Supplementary Table S7. Confounding analyses for the association between the interaction of the TGF-B-Polygenic Risk Score and red meat intake in relation to colorectal cancer risk.

Supplementary Figure S1, LocusZoom plots.

Supplementary Table S3. Weights used for polygenic risk score estimation and coordinates from single nucleotide polymorphisms considered in the study.

Current findings on the relationship between wholegrain intake and breast cancer are inconsistent. We aimed to estimate the association between long-term wholegrain intake and breast cancer risk, specifically investigating: (i) adherence to the updated Nordic Nutrition Recommendations (NNR2023) guidelines on wholegrain intake, and (ii) consumption of specific wholegrain products. Data from food frequency questionnaires were used to assess adherence to NNR2023 guidelines on wholegrain intake and consumption of wholegrain products among 36,479 women (48–83 years) in the Swedish Mammography Cohort at two timepoints. Time-updated Cox proportional hazards regression models were used to estimate multivariable-adjusted hazard ratios (HR) and 95

Supplementary Table S5. Results from multinomial logistic regression models to evaluate pathway-based polygenic risk score interactions with red meat and processed meat intake by topological tumor location.

Colorectal cancer (CRC) is a leading cause of cancer-related death, with incidence rising substantially among individuals under 50 years of age. Polygenic risk scores (PRS) hold promise for identifying high-risk individuals; when combined with lifestyle factors, they substantially improve prediction accuracy compared with models based on lifestyle factors alone. However, few clinical tools currently exist that facilitate this integrated, PRS-enhanced risk assessment. To bridge this gap, we developed MyGeneRisk Colo n, a publicly accessible web portal that delivers individualized CRC risk prediction by incorporating genetic, demographic, family history, and lifestyle factors. This paper details the development of the underlying risk prediction model, the portal's architecture and data security, our reporting framework, and engagement with a community advisory panel. Designed as a user-friendly platform, MyGeneRisk Colon aims to effectively communicate personalized CRC risk profiles and educate users and healthcare providers about prevention strategies.

BACKGROUND:Observational studies have reported lower ovarian cancer risk among individuals taking aspirin frequently (i.e. daily/near daily). However, most studies relied on a single assessment of aspirin use, which may have led to misclassification and precluded the examination of patterns of use over time. We examined the association between aspirin use, assessed at multiple time points, and ovarian cancer risk. METHODS:Data were pooled from 10 prospective cohort studies from the Ovarian Cancer Cohort Consortium (n = 675 901 participants; 5528 cases; median follow-up = 13 years). Frequent aspirin use was self-reported via repeat questionnaires. We examined multiple time-updated, lagged aspirin-exposure metrics and risk of ovarian cancer by using pooled logistic regression adjusted for time-updated confounders. RESULTS:While ever frequent aspirin use was not associated with ovarian cancer [odds ratio (OR) 0.97; 95% confidence interval (CI): 0.91-1.03], individuals who reported long-term use experienced a 14% reduction in ovarian cancer risk (>6 years; OR 0.86; 95% CI: 0.77-0.97). This risk reduction was evident among individuals with at least three ovarian cancer risk factors (OR 0.65; 95% CI: 0.50-0.85) but not among individuals with fewer than three ovarian cancer risk factors (OR 0.94; 95% CI: 0.82-1.08), P-interaction = .02). Reduced ovarian cancer risks were also observed for low-dose aspirin use (OR 0.90; 95% CI: 0.80-1.01 for ever low-dose use; OR 0.75; 95% CI: 0.56-0.99 for long-term low-dose use) but not ever regular-dose use (OR 1.09; 95% CI: 0.94-1.27). CONCLUSION:Long-term use of aspirin, and particularly low-dose aspirin, is associated with lower ovarian cancer risk, especially among individuals with other established risk factors for ovarian cancer. Research should continue to explore the potential role of long-term, low-dose aspirin use for ovarian cancer primary prevention.

Background:Risk stratification for prostate cancer (PCa) progression or aggressiveness is often based on clinicopathologic features, some of which may be influenced by genetic factors. We developed a novel, germline polygenic risk score (PRSagg) to predict likelihood of developing aggressive PCa. Methods:PRSagg was developed using data from 38,688 patients with PCa (case-only analysis) from the Million Veteran Program (MVP) through a genome-wide search for variants associated with PCa grade group at diagnosis. We tested associations of PRSagg with grade group using the entire MVP dataset using the .632 bootstrap method. In an MVP cohort with localized PCa that was initially monitored without treatment, we tested PRSagg for association with unfavorable outcomes (subsequent development of grade group 4-5, metastasis, and/or biochemical recurrence after definitive treatment). We performed external validation in data from patients in the PRACTICAL Consortium (n=45,214) and from participants in the ProtecT randomized trial who underwent active monitoring (n=316). Odds ratios (ORs) were calculated per standard deviation (SD) increase with 95% confidence intervals, while adjusting for age, genetic ancestry, a previously developed polygenic score for risk of PCa (PHS601), and a polygenic score for benign elevated prostate-specific antigen (PRSPSA). For the outcome of metastasis, we additionally adjusted for PSA at diagnosis. Results:In the MVP training dataset, PRSagg (172 variants) was associated with higher grade group at diagnosis (OR = 1.53 [1.51-1.56]) and with increased risk of unfavorable outcomes during monitoring (OR = 1.13 [1.09-1.18]). These findings were confirmed in the external datasets. PRSagg was associated with greater odds of higher grade group at diagnosis (OR = 1.09 [1.061.11]). Among ProtecT participants undergoing active monitoring, PRSagg was associated with higher risk of metastasis (OR = 2.15 [1.02-3.88]). Among MVP participants with high polygenic risk of developing any PCa, the risk of aggressive disease was highest in men with high PRSagg and low genetic risk of PSA elevation. Conclusions:Among men who develop PCa, a weighted sum of common germline variants (PRSagg) is independently associated with PCa aggressiveness. These findings may inform future study of germline influence on tumor evolution and risk-stratified intensity of active surveillance.

Supplementary Table S6. Associations between red meat/processed meat intake with colorectal cancer risk stratified by quartiles of pathway-based polygenic risk scores.

BACKGROUND:Stomach cancer presents complex etiologic heterogeneity. Ethanol in alcoholic beverages and its metabolite acetaldehyde are carcinogens causally linked to several cancers, but their role in gastric carcinogenesis has not been established. We analyzed harmonized, individual-level prospective data to examine associations between alcohol intake and risk of stomach cancer and its subtypes. METHODS:2,009,951 participants in 20 cohorts (mean follow-up=9-29 years) within the Pooling Project of Prospective Studies of Diet and Cancer (n = 8,357 incident invasive gastric adenocarcinomas) were included. We used Cox regression to assess associations between alcohol intake and risk of stomach cancer overall and by anatomical and histological subtype and population subgroup, adjusting for confounders. RESULTS:Evidence for an association between alcohol intake and overall stomach cancer risk was weak (hazard ratio, HR, for ≥30 v 0.1-<5 g/day: 1.06 [95% confidence interval, CI, 0.96 to 1.16], P between-studies heterogeneity=0.43). Positive associations with stomach cancer risk were observed in never smokers (HR, for ≥30 v 0.1-<5 g/day: 1.20 [95% CI, 1.02 to 1.42]; P interaction=0.02) and for Asian studies (HR, 1.21 [95% CI, 1.02 to 1.42]; P interaction=0.01). Modest increased risks were observed for non-cardia cancers such as those of the fundus, body and greater curvature, but not distally located non-cardia cancers. HRs did not differ materially between diffuse- and intestinal-type cancers (P heterogeneity>0.05). CONCLUSION:There was little evidence of an overall association between alcohol intake and stomach cancer risk, although modest positive associations were observed among never smokers and in Asian cohorts.

Supplementary Table S4. Pathway annotation, mapped genes, and putative effect for single nucleotide polymorphisms that were overrepresented in PANTHER pathways.

OBJECTIVES:This study aimed to investigate the association between dietary total antioxidant capacity (TAC) and the risks of clinical outcomes, including surgery, gastrointestinal cancer, and mortality, among middle-aged and older individuals with IBD. DESIGN:Nationwide prospective cohort study. SETTING AND PARTICIPANTS:We included middle-aged and older participants with IBD when recruited in the UK Biobank. MEASUREMENTS:Dietary TAC was calculated by the oxygen radical absorbance capacity from the food by repeated dietary recalls. The outcomes representing IBD prognosis include IBD-related surgery, gastrointestinal cancer, and death events. Hazard ratios (HRs) with 95% confidence intervals (CIs) were estimated using Cox proportional hazard models. Polymorphism of antioxidant-related enzymes genes was ascertained via genotype data. RESULTS:With a median follow-up period of 10.9 years, we documented 174 cases of IBD-related surgery, 52 gastrointestinal cancer, and 189 death events among 2487 IBD participants. Compared to the lowest quartile of dietary TAC, participants in the highest quartile presented lower risks of IBD-related surgery (HR 0.53; 95% CI 0.34-0.84; P-trend = 0.005) and all-cause mortality (HR 0.61; 95% CI 0.39-0.96; P-trend = 0.014). Compared to the lowest decile, participants in the higher deciles of dietary TAC had a lower risk of gastrointestinal cancer (HR 0.39; 95% CI 0.19-0.83; P = 0.014). We also found genetic variants in catalase gene CAT and antioxidant transporter gene SLC2A14 modified the association between dietary TAC and IBD prognosis. CONCLUSIONS:Higher dietary TAC was associated with better prognosis of middle-aged and older individuals with IBD, including lower risk of related surgery, gastrointestinal cancer, and all-cause mortality, suggesting the importance of adherence to high-TAC diet in IBD management.

Cross-sectional studies link gut microbiome alterations to type 2 diabetes (T2D), but prospective evidence remains limited. We aim to identify taxonomic and functional features associated with future T2D risk. We analyze shotgun metagenomic data from 4,685 participants (mean age, 73.9 years; 49.0% women) in the Swedish SIMPLER cohort, followed for a median 5.3 years, during which 383 developed T2D. Six species are associated with increased T2D risk: Desulfovibrio piger, Alistipes communis, Alistipes finegoldii, Akkermansia muciniphila, Ruminococcus gnavus, and GGB3614_SGB4886 (Lachnospiraceae), while three are protective: Erysipelotrichaceae bacterium, Coprococcus catus, and Clostridia unclassified SGB6317. We observe context-specific associations, including a dietary fiber-modified effect for A. muciniphila indicative of diet-dependent patterns. Three gut metabolic modules are associated with incident T2D: asparagine degradation (higher risk), mannose degradation, and the non-oxidative pentose phosphate pathway (lower risk). These prospective findings offer insights into T2D etiology and may support microbiome-informed strategies for risk prediction and prevention.

Pancreatic cancer incidence is rising, yet few modifiable risk factors have been identified. The Mediterranean diet, which lowers inflammation and improves healthy weight maintenance and insulin control, may lower pancreatic cancer risk, yet the evidence for this association is inconsistent. To investigate the association, we conducted a pooled analysis of 2,315,406 individuals from 23 prospective cohorts in the Pooling Project of Prospective Studies of Diet and Cancer (DCPP), of whom 10,748 developed incident pancreatic cancer over a mean follow-up duration ranging from 8.1 to 23.3 years across studies. Adherence to the Mediterranean diet was assessed using the alternative Mediterranean diet score (aMED) and a modified score excluding alcohol (maMED). Study- and sex-specific hazard ratios (HRs) and 95

AIMS:Little evidence exists on the health implications of adherence to a diet in line with the updated Nordic Nutrition Recommendations (NNR2023). We estimated the association between long-term adherence to NNR2023 and (i) incidence of cardiovascular disease (CVD), and (ii) biomarkers of cardiometabolic health. METHODS:The study population consisted of 76,028 participants from the Swedish Mammography Cohort (SMC) and Cohort of Swedish Men, and 4,267 women in a clinical sub-cohort of SMC. Data from food frequency questionnaires were used to assess NNR2023 adherence at baseline (in 1997) and upon re-investigation in 2009 and 2019. Time-varying multivariable Cox proportional hazards regression models were used to estimate the association between NNR2023 adherence and incidence of major adverse cardiovascular events (MACE) - a composite of acute myocardial infarction, stroke, and CVD mortality - as well as specific CVD events. Quantile regression was used to assess the association between NNR2023 adherence and cardiometabolic biomarkers. RESULTS:During a mean follow-up of 18.7 years (1.48 million person-years), we identified 24,041 cases of MACE. Participants in the highest vs lowest quartile of NNR2023 adherence had 17% (hazard ratio: 0.83; 95% confidence interval: 0.80, 0.86) lower risk of MACE, as well as lower risks of the individual MACE components. Higher NNR2023 adherence was associated with a more favourable blood lipid profile and insulin sensitivity (all p-values < 0.05). CONCLUSION:This study provides evidence for a positive impact of adherence to NNR2023 on cardiovascular health.

AbstractBackground: Red meat and/or processed meat are established colorectal cancer risk factors. Genome-wide association studies (GWAS) have reported more than 200 variants associated with colorectal cancer risk. We used functional annotation data to identify subsets of variants within known pathways to construct pathway-based polygenic risk scores (pPRS) to assess interactions with meat intake. Methods: A pooled sample of 30,812 cases and 40,504 colorectal cancer controls from 27 studies was analyzed. Quantiles for red and processed meat intake were constructed. A total of 204 GWAS variants were annotated to genes with Annotation Query (AnnoQ) and assessed for overrepresentation in PANTHER-reported pathways. pPRSs were constructed from significantly overrepresented pathways. Covariate-adjusted logistic regression models evaluated interactions between pPRS and red or processed meat intake in relation to colorectal cancer risk. Results: A total of 30 variants were overrepresented in four pathways: presenilin/Alzheimer disease, cadherin/WNT signaling, gonadotropin-releasing hormone receptor, and transforming growth factor-β (TGF-β) signaling. We found a significant interaction between TGF-β pPRS and red meat intake [ORint = 0.95; 95% confidence interval (CI) = 0.92–0.98; P = 0.003). When variants in the TGF-β pathway were assessed, we observed significant interactions of red meat with rs2337113 [intron SMAD family member 7 (SMAD7) gene, Chr18] and rs2208603 [intergenic region bone morphogenetic protein 5 (BMP5), Chr6; P = 0.0005 and 0.036, respectively]. There was no evidence of pPRS × red meat interactions for other pathways or with processed meat. Conclusions: This pathway-based interaction analysis revealed a statistically significant interaction between variants in the TGF-β pathway and red meat consumption that influences colorectal cancer risk. Impact: These findings shed light on the possible mechanistic link between red meat consumption and colorectal cancer risk.

Abstract Background Prostate cancer (PCa) is heterogeneous, making risk stratification essential for clinical care. Although polygenic risk scores (PRSs) with main effects of single-nucleotide polymorphisms (SNPs) can help identify individuals at high risk before biological and clinical onset, a PRS for predicting PCa aggressiveness remains underdeveloped. The KLK3 , which encodes prostate-specific antigen (PSA), is linked to PCa aggressiveness. Recent findings on KLK3 SNP-SNP interactions show promise for predicting PCa aggressiveness. The objective of this study is to develop a PRS (PRS-KLK3int) by examining KLK3 SNP-SNP interaction pairs. Methods The PRS-KLK3int was developed based on a discovery set (10,836 PCa patients) and two validation sets with 14,348 and 16,584 patients of European ancestry. A total of 3145 SNP pairs and two published PRSs were evaluated. Results This study developed a PRS-KLK3int with 284 SNPs, combining an existing PRS with 270 SNPs and 12 SNP-SNP interaction pairs with 15 SNPs (one overlapped). All these 12 pairs were involved with at least one SNP from KLK3 . The PRS-KLK3int outperformed two existing PRSs in predicting PCa aggressiveness (p-values: 3.5×10 −18 , 9×10 −14 , and 1.7×10 −20 for the three sets). It effectively distinguished high-risk from low-risk groups across all datasets. The top 1% high-risk group had a higher prevalence of PCa aggressiveness than the middle 50% group (45.5% vs. 25.9%, OR = 2.38, p = 2.2×10 −5 ) in the discovery set, and similar results were observed in validation sets (OR = 2.56, p = 4.3×10 −6 ; OR = 2.07, p = 2.1×10 −5 ). Conclusions These findings support PRS-KLK3int as a valuable tool for PCa severity stratification, especially in identifying extremely high-risk PCa patients.

Supplementary Table S2. Summary statistics for colorectal cancer-related risk factors in study participants.

Physical activity is an established protective factor for colorectal cancer (CRC), but it is unclear if genetic variants modify this effect. To investigate this possibility, we conducted a genome-wide gene–physical activity interaction analysis. Using logistic regression (1-d.f), two-step screening and testing method (EDGE), and joint tests (3-d.f), we analyzed interactions between common genetic variants across the genome and physical activity in relation to CRC risk. Self-reported physical activity levels were categorized as active (≥ 8.75 MET-h/wk) vs. inactive (< 8.75 MET-h/wk; 39,992 participants) and as study- and sex-specific quartiles of activity (42,602 participants). Physical activity was inversely associated with CRC risk overall (OR [active vs. inactive] = 0.85; 95

BACKGROUND:Dietary nitrate exposure originates from vegetables, drinking water, and is, together with nitrite, used as food additives in animal products. Both compounds can generate N-nitroso compounds, some of which are known animal carcinogens. However, epidemiological evidence regarding nitrate and nitrite intake in relation to colorectal cancer (CRC) risk and its subsites remains limited. METHODS:Nitrate and nitrite intake was assessed by linking a food and drinking water database to food frequency questionnaires completed in 1997 and updated in 2009 and 2019, by 82,009 middle-aged to elderly men and women of two population-based cohorts from the Swedish Infrastructure for Medical Population-based Life-course and Environmental Research. We ascertained incident CRC through the Swedish Cancer Registry from 1998 to 2022. Cox proportional hazards models were fitted to evaluate exposure-outcome associations, presented as hazard ratios (HR) with 95% confidence intervals (CI). RESULTS:We ascertained 3,170 CRC cases. No associations were observed for nitrate intake with CRC. In contrast, when comparing the highest to the lowest quintile, nitrite intake was associated with a dose-dependent higher risk of CRC in men (HR 1.23; 95%CI 1.06-1.43; p-trend<0.05) but not in women. CRC subsite analyses in men indicated the strongest association for distal colon cancer (HR 1.50; 95% CI: 1.13-1.98). CONCLUSION:A higher nitrite intake was associated with a higher CRC risk in men, particularly distal colon cancer. These findings indicate potential sex differences and differential susceptibilities across the colorectum in nitrite-related cancer risk.