly upregulated in NSCLC-related MPE. Exploratory analyses suggested that predicted targets of these small RNAs are associated with biological processes relevant to NSCLC. Conclusions: This study provides initial evidence that PF, specifically its sEV compartment, contains a broad spectrum of small RNAs beyond miRNAs and identifies a subset that is differentially expressed in NSCLC-associated MPE. Although limited by sample size, these findings support the feasibility of expanded small RNA profiling in PF and provide a foundation for future exploratory and validation studies.

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