Jongwan Kim | Search PubMed

PubMed2026

Evaluation of the subtype-specific epigenetic prognostic association of HELLS in non-small cell lung cancer: integrated clinical and molecular insights.

BACKGROUND: Helicase, lymphoid-specific (HELLS) is an epigenetic chromatin remodeler implicated in several cancers, but its prognostic role in non-small cell lung cancer (NSCLC) subtypes remains unclear. We investigated the expression, prognostic significance, and subtype-specific associations of HELLS in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). METHODS: The Cancer Genome Atlas (TCGA) and independent Gene Expression Omnibus (GEO) datasets were analyzed. HELLS expression was compared between tumor and normal tissues, survival was evaluated separately in LUAD and LUSC, and gene set enrichment analysis (GSEA) was performed. Multivariable analyses were used to assess associations between HELLS and selected oncogenic and immune-related genes after adjustment for clinical variables. RESULTS: HELLS was significantly upregulated in both LUAD and LUSC compared with normal lung tissues (P<0.001). High HELLS expression was associated with shorter overall survival (OS) in LUAD (log-rank P=0.001) and in the TCGA-LUSC cohort (log-rank P=0.002); however, external validation in GSE42127 (LUSC, n=43) was not significant [log-rank P=0.12; hazard ratio (HR) =0.49, 95% confidence interval (CI): 0.20-1.22, P=0.13]. HELLS-high LUAD tumors showed enrichment trends enriched in proliferation-related pathways, whereas HELLS-low LUSC tumors were enriched in inflammatory and apoptotic pathways. HELLS expression remained associated with KRAS, BRAF, and CD274 in LUAD after adjustment for age, sex, and stage, while only limited associations were observed in LUSC. CONCLUSIONS: HELLS shows a subtype-dependent prognostic and molecular association in NSCLC, with the strongest and most reproducible signal in LUAD; however, its prognostic value is attenuated after multivariable adjustment and is not consistently reproduced across external cohorts.

Helicase, lymphoid-specific (HELLS)↗

PubMed2026

Evaluation of amplicon-based nanopore sequencing for foot-and-mouth disease viruses in clinical and environmental samples.

Foot-and-mouth disease (FMD) causes severe global economic loss, necessitating rapid viral characterization. Nanopore sequencing provides a simple, real-time workflow suitable for on-site outbreak response, addressing the limitations of conventional methods. In this study, we optimized a previously published amplicon-based protocol and used this method to characterize a diverse range of samples (vesicular fluid, epithelium, serum, nasal/oral swabs, and environmental samples) collected during FMD outbreaks in 2025 in the Republic of Korea. Of the 129 samples collected, we successfully recovered complete genomes from 37 samples and VP1 sequences from 85 samples. Amplifying the S-fragment in isolation and separately barcoding each pool of PCR amplicons markedly improved sequence recovery. Furthermore, sequencing success depended on viral load and sample type. Based on comparisons with real-time RT-PCR results, whole-genome sequence (WGS) recovery exceeded 77.3% at cycle threshold (Ct) values ≤25 across all clinical samples. In the Ct > 30 category, serum samples yielded the highest WGS recovery rates (44.4%). This rate was markedly higher than the success rates observed for epithelium (20.0%) and nasal swabs (9.1%), whereas oral swabs and environmental samples failed to yield any sequences (0%). However, VP1 recovery from environmental samples reached 80% at Ct ≤ 30 (8/10), providing an approach to enable non-invasive monitoring. These findings demonstrate that amplicon-based nanopore sequencing is a practical method for the rapid generation of genomic data during FMD outbreaks.IMPORTANCEAlthough rapid detection and genomic data analysis are crucial for effective foot-and-mouth disease (FMD) control, the collection of these data can be challenging for certain sample types and impacted by reduced viral loads that result from nationwide FMD vaccination. This study provides a practical solution through large-scale evaluation of an optimized amplicon-based nanopore sequencing protocol to enhance the sequencing success rates for both clinical and environmental samples. Using a modified protocol to enhance genome recovery, we demonstrated that sequence data could be retrieved from diverse sample types (even with high real-time RT-PCR cycle threshold values). We identified serum as the most suitable sample, with environmental sample sequencing allowing for non-invasive monitoring during outbreaks. These results support the use of nanopore sequencing for rapid genomic analysis, particularly in outbreak responses, such as rapid surveillance, emergency vaccine selection, and epidemiological monitoring.

Foot-and-Mouth Disease↗