Effect of postbiotic Lactiplantibacillus plantarum LRCC5314 supplemented in powdered milk on type 2 diabetes in mice

Type 2 diabetes (T2D) is a chronic multifactorial disease characterized by a combination of insulin resistance and impaired glucose regulation. The alleviative effects of probiotics on T2D have been widely studied. However, studies on the effects of postbiotics, known as inactivated probiotics, on dairy products are limited. This study aimed to evaluate the effectiveness of postbiotic Lactiplantibacillus plantarum LRCC5314 in milk powder (MP-LRCC5314) in a stress-T2D mouse model. Compared with probiotic MP-LRCC5314, postbiotic MP-LRCC5314 significantly influenced stress-T2D-related factors. The administration of heat-killed MP-LRCC5314 reduced corticosterone levels, increased short-chain fatty acid production by modulating gut microbiota, and regulated immune response, glucose metabolism, stress-T2D-related biomarkers in the brain, gut, and adipose tissues, as well as glucose and insulin sensitivity. Additionally, heat-killed MP-LRCC5314 treatment led to a decrease in pro-inflammatory cytokine levels and an increase in anti-inflammatory cytokine levels. Overall, these findings suggest that adding postbiotic MP-LRCC5314 to milk powder could serve as a potential supplement for stress-T2D mitigation.

Ameliorating effect of 2'-Fucosyllactose and 6'-Sialyllactose on lipopolysaccharide-induced intestinal inflammation

Human milk oligosaccharides (HMO) affect gut microbiota during neonatal development, particularly with respect to the immune system. Bovine milk-based infant formulas have low oligosaccharide contents. Thus, efforts to fortify infant formulas with HMO are being undertaken. Two major HMO, 2'-fucosyllactose (2'-FL) and 6'-sialyllactose (6'-SL), exert anti-inflammatory effects; however, the associations between anti-inflammatory effects induced by 2'-FL and 6'-SL co-treatment and gut microbiota composition and metabolite modulation remain unclear. Therefore, in this study, we evaluated the effects of a mixture of these HMO. To determine the optimal HMO ratio for anti-inflammatory effects and elucidate its mode of action, LPS-induced inflammatory HT-29 epithelial cells and intestinal inflamed suckling mice were treated with various mixtures of 2'-FL and 6'-SL. 2'-FL:6'-SL ratio of 5:1 was identified as the most effective pre-treatment HMO mixture in vitro; thus, this ratio was selected and used for low, middle, and high-dose treatments for subsequent in vivo studies. In vivo, high-dose HMO treatment restored LPS-induced inflammation symptoms, such as body weight loss, colon length reduction, histological structural damage, and intestinal gene expression related to inflammatory responses. High-dose HMO was the only treatment that modulated the major phyla Bacteroidetes and Firmicutes and the genera Ihubacter, Mageeibacillus, and Saccharofermentans. These changes in microbial composition were correlated with intestinal inflammation-related gene expression and short-chain fatty acid production. To our knowledge, our study is the first to report the effects of Ihubacter, Mageeibacillus, and Saccharofermentans on short chain fatty acid levels, which can subsequently affect inflammatory cytokine and tight junction protein levels. Conclusively, the HMO mixture exerted anti-inflammatory effects through changes in microbiota and metabolite production. These findings suggested that supplementation of infant formula with HMO may benefit formula-fed infants by forming unique microbiota contributing to neonatal development.

Now or Later? Patient Satisfaction and Anxiety Among Women Undergoing Breast Biopsies Performed the Same Day as Recommended Versus a Later Day

PURPOSE

The aim of this study was to determine differences in patient satisfaction and anxiety among women undergoing core-needle breast biopsies performed the same day as recommended versus a future date.

METHODS

After institutional review board exemption was granted, a survey was administered to patients at four sites on the day of imaging-guided core-needle breast biopsy. The survey was available from November 2020 through January 2022. Questions pertained to biopsy timing (same day versus later day), pre- and postbiopsy satisfaction with overall breast-care experience, biopsy wait-time satisfaction, pre- and postbiopsy anxiety, radiologist-patient communication, demographics, life stressors, breast cancer history, and risk factors. Comparisons were made between same-day and later-day biopsies by multivariable analysis.

RESULTS

Of 974 respondents (response rate 65.6%), almost half were scheduled for same-day biopsies (47.8% [466 of 974]). In multivariate analyses, same-day biopsies were associated with higher prebiopsy overall breast-care satisfaction (P < .001), higher wait-time satisfaction (P < .001), and higher prebiopsy (P = .001) and postbiopsy anxiety (P = .001). Better radiologist-patient communication was associated with lower prebiopsy anxiety (P < .001) and greater prebiopsy overall (P < .001) and wait-time (P < .001) satisfaction. Compared with White women, Black women reported lower postbiopsy anxiety (P < .001) but also lower prebiopsy satisfaction (P = .03) and wait-time satisfaction (P < .001).

CONCLUSIONS

Same-day versus later-day biopsies resulted in better prebiopsy overall breast-care and wait-time patient satisfaction scores; however, no satisfaction differences were noted after biopsy. Clinically significant anxiety was associated with both same- and later-day biopsies but was higher for same-day biopsies. Higher anxiety levels correlated with lower overall satisfaction, suggesting that interventions to reduce anxiety and improve communication could improve patient experiences during same-day biopsies.

Elimination microplastic particles in brine process water for ensuring the safety of brined cabbage

Various studies have investigated the presence of microplastics (MPs) in food and their potential hazardous impact on human health. The frequency of human exposure to MPs, particularly through the consumption of manufactured food and drinking water, is increasing. However, data regarding MP contamination in brine and brined cabbage used for the production of kimchi are limited. Here, we quantified MPs in brine process water during the production of brined cabbage. Pretreatment of the brine process water by performing a filtration step resulted in an MP-removal efficiency of 98.7-100%; 3671 ± 174 MP particles were observed in brining process water that was not filtered. A glass filter, STS filter, and Si Filter showed significant MP-removal efficiency, decreasing the number of MP particles in brining process water to 2,361, 2,775, and 3,490, respectively (p < 0.05). Our results provide data on how filtering of brine can effectively safeguard kimchi from MP contamination and e can be produced. However, to overcome the limitations of our laboratory-scale study, additional technologies should be used in the future for large-scale filtration processes.

Disruption of H3K36 methylation provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis

Chromatin organization is essential for maintaining cell-fate trajectories and developmental programs. Here, we find that disruption of H3K36 methylation dramatically impairs normal epithelial differentiation and development, which promotes increased cellular plasticity and enrichment of alternative cell fates. Specifically, we observe a striking increase in the aberrant generation of excessive epithelial glandular tissues, including hypertrophic salivary, sebaceous, and meibomian glands, as well as enhanced squamous tumorigenesis. These phenotypic and gene expression manifestations are associated with loss of H3K36me2 and rewiring of repressive H3K27me3, changes we also observe in human patients with glandular hyperplasia. Collectively, these results have identified a critical role for H3K36 methylation in both in vivo epithelial cell-fate decisions and the prevention of squamous carcinogenesis and suggest that H3K36 methylation modulation may offer new avenues for the treatment of numerous common disorders driven by altered glandular function, which collectively affect large segments of the human population.

Are All Prognostic Stage IB Breast Cancers Equivalent?

PURPOSE/OBJECTIVE(S)

The 8th edition of the American Joint Committee on Cancer (AJCC) has recognized the prognostic influence of histologic grade and biomarker status for breast cancer (BC). Contemporary BC staging includes both anatomic tumor extent and prognostic stage. However, prognostic stage IB remains heterogeneous and includes patients with locally advanced anatomic pathologic stage IIIA-B (pT3N1 or pT1-3N2, G1-2) hormone-receptor positive/HER2-negative BC (LA-HR+/HER2-) as well as patients with early-stage anatomic clinical/pathologic stage IA (T1cN0, G2-3) triple-negative BC (ES-TNBC). We hypothesized that although both are classified as prognostic stage IB BC, overall survival (OS) is worse for LA-HR+/HER2- compared to ES-TNBC.

MATERIALS/METHODS

We used the National Cancer Database to identify patients with surgically-resected LA-HR+/HER2- BC (pT3N1 or pT1-3N2, grade 1-2) and those with ES-TNBC (T1N0, grade 2-3) from 2004-2017. Patients were excluded if receptor status, tumor grade, and/or TNM staging data were unknown. HR+/HER2- patients treated with neoadjuvant therapy were also excluded. The primary endpoint was OS. Multivariable Cox regression analysis was used to evaluate differences in OS between LA-HR+/HER2- BC and ES-TNBC (adjusting for baseline patient demographic characteristics) in the entire cohort and in the subset of patients that received appropriate treatment based on anatomic stage: radiation (RT), chemotherapy (CT) and hormone therapy for LA-HR+/HER2- BC and CT or CT+RT for ES-TNBC treated with mastectomy or lumpectomy, respectively. We report hazard ratios (HR) with 95% confidence intervals (CI) with p<0.05 considered statistically significant.

RESULTS

A total of 45,818 patients met inclusion criteria (N = 17,359 with LA-HR+/HER2- BC and N = 28,459 with ES-TNBC). Over 75% of the LA-HR+/HER2- BC patients have anatomic pathologic stage IIIB disease (pT1-3N2, G1-2). With a median follow-up of 56 months, the 6-year OS rates were 86.1% (LA-HR+/HER2-) vs. 90.4%patients (ES-TNBC) which corresponded to a 63% relative increased risk of death in LA-HR+/HER2- patients compared to ES-TNBC patients (HR = 1.63, 95% CI 1.53-1.73, p<0.0001) after adjusting for all covariates. Approximately 66% (N = 11,533) LA-HR+/HER2- and 69% (N = 19,512) ES-TNBC received appropriate therapy. The 6-year OS was 91.8% (LA-HR+/HER2-) vs. 93.3% (ES-TNBC) which corresponded to a 35% increased risk of death in the LA-HR+/HER2- patients compared to ES-TNBC (adjusted HR = 1.35, 95% 1.24-1.48, p<0.0001). Other covariates associated with OS were age, income, insurance status, facility type, and ethnicity/race.

CONCLUSION

We found that LA-HR+/HER2- BC has significantly worse OS compared to ES-TNBC despite both being classified as prognostic stage IB, even when accounting for treatments delivered. The categorization of pT3N1 or pT1-3N2, G1-2 HR+/HER2- BC as prognostic stage IB needs to be reconsidered in order to provide patients with more accurate information regarding expected OS.

Omission of Adjuvant Radiotherapy in Low-Risk Elderly Males with Breast Cancer

PURPOSE/OBJECTIVE(S)

Randomized clinical trials demonstrate that lumpectomy + hormone therapy (HT) without radiation therapy (RT) yields equivalent survival and acceptable local-regional outcomes in elderly women with early-stage, node-negative (T1-2N0) hormone-receptor positive (HR+) breast cancer. Whether these data apply to men with the same inclusion criteria remains unknown. We hypothesized that outcomes in males would be comparable to those seen in females, with RT not conferring an overall survival (OS) benefit over HT alone.

MATERIALS/METHODS

We conducted a retrospective matched-cohort study using the National Cancer Database for males ≥65 years with pathologic T1-2N0 (≤3 cm) HR+ breast cancer treated with breast conserving surgery with negative margins from 2004-2019. Patients who received chemotherapy, had nodal or distant metastases, or unknown follow-up were excluded. Adjuvant treatment was classified as HT alone, RT alone, or HT+RT. Due to limitations of survival analysis on retrospective data, male patients were matched with female patients to determine comparable outcomes based on age (± 3 years), Charlson Deyo comorbidity score, T-stage, and adjuvant treatment. Survival analysis was performed using Cox regression and Kaplan-Meier analysis. To adjust for confounding, inverse probability of treatment weighting (IPTW) was used.

RESULTS

A total of 523 patients met inclusion criteria, with 24.4% receiving HT, 16.3% receiving RT, and 59.2% receiving HT+RT. Median follow-up was 6.9 years (IQR: 5.0-9.4 years). Unadjusted 5-yr OS rates in the HT, RT, and HT+RT cohorts were 79.2% (95% CI 70.7-85.5%), 80.9% (95% CI 70.3-88.0%), and 93.3% (95% CI 89.7-95.7%), respectively. Adjusted 10-yr OS rates in the HT, RT, and HT+RT cohorts were 82.3% (95% CI 78.6-85.5%), 83.6% (95% CI 80.0-86.7%), and 92.8% (95% CI 90.1-94.8%), respectively. On unadjusted multivariable Cox regression analysis (MVA), relative to HT, receipt of HT+RT was associated with improvements in OS (HR: 0.603; 95% CI: 0.410-0.888; p = 0.01). RT alone was not associated with improved OS (HR: 1.116; 95% CI: 0.710-1.755; p = 0.633). On adjusted MVA, relative to HT, receipt of HT+RT was associated with improvements in OS (HR: 0.551; 95% CI: 0.370-0.820; p = 0.003). Again, RT alone was not associated with improved OS (HR: 0.991; 95% CI: 0.613-1.604; p = 0.972). Other factors associated with OS included age, Charlson Deyo score, T stage, and grade. Overall, in the matched women, the same trends were found as in the men, the best survival was in HT+RT, but no difference in OS between HT vs. RT.

CONCLUSION

Among men ≥65 years old with T1-2N0 HR+ breast cancer, RT alone did not confer an OS benefit over HT alone. Combined RT+HT did yield improvements in OS, though there are likely significant unmeasured confounders contributing to these outcomes in patients treated with the most aggressive approach. Our findings support that RT omission may be a reasonable option in elderly men with T1-2N0 HR+ breast cancer treated with lumpectomy + HT.

High-throughput Oligopaint screen identifies druggable 3D genome regulators

The human genome functions as a three-dimensional chromatin polymer, driven by a complex collection of chromosome interactions1-3. Although the molecular rules governing these interactions are being quickly elucidated, relatively few proteins regulating this process have been identified. Here, to address this gap, we developed high-throughput DNA or RNA labelling with optimized Oligopaints (HiDRO)-an automated imaging pipeline that enables the quantitative measurement of chromatin interactions in single cells across thousands of samples. By screening the human druggable genome, we identified more than 300 factors that influence genome folding during interphase. Among these, 43 genes were validated as either increasing or decreasing interactions between topologically associating domains. Our findings show that genetic or chemical inhibition of the ubiquitous kinase GSK3A leads to increased long-range chromatin looping interactions in a genome-wide and cohesin-dependent manner. These results demonstrate the importance of GSK3A signalling in nuclear architecture and the use of HiDRO for identifying mechanisms of spatial genome organization.

Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation

Multi-enhancer hubs are spatial clusters of enhancers present across numerous developmental programs. Here, we studied the functional relevance of these three-dimensional structures in T cell biology. Mathematical modeling identified a highly connected multi-enhancer hub at the Ets1 locus, comprising a noncoding regulatory element that was a hotspot for sequence variation associated with allergic disease in humans. Deletion of this regulatory element in mice revealed that the multi-enhancer connectivity was dispensable for T cell development but required for CD4+ T helper 1 (Th1) differentiation. These mice were protected from Th1-mediated colitis but exhibited overt allergic responses. Mechanistically, the multi-enhancer hub controlled the dosage of Ets1 that was required for CTCF recruitment and assembly of Th1-specific genome topology. Our findings establish a paradigm wherein multi-enhancer hubs control cellular competence to respond to an inductive cue through quantitative control of gene dosage and provide insight into how sequence variation within noncoding elements at the Ets1 locus predisposes individuals to allergic responses.

Safety and efficacy of trastuzumab biosimilar plus irinotecan or gemcitabine in patients with previously treated HER2 (ERBB2)-positive non-breast/non-gastric solid tumors: a phase II basket trial with circulating tumor DNA analysis

BACKGROUND

Human epidermal growth factor receptor 2 (HER2) (ERBB2)-directed agents are standard treatments for patients with HER2-positive breast and gastric cancer. Herein, we report the results of an open-label, single-center, phase II basket trial to investigate the efficacy and safety of trastuzumab biosimilar (Samfenet®) plus treatment of physician's choice for patients with previously treated HER2-positive advanced solid tumors, along with biomarker analysis employing circulating tumor DNA (ctDNA) sequencing.

METHODS

Patients with HER2-positive unresectable or metastatic non-breast, non-gastric solid tumors who failed at least one prior treatment were included in this study conducted at Asan Medical Center, Seoul, Korea. Patients received trastuzumab combined with irinotecan or gemcitabine at the treating physicians' discretion. The primary endpoint was the objective response rate as per RECIST version 1.1. Plasma samples were collected at baseline and at the time of disease progression for ctDNA analysis.

RESULTS

Twenty-three patients were screened from 31 December 2019 to 17 September 2021, and 20 were enrolled in this study. Their median age was 64 years (30-84 years), and 13 patients (65.0%) were male. The most common primary tumor was hepatobiliary cancer (seven patients, 35.0%), followed by colorectal cancer (six patients, 30.0%). Among 18 patients with an available response evaluation, the objective response rate was 11.1% (95% confidence interval 3.1% to 32.8%). ERBB2 amplification was detected from ctDNA analysis of baseline plasma samples in 85% of patients (n = 17), and the ERBB2 copy number from ctDNA analysis showed a significant correlation with the results from tissue sequencing. Among 16 patients with post-progression ctDNA analysis, 7 (43.8%) developed new alterations. None of the patients discontinued the study due to adverse events.

CONCLUSIONS

Trastuzumab plus irinotecan or gemcitabine was safe and feasible for patients with previously treated HER2-positive advanced solid tumors with modest efficacy outcomes, and ctDNA analysis was useful for detecting HER2 amplification.

Benchmarking integration of single-cell differential expression

Integration of single-cell RNA sequencing data between different samples has been a major challenge for analyzing cell populations. However, strategies to integrate differential expression analysis of single-cell data remain underinvestigated. Here, we benchmark 46 workflows for differential expression analysis of single-cell data with multiple batches. We show that batch effects, sequencing depth and data sparsity substantially impact their performances. Notably, we find that the use of batch-corrected data rarely improves the analysis for sparse data, whereas batch covariate modeling improves the analysis for substantial batch effects. We show that for low depth data, single-cell techniques based on zero-inflation model deteriorate the performance, whereas the analysis of uncorrected data using limmatrend, Wilcoxon test and fixed effects model performs well. We suggest several high-performance methods under different conditions based on various simulation and real data analyses. Additionally, we demonstrate that differential expression analysis for a specific cell type outperforms that of large-scale bulk sample data in prioritizing disease-related genes.

Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation

Innate lymphoid cells (ILCs) are well-characterized immune cells that play key roles in host defense and tissue homeostasis. Yet, how the three-dimensional (3D) genome organization underlies the development and functions of ILCs is unknown. Herein, we carried out an integrative analysis of the 3D genome structure, chromatin accessibility and gene expression in mature ILCs. Our results revealed that the local 3D configuration of the genome is rewired specifically at loci associated with ILC biology to promote their development and functional differentiation. Importantly, we demonstrated that the ontogenesis of ILC2s and the progression of allergic airway inflammation are determined by a unique local 3D configuration of the region containing the ILC-lineage-defining factor Id2, which is characterized by multiple interactions between the Id2 promoter and distal regulatory elements bound by the transcription factors GATA-3 and RORα, unveiling the mechanism whereby the Id2 expression is specifically controlled in group 2 ILCs.

Sync and Swarm: Solvable Model of Nonidentical Swarmalators

We study a model of nonidentical swarmalators, generalizations of phase oscillators that both sync in time and swarm in space. The model produces four collective states: asynchrony, sync clusters, vortexlike phase waves, and a mixed state. These states occur in many real-world swarmalator systems such as biological microswimmers, chemical nanomotors, and groups of drones. A generalized Ott-Antonsen ansatz provides the first analytic description of these states and conditions for their existence. We show how this approach may be used in studies of active matter and related disciplines.

OS10.6.A What is the initial cell in the subventricular zone for human glioblastoma genesis?

Background

We all have a fundamental question about why glioblastoma (GBM) develops. In order to find the answer to this fundamental question, if you find out what the first cell is, you will get closer to the answer. GBM arises from the subventricular zone (SVZ). GBM is one of the most devastating tumour of human brain as the most optimal treatment barely prolongs the survival, and it does not cure the disease. As the majority of GBM tissues show copy number variations (CNV) of co-altered chromosomal 7 gain and 10 loss, we hypothesized the origin cell (Oc) of SVZ may be traced back with these markers. The cellular identity of the Oc is still unknown and it is different from the tumour-derived progenitor-like cells. We aimed to define these cells from the SVZ that have a potential to get activated into GBM.

Material and Methods

We compared bulk RNA sequencing (RNAseq) data of IDHwt GBM tumor tissue (n=122), tumor free SVZ from GBM patients (n=40), tumor-free control SVZ of non-glial tumor (n=9). Pared single nucleus RNAseq (snRNAseq) or single cell RNAseq (scRNAseq) samples of tumor free SVZ (n=11) and GBM tumor (n=8), were done to see cell specific CNVs. We developed genetically engineered mouse models for GBM genesis introducing three driver mutations (TP53, PTEN, and EGFRviii) into SVZ to isolate mouse Oc (mOc) and mouse cancer cells (mCc). The biological characteristics of separated mOc and mCc were compared. Bulk RNAseq and scRNAseq were performed on these cells (mOc, mCc), and their cellular state was compared with the human gene set.

Results

In this work, we found two types of the Oc in the RNA sequencing of 60 human tumour free-SVZ samples. Furthermore, single-cell level analysis revealed that two Oc types in SVZ harbor ongoing patterns of CNV co-alterations from Oc1 to Oc2, and finally to GBM. The Oc1 type cells contained the CNV signature of Oc2 ancestor with neural progenitor cell (NPC) signature. Oc2 type cells expressed a high level of EGFR than other cells with astrocyte-like cell signature. Both of these cells expressed oligodendrocyte progenitor cell (OPC)-like signatures in the SVZ. We validated the human-based findings by using the P53/PTEN/EGFR-mutant mouse model with EGFR/tdTomato overexpression and P53/PTEN knockout in the SVZ cells. As a result, non-tumourigenic and highly motile Oc-like cell-states are found in the mouse models, supporting the firework-like migration pattern from the SVZ.

Conclusion

Our results demonstrate how members of Oc preoccupy the SVZ, known as the stem cell niche and give rise to the tumour. We anticipate that a new therapy may emerge by targeting the Oc in the SVZ.

Fully automatic AI-based valve motion parameter extraction on long axis CINE images - application on N=11000 patient datasets

Funding Acknowledgements

Type of funding sources: Private company. Main funding source(s): Research support from Siemens Healthineers GmbH.

Background

Mitral valve (MV) motion parameters, assessable using CMR [1, 2], have been shown to help the diagnosis of cardiac dysfunction. To extract valve motion parameters, we propose a fully automatic AI-based prototype system that tracks annulus and apex landmarks by the registration network on time-resolved two- and four-chamber CMR cine views. Parameters such as displacements, velocities, mitral annular plane systolic excursion (MAPSE), or longitudinal shortening (LS) are automatically extracted and evaluated on a large CMR dataset (N=11000).

Methods

The system consists of two sequential neural networks with a processing step in between (Fig. 1a) [3]. Initially, a 2D UNet is applied to localize both MV annulus insertion points as well as the apex. Based on these points, the image processing step consists of rotating, cropping, and interpolating the images, allowing a standardized image impression for both long axis views. Finally, the registration network (VoxelMorph framework [4]) is applied to the processed series and tracks the MV annulus insertion points and apex over the cardiac cycle by the deformation fields obtained by the network. The system was trained on (N=166) multivendor, multi-field strength, ground-truth annotated datasets [5].

A total of 11000 datasets, acquired on a 1.5T scanner (MAGNETOM Aera, Siemens Healthcare, Erlangen, Germany) from January 2016 to September 2017 [6], were used for parameter extraction. 200 of these datasets were additionally annotated semi-automatically for the performance evaluation of the system.

Five motion parameters were automatically derived by the system that are defined as follows (Fig. 1b): (1) The atrioventricular plane displacement (AVPD) as the distance of the plane spanned by the MV annulus points relative to the first frame, (2) the atrioventricular plane velocity (AVPV) as the discrete temporal derivate of the AVPD, (3) the diameter of the annulus as the maximum distance between the MV annulus points, (4) the lateral/inferior and septal/superior MAPSE, as the maximum MV points’ excursion, and (5) the LS as the percentage size difference of the distance between the mid valvular point and the apex point at end-systole and end-diastole.

Results

The accuracy of the system resulted in deviations on the annotated dataset of 1.02 ± 0.87 mm, 0.01 ± 0.02 mm/s, 1.54 ± 1.21 mm, 2.30 ± 1.35 mm, 2.1 ± 1.8 mm for AVPD, AVPV, diameter, MAPSE, and LS respectively. Initial statistics on all datasets (Fig. 2) revealed a mean lateral/inferior, septal/superior MAPSE and LS of 8.7 ± 2.7 mm, 10.5 ± 3.2 mm and 16.3 ± 4.2 % for two-chamber and 9.6 ± 2.6 mm, 8.7 ± 2.6 mm and 15.5 ± 3.9 % for four-chamber views, respectively.

Conclusions

The results demonstrate the versatility of the proposed system for automatic extraction of various MV motion parameters. The proposed system enables automatic extraction of clinically relevant parameters and can improve the automation of MV-based analyses. System overview & Parameter of interestsAnalysis of the extracted parameters

Fully automated machine learning-based selection of optimal bSSFP frequency offset for artifact reduction in cardiac MRI

Funding Acknowledgements

Type of funding sources: Private company. Main funding source(s): Research Support from Siemens Healthineers GmbH.

Background

In bSSFP sequences commonly used for cardiac MRI, signal modulation (e.g. banding artifacts) due to B0 inhomogeneity is often observed, especially at higher field strengths. The spatial position of these artifacts can be shifted by a frequency offset to reduce artifacts in a region of interest (ROI), e.g. the heart. To this end, frequency scout (FS) scans are acquired to visually select the optimal frequency offset [1,2]. In this work, we propose a fully automated image-based system for selecting the optimal frequency offset on FS images based on machine learning.

Methods

The proposed prototype system consists of four main steps (Fig.1). First, a pre-trained deep-learning-based whole heart segmentation network is applied on a four chamber-view FS image to localize the ROI where artifacts should be reduced. Second, high frequency components within the ROI (for each frequency offset in the FS series) are extracted by successive processing of Fourier transformation, high-pass filtering, inverse Fourier transformation and subtraction over series. and N images with the lowest high-frequency content are selected. Third, an adaptive weighting map for each FS image is generated which penalizes signal deviations from a pixel-wise median that is calculated based on the selected images [3]. By averaging the maps and selecting the frame with maximum percentage, the optimal frequency offset is selected.

A total of 38 datasets, acquired on multiple clinical 3T MRI scanners (MAGNETOM Skyra, Vida, Prisma, Lumina; Siemens Healthcare, Erlangen, Germany), were used to evaluate the proposed system. All FS series were annotated manually and used to compare with the system output. The experts were allowed to select multiple possible optimal FS images within a FS series. In case of multiple annotations, the system output was labelled as correct when it selected one of the offsets chosen by the expert. Further, the generated weighting maps were visually evaluated.

Results

The proposed system achieved an accuracy of 92.1% compared to experts’ ground truth annotations. From the failed cases (n=3), the maximum difference was off by 2 frames. Based on the generated weighting maps, a reasonable decision on the selection of the optimal frequency offset is made. The algorithm successfully selects an FS image with minimized banding and flow artifacts within the ROI (Fig. 2a). Further, it reveals that the generated weighting map correctly suppress areas containing artifacts (Fig. 2b).

Conclusions

Initial results demonstrate the feasibility of the proposed system to automatically select the optimal frequency offset on FS scans. Therefore, it can improve the automation of a cardiac MRI workflow. An example of the result of each step

MicroRNA-29 Ameliorates Fibro-Inflammation and Insulin Resistance in HIF1α-Deficient Obese Adipose Tissue by Inhibiting Endotrophin Generation

Dysregulation of extracellular matrix proteins in obese adipose tissue (AT) induces systemic insulin resistance. The metabolic roles of type VI collagen and its cleavage peptide endotrophin in obese AT are well established. However, the mechanisms regulating endotrophin generation remain elusive. Herein, we identified that several endotrophin-containing peptides (pre-endotrophins) were generated from the COL6A3 chain in a stepwise manner for the efficient production of mature endotrophin, partly through the action of hypoxia-induced matrix metalloproteinases (MMPs), including MMP2, MMP9, and MMP16. Hypoxia is an upstream regulator of COL6A3 expression and the proteolytic processing that regulates endotrophin generation. Hypoxia-inducible factor 1α (HIF1α) and the hypoxia-associated suppression of microRNA-29 (miR-29) cooperatively control the levels of COL6A3 and MMPs, which are responsible for endotrophin generation in hypoxic ATs. Adipocyte-specific Hif1α knock-out (APN-HIF1αKO) mice fed a chronic high-fat diet exhibited the significant amelioration of both local fibro-inflammation in AT and systemic insulin resistance compared with their control littermates, partly through the inhibition of endotrophin generation. Strikingly, adenovirus-mediated miR-29 overexpression in the ATs of APN-HIF1αKO mice in obesity significantly decreased endotrophin levels, suggesting that miR-29, combined with HIF1α inhibition in AT, could be a promising therapeutic strategy for treating obesity and related metabolic diseases.

A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages

The ability to study cancer-immune cell communication across the whole tumor section without tissue dissociation is needed, especially for cancer immunotherapy development, which requires understanding of molecular mechanisms and discovery of more druggable targets. In this work, we assembled and evaluated an integrated experimental framework and analytical process to enable genome-wide scale discovery of ligand-receptors potentially used for cellular crosstalks, followed by targeted validation. We assessed the complementarity of four different technologies: single-cell RNA sequencing and Spatial transcriptomic (measuring over >20,000 genes), RNA In Situ Hybridization (RNAscope, measuring 4-12 genes) and Opal Polaris multiplex protein staining (4-9 proteins). To utilize the multimodal data, we implemented existing methods and also developed STRISH (Spatial TRanscriptomic In Situ Hybridization), a computational method that can automatically scan across the whole tissue section for local expression of gene (e.g. RNAscope data) and/or protein markers (e.g. Polaris data) to recapitulate an interaction landscape across the whole tissue. We evaluated the approach to discover and validate cell-cell interaction in situ through in-depth analysis of two types of cancer, basal cell carcinoma and squamous cell carcinoma, which account for over 70% of cancer cases. We showed that inference of cell-cell interactions using scRNA-seq data can misdetect or detect false positive interactions. Spatial transcriptomics still suffers from misdetecting lowly expressed ligand-receptor interactions, but reduces false discovery. RNAscope and Polaris are sensitive methods for defining the location of potential ligand receptor interactions, and the STRISH program can determine the probability that local gene co-expression reflects true cell-cell interaction. We expect that the approach described here will be widely applied to discover and validate ligand receptor interaction in different types of solid cancer tumors.

TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors

The high mobility group (HMG) transcription factor TCF-1 is essential for early T cell development. Although in vitro biochemical assays suggest that HMG proteins can serve as architectural elements in the assembly of higher-order nuclear organization, the contribution of TCF-1 on the control of three-dimensional (3D) genome structures during T cell development remains unknown. Here, we investigated the role of TCF-1 in 3D genome reconfiguration. Using gain- and loss-of-function experiments, we discovered that the co-occupancy of TCF-1 and the architectural protein CTCF altered the structure of topologically associating domains in T cell progenitors, leading to interactions between previously insulated regulatory elements and target genes at late stages of T cell development. The TCF-1-dependent gain in long-range interactions was linked to deposition of active enhancer mark H3K27ac and recruitment of the cohesin-loading factor NIPBL at active enhancers. These data indicate that TCF-1 has a role in controlling global genome organization during T cell development.

AB0344 EFFICACY OF SUBCUTANEOUS INFLIXIMAB (CT-P13 SC) COMPARED WITH INTRAVENOUS INFLIXIMAB IN RHEUMATOID ARTHRITIS: A POST-HOC ANALYSIS OF A PHASE 3 RANDOMIZED CONTROLLED TRIAL

Background

Subcutaneous (SC) CT-P13 is the first and only subcutaneous formulation of infliximab (IFX) approved by the EMA.1 In the pivotal study (NCT03147248), non-inferiority of SC IFX to intravenous (IV) was demonstrated in rheumatoid arthritis (RA) patients using 28-joint Disease Activity Score (DAS28) C-reactive protein (CRP) improvement at Week 22, with a statistically significant treatment difference of 0.27 (95% CI 0.02, 0.52) favoring the SC versus the IV arm.2,3 At Week 30, numerical differences in efficacy outcomes were shown between SC and IV IFX favoring SC IFX. IV group patients switched to SC IFX by Week 30, and the difference between the groups was reduced at Week 54.2

Objectives

To investigate whether there was a statistically significant difference between SC and IV IFX at Weeks 30 and 54 in the phase 3 pivotal study of CT-P13 SC using conservative missing imputation methods.

Methods

Patients with active RA who had an inadequate response to MTX received IV IFX 3mg/kg at Weeks 0 and 2 for induction and were randomized at a 1:1 ratio to receive SC IFX 120mg every 2 weeks or IV 3mg/kg every 8 weeks thereafter for maintenance. Patients who were randomized to receive IV IFX switched to SC at Week 30. In this post-hoc analysis, non-responder imputation (NRI) and last observation carried forward (LOCF) methods were used to investigate whether the difference in efficacy outcomes between SC and IV IFX at Weeks 30 and 54 was statistically significant. Assessments included EULAR (CRP/ESR)/ACR response; remission rate and low disease activity (LDA) rate based on DAS28 (CRP/ESR), Clinical Disease Activity Index (CDAI) and Simplified Disease Activity Index (SDAI); Boolean remission rate; and the proportion of patients achieving a minimal clinically important difference (MCID) in Health Assessment Questionnaire (HAQ).

Results

Of the 343 randomized patients, 165 patients who received SC IFX and 174 patients who received IV IFX from the efficacy population were included in the analysis. There was a statistically significant difference in SC IFX compared to IV treated patients at Week 30 using both NRI and LOCF methods in almost all the clinical variables. However, the difference in efficacy outcomes between SC IFX and IV was reduced at Week 54 after the IV group switched to SC. This supports the improved efficacy of SC IFX at Week 30. Some of the key results (EULAR [CRP] responses, LDA rates based on DAS28 [CRP], CDAI, and SDAI) were presented in Figure 1. Analysis using LOCF and NRI methods yielded consistent results across most of the efficacy outcomes.

Figure 1.

Comparison of clinical outcomes between SC IFX and IV IFX in patients with active rheumatoid arthritis.

*P<0.05.

P-value for difference in proportion between SC and IV treatment group was obtained by asymptotic Wald test.

Low disease activity based on DAS28 (CRP) (< 3.2), CDAI (eatment group AI (≤ 11.0).

Conclusion

Statistical analyses using conservative missing imputation methods showed significantly greater improvements in clinical outcomes with SC IFX compared to IV at Week 30 in patients with RA. Between-group differences was reduced at Week 54, suggesting improved responses after switching from IV to SC.

References

[1]Remsima summary of product characteristics. https://www.ema.europa.eu/en/documents/product-information/remsima-epar-product-information_en.pdf. Published 2021. Accessed 10 January 2022.

[2]Westhovens R, Wiland P, Zawadzki M, et al. Efficacy, pharmacokinetics and safety of subcutaneous versus intravenous CT-P13 in rheumatoid arthritis: a randomized phase I/III trial. Rheumatology (Oxford). 2021;60(5):2277-2287.

[3]Combe B, Allanore Y, Alten R, et al. Comparative efficacy of subcutaneous (CT-P13) and intravenous infliximab in adult patients with rheumatoid arthritis: a network meta-regression of individual patient data from two randomised trials. Arthritis Res Ther. 2021;23(1):119.

Disclosure of Interests

Arnaud Constantin Speakers bureau: Abbvie, Amgen, Boehringer, Celltrion, Galapagos, Janssen, Lilly, Novartis, Sanofi, UCB, Consultant of: Abbvie, Amgen, Boehringer, Celltrion, Galapagos, Janssen, Lilly, Novartis, Sanofi, UCB, Roberto Caporali Speakers bureau: Abbvie, Amgen, BMS, Celltrion, Galapagos, Lilly, Pfizer, Fresenius-Kabi, MSD, UCB, Roche,Janssen, Novartis, Sandoz, Consultant of: Abbvie, Amgen, BMS, Celltrion, Galapagos, Lilly, Pfizer, MSD, UCB, Janssen, Novartis, Sandoz, Christopher John Edwards Speakers bureau: Abbvie, Astra Zeneca, Celltrion, Chugai, Fresenius, Galapagos, Gilead, GSK, Lilly, Janssen, Pfizer, Roche, Consultant of: Abbvie, Astra Zeneca, Chugai, Galapagos, Gilead, GSK, Lilly, Janssen, Pfizer, Roche, Grant/research support from: Celltrion, Pfizer, Abbvie, Joao Eurico Fonseca Speakers bureau: Abbvie, Ache, Janssen, Lilly, Medac, Novartis, Pfizer, Consultant of: Abbvie, Celltrion, Janssen, Lilly, Pfizer, Grant/research support from: Abbvie, Janssen, Lilly, MSD, Novartis, Pfizer, Roche, Florenzo Iannone Speakers bureau: Abbvie, BMS, Celltrion, Galapagos, MSD, Eli-Lilly, Janssen, Novartis, Pfizer, UCB, Consultant of: Abbvie, BMS, Celltrion, Galapagos, MSD, Eli-Lilly, Janssen, Pfizer, Grant/research support from: BMS, MSD, Edward Keystone Speakers bureau: Amgen, AbbVie, Celltrion, F. Hoffmann-La Roche Inc., Janssen Inc., Merck, Pfizer Pharmaceuticals, Sandoz, Sanofi Genzyme, Consultant of: AbbVie, Amgen, Celltrion, Myriad Autoimmune, F. Hoffmann-La Roche Inc, Janssen Inc, Lilly Pharmaceuticals, Merck, Pfizer Pharmaceuticals, Sandoz, Sanofi-Genzyme, Samsung Bioepsis, Grant/research support from: Amgen, Merck, Pfizer Pharmaceuticals, Hendrik Schulze-Koops Consultant of: Celltrion, Taeksang Kwon Employee of: Celltrion Healthcare, Seungmin Kim Employee of: Celltrion Healthcare, Sangwook Yoon Employee of: Celltrion Healthcare, Dong-Hyeon Kim Employee of: Celltrion Healthcare, Gahee Park Employee of: Celltrion Inc., DaeHyun Yoo Speakers bureau: Celltrion, Celltrion Healthcare

Stripenn detects architectural stripes from chromatin conformation data using computer vision

Architectural stripes tend to form at genomic regions harboring genes with salient roles in cell identity and function. Therefore, the accurate identification and quantification of these features are essential for understanding lineage-specific gene regulation. Here, we present Stripenn, an algorithm rooted in computer vision to systematically detect and quantitate architectural stripes from chromatin conformation measurements using various technologies. We demonstrate that Stripenn outperforms existing methods and highlight its biological applications in the context of B and T lymphocytes. By comparing stripes across distinct cell types and different species, we find that these chromatin features are highly conserved and form at genes with prominent roles in cell-type-specific processes. In summary, Stripenn is a computational method that borrows concepts from widely used image processing techniques to demarcate and quantify architectural stripes.

BRD4 orchestrates genome folding to promote neural crest differentiation

Higher-order chromatin structure regulates gene expression, and mutations in proteins mediating genome folding underlie developmental disorders known as cohesinopathies. However, the relationship between three-dimensional genome organization and embryonic development remains unclear. Here we define a role for bromodomain-containing protein 4 (BRD4) in genome folding, and leverage it to understand the importance of genome folding in neural crest progenitor differentiation. Brd4 deletion in neural crest results in cohesinopathy-like phenotypes. BRD4 interacts with NIPBL, a cohesin agonist, and BRD4 depletion or loss of the BRD4-NIPBL interaction reduces NIPBL occupancy, suggesting that BRD4 stabilizes NIPBL on chromatin. Chromatin interaction mapping and imaging experiments demonstrate that BRD4 depletion results in compromised genome folding and loop extrusion. Finally, mutation of individual BRD4 amino acids that mediate an interaction with NIPBL impedes neural crest differentiation into smooth muscle. Remarkably, loss of WAPL, a cohesin antagonist, rescues attenuated smooth muscle differentiation resulting from BRD4 loss. Collectively, our data reveal that BRD4 choreographs genome folding and illustrates the relevance of balancing cohesin activity for progenitor differentiation.

Impact of field heterogeneity on the dynamics of the forced Kuramoto model

We studied the impact of field heterogeneity on entrainment in a system of uniformly interacting phase oscillators. Field heterogeneity is shown to induce dynamical heterogeneity in the system. In effect, the heterogeneous field partitions the system into interacting groups of oscillators that feel the same local field strength and phase. Based on numerical and analytical analysis of the explicit dynamical equations derived from the periodically forced Kuramoto model, we found that the heterogeneous field can disrupt entrainment at different field frequencies when compared to the homogeneous field. This transition occurs when the phase- and frequency-locked synchronization between groups of oscillators is broken at a critical field frequency, causing each group to enter a new dynamical state (disrupted state). Strikingly, it is shown that disrupted dynamics can differ between groups.

Empirical assessment of biases in cerebrospinal fluid biomarkers of Alzheimer's disease: an umbrella review and re-analysis of data from meta-analyses

OBJECTIVE

Alzheimer's disease (AD) is a leading cause of years lived with disability in older age, and several cerebrospinal fluid (CSF) markers have been proposed in individual meta-analyses to be associated with AD but field-wide evaluation and scrutiny of the literature is not available.

MATERIALS AND METHODS

We performed an umbrella review for the reported associations between CSF biomarkers and AD. Data from available meta-analyses were reanalyzed using both random and fixed effects models. We also estimated between-study heterogeneity, small-study effects, excess significance, and prediction interval.

RESULTS

A total of 38 meta-analyses on CSF markers from 11 eligible articles were identified and reanalyzed. In 14 (36%) of the meta-analyses, the summary estimate and the results of the largest study showed non-concordant results in terms of statistical significance. Large heterogeneity (I2≥75%) was observed in 73% and small-study effects under Egger's test were shown in 28% of CSF biomarkers.

CONCLUSIONS

Our results suggest that there is an excess of statistically significant results and significant biases in the literature of CSF biomarkers for AD. Therefore, the results of CSF biomarkers should be interpreted with caution.

POS1413 INTERVAL BETWEEN SYMPTOM ONSET AND DIAGNOSIS AMONG PATIENTS WITH AUTOIMMUNE RHEUMATIC DISEASES IN A MULTI-ETHNIC ASIAN POPULATION

Background:

The interval between symptom onset and diagnosis can often be longer than is ideal in autoimmune rheumatic diseases (ARDs).

Objectives:

We aimed to characterise this interval among patients newly diagnosed with ARDs in a multi-ethnic Asian population and to identify factors associated with a longer interval.

Methods:

We used Scott’s model of pathways to treatment to characterise the interval between symptom onset and diagnosis into 4 intervals: #1 between symptom onset and first seeking medical attention, #2 between first medical attention and rheumatology referral, #3 between rheumatology referral and first rheumatology assessment, and #4 between first rheumatology assessment and diagnosis. Linear regression models were used to identify factors associated with a longer the overall interval between symptom onset and diagnosis and Interval #1.

Results:

Among 259 patients (age: 51±15 years, female: 71%, most common three ARDs: rheumatoid arthritis (n = 75), axial spondyloarthritis (n = 40) and psoriatic arthritis (n = 35)), the median overall interval was 11.5 months. Interval #1 (median = 4.9 months) was significantly longer than the other intervals (Table 1). Patients with axial spondyloarthritis had a significantly longer overall interval (median = 38.7 months) and Interval #1 (median = 26.6 months) compared to patients with RA (median = 7.6 and 3.5 months, respectively), PsA (median = 7.0 and 2.6 months, respectively) and the other ARDs. Gender was the only patient-related factor significantly associated with the overall interval (reference = male, coefficient = -15.3, p = 0.033) in regression models.

Conclusion:

A longer than ideal interval between symptom onset and diagnosis was observed among patients with ARDs. This was primarily due to a relatively long interval between symptom onset and first seeking medical attention, and highlights the importance of interventions targeting patients prior to first medical attention in reducing the duration between symptom onset and diagnosis.

References:

[1]Scott SE, Walter FM, Webster A, Sutton S, Emery J. The model of pathways to treatment: conceptualization and integration with existing theory. Br J Health Psychol. 2013;18(1):45-65.

Table 1.

Interval between symptom onset and diagnosis

Overall interval, months, median (lower and upper quartiles)†Interval #1, months, median (lower and upper quartiles)Interval #2, months, median (lower and upper quartiles)Interval #3, months, median (lower and upper quartiles)Interval #4, months, median (lower and upper quartiles)Overall(n = 259)11.5(4.7 – 36.0)4.9(1.0 – 24.0)0.3(0.0 – 3.9)1.5(0.8 – 1.8)0.0(0.0 – 1.2)RA(n = 75)7.6(3.1 – 14.8)3.5(1.3 – 11.6)0.2(0.0 – 2.5)1.3(0.6 – 1.6)0.0(0.0 – 0.2)AxSpA(n = 40)38.7(9.6 – 66.7)26.6(4.2 – 56.1)1.6(0.0 – 7.6)1.6(1.2 – 2.3)0.0(0.0 – 2.0)PsA(n = 35)7.0(3.0 – 28.4)2.6(0.2 – 11.3)0.5(0.2 – 3.9)1.6(0.6 – 1.7)0.0(0.0 – 0.0)Seronegative IA(n = 21)12.0(4.7 – 22.8)6.4(1.9 – 34.4)0.1(0.0 – 4.6)1.4(1.3 – 1.5)0.0(0.0 – 0.8)SjS(n = 27)14.2(6.0 – 48.0)4.6(0.6 – 19.0)0.3(0.0 – 3.9)1.6(0.9 – 1.9)0.8(0.0 – 2.3)UCTD(n = 27)15.7(5.1 – 39.8)2.2(0.7 – 24.0)0.8(0.1 – 8.1)1.6(0.5 – 1.8)1.2(0.0 – 2.1)Other ARDs(n = 34)8.1(5.3 – 36.0)6.3(0.9 – 31.7)0.2(0.0 – 1.1)1.5(1.2 – 1.8)0.3(0.0 – 1.1)

Overall interval and Intervals #1-4: refer to abstract for definitions; RA: rheumatoid arthritis; axSpA: axial spondyloarthritis; PsA: psoriatic arthritis; IA: inflammatory arthritis; SjS: Sjögren’s syndrome; UCTD: undifferentiated connective tissue disease; other ARDs: systemic lupus erythematosus, systemic sclerosis, idiopathic inflammatory myopathies, palindromic rheumatism and overlap syndromes.

†Intervals #1-4 did not sum to the overall interval mainly due to the fact that Intervals #1-4 might not available for all patients.

Disclosure of Interests:

None declared

Virtual reality as a learning tool in spinal anatomy and surgical techniques

Background

Surgical simulation is a valuable educational tool for trainees to practice in a safe, standardized, and controlled environment. Interactive feedback-based virtual reality (VR) has recently moved to the forefront of spine surgery training, with most commercial products focusing on instrumentation. There is a paucity of learning tools directed at decompression principles. The purpose of this study was to evaluate the efficacy of VR simulation and its educational role in learning spinal anatomy and decompressive techniques.

Methods

A VR simulation module was created with custom-developed software. Orthopaedic and neurosurgical trainees were prospectively enrolled and interacted with patient-specific 3D models of lumbar spinal stenosis while wearing a headset. A surgical toolkit allowed users to perform surgical decompression, specifically removing soft tissues and bone. The module allowed users to perform various techniques in posterior decompressions and comprehend anatomic areas of stenosis. Pre- and post-module testing, and utility questionnaires were administered to provide both quantitative and qualitative evaluation of the module as a learning device.

Results

28 trainees were enrolled (20-orthopaedic, 8-neurosurgery) in the study. Pre-test scores on anatomic knowledge progressively improved and showed strong positive correlation with year-in-training (Pearson's r = 0.79). Following simulation, the average improvement in post-test scores was 11.4% in junior trainees (PGYI-III), and 1.0% in senior trainees (PGYIII-Fellows). Knowledge improvement approached statistical significance amongst junior trainees (p = 0.0542). 89% of participants found the VR module useful in understanding and learning the pathology of spinal stenosis. 71% found it useful in comprehending decompressive techniques. 96% believed it had utility in preoperative planning with patient-specific models.

Conclusions

Our original VR spinal decompression simulation has shown to be overwhelmingly positively received amongst trainees as both a learning module of patho-anatomy and patient-specific preoperative planning, with particular benefit for junior trainees.

Powerful p-value combination methods to detect incomplete association

Meta-analyses increase statistical power by combining statistics from multiple studies. Meta-analysis methods have mostly been evaluated under the condition that all the data in each study have an association with the given phenotype. However, specific experimental conditions in each study or genetic heterogeneity can result in "unassociated statistics" that are derived from the null distribution. Here, we show that power of conventional meta-analysis methods rapidly decreases as an increasing number of unassociated statistics are included, whereas the classical Fisher's method and its weighted variant (wFisher) exhibit relatively high power that is robust to addition of unassociated statistics. We also propose another robust method based on joint distribution of ordered p-values (ordmeta). Simulation analyses for t-test, RNA-seq, and microarray data demonstrated that wFisher and ordmeta, when only a small number of studies have an association, outperformed existing meta-analysis methods. We performed meta-analyses of nine microarray datasets (prostate cancer) and four association summary datasets (body mass index), where our methods exhibited high biological relevance and were able to detect genes that the-state-of-the-art methods missed. The metapro R package that implements the proposed methods is available from both CRAN and GitHub ( http://github.com/unistbig/metapro ).

Diffusible Signaling Factor, a Quorum-Sensing Molecule, Interferes with and Is Toxic Towards Bdellovibrio bacteriovorus 109J

Bdellovibrio bacteriovorus 109J is a predatory bacterium which lives by predating on other Gram-negative bacteria to obtain the nutrients it needs for replication and survival. Here, we evaluated the effects two classes of bacterial signaling molecules (acyl homoserine lactones (AHLs) and diffusible signaling factor (DSF)) have on B. bacteriovorus 109J behavior and viability. While AHLs had a non-significant impact on predation rates, DSF considerably delayed predation and bdelloplast lysis. Subsequent experiments showed that 50 μM DSF also reduced the motility of attack-phase B. bacteriovorus 109J cells by 50% (38.2 ± 14.9 vs. 17 ± 8.9 μm/s). Transcriptomic analyses found that DSF caused genome-wide changes in B. bacteriovorus 109J gene expression patterns during both the attack and intraperiplasmic phases, including the significant downregulation of the flagellum assembly genes and numerous serine protease genes. While the former accounts for the reduced speeds observed, the latter was confirmed experimentally with 50 μM DSF completely blocking protease secretion from attack-phase cells. Additional experiments found that 30% of the total cellular ATP was released into the supernatant when B. bacteriovorus 109J was exposed to 200 μM DSF, implying that this QS molecule negatively impacts membrane integrity.