Chanock, Stephen J

Abstract Background Lung adenocarcinoma in never-smokers is a major public health burden, especially among East Asian women. Polygenic risk scores (PRSs) are promising for risk stratification but are primarily developed in European-ancestry populations. We aimed to develop and validate single- and multi-ancestry PRSs for East Asian never-smokers to improve lung adenocarcinoma risk prediction. Methods PRSs were developed using genome-wide association study summary statistics from East Asian (8002 cases; 20 782 controls) and European (2058 cases; 5575 controls) populations. Single-ancestry models included a PRS with 25 single nucleotide variants (PRS-25), PRS clumping and thresholding (CT), and LDpred2; multi-ancestry models included LDpred2 plus European PRS-128, PRS-CSx, and clumping and thresholding, super learning, empirical Bayes (CT-SLEB). Performance was evaluated in independent East Asian data from the Female Lung Cancer Consortium and externally validated in the Nanjing Lung Cancer Cohort. We assessed predictive accuracy via area under the curve operating procedure (AUC), with 10-year and (ages 30-80 years) absolute risks estimates. Results The best multi-ancestry PRS, using East Asian and European data via CT-SLEB, outperformed the best East Asian-only (LDpred2; AUC = 0.629, 95% confidence interval [CI] = 0.618 to 0.641), achieving an AUC of 0.640 (95% CI = 0.629 to 0.653) and odds ratio of 1.71 (95% CI = 1.61 to 1.82) per standard deviation increase. Nanjing Lung Cancer Cohort validation confirmed robust performance (AUC = 0.649, 95% CI = 0.623 to 0.676). The top 20% PRS group had a 3.92-fold higher lung adenocarcinoma risk than the bottom 20%. Further, the top 5% PRS group reached a 6.69% lifetime absolute risk. Notably, this group reached the average population 10-year lung adenocarcinoma risk at age 50 years (0.42%) by age 41 years, 9 years earlier. Conclusions Multi-ancestry PRS approaches enhance lung adenocarcinoma risk stratification in East Asian never-smokers, with consistent external validation, suggesting future clinical utility.

Introduction: Over 80,000 new cases of Non-Hodgkin's Lymphoma (NHL) are diagnosed annually, but modifiable risk factors are largely unknown. Circadian disruption has been identified as a risk factor for several cancers, including breast and prostate cancer, and affects immune cells such as Natural Killer (NK) cells and T-helper cells. Disruptions in circadian rhythms can lead to aberrant immune cell trafficking and proliferation. Despite this biological connection, evidence linking circadian disruptions to NHL remains inconclusive. Only single Mendelian Randomization (MR) study (PMID: 32895918) has explored the causal relationship between sleep traits and overall NHL risk, without examining NHL subtypes. Studies have shown distinct risk factor profiles among NHL subtypes. Therefore, this study aims to investigate the causal relationship between sleep traits and NHL subtypes in European populations using MR. Methods: We conducted a two-sample MR analyses using genome-wide association studies (GWAS) summary data on sleep traits and NHL subtypes. The GWAS summary statistics on sleep traits were obtained from publicly available UKBiobank datasets. The sleep traits analyzed included chronotype (N=449,734), insomnia (N=237,627), sleep duration (N=446,118), daytime sleepiness (N=452,071), short sleep (N=411,934), and long sleep (N=339,926). Only independent, genome-wide significant SNPs (p < 5×10-8) were considered as valid instruments. The NHL subtype-specific summary statistics came from the InterLymph including follicular lymphoma (FL: N=6,508 cases / 64,183 controls), mantle cell lymphoma (MCL: N=1,169 cases / 61,603 controls), and Waldenström macroglobulinemia/lymphoplasmacytic lymphoma (WM/LPL: N=1,697 cases / 59,333 controls). Our primary analysis used the random-effects inverse-variance weighted (IVW) method. In addition, we employed MR-Egger to adjust for directional pleiotropy. Heterogeneity in the MR results was evaluated with Cochran's Q statistic. Results: The IVW method did not identify any statistically significant causal association between sleep traits and the risk of NHL subtypes (FL,MCL,WM/LPL), but did yield several intriguing associations. Chronotype (early rising) showed a tendency towards a marginally an increased NHL risk across subtypes [Odds ratio (OR) range: 1.07 - 2.56]. Conversely, a decreased risk was noted for long sleep (≥ 9 hours vs. 7-8 hours) [OR range: 0.19 - 0.62], insomnia [OR range: 0.72 - 0.88], and short sleep (excludes MCL) [OR range: 0.12 - 0.72]. Confidence limit for long sleep was wide due to small number of variants (N=8). The MR-Egger regression analysis did not provide evidence of significant directional horizontal pleiotropy. The F-statistics for all sleep traits were greater than 10 indicating absences of weak instrument bias. Conclusions: Our study found no statistically significant associations between sleep traits and three NHL subtypes (FL, MCL, WM/LPL) in European populations. However, we observed potential influences of chronotype, long and short sleep, and insomnia on NHL risk. These findings align with and extend previous MR study by providing subtype-specific insights. Future directions include expanding our analysis to additional NHL subtypes, generating polygenic risk scores, and conducting stratified analyses using the InterLymph population. These efforts aim to further elucidate the complex relationship between sleep characteristics and NHL risk across diverse subtypes and populations.

Abstract Background: Genome-wide association studies (GWAS) have linked single nucleotide polymorphisms (SNPs) to pancreatic ductal adenocarcinoma (PDAC) risk at over 20 genomic loci. The Pancreatic Cancer Cohort Consortium and Pancreatic Cancer Case-Control Consortium are currently expanding on previous GWAS studies for PDAC from ∼9,000 cases and ∼12,000 controls to ∼36,000 cases and ∼800,000 controls in individuals of European and Asian ancestry. This ongoing GWAS phase is estimated to detect up to 50 new risk signals. Post-GWAS studies aim to fine-map and functionally assess risk variants in disease-relevant cell types and contexts to identify target genes and underlying mechanisms of risk. Massively parallel reporter assays (MPRAs) are a powerful method of assessing allele-specific gene regulatory effects. Integrating sequences into the genome using lentiviruses (Lenti-MPRA) enables the capture of variant function in the context of the native cellular chromatin. An added benefit is that Lenti-MPRAs can be used for difficult to transfect cells such as primary cells, that often reflect the disease relevant cell types. Methods: We have used a lentiviral MPRA to test 228 fine-mapped SNPs at the chr5p15.33 multi-cancer risk locus in PDAC cell lines (MIA PaCa-2, PANC-1) and the normal-derived ductal pancreas (HPDE) cell line. Additionally, we have optimized the transduction of large MPRA libraries into primary pancreas cells. Tunicamycin was used to induce ER stress in cell lines and primary cells, assessing downstream gene expression using RT-qPCR. Results: Our pilot MPRA demonstrated high reproducibility in PDAC cell lines (r2=0.93-0.97, MIA PaCa-2, PANC-1 cells) and normal-derived pancreatic ductal cells (r2=0.68-0.86, HPDE cells). We identified 33 SNPs out of 228 with significant allele-specific transcriptional activity in PDAC cell lines and 5 in HPDE cells (FDR ≤0.05). An additional 6-15% of variants exhibited significant allele-specific transcriptional activity when in the frames of the SNP-centered tested oligos were shifted left or right. We demonstrate the inducibility of ER-stress with tunicamycin treatment over 24 hours in cells lines and primary pancreatic cells. Additionally, we observed increased expression of CLPTM1IL at the chr5p15.33 locus after tunicamycin treatment over 24 hours in cell lines and primary pancreatic cells, suggesting ER-stress and inflammation may influence gene expression at this locus. Conclusions: Lentiviral MPRA assays in commonly used PDAC cell lines have demonstrated good reproducibility. The optimization studies and preliminary work in primary pancreatic cells provide a solid foundation for the next steps of assessing all GWAS loci in ER stress, an important disease relevant condition. Citation Format: Minal B Patel, Aidan O'Brien, Jun Zhong, Irene Collins, Jason W Hoskins, Stephen J Chanock, Samuel O Antwi, Rachel Z Stolzenberg-Solomon, Alison P Klein, Brian M Wolpin, Sara Lindström, H. Efsun Arda, Kevin M Brown, Katelyn E Connelly, Laufey T Amundadottir, Meagan Jezek. The functional characterization of pancreatic ductal adenocarcinoma GWAS risk variants in primary pancreatic cells – A pilot study [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A018.