The most near-term clinical application of genome-wide association studies in lung cancer is a polygenic risk score (PRS). A case-control dataset was generated consisting of 4002 lung cancer cases from the LORD project and 20,010 ethnically matched controls from CARTaGENE. A genome-wide PRS including >1.1 million genetic variants was derived and validated in UK Biobank (n = 5419 lung cancer cases). The predictive ability and diagnostic discrimination performance of the PRS was tested in LORD/CARTaGENE and benchmarked against previous PRSs from the literature. Stratified analyses were performed by smoking status and genetic risk groups defined as low (80th percentile) PRS. The phenotypic variance explained and the effect size of the genome-wide PRS numerically outperformed previous PRSs. Individuals with high genetic risk had a 2-fold odds of lung cancer compared to low genetic risk. The PRS was an independent predictor of lung cancer beyond conventional clinical risk factors, but its diagnostic discrimination performance was incremental in an integrated risk model. Smoking increased the odds of lung cancer by 7.7-fold in low genetic risk and by 11.3-fold in high genetic risk. Smoking with high genetic risk was associated with a 17-fold increase in the odds of lung cancer compared to individuals who never smoked and with low genetic risk. Individuals at low genetic risk are not protected against the smoking-related risk of lung cancer. The joint multiplicative effect of PRS and smoking increases the odds of lung cancer by nearly 20-fold. This work was supported by the CQDM and the IUCPQ Foundation owing to a generous donation from Mr. Normand Lord.

Whether single-cell RNA-sequencing (scRNA-seq) captures the same biological information as single-nucleus RNA-sequencing (snRNA-seq) remains uncertain and likely to be context-dependent. Herein, a head-to-head comparison was performed in matched normal-adenocarcinoma human lung samples to assess biological insights derived from scRNA-seq versus snRNA-seq and better understand the cellular transition that occurs from normal to tumoral tissue. Here, the transcriptome of 160,621 cells/nuclei was obtained. In non-tumor lung, cell type proportions varied widely between scRNA-seq and snRNA-seq with a predominance of immune cells in the former (81.5%) and epithelial cells (69.9%) in the later. Similar results were observed in adenocarcinomas, in addition to an overall increase in cell type heterogeneity and a greater prevalence of copy number variants in cells of epithelial origin, which suggests malignant assignment. The cell type transition that occurs from normal lung tissue to adenocarcinoma was not always concordant whether cells or nuclei were examined. As expected, large differential expression of the whole-cell and nuclear transcriptome was observed, but cell-type specific changes of paired normal and tumor lung samples revealed a set of common genes in the cells and nuclei involved in cancer-related pathways. In addition, we showed that the ligand-receptor interactome landscape of lung adenocarcinoma was largely different whether cells or nuclei were evaluated. Immune cell depletion in fresh specimens partly mitigated the difference in cell type composition observed between cells and nuclei. However, the extra manipulations affected cell viability and amplified the transcriptional signatures associated with stress responses. In conclusion, research applications focussing on mapping the immune landscape of lung adenocarcinoma benefit from scRNA-seq in fresh samples, whereas snRNA-seq of frozen samples provide a low-cost alternative to profile more epithelial and cancer cells, and yield cell type proportions that more closely match tissue content.

Circulating tumor DNA (ctDNA) positivity at diagnosis, which is associated with worse outcomes in multiple solid tumors including stage I-III non-small cell lung cancer (NSCLC), may have utility to guide (neo)adjuvant therapy. In this retrospective study, 260 patients with clinical stage I NSCLC (180 adenocarcinoma, 80 squamous cell carcinoma) were allocated (2:1) to high- and low-risk groups based on relapse versus disease-free status ≤5 years post-surgery. We evaluated the association of preoperative ctDNA detection by a plasma-only targeted methylation-based multi-cancer early detection (MCED) test with NSCLC relapse ≤5 years post-surgery in the overall population, followed by histology-specific subgroup analyses. Across clinical stage I patients, preoperative ctDNA detection did not associate with relapse within 5 years post-surgery. Sub-analyses confined to lung adenocarcinoma suggested a histology-specific association between ctDNA detection and outcome. In this group, ctDNA positivity tended to associate with relapse within 2 years, suggesting prognostic implications of MCED test positivity may be histology- and time-dependent in stage I NSCLC. Preoperative ctDNA detection was associated with upstaging of clinical stage I to pathological stage II-III NSCLC. Our findings suggest preoperative ctDNA detection in patients with resectable clinical stage I NSCLC using MCED, a pan-cancer screening test developed for use in an asymptomatic population, has no detectable prognostic value for relapse ≤5 years post-surgery. MCED detection may be associated with early adenocarcinoma relapse and increased pathological upstaging rates in stage I NSCLC. However, given the exploratory nature of these findings, independent validation is required.

Background: Data are scarce about tumor mutational burden (TMB) as a biomarker in never smokers with non–small cell lung cancer (NSCLC). Methods: TMB was assessed by whole-genome sequencing (WGS) and compared with in silico reduced whole-exome sequencing (WES) and targeted commercial next-generation sequencing (NGS) gene panels in 92 paired tumor-normal samples from never smokers who underwent NSCLC resection with curative intent. Analyses were performed to test for association with survival after surgery and to identify the optimal prognostic TMB cutoff. Results: Tumors of never smokers with NSCLC had low TMB scores (median 1.57 mutations/Mb; range, 0.13–17.94). A TMB cutoff of 1.70 mutations/Mb was associated with a 5-year overall survival of 58% in the high-TMB (42% of cases) compared with 86% in low-TMB patients (Wald P = 0.0029). TMB scores from WGS and WES were highly correlated (Spearman ρ = 0.93, P < 2.2e−16). TMB scores from NGS panels demonstrated high intraindividual fluctuations and identified high-TMB patients with 65% concordance in average compared with WGS. Conclusions: In resected NSCLC of never smokers, high TMB was associated with worse prognosis. WES provided a good estimate of TMB while targeted NGS panels seem to lack adequate depth and resolution in the setting of low mutation burden. Impact: TMB is a prognostic indicator of survival in resected NSCLC from individuals who never smoked. In this setting of low mutation counts, TMB can be accurately measured by WGS or WES, but not NGS panels.

There is still limited data on the prevalence of actionable molecular alterations in patients with early-stage resectable lung adenocarcinoma and prior studies reported important differences across geographic locations, demographic and pathologic characteristics. The tumors of 1,603 French Canadian patients with pathologically confirmed lung adenocarcinoma were interrogated using a 50-gene next-generation sequencing panel. The goal was to assess the prevalence of genetic alterations in eleven guideline-based oncogenic genes in resectable lung adenocarcinoma. Age, sex, pathological stage, smoking history and predominant histologic patterns were associated with molecular subtypes defined by oncogenic drivers. Age at surgery for the 1,603 patients was 65 ± 8 and includes 61 % of females, 6 % of patients without a smoking history and 70 % of stage I. The overall prevalence of targetable alterations for approved and investigational therapies was 65.9 % and 56.7 % of patients had tumors harboring at least one variant of strong clinical significance (tier I of the AMP/ASCO/CAP categorization). The most frequently mutated genes were KRAS (45.3 %), EGFR (11.5 %) and BRAF (3.9 %). MET exon 14 skipping alterations were identified in 47 patients (2.9 %) and oncogenic fusions in ALK, ROS1, RET and MET were found in 1.7 % of cases. As expected, EGFR activating mutations were associated with patients who never smoked, females, earlier disease stages, with more lepidic/acinar and less solid predominant patterns. Quasi similar but inverted relationships with clinico-pathological features were observed in one third of patients (n = 534) free of molecular alterations characterized by more males, patients who smoked, with later stage diagnosis and with more solid and less lepidic/acinar adenocarcinomas. This study highlights the epidemiology of guideline-based targetable alterations in French-Canadian patients with resectable lung adenocarcinoma. The large proportion of patients eligible for targeted therapies will have important impact on oncological practices in the current era of neoadjuvant and perioperative treatments.

Introduction: Lung adenocarcinoma (LUAD) is the leading cause of cancer-related mortality worldwide. Acinar is the most prevalent architectural pattern and is associated with an intermediate prognosis. Several studies have investigated the prognosis of acinar-predominant LUAD patients. Here, we aimed to move beyond the acinar-predominant classification and gain a more comprehensive understanding of how acinar minor components influence prognosis specifically when accompanying other histological patterns in LUAD. Methods: Patients were grouped by the proportion of acinar patterns in their tumors: acinar-predominant (AP), and acinar component (AC; non-acinar predominant LUAD with an acinar component of ≥5%). The clinicopathologic characteristics, recurrence-free survival (RFS), and a panel of well-characterized driver mutations, including KRAS, EGFR, BRAF, MET, and PIK3CA, were investigated in the two groups of patients. Results: Among 1263 LUAD patients, 716 (56.7%) were AP, and 547 (43.3%) were AC. In AP, the frequency of EGFR exon 19 deletions (EGFR-Del 19) was significantly higher than in AC (p = 0.014). AC demonstrated a worse RFS than AP in the unadjusted analysis (log-rank p: 0.006). In stage I, the difference in the RFS of AC in comparison to AP remained significant (p = 0.048). In the multivariable analysis, AC was significantly associated with a worse RFS in comparison to AP (hazard ratio [HR] AC vs. AP: 1.240, 95% CI: 1.103–1.312, p: 0.04), even after adjusting for other histological patterns, the mutational status, and relevant clinicopathological features. The post-recurrence survival was significantly better in patients with an acinar component of ≥5% who received EGFR tyrosine kinase inhibitors (TKIs) compared to those who did not receive TKIs (p = 0.033). Conclusions: While the predominant pattern primarily dictates prognosis in LAUD, the presence of an acinar minor component alongside other high-grade patterns may further worsen outcomes. This underscores the necessity of considering the broader histological landscape rather than focusing solely on predominant patterns, as our findings show that minor acinar components can impact RFS alongside other histological patterns.