Common and rare variant association analyses in Amyotrophic Lateral Sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology
Abstract Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a life-time risk of 1 in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry GWAS in ALS including 29,612 ALS patients and 122,656 controls which identified 15 risk loci in ALS. When combined with 8,953 whole-genome sequenced individuals (6,538 ALS patients, 2,415 controls) and the largest cortex-derived eQTL dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, repeat expansions or regulatory effects. ALS associated risk loci were shared with multiple traits within the neurodegenerative spectrum, but with distinct enrichment patterns across brain regions and cell-types. Of the environmental and life-style risk factors obtained from literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. All ALS associated signals combined reveal a role for perturbations in vesicle mediated transport and autophagy, and provide evidence for cell-autonomous disease initiation in glutamatergic neurons.
Loss of Tmem106b leads to cerebellum Purkinje cell death and motor deficits
Abstract Low-grade inflammation associated with metabolic syndrome (MS) triggers alterations in several organs, but its effects on pulmonary functional and immunological response in older adults are unknown. This cross-sectional study investigated such responses in older adults with and without MS. The study consisted of 77 older adults with MS (68 ± 3 years old) and without MS (67 ± 3 years old). Impulse oscillometry (IOS) was used to evaluate airway and tissue resistance and reactance. Biomarkers of systemic and pulmonary inflammation and fibrosis were studied. Total resistance of respiratory system (R5Hz; p < 0.009), and resistance of proximal (R20Hz; p < 0.001) and distal (R5Hz-R20Hz; p < 0.004) airways were impaired in MS individuals compared to those without MS. The levels of pro-inflammatory (leptin; IL-1beta; IL-8, p < 0.001; TNF-alpha, p < 0.04) and pro-fibrotic (VEGF, p < 0.001) factor increased in MS, while reduced levels of anti-inflammatory cytokines (adiponectin; IL-1ra; IL-10; p < 0.001), and anti-fibrotic (relaxin 1; relaxin 3; Klotho, p < 0.001) factors were found. We conclude that MS accelerates lung function and mechanics impairment in older adults in detriment of an imbalance between pro and anti-inflammatory and fibrotic mediators. Furthermore, this study shows that the lungs also are a target organ in MS, deserving clinical assessment in older adults’ population.
Smoking Modifies Pancreatic Cancer Risk Loci on 2q21.3
Abstract Germline variation and smoking are independently associated with pancreatic ductal adenocarcinoma (PDAC). We conducted genome-wide smoking interaction analysis of PDAC using genotype data from four previous genome-wide association studies in individuals of European ancestry (7,937 cases and 11,774 controls). Examination of expression quantitative trait loci data from the Genotype-Tissue Expression Project followed by colocalization analysis was conducted to determine whether there was support for common SNP(s) underlying the observed associations. Statistical tests were two sided and P < 5 × 10–8 was considered statistically significant. Genome-wide significant evidence of qualitative interaction was identified on chr2q21.3 in intron 5 of the transmembrane protein 163 (TMEM163) and upstream of the cyclin T2 (CCNT2). The most significant SNP using the Empirical Bayes method, in this region that included 45 significantly associated SNPs, was rs1818613 [per allele OR in never smokers 0.87, 95% confidence interval (CI), 0.82–0.93; former smokers 1.00, 95% CI, 0.91–1.07; current smokers 1.25, 95% CI 1.12–1.40, Pinteraction = 3.08 × 10–9). Examination of the Genotype-Tissue Expression Project data demonstrated an expression quantitative trait locus in this region for TMEM163 and CCNT2 in several tissue types. Colocalization analysis supported a shared SNP, rs842357, in high linkage disequilibrium with rs1818613 (r2 = 0. 94) driving both the observed interaction and the expression quantitative trait loci signals. Future studies are needed to confirm and understand the differential biologic mechanisms by smoking status that contribute to our PDAC findings. Significance: This large genome-wide interaction study identifies a susceptibility locus on 2q21.3 that significantly modified PDAC risk by smoking status, providing insight into smoking-associated PDAC, with implications for prevention.
AbstractTo examine the length of a hexanucleotide expansion in C9orf72, which represents the most frequent genetic cause of frontotemporal lobar degeneration and motor neuron disease, we employed a targeted amplification-free long-read sequencing technology: No-Amp sequencing. In our cross-sectional study, we assessed cerebellar tissue from 28 well-characterized C9orf72 expansion carriers. We obtained 3507 on-target circular consensus sequencing reads, of which 814 bridged the C9orf72 repeat expansion (23%). Importantly, we observed a significant correlation between expansion sizes obtained using No-Amp sequencing and Southern blotting (P = 5.0 × 10−4). Interestingly, we also detected a significant survival advantage for individuals with smaller expansions (P = 0.004). Additionally, we uncovered that smaller expansions were significantly associated with higher levels of C9orf72 transcripts containing intron 1b (P = 0.003), poly(GP) proteins (P = 1.3 × 10− 5), and poly(GA) proteins (P = 0.005). Thorough examination of the composition of the expansion revealed that its GC content was extremely high (median: 100%) and that it was mainly composed of GGGGCC repeats (median: 96%), suggesting that expanded C9orf72 repeats are quite pure. Taken together, our findings demonstrate that No-Amp sequencing is a powerful tool that enables the discovery of relevant clinicopathological associations, highlighting the important role played by the cerebellar size of the expanded repeat in C9orf72-linked diseases.
Cirrhosis Is Associated With High Mortality and Readmissions Over 90 Days Regardless of COVID‐19: A Multicenter Cohort
Objective: The aim of this work is to formulate recommendations based on global expert consensus to guide the surgical community on the safe resumption of surgical and endoscopic activities. Background: The COVID-19 pandemic has caused marked disruptions in the delivery of surgical care worldwide. A thoughtful, structured approach to resuming surgical services is necessary as the impact of COVID-19 becomes better controlled. The Coronavirus Global Surgical Collaborative sought to formulate, through rigorous scientific methodology, consensus-based recommendations in collaboration with a multidisciplinary group of international experts and policymakers. Methods: Recommendations were developed following a Delphi process. Domain topics were formulated and subsequently subdivided into questions pertinent to different aspects of surgical care in the COVID-19 crisis. Forty-four experts from 15 countries across 4 continents drafted statements based on the specific questions. Anonymous Delphi voting on the statements was performed in 2 rounds, as well as in a telepresence meeting. Results: One hundred statements were formulated across 10 domains. The statements addressed terminology, impact on procedural services, patient/staff safety, managing a backlog of surgeries, methods to restart and sustain surgical services, education, and research. Eighty-three of the statements were approved during the first round of Delphi voting, and 11 during the second round. A final telepresence meeting and discussion yielded acceptance of 5 other statements. Conclusions: The Delphi process resulted in 99 recommendations. These consensus statements provide expert guidance, based on scientific methodology, for the safe resumption of surgical activities during the COVID-19 pandemic.
Identification of NPTX2 as a prognostic biomarker of Alzheimer’s disease through a longitudinal CSF proteomics study in ADNI subjects
AbstractBackgroundMany biomarkers have been identified which are relevant to studies of Alzheimer’s disease (AD), especially pertaining to the evolution of amyloid plaque, tau tangle pathology and loss of brain tissue. There remains, however, the need for additional biomarkers that reflect pathologic processes affecting neuronal function during pre‐clinical and prodromal stages, to help accelerate drug development efforts.MethodA retrospective investigation of longitudinal changes in concentrations of five analytes (CgA, NPTX2, VGF, SCG2, FABP3) was performed in CSF of ADNI subjects. Rates of longitudinal change in these candidate proteins were compared between: a) Cognitively normal subjects (CN; n = 76) versus subjects with mild cognitive impairment (MCI; n = 111) at baseline; b) Subjects categorized as p‐Tau181/Aβ1‐42 ratio positive versus negative at baseline; and c) ‘Progressors’, i.e., subjects who progressed from CN to MCI or MCI to Dementia within a predefined period versus subjects categorized as ‘non‐progressors’. Following a pre‐specified analysis plan involving mixed‐effects linear models adjusting for relevant covariates, the association between changes in each analyte’s concentration and subjects’ clinical progression was quantified.ResultNPTX2, a protein involved in synaptic function, showed the strongest association with baseline clinical diagnosis of MCI, and a positive p‐Tau181/Aβ1‐42 ratio – the biomarker profile indicative of AD. Differences in the rates of decline in NPTX2 concentration between subjects classified as CN and MCI as well as between p‐Tau181/Aβ1‐42 ratio positive and negative subjects were highly significant (p=0.008 and p<0.0001 resp.), suggesting a complex interaction between the rate of decline in subjects at various stages along the disease continuum. Of the five analytes, only the rates of change in NPTX2 concentrations differed between progressors and non‐progressors (mean difference: 0.08 ± 0.02 ng/mL/year); p = 0.0004), further validating the association of changes in NPTX2 concentration and clinical prognosis. Additional exploratory analyses indicated the presence of a correlation between NPTX2 rates of change and declining cognition measured by MMSE (coef. = 0.3, p = 0.02), and Adas‐Cog 13 (coef. = ‐0.3, p = 0.01).ConclusionThese results suggest that NPTX2 concentration may serve as a prognostic biomarker of accelerated cognitive decline in at least a subset of individuals with AD.