False Discovery Rate Threshold Research Articles

Potential drug targets for tumors identified through Mendelian randomization analysis.

According to the latest cancer research data, there are a significant number of new cancer cases and a substantial mortality rate each year. Although a substantial number of clinical patients are treated with existing cancer drugs each year, the efficacy is unsatisfactory. The incidence is still high and the effectiveness of most cancer drugs remains unsatisfactory. Therefore, we evaluated the human proteins for their causal relationship to for cancer risk and therefore also their potential as drug targets. We used summary tumors data from the FinnGen and cis protein quantitative trait loci (cis-pQTL) data from a genome-wide association study, and employed Mendelian randomization (MR) to explore the association between potential drug targets and nine tumors, including breast, colorectal, lung, liver, bladder, prostate, kidney, head and neck, pancreatic caners. Furthermore, we conducted MR analysis on external cohort. Moreover, Bidirectional MR, Steiger filtering, and colocalization were employed to validate the main results. The DrugBank database was used to discover potential drugs of tumors. Under the threshold of False discovery rate (FDR) < 0.05, results showed that S100A16 was protective protein and S100A14 was risk protein for human epidermal growth factor receptor 2-positive (HER-positive) breast cancer, phosphodiesterase 5A (PDE5A) was risk protein for colorectal cancer, and melanoma inhibitory activity (MIA) was protective protein for non-small cell lung carcinoma (NSCLC). And there was no reverse causal association between them. Colocalization analysis showed that S100A14 (PP.H4.abf = 0.920) and S100A16 (PP.H4.abf = 0.932) shared causal variation with HER-positive breast cancer, and PDE5A (PP.H4.abf = 0.857) shared causal variation with colorectal cancer (CRC). The MR results of all pQTL of PDE5A and MIA were consistent with main results. In addition, the MR results of MIA and external outcome cohort were consistent with main results. In this study, genetic predictions indicate that circulating S100 calcium binding protein A14 (S100A14) and S100 calcium binding protein A16 (S100A16) are associated with increase and decrease in the risk of HER-positive breast cancer, respectively. Circulating PDE5A is associated with increased risk of CRC, while circulating MIA is associated with decreased risk of NSCLC. These findings suggest that four proteins may serve as biomarkers for cancer prevention and as potential drug targets that could be expected for approval.

GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight.

Genetic enhancement of grain production and quality is a priority in wheat breeding projects. In this study, we assessed two key agronomic traits-grain protein content (GPC) and thousand kernel weight (TKW)-across 179 Bulgarian contemporary and historic varieties and landraces across three growing seasons. Significant phenotypic variation existed for both traits among genotypes and seasons, and no discernible difference was evident between the old and modern accessions. To understand the genetic basis of the traits, we conducted a genome-wide association study with MLM using phenotypic data from the crop seasons, best linear unbiased estimators, and genotypic data from the 25K Infinium iSelect array. As a result, we detected 16 quantitative trait nucleotides (QTNs) associated with GPC and 15 associated with TKW, all of which passed the false discovery rate threshold. Seven loci favorably influenced GPC, resulting in an increase of 1.4% to 8.1%, while four loci had a positive impact on TKW with increases ranging from 1.9% to 8.4%. While some loci confirmed previously published associations, four QTNs linked to GPC on chromosomes 2A, 7A, and 7B, as well as two QTNs related to TKW on chromosomes 1B and 6A, may represent novel associations. Annotations for proteins involved in the senescence-associated nutrient remobilization and in the following buildup of resources required for seed germination have been found for selected putative candidate genes. These include genes coding for storage proteins, cysteine proteases, cellulose-synthase, alpha-amylase, transcriptional regulators, and F-box and RWP-RK family proteins. Our findings highlight promising genomic regions for targeted breeding programs aimed at improving grain yield and protein content.

Impact of PAP on the gut microbiome in OSA: A pilot study

Objective/backgroundMicrobes within the gastrointestinal tract have emerged as modulators of the host's health. Obstructive sleep apnea (OSA) is characterized by intermittent partial, or complete, airway closure during sleep and is associated with increased risk of non-communicable diseases as well as dysbiosis of the gut microbiome. Thus, we investigated if improving nocturnal airway patency via positive airway pressure (PAP) therapy improves gut microbial diversity in recently diagnosed patients with moderate-to-severe OSA (apnea-hypopnea index ≥15.0 events/hr). Patients/methodsEight subjects (3 F, 56±9yrs, 33.5 ± 7.7 kg/m2, 45.0 ± 38.4 events/hr) provided stool samples before, and two months after, PAP therapy (mean adherence of 95 ± 6%, residual apnea-hypopnea index of 4.7 ± 4.6 events/hr). ResultsWhile the Shannon diversity index tended to increase following PAP (3.96 ± 0.52 to 4.18 ± 0.56, p = 0.08), there were no changes in the Observed (1,088 ± 237 to 1,136 ± 289, p = 0.28) nor Inverse-Simpson (22.4 ± 12.99 to 26.6 ± 18.23, p = 0.28) alpha diversity indices. There were also no changes in beta diversity assessed using the Bray-Curtis (p = 0.98), Jaccard (p = 0.99), WUniFrac (p = 0.98), GUniFrac (p = 0.98), or UniFrac (p = 0.98) methods. No changes in differential abundance taxa were found using a false discovery rate threshold of <0.20. ConclusionsOur data are the first to report that PAP therapy may not offset, or reverse, gut dysbiosis in patients with OSA. Accordingly, interventions which improve gut microbial health should be explored as potential adjunctive treatment options in patients with OSA to reduce their risk of developing non-communicable diseases.

Abstract 5480: Single cell and spatial transcriptomic profile of appendiceal tumour peritoneal disease

Abstract Introduction: Appendiceal tumors (AT) are rare and often develop peritoneal disease (PD), with 5 year survival of 15-63% for high grade adenocarcinomas (HG) and 46-96% for low grade mucinous neoplasms (LG). While the mainstay of treatment is cytoreductive surgery and heated intraperitoneal chemotherapy (CRS/HIPEC), the role of systemic chemotherapy is less clear with limited biological characterization of AT and its tumor microenvironment (TME). The purpose of this study was to evaluate the TME of AT PD. Here we present an atlas of AT PD cells alongside a spatially resolved transcriptomic profile comparing HG and LG. Methods: We collected tissue from 29 patients with AT PD during CRS prior to HIPEC (18 LG, nine HG and two no tumor control). We performed comprehensive single-cell RNA sequencing (38224 cells) on fresh tissue specimens from nine patients (four HG, five LG), and whole transcriptome spatial analysis (&amp;gt;18000 genes) using the GeoMx Digital Spatial Profiler on formalin-fixed paraffin-embedded tissue from 22 patients (five HG, 13 LG). In the spatial profiling, we used anti-CK20, anti-CD45 and SYTO 83 as morphology markers to select areas of interest (AOIs): tumor (CK20), immune (CD45) and stroma (non-CK20/CD45). Analyses were performed with R and a false discovery rate threshold of 0.05. Results: Single-cell RNA sequencing showed that both LG and HG have a preponderance of T-lineage cells including CD8, CD4 and NK T-cells. Both LG and HG tumors display association of mesothelial cells with cancer-associated fibroblasts (CAF), and CAF subsets expressing genes of epithelial-mesenchymal transition (EMT). LG and HG tumors display different patterns of mucin gene expression - epithelial cells of HG express the secreted mucin MUC20 in addition to MUC2 and MUC5B also expressed in LG; a subset of mesothelial cells in LG but not HG express the transmembrane mucin genes MUC1, MUC3A, MUC12 and MUC16. Spatial analysis of tumor AOIs revealed HG compared to LG had increased expression of genes associated with MYC targets, oxidative phosphorylation, anti-tumor immune pathways (IFNα/γ response, intestinal immune network for IGA production), cell cycle pathways (E2F targets, G2M checkpoint) and EMT. LG compared to HG had increased expression of genes associated with inflammation-mediated disease (TNFα signaling via NFKB, inflammatory response), regulation of tumor growth (P53), hypoxia and early cell cycle (estrogen response) and glycosylation pathways. Immune and stromal AOIs did not have significant transcriptomic differences between LG and HG. Conclusion: This study provides novel insights into the biological profile of AT PD by describing TME cell types, immune function, tumor growth and cell cycle pathways. These findings may be used to identify clinically relevant biomarkers and new therapeutic targets. Citation Format: Madeleine C. Strach, Nicole Yeung, Eva Apostolov, Tony Wang, Hui-Ming Lin, Nabila Ansari, Cherry Koh, Joo-Shik Shin, James Kench, Alexander Swarbrick, Lisa Horvath, Kate L. Mahon. Single cell and spatial transcriptomic profile of appendiceal tumour peritoneal disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5480.

Dioxin(-like)-Related Biological Effects through Integrated Chemical-wide and Metabolome-wide Analyses.

Dioxin(-like) exposures are linked to adverse health effects, including cancer. However, metabolic alterations induced by these chemicals remain largely unknown. Beyond known dioxin(-like) compounds, we leveraged a chemical-wide approach to assess chlorinated co-exposures and parent compound products [termed dioxin(-like)-related compounds] among 137 occupational workers. Endogenous metabolites were profiled by untargeted metabolomics, namely, reversed-phase chromatography with negative electrospray ionization (C18-negative) and hydrophilic interaction liquid chromatography with positive electrospray ionization (HILIC-positive). We performed a metabolome-wide association study to select dioxin(-like) associated metabolic features using a 20% false discovery rate threshold. Metabolic features were then characterized by pathway enrichment analyses. There are no significant features associated with polychlorinated dibenzo-p-dioxins (PCDDs), a subgroup of known dioxin(-like) compounds. However, 3,110 C18-negative and 2,894 HILIC-positive features were associated with at least one of the PCDD-related compounds. Abundant metabolic changes were also observed for polychlorinated dibenzofuran-related and polychlorinated biphenyl-related compounds. These metabolic features were primarily enriched in pathways of amino acids, lipid and fatty acids, carbohydrates, cofactors, and nucleotides. Our study highlights the potential of chemical-wide analysis for comprehensive exposure assessment beyond targeted chemicals. Coupled with advanced endogenous metabolomics, this approach allows for an in-depth exploration of metabolic alterations induced by environmental chemicals.

Sodium intake and the risk of various types of cardiovascular diseases: a Mendelian randomization study.

The existing literature on the link between sodium intake and cardiovascular disease (CVD) largely consists of observational studies that have yielded inconsistent conclusions. In this study, our objective is to assess the causal relationship between sodium intake and 50 CVDs using two-sample Mendelian randomization (MR) analysis. MR analyses were performed to investigate the associations between urinary sodium/creatinine ratio (UNa/UCr), an indicator of sodium intake, and 50 CVDs. The genome-wide association study (GWAS) for UNa/UCr was from the UK Biobank (UKBB), and the GWASs for CVDs were from FinnGen. A false discovery rate (FDR) threshold of 5% was applied for multiple comparison correction. The inverse-variance weighted method indicated that the genetically predicted UNa/UCr was significantly associated with 7 of 50 CVDs, including "Coronary atherosclerosis" (OR = 2.01; 95% CI: 1.37, 2.95), "Diseases of arteries, arterioles and capillaries" (OR = 1.88; 95% CI: 1.20, 2.94), "Hard cardiovascular diseases" (OR = 1.71; 95% CI: 1.24, 2.35), "Ischemic heart diseases" (OR = 2.06; 95% CI: 1.46, 2.93), "Major coronary heart disease event" (OR = 1.99; 95% CI: 1.36, 2.91), "Myocardial infarction" (OR = 2.03; 95% CI: 1.29, 3.19), and "Peripheral artery disease" (OR = 2.50; 95% CI: 1.35, 4.63). Similar results were obtained with the MR-Egger and weighted median methods. No significant heterogeneity or horizontal pleiotropy was found in this analysis. Our study has uncovered a significant positive causal relationship between UNa/UCr and various CVDs. These results offer a new theoretical foundation for advocating the restriction of sodium intake as a preventive measure against CVD.

Abstract 13280: Plasma Extracellular microRNAs Associated With Cardiovascular Disease Risk Factors in Middle-Aged and Older Populations

Background: Extracellular microRNAs (miRNAs) are a class of non-coding RNAs that resist degradation and remain stable in the extracellular milieu where they contribute to various physiological and pathological processes by facilitating intercellular signaling. Previous studies have reported associations between miRNAs and cardiovascular diseases (CVD); however, the plasma miRNA signatures of CVD and its risk factors have not been fully elucidated at the population level. Methods: Plasma miRNA levels were measured in 4,440 Framingham Heart Study (FHS) participants from the Third Generation and Omni II cohorts using qRT-PCR. Linear regression analyses were conducted to test the cross-sectional associations of each miRNA with CVD risk factors, including systolic blood pressure (SBP), diastolic blood pressure (DBP), triglycerides, HDL and total cholesterol, blood glucose, BMI, and cigarette smoking. Prospective analyses of the associations of miRNAs with new-onset obesity, hypertension, type 2 diabetes, CVD, and all-cause mortality were conducted using proportional hazards regression. A false discovery rate threshold of 0.05 was applied for each risk factor and outcome individually. Replication was carried out in 2,000 Rotterdam Study (RS) participants with data on plasma miRNA levels measured using RNA-seq. Pathway enrichment analyses were conducted and gene targets were predicted for miRNAs associated with five or more risk factors in FHS. Results and Conclusions: In FHS, six miRNAs (miR-193b-3p, miR-122-5p, miR-365a-3p, miR-194-5p, miR-192-5p, miR-193a-5p) were associated with five or more CVD risk factors. This miRNA signature was enriched for biological processes and cellular pathways associated with CVD; many of the genes annotated to these pathways are predicted targets of the identified miRNAs. In RS, miR-193b-3p, miR-194-5p, and miR-193a-5p were associated with two or more risk factors. Prospective analysis revealed eight miRNAs associated with all-cause mortality only in FHS, including miR-193b-3p, miR-122-5p, miR-192-5p, and miR-193a-5p. These findings suggest plasma miRNA levels are associated with CVD risk factors and could provide opportunities to investigate their possible contributions to CVD pathogenesis.

Does right hemisphere compensate for the left in school-age children with large left middle fossa arachnoid cysts?

BackgroundTo assess the cognitive function changes and brain network neuroplasticity in school-age children having large (diameter > 5 cm) left middle fossa arachnoid cyst (MFACs).MethodsEleven patients and 22 normal controls (NC) between 6 and 14 years of age were included. The CNS Vital Signs (CNS VS) were administered for cognitive assessment. The differences of cognitive data and functional connectivity (FC) in resting-state functional magnetic resonance imaging (rs-fMRI) were compared between the patient group and the NC group. The correlations between the altered FC and cognitive data in the patient group were assessed.ResultsPatient group had significantly poorer attention (including Complex Attention, Sustained Attention, Simple Attention, Cognitive Flexibility, and Executive Function) and memory function (Visual Memory and Working Memory) than the NC group (uncorrected p-value, p-unc < 0.05). Whole-brain local correlation (LCOR) analysis showed an extensively lower LCOR in the patient group (voxel threshold p-unc < 0.001, cluster-size threshold of false discovery rate adjusted p (p-FDR) < 0.001). Functional connectivity (FC) analysis showed that bilateral frontal and temporal lobes connectivity in the patient group was significantly lower than the NC group (p-FDR < 0.05). Seed-based FC analysis indicated that there was altered FC between the right temporal lobe and the left temporal-parietal/temporal-occipital area (p-FDR < 0.05). In the patient group, most of the altered FC had a negative correlation to the cognitive score, while the FC in the right temporal lobe-left temporal-occipital area positively correlated to Verbal/Visual Memory (r = 0.41–0.60, p-FDR < 0.05). In correlation analysis between clinical data and cognitive score, the only significant result was a low correlation between cyst size and Reaction Time (-0.30–-0.36, P-FDR < 0.05).ConclusionsSchool-aged children with large left MFAC showed significantly lower cognitive performance primarily in attention and memory domains. Distinct from neuroplasticity in a unilateral brain lesion, compensation in the healthy hemisphere in MFAC patients was sparse.

DNA methylation is not associated with sensitization to or dietary introduction of highly allergenic foods in a subset of the CHILD cohort at age 1 year.

In the first year of life, DNA methylation (DNAm) patterns are established and are particularly susceptible to exposure-induced changes. Some of these changes may leave lasting effects by persistently altering gene expression or cell type composition or function, contributing to disease. In this discovery study, we investigated DNAm associations with sensitization to peanut, egg, or cow's milk and hypothesized that genes demonstrating DNAm differences in immune cells may play a role in the development of food sensitization. Infant sensitization (a skin prick test wheal size that is at least 2 mm greater than the negative control) was measured to peanut, egg, and cow's milk at age 1 year, and ages of food introduction were reported prospectively. PBMC DNAm was measured in blood samples at 1 year in 144 infants, oversampled for atopy or wheeze. Statistical analysis of Illumina 450k array DNAm data was conducted in R with adjustment for clinical and genetic covariables and a minimum effect size of 1%, false discovery rate of 5%, and medium-confidence false discovery rate threshold of 20%. There were no DNAm differences between infants with and without peanut, egg, or cow's milk sensitization. Borderline significant sites with high effect sizes were enriched for methylation quantitative trait loci, hinting at genetic factors influencing DNAm at these sites. DNAm patterns did not differ by peanut or egg introduction before or after 12 months. This small pilot study did not show differences inmethylation by food sensitization or introduction, but it diddemonstrate DNAm patterns linked to genetic variants.

Wheat Grains as a Sustainable Source of Protein for Health.

Protein deficiency is recognized among the major global health issues with an underestimation of its importance. Genetic biofortification is a cost-effective and sustainable strategy to overcome global protein malnutrition. This study was designed to focus on protein-dense grains of wheat (Triticum aestivum L.) and identify the genes governing grain protein content (GPC) that improve end-use quality and in turn human health. Genome-wide association was applied using the 90k iSELECT Infinium and 35k Affymetrix arrays with GPC quantified by using a proteomic-based technique in 369 wheat genotypes over three field-year trials. The results showed significant natural variation among bread wheat genotypes that led to detecting 54 significant quantitative trait nucleotides (QTNs) surpassing the false discovery rate (FDR) threshold. These QTNs showed contrasting effects on GPC ranging from -0.50 to +0.54% that can be used for protein content improvement. Further bioinformatics analyses reported that these QTNs are genomically linked with 35 candidate genes showing high expression during grain development. The putative candidate genes have functions in the binding, remobilization, or transport of protein. For instance, the promising QTN AX-94727470 on chromosome 6B increases GPC by +0.47% and is physically located inside the gene TraesCS6B02G384500 annotated as Trehalose 6-phosphate phosphatase (T6P), which can be employed to improve grain protein quality. Our findings are valuable for the enhancement of protein content and end-use quality in one of the major daily food resources that ultimately improve human nutrition.

Unbiased gene expression analysis of the delayed fracture healing observed in Zucker diabetic fatty rats.

Impaired fracture repair in patients with type 2 diabetes mellitus (T2DM) is not fully understood. In this study, we aimed to characterize the local changes in gene expression (GE) associated with diabetic fracture. We used an unbiased approach to compare GE in the fracture callus of Zucker diabetic fatty (ZDF) rats relative to wild-type (WT) littermates at three weeks following femoral osteotomy. Zucker rats, WT and homozygous for leptin receptor mutation (ZDF), were fed a moderately high-fat diet to induce T2DM only in the ZDF animals. At ten weeks of age, open femoral fractures were simulated using a unilateral osteotomy stabilized with an external fixator. At three weeks post-surgery, the fractured femur from each animal was retrieved for analysis. Callus formation and the extent of healing were assessed by radiograph and histology. Bone tissue was processed for total RNA extraction and messenger RNA (mRNA) sequencing (mRNA-Seq). Radiographs and histology demonstrated impaired fracture healing in ZDF rats with incomplete bony bridge formation and an influx of intramedullary inflammatory tissue. In comparison, near-complete bridging between cortices was observed in Sham WT animals. Of 13,160 genes, mRNA-Seq analysis identified 13 that were differentially expressed in ZDF rat callus, using a false discovery rate (FDR) threshold of 10%. Seven genes were upregulated with high confidence (FDR = 0.05) in ZDF fracture callus, most with known roles in inflammation. These findings suggest that elevated or prolonged inflammation contributes to delayed fracture healing in T2DM. The identified genes may be used as biomarkers to monitor and treat delayed fracture healing in diabetic patients.

Genetic Parameter and Hyper-Parameter Estimation Underlie Nitrogen Use Efficiency in Bread Wheat.

Estimation and prediction play a key role in breeding programs. Currently, phenotyping of complex traits such as nitrogen use efficiency (NUE) in wheat is still expensive, requires high-throughput technologies and is very time consuming compared to genotyping. Therefore, researchers are trying to predict phenotypes based on marker information. Genetic parameters such as population structure, genomic relationship matrix, marker density and sample size are major factors that increase the performance and accuracy of a model. However, they play an important role in adjusting the statistically significant false discovery rate (FDR) threshold in estimation. In parallel, there are many genetic hyper-parameters that are hidden and not represented in the given genomic selection (GS) model but have significant effects on the results, such as panel size, number of markers, minor allele frequency, number of call rates for each marker, number of cross validations and batch size in the training set of the genomic file. The main challenge is to ensure the reliability and accuracy of predicted breeding values (BVs) as results. Our study has confirmed the results of bias-variance tradeoff and adaptive prediction error for the ensemble-learning-based model STACK, which has the highest performance when estimating genetic parameters and hyper-parameters in a given GS model compared to other models.

CSF metabolites associated with biomarkers of Alzheimer's disease pathology.

Metabolomics technology facilitates studying associations between small molecules and disease processes. Correlating metabolites in cerebrospinal fluid (CSF) with Alzheimer's disease (AD) CSF biomarkers may elucidate additional changes that are associated with early AD pathology and enhance our knowledge of the disease. The relative abundance of untargeted metabolites was assessed in 161 individuals from the Wisconsin Registry for Alzheimer's Prevention. A metabolome-wide association study (MWAS) was conducted between 269 CSF metabolites and protein biomarkers reflecting brain amyloidosis, tau pathology, neuronal and synaptic degeneration, and astrocyte or microglial activation and neuroinflammation. Linear mixed-effects regression analyses were performed with random intercepts for sample relatedness and repeated measurements and fixed effects for age, sex, and years of education. The metabolome-wide significance was determined by a false discovery rate threshold of 0.05. The significant metabolites were replicated in 154 independent individuals from then Wisconsin Alzheimer's Disease Research Center. Mendelian randomization was performed using genome-wide significant single nucleotide polymorphisms from a CSF metabolites genome-wide association study. Metabolome-wide association study results showed several significantly associated metabolites for all the biomarkers except Aβ42/40 and IL-6. Genetic variants associated with metabolites and Mendelian randomization analysis provided evidence for a causal association of metabolites for soluble triggering receptor expressed on myeloid cells 2 (sTREM2), amyloid β (Aβ40), α-synuclein, total tau, phosphorylated tau, and neurogranin, for example, palmitoyl sphingomyelin (d18:1/16:0) for sTREM2, and erythritol for Aβ40 and α-synuclein. This study provides evidence that CSF metabolites are associated with AD-related pathology, and many of these associations may be causal.

Prediction of worsening heart failure in hypertrophic cardiomyopathy using plasma proteomics

ObjectiveHeart failure (HF) is one of the most common and lifestyle-limiting complications of hypertrophic cardiomyopathy (HCM). Prediction of worsening HF using clinical measures alone remains limited. Moreover, the mechanisms by...

280-OR: Metabolomic Signatures of Excess Fetal Growth in Pregnancies Complicated by Type 1 Diabetes (T1D)

Background: In pregnancies complicated by T1D, glycemic control is only moderately associated with excess fetal growth, suggesting that nutrients other than glucose may be involved. Aims: We analyzed associations between metabolites in maternal and newborn plasma, and fetal growth patterns, in T1D pregnancies. Methods: We obtained maternal plasma samples in the 2nd and 3rd trimester and at delivery, and cord blood samples immediately after delivery, in 22 mother/infant dyads. We used an untargeted metabolomic platform (Broad Institute) and calculated correlation coefficients between individual metabolites and newborn growth percentiles adjusted for gestational age, sex, parity, and ethnicity (GROW percentile). We used a false discovery rate threshold of FDR&amp;lt;0.2. Large for gestational age (LGA) was defined as GROW percentile ≥90 and appropriate for gestational age (AGA) as between the 10th and 90th percentiles. Results: Forty-five percent of newborns were classified as LGA. Maternal age, BMI, diabetes duration, insulin dose and pump use did not differ between LGA vs. AGA. We identified stronger associations between GROW percentiles and metabolites in cord blood than with metabolites in maternal plasma during the 2nd or 3rd trimester. In cord blood, 29 metabolites were associated with GROW percentile (FDR&amp;lt;0.2). For 51 metabolites, the ratio between abundance in cord blood to abundance in maternal blood at delivery was associated with the GROW percentile (FDR &amp;lt;0.2). Many of the top-ranking metabolites positively associated with infant growth were long-chain glycerophosphocholines (e.g., LPC(20:3) β 0.035, p=0.0002, FDR 0.01; LPC(22:5) β 0.033, p=0.0008, FDR 0.03). Conclusion: Glycerophospholipids in cord blood were associated with excess fetal growth in T1D pregnancies, suggesting alterations in lipid metabolism. We also report associations between fetal growth and ratios of metabolites in cord blood to maternal blood, suggesting differences in placental transport. Disclosure E.M.Isganaitis: None. D.Wolfs: None. J.C.O'connell: None. G.A.Hansbury: None. S.Wolpowitz: None. C.B.Clish: None. T.James-todd: None. F.M.Brown: Other Relationship; Dexcom, Inc. Funding National Institute of Diabetes and Digestive and Kidney Diseases (P30DK036836, P30DK057521); Broad Institute

Influence of chemical dose and exposure duration on protein synthesis in green sea turtle primary cells

Understanding the impacts of chemical exposure in marine wildlife is challenging, due to practical and ethical constraints that preclude traditional toxicology research on these animals. This study addressed some of these limitations by presenting an ethical and high throughput cell-based approach to elucidate molecular-level effects of contaminants on sea turtles. The experimental design addressed basic questions of cell-based toxicology, including chemical dose and exposure time. Primary green turtle skin cells were exposed to polychlorinated biphenyl (PCB) 153 and perfluorononanoic acid (PFNA) for 24 and 48 h, at three sub-lethal, environmentally relevant concentrations (1, 10 and 100 μg/L). Sequential window acquisition of all theoretical mass spectra (SWATH-MS) identified over 1000 differentially abundant proteins within the 1% false discovery rate (FDR) threshold. The 24 h exposure resulted in a greater number of differentially abundant proteins, compared to 48 h exposure, for both contaminants. However, there were no statistically significant dose-response relationships for the number of differentially synthesised proteins, nor differences in the proportion of increased vs decreased proteins between or within exposure times. Known in vivo markers of contaminant exposure, superoxide dismutase and glutathione S-transferase, were differentially abundant following exposure to PCB153 and PFNA. SignificanceCell-based (in vitro) proteomics provides an ethical and high throughput approach to understanding the impacts of chemical contamination on sea turtles. Through investigating effects of chemical dose and exposure duration on unique protein abundance in vitro, this study provides an optimised framework for conducting cell-based studies in wildlife proteomics, and highlights that proteins detected in vitro could act as biomarkers of chemical exposure and effect in vivo.

Bridging the False Discovery Gap.

Controlling the false discovery rate (FDR) among discoveries from a tandem mass spectrometry proteomics experiment using target decoy competition (TDC) controls only the proportion of false discoveries in an average sense. Thus, for any particular analysis, even with a valid FDR control procedure, the proportion of false discoveries (the FDP) may be higher than the specified FDR threshold. We demonstrate this phenomenon using real data and describe two recently developed methods that help bridge the gap between controlling the expected or average rate of false discoveries and the empirical rate (FDP). The FDP Stepdown method controls the FDP at any desired confidence level, and the TDC Uniform Band provides a confidence, or upper prediction bound, on the FDP in TDC's list of discoveries.

MYC amplification segment-size mutual exclusivity analysis with other oncogenic events in a pan-cancer sequencing cohort.

3073 Background: MYC gene alterations resulting in increased copy number are recurrent oncogenic alterations across human malignancies. Presently no clear data exists to aid in interpreting MYC amplification characteristics for identifying MYC-dependent tumors. Methods: Analysis was conducted on a center-wide cohort of 68,920 tumor-normal matched samples from pediatric and adult patients sequenced with an FDA-authorized targeted sequencing panel (MSK-IMPACT). To ascertain tumor content, ploidy and allelic specific gene copy number, tumor-normal samples were analyzed with FACETS. Samples with tumor purity &lt;20% were excluded. MYC amplification was defined as total copy number (TCN) minus ploidy ≥ 4. All samples were queried for presence of concurrent oncogenic or likely-oncogenic alterations based on OncoKb annotation. Co-occurrence (Co) and mutual-exclusivity (Me) analysis between MYC amplification according to segment size and other oncogenic alterations was performed with DISCOVER (false discovery rate threshold of 0.01) for each tumor type. Results: After removing low-quality samples (n=19,010/68,920), 49,910 samples were included in the analysis. 3,219 (6.4%) samples harbored MYC amplification, with segment size ranging from less than 100Kb to more than 100Mb, with 38% samples displaying focal amplifications shorter than 10 Mb and 62% broad amplifications longer than 10 Mb. TCN was inversely correlated with segment size (R= -0.34, p=2.2e-16). Triple-negative breast cancer (13.3%), hepatocellular carcinoma (8.7%), neuroendocrine tumors of the rectum (8.3%), high-grade serous ovarian cancer (7.6%) and large cell neuroendocrine carcinomas of the lung (6.7%) had the highest prevalence of MYC amplification without concurrent potentially driver oncogene mutations, amplifications or fusions. CoMe analysis demonstrated mutual exclusivity of MYC gene amplification regardless of segment size with most major tumor-type specific oncogenic events. All MYC amplifications were mutually exclusive with MET splice variants and mutations (q&lt; 0.001) and KRAS mutations (q&lt; 0.001) in lung adenocarcinoma (LUAD), FGFR3 mutations (q&lt; 0.001) and fusions (q&lt; 0.001) in bladder cancer, PTEN mutations (q&lt; 0.001) in hormone receptor-positive breast cancer, KRAS mutations (q&lt; 0.001) in colorectal cancer and CDK4 amplifications (q&lt; 0.001) in sarcomas. Broad MYC amplifications were mutually exclusive with RET, ROS1 and ALK fusions in LUAD, while focal ones co-occurred with RET (q=0.007) and ALK fusions (q&lt; 0.001) or secondary mutations (q&lt; 0.001). Conclusions: This dataset defines a subgroup of MYC amplified cancers without co-occurring drivers and further subdivided by segment size, providing information that may help better identify patients for trials of novel MYC-directed therapies.

Aberrantly Expressed Hsa_circ_0060762 and CSE1L as Potential Peripheral Blood Biomarkers for ALS.

Amyotrophic lateral sclerosis (ALS) is a rapidly progressive adult-onset neurodegenerative disease that is often diagnosed with a delay due to initial non-specific symptoms. Therefore, reliable and easy-to-obtain biomarkers are an absolute necessity for earlier and more accurate diagnostics. Circular RNAs (circRNAs) have already been proposed as potential biomarkers for several neurodegenerative diseases. In this study, we further investigated the usefulness of circRNAs as potential biomarkers for ALS. We first performed a microarray analysis of circRNAs on peripheral blood mononuclear cells of a subset of ALS patients and controls. Among the differently expressed circRNA by microarray analysis, we selected only the ones with a host gene that harbors the highest level of conservation and genetic constraints. This selection was based on the hypothesis that genes under selective pressure and genetic constraints could have a major role in determining a trait or disease. Then we performed a linear regression between ALS cases and controls using each circRNA as a predictor variable. With a False Discovery Rate (FDR) threshold of 0.1, only six circRNAs passed the filtering and only one of them remained statistically significant after Bonferroni correction: hsa_circ_0060762 and its host gene CSE1L. Finally, we observed a significant difference in expression levels between larger sets of patients and healthy controls for both hsa_circ_0060762 and CSE1L. CSE1L is a member of the importin β family and mediates inhibition of TDP-43 aggregation; the central pathogenicity in ALS and hsa_circ_0060762 has binding sites for several miRNAs that have been already proposed as biomarkers for ALS. In addition, receiver operating characteristics curve analysis showed diagnostic potential for CSE1L and hsa_circ_0060762. Hsa_circ_0060762 and CSE1L thus represent novel potential peripheral blood biomarkers and therapeutic targets for ALS.

Schizophrenia and co-morbidity risk: Evidence from a data driven phenomewide association study

Schizophrenia is a chronic debilitating psychiatric disorder with significant morbidity and mortality. In this study, we used information from 337,484 UK Biobank participants and performed PheWAS using schizophrenia genetic risk score on 1135 disease outcomes. Signals that passed the false discovery rate threshold were further analyzed for evidence on the causality of the association. We extended the analysis to 30 serum, four urine, and six neuroimaging biomarkers to identify biomarkers that could be affected by schizophrenia. Schizophrenia GRS was associated with 54 (39 distinct) disease outcomes including schizophrenia in the PheWAS analysis. Of these, a causal association were found with 10 distinct diseases in the MR analysis. Schizophrenia causally linked with higher odds of anxiety (OR = 1.41, 95%CI 1.12 to 1.21), bipolar disorder (OR = 1.52, 95%CI 1.36 to 1.70), major depressive disorder (OR = 1.12, 95%CI 1.08 to 1.16) and suicidal ideation (OR = 1.30, 95%CI 1.19 to 1.42). Lower odds were found for several diseases including type 1 diabetes, coronary atherosclerosis and some musculoskeletal disorders. In analyses using biomarkers, schizophrenia was associated with lower serum 25(OH)D, gamma glutamyltransferase, cystatin C, serum creatinine. However, we did not find association with any of the brain imaging markers. Our analyses confirmed the co-existence of schizophrenia with other mental health disorders but did not otherwise suggest strong effects on disease risk. Biomarker analyses reflected associations which could be explained by unhealthy lifestyles, suggesting patients with schizophrenia may benefit from screening for and managing broader health aspects.