Correction For Multiple Testing Research Articles

Risk Factors for Intracerebral Hemorrhage: Genome-Wide Association Study and Mendelian Randomization Analyses.

The genetic and nongenetic causes of intracerebral hemorrhage (ICH) remain obscure. The present study aimed to uncover the genetic and modifiable risk factors for ICH. We meta-analyzed genome-wide association study data from 3 European biobanks, involving 7605 ICH cases and 711 818 noncases, to identify the genomic loci linked to ICH. To uncover the potential causal associations of cardiometabolic and lifestyle factors with ICH, we performed Mendelian randomization analyses using genetic instruments identified in previous genome-wide association studies of the exposures and ICH data from the present genome-wide association study meta-analysis. We performed multivariable Mendelian randomization analyses to examine the independent associations of the identified risk factors with ICH and evaluate potential mediating pathways. We identified 1 ICH risk locus, located at the APOE genomic region. The lead variant in this locus was rs429358 (chr19:45411941), which was associated with an odds ratio of ICH of 1.17 (95% CI, 1.11-1.20; P=6.01×10-11) per C allele. Genetically predicted higher levels of body mass index, visceral adiposity, diastolic blood pressure, systolic blood pressure, and lifetime smoking index, as well as genetic liability to type 2 diabetes, were associated with higher odds of ICH after multiple testing corrections. Additionally, a genetic increase in waist-to-hip ratio and liability to smoking initiation were consistently associated with ICH, albeit at the nominal significance level (P<0.05). Multivariable Mendelian randomization analysis showed that the association between body mass index and ICH was attenuated on adjustment for type 2 diabetes and further that type 2 diabetes may be a mediator of the body mass index-ICH relationship. Our findings indicate that the APOE locus contributes to ICH genetic susceptibility in European populations. Excess adiposity, elevated blood pressure, type 2 diabetes, and smoking were identified as the chief modifiable cardiometabolic and lifestyle factors for ICH.

Genetically predicted systemic inflammation and the risk of atrial fibrillation: A bidirectional two-sample Mendelian randomization study

BackgroundSystemic inflammation has been proposed to be associated with the incidence of atrial fibrillation (AF), but whether it is a cause or a consequence of AF remains uncertain. We sought to explore the causal associations between systemic inflammation and AF using bidirectional Mendelian randomization (MR) analysis. MethodsIndependent genetic variants strongly associated with AF were selected as instrumental variables from the largest genome-wide association study (GWAS) with up to 1,030,836 individuals. Regarding inflammation traits, genetic associations with 41 inflammatory cytokines and 5 inflammatory biomarkers were obtained from their corresponding GWASs databases. Effect estimates were primarily evaluated using the inverse-variance weighted (IVW) method, supplemented by sensitivity analyses using MR-Egger, weighted median, and MR-PRESSO methods. ResultsIn our initial MR analyses, we observed suggestive associations of genetically predicted interleukin-17 (IL-17), interleukin-2 receptor subunit alpha (IL-2rα), and procalcitonin (PCT) with AF. One standard deviation (SD) increase in IL-17, IL-2rα, and PCT caused an increase in AF risk by 6.3 % (OR 1.063, 95 %CI 1.011–––1.118, p = 0.018), 4.9 % (OR 1.049, 95 %CI 1.007–––1.094, p = 0.023) and 3.4 % (OR 1.034, 95 %CI 1.005–––1.064, p = 0.022), respectively. Furthermore, our reverse MR analyses indicated that genetically predicted AF contributed to a suggestive increase in the levels of macrophage inflammatory protein-1β (MIP1β) (β 0.055, 95 %CI 0.006 to 0.103, p = 0.028), while a decrease in the levels of fibrinogen (Fbg) (β −0.091, 95 %CI −0.140 to −0.041, p < 0.001), which remained significant after multiple test correction. ConclusionsOur MR study identified several inflammatory biomarkers with suggestive causal associations regarding the upstream and downstream regulation of AF occurrence, offering new insights for therapeutic exploitation of AF. Further research is required to validate the underlying link between systemic inflammation and AF in larger cohorts.

Poor subjective sleep quality and trait impulsivity in patients with bipolar disorder.

Sleep disturbance and impulsivity are key components of mood vulnerability in bipolar disorder (BD), but few studies have assessed the association between these two symptoms among patients with BD. Forty-seven euthymic patients with bipolar I disorder (BDI) or bipolar II disorder (BDII) and 58 age- and sex-matched healthy controls were enrolled in this cross-sectional study. Trait impulsivity was measured using the Barratt Impulsiveness Scale Version 11 (BIS-11), which yielded 3 second-order factors: attention, motor, and non-planning. Subjective sleep quality was assessed using the self-reported Pittsburgh Sleep Quality Index (PSQI). General linear models (GLMs) were used to assess the associations between subjective poor sleep and trait impulsivity with multiple testing corrections. Patients with BD scored higher in BIS-11 and PSQI than healthy controls. PSQI total scores positively correlated with BIS-11 total scores, while sleep disturbance and daytime dysfunction were associated with attentional impulsiveness after controlling for covariates. Participants with higher PSQI total scores (>10) had higher scores in BIS-11 total, attention, and non-planning than those with low PSQI scores (≤5). These findings support the hypothesis that poor sleep quality might lead to impulsivity and add to the growing evidence that improving sleep quality may be a therapeutic target for patients with BD.

Plasma thrombin generation in the presence of TIX-5 may contribute significantly to a prediction model for major bleeding in patients on VKA anticoagulant therapy

IntroductionOral anticoagulant therapy comes at the cost of a significant bleeding risk. However, it is hard to predict which patients are at risk of major bleeding. Previously we found associations of Calibrated Automated Thrombinography (CAT) parameters obtained in the presence of TIX-5 (an inhibitor of the FV activation by FXa), and plasma levels of TFPIα, γ’-fibrinogen and soluble thrombomodulin with major bleeding in the BLEEDS cohort, a cohort especially powered to find new biomarkers of major bleeding during VKA therapy. MethodsTo determine and compare the predictive capability for major bleeding in the BLEEDS cohort of the above biomarkers, also in a combined model with clinical risk factors, we performed Univariable Prentice-weighted Cox regression analyses and Bayesian variable selection. ResultsThe highest predictive value among the laboratory measures were found for thrombin generation lagtime in the presence of TIX-5 (TIX-5 lagtime per 25% increase, hazard ratio (HR) 1.11, 95%CI 1.04–1.18, p=0.001) and full-length tissue factor pathway inhibitor (TFPIα) (per 25% increase HR 1.12, 95%CI 1.03–1.21, p=0.008), which remained significant after correction for multiple testing, and independently associated with major bleeding after Bayesian variable selection. Only the addition of TIX-5 lagtime to the clinical risk factors improved prediction of major bleeding significantly (p<0.001). ConclusionWe established predictive value of the lagtime of thrombin generation measured in the presence of TIX-5 for the risk of a major bleeding of patients on VKA therapy.

Plasma fatty acids and attention deficit hyperactivity disorder: a Mendelian randomization investigation.

Attention deficit hyperactivity disorder (ADHD) is the most common neurodevelopmental disorder of childhood, and pathogenesis is not fully understood. Observational studies suggest an association between fatty acids abnormalities and ADHD, but there are contradictions and differences between these findings. To address this uncertainty, we employed a two-sample bidirectional Mendelian Randomization (MR) analysis to investigate the causal relationship between fatty acids and ADHD. We conducted a two-sample Mendelian Randomization (MR) study, selecting single nucleotide polymorphisms (SNPs) highly correlated with fatty acid levels from the CHARGE Consortium as our instruments. The outcome data were sourced from the Psychiatric Genomics Consortium (PGC) dataset on ADHD, comprising 225,534 individuals, with 162,384 cases and 65,693 controls. Inverse variance weighting, MR-Egger, and weighted median methods were employed to estimate the causal relationship between fatty acids and ADHD. Cochran's Q-test was used to quantify heterogeneity of instrumental variables. Sensitivity analyses included MR-Egger intercept tests, leave-one-out analyses, and funnel plots. The MR analysis revealed no significant associations between genetically predicted levels of various saturated, monounsaturated, and polyunsaturated fatty acids (including omega-3 and omega-6) and ADHD risk in the CHARGE and PGC cohorts. Notably, an initial association with Dihomo-gamma-linolenic acid (DGLA) (OR = 1.009, p = 0.032 by IVW) did not persist after correction for multiple testing (adjusted p-value = 0.286). Sensitivity analysis supported our findings, indicating robustness. Moreover, there was a lack of evidence supporting a causal link from ADHD to fatty acids. While our study on the basis of genetic data does not provide evidence to support the causal role of fatty acids in ADHD, it does not preclude their potential involvement in reducing the risk of ADHD. Further research is needed to explore this possibility.

Self-perceived oral health and orofacial appearance in older adults - an 18-year follow-up study in Karlskrona, Sweden.

To analyze whether self-perceived oral health and orofacial appearance change with increasing age. This longitudinal study is based on data from a questionnaire used in the Swedish National Study of Aging and Care. The sample comprises 160 participants 60 years of age at baseline 2001-2003. The same participants were re-examined at 66-, 72-, and 78 years of age. To analyze whether perceptions of oral health and orofacial appearance changed with increasing age, Cochran's Q test was conducted. Statistical significance was considered at p ≤ 0.05, and the calculated value Q must be equal to or greater than the critical chi-square value (Q ≥ 7.82). Significance values have been adjusted for the Bonferroni correction for multiple tests. Self-perceived mouth dryness, both day (Q = 7.94) and night (Q = 23.41), increased over the 18-year follow-up. When divided by gender, significant differences were only seen for mouth dryness at nighttime. A decrease in sensitive teeth was perceived with increasing age, and an increase in self-perceived satisfaction with dental appearance, and a decrease in self-perceived problems with dental gaps between the ages of 60 and 78. These changes were, however, not statistically significant. Men experienced a higher proportion of discomfort with discolored teeth at age 78 than at 60 (Q = 9.09). Self-perceived oral health and orofacial appearance were relatively stable, with few changes over an 18-year follow-up.

Abstract PS10-04: The Landscape of Somatic Genetic Alterations in Breast Cancers from Carriers of Germline Pathogenic Variants in DNA-repair Genes

Abstract Background: Hereditary breast cancer in carriers of germline pathogenic or likely pathogenic variants (PVs) in ATM, BRCA1, BRCA2, CHEK2, and PALB2 have unique clinicopathological characteristics compared to sporadic breast cancer. However, very little is known about the underlying differences in somatic genetic alterations between hereditary and sporadic breast cancer. Methods: The study included 7,533 individuals with breast cancer subjected to Tempus xT tumor-normal matched sequencing (596-648 genes). The frequencies of the somatic genetic alterations in each gene were compared separately between tumors arising in individuals with incidental germline PVs (gATM, gBRCA1, gBRCA2, gCHEK2, gPALB2) and sporadic breast tumors. Sporadic tumors were identified as individuals with no detected incidental germline PVs in these 5 genes. Comparisons were made by either Pearson’s Chi-squared or Fisher’s exact test, with false discovery rate (FDR) correction for multiple testing. Breast cancer subtype was determined based on the record of IHC positivity for ER, PR, or HER2. Detection of ERBB2 (HER2) gene amplifications via DNA sequencing was also used to classify samples as HER2+ in the absence of available IHC data. Results: The median age at breast cancer diagnosis for the cohort was 56 years. More than two-thirds of the patients were White (73%) while 14% identified as Black or African American. The overall frequency of incidental germline PVs in each gene was 0.8% for gATM, 1.4% for gBRCA1, 2.1% for gBRCA2, 1.0% for CHEK2, and 0.7% for PALB2. A total of 3,648 (48.4%) tumors were ER+/PR+/HER2-, 1,297 (17.2%) were triple-negative (TNBC), 841 (11.2%) were HER2+ and 1,747 (23.2%) could not be classified due to missing ER, PR or HER2 status, or absence of detected ERBB2 amplifications. Among ER+/PR+/HER2- breast cancers, compared to sporadic tumors, ESR1 mutations were significantly enriched in gATM carriers (33% vs. 11%, q-value 0.05), TP53 alterations were significantly enriched in gBRCA1 PV carriers (69% vs. 30%, q-value &amp;lt; 0.001) but depleted in gATM (12% vs. 30%, q-value 0.4) and gCHEK2 PV carriers (5.4% vs. 30%, q-value 0.06), and PIK3CA (14% vs. 35%, q-value 0.001) and CCND1 (3.4% vs. 17%, q-value 0.02) alterations were significantly lower in gBRCA2 PV carriers. Among TNBC, TP53 alterations were also significantly higher in gBRCA1 PV carriers compared to sporadic tumors (96% vs. 69%, q-value 0.004). In HER2+ breast cancers, ERBB2 alterations were observed in approximately two-thirds of the tumors, and a significant difference was not observed between incidental hereditary and sporadic tumors. Among ER+/PR+/HER2- tumors, although not statistically significant, the frequency of ESR1 (3.1% vs. 11%, q-value &amp;gt;0.9), PIK3CA (12% vs. 35%, q-value 0.2) alterations were lower in incidental gBRCA1 versus sporadic tumors, FGFR1 alterations were lower in incidental gBRCA1 (6.2% vs. 13%, q-value &amp;gt;0.9) and incidental gBRCA2 (3.4% vs. 13%, q-value 0.13) but enriched in incidental gATM (33% vs. 13%, q-value 0.05). Conclusions: The observed differences in the frequencies of CCND1, ESR1, PIK3CA, TP53, and other key genetic alterations between incidental hereditary and sporadic breast cancer highlight the unique tumor biology of breast cancer in germline PV carriers and have significant implications for understanding tumorigenesis and identifying therapeutic strategies for the management of hereditary breast cancer. Citation Format: Minxuan Huang, Melissa Stoppler. The Landscape of Somatic Genetic Alterations in Breast Cancers from Carriers of Germline Pathogenic Variants in DNA-repair Genes [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS10-04.

Abstract PO5-15-09: DNA damage induced necroptosis predicts response to radioimmunotherapy

Abstract Background: More than half of all cancer patients receive radiotherapy (RT) during their cancer experience. DNA damage induced by RT can initiate a pro-inflammatory immune response within the tumor microenvironment (TME), yet this response is not uniformly observed across all tumors. Mre11 is one of the first responders to double stranded breaks and coordinates the DNA damage response. Recent work in our lab reveals that Mre11 is required for cGAS mediated detection of cytoplasmic DNA, in turn activating STING to engage the type I interferon signaling pathway, downstream of which can activate ZBP1/RIPK3/MLKL mediated necroptosis. The purpose of this study is to determine if expression of the necroptotic pathway may predict whether breast tumors benefit from RT to overcome ICI resistance and induce systemic anti-tumor immunity in the form of an abscopal response. Methods: Four Trp53-/- Balb/c breast cancer syngeneic allograft models with low tumor mutational burden and resistance to dual ICI (anti-PD1 and anti-CTLA4, BioXcell) were used. Mice were implanted with bilateral tumors and randomly divided into four treatment cohorts: untreated, RT, ICI, or RT+ICI, where RT (8Gyx3) was administered to one tumor. Two lines exhibited abscopal responses to RT+ICI (i.e., “abscopal models”), whereas the other two did not (i.e., “non-abscopal models”). To identify gene expression patterns associated with abscopal responding breast tumors, we performed spatial transcriptomic analysis of tumors 10 days after initiating treatment using the GeoMx whole transcriptome assay targeting panCK+ tumor cells and tumor adjacent CD45+ immune cells (N &amp;gt;5 for each treatment group and tumor type). Unsupervised hierarchical clustering was performed to identify gene expression patterns across areas of interest. Genes selectively induced by RT+ICI in abscopal models that were not induced in non-abscopal models were identified using two-tailed t-test and FDR correction for multiple testing (FDR&amp;lt; 5%). DeSEQ2 and GSEA analysis were performed using publicly available mouse gene sets (Broad Institute). Results: The TME in untreated tumors in the abscopal models demonstrate upregulation in the B cell survival pathway and apoptotic pathways compared to untreated tumors in non-abscopal models. Hierarchical clustering of immune related genes in CD45+ segments of RT+ICI treated tumors exhibiting an abscopal response revealed a global shift in gene expression profiles after treatment. GSEA analysis of CD45+ segments from abscopal models shows that RT+ICI treatment results in enrichment of the interferon mediated signaling pathway including interferon alpha (p&amp;lt; 0.0001), interferon beta (p&amp;lt; 0.0001), type II interferon response (p&amp;lt; 0.0001), and antigen processing and presentation (p&amp;lt; 0.0001). In tumor cells of breast cancers demonstrating the abscopal response, Isg15 and Zbp1 are highly induced by RT+ICI. The necroptotic pathway, including Zbp1, Ripk3, and Mlkl, are significantly higher expressed in the panCK+ tumors known to demonstrate the abscopal response. Conclusion: Breast cancer models with an abscopal response to RT+ICI demonstrate higher expression of Isg15 and Zbp1, both of which are involved in secreted inflammatory signaling. The TME in these models have increased interferon signaling and antigen presentation in response to RT+ICI. The role of DNA damage induced necroptosis in generating an abscopal response in breast cancer warrants further investigation as a potential biomarker for response to RT+ICI combination therapy. Citation Format: Anna Goddard, Qinhong Wang, Minguk Cho, Lynn Lerner, Gaorav Gupta. DNA damage induced necroptosis predicts response to radioimmunotherapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-15-09.

Long-Term Survivability of Surgical and Non-Surgical Management of Spinal Epidural Abscess

Spinal epidural abscess (SEA) is a rare and life-threatening infection within the epidural space with significant functional impairment and morbidity. Active debate remains over whether to operate for SEAs, with limited existing data comparing the long-term survivability after surgical versus nonsurgical management. This study aims to determine the long-term survival of patients who underwent surgical and nonsurgical management for SEA. Retrospective cohort study. A total of 250 consecutive SEA patients. Survival and mortality rates, complications. All patients treated at a tertiary medical center for a primary SEA from January 2000 to June 2020 are identified. Data collection is by retrospective chart review. Cox proportional hazards regression models are used for all survival analyses while controlling for potential confounding variables and with multiple testing corrections. A total of 35 out of 250 patients died with an overall all-cause mortality of 14%. More than half of all deaths occurred within 90 days after treatment. The 90-day, 3-year, and 5-year survival rates are 92.8%, 89.2%, and 86.4%, respectively. Among surgery patients, the all-cause mortality was 13.07%, compared to 16.22% for medically-managed patients. Surgical treatment (decompression, fusion, debridement) significantly reduced the risk of death by 62.4% compared to medical therapy (p=.03), but surgery patients experienced a significantly longer mean length of stay (p=.01). Risk factors of short-term mortality included hypoalbuminemia (<3.5 g/dL), American Society of Anesthesiologists (ASA) 4+, and cardiac arrest. Risk factors of long-term mortality were immunocompromised state, elevated WBC count >12,000, sepsis, septic shock, ASA 4+, and cardiac arrest (p<.05). In terms of complications, surgically-managed patients experienced a higher proportion of deep vein thrombosis (p<.05). The overall long-term survivability of SEA treatment is relatively high at (86% at 5-year) in this study. The following SEA mortality risk factors were identified: hypoalbuminemia (short-term), immunocompromised state (long-term), leukocytosis (long-term), sepsis and septic shock (long-term), ASA 4+ and cardiac arrest (overall). For primary SEA patients, surgical management may reduce mortality risk compared to nonsurgical management.

Oral pathology following treatment of brain tumors in childhood

Relevance. The limited selectivity of antitumor therapy for central nervous system neoplasms entails the risk of dental morbidity in patients.The aim of the study is to assess the severity of damage to the dental hard tissues in patients with tumors of the posterior cranial fossa (medulloblastoma, astrocytoma) and other tumors of the central nervous system.Materials and methods. Three comparison groups were established based on the toxicity profiles of antitumor therapy among 251 patients at the "Russian Field" treatment and rehabilitation scientific center, to assess the characteristics of oral health status. The assessment of oral health status included diagnosing the carious process and calculating the DMFT index. The degree of damage to the dental hard tissues was evaluated on a four-point scale. The clinical manifestations of oral cavity pathology were compared using the Z-criterion for multiple pairwise comparisons of data, with adjustments for multiple testing (Multiple pairwise comparison Z-test for proportions with multiple testing correction) using the free R software version 3.5.2. The null hypothesis of equal indicators in the compared groups was rejected with a 95% confidence probability when comparing groups of patients.Results. Dental hard tissue pathology was significantly more prevalent in patients with medulloblastoma compared to those diagnosed with astrocytomas and other central nervous system tumors. Additionally, the prevalence of dental hard tissue pathology progressively decreased as the observation period following the completion of antitumor remission was extended.Conclusion. The most severe damage to dental hard tissues is observed in patients with medulloblastoma, who undergo more intensive antitumor therapy compared to those with CNS tumors of other histological types.

Causal association of metformin treatment with diverse cardiovascular diseases: a Mendelian randomization analysis.

The cardiovascular effects of metformin continue to be a subject of debate within the medical community. The Mendelian randomization (MR) study used data from genome-wide association studies (GWAS) to explore the causal association with six diseases that are associated with bimatoprost treatment and myocardial infarction, chronic heart failure, atrial fibrillation, hypertrophic and dilated cardiomyopathy, and valvular disease. Genome-wide significant single nucleotide polymorphisms (SNPs), that are associated with metformin use were selected as the instrumental variables. To determine the causal relationship between metformin use and various cardiovascular diseases, MR analysis was conducted, employing methods such as Instrumental Variable Weighting (IVW). The IVW analysis demonstrated a positive association between metformin treatment and the risk of myocardial infarction (OR = 22.67, 95% CI 3.22-34.01; P = 0.002). Conversely, metformin treatment exhibited a negative association with the risk of developing valvular disease (OR = 0.98, 95% CI 0.95-1.00; P = 0.046) and hypertrophic cardiomyopathy (OR = 0.01, 95% CI 0.00-0.22; P = 0.016). Multiple test correction found that metformin treatment was causally associated with the risk of both hypertrophic cardiomyopathy (PFDR = 0.048) and myocardial infarction (PFDR = 0.012). The analysis revealed limited heterogeneity in the individual results, absence of pleiotropy evidence, and indications of stability in the findings. The MR study discovered from a genetic standpoint that metformin may lower the risk of hypertrophic cardiomyopathy and valvular heart disease, yet it could elevate the risk of myocardial infarction.

Blood parameters in pediatric myelin oligodendrocyte glycoprotein antibody-associated disorders

Background and objectivesPatients with myelin oligodendrocyte glycoprotein antibody-associated disorders (MOGAD) clinically present e.g. with acute disseminated encephalomyelitis (ADEM), optic neuritis (ON), transverse myelitis (TM) or aquaporin-4-IgG (AQP4-IgG) negative neuromyelitis optica spectrum disorders (NMOSD)-like phenotypes. We aimed to analyze and compare blood parameters in children with MOGAD, AQP4-IgG-positive NMOSD (hence NMOSD), multiple sclerosis (MS) and healthy controls (HC). MethodsWe evaluated differences in complete blood counts (CBC), neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), monocyte-to-lymphocyte ratio (MLR) and C-reactive protein (CRP) between these four groups and within the groups between clinical attack, acute treatment and remission. ResultsOur cohort consisted of 174 children and adolescents with a total of 550 timepoints: 66 patients had MOGAD (202 timepoints), 11 NMOSD (76 timepoints), 58 MS (219 timepoints) and 39 were HC (53 timepoints). At clinical attack, leukocyte counts were elevated in MOGAD compared to remission (p < 0.001) and compared to all other groups (p < 0.001). NLR was high in MOGAD and NMOSD, and PLR was high in NMOSD, however, after correction for multiple testing these findings did not remain significant. While glucocorticoids caused an increase of leukocyte counts and NLR in NMOSD and MS, these values remained stable during acute treatment in MOGAD. In remission, NLR normalized in MOGAD, while it stayed high in NMOSD. PLR increased in NMOSD and was significantly higher compared to all other groups. DiscussionSome blood parameters, mainly leukocyte and differential counts, might help clinicians to evaluate disease activity, differentiate relapses from pseudo-relapses and even distinguish between different disease entities.

Genome-wide meta-analysis of short-tandem repeats for Parkinson's disease risk using genotype imputation.

Idiopathic Parkinson's disease is determined by a combination of genetic and environmental factors. Recently, the first genome-wide association study on short-tandem repeats in Parkinson's disease reported on eight suggestive short-tandem repeat-based risk loci (α = 5.3 × 10-6), of which four were novel, i.e. they had not been implicated in Parkinson's disease risk by genome-wide association analyses of single-nucleotide polymorphisms before. Here, we tested these eight candidate short-tandem repeats in a large, independent Parkinson's disease case-control dataset (n = 4757). Furthermore, we combined the results from both studies by meta-analysis resulting in the largest Parkinson's disease genome-wide association study of short-tandem repeats to date (n = 43 844). Lastly, we investigated whether leading short-tandem repeat risk variants exert functional effects on gene expression regulation based on methylation quantitative trait locus data in human 'post-mortem' brain (n = 142). None of the eight previously reported short-tandem repeats were significantly associated with Parkinson's disease in our independent dataset after multiple testing correction (α = 6.25 × 10-3). However, we observed modest support for short-tandem repeats near CCAR2 and NCOR1 in the updated meta-analyses of all available data. While the genome-wide meta-analysis did not reveal additional study-wide significant (α = 6.3 × 10-7) short-tandem repeat signals, we identified seven novel suggestive Parkinson's disease short-tandem repeat risk loci (α = 5.3 × 10-6). Of these, especially a short-tandem repeat near MEIOSIN showed consistent evidence for association across datasets. CCAR2, NCOR1 and one novel suggestive locus identified here (LINC01012) emerged from colocalization analyses showing evidence for a shared causal short-tandem repeat variant affecting both Parkinson's disease risk and cis DNA methylation in brain. Larger studies, ideally using short-tandem repeats called from whole-sequencing data, are needed to more fully investigate their role in Parkinson's disease.

Pathologic Features of Anti-Ku Myositis.

Characteristics of myositis with anti-Ku antibodies are poorly understood. The purpose of this study was to elucidate the pathologic features of myositis associated with anti-Ku antibodies, compared with immune-mediated necrotizing myopathy (IMNM) with anti-signal recognition particle (SRP) and anti-3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) antibodies, in muscle biopsy-oriented registration cohorts in Japan and Germany. We performed a retrospective pathology review of patients with anti-Ku myositis samples diagnosed in the Japanese and German cohorts. We evaluated histologic features and performed HLA phenotyping. Fifty biopsied muscle samples in the Japanese cohort and 10 in the German cohort were obtained. After exclusion of myositis-specific autoantibodies or other autoimmune connective tissue diseases, 26 samples (43%) of anti-Ku antibody-positive myositis were analyzed. All the samples shared some common features with IMNM, whereas they showed expression of MHC class II and clusters of perivascular inflammatory cells more frequently than the anti-SRP/HMGCR IMNM samples (71% vs 7%/16%; p < 0.005/<0.005; 64% vs 0%/0%; p < 0.005/<0.005). Anti-Ku myositis biopsies could be divided into 2 subgroups based on the extent of necrosis and regeneration. The group with more abundant necrosis and regeneration showed a higher frequency of MHC class II expression and perivascular inflammatory cell clusters. HLA phenotyping in the 44 available patients showed possible associations of HLA-DRB1*03:01, HLA-DRB1*11:01, and HLA-DQB1*03:01 (p = 0.0045, 0.019, and 0.027; odds ratio [OR] 50.2, 4.6, and 2.8; 95% CI 2.6-2942.1, 1.1-14.5, and 1.0-7.0) in the group with less conspicuous necrosis and regeneration. On the contrary, in the group of more abundant necrosis and regeneration, the allele frequencies of HLA-A*24:02, HLA-B*52:01, HLA-C*12:02, and HLA-DRB1*15:02 were lower than those of healthy controls (p = 0.0036, 0.027, 0.016, and 0.026; OR = 0.27, 0, 0, and 0; 95% CI 0.1-0.7, 0-0.8, 0-0.8, and 0-0.8). However, these HLA associations did not remain significant after statistical correction for multiple testing. While anti-Ku myositis shows necrotizing myopathy features, they can be distinguished from anti-SRP/HMGCR IMNM by their MHC class II expression and clusters of perivascular inflammatory cells. The HLA analyses suggest that anti-Ku myositis may have different subsets associated with myopathologic subgroups.

Impact of loss-of-function in angiopoietin-like 4 on the human phenome

BackgroundCarriers of the E40K loss-of-function variant in Angiopoietin-like 4 (ANGPTL4), have lower plasma triglyceride levels as well as lower rates of coronary artery disease (CAD) and type 2 diabetes (T2D). These genetic data suggest ANGPTL4 inhibition as a potential therapeutic target for cardiometabolic diseases. However, it is unknown whether the association between E40K and human diseases is due to linkage disequilibrium confounding. The broader impact of genetic ANGPTL4 inhibition is also unknown, raising uncertainties about the safety and validity of this target. MethodsTo assess the impact of ANGPLT4 inhibition, we evaluated whether E40K and other loss-of-function variants in ANGPTL4 influenced a wide range of health markers and diseases using 29 publicly available genome-wide association meta-analyses of cardiometabolic traits and diseases, as well as 1589 diseases assessed in electronic health records within FinnGen (n = 309,154). To determine whether these relationships were likely causal, and not driven by other correlated variants, we used the Bayesian fine mapping algorithm CoPheScan. ResultsThe CoPheScan posterior probability of E40K being the causal variant for triglyceride levels was 99.99 %, validating the E40K to proxy lifelong lower activity of ANGPTL4. The E40K variant was associated with lower risk of CAD (odds ratio [OR] = 0.84, 95 % CI = 0.81 to 0.87, p=3.6e-21) and T2D (OR = 0.91, 95 % CI = 0.87 to 0.95, p=2.8e-05) in GWAS meta-analyses, with results replicated in FinnGen. These significant results were also replicated using other rare loss-of-function variants identified through whole exome sequencing in 488,278 participants of the UK Biobank. Using a Mendelian randomization study design, the E40K variant effect on cardiometabolic diseases was concordant with lipoprotein lipase enhancement (r = 0.82), but not hepatic lipase enhancement (r = −0.10), suggesting that ANGPTL4 effects on cardiometabolic diseases are potentially mainly mediated through lipoprotein lipase. After correction for multiple testing, the E40K variant did not significantly increase the risk of any of the 1589 diseases tested in FinnGen. ConclusionsANGPTL4 inhibition may represent a potentially safe and effective target for cardiometabolic diseases prevention or treatment.

Recalling and anticipating positive events to improve the positive affect and mental health of adolescents: A cluster randomized controlled trial in secondary schools

This cluster randomized controlled trial examined the effectiveness of Positive Events Training (PET), a combined group training aimed at simultaneously improving positive autobiographical memory (AM) and episodic future thinking (EFT) among adolescents (12–16 years). Delivered as a universal school-based program, PET was compared with an active (creative writing) control group (CREAT). Effects on resilience, wellbeing, positive emotions, emotional response styles towards positive emotions (savoring, dampening), anhedonia, depressive symptoms, and multiple AM and EFT indices were examined. Adolescents (NPET = 95, NCREAT = 93) completed self-report scales at baseline, post-training and two-month follow-up. Multilevel models revealed that PET led to significant improvements in certain AM and EFT skills. Moreover, a decrease in anhedonia was observed at post-training. However, this effect did not withstand correction for multiple testing. Absence of changes in the other outcomes should be interpreted within the context of the universal school-based approach and the potential limited scope for detectable changes. Exploratory analyses suggest the importance of further investigating PET's potential in addressing positive affect dysregulations in indicated samples, and exploring perceived likelihood of generated future events and dampening as potential underlying mechanisms. Study limitations and future directions to maximize the demonstrated potential of PET are discussed.

Investigating the role of common cis-regulatory variants in modifying penetrance of putatively damaging, inherited variants in severe neurodevelopmental disorders

Recent work has revealed an important role for rare, incompletely penetrant inherited coding variants in neurodevelopmental disorders (NDDs). Additionally, we have previously shown that common variants contribute to risk for rare NDDs. Here, we investigate whether common variants exert their effects by modifying gene expression, using multi-cis-expression quantitative trait loci (cis-eQTL) prediction models. We first performed a transcriptome-wide association study for NDDs using 6987 probands from the Deciphering Developmental Disorders (DDD) study and 9720 controls, and found one gene, RAB2A, that passed multiple testing correction (p = 6.7 × 10–7). We then investigated whether cis-eQTLs modify the penetrance of putatively damaging, rare coding variants inherited by NDD probands from their unaffected parents in a set of 1700 trios. We found no evidence that unaffected parents transmitting putatively damaging coding variants had higher genetically-predicted expression of the variant-harboring gene than their child. In probands carrying putatively damaging variants in constrained genes, the genetically-predicted expression of these genes in blood was lower than in controls (p = 2.7 × 10–3). However, results for proband-control comparisons were inconsistent across different sets of genes, variant filters and tissues. We find limited evidence that common cis-eQTLs modify penetrance of rare coding variants in a large cohort of NDD probands.

A pleiotropy scan to discover new susceptibility loci for pancreatic ductal adenocarcinoma.

Pleiotropic variants (i.e., genetic polymorphisms influencing more than one phenotype) are often associated with cancer risk. A scan of pleiotropic variants was successfully conducted ten years ago in relation to pancreatic ductal adenocarcinoma susceptibility. However, in the last decade, genetic association studies performed on several human traits have greatly increased the number of known pleiotropic variants. Based on the hypothesis that variants already associated with a least one trait have a higher probability of association with other traits, 61,052 variants reported to be associated by at least one genome wide association study (GWAS) with at least one human trait were tested in the present study consisting of two phases (discovery and validation), comprising a total of 16,055 pancreatic ductal adenocarcinoma (PDAC) cases and 212,149 controls. The meta-analysis of the two phases showed two loci (10q21.1-rs4948550 (P=6.52×10-5) and 7q36.3-rs288762 (P=3.03×10-5) potentially associated with PDAC risk. 10q21.1-rs4948550 shows a high degree of pleiotropy and it is also associated with colorectal cancer risk while 7q36.3-rs288762 is situated 28,558 base pairs upstream of the Sonic Hedgehog (SHH) gene, which is involved in the cell differentiation process and PDAC etiopathogenesis. In conclusion, none of the single nucleotide polymorphisms (SNPs) showed a formally statistically significant association after correction for multiple testing. However, given their pleiotropic nature and association with various human traits including colorectal cancer, the two SNPs showing the best associations with PDAC risk merit further investigation through fine mapping and ad hoc functional studies.

The landscape of rare genetic variants in familial Waldenström macroglobulinemia

AbstractWaldenström macroglobulinemia (WM) is a rare hematological malignancy. Risk for WM is elevated 20-fold among first-degree relatives of patients with WM. However, the list of variants and genes that cause WM remains incomplete. In this study we analyzed exomes from 64 WM pedigrees for evidence of genetic susceptibility for this malignancy. We determined the frequency of pathogenic (P) or likely pathogenic (LP) variants among patients with WM; performed variant- and gene-level association analyses with the set of 166 WM cases and 681 unaffected controls; and examined the segregation pattern of deleterious variants among affected members in each pedigree. We identified P/LP variants in TREX1 and SAMHD1 (genes that function at the interface between innate immune response, genotoxic surveillance, and DNA repair) segregating in patients with WM from 2 pedigrees. There were additional P/LP variants in cancer-predisposing genes (eg, POT1, RECQL4, PTPN11, PMS2). In variant- and gene-level analyses, no associations were statistically significant after multiple testing correction. On a pathway level, we observed involvement of genes that play a role in telomere maintenance (q-value = 0.02), regulation of innate immune response (q-value = 0.05), and DNA repair (q-value = 0.08). Affected members of each pedigree shared multiple deleterious variants (median, n = 18), but the overlap between the families was modest. In summary, P/LP variants in highly penetrant genes constitute a modest proportion of the deleterious variants; each pedigree is largely unique in its genetic architecture, and multiple genes are likely involved in the etiology of WM.

Neuron enriched extracellular vesicles’ MicroRNA expression profiles as a marker of early life alcohol consumption

Alcohol consumption may impact and shape brain development through perturbed biological pathways and impaired molecular functions. We investigated the relationship between alcohol consumption rates and neuron-enriched extracellular vesicles’ (EVs’) microRNA (miRNA) expression to better understand the impact of alcohol use on early life brain biology. Neuron-enriched EVs’ miRNA expression was measured from plasma samples collected from young people using a commercially available microarray platform while alcohol consumption was measured using the Alcohol Use Disorders Identification Test. Linear regression and network analyses were used to identify significantly differentially expressed miRNAs and to characterize the implicated biological pathways, respectively. Compared to alcohol naïve controls, young people reporting high alcohol consumption exhibited significantly higher expression of three neuron-enriched EVs’ miRNAs including miR-30a-5p, miR-194-5p, and miR-339-3p, although only miR-30a-5p and miR-194-5p survived multiple test correction. The miRNA-miRNA interaction network inferred by a network inference algorithm did not detect any differentially expressed miRNAs with a high cutoff on edge scores. However, when the cutoff of the algorithm was reduced, five miRNAs were identified as interacting with miR-194-5p and miR-30a-5p. These seven miRNAs were associated with 25 biological functions; miR-194-5p was the most highly connected node and was highly correlated with the other miRNAs in this cluster. Our observed association between neuron-enriched EVs’ miRNAs and alcohol consumption concurs with results from experimental animal models of alcohol use and suggests that high rates of alcohol consumption during the adolescent/young adult years may impact brain functioning and development by modulating miRNA expression.