Predictive value of spectral dual-detector computed tomography for PD-L1 expression in stage I lung adenocarcinoma: development and validation of a novel nomogram.

Background: Programmed death ligand-1 (PD-L1) expression serves a predictive biomarker for the efficacy of immune checkpoint inhibitors (ICIs) in the treatment of patients with early-stage lung adenocarcinoma (LA). However, only a limited number of studies have explored the relationship between PD-L1 expression and spectral dual-layer detector-based computed tomography (SDCT) quantification, qualitative parameters, and clinical biomarkers. Therefore, this study was conducted to clarify this relationship in stage I LA and to develop a nomogram to assist in preoperative individualized identification of PD-L1-positive expression. Methods: We analyzed SDCT parameters and PD-L1 expression in patients diagnosed with invasive nonmucinous LA through postoperative pathology. Patients were categorized into PD-L1-positive and PD-L1-negative expression groups based on a threshold of 1%. A retrospective set (N=356) was used to develop and internally validate the radiological and biomarker features collected from predictive models. Univariate analysis was employed to reduce dimensionality, and logistic regression was used to establish a nomogram for predicting PD-L1 expression. The predictive performance of the model was evaluated using receiver operating characteristic (ROC) curves, and external validation was performed in an independent set (N=80). Results: The proportions of solid components and pleural indentations were higher in the PD-L1-positive group, as indicated by the computed tomography (CT) value, CT at 40 keV (CT40keV; a/v), electron density (ED; a/v), and thymidine kinase 1 (TK1) exhibiting a positive correlation with PD-L1 expression. In contrast, the effective atomic number (Zeff; a/v) showed a negative correlation with PD-L1 expression [r=-0.4266 (Zeff.a), -0.1131 (Zeff.v); P<0.05]. After univariate analysis, 18 parameters were found to be associated with PD-L1 expression. Multiple regression analysis was performed on significant parameters with an area under the curve (AUC) >0.6, and CT value [AUC =0.627; odds ratio (OR) =0.993; P=0.033], CT40keV.a (AUC =0.642; OR =1.006; P=0.025), arterial Zeff (Zeff.a) (AUC =0.756; OR =0.102; P<0.001), arterial ED (ED.a) (AUC =0.641; OR =1.158, P<0.001), venous ED (ED.v) (AUC =0.607; OR =0.864; P<0.001), TK1 (AUC =0.601; OR =1.245; P=0.026), and diameter of solid components (Dsolid) (AUC =0.632; OR =1.058; P=0.04) were found to be independent risk factors for PD-L1 expression in stage I LA. These seven predictive factors were integrated into the development of an SDCT parameter-clinical nomogram, which demonstrated satisfactory discrimination ability in the training set [AUC =0.853; 95% confidence interval (CI): 0.76-0.947], internal validation set (AUC =0.824; 95% CI: 0.775-0.874), and external validation set (AUC =0.825; 95% CI: 0.733-0.918). Decision curve analyses also revealed the highest net benefit for the nomogram across a broad threshold probability range (20-80%), with a clinical impact curve (CIC) indicating its clinical validity. Comparisons with other models demonstrated the superior discriminatory accuracy of the nomogram over any individual variable (all P values <0.05). Conclusions: Quantitative parameters derived from SDCT demonstrated the ability to predict for PD-L1 expression in early-stage LA, with Zeff.a being notably effective. The nomogram established in combination with TK1 showed excellent predictive performance and good calibration. This approach may facilitate the improved noninvasive prediction of PD-L1 expression.

An R package for Survival-based Gene Set Enrichment Analysis.

Functional enrichment analysis is usually used to assess the effects of experimental differences. However, researchers sometimes want to understand the relationship between transcriptomic variation and health outcomes like survival. Therefore, we suggest the use of Survival-based Gene Set Enrichment Analysis (SGSEA) to help determine biological functions associated with a disease's survival. We developed an R package and corresponding Shiny App called SGSEA for this analysis and presented a study of kidney renal clear cell carcinoma (KIRC) to demonstrate the approach. In Gene Set Enrichment Analysis (GSEA), the log-fold change in expression between treatments is used to rank genes, to determine if a biological function has a non-random distribution of altered gene expression. SGSEA is a variation of GSEA using the hazard ratio instead of a log fold change. Our study shows that pathways enriched with genes whose increased transcription is associated with mortality (NES > 0, adjusted p-value < 0.15) have previously been linked to KIRC survival, helping to demonstrate the value of this approach. This approach allows researchers to quickly identify disease variant pathways for further research and provides supplementary information to standard GSEA, all within a single R package or through using the convenient app.

Identification of tumor mutations in plasma based on mutation variant frequency change (MVFC).

To overcome the dependency of strategies utilizing cell-free DNA (cfDNA) on tissue sampling, the emergence of sequencing panels for non-invasive mutation screening was promoted. However, cfDNA sequencing with panels still suffers from either inaccuracy or omission, and novel approaches for accurately screening tumor mutations solely based on plasma without gene panel restriction are urgently needed. We performed unique molecular identifier (UMI) target sequencing on plasma samples and peripheral blood mononuclear cells (PBMCs) from 85 hepatocellular carcinoma (HCC) patients receiving surgical resection, which were divided into an exploration dataset (20 patients) or an evaluation dataset (65 patients). Plasma mutations were identified in pre-operative plasma, and the mutation variant frequency change (MVFC) between post- and pre-operative plasma was then calculated. In the exploration dataset, we observed that plasma mutations with MVFC < 0.2 were enriched for tumor mutations identified in tumor tissues and had frequency changes that correlated with tumor burden; these plasma mutations were therefore defined as MVFC-identified tumor mutations. The presence of MVFC-identified tumor mutations after surgery was related to shorter relapse-free survival (RFS) in both datasets and thus indicated minimum residual disease (MRD). The combination of MVFC-identified tumor mutations and Alpha Fetoprotein (AFP) could further improve MRD detection (P < 0.0001). Identification of tumor mutations based on MVFC was also confirmed to be applicable with a different gene panel. Overall, we proposed a novel strategy for non-invasive tumor mutation screening using solely plasma that could be utilized in HCC tumor-burden monitoring and MRD detection.