Biology subjects

Oni, L.

Publications and source records attributed to Oni, L..

3 recordsLinked to original sources

bioRxiv2026

Optimised haemoglobin depletion improves clinical proteomics from dried blood spots

Equitable access to large sample cohorts for robust, high-throughput proteomics for biomarker discovery is a major barrier to widescale clinical implementation. Dried blood spots (DBS) offer a minimally invasive alternative to venous blood draws, enabling at-home microsampling (<50 {micro}L) for centralised analysis, thus enhancing research participation. This approach is particularly relevant for under-represented groups, including children, the elderly, minority backgrounds and those with long-term health conditions such as chronic kidney disease (CKD), where disease fluctuations may occur outside the clinic, and vein preservation is critical. Proteomic analysis has demonstrated great utility in monitoring disease progression, and for biomarker/therapeutic target discovery. However, liquid chromatography-tandem mass spectrometry (LC-MS/MS) of whole blood is hindered by the wide dynamic range and the relatively high abundance of proteins such as haemoglobin, compromising biomarker discovery. Here, we establish an optimised workflow for protein extraction and haemoglobin depletion from microsamples obtained using DBS, enabling sensitive and high-throughput proteomic analysis. We demonstrate that haemoglobin depletion increases protein identifications by [~]50%, mitigating ion suppression and dynamic range effects, enabling the identification of putative biomarkers from patients with stage 5 CKD on dialysis. We also evaluated a commercial cell-free DBS device which yielded a sample more representative of plasma compared to traditional DBS and enabled greater depletion of haemoglobin compared to traditional DBS with haemoglobin depletion methods. Our findings offer a scalable approach for biomarker discovery, facilitating remote, longitudinal clinical studies.

biochemistry↗

bioRxiv2026

Deletion of the MALAT1 RNA 3' end Promotes Transcript Decay, TALAM1 downregulation, and Inhibits Proliferation in Gastric and Breast Cancer Cells

The long non-coding RNA MALAT1 is a conserved oncogenic driver whose function relies on a 3 triple-helix motif. While its biochemistry is well-characterized in vitro, the endogenous requirement for this motif in regulating the stability of the transcript and other genes residing in its locus remains unclear. In this study, we employed a dual-sgRNA CRISPR-Cas9 approach to systematically excise triple-helix-forming sequences from the native MALAT1 locus in gastric (AGS) and breast (MCF7) cancer cells. Our findings demonstrate that the 3 end strongly contributes to MALAT1 stability. Perturbations ranging from genomic deletions to a single-base changes trigger transcript collapse and rapid exonucleolytic decay, while the biogenesis of the small RNA mascRNA (a byproduct of MALAT1, also involved in cancer) remains decoupled and unaffected. In cellulo, DMS probing reveals that edited transcripts retain structural complexity in the 3 region. Phenotypically, structural disruption of the 3 end significantly impairs proliferation of both cancer cellular models. These results identify the 3 triple-helix as a determinant of MALAT1 stability and provide endogenous validation for its role in the analyzed AGS and MCF7 cells.

molecular biology↗

bioRxiv2025

The Liver-Enriched Long Non-Coding RNA FAM99A Suppresses Tumorigenesis through Negative Regulation of Protein Synthesis

Primary liver cancer represents a significant global health burden, with limited therapeutic options for advanced disease. Long non-coding RNAs (lncRNAs) are increasingly found to play crucial roles in hepatic biology and disease progression. Here, we identify FAM99A as a highly liver-specific lncRNA that is systematically downregulated across liver malignancies, with reduced expression correlating with poor clinical outcomes. FAM99A exhibits remarkable tissue specificity with minimal expression outside the liver, and its levels rapidly decline during primary hepatocyte dedifferentiation in culture. Through isoform analysis, we establish FAM99A-203 as the predominant transcript in normal liver tissue and observe altered isoform distribution in liver cancers. Functionally, FAM99A overexpression inhibits anchorage-independent growth in liver cancer cell lines. Transcriptomic analysis reveals that FAM99A negatively regulates translation-related pathways in both liver cancer cells and primary hepatocytes. This is corroborated by protein synthesis assays showing that FAM99A overexpression substantially reduces global translation rates. Targeted RNase H-mediated extraction coupled with mass spectrometry identifies multiple components of the translation machinery as direct FAM99A binding partners, including eukaryotic translation initiation factors and RNA helicases involved in ribosome biogenesis. Clinical data analysis demonstrates significant inverse correlations between FAM99A expression and ribosomal protein genes in liver cancer patients. Additionally, hepatitis B virus appears to downregulate FAM99A expression, potentially contributing to its oncogenic properties. Our findings establish FAM99A as a liver-specific translational regulator that exerts tumor-suppressive effects by restraining protein synthesis rates, offering insights into hepatocarcinogenesis and the potential of FAM99A as both a biomarker and agent in new therapeutic avenues.

cancer biology↗