Adjustment For Multiple Comparisons Research Articles

PS-P10-6: IDENTIFYING A URINARY PEPTIDOMICS PROFILE FOR HYPERTENSION IN YOUNG ADULTS: THE AFRICAN-PREDICT STUDY

Background and Aims: Hypertension is one of the most important and complex risk factors for cardiovascular diseases. Identifying biomarkers in hypertension may lead to better strategies to understand the development of hypertension. Biomarker discovery through the use of peptidomics may also provide essential information for the prediction and prevention of premature CVD development. Methods and Results: We included 78 hypertensive (based on 24-hour ambulatory blood pressure) and 79 normotensive age (20–30-years old), sex and ethnicity (62% black and 48% white) matched participants from the African-PREDICT study. Urinary peptidomics were analysed with capillary electrophoresis time-of-flight mass spectrometry. Hypertension-specific peptide profiles were combined into a single summary multidimensional classifier. When comparing the peptide data between the normotensive and hypertensive groups, 354 peptides were nominally differentially expressed (Wilcoxon p-value less than 0.05). Nonetheless, only three peptides (ID10000 (SHANK1), ID8939 (unsequenced) and ID6841 (unsequenced)) remained significant after rigorous adjustments for multiple comparisons (maxT test) and were more abundant in the hypertensive compared to the normotensive group (all p-value less than 0.001). Furthermore, the 15 nominally most significant peptides (all p-value less than or equal to 0.0013) were combined into a unifying score which differed significantly between the groups (p-value less than 0.001) but had an insufficient prediction capability for hypertension. Conclusion: Apart from differential expression of single peptides in hypertensive adults, including ID10000 (SHANK1), no unifying urinary hypertension peptidomics profile was identified with a sufficient prediction capability. Our findings suggest that a downstream multimarker approach cannot reliably represent a complex multifactorial condition such as hypertension.

Data driven clusters derived from resting state functional connectivity: Findings from the EMBARC study

BackgroundTo address the clinical heterogeneity of Major Depressive Disorder (MDD), this investigation determined whether resting state functional magnetic resonance imaging (fMRI) could be deployed to identify circuit based homogeneous subgroups, and whether subgroups identified show differential treatment outcomes. MethodsPretreatment resting state fMRIs obtained from 278 outpatients with nonpsychotic MDD from Establishing Moderators and Biosignatures of Antidepressant Response for Clinical Care for Depression Study were used to create data-driven subgroups using CLICK clustering. These subgroups were then compared using baseline clinical data, as well as baseline-to-week 8 changes in depression severity measured using the 17-item Hamilton Rating Scale for Depression (HAMD17) and response/remission rates by treatment group. ResultsThree subgroups were identified. Cluster-1 was characterized by overallhyperconnectivity coupled with profound hypoconnectivity between the supramarginal gyrus (executive control network; ECN) and the superior frontal cortex (dorsal attention network; DAN). Cluster-2 was characterized by overall hypoconnectivity coupled with hyperconnectivity between supramarginal gyrus (ECN) and superior frontal cortex (DAN). Cluster-3 showed hypoconnectivity, especially profound between the angular cortex (default mode network; DMN) and middle frontal cortex (ECN). While baseline clinical measures did not differentiate the three clusters, Cluster-3 had the remission rate (51.6%) compared to Cluster-1 and Cluster-2 (32.7% and 31.9%) when treated with sertraline. LimitationsDue to the exploratory nature of these analyses, there were no adjustments for multiple comparisons. ConclusionsBaseline functional connectivity can be used to subgroup patients with MDD that differ in acute phase treatment outcomes. Measures of connectivity may address the heterogeneity of MDD.

Effect of a diet based on the dietary guidelines for americans on inflammation markers in women at risk for cardiometabolic disease: results of a randomized, controlled trial

ObjectiveTo evaluate the effect of a diet pattern based on Dietary Guidelines for Americans (DGA), in a controlled feeding setting, on plasma markers of inflammation and on cytokine production by peripheral blood mononuclear cells (PBMC).DesignWomen (n = 44) with one or more risk factors of metabolic syndrome (and BMI: 25.2-39.8 kg/m2) completed an 8-wk controlled feeding study. They were randomized to either a group following a diet based on DGA 2010 (DGA), or a group given a ‘typical American diet’ (TAD), based largely on a Western diet pattern. By design, women maintained their body weight. Fasting plasma and PBMC were collected at wk. 0 (baseline) and at wk. 8 (post-intervention). Sixteen plasma markers of inflammation and eight PBMC cytokines were measured at both time points, to evaluate if the diet had a significant effect on concentrations of these inflammatory markers. Data were analyzed using ANCOVA, followed by multiple-comparison adjustment using Benjamini-Hochberg method.ResultsSignificant changes observed in Serum Amyloid A (SAA) and Matrix Metalloproteinase 3 (MMP3) in plasma did not retain significance upon multiple comparison adjustment. SAA: p = 0.044, adj p = 0.450; DGA mean change [95% CI] = − 12.6[− 32.3 to 7.04]; TAD mean change [95% CI] = − 2.24 [− 9.99 to 5.51]. MMP3: p = 0.014, adj p = 0.35; DGA mean change [95% CI] = 2.72[− 4.16 to 9.59]; TAD mean change [95% CI] = − 0.98[− 16.7 to 14.7]). Other inflammation markers were not differently altered by DGA relative to TAD. Effect size of change (Cohens d) indicated a large/medium-large effect of intervention on MMP3 and CRP, and medium effect on IL-6.ConclusionsNo statistically significant changes were observed in the immune markers examined in this study. The biological roles and magnitude of the non-significant differences seen with two variables, CRP and MMP3, suggest that they be examined in future studies.Trial registrationClinicaltrials.gov identifier NCT02298725.

Childhood adiposity, serum metabolites and breast density in young women

BackgroundChildhood adiposity is inversely associated with young adult percent dense breast volume (%DBV) and absolute dense breast volume (ADBV), which could contribute to its protective effect for breast cancer later in life. The objective of this study was to identify metabolites in childhood serum that may mediate the inverse association between childhood adiposity and young adult breast density.MethodsLongitudinal data from 182 female participants in the Dietary Intervention Study in Children (DISC) and the DISC 2006 (DISC06) Follow-Up Study were analyzed. Childhood adiposity was assessed by anthropometry at the DISC visit with serum available that occurred closest to menarche and expressed as a body mass index (BMI) z-score. Serum metabolites were measured by untargeted metabolomics using ultra-high-performance liquid chromatography–tandem mass spectrometry. %DBV and ADBV were measured by magnetic resonance imaging at the DISC06 visit when participants were 25–29 years old. Robust mixed effects linear regression was used to identify serum metabolites associated with childhood BMI z-scores and breast density, and the R package mediation was used to quantify mediation.ResultsOf the 115 metabolites associated with BMI z-scores (FDR < 0.20), 4 were significantly associated with %DBV and 6 with ADBV before, though not after, adjustment for multiple comparisons. Mediation analysis identified 2 unnamed metabolites, X-16576 and X-24588, as potential mediators of the inverse association between childhood adiposity and dense breast volume. X-16576 mediated 14% (95% confidence interval (CI) = 0.002, 0.46; P = 0.04) of the association of childhood adiposity with %DBV and 11% (95% CI = 0.01, 0.26; P = 0.02) of its association with ADBV. X-24588 also mediated 7% (95% CI = 0.001, 0.18; P = 0.05) of the association of childhood adiposity with ADBV. None of the other metabolites examined contributed to mediation of the childhood adiposity–%DBV association, though there was some support for contributions of lysine, valine and 7-methylguanine to mediation of the inverse association of childhood adiposity with ADBV.ConclusionsAdditional large longitudinal studies are needed to identify metabolites and other biomarkers that mediate the inverse association of childhood adiposity with breast density and possibly breast cancer risk.

Mitochondrial DNA haplogroup analysis in Saudi Arab patients with multiple sclerosis.

Previous studies have suggested that mitochondrial DNA (mtDNA) variants are associated with multiple sclerosis (MS), a complex neurodegenerative immune-mediated disease of the central nervous system. Since mtDNA is maternally inherited without recombination, specific mtDNA variants defining genetic background are associated with the susceptibility to human diseases. To assess the contribution of mtDNA haplogroups to the predisposition of MS in an Arab population, we analysed sequencing data of mitochondrial genomes from 47 native Saudi Arab individuals including 23 patients with relapsing-remitting MS (RRMS) and 24 healthy controls. All patients and controls could be classified into ten haplogroups. The European-specific haplogroup U was more prevalent in patients than in the controls (26.1% vs. 4.2%), whereas haplogroup T was only present in patients and haplogroups HV and N were only found in controls. Haplogroup U was significantly association with increased risk of MS (odds ratio = 6.26, p<0.05), although the association did not maintain significance after adjustment for multiple comparisons. Haplotype U was more prevalent in patients with younger age of onset (p = 0.006), but there was no relationship between haplotype U and disease severity, disease duration or EDSS and age-matched carriers and non-carriers of haplogroup U (p>0.05). Definition site of haplogroup U include the variant m.12308A>G in MT-TL2 gene which was found to affect highly conserved position within the variable arm of tRNALeu(CUN) and thus may impact mitochondrial protein synthesis, and two other variants namely m.11467A>G in MT-ND4 gene and m.12372G>A in MT-ND5 gene which were previously linked with mitochondrial function. Despite the small number of subjects, which may limit the statistical power of the study, our results showed for the first time a possible contribution of haplogroup U to the predisposition to MS in an Arab population. These findings warrant further validation in a large cohort to distinguish a genuine effect specific to MS from a chance finding due to small sampling.

Lung proteome and metabolome endotype in HIV-associated obstructive lung disease.

Obstructive lung disease is increasingly common among persons with HIV, both smokers and nonsmokers. We used aptamer proteomics to identify proteins and associated pathways in HIV-associated obstructive lung disease. Bronchoalveolar lavage fluid (BALF) samples from 26 persons living with HIV with obstructive lung disease were matched to persons living with HIV without obstructive lung disease based on age, smoking status and antiretroviral treatment. 6414 proteins were measured using SomaScan® aptamer-based assay. We used sparse distance-weighted discrimination (sDWD) to test for a difference in protein expression and permutation tests to identify univariate associations between proteins and forced expiratory volume in 1 s % predicted (FEV1 % pred). Significant proteins were entered into a pathway over-representation analysis. We also constructed protein-driven endotypes using K-means clustering and performed over-representation analysis on the proteins that were significantly different between clusters. We compared protein-associated clusters to those obtained from BALF and plasma metabolomics data on the same patient cohort. After filtering, we retained 3872 proteins for further analysis. Based on sDWD, protein expression was able to separate cases and controls. We found 575 proteins that were significantly correlated with FEV1 % pred after multiple comparisons adjustment. We identified two protein-driven endotypes, one of which was associated with poor lung function, and found that insulin and apoptosis pathways were differentially represented. We found similar clusters driven by metabolomics in BALF but not plasma. Protein expression differs in persons living with HIV with and without obstructive lung disease. We were not able to identify specific pathways differentially expressed among patients based on FEV1 % pred; however, we identified a unique protein endotype associated with insulin and apoptotic pathways.

Comparative Evaluation of Artifacts Originated by Four Different Post Materials Using Different CBCT Settings.

Forty premolar teeth were used in this study. Root canals were treated, and teeth were randomly distributed into four subgroups (n = 10) for the preparation of post materials: titanium, gold (Nordin), quartz fiber (Bisco DT Light), and glass fiber (Rely X). The CBCT images were taken with two different kVps, three different metal artifact reduction (MAR) algorithm options, and two different resolutions. For each protocol, the effective dose was calculated according to the dose area production (DAP) value. The standard analysis of variance technique and the Tukey multiple comparison adjustment method were used to assess interactions among material types, kVp, MAR, and voxel settings. More artifacts were found in the middle third than in the cervical third (p &lt; 0.05). The mean value of artifacts was highest for gold (Nordin), 90 kVp, no MAR, and 100 voxel size. Glass or quartz fiber posts at low resolution, with high MAR and 96 kVp, originated fewer artifacts. Moreover, the use of 90 and 96 kVp with 200 voxel size and high MAR provided the least amount of radiation. The best setting for radiographic follow-up of post materials on the Planmeca ProMax is 96 kVp with low resolution and high MAR; this setting produced one of the lowest effective doses. This study estimated the best scanning protocol by lowering the effective dose to a minimum level according to the "as low as reasonably achievable" principle, as well as assessing the tooth region and the post material generating the fewest artifacts, in order to prevent image interpretation challenges such as false-positive and false-negative results stemming from the deterioration of the visibility of the root canal due to perforation, fractures, and voids in the root canal region.

High-resolution surface electromyographic activities of facial muscles during mimic movements in healthy adults: A prospective observational study.

Surface electromyography (sEMG) is a standard tool in clinical routine and clinical or psychosocial experiments also including speech research and orthodontics to measure the activity of selected facial muscles to objectify facial movements during specific facial exercises or experiments with emotional expressions. Such muscle-specific approaches neglect that facial muscles act more as an interconnected network than as single facial muscles for specific movements. What is missing is an optimal sEMG setting allowing a synchronous measurement of the activity of all facial muscles as a whole. A total of 36 healthy adult participants (53% women, 18-67 years) were included. Electromyograms were recorded from both sides of the face using an arrangement of electrodes oriented by the underlying topography of the facial muscles (Fridlund scheme) and simultaneously by a geometric and symmetrical arrangement on the face (Kuramoto scheme). The participants performed a standard set of different facial movement tasks. Linear mixed-effects models and adjustment for multiple comparisons were used to evaluate differences between the facial movement tasks, separately for both applied schemes. Data analysis utilized sEMG amplitudes and also their maximum-normalized values to account for amplitude differences between the different facial movements. Surface electromyography activation characteristics showed systematic regional distribution patterns of facial muscle activation for both schemes with very low interindividual variability. The statistical significance to discriminate between the different sEMG patterns was good for both schemes (significant comparisons for sEMG amplitudes: 87.3%, both schemes, normalized values: 90.9%, Fridlund scheme, 94.5% Kuramoto scheme), but the Kuramoto scheme performed considerably superior. Facial movement tasks evoke specific patterns in the complex network of facial muscles rather than activating single muscles. A geometric and symmetrical sEMG recording from the entire face seems to allow more specific detection of facial muscle activity patterns during facial movement tasks. Such sEMG patterns should be explored in more clinical and psychological experiments in the future.

Mechanical chest compression and extracorporeal life support for out-of-hospital cardiac arrest. A 30-month observational study in the metropolitan area of Milan, Italy

BackgroundReturn of spontaneous circulation (ROSC) is achieved in 25% of out-of-hospital cardiac arrest (OHCA) patients. Mechanical chest compression (mechCPR) may maintain better perfusion during transport, allowing hospital treatments like extracorporeal circulation life support (ECLS). We aim to assess the effectiveness of a pre-hospital protocol introduction. MethodsObservational, retrospective study assessing all OHCA patients aged 12–75, with no-flow time <20 min in a metropolitan area (Milan, Italy, 2013–2016). Primary outcomes: ROSC and Cerebral Performance Category score (CPC) ≤2 at hospital discharge. Logistic regressions with multiple comparison adjustments balanced with propensity scores calculated with inverse probability of treatment weighting were performed. Results1366 OHCA were analysed; 305 received mechCPR, 1061 manual chest compressions (manCPR), and 108 ECLS. ROSC and CPC ≤2 were associated with low-flow minutes (odds ratio [95% confidence interval] 0.90 [0.88–0.91] and 0.90 [0.87–0.93]), shockable rhythm (2.52 [1.71–3.72] and 10.68 [5.63–20.28]), defibrillations number (1.15 [1.07–1.23] and 1.15 [1.04–1.26]), and mechCPR (1.86 [1.17–2.96] and 2.06 [1.11–3.81]). With resuscitation times >13 min, mechCPR achieved more frequently ROSC compared to manCPR. Among ECLS patients, 70% had time exceeding protocol: 8 (7.5%) had CPC ≤2 (half of them with low-flow times between 45 and 90 min), 2 (1.9%) survived with severe neurological disabilities, and 13 brain-dead (12.0%) became organ donors. ConclusionsMechCPR patients achieved ROSC more frequently than manual CPR patients; mechCPR was a crucial factor in an ECLS protocol for refractory OHCA. ECLS offered a chance of survival to patients who would otherwise die.

A proteomic approach for investigating the pleiotropic effects of statins in the atherosclerosis risk in communities (ARIC) study

BackgroundStatins are prescribed to reduce LDL-c and risk of CVD. Statins have pleiotropic effects, affecting pathophysiological functions beyond LDL-c reduction. We compared the proteome of statin users and nonusers (controls). We hypothesized that statin use is associated with proteins unrelated to lipid metabolism. MethodsAmong 10,902 participants attending ARIC visit 3 (1993–95), plasma concentrations of 4955 proteins were determined using SOMAlogic's DNA aptamer-based capture array. 379 participants initiated statins within the 2 years prior. Propensity scores (PS) were calculated based on visit 2 (1990–92) LDL-c levels and visit 3 demographic/clinical characteristics. 360 statin users were PS matched to controls. Log2-transformed and standardized protein levels were compared using t-tests, with false discovery rate (FDR) adjustment for multiple comparisons. Analyses were replicated in visit 2. ResultsCovariates were balanced after PS matching, except for higher visit 3 LDL-c levels among controls (125.70 vs 147.65 mg/dL; p < 0.0001). Statin users had 11 enriched and 11 depleted protein levels after FDR adjustment (q < 0.05). Proteins related and unrelated to lipid metabolism differed between groups. Results were largely replicated in visit 2. ConclusionProteins unrelated to lipid metabolism differed by statin use. Pending external validation, exploring their biological functions could elucidate pleiotropic effects of statins. SignificanceStatins are the primary pharmacotherapy for lowering low-density lipoprotein (LDL) cholesterol and preventing cardiovascular disease. Their primary mechanism of action is through inhibiting the protein 3hydroxy-3-methylglutaryl CoA reductase (HMGCR) in the mevalonate pathway of LDL cholesterol synthesis. However, statins have pleiotropic effects and may affect other biological processes directly or indirectly, with hypothesized negative and positive effects. The present study contributes to identifying these pathways by comparing the proteome of stain users and nonusers with propensity score matching. Our findings highlight potential biological mechanisms underlying statin pleiotropy, informing future efforts to identify statin users at risk of rare nonatherosclerotic outcomes and identify health benefits of statin use independent of LDL-C reduction.

Laparoscopic fundoplication after lung transplantation does not appear to alter lung function trajectory

The primary aim of this study was to determine if allograft function in lung transplant (LTx) recipients improves or stabilizes after laparoscopic fundoplication (LF). The secondary aim was to examine the differences in forced expiratory volume in 1 second (FEV1) before and after LF for various subgroups to identify patients who obtained a superior respiratory outcome after LF, and potential predictive factors for this outcome. Retrospective analysis of consecutive LTx recipients undergoing LF at a single centre in Brisbane, Australia between 2004 and 2018. 149/431 proceeded to LF after clinical review and pH study. Regular pre- and post-fundoplication pulmonary function tests were collected from participants. Data were analyzed with linear mixed models, random intercept models, the Reliable Change Index (RCI), and graphical and visual analysis of the trajectory of FEV1. There was 100% follow-up. After Bonferroni adjustment for multiple comparison was performed, none of the models demonstrated statistical significance. The Reliable Change Index showed one patient had a significant improvement in lung function across that time period, while nine had a significant reduction. The rate of change before and after LF was similar for the 132/149 patients for whom the first and last pre- and post-LF FEV1 values were available. A subset of patients had a considerable reduction in their FEV1 in the peri-operative period (i.e., a large difference between the first measurement post-LF and the final measurement pre-LF). In the largest published cohort to date, LF performed in a high-volume center did not appear to alter the reduction in allograft function seen with time.

General Anesthesia and Cerebral Function: Changes in Cognition and Regional Brain Metabolism in Patients following Surgery

AbstractBackgroundImproved understanding of relationships between general anesthesia and subsequent cognitive decline is critically needed. In this study, previously healthy and mildly impaired subjects were compared pre‐ and post‐surgery, with respect to longitudinal assessments of their neuropsychologic performance and regional brain metabolism.MethodWe screened records of 1,450 Alzheimer’s Disease Neuroimaging Initiative subjects to identify all those undergoing non‐cancer surgeries involving general anesthesia with a minimum of two pre‐surgical and two post‐surgical ADNI visits, yielding neuropsychological data for this analysis acquired during 256 visits by 64 subjects – 32 surgical patients meeting the above criteria, and 32 controls who were demographically matched but with no reported surgeries during enrollment. Cognitive domain scores were correlated with rates of decline in regional cerebral metabolism based on interval changes in pairs of FDG‐PET scans acquired pre‐ and post‐surgery; analogous calculations were performed in the non‐surgical group by setting “surgery” dates according to median elapsed time from first visit to surgery in the surgical group. Imaging data were quantitatively examined by both standardized volume of interest (sVOI) and statistical parametric mapping (spm) methods of analysis.ResultsVOIs included bilaterally 6 frontal, 5 temporal, 4 parietal, 2 occipital, and sensorimotor cerebral cortical volumes, as well as 7 noncortical volumes. Compared to the non‐surgical group, the surgical group showed greater post‐surgical decline in the two anterior temporal volumes measured (p=0.01), both medially (including the hippocampus and adjacent cortex) and laterally. Within the surgery group, comparing pre‐ versus post‐ timeframes also identified most significant accelerated decline in the two anterior temporal volumes. The spm analyses corroborated significant acceleration of metabolic decline postsurgically in temporal cortex, predominantly in the right hemisphere, with cluster size significant after statistical adjustment for multiple comparisons (P&lt;0.0005, Pcorr = 0.047). Finally, pre‐ and post‐surgical differences in rates of temporal metabolic decline correlated with differences in executive function decline within the surgical group (r=0.785).ConclusionMajor surgeries involving general anesthesia were associated with significantly accelerated decline in temporal metabolism postsurgically. This in turn was correlated with greater acceleration of decline in cognitive function of surgical patients.

In Vitro Study Comparing Retention of Custom Post and Cores Fabricated Using Conventional, CAD/CAM Milling and 3D-Printing Techniques

This study aimed to evaluate the differences in the retention of custom-cast non-precious post and cores (CCNPPCs) (control group), custom-milled titanium post and cores (CMTPCs), custom-printed titanium post and cores (CPTPCs), and custom-milled zirconia post and cores (CMZPCs), and to evaluate their mode of failure. The tested null hypothesis was that there were no differences in the retention of the various custom post and cores tested. A total of 80 post-and-core patterns were made using pattern resin and were divided into four groups: Group 1—fabricated via conventional casting using a non-precious casting alloy; Group 2—fabricated using a computer-aided design/computer-aided manufacturing (CAD/CAM) subtractive technique using titanium; Group 3—fabricated using a CAD/CAM additive (3D printing) technique using titanium; and Group 4—fabricated using a CAD/CAM subtractive technique using zirconia. The post and cores were cemented with resin cement and a universal pull-out test was used to check the retention. The data were statistically analyzed using one-way ANOVA tests, post hoc tests, and Tukey’s adjustment for multiple comparisons. The pull-out test revealed higher retention values for CPTPCs and CMTPCs. When compared with CMZPCs, the conventional CCNPPCs revealed significantly better retention values (p &lt; 0.05). Cohesive failure was observed in Groups 1, 2, and 4. However, Group 3 revealed a mixed type of failure. The CCNPPCs revealed clinically acceptable values, while the CPTPC and CMTPC groups revealed better overall values of retention and time to failure. The titanium alloy was assessed to be a promising choice for fabricating dental post-and-core restorations.

Apathy in depression: An arterial spin labeling perfusion MRI study

IntroductionApathy, as defined as a deficit in goal-directed behaviors, is a critical clinical dimension in depression associated with chronic impairment. Little is known about its cerebral perfusion specificities in depression. To explore neurovascular mechanisms underpinning apathy in depression by pseudo-continuous arterial spin labeling (pCASL) magnetic resonance imaging (MRI). MethodsPerfusion imaging analysis was performed on 90 depressed patients included in a prospective study between November 2014 and February 2017. Imaging data included anatomical 3D T1-weighted and perfusion pCASL sequences. A multiple regression analysis relating the quantified cerebral blood flow (CBF) in different regions of interest defined from the FreeSurfer atlas, to the Apathy Evaluation Scale (AES) total score was conducted. ResultsAfter confound adjustment (demographics, disease and clinical characteristics) and correction for multiple comparisons, we observed a strong negative relationship between the CBF in the left anterior cingulate cortex (ACC) and the AES score (standardized beta = −0.74, corrected p value = 0.0008). ConclusionOur results emphasized the left ACC as a key region involved in apathy severity in a population of depressed participants. Perfusion correlates of apathy in depression evidenced in this study may contribute to characterize different phenotypes of depression.

Infertility and treatments used have minimal effects on first-trimester placental DNA methylation and gene expression

To determine if DNA methylation alterations exist in first trimester human placenta between conceptions utilizing fertility treatments and those that do not, and if so, if they are the result of underlying infertility or fertility treatments. We also assessed if significant alterations led to changes in gene expression. We compared DNA methylation of first trimester placenta from singleton pregnancies that resulted in live births from unassisted, non-IVF fertility treatment (NIFT), and IVF conceptions using the Infinium MethylationEPIC BeadChip array. Significant CpG sites were compared to corresponding RNA-seq analysis in similar cohorts to determine if methylation alterations lead to differences in gene expression. 138 singleton pregnancies undergoing chorionic villus sampling resulting in a live birth were recruited for methylation analysis (56 unassisted, 38 NIFT, 44 IVF conceptions). RNA-seq data consisted of 141 subjects (74 unassisted, 33 NIFT, and 34 IVF) of which 116 overlap with the methylation cohort. IVF conceived pregnancy, or pregnancy conceived via non-IVF fertility treatment such as ovulation induction and/or intrauterine insemination. Significant methylation changes at CpG sites after adjustment for multiple comparisons. Secondary outcome is gene expression changes of significant CpG sites. Of the 741,145 probes analyzed in placenta, few were significant at Bonferroni<0.05: 185 CpG sites (0.025%) significant in pregnancies conceived with fertility treatment (NIFT+IVF) vs unassisted conceptions; 28 in NIFT vs unassisted; 195 in IVF vs unassisted; and only 13 (0.0018%) significant in IVF vs NIFT conceptions. Of all significant CpG sites combined, 10% (35 total) were located in genes with suggestive gene expression changes (RNA-seq P<0.05), but none were significant after adjustment for multiple comparisons (RNA-seq FDR<0.05). None of the 13 differentially methylated probes in IVF vs NIFT placenta were located in genes with suggestive IVF vs NIFT gene expression differences. Underlying infertility is the most significant contributor to the minimal differences in first trimester placental methylation, and not the specific fertility treatment utilized, such as IVF.

PIK3CA mutations are associated with pathologic complete response rate to neoadjuvant pyrotinib and trastuzumab plus chemotherapy for HER2-positive breast cancer

BackgroundNeoadjuvant treatment with a dual anti-human epidermal growth factor receptor 2 (HER2) blockade with pyrotinib and trastuzumab has been shown to be effective for HER2-positive breast cancer.MethodsThe genomic characteristics of 425 cancer-related genes from the archived tumour blocks of 50 patients enrolled in a prospective neoadjuvant pyrotinib and trastuzumab plus chemotherapy clinical trial (ChiCTR1900022293) were assessed by next-generation sequencing (NGS). The relationship between tumour biomarkers and the postoperative pathological complete response (pCR) were explored.ResultsForty-five patients completed neoadjuvant chemotherapy and final surgery, of which 26 (58%) achieved a pCR. Among all driver gene mutations, PIK3CA mutation was screened out for having a significant relationship with the treatment response. The pCR rate of patients with wild-type PIK3CA was significantly higher than patients with mutated PIK3CA (80.8% vs. 26.3%; P = 0.00057), and remained significant after a multiple comparison adjustment (Padjusted = 0.024). We further evaluated the predictive value with logistic regression model of clinical features, genetic biomarkers or both, an AUC of 0.912 (95% CI: 0.827−0.997) was achieved in the integrated model.ConclusionsOur data suggest that HER2-positive breast cancers with activating mutations in PIK3CA are less likely to benefit from pyrotinib combined with trastuzumab neoadjuvant therapy.

The Roles of MTRR and MTHFR Gene Polymorphisms in Colorectal Cancer Survival.

Paradoxically epidemiological data illustrate a negative relationship between dietary folate intake and colorectal cancer (CRC) risk. The occurrence and progression of CRC may be influenced by variants in some key enzyme coding genes in the folate metabolic pathway. We investigated the correlation between genetic variants in methionine synthase reductase (MTRR) and methylenetetrahydrofolate reductase (MTHFR) and CRC survival. This study used data collected from the Newfoundland Familial Colorectal Cancer Study. A total of 532 patients diagnosed with CRC for the first time from 1999 to 2003 were enrolled, and their mortality were tracked until April 2010. DNA samples were genotyped by Illumina's integrated quantum 1 million chip. Cox models were established to assess 33 tag single-nucleotide polymorphisms in MTRR and MTHFR in relation to overall survival (OS), disease-free survival (DFS) and CRC-specific survival. The MTRR and MTHFR genes were associated with DFS and CRC-specific survival in CRC patients at the gene level. After multiple comparison adjustment, MTRR rs1801394 A (vs. G) allele was associated with increased DFS (p = 0.024), while MTHRT rs3737966 (G vs. A), rs4846049 (T vs. G), rs1476413 (A vs. G), rs1801131 (C vs. A), rs12121543 (A vs. C), rs1801133 (C vs. T), rs4846052 (T vs. C), rs2066471 (A vs. G) and rs7533315 (T vs. C) were related to worse CRC-specific survival. Additionally, significant interactions were seen among pre-diagnostic alcohol consumption with MTRR rs1801394, rs3776467, rs326124, rs162040, and rs3776455, with superior OS associated with those protective variant alleles limited to patients with alcohol consumption under the median. The MTHFR rs3737966 (G vs. A) allele seemed to be detrimental to CRC survival only among subjects with fruit intake below the median. Polymorphic variants in MTRR and MTHFR genes that code for key enzymes for folate metabolism may be associated with survival in patients with CRC. The gene-CRC outcome association seems modulated by alcohol drinking and fruit intake.

OR02-1 Differences in HDL Particle Composition in Patients with Nonalcoholic Fatty Liver Disease (NAFLD) and Advanced Liver Fibrosis May Explain Higher Cardiovascular Risk

Abstract The severity of liver fibrosis in patients with NAFLD is a strong predictor of cardiovascular mortality, independently of other well-known cardiovascular risk factors. However, the exact mechanisms leading to cardiovascular disease in patients with advanced liver fibrosis remain incompletely understood. As many of the apolipoproteins are synthesized in the liver, we hypothesized that lipoprotein composition may explain the association between liver disease and cardiovascular disease. Patients (n=185) underwent a liver proton magnetic resonance spectroscopy (1H-MRS) to measure intrahepatic triglyceride accumulation and a percutaneous liver biopsy if they had NAFLD. Advanced lipid testing and lipoprotein subfractions were measured by ion mobility. ApoA-I containing particles (i.e., HDL) were isolated and a novel targeted proteomic approach utilizing multiple reaction monitoring (MRM) by liquid chromatography and tandem mass spectrometry (LC-MS/MS) was undertaken to measure HDL-bound proteins that are associated with lipid metabolism. Forty-five patients did not have NAFLD by 1H-MRS and were used as controls for comparisons. One-hundred and forty patients had a liver biopsy, and 26 were diagnosed with advanced fibrosis. Patients with vs. without advanced fibrosis had similar clinical characteristics (Age: 54±9 vs. 52±11 years; sex: 77% vs. 76% males; BMI: 34.2±4.3 vs. 34.5±4.6 kg/m2). Patients with advanced fibrosis had lower HDL-C (34±8 vs. 38±9 mg/dl, p=0.024) and higher A1c (7.3±1.3% vs. 6.5±1.0%, p&amp;lt;0.001). No differences were observed in LDL or VLDL particle number or size between the groups. Patients with advanced fibrosis showed a mild reduction in HDL particle number, mainly driven by a reduction of small HDL particles (17269±3705 vs. 19057±4052 nmol/L, p=0.042). Despite this small difference in HDL particle number, a significant difference was observed in the proteomic signature of these particles. A panel of twenty-eight HDL-bound proteins were targeted and quantified by MRM LC-MS/MS. After adjustment for multiple comparisons based on a false discovery rate set at 10% (method of Benjamini-Krieger-Yekutieli), five proteins were found to be decreased in patients with advanced fibrosis (ApoC-I, ApoC-IV, ApoM, LCAT, and SAA4; all p&amp;lt;0.017). No differences were observed in these proteins in patients with vs. without NAFLD or steatohepatitis (NASH). The pCAD index [range from 0-100] is a well-validated model based on measurement of 5 HDL-associated apolipoproteins (Apolipoproteins A-I, C-I, C-II, C-III, and C-IV) that is associated with presence of coronary artery disease and cardiovascular mortality. We observed a stepwise increase in pCAD index with every stage of fibrosis among patients with NAFLD (F0: 84±3; F1: 88±3; F2: 90±6; F3-4: 97±1, p=0.037). Conclusion Patients with NAFLD with advanced fibrosis showed significant differences in the apolipoproteomic composition of HDL particles, and this translated into increased cardiovascular risk based on pCAD index. Different lipoprotein composition and function may explain the link between liver disease and increased cardiovascular mortality in these patients. Presentation: Saturday, June 11, 2022 11:30 a.m. - 11:45 a.m.

Comparisons of Patient-Reported Quality of Life and Swallowing Scores of Mucosal Sparing Radiation vs. Standard of Care for Oropharyngeal Tumors

<h3>Purpose/Objective(s)</h3> We hypothesized mucosal sparing radiation therapy (MSRT) would result in improved patient-reported quality of life (QOL) and modified barium swallowing impairment scores (MBSImp) compared to standard of care (SOC) post-operative adjuvant radiation for human papillomavirus related (HPV) oropharyngeal squamous cell carcinoma (OPSCC). <h3>Materials/Methods</h3> The results of two institutional prospective studies, the SOC arm of MC1675 (DART) and a MSRT trial, were compared to assess for differences in QOL and MBSImp. Both trials were performed with patients undergoing transoral surgery with negative margins and neck dissection. The SOC was 60 Gy to the primary mucosal site and at-risk nodal regions while MSRT excluded the primary mucosal site primarily using proton therapy. Chemotherapy was delivered in both as indicated. Shared endpoints between the studies included EORTC HN-35 (HN35) at baseline, end of treatment (EOT), 3-, 6-, 12-, 24-, and 36-months posttreatment and MBSimp studies at baseline and 12 months posttreatment. Baseline adjusted mixed models, with adjustments for multiple comparisons, were utilized to test the effect of treatment arm over time and their interaction, with statistical significance set at p<0.05. <h3>Results</h3> 127 patients were included, 64 from the SOC and 63 from the MSRT trial. Significant differences in patient characteristics included smoking history, insurance coverage, use of chemotherapy, and pathologic T and N categories. After treatment, improved QOL scores were significantly associated with MSRT for HN35 domains: pain, swallowing, speech problems, trouble with social eating, trouble with social contact, less sexuality, opening mouth, dry mouth, pain killers, nutritional supplements, feeding tube, and weight loss. When considering the interaction between treatment and time, the largest QOL difference occurred acutely (<3 months post-RT) with significant differences in pain, swallowing, senses problems, speech problems, trouble with social eating, trouble with social contact, less sexuality, opening mouth, dry mouth, sticky saliva, and feeling ill. Better scores with MSRT for trouble with social eating, pain, and dry mouth persisted 3 months post-RT, while no significant differences remained 6 months post-RT. When adjusted for baseline patient characteristics MSRT was still associated with superior scores for swallowing, senses problems, trouble with social eating, less sexuality, and feeding tube use. MBSimp from baseline to 12 months post-RT showed worsening of oral impairment (imp) score and overall imp score for SOC but not for MSRT. At 12 months MSRT was associated with less oral imp and overall imp than SOC. <h3>Conclusion</h3> MSRT for HPV+ OPSCC is associated with higher QOL scores compared to current SOC treatment in the acute and subacute setting and higher MBSimp scores at 12 months. Adding MSRT to the DART regimen for select HPV OSCC patients will be further studied.

Survival in Metastatic Renal Cell Carcinoma Treated with Immunotherapy and Stereotactic Radiation Therapy or Immunotherapy Alone: A National Cancer Database Analysis

<h3>Purpose/Objective(s)</h3> Immunotherapy (IO) has significantly improved outcomes in metastatic renal cell carcinoma (mRCC). Preclinical evidence suggests that responses to IO may be enhanced through the immunomodulatory effects of stereotactic radiation therapy (SRT). We hypothesized that clinical outcomes from the National Cancer Database (NCDB) would demonstrate improved overall survival (OS) in mRCC patients receiving IO+SRT versus IO alone. <h3>Materials/Methods</h3> Patients with mRCC diagnosed from 2012-2016 and receiving first-line IO±SRT were identified from the NCDB. Complete staging details and radiation treatment characteristics were required for study inclusion. The definition of SRT was ≥10 Gy in 1 fraction, ≥20 Gy in 2 fractions, ≥24 Gy in 3 fractions, or ≥25 Gy in 5 fractions. Conventional radiation therapy was allowed in the IO alone cohort. The primary endpoint was OS (from date of stage IV diagnosis) stratified by the receipt of SRT (IO+SRT versus IO alone). Secondary endpoints included OS stratified by the presence of brain metastases (BM) and timing of SRT (before or after IO). Events beyond 24 months were censored. Survival was estimated using Kaplan-Meier methodology and compared via the log-rank test. Adjustments for multiple comparisons were performed. <h3>Results</h3> Of 644 eligible patients, 63 (9.8%) received IO+SRT and 581 (90.2%) received IO alone. The median follow-up time was 17.7 months (range, 2-24 months). Baseline characteristics were similar between cohorts, although SRT+IO patients were more frequently <60 years old (57.1% vs 40.3%, P=0.010) and had higher rates of BM (71.4% vs 11.2%, P<0.001). There was no difference in metastatic tumor burden (defined as the number of involved organ systems) between cohorts (P=0.48). Sites treated with SRT included the brain (71.4%), lung/chest (6.4%), spine (6.4%), bones (3.2%), and other (12.6%). While there was no significant difference in OS for patients receiving IO+SRT vs IO alone (log-rank P=0.11), OS was consistently higher at 1-year (74.4% vs 65.0%) and 2-years (71.0% vs 58.4%). In patients with BM, 1-year survival rates were 73.0% (95% CI, 57.4-83.7) with IO+SRT and 54.7% (95% CI, 41.8-65.9) with IO alone (P=<0.026). The timing of SRT (before or after IO) did not appear to influence OS (P=0.32). <h3>Conclusion</h3> Patients with BM secondary to mRCC had prolonged OS with the addition of SRT to IO. Prospective clinical trials are warranted to better identify mRCC populations which may benefit from combined modality therapy. Potential synergistic factors, such as oligometastatic tumor burden, IO mechanism of action, and SRT dose should be considered in future analyses of mRCC patients receiving IO+SRT.