Regulation of non-canonical proteins from diverse origins through the nonsense-mediated mRNA decay pathway.

Immunotherapy harnesses neoantigens encoded within the human genome, but their therapeutic potential is hampered by low expression, which may be controlled by the nonsense-mediated mRNA decay (NMD) pathway. This study investigates the impact of UPF1-knockdown on the expression of non-canonical/mutant proteins, employing proteogenomic to explore UPF1 role within the NMD pathway. Additionally, we conducted a comprehensive pan-cancer analysis of UPF1 expression and evaluated UPF1 expression in Triple-Negative Breast Cancer (TNBC) tissue in-vivo. Our findings reveal that UPF1-knockdown leads to increased translation of non-canonical/mutant proteins, particularly those originating from retained-introns, pseudogenes, long non-coding RNAs, and unannotated transcript biotypes. Moreover, our analysis demonstrates elevated UPF1 expression in various cancer types, with notably heightened protein levels in patient-derived TNBC tumors compared to adjacent tissues. This study elucidates UPF1 role in mitigating transcriptional noise by degrading transcripts encoding non-canonical/mutant proteins. Targeting this mechanism may reveal a new spectrum of neoantigens accessible to the antigen presentation pathway. Our novel findings provide a strong foundation for the development of therapeutic strategies aimed at targeting UPF1 or modulating the NMD pathway.

A simple organic solvent precipitation method to improve detection of low molecular weight proteins.

Mass spectrometry-based proteomics revolutionized global proteomic profiling. Although high molecular weight abundant proteins are readily sampled in global proteomics studies, less abundant low molecular weight proteins are often underrepresented. This includes biologically important classes of low molecular weight proteins including ligands, growth factors, peptide hormones and cytokines. Although extensive fractionation can facilitate achieving better coverage of proteome, it requires additional infrastructure, mass spectrometry time and labour. There is need for a simple method that can selectively deplete high molecular weight abundant proteins and enrich for low molecular weight less abundant proteins to improve their coverage in proteomics studies. We present a simple organic-solvent based protein precipitation method that selectively depletes high molecular weight proteins and enriches low molecular weight proteins in the soluble fraction. Using this strategy, we demonstrate identification of low molecular weight proteins that are generally underrepresented in proteomics datasets. In addition, we show the utility of this approach in identifying functional cleavage products from precursor proteins and low molecular weight short open reading frame proteins encoded by non-coding regions such as lncRNAs and UTRs. As the method does not require additional infrastructure, it can complement existing proteomics workflows to increase detection and coverage of low molecular weight proteins that are less abundant.

Exploring the Association of Innate Immunity Biomarkers With MRI Features in Both Early and Late Stages Osteoarthritis.

Objective: To evaluate the association between biomarkers of innate immunity and the magnetic resonance imaging (MRI) features of earlier and later stages of knee osteoarthritis (KOA). Methods: From 139 and 20 participants with earlier and later stages of KOA, respectively, we analyzed knee MRIs scored using the Boston Leeds Osteoarthritis Knee Score (BLOKS) at recruitment with biomarkers. In paired serum (s) and synovial fluid (sf), we quantified three biomarkers related to innate immunity: lipopolysaccharide binding protein (LBP), CD14 and Toll-like receptor 4 (TLR4), and three proinflammatory biomarkers [interleukin-6 (IL6), IL8, and tumor necrosis factor alpha (TNFα)]. Results: In participants with earlier KOA, (s) LBP was statistically significantly associated with meniscal extrusion, and (sf) CD14 was associated with effusion after adjustment with age, sex, and body mass index. In participants with later stage of KOA, (sf) LBP was associated with effusion. (sf) CD14 was associated with cartilage loss and BML. In earlier stage of KOA, the proinflammatory biomarkers IL6, IL8, and TNFα were associated with most MRI features. Conclusion: Innate immunity biomarkers (s) LBP was associated with MRI meniscal extrusion; (sf) CD14 was associated with MRI synovial inflammation in earlier stage and BMLs in later stage of KOA. Associations between proinflammatory biomarkers and various MRI features in earlier stage of KOA were observed.

The association of plasma IL-1Ra and related cytokines with radiographic severity of early knee osteoarthritis.

Objective: We aimed to evaluate the association between inflammatory biomarkers in peripheral blood and severity of knee osteoarthritis (OA). Methods: We performed a cross-sectional study in participants with frequent knee pain, evaluated radiographic and clinical severity. We measured inflammatory biomarkers: plasma (p) IL-1Ra, IL-1ß, IL-18, serum (s) CD14, hsCRP and bone and cartilage biomarkers: urine (u) CTX-II, (s) HA, COMP, CTX-I, PIIANP. We assessed radiographic severity by Kellgren-Lawrence (KL) grading and Osteoarthritis Research Society International (OARSI) standardized scoring atlas; and clinical severity by the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC). Results: 139 participants (82% women, mean ± SD age: 55.5 ± 7.8 years) were included. (p) IL-1Ra was negatively associated with radiographic severity by KL grading (Spearman rho = -0.197, P = 0.021), osteophytes (Spearman rho = -0.217, P = 0.011), and joint space narrowing of index knee (Spearman rho = -0.172, P = 0.045); and KL sum score of both knees (Spearman rho = -0.180, P = 0.035), after adjustment for age, gender and body mass index (BMI). Other inflammatory markers were not associated with radiographic severity. Cartilage degradation markers (u) CTXII and (s) COMP were modestly associated with radiographic severity after adjustment. In multivariate models, (s) hsCRP and the bone and cartilage biomarkers, but not the inflammatory biomarkers, were associated with radiographic severity. Conclusion: Among the inflammatory biomarkers in peripheral blood, IL-1Ra was negatively associated with radiographic severity in this early knee OA cohort.