MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape.

MLL rearrangements produce fusion oncoproteins that drive leukemia development, but the direct effects of MLL-fusion inactivation remain poorly defined. We designed models with degradable MLL::AF9 where treatment with small molecules induces rapid degradation. We leveraged the kinetics of this system to identify a core subset of MLL::AF9 target genes where MLL::AF9 degradation induces changes in transcriptional elongation within 15 minutes. MLL::AF9 degradation subsequently causes loss of a transcriptionally active chromatin landscape. We used this insight to assess the effectiveness of small molecules that target members of the MLL::AF9 multiprotein complex, specifically DOT1L and MENIN. Combined DOT1L/MENIN inhibition resembles MLL::AF9 degradation, whereas single-agent treatment has more modest effects on MLL::AF9 occupancy and gene expression. Our data show that MLL::AF9 degradation leads to decreases in transcriptional elongation prior to changes in chromatin landscape at select loci and that combined inhibition of chromatin complexes releases the MLL::AF9 oncoprotein from chromatin globally.

Comprehensive single-cell transcriptome lineages of a proto-vertebrate.

Ascidian embryos highlight the importance of cell lineages in animal development. As simple proto-vertebrates, they also provide insights into the evolutionary origins of cell types such as cranial placodes and neural crest cells. Here we have determined single-cell transcriptomes for more than 90,000 cells that span the entirety of development-from the onset of gastrulation to swimming tadpoles-in Ciona intestinalis. Owing to the small numbers of cells in ascidian embryos, this represents an average of over 12-fold coverage for every cell at every stage of development. We used single-cell transcriptome trajectories to construct virtual cell-lineage maps and provisional gene networks for 41 neural subtypes that comprise the larval nervous system. We summarize several applications of these datasets, including annotating the synaptome of swimming tadpoles and tracing the evolutionary origin of cell types such as the vertebrate telencephalon.

Privacy-preserving model evaluation for logistic and linear regression using homomorphically encrypted genotype data.

OBJECTIVE: Linear and logistic regression are widely used statistical techniques in population genetics for analyzing genetic data and uncovering patterns and associations in large genetic datasets, such as identifying genetic variations linked to specific diseases or traits. However, obtaining statistically significant results from these studies requires large amounts of sensitive genotype and phenotype information from thousands of patients, which raises privacy concerns. Although cryptographic techniques such as homomorphic encryption offers a potential solution to the privacy concerns as it allows computations on encrypted data, previous methods leveraging homomorphic encryption have not addressed the confidentiality of shared models, which can leak information about the training data. METHODS: In this work, we present a secure model evaluation method for linear and logistic regression using homomorphic encryption for six prediction tasks, where input genotypes, output phenotypes, and model parameters are all encrypted. RESULTS: Our method ensures no private information leakage during inference and achieves high accuracy (≥93% for all outcomes) with each inference taking less than ten seconds for ∼200 genomes. CONCLUSION: Our study demonstrates that it is possible to perform linear and logistic regression model evaluation while protecting patient confidentiality with theoretical security guarantees. Our implementation and test data are available at https://github.com/G2Lab/privateML/.

Identification of MYH9 as a key regulator for synoviocyte migration and invasion through secretome profiling.

OBJECTIVES: 'Invasive pannus' is a pathological hallmark of rheumatoid arthritis (RA). This study aimed to investigate secretome profile of synovial fibroblasts of patients with RA (RA-FLSs), a major cell type comprising the invasive pannus. METHODS: Secreted proteins from RA-FLSs were first identified using liquid chromatography-tandem mass spectrometry analysis. Ultrasonography was performed for affected joints to define synovitis severity at the time of arthrocentesis. Expression levels of myosin heavy chain 9 (MYH9) in RA-FLSs and synovial tissues were determined by ELISA, western blot analysis and immunostaining. A humanised synovitis model was induced in immuno-deficient mice. RESULTS: We first identified 843 proteins secreted from RA-FLSs; 48.5% of the secretome was associated with pannus-driven pathologies. Parallel reaction monitoring analysis of the secretome facilitated discovery of 16 key proteins related to 'invasive pannus', including MYH9, in the synovial fluids, which represented synovial pathology based on ultrasonography and inflammatory activity in the joints. Particularly, MYH9, a key protein in actin-based cell motility, showed a strong correlation with fibroblastic activity in the transcriptome profile of RA synovia. Moreover, MYH9 expression was elevated in cultured RA-FLSs and RA synovium, and its secretion was induced by interleukin-1ß, tumour necrosis factor α, toll-like receptor ligation and endoplasmic reticulum stimuli. Functional experiments demonstrated that MYH9 promoted migration and invasion of RA-FLSs in vitro and in a humanised synovitis model, which was substantially inhibited by blebbistatin, a specific MYH9 inhibitor. CONCLUSIONS: This study provides a comprehensive resource of the RA-FLS-derived secretome and suggests that MYH9 represents a promising target for retarding abnormal migration and invasion of RA-FLSs.

Pre-application of dentin bonding agent prevents discoloration caused by mineral trioxide aggregate.

BACKGROUND: To evaluate tooth discoloration by newly developed calcium silicate-based materials, and to examine the pre-application of dentin bonding agent (DBA) for preventing discoloration caused by mineral trioxide aggregate (MTA). METHODS: The roots of 50 premolars were randomly divided into five groups (n = 10) and cavities were prepared from resected root surfaces. MTA was placed in the cavities of teeth belonging to the ProRoot MTA (MTA) and RetroMTA (RMTA) groups. For teeth belonging to the ProRoot + DBA (MTA-B) and RetroMTA + DBA (RMTA-B) groups, DBA was first applied to the cavities prior to the addition of MTA. Teeth in the control group were restored with composite resin only (i.e., without MTA). After 12 weeks, MTA was removed from the MTA and RMTA groups and bleaching agents were applied for 3 additional weeks. Color assessments were recorded at baseline, and 1, 4, and 12 weeks, as well as after bleaching. A one-way ANOVA was performed to assess the differences between the two types of MTAs and color changes following DBA pre-application in each MTA group. A p-value of < 0.05 was considered indicative of statistical significance. RESULTS: Following 12 weeks of MTA treatment, there was a significant difference between the discoloration in the MTA and RMTA groups (p < 0.05). However, no significant difference was observed between the RMTA and RMTA-B groups (p > 0.05). Following bleaching, the color changes (ΔE values) of the MTA group were not significantly different from those of the MTA-B group (p > 0.05). The difference of ΔE between the RMTA group after internal bleaching and the RMTA-B group was also not significant (p > 0.05). CONCLUSIONS: RetroMTA caused significantly less discoloration than ProRoot MTA. Pre-application of DBA reduced discoloration caused by ProRoot MTA. MTA discoloration was improved equally well between DBA pre-application and post-bleaching.

VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants.

Rare or de novo variants have substantial contribution to human diseases, but the statistical power to identify risk genes by rare variants is generally low due to rarity of genotype data. Previous studies have shown that risk genes usually have high expression in relevant cell types, although for many conditions the identity of these cell types are largely unknown. Recent efforts in single cell atlas in human and model organisms produced large amount of gene expression data. Here we present VBASS, a Bayesian method that integrates single-cell expression and de novo variant (DNV) data to improve power of disease risk gene discovery. VBASS models disease risk prior as a function of expression profiles, approximated by deep neural networks. It learns the weights of neural networks and parameters of Gamma-Poisson likelihood models of DNV counts jointly from expression and genetics data. On simulated data, VBASS shows proper error rate control and better power than state-of-the-art methods. We applied VBASS to published datasets and identified more candidate risk genes with supports from literature or data from independent cohorts. VBASS can be generalized to integrate other types of functional genomics data in statistical genetics analysis.

Hierarchical Concept Relations Improve Detection of Off-Label Drug Use in Electronic Health Records Data.

Real-world clinical practice commonly veers from formal drug approvals in off-label use, accounting for 21% of prescriptions for common drugs. Due to its ad hoc nature, off-label use typically goes undocumented, evading the safety and efficacy scrutiny of clinical trials. A systematic and automated approach to detection of these uses in the electronic health record (EHR) would enable improved safety monitoring, provide insight into prescribing patterns, and support real-world evidence appraisal. Domain knowledge provided by medication-indication knowledge bases has been shown to improve the accuracy of EHR-based automated detection of off-label use, but remains limited due to diverse concept representations and granularities across data sources. We present a method to leverage hierarchical concept knowledge to align medication-indication knowledge with EHR data for automated detection of off-label drug use in clinical practice. We demonstrate an over two-fold increase in detected off-label diagnoses when leveraging hierarchical knowledge relative to direct concept matching alone.

Morphological Characteristics and Classification of Mandibular First Molars Having 2 Distal Roots or Canals: 3-Dimensional Biometric Analysis Using Cone-beam Computed Tomography in a Korean Population.

INTRODUCTION: The aim of this study was to determine the morphologic characteristics of mandibular first molars having 2 canals in distal roots. Interorifice distance, buccal bone thickness, and root curvature were evaluated using cone-beam computed tomography images in a Korean population. METHODS: In total, 1958 mandibular first molars were evaluated in axial, coronal, sagittal, and paraxial planes. Distal roots having 2 canals were classified according to their root and canal shapes (2 roots, 2 canals [2R2C]; 1 root, 2 canals with 2 apical foramina [1R2C(2-2)]; and 1 root, 2 canals with 1 apical foramen [1R2C(2-1)]). The distances between orifices and the distance from the apex to the buccal bone plate were measured for each root canal shape (2R2C, 1R2C[2-2], and 1R2C[2-1]). The curvature of distolingual (DL) roots was classified according to severity using 3-dimensional reconstructed images, and the direction of curvature was determined. The relationships of these characteristics to sex and side were evaluated. RESULTS: The prevalences of 2R2C, 1R2C(2-2), and 1R2C(2-1) were 25.89%, 10.32%, and 14.15%, respectively. The distances between distobuccal (DB) and DL orifices were 3.77 ± 0.74 mm for 2R2C, 3.02 ± 0.65 mm for 1R2C(2-2), and 2.44 ± 0.64 mm for 1R2C(2-1). The distances from the buccal plate to the DB canal were 3.84 ± 1.35 mm for 2R2C, 5.33 ± 1.41 mm for 1R2C(2-2), and 5.96 ± 1.63 mm for 1R2C(2-1). The distance from the buccal plate to the DL canal was 9.85 ± 1.46 mm for 2R2C, and 8.28 ± 1.50 mm for 1R2C(2-2). All distances differed significantly according to root canal configurations, and all were greater in men than women (P < .05), except for the DB-DL orifice distance in 1R2C(2-2) and the DB to buccal cortical plate distance in all root configurations (P > .05). No significant difference between the left and right sides was found (P > .05). The prevalence of most severely curved DL roots (type III) was 62.92%, and the direction was commonly toward the buccal side (69.03%). CONCLUSIONS: The prevalence of mandibular first molars having 2 canals in distal roots was more than 50% in a Korean population. Interorifice distances between DB and DL canals and distances from the apex to the buccal cortical plate differed according to root and canal numbers and shapes.