False Discovery Rate Adjustment Research Articles

Screening and Predictive Biomarkers for Down Syndrome Through Amniotic Fluid Metabolomics.

Down syndrome (DS) is a congenital disorder caused by the presence of an extra copy of all or part of chromosome 21. It is characterized by significant intellectual disability, distinct facial features, and growth and developmental challenges. The utilization of metabolomics to analyze specific metabolic markers in maternal amniotic fluid may provide innovative tools and screening methods for investigating the early pathophysiology of trisomy 21 at the functional level. Amniotic fluid samples were obtained via amniocentesis from 57 pregnancies with DS and 55 control pregnancies between 173/7 and 240/7weeks of gestation. The targeted metabolomics focused on 34 organic acids, 17 amino acids, and 5 acylcarnitine metabolites. The untargeted metabolomics analysis concentrated on lipid profiles and included 602 metabolites that met quality control standards. Principal Component Analysis, Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA), and false discovery rate (FDR) adjustments were applied. MetaboAnalystR 5.0 was used to perform the metabolic pathway analysis on the identified differential metabolites. Fifty differential metabolites, including L-glutamine, eight organic acids, and 41 lipids, were significantly altered in DS based on three criteria: VIP > 1 in the OPLS-DA model, FDR-adjusted p-value < 0.05, and |log2FC|>log2(1.5) from a volcano plot of all detected metabolites. An analysis of 212 differential metabolites, selected from both targeted and untargeted approaches (VIP > 1 in the OPLS-DA model and FDR-adjusted p-value < 0.05), revealed significant changes in nine metabolic pathways. Fourteen key metabolites were identified to establish a screening model for DS, achieving an area under the curve of 1.00. Our results underscore the potential of metabolomics approaches in identifying concise and reliable biomarker combinations that demonstrate promising screening performance in DS.

GWAS of multiple neuropathology endophenotypes identifies new risk loci and provides insights into the genetic risk of dementia.

Genome-wide association studies (GWAS) have identified >80 Alzheimer's disease and related dementias (ADRD)-associated genetic loci. However, the clinical outcomes used in most previous studies belie the complex nature of underlying neuropathologies. Here we performed GWAS on 11 ADRD-related neuropathology endophenotypes with participants drawn from the following three sources: the National Alzheimer's Coordinating Center, the Religious Orders Study and Rush Memory and Aging Project, and the Adult Changes in Thought study (n = 7,804 total autopsied participants). We identified eight independent significantly associated loci, of which four were new (COL4A1, PIK3R5, LZTS1 and APOC2). Separately testing known ADRD loci, 19 loci were significantly associated with at least one neuropathology after false-discovery rate adjustment. Genetic colocalization analyses identified pleiotropic effects and quantitative trait loci. Methylation in the cerebral cortex at two sites near APOC2 was associated with cerebral amyloid angiopathy. Studies that include neuropathology endophenotypes are an important step in understanding the mechanisms underlying genetic ADRD risk.

The lung proteome in HIV-associated obstructive lung disease (OLD)

RationaleObstructive lung disease is increasingly common among persons living with HIV (PLWH). There are currently no validated biomarkers that identify individuals at risk of developing obstructive lung disease (OLD) and specific mechanisms contributing to HIV-associated OLD remain elusive, independent of smoking.ObjectivesWe sought to identify biomarkers and biological pathways associated with OLD using a broad proteomic approach.MethodsWe performed tandem mass tagging and mass spectrometry (MS) analysis on bronchoalveolar lavage fluid (BALF) samples from persons living with HIV with OLD (n=26) and without OLD (n=26). We combined untargeted MS with a targeted SomaScan aptamer-based approach. We used Pearson correlation tests to identify associations between each protein and lung function (FEV1pp). We adjusted for multiple comparisons using a false discovery rate (FDR) adjustment. Significant proteins were entered into a pathway overrepresentation analysis. Protein-driven endotypes were constructed using K-means clustering.Measurements and main resultsWe identified over 3800 proteins by MS and identified 254 proteins that correlated with FEV1pp when we combined the MS and SomaScan proteomes when adjusting for smoking status. Pathway analysis revealed cell adhesion molecules as significant.ConclusionsProtein expression differs in the lung of PWH and decreased lung function (FEV1pp). Pathway analysis reveals cell adhesion molecules having potentially important roles in this process.

Altered Resting-State Electroencephalogram Microstate Characteristics in Stroke Patients.

Stroke remains a leading cause of disability globally and movement impairment is the most common complication in stroke patients. Resting-state electroencephalography (EEG) microstate analysis is a non-invasive approach of whole-brain imaging based on the spatiotemporal pattern of the entire cerebral cortex. The present study aims to investigate microstate alterations in stroke patients. Resting-state EEG data collected from 24 stroke patients and 19 healthy controls matched by age and gender were subjected to microstate analysis. For four classic microstates labeled as class A, B, C and D, their temporal characteristics (duration, occurrence and coverage) and transition probabilities (TP) were extracted and compared between the two groups. Furthermore, we explored their correlations with clinical outcomes including the Fugl-Meyer assessment (FMA) and the action research arm test (ARAT) scores in stroke patients. Finally, we analyzed the relationship between the temporal characteristics and spectral power in frequency bands. False discovery rate (FDR) method was applied for correction of multiple comparisons. Microstate analysis revealed that the stroke group had lower occurrence of microstate A which was regarded as the sensorimotor network (SMN) compared with the control group (p = 0.003, adjusted p = 0.036, t = -2.959). The TP from microstate A to microstate D had a significant positive correlation with the Fugl-Meyer assessment of lower extremity (FMA-LE) scores (p = 0.049, r = 0.406), but this finding did not survive FDR adjustment (adjusted p = 0.432). Additionally, the occurrence and the coverage of microstate B were negatively correlated with the power of delta band in the stroke group, which did not pass adjustment (p = 0.033, adjusted p = 0.790, r = -0.436; p = 0.026, adjusted p = 0.790, r = -0.454, respectively). Our results confirm the abnormal temporal dynamics of brain activity in stroke patients. The study provides further electrophysiological evidence for understanding the mechanism of brain motor functional reorganization after stroke.

Metabolic phenotypes and vitamin D response in the critically ill: A metabolomic cohort study

Background & AimsAlthough vitamin D deficiency is common in critically ill patients, randomized controlled trials fail to demonstrate benefits of supplementation. We aimed to identify distinct vitamin D3 responsive metabolic phenotypes prior to trial intervention of high-dose vitamin D3 by applying machine learning clustering method to metabolomics data from the Correction of Vitamin D Deficiency in Critically Ill Patients (VITdAL-ICU) trial. MethodsIn the randomized, placebo-controlled VITdAL-ICU trial, critically ill adults received placebo or high-dose vitamin D3. To distinguish vitamin D3 responsive metabolic phenotypes prior to intervention, we implemented consensus clustering with partitioning around medoids algorithm to the plasma metabolome data before randomization. Individual metabolite differences were determined utilizing linear mixed-effects regression models stratified for metabolomic phenotypes with false discovery rate adjustment. The association between vitamin D3 supplementation and 180-day mortality was evaluated in each metabolic phenotype, applying multivariable logistic regression analysis. ResultsIn 453 critically ill adults, the study identified 4 distinct metabolic phenotypes (clusters A. N=134; B. N=123; C. N=92; D. N=104). We found differential metabolic pathway patterns in the four clusters. Specifically, branched chain amino acid catabolic metabolites, long-chain acylcarnitines and diacylglycerol species are significantly increased in a specific metabolic phenotype (cluster D) following high-dose vitamin D3. Further, in cluster D high-dose vitamin D3 supplementation had a significantly lower adjusted odds of 180-day mortality after controlling age, sex, Simplified Acute Physiology Score II, admission diagnosis, and baseline 25-hydroxyvitamin D (OR 0.28 (95%CI, 0.09–0.89); P=0.03). In metabotype A, B, and C, high-dose vitamin D3 supplementation was not significantly associated with lower 180-day mortality following multivariable adjustment. ConclusionIn this post-hoc cohort study of the VITdAL-ICU trial, the clustering analysis of plasma metabolome data identified biologically distinct metabolic phenotypes. Among clusters, we found the different associations between high-dose vitamin D3 supplementation and specific metabolite pathways as well as 180-day mortality. Our findings facilitate further research to validate metabolic phenotype-targeted strategies for critical illness treatments.

Causal relationship between immune cells and pulmonary arterial hypertension: Mendelian randomization analysis.

Immunity and inflammation in pulmonary arterial hypertension (PAH) has gained more attention. This research aimed to investigate the potential causal connections between 731 immunophenotypes and the likelihood of developing PAH. We obtained immunocyte data and PAH from openly accessible database and used Mendelian randomization (MR) analysis to evaluate the causal association between each immunophenotype and PAH. Various statistical methods were employed: the MR-Egger, weighted median, inverse variance weighted (IVW), simple mode, and weighted mode. In the study of 731 different types of immune cells, it was found that 9 showed a potential positive connection (IVW P < .05) with increased risk of PAH, while 19 had a possible negative link to decreased risk. Following false discovery rate (FDR) adjustment, the analysis using the IVW method demonstrated that 5 immune phenotypes were significantly associated with PAH (FDR < 0.05, OR > 1). Conversely, there was a negative correlation between PAH and 4 immune cell types (FDR < 0.05, OR < 1). Sensitivity analyses suggested the robustness of all MR findings. This research, for the first time, has revealed indicative evidence of a causal link between circulating immune cell phenotypes and PAH through genetic mechanisms. These results underscore the importance of immune cells in the pathogenesis of PAH.

Exploring the heart-brain and brain-heart axes: Insights from a bidirectional Mendelian randomization study on brain cortical structure and cardiovascular disease

IntroductionThe bidirectional relationship between the brain cortex and cardiovascular diseases (CVDs) remains inadequately explored. MethodsThis study used bidirectional Mendelian randomization (MR) analysis to explore the interactions between nine phenotypes associated with hypertension, heart failure, atrial fibrillation (AF), and coronary heart disease (CHD), and brain cortex measurements. These measurements included total surface area (SA), average thickness (TH), and the SA and TH of 34 regions defined by the Desikan-Killiany atlas. The nine traits were obtained from sources such as the UK Biobank and FinnGen, etc., while MRI-derived traits of cortical structure were sourced from the ENIGMA Consortium. The primary estimate was obtained using the inverse-variance weighted approach. A false discovery rate adjustment was applied to the p-values (resulting in q-values) in the analyses of regional cortical structures. ResultsA total of 1,260 two-sample MR analyses were conducted. Existing CHD demonstrated an influence on the SA of the banks of the superior temporal sulcus (bankssts) (q=0.018) and the superior frontal lobe (q=0.018), while hypertension was associated with changes in the TH of the lateral occipital region (q=0.02). Regarding the effects of the brain cortex on CVD incidence, total SA was significantly associated with the risk of CHD. Additionally, 16 and 3 regions exhibited significant effects on blood pressure and AF risk, respectively (q<0.05). These regions were primarily located in the frontal, temporal, and cingulate areas, which are associated with cognitive function and mood regulation. ConclusionThe detection of cortical changes through MRI could aid in screening for potential neuropsychiatric disorders in individuals with established CVD. Moreover, abnormalities in cortical structure may predict future CVD risk, offering new insights for prevention and treatment strategies.

Single gene mutations and prognosis in limited-stage follicular lymphoma treated with radiation therapy.

Radiotherapy is routinely used for management of limited-stage follicular lymphoma (FL), yet half of patients ultimately relapse. We hypothesized that the presence of specific gene mutations may predict outcomes. We performed targeted sequencing of a 69-gene panel in 117 limited-stage FL patients treated with radiotherapy and identified recurrently mutated genes. CREBBP was most frequently mutated, and mutated CREBBP was associated with inferior progression-free survival, though not after false discovery rate adjustment. This association failed to validate in an independent cohort. We conclude that recurrent gene mutations do not predict outcomes in this setting. Alternative biomarkers may offer better prognostic insight.

Awareness of Breast Cancer Risk Factors in Women with vs. Without High Breast Density.

Women with high breast density (HBD) carry an increased risk for breast cancer (BC). The aim of the study was to provide data on awareness and knowledge gaps among women with vs w/o HBD about BC risk factors (BCRFs), which is the basis for effective communication about screening. This was a web-based survey of 3000 women aged ≥30 and ≤70 from six countries. It comprised of 45 questions. T-tests and chi-square tests with False Discovery Rate adjustments were conducted as applicable, with significant differences reported at α=0.05. Three-thousand women were included in the analysis, 733 (24.4%) had HBD. Overall, 39% of women were familiar with the concept of HBD in the context of BC. Thirty-one percent of women were aware of HBD as BCRF and for 24% of women HBD was personally applicable. A significantly higher proportion of women with HBD were aware of almost all BCRFs compared to women w/o HBD (p ≤ 0.05). Similarly, a significantly higher proportion of women with HBD have undergone screening procedures compared to women w/o HBD (p ≤ 0.05). Women with HBD were significantly better aware of basic facts about BC (p ≤ 0.05). A total of 1617 women underwent mammography, 904 ultrasound and 150 MRI during their last screening. The most relevant source of information about BC was the health care professional, as reported by 63% of women. Overall 39% of women were familiar with HBD as BCRF. Lack of BCRF awareness may contribute to delayed screenings, missed opportunities for early detection, and potentially poorer outcomes for individuals with dense breast tissue. Thus, this information should be communicated more widely.

A Metabolomics Approach to Identify Metabolites Associated With Mortality in Patients Receiving Maintenance Hemodialysis

BackgroundUremic toxins contributing to increased risk of death remain largely unknown. We used untargeted metabolomics to identify plasma metabolites associated with mortality in patients receiving maintenance hemodialysis. MethodsWe measured metabolites in serum samples from 522 Longitudinal US/Canada Incident Dialysis (LUCID) study participants. We assessed the association between metabolites and 1-year mortality, adjusting for age, sex, race, cardiovascular disease, diabetes, body mass index, serum albumin, Kt/Vurea, dialysis duration, and country. We modeled these associations using limma, a metabolite-wise linear model with empirical Bayesian inference, and two machine learning (ML) models: LASSO and random forest (RF). We accounted for multiple testing using a false discovery rate (pFDR) adjustment. We defined significant mortality-metabolite associations as pFDR<0.1 in the limma model and metabolites of at least medium importance in both ML models. ResultsThe mean age of the participants was 64 years, the mean dialysis duration was 35 days, and there were 44 deaths (8.4%) during a 1-year follow-up period. Two metabolites were significantly associated with 1-year mortality. Quinolinate levels (kynurenine pathway metabolite) were 1.72-fold higher in patients who died by year 1 compared to those who did not (pFDR, 0.009), while mesaconate levels (an emerging immunometabolite) were 1.57-fold higher (pFDR, 0.002). An additional 42 metabolites had high importance by LASSO, 46 by RF, and 9 by both ML models but were not significant by limma. ConclusionQuinolinate and mesaconate were significantly associated with a 1-year risk of death in incident patients receiving maintenance hemodialysis. External validation of our findings is needed.

Ketamine vs Electroconvulsive Therapy for Treatment-Resistant Depression

The ELEKT-D: Electroconvulsive Therapy (ECT) vs Ketamine in Patients With Treatment Resistant Depression (TRD) (ELEKT-D) trial demonstrated noninferiority of intravenous ketamine vs ECT for nonpsychotic TRD. Clinical features that can guide selection of ketamine vs ECT may inform shared decision-making for patients with TRD. To evaluate whether selected clinical features were associated with differential improvement with ketamine vs ECT. This secondary analysis of an open-label noninferiority randomized clinical trial was a multicenter study conducted at 5 US academic medical centers from April 7, 2017, to November 11, 2022. Analyses for this study, which were not prespecified in the trial protocol, were conducted from May 10 to Oct 31, 2023. The study cohort included patients with TRD, aged 21 to 75 years, who were in a current nonpsychotic depressive episode of at least moderate severity and were referred for ECT by their clinicians. Eligible participants were randomized 1:1 to receive either 6 infusions of ketamine or 9 treatments with ECT over 3 weeks. Association between baseline factors (including 16-item Quick Inventory of Depressive Symptomatology Self-Report [QIDS-SR16], Montgomery-Asberg Depression Rating Scale [MADRS], premorbid intelligence, cognitive function, history of attempted suicide, and inpatient vs outpatient status) and treatment response were assessed with repeated measures mixed-effects model analyses. Among the 365 participants included in this study (mean [SD] age, 46.0 [14.5] years; 191 [52.3%] female), 195 were randomized to the ketamine group and 170 to the ECT group. In repeated measures mixed-effects models using depression levels over 3 weeks and after false discovery rate adjustment, participants with a baseline QIDS-SR16 score of 20 or less (-7.7 vs -5.6 points) and those starting treatment as outpatients (-8.4 vs -6.2 points) reported greater reduction in the QIDS-SR16 with ketamine vs ECT. Conversely, those with a baseline QIDS-SR16 score of more than 20 (ie, very severe depression) and starting treatment as inpatients reported greater reduction in the QIDS-SR16 earlier in course of treatment (-8.4 vs -6.7 points) with ECT, but scores were similar in both groups at the end-of-treatment visit (-9.0 vs -9.9 points). In the ECT group only, participants with higher scores on measures of premorbid intelligence (-14.0 vs -11.2 points) and with a comorbid posttraumatic stress disorder diagnosis (-16.6 vs -12.0 points) reported greater reduction in the MADRS score. Those with impaired memory recall had greater reduction in MADRS during the second week of treatment (-13.4 vs -9.6 points), but the levels of MADRS were similar to those with unimpaired recall at the end-of-treatment visit (-14.3 vs -12.2 points). Other results were not significant after false discovery rate adjustment. In this secondary analysis of the ELEKT-D randomized clinical trial of ECT vs ketamine, greater improvement in depression was observed with intravenous ketamine among outpatients with nonpsychotic TRD who had moderately severe or severe depression, suggesting that these patients may consider ketamine over ECT for TRD.

Lower Independent Self-Care Readiness Persists over Time in Teens with Type 1 Diabetes and Executive Function Challenges.

Management of type 1 diabetes is complex and benefits from adequate executive function (EF) (planning, organization, problem-solving). Teens with diabetes and executive dysfunction may have challenges with acquisition of self-care skills. Over 18 months, parents of teens with type 1 diabetes aged 13-17 completed the Diabetes Family Responsibility Questionnaire (DFRQ) and Readiness for Independent Self-Care Questionnaire (RISQ) every 6 months. Parents assessed teen EF, completing the Behavior Rating Inventory of Executive Function (BRIEF). T-score ≥60 defined EF challenges. EF, demographic, and diabetes treatment variables predicted RISQ score over time using longitudinal mixed modeling with false discovery rate adjustment. There were 169 teen participants (54% male) aged 15.9±1.3 years, diabetes duration 8.4±3.7 years, and A1c 8.6±1.2%. About a third (31.4%) of teens had parent-reported BRIEF Global Executive Composite (GEC) scores ≥60. After adjusting for age, gender, and DFRQ, those with GEC <60 had RISQ score 4.1 points higher than those with GEC ≥60, p=0.016. Behavioral regulation index (BRI; adjusted for age, CGM use, DFRQ, and A1c) did not predict RISQ while metacognition index (MI; adjusted for age, gender, and DFRQ) did; those with MI <60 had RISQ score 5.3 points higher than those with MI ≥60, p<0.001. In all models, older teen age (p<0.05) and less parental involvement (p<0.001) predicted higher RISQ score. EF skills, especially metacognition, appear important for acquisition of self-care behaviors in teens with type 1 diabetes. Evaluating EF during adolescence may identify teens needing extra support during the transition process.

Promoting equity in clinical research: The role of social determinants of health

ObjectiveThis study aims to investigate the association between social determinants of health (SDoH) and clinical research recruitment outcomes and recommends evidence-based strategies to enhance equity. Materials and MethodsData were collected from the internal clinical study manager database, clinical data warehouse, and clinical research registry. Study characteristics (e.g., study phase) and sociodemographic information were extracted. Median neighborhood income, distance from the study location, and Area Deprivation Index (ADI) were calculated. Mixed effect generalized regression was used for clustering effects and false discovery rate adjustment for multiple testing. A stratified analysis was performed to examine the impact in distinct medical departments. ResultsThe study sample consisted of 3,962 individuals, with a mean age of 61.5 years, 53.6 % male, 54.2 % White, and 49.1 % non-Hispanic or Latino. Study characteristics revealed a variety of protocols across different departments, with cardiology having the highest percentage of participants (46.4 %). Industry funding was the most common (74.5 %), and digital advertising and personal outreach were the main recruitment methods (58.9 % and 90.8 %). DiscussionThe analysis demonstrated significant associations between participant characteristics and research participation, including biological sex, age, ethnicity, and language. The stratified analysis revealed other significant associations for recruitment strategies. SDoH is crucial to clinical research recruitment, and this study presents evidence-based solutions for equity and inclusivity. Researchers can tailor recruitment strategies to overcome barriers and increase participant diversity by identifying participant characteristics and research involvement status. ConclusionThe findings highlight the relevance of clinical research inequities and equitable representation of historically underrepresented populations. We need to improve recruitment strategies to promote diversity and inclusivity in research.

Causal relationship between immune cells and aortic aneurysms: a Mendelian randomization study.

The causal association between immune cell traits and aortic aneurysm remains unknown. We performed a bidirectional two-sample Mendelian randomization analysis to explore the causality between 731 immune cell characteristics and the risk of abdominal aortic aneurysm and thoracic aortic aneurysms through publicly available genetic data, respectively. To examine heterogeneity and horizontal pleiotropy, Cochran's Q test and MR-Egger intercept were utilized. Additionally, multivariable Mendelian randomization analysis and meta-analysis were performed in further analysis. We found that 20 immune phenotypes had a suggestive causality on abdominal aortic aneurysm, and 15 immune phenotypes had a suggestive causal effect on thoracic aortic aneurysm. After further false discovery rate adjustment (q value <0.1), CD20 on IgD+ CD38- B cell (q = 0.053) and CD127 on CD28+ CD4+ T cell (q = 0.096) were associated with an increased risk of abdominal aortic aneurysm, respectively, indicating a significant causality between them. After adjusting for smoking, there is still statistical significance between CD127 on CD28+ CD4+ T cell and abdominal aortic aneurysm. However, after adjusting for lipids, no statistical significance can be observed between CD127 on CD28+ CD4+ T cells and abdominal aortic aneurysm. Furthermore, there is still statistical significance between CD20 on IgD+ CD38- B cells and abdominal aortic aneurysm after adjusting for lipids and smoking, which was further identified by meta-analysis. We found a causal association between immune cell traits and aortic aneurysm by genetic methods, thus providing new avenues for future mechanism studies.

Fasting and postprandial plasma metabolite responses to a 12-wk dietary intervention in tissue-specific insulin resistance: a secondary analysis of the PERSonalized glucose Optimization through Nutritional intervention (PERSON) randomized trial

BackgroundWe previously showed that dietary intervention effects on cardiometabolic health were driven by tissue-specific insulin resistance (IR) phenotype: individuals with predominant muscle IR (MIR) benefited more from a low-fat, high-protein, and high-fiber (LFHP) diet, whereas individuals with predominant liver insulin resistance (LIR) benefited more from a high-monounsaturated fatty acid (HMUFA) diet. ObjectivesTo further characterize the effects of LFHP and HMUFA diets and their interaction with tissue-specific IR, we investigated dietary intervention effects on fasting and postprandial plasma metabolite profile. MethodsAdults with MIR or LIR (40–75 y, BMI 25–40 kg/m2) were randomly assigned to a 12-wk HMUFA or LFHP diet (n = 242). After the exclusion of statin use, 214 participants were included in this prespecified secondary analysis. Plasma samples were collected before (T = 0) and after (T = 30, 60, 120, and 240 min) a high-fat mixed meal for quantification of 247 metabolite measures using nuclear magnetic resonance spectroscopy. ResultsA larger reduction in fasting VLDL-triacylglycerol (TAG) and VLDL particle size was observed in individuals with MIR following the LFHP diet and those with LIR following the HMUFA diet, although no longer statistically significant after false discovery rate (FDR) adjustment. No IR phenotype-by-diet interactions were found for postprandial plasma metabolites assessed as total area under the curve (tAUC). Irrespective of IR phenotype, the LFHP diet induced greater reductions in postprandial plasma tAUC of the larger VLDL particles and small HDL particles, and TAG content in most VLDL subclasses and the smaller LDL and HDL subclasses (for example, VLDL-TAG tAUC standardized mean change [95% CI] LFHP = −0.29 [−0.43, −0.16] compared with HMUFA = −0.04 [−0.16, 0.09]; FDR-adjusted P for diet × time = 0.041). ConclusionsDiet effects on plasma metabolite profiles were more pronounced than phenotype-by-diet interactions. An LFHP diet may be more effective than an HMUFA diet for reducing cardiometabolic risk in individuals with tissue-specific IR, irrespective of IR phenotype. Am J Clin Nutr 20xx;x:xx.This trial was registered at the clinicaltrials.gov registration (https://clinicaltrials.gov/study/NCT03708419?term=NCT03708419&rank=1) as NCT03708419 and CCMO registration (https://www.toetsingonline.nl/to/ccmo_search.nsf/fABRpop?readform&unids=3969AABCD9BA27FEC12587F1001BCC65) as NL63768.068.17.

Biomarker analysis and updated clinical outcomes: Neoadjuvant systemic treatment (NST) with nivolumab (nivo) and relatlimab (rela) in surgically resectable melanoma.

9587 Background: NST with immune checkpoint blockade (ICB) improves clinical outcomes over upfront surgery followed by adjuvant treatment (tx) in patients (pts) with stage III, surgically resectable melanoma. The NST platform also provides an opportunity for deep translational analysis to identify baseline (BL) biomarkers predicting pathologic response and to gain insights into resistance. BL biomarkers, including gene expression signatures (GES) such as IFN-γ/ tumor mutational burden, tumor infiltrating lymphocytes, and presence of tertiary lymphoid structures, have been associated with pathologic response to NST with anti-PD1 and/or anti-CTLA4 antibodies. These studies have not evaluated the newest ICB combination, nivo (anti-PD1) + rela (anti-LAG3), which achieved a major pathologic response rate (MPR) (≤10% viable tumor) of 63% in a Ph II study (NCT02519322). Here we report GES analysis from BL and longitudinal tumor tissues obtained on this study and correlations with outcomes. Methods: Longitudinal tissue was collected from 30 pts treated on the clinical trial and available RNA analyzed using the NanoString nCounter PanCancer IO360 panel. Clinical outcomes, including recurrence and event-free survival, were also updated with longer follow-up. Pts were grouped into MPR and non- major pathologic responders (non MPR). Normalization, differential expression / GES evaluation was performed using nSolver Advanced Analysis software. Differential expression is fit on a per signatures basis using a linear model for analysis. P-values were adjusted within each analysis and on the grouping variable level difference t-test using the Benjamini and Yekutieli False Discovery Rate adjustment to account for correlations amongst the tests. BL analysis was grouped based on pathologic response, MPR vs non-MPR. Results: Of the 30 pts (median follow up 44 months), 53 RNA samples from 26 patients (9 NR and 17 R) were included in the full analysis. Immune GES with significantly higher (adjusted p&lt; 0.05) differences at BL in MPR vs non-MPR included: B cells, CD45, CD-8+ T cells, TIGIT, IDO1, and IFN-γ. Significantly higher B7-H3 GES at BL was associated with non MPR. Additional analyses (i.e., cell population changes over time) and association with event outcomes are underway. Conclusions: To our knowledge, this is the first longitudinal RNA analysis reported from pts treated with nivo+rela. BL immune features associated with major pathologic response include higher GES of B cells, CD45+ cells, CD8 T cells, and increased expression of TIGIT, IDO and IFN-y. Additionally, higher B7-H3 in non MPR pts may indicate a clinically actionable strategy for further evaluation. Ongoing analyses of longitudinal samples and correlations with clinical outcomes are underway and will be presented. Clinical trial information: NCT02519322 .

The Metabolomic Profile of Microscopic Colitis Is Affected by Smoking but Not Histopathological Diagnosis, Clinical Course, Symptoms, or Treatment.

Microscopic colitis (MC) is classified as collagenous colitis (CC) and lymphocytic colitis (LC). Genetic associations between CC and human leucocyte antigens (HLAs) have been found, with smoking being a predisposing external factor. Smoking has a great impact on metabolomics. The aim of this explorative study was to analyze global metabolomics in MC and to examine whether the metabolomic profile differed regarding the type and course of MC, the presence of IBS-like symptoms, treatment, and smoking habits. Of the 240 identified women with MC aged ≤73 years, 131 completed the study questionnaire; the Rome III questionnaire; and the Visual Analog Scale for Irritable Bowel Syndrome (VAS-IBS). Blood samples were analyzed by ultra-high-performance liquid chromatograph mass spectrometry (UHLC-MS/UHPLC-MSMS). The women, 63.1 (58.7-67.2) years old, were categorized based on CC (n = 76) and LC (n = 55); one episode or refractory MC; IBS-like symptoms or not; use of corticosteroids or not; and smoking habits. The only metabolomic differences found in the univariate model after adjustment for false discovery rate (FDR) were between smokers and non-smokers. Serotonin was markedly increased in smokers (p < 0.001). No clear patterns appeared when conducting a principal component analysis (PCA). No differences in the metabolomic profile were found depending on the type or clinical course of the disease, neither in the whole MC group nor in the subgroup analysis of CC.

Abstract PO2-13-05: Deciphering pregnancy-associated breast cancer: distinctive molecular profile and clinical implications from GEICAM/2017-07 EMBARCAM study

Abstract Background: Pregnancy-Associated Breast Cancer (PABC) is defined as BC diagnosed during pregnancy, breastfeeding, or within the first year postpartum. This challenging entity has a distinct biology and worst prognosis and presents an increased risk for metastasis and death compared to non-PABC patients. Identification of molecular pathways that define this malignancy is crucial to explain its biological characteristics and potential association with pregnancy as well as serve to identify new biomarkers with preventive and clinical implications. This study assesses the gene expression profile of a PABC cohort from the Registry Study of Pregnancy and Breast Cancer (GEICAM/2017-07 EMBARCAM study, NCT04603820) to identify distinct molecular signatures and altered pathways for this entity. Methods: This was a multicenter, observational and ambispective age-matched cohort of PABC patients (n=46) and non-PABC patients (n=49). We analyzed the expression of 776 genes involved in 23 key breast cancer pathways, using the nCounter® Breast Cancer 360™ Panel (NanoString Technologies) on BC tumor samples, including molecular subtypes by PAM50 gene signature. Associations between individual differential genes and epidemiological and clinical features of these patients were explored. Normalized differential expression values were log2-transformed for statistical analysis in nSolver Software (NanoString Technologies). P-values were adjusted within each gene/signature and on the grouping variable level difference t-test using the Benjamini and Yekutieli False Discovery Rate (FDR) adjustment. Results: PABC patients’ clinical subtypes were distributed as 43,5% HR-positive/HER2-negative, 17,4% HER2-positive and 39,1% triple negative BC. These patients reported higher family history of BC/ovarian cancer compared to non-PABC (52.17% vs 26.53%; p=0.0124). Differential gene expression showed distinct molecular profiles in PABC and non-PABC patients: significantly genes enrichment involved in cell proliferation and p53 signature for PABC patients and higher expression of apoptosis, TGF-β, and PTEN signatures for non-PABC (adj p&amp;lt; 0.05). Furthermore, CDK4 expression signature (adj p=0.124) and DNA damage repair signatures Homologous Recombination Deficiency (HDR) (adj p=0.083) and BRCAness (adj p=0.220) were also upregulated in PABC tumors. The most significantly upregulated genes in PABC patients (CCNA2, DEPDC1, FAM83D, CDC20, CDKN3, TRIP13, TTK, MAD2L1, KIF2C, and UBE2C) (adj p&amp;lt; 0.05) were involved in cell cycle regulation and DNA damage repair. PABC basal-like tumors were found to be significantly more prevalent than non-PABC, as per the PAM50 classification (45.7% vs 20.4%; p=0.020). Interestingly, basal-like PABC showed higher expression of ESR1 than basal-like non-PABC (logFC=1.486; p=0.022). In contrast, luminal A PABC tumors exhibited lower ESR1 expression vs non-PABC (logFC=-1.5; p=0.021). Additionally, HER2-enriched PABC tumors displayed lower B7-H3/CD276 expression compared to HER2-enriched non-PABC (adj p=0.031). Conclusions: Our study shows that PABC is potentially a clinical and molecular different entity with predominance of the basal-like subtype. Moreover, our results suggest the activation of oncogenic pathways related to cell proliferation, DNA damage repair and p53 mutations which may lead to a clinically more aggressive phenotype for PABC patients. Likewise, the enrichment of BRCAness and HRD signatures found in PABC patients in our study may suggest an increased genetic instability due to a breakdown in the DNA damage repair. These findings may be clinically relevant and translate to new treatment options in PABC patients, who may benefit from therapies targeting DNA repair or cell-cycle checkpoints, such as PARP inhibitors. Citation Format: Juan de la Haba-Rodríguez, Regina Peña, Marina Pollan, Yolanda Jerez Gilarranz, Jose Ponce, Antonio Fernández Aramburu, Blanca Cantos, Ana Santaballa Bertrán, Elena Galve, María Eva Pérez, Susana de la Cruz, María Helena López-Ceballos, Yolanda Fernández, Fernando Moreno, Sonia González, Manuel Ruíz - Borrego, Isabel Blancas, José L Alonso-Romero, Álvaro Jiménez-Arranz, Raúl Rincón, Silvia Guil, Alejandra Díaz-Chacón, Rosalía Caballero, Begoña Bermejo, Angel Guerrero. Deciphering pregnancy-associated breast cancer: distinctive molecular profile and clinical implications from GEICAM/2017-07 EMBARCAM study [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 PO2-13-05.

Association of the bitter taste genes TAS2R38 and CA6 and breast cancer risk; a case-control study of Polish women in Poland and Polish immigrants in USA.

It is known that the perception of bitterness is mediated by type 2 bitter taste receptors (TAS2Rs). However, recent reports have suggested that the carbonic anhydrase 6 (CA6) gene may also influence bitterness sensing. Genetic variants in these genes could influence dietary intake of brassica vegetables, whose increased consumption has been observed in the literature, though inconsistently, to decrease breast cancer (BC) risk. We hypothesized that the estimated odds ratios (ORs) for the association between BC and taster diplotype (PAV/PAV) and/or genotype A/A, will be in the direction of increased BC risk, potentially due to reduced consumption of brassica vegetables. Using a case-control study of BC in Polish women in Poland (210 cases and 262 controls) and Polish immigrant women to USA (78 cases and 170 controls) we evaluated the association of the taster diplotypes in TAS2R38 gene and genotypes in the CA6 gene and BC risk in these two populations individually and jointly. No significant increase in risk was observed for the TAS2R38 PAV/PAV diplotype (tasters) in each population individually or in the joint population. For the CA6 gene, in the joint population, we observed an increased BC risk for the combined G/A and G/G genotypes (non-tasters) vs A/A (tasters), OR = 1.41 (95% CI 1.04-1.90, p = 0.026) which after adjustment for False Discovery Rate (FDR), was not significant at p≤0.05 level. However, for the joint population and for the combined genotype of the two genes AVI/AVI+G* (non-tasters) vs. PAV/*+A/A (tasters), we observed a significant increase in BC risk, OR = 1.77 (95%CI 1.47-2.74, p = 0.01), for the non-tasters, which remained significant after FDR adjustment. In conclusion for the joint population and the joint effect for the two bitter sensing genes, we observed an increase in BC risk for the bitterness non-tasters, association which is in the opposite direction to our original hypothesis.

Investigating causal relationships between extensive peripheral immune cell phenotypes and preeclampsia: A bi-directional Mendelian randomization analysis.

Preeclampsia, a multifaceted condition during pregnancy characterized by hypertension and organ dysfunction, poses significant risks to both maternal and fetal health. This study aims to investigate the bidirectional causal relationship between peripheral immune cell phenotypes and preeclampsia using a two-sample Mendelian randomization (MR) approach. Genetic data from two sizable cohorts were utilized: 3757 individuals from Sardinia, providing information on 731 immune traits, and 200929 Finnish adult females, encompassing 6663 preeclampsia cases. Single-nucleotide polymorphisms served as instrumental variables. The MR analyses employed the inverse variance-weighted (IVW) method as the primary tool, supplemented by MR-Egger, weighted median, and weighted mode methods to enhance reliability and address potential heterogeneity and horizontal pleiotropy. Among the 731 immune cell phenotypes studied, 18 displayed a suggestive positive association (IVW p<.05) with heightened preeclampsia risk, while 20 exhibited a suggestive negative association linked to reduced risk. Following false discovery rate (FDR) adjustment, four immune phenotypes showed significant associations with decreased preeclampsia risk: CD27 on CD24+ CD27+ B cells (B-cell panel) (odds ratio [OR]=0.927, PFDR=0.061), CD33+ HLA DR+ CD14- absolute count (OR=0.963, PFDR=0.061), CD80 on plasmacytoid dendritic cells (OR=0.923, PFDR=0.061); and CD80 on CD62L+ plasmacytoid dendritic cells (OR=0.923, PFDR=0.061). In the reverse-direction MR analysis, no significant causal effects of preeclampsia on immune cell phenotypes were observed. This study provides quantifiable evidence linking specific immune cell phenotypes to the risk of developing preeclampsia. This novel understanding of the immunological aspects underlying preeclampsia's pathogenesis could lead to innovative therapeutic strategies centered on immune modulation.