Methods
Genetic associations with lean mass
As genetic proxies for lean mass, we selected single nucleotide polymorphisms (SNPs, used interchangeably with genetic variants) that were associated in a genome wide association study (GWAS) with appendicular lean mass at genome wide significance (P<5×10-8).11 This GWAS used phenotypic and genetic data from 450 243 participants in the UK Biobank cohort (mean age 57 years).11 12 Appendicular lean mass more accurately reflects the effects of lean mass than whole body lean mass, which includes smooth and cardiac muscle.11 Fat free mass (used interchangeably with lean mass) was determined with bioimpedance, measured by the Tanita BC418MA body composition analyser, with a standardised UK Biobank protocol.12
Appendicular lean mass was calculated as the sum of lean mass in the arms and legs. Appendicular lean mass was residualised for age, age2, UK Biobank genotyping array, top 10 principal components of ancestry, UK Biobank assessment centre, and appendicular fat mass (the sum of fat mass in all four extremities). Adjustment for the principal components of ancestry minimises confounding of genetic associations by ancestry, which is a key assumption of mendelian randomisation. These residuals were normalised into normalised quantiles of a standard normal distribution and therefore the effects of SNPs are reported in standard deviation units. The measure of appendicular lean mass derived from bioimpedance was validated in a subset of UK Biobank individuals with measurements of body composition by dual energy x ray absorptiometry (DEXA).11 Moreover, the association between the variants and appendicular lean mass was consistent across all age groups included in the analysis (38-45, 46-50, 51-55, 56-60, 61-65, and 66-74 years).11
In secondary analyses, we used genetic variants associated with trunk lean mass (n=447 990) and whole body lean mass (n=448 322) in GWAS performed in the UK Biobank. These GWAS were adjusted for age, age2, sex, age×sex, age2×sex, and the top 20 principal components of ancestry. In these analyses, we also performed multivariable mendelian randomisation analyses adjusting, respectively, for trunk fat mass (n=448 068) and whole body fat mass (n=447 626). All SNP effects are in standard deviation units.
Genetic associations with Alzheimer’s disease, cognitive performance, and hippocampal volume
Recent GWAS of Alzheimer’s disease13 included proxy patients that were identified based on a family history of dementia, and so were likely to include patients with non-Alzheimer’s disease dementia. To ensure the relevance of our results to Alzheimer’s disease, we restricted analysis to the primary analytic outcome of clinically diagnosed late onset Alzheimer’s disease. We obtained genetic associations with Alzheimer’s disease from the first stage of the 2019 International Genomics of Alzheimer’s Project meta-analysis of GWAS of Alzheimer’s disease.14 All participants were of European ancestry. Genetic associations were adjusted for age, sex, and principal components of ancestry.
For replication, we obtained genetic associations with Alzheimer’s disease from release six of the FinnGen consortium.15 FinnGen is a Finnish cohort that combines health record data with genomic data. We used the curated G6_AD_WIDE phenotype, which combines the ICD-10 (international classification of diseases, 10th revision) codes (F00 and G30) and ICD-9 (international classification of diseases, ninth revision) codes (3310) with the purchase history of drug treatments for Alzheimer’s disease (including donepezil, memantine, and rivastigmine). These drug treatments are not exclusively prescribed to patients with Alzheimer’s disease, and so we anticipated that some patients were misclassified. ICD codes were obtained from inpatient and outpatient settings. No sample overlap was present between the risk factor sample (UK Biobank) and either of these cohorts of Alzheimer’s disease.
Genetic associations with cognitive tasks were obtained from the largest available meta-analysis of 14 GWAS of cognitive performance in individuals of European ancestry (n=269 867).16 Each cohort extracted a score representing a common latent g factor (or general intelligence) that contributes to multiple dimensions of cognition.17 18 Genetic associations with cognitive tasks are reported in standard deviation units. Genetic associations with hippocampal volume were obtained from the largest publicly available GWAS meta-analysis of hippocampal volume, defined by magnetic resonance imaging, that did not overlap with the UK Biobank (n=30 717, all individuals of European ancestry).19 Genetic associations were adjusted for intracranial volume (reported as mm3).
Selection of genetic proxies for lean mass
The mendelian randomisation method requires that genetic variants used as proxies are strongly associated with the risk factor of interest and are not in high linkage disequilibrium with one another. To select independent variants meeting these criteria, we first identified the set of genome wide significant (P<0.001) variants overlapping between the risk factor GWAS (eg, lean mass) and the respective outcome GWAS (eg, Alzheimer’s disease). We then clumped the variants within a 10 Mb window using a between-SNP r2<0.001 (the r2 value is a measure of the tendency for genetic variants to be inherited together; calculated using the 1000G European reference panel).20 We calculated the variance explained by the variants used to proxy appendicular lean mass.21 We also checked the appendicular lean mass variant list to ensure that no genetic proxies were present within the APOE gene region (Chr19:45,116,911-46,318,605).14 This variant selection process was used for all analyses.
Statistical analysis
Genetic associations between lean mass and Alzheimer’s disease were harmonised by aligning beta coefficients to the same effect allele.20 We used the random effects inverse variance weighted method as the primary mendelian randomisation approach. This method regresses the SNP-outcome association on the SNP-risk-factor association and weights the regression by the inverse of the standard error of the SNP-outcome association. The estimand is the effect of a standard deviation increase in lean mass on the risk of Alzheimer’s disease (or on standard deviation units of cognitive performance). All mendelian randomisation analyses were performed with the TwoSampleMR version 4.2.1.20 Online supplemental figure 1 shows a causal diagram illustrating the hypotheses for our analyses.
We performed several sensitivity analyses. The causal effect estimated in a mendelian randomisation analysis is unbiased if the effect of the genetic proxies on Alzheimer’s disease is mediated through lean mass and not through other causal pathways. To test this assumption of no horizontal pleiotropy, we performed sensitivity analyses that are more robust to the inclusion of pleiotropic variants including the following methods: weighted median,22 mendelian randomisation Egger,23 and penalised weighted median.24
To test for associations in the reverse direction, we performed mendelian randomisation analyses to test for the association between genetically proxied liability to Alzheimer’s disease14 and appendicular lean mass. The appendicular lean mass GWAS adjusted for appendicular fat mass, and the use of GWAS adjusted for heritable covariates that might introduce collider bias in a mendelian randomisation analysis.25 This bias can be overcome with multivariable mendelian randomisation rather than genetic associations adjusted for covariates.26 We therefore repeated the analyses with genetically predicted lean mass and trunk mass adjusted, respectively, for genetically predicted lean fat mass and trunk fat mass in multivariable mendelian randomisation analyses.27 This multivariable mendelian randomisation approach also allows estimation of the association between genetically proxied fat mass and Alzheimer’s disease adjusted for lean mass.
Genetic variants for use in multivariable mendelian randomisation were identified by pooling all genome wide significant SNPs for both risk factors, ordering by lowest P value, and clumping as described above. We used the regression based multivariable mendelian randomisation method which regresses the SNP-outcome associations on the two SNP-risk-factor associations, with the intercept fixed at zero with a random effects model.20 We also performed multivariable mendelian randomisation analyses adjusting for genetically proxied height with a dataset that did not overlap with the UK Biobank (n=253 288 participants of European ancestry).28 Finally, we compared associations between genetically proxied lean mass and Alzheimer’s disease with conventional epidemiological proxies for adiposity, such as body mass index (n=806 834 participants of European ancestry, 451 SNPs) and waist-hip ratio adjusted for body mass index (WHRadjBMI; n=694 649 participants of European ancestry, 258 SNPs).29
To examine whether the effect of lean mass on cognitive performance is mediated through Alzheimer’s disease, we performed multivariable mendelian randomisation analyses adjusting the lean mass effect for liability to Alzheimer’s disease. To examine whether the effect of lean mass on Alzheimer’s disease is mediated through cognitive performance, we performed multivariable mendelian randomisation analyses controlling the lean mass association for cognitive performance. Finally, in post hoc analyses, we tested whether coronary artery disease (132 variants30) could function as a putative mediator for the association between appendicular lean mass and risk of Alzheimer’s disease by first examining its association with Alzheimer’s disease. If this association was significant, we planned to perform multivariable mendelian randomisation analyses adjusting the association between appendicular lean mass and Alzheimer’s disease for effects of the proxies on the risk of coronary artery disease.
Patient and public involvement
Patients or members of the public were not involved in the design of the study, interpretation of the results, or drafting of the manuscript. We currently have no plans to share the results with research participants or public communities. Results will be disseminated through a press release.