A comprehensive re-assessment of the association between vitamin D and cancer susceptibility using Mendelian randomization.

Previous Mendelian randomization (MR) studies on 25-hydroxyvitamin D (25(OH)D) and cancer have typically adopted a handful of variants and found no relationship between 25(OH)D and cancer; however, issues of horizontal pleiotropy cannot be reliably addressed. Using a larger set of variants associated with 25(OH)D (74 SNPs, up from 6 previously), we perform a unified MR analysis to re-evaluate the relationship between 25(OH)D and ten cancers. Our findings are broadly consistent with previous MR studies indicating no relationship, apart from ovarian cancers (OR 0.89; 95% C.I: 0.82 to 0.96 per 1 SD change in 25(OH)D concentration) and basal cell carcinoma (OR 1.16; 95% C.I.: 1.04 to 1.28). However, after adjustment for pigmentation related variables in a multivariable MR framework, the BCC findings were attenuated. Here we report that lower 25(OH)D is unlikely to be a causal risk factor for most cancers, with our study providing more precise confidence intervals than previously possible

A comprehensive re-assessment of the association between vitamin D and cancer susceptibility using Mendelian randomization

Abstract: Previous Mendelian randomization (MR) studies on 25-hydroxyvitamin D (25(OH)D) and cancer have typically adopted a handful of variants and found no relationship between 25(OH)D and cancer; however, issues of horizontal pleiotropy cannot be reliably addressed. Using a larger set of variants associated with 25(OH)D (74 SNPs, up from 6 previously), we perform a unified MR analysis to re-evaluate the relationship between 25(OH)D and ten cancers. Our findings are broadly consistent with previous MR studies indicating no relationship, apart from ovarian cancers (OR 0.89; 95% C.I: 0.82 to 0.96 per 1 SD change in 25(OH)D concentration) and basal cell carcinoma (OR 1.16; 95% C.I.: 1.04 to 1.28). However, after adjustment for pigmentation related variables in a multivariable MR framework, the BCC findings were attenuated. Here we report that lower 25(OH)D is unlikely to be a causal risk factor for most cancers, with our study providing more precise confidence intervals than previously possible

Genetics of Skin Cancer

Three major types of skin cancers (melanoma, basal cell carcinoma (BCC) and squamous cellcarcinoma (SCC)) are a significant health burden mainly for the fair-skinned population.Melanoma is the most lethal form of skin cancer while BCC is the commonest form of skincancer. Cutaneous squamous cell carcinoma is more frequent than melanoma and moreaggressive than BCC. Ultraviolet radiation, pigmentation phenotypes and genetic factorsplay a role in skin cancer etiology. The objective of this work is to expand the currentunderstanding of genetic architecture of skin cancer. Furthermore, finding the causalassociation of various risk factors and skin cancer may strengthen preventive efforts. Thus, Ihave used genetic data to help evaluate the causal association of polyunsaturated fattyacids (PUFAs), vitamin D and melanoma and overall-cancer risk and mortality.In Chapter 1, I have included an introduction to skin cancer and its various risk factors aswell as a general overview of the statistical and computational methods used in the studiesincluded in the thesis.In Chapter 2, I performed Mendelian randomisation (MR) of melanoma on PUFAs. The studysample comprised 12,874 melanoma cases and 23,203 controls. PUFA Instrumentalvariables were derived from publicly available CHARGE consortium data. By using theinverse variance weighted method, I identified that even with a large change of fatty acidlevels (Docosapentaenoic acid (DPA- moving a person from the 17 th percentile to themedian)) there is no causal association between PUFAs and risk of melanoma odds ratio[OR] = 1.03 (95% confidence interval [CI] = 0.96-1.10). Other PUFAs yielded similar results.In Chapter 3, I used the same instruments of PUFAs to determine the causal association ofoverall cancer risk and mortality (46,155 cases for risk, 6,998 cases for morality and 270,342controls from UK Biobank). I further performed individual cancer analysis for 6 cancer types.I identified that there is no causal association between PUFAs and overall cancer risk andmortality except arachidonic acid (AA) overall cancer risk (OR = 1.02, 95% CI = 1.00 – 1.03).Colorectal cancer risk was increased with higher AA levels (OR = 1.05, 95% CI =1.03 – 1.07).In Chapter 4, I present MR analysis of vitamin D on melanoma risk. Observational studieshave shown many health benefits of vitamin D. To determine the causality of melanoma andvitamin D, I used melanoma meta-analysis consortium data with vitamin D instruments fromprevious publications. I found that changing vitamin D levels by a large amount (20nmol/Ldecrease), did not change the melanoma risk, OR =1.06 (95% CI = 0.95 – 1.19).In Chapter 5, I present the multi-trait analysis of GWAS (MTAG) of keratinocyte cancer (KC)which revealed 29 novel loci for KC risk. From individual cancer meta-analysis of either BCCor SCC, I further identified 12 loci and 1 locus, respectively. I used data from UKBB, QSkin,23andMe and eMERGE (47,742 cases, 634,413 controls) for KC MTAG analysis. I identifiedseveral drug targets; these included the important immune regulation locus CTLA4, which isa target of immunotherapy in melanoma treatment.In Chapter 6, I present the MTAG analysis of melanoma and correlated traits (biochemicaltraits, autoimmune traits) which revealed 74 loci. 18 of them are novel for melanoma risk.New loci included NDUFC2 is a drug target for diabetes mellitus, CTLA4 which is already adrug target for melanoma immunotherapy. My studies may provide future avenues formelanoma and KC treatments. Finally, in Chapter 7 I provide a general discussion withfuture directions for genetic epidemiology, particularly about GWAS, MR and MTAG and theusage of polygenic risk scores.In conclusion, I identified new genetic variants associated with KC and melanoma risk whichwill be potentially useful for future MR and polygenic risk score construction. My causalinference on overall cancer risk and melanoma may inform public health policies. Thesefindings may provide insight for future personalised treatments for skin cancer

Mendelian randomization study for genetically predicted polyunsaturated fatty acids levels on overall cancer risk and mortality

Background: Observational studies evaluating the link between polyunsaturated fatty acids (PUFA) and cancers have yielded mixed findings. We used Mendelian randomization (MR) to evaluate whether genetic evidence supports a causal role for PUFAs on overall cancer outcomes. Methods: We identified genetic instruments for six PUFAs from previous literature and evaluated their association with overall cancer risk (46,155 cases, 270,342 controls) and cancer mortality (6,998 deaths, 270,342 controls) among the UK Biobank cohort. We used the inverse variance weighted model to combine SNP estimates, and derived log (OR) estimates per SD change in each PUFA. Results: None of the six PUFAs showed association with overall cancer risk or mortality, with narrow confidence interval (CI) ruling out all but very small effects, for example, arachidonic acid (AA) overall cancer risk (OR, 1.02; 95% CI, 1.00–1.03). Sex-specific analysis revealed no associations except α-linolenic acid for potentially reducing cancer risk in men (OR, 0.92; 95% CI, 0.86–0.98; P = 0.02); however, this was nonsignificant after multiple testing correction. From individual cancers, only colorectal cancer showed evidence for a causal association for higher AA levels (OR, 1.05; 95% CI, 1.03–1.07), with similar results for the other correlated PUFAs. Conclusions: Our study provides no support for the hypothesis that PUFAs reduce overall cancer risk or mortality. Higher AA levels increased the risk for colorectal cancer. Impact: Our well-powered MR study provides robust causal inferences for the PUFAs on overall cancer risk and mortality. Future larger studies are warranted to replicate the individual cancer findings

Host genetic polymorphisms associated with beta human papillomavirus seropositivity

Human papillomaviruses (HPVs) cause superficial epidermal infections and are only cleared if they trigger an immunological response. We analysed SNPs that had previously been investigated for association with HPV infection to determine whether they play a role in the serological response to cutaneous beta-HPVs in an Australian population. Serum samples from 1,142 participants were analysed for seropositivity against the L1 protein of 21 beta-HPV types. Associations between seropositivity to beta-HPV types and the SNPs rs9264942 (HLA-C; HPV-9, p = 0.022, HPV-15, p = 0.043 and HPV-17, p = 0.004), rs12449858 (EVER1; HPV-23, p = 0.029), and rs2981451 (FGFR2; HPV-22, p = 0.049) were identified. We found that certain SNPs could be involved in the serological response to beta-HPVs

Dark Green Leafy Vegetable Intake, MTHFR Genotype, and Risk of Cutaneous Squamous Cell Carcinoma

Background: Evidence suggests that consumption of dark green leafy vegetables may influence the decrease in the risk of cutaneous squamous cell carcinoma (SCC). Dark green leafy vegetables contain folate as a main component among other nutrients; thus, we hypothesised that their possible observed protective effect on SCC, observed in previous studies, would be more evident in persons with specific genotypes related to folate metabolism. Methods: Genotyping of methylenetetrahydrofolate reductase (MTHFR) gene variants rs1801133 (C677T) and rs1801131 (A1298C) was carried out for 1,128 participants in an Australian community-based longitudinal study of skin cancer. Dietary intakes were assessed through repeated Food Frequency Questionnaires (1992–1996), and all incident skin cancers were recorded in 1992–2007 and histologically confirmed. We assessed associations between intake of dark green leafy vegetables and SCC development in strata defined by genotype, by calculating relative risks (RRs) with 95% confidence intervals (CIs) using generalised linear models with negative binomial distribution and person-years of follow-up as offset. Results: High versus low intake of dark green leafy vegetables was associated with a lower risk of SCC tumours in carriers of the C677T variant allele (RR = 0.42, 95% CI = 0.23–0.75), and within wild-type A1298C homozygotes (RR = 0.43, 95% CI = 0.22–0.85). Conclusion: The protective effect of dark green leafy vegetables on cutaneous SCC may be genotype-dependent. Folate metabolism-related gene polymorphisms should be considered when assessing the relation of green leafy vegetables to cancer risk

Associations of keratinocyte cancers with snp variants in the sonic hedgehog pathway

Background: Sonic Hedgehog (SHH) pathway dysregulation is implicated in basal cell carcinoma (BCC) development. To evaluate the possible wider role of SHH gene variants in skin carcinogenesis, we assessed associations of genes in the SHH pathway with lifetime development of any keratinocyte cancer (KC), and with developing either BCCs or squamous cell carcinomas (SCCs) exclusively, in a 25-year prospective, population-based study of 1,621 Australians. Methods: We genotyped 795 unrelated adults with available blood samples: 311 cases with any KC (186 developing BCCs-only, 55 SCCs-only, 70 BCCs and SCCs) and 484 controls. We compared allele frequencies of 158 independent SNPs across 43 SHH genes between cases and controls, and performed a gene-based analysis. Results: We found associations between SNP rs4848627 (GLI2) (related to DNA synthesis in keratinocytes) and development of any KC (OR = 1.53; 95% CI = 1.06–2.13, P < 0.01) and SCCs exclusively (OR = 2.12; 95%CI = 1.39–3.23, P < 0.01). SNP rs3217882 located in CCND2 was associated with exclusive BCC development (OR = 1.43, CI = 1.12–1.82, P < 0.01). The gene-based analysis suggested an association of PRKACG (protein kinase cAMP-activated catalytic subunit gamma) with any KC (P = 0.013). Conclusion: We conclude that variants located in genes in the SHH pathway may are involved in SCC as well as BCC development.</p

Combined analysis of keratinocyte cancers identifies novel genome-wide loci

The keratinocyte cancers (KC) basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are the most common cancers in fair-skinned people. KC treatment represents the second highest cancer healthcare expenditure in Australia. Increasing our understanding of the genetic architecture of KC may provide new avenues for prevention and treatment.We first conducted a series of Genome-wide association studies (GWAS) of KC across three European ancestry datasets from Australia, Europe and USA, and used linkage disequilibrium (LD) Score regression (LDSC) to estimate their pairwise genetic correlations. We employed a multiple-trait approach to map genes across the combined set of KC GWAS (total N = 47,742 cases, 634,413 controls). We also performed meta-analyses of BCC and SCC separately to identify trait specific loci.We found substantial genetic correlations (generally 0.5-1) between BCC and SCC suggesting overlapping genetic risk variants. The multiple trait combined KC GWAS identified 63 independent genome-wide significant loci, 29 of which were novel. Individual separate meta-analyses of BCC and SCC identified an additional 13 novel loci not found in the combined KC analysis. Three new loci were implicated using gene-based tests. New loci included common variants in BRCA2 (distinct to known rare high penetrance cancer risk variants), and in CTLA4, a target of immunotherapy in melanoma.We found shared and trait specific genetic contributions to BCC and SCC. Considering both, we identified a total of 79 independent risk loci, 45 of which are novel

Genetically determined risk of keratinocyte carcinoma and risk of other cancers

Background: Epidemiological studies have consistently documented an increased risk of developing primary non-cutaneous malignancies among people with a history of keratinocyte carcinoma (KC). However, the mechanisms underlying this association remain unclear. We conducted two separate analyses to test whether genetically predicted KC is related to the risk of developing cancers at other sites. Methods: In the first approach (one-sample), we calculated the polygenic risk scores (PRS) for KC using individual-level data in the UK Biobank (n = 394 306) and QSkin cohort (n = 16 896). The association between the KC PRS and each cancer site was assessed using logistic regression. In the secondary (two-sample) approach, we used genome-wide association study (GWAS) summary statistics identified from the most recent GWAS meta-Analysis of KC and obtained GWAS data for each cancer site from the UK-Biobank participants only. We used inverse-variance-weighted methods to estimate risks across all genetic variants. Results: Using the one-sample approach, we found that the risks of cancer at other sites increased monotonically with KC PRS quartiles, with an odds ratio (OR) of 1.16, 95% confidence interval (CI): 1.13-1.19 for those in KC PRS quartile 4 compared with those in quartile 1. In the two-sample approach, the pooled risk of developing other cancers was statistically significantly elevated, with an OR of 1.05, 95% CI: 1.03-1.07 per doubling in the odds of KC. We observed similar trends of increasing cancer risk with increasing KC PRS in the QSkin cohort. Conclusion: Two different genetic approaches provide compelling evidence that an instrumental variable for KC constructed from genetic variants predicts the risk of cancers at other sites. </p

A comprehensive re-assessment of the association between vitamin D and cancer susceptibility using Mendelian randomization

Previous Mendelian randomization (MR) studies on 25-hydroxyvitamin D (25(OH)D) and cancer have typically adopted a handful of variants and found no relationship between 25(OH)D and cancer; however, issues of horizontal pleiotropy cannot be reliably addressed. Using a larger set of variants associated with 25(OH)D (74 SNPs, up from 6 previously), we perform a unified MR analysis to re-evaluate the relationship between 25(OH)D and ten cancers. Our findings are broadly consistent with previous MR studies indicating no relationship, apart from ovarian cancers (OR 0.89; 95% C.I: 0.82 to 0.96 per 1 SD change in 25(OH)D concentration) and basal cell carcinoma (OR 1.16; 95% C.I.: 1.04 to 1.28). However, after adjustment for pigmentation related variables in a multivariable MR framework, the BCC findings were attenuated. Here we report that lower 25(OH)D is unlikely to be a causal risk factor for most cancers, with our study providing more precise confidence intervals than previously possible.</p