The Genetics of Cognitively Healthy Centenarians

The overall objective of this thesis was to investigate the genetic factors underlying extreme human longevity and the escape of Alzheimer’s disease, for which we explore the genetic architecture of the cognitively healthy centenarians from the 100-plus Study. In the first part of the thesis, we focus on the comparison of the cognitively healthy centenarians with young AD patients and population controls in the context of Alzheimer’s disease and human longevity. In chapter 2, we exploited extreme phenotypes in the genetic research of AD by comparing extreme controls and young AD cases in a case-control study of AD. We report that cognitively healthy centenarians have a lower frequency of genetic variants associated with increased AD risk compared to the general population, and a higher frequency of protective genetic variants. In chapter 3, we investigated the molecular pathways that are known to play a role in AD pathogenesis and their association with the resilience against AD. In this study, we combined the effect of multiple variants together into polygenic risk scores (PRS) and pathway- specific polygenic risk scores, which incorporate the effect of multiple genetic variants acting on the same molecular pathway. We report that cognitively healthy centenarians have the lowest PRS and pathway-specific PRS for all major AD-associated pathways. Moreover, only the PRS of immune system and endocytosis pathways significantly influenced the resilience against AD, even after excluding APOE variants. In chapter 4, we attempted to disentangle the effect on longevity from the effect on AD risk of the genetic variants that are associated with AD. We found that most genetic variants that increase the risk of AD were associated with lower odds of longevity. Based on our analysis, most AD-associated variants negatively affect longevity through their increased risk of AD. However, a subset of variants preferentially involved in immune-related processes seemed to affect not only AD but also other age-related diseases, such that the cumulative effect on longevity was larger than the effect on AD alone. In chapter 5, we focused on human longevity and we constructed a polygenic risk score (PRS) that associated with becoming a cognitively healthy centenarians and independently with survival. This PRS included 330 genetic variants, did not include APOE variants, associated with up to 4-years longer survival, and showed functional enrichment for hallmarks of longevity. In the second part of the thesis, we present the contribution of the cognitively healthy centenarians from the 100-plus Study to large, collaborative GWAS of AD and longevity. In chapter 6, we participated to one of the largest GWAS of AD. This collaborative effort led to the discovery of six additional genetic variants associated with AD. Furthermore, we add on the growing literature showing the applicability of polygenic risk score (PRS) of AD in order to stratify patients and to identify those at highest risk for the disease. In chapter 7, we collaborated on the largest GWAS of longevity. We introduced a new, unbiased, method to identify cases and controls based on country- and sex-specific survival percentiles. In addition to APOE variants, we found a novel association near GPR78 gene, and through genetic correlation and gene expression analyses, we showed a marked overlap between the genetics of diseases and the genetics of longevity. In chapter 8, we present snpXplorer, a tool freely available to the scientific community to explore summary statistics of genetic studies, compare levels of association between different traits, and functionally annotate sets of genetic variants

Analysis of Helicopter Activities in Forest Fire-Fighting

In Southern European countries wildfires are the most natural threat to forests and wooded areas. Over the last decade, public and scientific debates on forest fire management have increased. Helicopters and airtankers are extremely effective fire suppression means, but they are also very expensive. Studies on the improved performance of suppression for the enhancement of firefighting organization are still needed. Consequently to make a plan for the distribution of financial resources to be divided between fire suppression and fire prevention actions in terms of fuel management is not possible. The aim of this study is to compare the helicopter’s forest fire-fighting activity in Tuscany (central Italy) over two periods: between 1998–2000 and 2001–2005 when five and ten helicopters were respectively assigned. For both periods (1998–2000 and 2001–2005) the following were analyzed: the number of forest fires and the burned area with or without helicopter intervention and the position of the helicopter bases in relation to the fire. The results showed that a fleet of 10 helicopters is oversized, in relation to the fire regime of Tuscany, suggesting the need to evaluate a reduction in the fleet. Financial resources may be thus made available for more profitable fire prevention activities, such as, active fuel management. The results also showed where there is the need to improve the helicopter efficiency via the re–management as regards the positioning of their bases

XIAP inhibitors induce differentiation and impair clonogenic capacity of acute myeloid leukemia stem cells.

Acute myeloid leukemia (AML) is a neoplasia characterized by the rapid expansion of immature myeloid blasts in the bone marrow, and marked by poor prognosis and frequent relapse. As such, new therapeutic approaches are required for remission induction and prevention of relapse. Due to the higher chemotherapy sensitivity and limited life span of more differentiated AML blasts, differentiation-based therapies are a promising therapeutic approach. Based on public available gene expression profiles, a myeloid-specific differentiation-associated gene expression pattern was defined as the therapeutic target. A XIAP inhibitor (Dequalinium chloride, DQA) was identified in an in silico screening searching for small molecules that induce similar gene expression regulation. Treatment with DQA, similarly to Embelin (another XIAP inhibitor), induced cytotoxicity and differentiation in AML. XIAP inhibition differentially impaired cell viability of the most primitive AML blasts and reduced clonogenic capacity of AML cells, sparing healthy mature blood and hematopoietic stem cells. Taken together, these results suggest that XIAP constitutes a potential target for AML treatment and support the evaluation of XIAP inhibitors in clinical trials

A meta-analysis of genome-wide association studies identifies multiple longevity genes

Publisher's version (útgefin grein).Human longevity is heritable, but genome-wide association (GWA) studies have had limited success. Here, we perform two meta-analyses of GWA studies of a rigorous longevity phenotype definition including 11,262/3484 cases surviving at or beyond the age corresponding to the 90th/99th survival percentile, respectively, and 25,483 controls whose age at death or at last contact was at or below the age corresponding to the 60th survival percentile. Consistent with previous reports, rs429358 (apolipoprotein E (ApoE) ε4) is associated with lower odds of surviving to the 90th and 99th percentile age, while rs7412 (ApoE ε2) shows the opposite. Moreover, rs7676745, located near GPR78, associates with lower odds of surviving to the 90th percentile age. Gene-level association analysis reveals a role for tissue-specific expression of multiple genes in longevity. Finally, genetic correlation of the longevity GWA results with that of several disease-related phenotypes points to a shared genetic architecture between health and longevity.Alexander von Humboldt-StiftungPeer Reviewe

A meta-analysis of genome-wide association studies identifies multiple longevity genes

Human longevity is heritable, but genome-wide association (GWA) studies have had limited success. Here, we perform two meta-analyses of GWA studies of a rigorous longevity phenotype definition including 11,262/3484 cases surviving at or beyond the age corresponding to the 90th/99th survival percentile, respectively, and 25,483 controls whose age at death or at last contact was at or below the age corresponding to the 60th survival percentile. Consistent with previous reports, rs429358 (apolipoprotein E (ApoE) ε4) is associated with lower odds of surviving to the 90th and 99th percentile age, while rs7412 (ApoE ε2) shows the opposite. Moreover, rs7676745, located near GPR78, associates with lower odds of surviving to the 90th percentile age. Gene-level association analysis reveals a role for tissue-specific expression of multiple genes in longevity. Finally, genetic correlation of the longevity GWA results with that of several disease-related phenotypes points to a shared genetic architecture between health and longevity

Common variants in Alzheimer's disease: Novel association of six genetic variants with AD and risk stratification by polygenic risk scores

BACKGROUND: Disentangling the genetic constellation underlying Alzheimer's disease (AD) is important. Doing so allows us to identify biological pathways underlying AD, point towards novel drug targets and use the variants for individualised risk predictions in disease modifying or prevention trials. In the present work we report on the largest genome-wide association study (GWAS) for AD risk to date and show the combined utility of proven AD loci for precision medicine using polygenic risk scores (PRS). METHODS: Three sets of summary statistics were included in our meta-GWAS of AD: an Spanish case-control study (GR@ACE/DEGESCO study, n = 12,386), the case-control study of International Genomics of Alzheimer project (IGAP, n = 82,771) and the UK Biobank (UKB) AD-by-proxy case-control study (n=314,278). Using these resources, we performed a fixed-effects inverse-variance-weighted meta-analysis. Detected loci were confirmed in a replication study of 19,089 AD cases and 39,101 controls from 16 European-ancestry cohorts not previously used. We constructed a weighted PRS based on the 39 AD variants. PRS were generated by multiplying the genotype dosage of each risk allele for each variant by its respective weight, and then summing across all variants. We first validated it for AD in independent data (assessing effects of sub-threshold signal, diagnostic certainty, age at onset and sex) and tested its effect on risk (odds for disease) and age at onset in the GR@ACE/DEGESCO study. FINDINGS: Using our meta-GWAS approach and follow-up analysis, we identified novel genome-wide significant associations of six genetic variants with AD risk (rs72835061-CHRNE, rs2154481-APP, rs876461-PRKD3/NDUFAF7, rs3935877-PLCG2 and two missense variants: rs34173062/rs34674752 in SHARPIN gene) and confirmed a stop codon mutation in the IL34 gene increasing the risk of AD (IL34-Tyr213Ter), and two other variants in PLCG2 and HS3ST1 regions. This brings the total number of genetic variants associated with AD to 39 (excluding APOE). The PRS based on these variants was associated with AD in an independent clinical AD-case control dataset (OR=1.30, per 1-SD increase in the PRS, 95%CI 1.18-1.44, p = 1.1x10-7), a similar effect to that in the GR@ACE/DEGESCO (OR=1.27, 95%CI 1.23-1.32, p = 7.4x10-39). We then explored the combined effects of these 39 variants in a PRS for AD risk and age-at-onset stratification in GR@ACE/DEGESCO. Excluding APOE, we observed a gradual risk increase over the 2% tiles; when comparing the extremes, those with the 2% highest risk had a 2.98-fold (95% CI 2.12-4.18, p = 3.2x10-10) increased risk compared to those with the 2% lowest risk (p = 5.9x10-10). Using the PRS we identified APOE ε33 carriers with a similar risk as APOE ε4 heterozygotes carriers, as well as APOE ε4 heterozygote carriers with a similar risk as APOE ε4 homozygote. Considering age at onset; there was a 9-year difference between median onset of AD the lowest risk group and the highest risk group (82 vs 73 years; p = 1.6x10-6); a 4-year median onset difference (81 vs 77 years; p = 6.9x10-5) within APOE ε4 heterozygotes and a 5.5-year median onset difference (78.5 vs 73 years; p = 4.6x10-5) within APOE ε4 carriers. INTERPRETATION: We identified six novel genetic variants associated with AD-risk, among which one common APP variant. A PRS of all genetic loci reported to date could be a robust tool to predict the risk and age at onset of AD, beyond APOE alone. These properties make PRS instrumental in selecting individuals at risk in order to apply preventative strategies and might have potential use in diagnostic work-up

The Effect of Alzheimer’s Disease-Associated Genetic Variants on Longevity

Human longevity is influenced by the genetic risk of age-related diseases. As Alzheimer’s disease (AD) represents a common condition at old age, an interplay between genetic factors affecting AD and longevity is expected. We explored this interplay by studying the prevalence of AD-associated single-nucleotide-polymorphisms (SNPs) in cognitively healthy centenarians, and replicated findings in a parental-longevity GWAS. We found that 28/38 SNPs that increased AD-risk also associated with lower odds of longevity. For each SNP, we express the imbalance between AD- and longevity-risk as an effect-size distribution. Based on these distributions, we grouped the SNPs in three groups: 17 SNPs increased AD-risk more than they decreased longevity-risk, and were enriched for β-amyloid metabolism and immune signaling; 11 variants reported a larger longevity-effect compared to their AD-effect, were enriched for endocytosis/immune-signaling, and were previously associated with other age-related diseases. Unexpectedly, 10 variants associated with an increased risk of AD and higher odds of longevity. Altogether, we show that different AD-associated SNPs have different effects on longevity, including SNPs that may confer general neuro-protective functions against AD and other age-related diseases

Centenarian controls increase variant effect sizes by an average twofold in an extreme case-extreme control analysis of Alzheimer's disease

The detection of genetic loci associated with Alzheimer’s disease (AD) requires large numbers of cases and controls because variant effect sizes are mostly small. We hypothesized that variant effect sizes should increase when individuals who represent the extreme ends of a disease spectrum are considered, as their genomes are assumed to be maximally enriched or depleted with disease-associated genetic variants. We used 1,073 extensively phenotyped AD cases with relatively young age at onset as extreme cases (66.3 ± 7.9 years), 1,664 age-matched controls (66.0 ± 6.5 years) and 255 cognitively healthy centenarians as extreme controls (101.4 ± 1.3 years). We estimated the effect size of 29 variants that were previously associated with AD in genome-wide association studies. Comparing extreme AD cases with centenarian controls increased the variant effect size relative to published effect sizes by on average 1.90-fold (SE = 0.29, p = 9.0 × 10−4). The effect size increase was largest for the rare high-impact TREM2 (R74H) variant (6.5-fold), and significant for variants in/near ECHDC3 (4.6-fold), SLC24A4-RIN3 (4.5-fold), NME8 (3.8-fold), PLCG2 (3.3-fold), APOE-ε2 (2.2-fold), and APOE-ε4 (twofold). Comparing extreme phenotypes enabled us to replicate the AD association for 10 variants (p < 0.05) in relatively small samples. The increase in effect sizes depended mainly on using centenarians as extreme controls: the average variant effect size was not increased in a comparison of extreme AD cases and age-matched controls (0.94-fold, p = 6.8 × 10−1), suggesting that on average the tested genetic variants did not explain the extremity of the AD cases. Concluding, using centenarians as extreme controls in AD case–control studies boosts the variant effect size by on average twofold, allowing the replication of disease-association in relatively small samples

XIAP inhibitors induce differentiation and impair clonogenic capacity of acute myeloid leukemia stem cells.

Acute myeloid leukemia (AML) is a neoplasia characterized by the rapid expansion of immature myeloid blasts in the bone marrow, and marked by poor prognosis and frequent relapse. As such, new therapeutic approaches are required for remission induction and prevention of relapse. Due to the higher chemotherapy sensitivity and limited life span of more differentiated AML blasts, differentiation-based therapies are a promising therapeutic approach. Based on public available gene expression profiles, a myeloid-specific differentiation-associated gene expression pattern was defined as the therapeutic target. A XIAP inhibitor (Dequalinium chloride, DQA) was identified in an in silico screening searching for small molecules that induce similar gene expression regulation. Treatment with DQA, similarly to Embelin (another XIAP inhibitor), induced cytotoxicity and differentiation in AML. XIAP inhibition differentially impaired cell viability of the most primitive AML blasts and reduced clonogenic capacity of AML cells, sparing healthy mature blood and hematopoietic stem cells. Taken together, these results suggest that XIAP constitutes a potential target for AML treatment and support the evaluation of XIAP inhibitors in clinical trials