Citations

Abstract Background: Alterations in innate immunity are pathologically associated with and genetically implicated in Alzheimer’s disease (AD). In the whole exome sequence (WES) dataset generated by the Alzheimer’s Disease Sequencing Project (ADSP), only the previously identified p.R47H variant in the innate immunity gene, TREM2, shows study-wide association with risk of AD. Using a novel approach, we searched the ADSP WES data to identify additional immune pathway genes with deleterious variants that, like TREM2.pR47H, show strong association with AD. Methods: Using polygenic risk scores (PRS) to analyze association with AD, we evaluated deleterious variants (CADD Phred-scaled score > 20) with a minor allele count of 20 or more in 228 genes comprising an immune co-expression network containing TREM2 (CENTREM2). A significant polygenic component composed of deleterious stop-gain and non-synonymous variants was identified, and false discovery rates were determined for the variants in this component. In genes harboring a significant variant, PRS for all variants in the genes were then analyzed. Results: The PRS for the 182 deleterious variants in CENTREM2 showed significant association with AD that was driven by 142 deleterious variants (136 non-synonymous, 6 stop-gain). In the 142 variant polygenic component, four variants had significant AD risk association: TREM2.pR47H, two deleterious stop-gain variants (FCGR1A.pR92X, and LILRB1.pY331X) in novel AD genes and 1 non-synonymous variant (ATP8B4.pG395S). Remarkably, PRS for the 36 additional variants in these four genes also showed significant association with AD. The PRS for all 40 variants in the 4 genes, showed significant, replicable association with AD and 3 additional variants in this polygenic component had significant false discovery rates: ATP8B4.pR1059Q, LILRB1.pP7P, and LILRB1.pY327Y. Conclusions: Here, we identify 3 immune pathway genes (ATP8B4, LILRB1, and FCGR1A) with a variant that associates with AD. Like TREM2.pR47H, each of the variants has a minor allele frequency less than 1% and is a deleterious, protein altering variant with a strong effect that increases or decreases (LILRB1.pY331X) risk of AD. Additional variants in these genes also alter risk of AD. The variants identified here are ideally suited for studies aimed at understanding how the innate immune system may be modulated to alter risk of AD.

Abstract Purpose: To identify molecular predictors of grade 3/4 neutropenic or leukopenic events (NLE) after chemotherapy using a genome-wide association study (GWAS). Experimental Design: A GWAS was performed on patients in the phase III chemotherapy study SUCCESS-A (n = 3,322). Genotyping was done using the Illumina HumanOmniExpress-12v1 array. Findings were functionally validated with cell culture models and the genotypes and gene expression of possible causative genes were correlated with clinical treatment response and prognostic outcomes. Results: One locus on chromosome 16 (rs4784750; NLRC5; P = 1.56E-8) and another locus on chromosome 13 (rs16972207; TNFSF13B; P = 3.42E-8) were identified at a genome-wide significance level. Functional validation revealed that expression of these two genes is altered by genotype-dependent and chemotherapy-dependent activity of two transcription factors. Genotypes also showed an association with disease-free survival in patients with an NLE. Conclusions: Two loci in NLRC5 and TNFSF13B are associated with NLEs. The involvement of the MHC I regulator NLRC5 implies the possible involvement of immuno-oncological pathways.

Abstract Work history is associated with long term health outcomes We hypothesize that characteristics of the first work experience, such as age at first job and length of work (hereafter job) are associated with future risk of hospitalization. We further hypothesize that the length of work will be associated with hospitalization. We conducted a survey of adults >60 years using a nested case-control approach within the Mayo Clinic Biobank. We collected job related variables including age at job start, reason for ending, and length of time. To test associations between each variable and hospitalization, we used age and gender adjusted logistic regression models. Our study included 4,024 subjects: 1,801 cases and 2223 controls. The mean age at time of match was 77.3 years (SD 7.2 years) with 49.2% males. Older age at the first full-time job was associated with lower chance of hospitalization later in life (OR=0.81 [0.67, 0.97] for those who started the job over 22 compared to those started at 18 or less). Cases were more likely to have stopped working because of illness (OR=2.04 [95% CI 1.29,3.27]). Cases were less likely to have stopped working because of retirement (OR=0.82 [95% CI: 0.72, 0.93]). We found cases were employed with a slightly shorter time (20.5 yrs. (SD 16.6)) compared to controls (21.8 yrs. (SD 16.3)) (p=0.005). Cases started work earlier and stopped work more frequently because of illness/disability compared to controls. This could reflect educational attainment in controls. This study highlights work history as potential predictor of future hospitalization.

Introduction: Phenome-wide association studies (PheWAS) using electronic medical record (EMR)-linked biobanks have been used not only to identify and replicate known associations of genetic variants with disease phenotypes but have also resulted in the discovery of potentially novel genotype-phenotype relationships. The natriuretic peptide (NP) system plays an important role in a broad range of disease processes including cardiovascular and inflammatory diseases. We hypothesized that performing a PheWAS using previously known functional genetic variants of the NP system may result in novel disease associations that could provide mechanistic insights in an unbiased manner. Methods: We scanned for associations between 9 single-nucleotide polymorphisms (SNPs) in the NP system and 27 EMR-derived chronic disease phenotypes in 3,025 individuals participating in a case-control study of peripheral arterial disease. The EMR phenotypes were identified using two or more ICD-9-CM diagnosis codes based on the AHRQ Clinical Classifications Software (CCS). The relationship of SNPs and phenotypes were modeled using logistic regression adjusting for gender. Results: We identified rs5065, a SNP located in the stop codon of exon 3 of the NPPA gene, to be the strongest associated SNP with rheumatoid arthritis (RA) (OR=0.78, p=0.0008, q-value=0.11). The SNP leads to the extension of atrial natriuretic peptide (ANP) by 2 additional arginines at the C terminus. Cardiovascular disease is known to be the leading cause of death in patients with RA and ANP plays an important immunomodulatory role by inhibiting inducible nitric oxide synthase, reducing TNF-α production and attenuating prostaglandin E2 production in macrophages. Circulating NPs have been used to screen for occult cardiac disease and are associated with mortality in RA. This study demonstrates for the first time the importance of the relationship between genetic variation in the NP system and RA. Conclusions: PheWAS was successfully used as a tool to identify a novel association of functional genetic variation in the NPPA gene with RA. The observation is hypothesis generating and further replication studies are required to determine the role of rs5065 in cardiovascular outcomes of RA.

Thiopurine drugs such as 6‐mercaptopurine (6‐MP) and 6‐thioguanine (6‐TG) are effective immunosuppressants and antineoplastic agents. We used a genome‐wide approach to identify genes that might contribute to individual variation in thiopurine response. Basal gene expression profiles, genome‐wide SNP data, and 6‐MP and 6‐TG Cell growth inhibition (GI50) values were generated for 200 Coriell Institute “Human Variation Panel” lymphoblastoid cell lines. Gene expression and genome‐wide SNPs were correlated with GI50 values to identify candidate genes that might contribute to thiopurine response. We identified 104 expression probes and 161 SNPs, as well as 315 gene probes and 579 SNPs that correlated significantly with GI50 values for 6‐MP and 6‐TG, respectively (P<10 −5 and 10 −6 , respectively). Three genes, CD83 , TXNDC13 and SNAP23 , contained SNPs that contributed significantly to both 6‐MP and 6‐TG cytotoxicity and were also significantly associated with expression levels (P<10 −4 ), suggesting a “three‐way model” involving genotype, gene expression and cytotoxicity. GBP5 , a gene with an expression level that correlated negatively with 6‐MP and 6‐TG GI50 values, sensitized leukemia cells when overexpressed. Functional studies of the remainder of the candidate genes are being performed. These results may enhance our ability to predict thiopurine response phenotypes. NIH GM28157.

Objectives Betaine‐homocysteine methyltransferase (BHMT) catalyzes the remethylation of homocysteine. BHMT in the human liver is responsible for up to 25% of homocysteine metabolism. Knowledge of the relationship between genetic polymorphisms and BHMT phenotypes could enhance our understanding of the role of this reaction in drug metabolism. Methods Levels of BHMT enzyme activity and immunoreactive protein were measured in 268 human liver biopsies. Twelve tag BHMT SNPs from our own gene resequencing and HapMap data were used to genotype DNA from these samples. Genotype‐phenotype association analysis was then performed. BHMT enzyme activity averaged 0.077 ± 0.028 units/μg, with a 12 fold variation. Results BHMT protein levels averaged 6.9 ± 3.3 units/μg, with a 50‐fold variation. Three SNPs (rs41272270, rs16876512, and rs6875201), located 28kb upstream, in the 5′‐UTR and in intron 1 of BHMT , respectively, were significantly correlated with both phenotypes (p<10 −8 for enzyme activity and p<10 −5 for protein level). rs41272270 was associated with altered protein binding during electrophoresis mobility shift assay. Conclusions Three tag SNPs were significantly associated with human hepatic BHMT enzyme activity and immunoreactive protein. These observations may help us understand the regulation of BHMT in the human liver and its role in drug metabolism. Supported by NIH U01 GM61388, R01 GM28157, R01 CA132780.

AbstractAimsLong‐term lithium therapy (LTLT) has been associated with kidney insufficiency in bipolar disorder (BD). We aimed to investigate the risk factors of chronic kidney disease (CKD) development and progression among BD patients receiving LTLT.MethodsWe included adult patients with BD on LTLT (≥1 year) who were enrolled in the Mayo Clinic Bipolar Biobank, Rochester, Minnesota. We reviewed electronic medical records to extract information related to lithium therapy and kidney‐related data to assess changes in the estimated glomerular filtration rate (eGFR). CKD severity was assessed based on eGFR.ResultsAmong 154 patients who received LTLT, 41 patients (27%) developed CKD, of whom 20 (49%) patients continued lithium (continuers) and 19 (46%) discontinued it (discontinuers). The median time to stage 3 CKD development was 21.7 years from the start of Li treatment. Type‐2 diabetes mellitus and benzodiazepine use were independent predictors for CKD development in the survival analysis, after controlling for age. The subsequent CKD progression rate did not differ between continuers and discontinuers (mean GFR 48.6 vs. 44.1, p = 0.13) at the end of follow‐up duration (mean duration: 3.5 ± 4.4 years for continuers and 4.9 ± 5.3 years for discontinuers).ConclusionCKD was observed in one fourth of patients with BD receiving LTLT. There was no significant difference in the progression of CKD among Li continuers versus discontinuers, at the mean follow‐up duration of 4.2 years, after the CKD diagnosis. Progression of CKD could be influenced by existing comorbidities and may not necessarily be due to lithium alone.

Abstract Incidence rates for endometrial cancer (EC) are rising, particularly in postmenopausal and obese women. Our previous work has showed that the uterine and vaginal microbiome distinguishes patients with EC from those without. We now examine the impact of patient factors (such as menopause status, body mass index, and vaginal pH) in the microbiome in the absence of EC and how these might contribute to the microbiome signature in EC. We find that each factor independently alters the microbiome and identified postmenopausal status as the main driver of a polymicrobial network associated with EC (ECbiome). Of the 17 taxa we found enriched in EC patients, 8 were also enriched by postmenopause. Because postmenopausal status is a main risk factor for endometrial cancer, this system can be thought of as an ecological succession towards a disease state. Organisms within the ECbiome have been previously identified as polymicrobial associations in chronic soft tissue infections, ulcers, morbid obesity, and bacterial vaginosis. This suggests that this microbiome network is likely involved in mechanisms of host disease. Within the ECbiome, Porphyromonas somerae stands out because of its very significant and specific association with EC (p = 5.73E-6; Q = 0.009). We had previously identified this species as significantly associated with EC, and hereby validate that finding. Because the association of P. somerae with EC was robust and specific enough to potentially be considered as a biomarker for the disease (AUC 76.7%, CI: 67.9-85.5%), we developed a P. somerae-specific qPCR assay to detect this species in vaginal swabs. This becomes of particular interest because the lower tract and uterine microbiome are significantly correlated in these patients (p = 0.01), indicating that the vaginal microbiome can be used as a proxy for the uterine environment in EC. In agreement with the 16S rRNA gene sequencing data, P. somerae was detected significantly more frequently in vaginal swabs of patients with EC than those without EC (p = 3.02E-7). Overall, the test achieved a sensitivity of 74% and specificity of 63%, with a positive predictive value of 0.86 for obese and postmenopausal patients. In summary, we identify Porphyromas somerae presence as the most predictive microbial marker of EC, and we confirm this using targeted qPCR, which could be of use in detecting EC in high-risk, asymptomatic women. Given the established pathogenic behavior of P.somerae, we have also explored mechanistic routes through which this microbe and associated consortia may be involved in the mechanisms of disease. Citation Format: Marina Walther-Antonio, Dana Walsh, Alexis Hokenstad, Jun Chen, Jayeun Sung, Gregory Jenkins, Nicholas Chia, Heidi Nelson, Andrea Mariani. Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome): Putative role of Porphyromonas somerae in the disease [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr PR09.