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We report the total and differential cross sections for J/ψ photoproduction with the large acceptance GlueX spectrometer for photon beam energies from the threshold at 8.2 GeV up to 11.44 GeV and over the full kinematic range of momentum transfer squared, t. Such coverage facilitates the extrapolation of the differential cross sections to the forward (t=0) point beyond the physical region. The forward cross section is used by many theoretical models and plays an important role in understanding J/ψ photoproduction and its relation to the J/ψ-proton interaction. These measurements of J/ψ photoproduction near threshold are also crucial inputs to theoretical models that are used to study important aspects of the gluon structure of the proton, such as the gluon generalized parton distribution of the proton, the mass radius of the proton, and the trace anomaly contribution to the proton mass. We observe possible structures in the total cross section energy dependence and find evidence for contributions beyond gluon exchange in the differential cross section close to threshold, both of which are consistent with contributions from open-charm intermediate states.

Sara S McCoy,1 Zubin Mukadam,2 Keith C Meyer,2 Jeffrey P Kanne,3 Cristopher A Meyer,3 Maria D Martin,3 Emmanuel Sampene,4 Scott W Aesif,5 Laurie N Rice,6 Christie M Bartels1 1Division of Rheumatology, Department of Internal Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA; 2Division of Pulmonary and Critical Care, Department of Internal Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA; 3Department of Radiology, University of Wisconsin, Madison, WI 53792-3252, USA; 4Department of Biostatistics, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA; 5Department of Pathology, University of Wisconsin, Madison, WI 53792-3252, USA; 6Department of Pulmonology, SSM Health Dean Medical Group, Madison, WI 53715, USA Objectives: International experts recently characterized interstitial pneumonia with autoimmune features (IPAF) as a provisional diagnosis for patients with interstitial lung disease who have characteristics of autoimmune disease but do not meet criteria for a specific autoimmune disease. We describe clinical characteristics of IPAF patients and examine responses to mycophenolate as a therapy for IPAF.Methods: This retrospective cohort included adult patients meeting European Respiratory Society/American Thoracic Society classification criteria for IPAF. Sociodemographic, clinical, and pulmonary function test data were abstracted for patients with and without mycophenolate treatment and followed longitudinally from interstitial lung disease diagnosis for change in pulmonary function test results.Results: We identified 52 patients who met criteria for IPAF. Of 52 IPAF patients, 24 did not receive mycophenolate and 28 did, with median time to mycophenolate treatment 22 months. Changes in FVC% and percentage predicted lung diffusion capacity for carbon monoxide (DLCO%) between the mycophenolate-treated and untreated groups were not significantly different (FVC% change P=0.08, DLCO% change P=0.17). However, there was a trend toward more rapid baseline decline of both FVC% and DLCO% in the mycophenolate-treated cohort before vs after mycophenolate therapy. The slope of both FVC% and DLCO% values improved after onset of mycophenolate exposure for the treated group, although this finding was not statistically significant.Conclusion: Patients with IPAF might benefit from mycophenolate therapy. Larger prospective clinical trials are needed to evaluate the efficacy of mycophenolate for patients who meet criteria for IPAF. Keywords: interstitial lung disease, autoimmune disease, connective tissue disease, myco­phenolate

Rationale and Objectives: Digital chest imaging has replaced film chest radiographs in many centers, but the International Labour Organization classification system, which is the most widely used system for recognition and classification of dust-related abnormalities, is predicated on film chest radiographs. The purpose of this study was to evaluate the equivalency of digital chest radiographs (including both hard copy and soft copy) with film radiographs for the recognition and quantification of abnormalities consistent with pneumoconiosis using the International Labour Organization classification system. Materials and Methods: Digital chest images and film images, obtained from 107 subjects with a range of parenchymal and pleural abnormalities, were classified in random order by six B readers. Results: Readings of film and soft copy images were equivalent for small opacity profusion; readings of hard copy images had significantly greater prevalence of small opacities compared to film and soft copy. The prevalence of large opacities differed significantly among all three image formats: hard copy greater than film greater than soft copy. However, film and soft copy readings for large opacities did not differ significantly when images demonstrating the coalescence of small opacities that had not yet become a large opacity were grouped with large opacities. The prevalence of pleural abnormalities differed significantly among all three image formats: film greater than hard copy greater than soft copy. Conclusions: Film and soft copy images can be recommended for the recognition and classification of dust-related parenchymal abnormalities using International Labour Organization classifications. The role of digital radiography in reading for pleural abnormalities requires additional investigation. [ABSTRACT FROM AUTHOR]

Solitary fibrous tumor (SFT) is a rare, non-hereditary soft tissue sarcoma thought to originate from fibroblastic mesenchymal stem cells. The etiology of SFT is thought to be due to an environmental intrachromosomal gene fusion between NGFI-A-binding protein 2 (NAB2) and signal transducer and activator protein 6 (STAT6) genes on chromosome 12, wherein the activation domain of STAT6 is fused with the DNA-binding domain of NAB2 resulting in the oncogenesis of SFT. All NAB2-STAT6 fusion variations discovered in SFTs contain the C-terminal of STAT6 transcript, and thus can serve as target site for antisense oligonucleotides (ASOs)-based therapies. Indeed, our in vitro studies show the STAT6 3' untranslated region (UTR)-targeting ASO (ASO 993523) was able to reduce expression of NAB2-STAT6 fusion transcripts in multiple SFT cell models with high efficiency (half-maximal inhibitory concentration: 116-300 nM). Encouragingly, in vivo treatment of SFT patient-derived xenograft mouse models with ASO 993523 resulted in acceptable tolerability profiles, reduced expression of NAB2-STAT6 fusion transcripts in xenograft tissues (21.9%), and, importantly, reduced tumor growth (32.4% decrease in tumor volume compared with the untreated control). Taken together, our study established ASO 993523 as a potential agent for the treatment of SFTs., Competing Interests: We declare that we have no competing interests., (© 2024 The Authors.)

The Cistrome Data Browser is a resource of ChIP-seq, ATAC-seq and DNase-seq data from humans and mice. It provides maps of the genome-wide locations of transcription factors, cofactors, chromatin remodelers, histone post-translational modifications and regions of chromatin accessible to endonuclease activity. Cistrome DB v3.0 contains approximately 45 000 human and 44 000 mouse samples with about 32 000 newly collected datasets compared to the previous release. The Cistrome DB v3.0 user interface is implemented as a single page application that unifies menu driven and data driven search functions and provides an embedded genome browser, which allows users to find and visualize data more effectively. Users can find informative chromatin profiles through keyword, menu, and data-driven search tools. Browser search functions can predict the regulators of query genes as well as the cell type and factor dependent functionality of potential cis-regulatory elements. Cistrome DB v3.0 expands the display of quality control statistics, incorporates sequence logos into motif enrichment displays and includes more expansive sample metadata. Cistrome DB v3.0 is available at http://db3.cistrome.org/browser., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Editor's Note. - RadioGraphics Update articles supplement or update information found in full-length articles previously published in RadioGraphics . These updates, written by at least one author of the previous article, provide a brief synopsis that emphasizes important new information such as technological advances, revised imaging protocols, new clinical guidelines involving imaging, or updated classification schemes.

Cell state atlases constructed through single-cell RNA-seq and ATAC-seq analysis are powerful tools for analyzing the effects of genetic and drug treatment-induced perturbations on complex cell systems. Comparative analysis of such atlases can yield new insights into cell state and trajectory alterations. Perturbation experiments often require that single-cell assays be carried out in multiple batches, which can introduce technical distortions that confound the comparison of biological quantities between different batches. Here we propose CODAL, a variational autoencoder-based statistical model which uses a mutual information regularization technique to explicitly disentangle factors related to technical and biological effects. We demonstrate CODAL's capacity for batch-confounded cell type discovery when applied to simulated datasets and embryonic development atlases with gene knockouts. CODAL improves the representation of RNA-seq and ATAC-seq modalities, yields interpretable modules of biological variation, and enables the generalization of other count-based generative models to multi-batched data., (© 2023. The Author(s).)

Solitary fibrous tumor (SFT) is a rare soft-tissue sarcoma. This nonhereditary cancer is the result of an environmental intrachromosomal gene fusion between NAB2 and STAT6 on chromosome 12, which fuses the activation domain of STAT6 with the repression domain of NAB2. Currently there is not an approved chemotherapy regimen for SFTs. The best response on available pharmaceuticals is a partial response or stable disease for several months. The purpose of this study is to investigate the potential of RNA-based therapies for the treatment of SFTs. Specifically, in vitro SFT cell models were engineered to harbor the characteristic NAB2-STAT6 fusion using the CRISPR/SpCas9 system. Cell migration as well as multiple cancer-related signaling pathways were increased in the engineered cells as compared to the fusion-absent parent cells. The SFT cell models were then used for evaluating the targeting efficacies of NAB2-STAT6 fusion-specific antisense oligonucleotides (ASOs) and CRISPR/CasRx systems. Our results showed that fusion specific ASO treatments caused a 58% reduction in expression of fusion transcripts and a 22% reduction in cell proliferation after 72 h in vitro. Similarly, the AAV2-mediated CRISPR/CasRx system led to a 59% reduction in fusion transcript expressions in vitro, and a 55% reduction in xenograft growth after 29 days ex vivo.

Recent advances in single-cell RNA sequencing have shown heterogeneous cell types and gene expression states in the non-cancerous cells in tumors. The integration of multiple scRNA-seq datasets across tumors can indicate common cell types and states in the tumor microenvironment (TME). We develop a data driven framework, MetaTiME, to overcome the limitations in resolution and consistency that result from manual labelling using known gene markers. Using millions of TME single cells, MetaTiME learns meta-components that encode independent components of gene expression observed across cancer types. The meta-components are biologically interpretable as cell types, cell states, and signaling activities. By projecting onto the MetaTiME space, we provide a tool to annotate cell states and signature continuums for TME scRNA-seq data. Leveraging epigenetics data, MetaTiME reveals critical transcriptional regulators for the cell states. Overall, MetaTiME learns data-driven meta-components that depict cellular states and gene regulators for tumor immunity and cancer immunotherapy., (© 2023. The Author(s).)

The arrival of COVID-19 restrictions and the increasing demand of online instruction options posed challenges to education communities worldwide, especially in human anatomy. In response, Colorado State University developed and deployed an 8-week-long large-scale virtual reality (VR) course to supplement online human anatomy instruction. Students ( n  = 75) received a VR-capable laptop and head-mounted display and participated in weekly synchronous group laboratory sessions with instructors. The software enabled students to remotely collaborate in a common virtual space to work with human anatomy using an artist-rendered cadaver. Qualitative data were collected on student engagement, confidence, and reactions to the new technology. Quantitative data assessed student knowledge acquisition and retention of anatomical spatial relationships. Results indicated that students performed better in the online course (mean = 82.27%) when compared to previous in-person laboratories (mean = 80.08%). The utilization of VR promoted student engagement and increased opportunities for student interaction with teaching assistants, peers, and course content. Notably, students reported benefits that focused on unique aspects of their virtual learning environment, including the ability to infinitely scale the cadaver and walk inside and around anatomical structures. Results suggested that using VR was equivalent to 2D methods in student learning and retention of anatomical relationships. Overall, the virtual classroom maintained the rigor of traditional gross anatomy laboratories without negatively impacting student examination scores and provided a high level of accessibility, without compromising learner engagement., Supplementary Information: The online version contains supplementary material available at 10.1007/s40670-023-01751-w., Competing Interests: Conflict of InterestTod R. Clapp is the Chief Science Officer of Perspectus, Inc., and owns stock in the company. All other authors have no conflict of interest to disclose., (© The Author(s) under exclusive licence to International Association of Medical Science Educators 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Summary: The regulation of genes by cis-regulatory elements (CREs) is complex and differs between cell types. Visual analysis of large collections of chromatin profiles across diverse cell types, integrated with computational methods, can reveal meaningful biological insights. We developed Cistrome Explorer, a web-based interactive visual analytics tool for exploring thousands of chromatin profiles in diverse cell types. Integrated with the Cistrome Data Browser database which contains thousands of ChIP-seq, DNase-seq and ATAC-seq samples, Cistrome Explorer enables the discovery of patterns of CREs across cell types and the identification of transcription factor binding underlying these patterns., Availability and Implementation: Cistrome Explorer and its source code are available at http://cisvis.gehlenborglab.org/ and released under the MIT License. Documentation can be accessed via http://cisvis.gehlenborglab.org/docs/., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2023. Published by Oxford University Press.)

3D patient tumor avatars (3D-PTAs) hold promise for next-generation precision medicine. Here, we describe the benefits and challenges of 3D-PTA technologies and necessary future steps to realize their potential for clinical decision making. 3D-PTAs require standardization criteria and prospective trials to establish clinical benefits. Innovative trial designs that combine omics and 3D-PTA readouts may lead to more accurate clinical predictors, and an integrated platform that combines diagnostic and therapeutic development will accelerate new treatments for patients with refractory disease., Competing Interests: Declarations of interests S.B., M.B., H.M., Z.P., C.A.M., K.M.N., M.F.P., R.C.S., K.S. and J.H.C. have no competing interests to declare. S.E.K. is an advisor to Xilis, Inc. F.M.B. declares consulting/advisory fees from AbbVie, Aduro BioTech Inc., Alkermes, AstraZeneca, Daiichi Sankyo Co. Ltd., DebioPharm, eFFECTOR Therapeutics, F. Hoffman-La Roche Ltd., Genentech Inc., Harbinger Health, IBM Watson, Infinity Pharmaceuticals, Jackson Laboratory, Kolon Life Science, Lengo Therapeutics, OrigiMed, PACT Pharma, Parexel International, Pfizer Inc., Protai Bio Ltd, Samsung Bioepis, Seattle Genetics Inc., Tallac Therapeutics, Tyra Biosciences, Xencor, Zymeworks, Black Diamond, Biovica, Eisai, FogPharma, Immunomedics, Inflection Biosciences, Karyopharm Therapeutics, Loxo Oncology, Mersana Therapeutics, OnCusp Therapeutics, Puma Biotechnology Inc., Seattle Genetics, Sanofi, Silverback Therapeutics, Spectrum Pharmaceuticals, and Zentalis; sponsored research to her institution from Aileron Therapeutics, Inc., AstraZeneca, Bayer Healthcare Pharmaceutical, Calithera Biosciences Inc., Curis Inc., CytomX Therapeutics Inc., Daiichi Sankyo Co. Ltd., Debiopharm International, eFFECTOR Therapeutics, Genentech Inc., Guardant Health Inc., Klus Pharma, Takeda Pharmaceutical, Novartis, Puma Biotechnology Inc., and Taiho Pharmaceutical Co.; and honoraria for a speaking engagement from Chugai Biopharmaceuticals. S.K. is a consultant for FGH BioTech and has received research funding from FGH BioTech and Systems Oncology. K.A.P. is co-inventor on a patent for EGFRT790M mutation testing issued, licensed, and with royalties paid from Molecular Diagnostics/Memorial Sloan Kettering Cancer Center. She reports research funding to the institution from AstraZeneca, Roche/Genentech, Boehringer Ingelheim, and D2G Oncology and consulting for AstraZeneca and Jannssen. M.G.C. reports grants from NeoImmuneTech, as well as other support from Orbus Therapeutics, Incyte, Merck, and UpToDate outside the submitted work; in addition, M.G.C. has a patent for Zika virus strains for the treatment of glioblastoma pending. E.E.’s full disclosures are given here: www.bit.ly/3xuWMer. J.T. reports personal financial interest in form of scientific consultancy role for Array Biopharma, AstraZeneca, Bayer, Boehringer Ingelheim, Chugai, Daiichi Sankyo, F. Hoffmann-La Roche Ltd, Genentech Inc, HalioDX SAS, Hutchison MediPharma International, Ikena Oncology, Inspirna Inc, IQVIA, Lilly, Menarini, Merck Serono, Merus, MSD, Mirati, Neophore, Novartis, Ona Therapeutics, Orion Biotechnology, Peptomyc, Pfizer, Pierre Fabre, Samsung Bioepis, Sanofi, Scandion Oncology, Scorpion Therapeutics, Seattle Genetics, Servier, Sotio Biotech, Taiho, Tessa Therapeutics, and TheraMyc; and holds stocks in Oniria Therapeutics and also educational collaboration with Imedex/HMP, Medscape Education, MJH Life Sciences, PeerView Institute for Medical Education and Physicians Education Resource (PER). D.A.T. is a member of the Scientific Advisory Board and receives stock options from Leap Therapeutics, Surface Oncology, Cygnal Therapeutics, Mestag Therapeutics, and Xilis, Inc. outside the submitted work. D.A.T. is scientific co-founder of Mestag Therapeutics. D.A.T. has received research grant support from Fibrogen, Mestag, and ONO Therapeutics. D.A.T. receives grant funding from the Lustgarten Foundation, the NIH, and the Thompson Foundation. None of this work is related to the publication. No other disclosures were reported. C.D.W. is a part-time consultant for LifeNet Health and receives grant funding from AACR-Novocure and Varian Medical Systems. X.S. and H.C. are cofounders of Xilis, Inc. and inventors on patents related to organoid research and micro-organospheres. X.S. is CEO of Xilis, Inc. H.C.’s full disclosure is given here: www.uu.nl/staff/JCClevers/Additionalfunctions. M.S., B.J.R., P.R., X.L., B.E.W., and A.L.W. do not report any conflicts., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Despite advancements in early detection and treatment, atherosclerosis remains the leading cause of death across all cardiovascular diseases (CVD). Biomechanical analysis of atherosclerotic lesions has the potential to reveal biomechanically instable or rupture-prone regions. Treatment decisions rarely consider the biomechanics of the stenosed lesion due in-part to difficulties in obtaining this information in a clinical setting. Previous 3D FEA approaches have incompletely incorporated the complex curvature of arterial geometry, material heterogeneity, and use of patient-specific data. To address these limitations and clinical need, herein we present a user-friendly fully automated program to reconstruct and simulate the wall mechanics of patient-specific atherosclerotic coronary arteries. The program enables 3D reconstruction from patient-specific data with heterogenous tissue assignment and complex arterial curvature. Eleven arteries with coronary artery disease (CAD) underwent baseline and 6-month follow-up angiographic and virtual histology-intravascular ultrasound (VH-IVUS) imaging. VH-IVUS images were processed to remove background noise, extract VH plaque material data, and luminal and outer contours. Angiography data was used to orient the artery profiles along the 3D centerlines. The resulting surface mesh is then resampled for uniformity and tetrahedralized to generate the volumetric mesh using TetGen. A mesh convergence study revealed edge lengths between 0.04 mm and 0.2 mm produced constituent volumes that were largely unchanged, hence, to save computational resources, a value of 0.2 mm was used throughout. Materials are assigned and finite element analysis (FEA) is then performed to determine stresses and strains across the artery wall. In a representative artery, the highest average effective stress was in calcium elements with 235 kPa while necrotic elements had the lowest average stress, reaching as low as 0.79 kPa. After applying nodal smoothening, the maximum effective stress across 11 arteries remained below 288 kPa, implying biomechanically stable plaques. Indeed, all atherosclerotic plaques remained unruptured at the 6-month longitudinal follow up diagnosis. These results suggest our automated analysis may facilitate assessment of atherosclerotic plaque stability., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2022 Warren, Yoo, Meyer, Molony, Samady and Hayenga.)

Genome-wide profiling of chromatin accessibility by DNase-seq or ATAC-seq has been widely used to identify regulatory DNA elements and transcription factor binding sites. However, enzymatic DNA cleavage exhibits intrinsic sequence biases that confound chromatin accessibility profiling data analysis. Existing computational tools are limited in their ability to account for such intrinsic biases and not designed for analyzing single-cell data. Here, we present Simplex Encoded Linear Model for Accessible Chromatin (SELMA), a computational method for systematic estimation of intrinsic cleavage biases from genomic chromatin accessibility profiling data. We demonstrate that SELMA yields accurate and robust bias estimation from both bulk and single-cell DNase-seq and ATAC-seq data. SELMA can utilize internal mitochondrial DNA data to improve bias estimation. We show that transcription factor binding inference from DNase footprints can be improved by incorporating estimated biases using SELMA. Furthermore, we show strong effects of intrinsic biases in single-cell ATAC-seq data, and develop the first single-cell ATAC-seq intrinsic bias correction model to improve cell clustering. SELMA can enhance the performance of existing bioinformatics tools and improve the analysis of both bulk and single-cell chromatin accessibility sequencing data., (© 2022. The Author(s).)

Polycomb repressive epigenetic complexes are recurrently dysregulated in cancer. Unlike polycomb repressive complex 2 (PRC2), the role of PRC1 in oncogenesis and therapy resistance is not well-defined. Here, we demonstrate that highly recurrent mutations of the PRC1 subunits BCOR and BCORL1 in leukemia disrupt assembly of a noncanonical PRC1.1 complex, thereby selectively unlinking the RING-PCGF enzymatic core from the chromatin-targeting auxiliary subcomplex. As a result, BCOR-mutated PRC1.1 is localized to chromatin but lacks repressive activity, leading to epigenetic reprogramming and transcriptional activation at target loci. We define a set of functional targets that drive aberrant oncogenic signaling programs in PRC1.1-mutated cells and primary patient samples. Activation of these PRC1.1 targets in BCOR-mutated cells confers acquired resistance to treatment while sensitizing to targeted kinase inhibition. Our study thus reveals a novel epigenetic mechanism that explains PRC1.1 tumor-suppressive activity and identifies a therapeutic strategy in PRC1.1-mutated cancer., Significance: We demonstrate that BCOR and BCORL1 mutations in leukemia unlink PRC1.1 repressive function from target genes, resulting in epigenetic reprogramming and activation of aberrant cell signaling programs that mediate treatment resistance. Our study provides mechanistic insights into the pathogenesis of PRC1.1-mutated leukemia that inform novel therapeutic approaches. This article is highlighted in the In This Issue feature, p. 85., (©2021 American Association for Cancer Research.)

As sequencing depth of chromatin studies continually grows deeper for sensitive profiling of regulatory elements or chromatin spatial structures, aligning and preprocessing of these sequencing data have become the bottleneck for analysis. Here we present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times faster than traditional workflows on bulk ChIP-seq/Hi-C profiles and than 10x Genomics' CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles., (© 2021. The Author(s).)

Despite remarkable clinical efficacy of immune checkpoint blockade (ICB) in cancer treatment, ICB benefits for triple-negative breast cancer (TNBC) remain limited. Through pooled in vivo CRISPR knockout (KO) screens in syngeneic TNBC mouse models, we found that deletion of the E3 ubiquitin ligase Cop1 in cancer cells decreases secretion of macrophage-associated chemokines, reduces tumor macrophage infiltration, enhances anti-tumor immunity, and strengthens ICB response. Transcriptomics, epigenomics, and proteomics analyses revealed that Cop1 functions through proteasomal degradation of the C/ebpδ protein. The Cop1 substrate Trib2 functions as a scaffold linking Cop1 and C/ebpδ, which leads to polyubiquitination of C/ebpδ. In addition, deletion of the E3 ubiquitin ligase Cop1 in cancer cells stabilizes C/ebpδ to suppress expression of macrophage chemoattractant genes. Our integrated approach implicates Cop1 as a target for improving cancer immunotherapy efficacy in TNBC by regulating chemokine secretion and macrophage infiltration in the tumor microenvironment., Competing Interests: Declaration of interests X.S.L. is a cofounder, board member, scientific advisor board member, and consultant of GV20 Oncotherapy and a stockholder of BMY, TMO, WBA, ABT, ABBV, and JNJ and receives research funding from Takeda, Sanofi, Bristol Myers Squibb, and Novartis. M.B. receives sponsored research support from and is a consultant to Novartis. M.B. serves on the scientific advisory boards of GV20 Oncotherapy, Kronos Bio, and H3 Biomedicine. T.X. is a cofounder, board member, and full-time employee of GV20 Oncotherapy., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Numerical simulations of coupled hemodynamics and leukocyte transport and adhesion inside coronary arteries have been performed. Realistic artery geometries have been obtained for a set of four patients from intravascular ultrasound and angiography images. The numerical model computes unsteady three-dimensional blood hemodynamics and leukocyte concentration in the blood. Wall-shear stress dependent leukocyte adhesion is also computed through agent-based modeling rules, fully coupled to the hemodynamics and leukocyte transport. Numerical results have a good correlation with clinical data. Regions where high adhesion is predicted by the simulations coincide to a good approximation with artery segments presenting plaque increase, as documented by clinical data from baseline and six-month follow-up exam of the same artery. In addition, it is observed that the artery geometry and, in particular, the tortuosity of the centerline are a primary factor in determining the spatial distribution of wall-shear stress, and of the resulting leukocyte adhesion patterns. Although further work is required to overcome the limitations of the present model and ultimately quantify plaque growth in the simulations, these results are encouraging towards establishing a predictive methodology for atherosclerosis progress.

The diaphragm serves as an anatomic border between the abdominal and thoracic cavities. Pathologic conditions traversing the diaphragm are often incompletely described and may be overlooked, resulting in diagnostic delays. Several routes allow abdominal contents or pathologic processes to spread into the thorax, including along normal transphrenic structures, through congenital defects in the diaphragm, through inherent areas of weakness between muscle groups, or by pathways created by tissue destruction, trauma, or iatrogenic injuries. A thorough knowledge of the anatomy of the diaphragm can inform an accurate differential diagnosis. Often, intraperitoneal pathologic conditions crossing the diaphragm may be overlooked if axial imaging is the only approach to this complex region because of the horizontal orientation of much of the diaphragm. Multiplanar capabilities of volumetric CT and MRI provide insight into the pathways where pathologic conditions may traverse this border. Knowledge of these characteristic routes and use of multiplanar imaging are critical for depiction of specific transdiaphragmatic pathologic conditions. © RSNA, 2020.

The blood-retina barrier and blood-brain barrier (BRB/BBB) are selective and semipermeable and are critical for supporting and protecting central nervous system (CNS)-resident cells. Endothelial cells (ECs) within the BRB/BBB are tightly coupled, express high levels of Claudin-5 (CLDN5), a junctional protein that stabilizes ECs, and are important for proper neuronal function. To identify novel CLDN5 regulators (and ultimately EC stabilizers), we generated a CLDN5-P2A-GFP stable cell line from human pluripotent stem cells (hPSCs), directed their differentiation to ECs (CLDN5-GFP hPSC-ECs), and performed flow cytometry-based chemogenomic library screening to measure GFP expression as a surrogate reporter of barrier integrity. Using this approach, we identified 62 unique compounds that activated CLDN5-GFP. Among them were TGF-β pathway inhibitors, including RepSox. When applied to hPSC-ECs, primary brain ECs, and retinal ECs, RepSox strongly elevated barrier resistance (transendothelial electrical resistance), reduced paracellular permeability (fluorescein isothiocyanate-dextran), and prevented vascular endothelial growth factor A (VEGFA)-induced barrier breakdown in vitro. RepSox also altered vascular patterning in the mouse retina during development when delivered exogenously. To determine the mechanism of action of RepSox, we performed kinome-, transcriptome-, and proteome-profiling and discovered that RepSox inhibited TGF-β, VEGFA, and inflammatory gene networks. In addition, RepSox not only activated vascular-stabilizing and barrier-establishing Notch and Wnt pathways, but also induced expression of important tight junctions and transporters. Taken together, our data suggest that inhibiting multiple pathways by selected individual small molecules, such as RepSox, may be an effective strategy for the development of better BRB/BBB models and novel EC barrier-inducing therapeutics., Competing Interests: Competing interest statement: This study is supported by F. Hoffmann-La Roche Ltd. F. Roudnicky, J.D.Z., B.K.K., N.J.P., Y.L., L.S.-P., H.R., P.S., S.G., M.L., S.U., F. Revelant, O.E., G.S., V.K., K.C., M.T., B.B., M.G., C.P., M.B., C.A.M., and P.D.W. are employees of F. Hoffmann-La Roche. L.D.G. and Z.M. are employees of Genentech Inc. F. Roudnicky, N.J.P., and V.K. were supported by a Roche postdoctoral fellowship. B.K.K. was supported by a Roche doctoral fellowship. C.A.C. is a founder and chief scientific officer of Sana Biotechnology. Neither a reagent nor any funding from Sana Biotechnology was used in this study.

We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow ( http://github.com/liulab-dfci/MAESTRO ) for the integrative analyses of single-cell RNA-seq (scRNA-seq) and ATAC-seq (scATAC-seq) data from multiple platforms. MAESTRO provides functions for pre-processing, alignment, quality control, expression and chromatin accessibility quantification, clustering, differential analysis, and annotation. By modeling gene regulatory potential from chromatin accessibilities at the single-cell level, MAESTRO outperforms the existing methods for integrating the cell clusters between scRNA-seq and scATAC-seq. Furthermore, MAESTRO supports automatic cell-type annotation using predefined cell type marker genes and identifies driver regulators from differential scRNA-seq genes and scATAC-seq peaks.

Using cadaveric instruction in a graduate-level anatomy course is an expensive and time-consuming undertaking. While this is a worthwhile endeavor, most first-year medical students and students in the health fields struggle with the independent, self-directed learning approach in the cadaveric laboratory, and going beyond rote memorization of the material. As such, effective assessment tools that maximize student learning in the cadaveric laboratory are critical, especially if no lecture component is present. Dissection quality often reflects student attention to detail and therefore may be tied to overall performance in the course. The aim of this study was to investigate the relationship between weekly table quizzes and the overall student outcomes in a graduate biomedical human dissection class as well as examining the benefits and implications of this approach. In this course, a uniquely structured weekly quiz assessed dissection quality and probed student understanding in human anatomy. Student data compiled from 5 years of dissection courses were analyzed to evaluate the relationship between performance in the weekly assessment and on the unit examinations. The results showed a statistically significant relationship between the weekly quizzes and the student examinations at the end of each dissection block in 2013, 2015, 2016, and 2017. The data suggest a potential correlation between performance on weekly quizzes and on unit examinations. The unique nature of the table quizzes provides the students with the opportunity to practice the retrieval of their knowledge, feel more guided throughout their dissection, and receive immediate feedback on their performance. This assessment tool also provides a way to predict student outcomes and an opportunity for early intervention to help at-risk students. The analysis of this research study contributes to the need for more data on the usage of assessment tools in a graduate human dissection class., Competing Interests: Declaration of Conflicting Interests:The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2020.)

Cytotoxic T cells play a key role in adaptive immunity by killing infected or cancerous cells. While the transcriptional control of CD8 T cell differentiation and effector function following T cell activation has been extensively studied, little is known about epigenetic regulation of these processes. Here we show that the histone deacetylase HDAC3 inhibits CD8 T cell cytotoxicity early during activation and is required for persistence of activated CD8 T cells following resolution of an acute infection. Mechanistically, HDAC3 inhibits gene programs associated with cytotoxicity and effector differentiation of CD8 T cells including genes encoding essential cytotoxicity proteins and key transcription factors. These data identify HDAC3 as an epigenetic regulator of the CD8 T cell cytotoxicity program., Competing Interests: Disclosures: Dr. Fisher reported a financial interest in Soltego, Inc., a company developing SIK inhibitors for topical skin darkening treatments that might be used for a broad set of human applications. Dr. Fisher's interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies. Dr. Brown reported grants from Novartis and personal fees from H3 Biomedicine, Kronos Bio, Aleta Biotherapeutics, and GV20 Therapeutics outside the submitted work. Dr. Wucherpfennig reported grants from Novartis during the conduct of the study; personal fees from TCR2 Therapeutics, T-Scan Therapeutics, Immunitas Therapeutics, and Nextechinvest outside the submitted work. No other disclosures were reported., (© 2020 Tay et al.)

Gene editing in human pluripotent stem cells (hPSC) is a powerful tool for understanding biology, for drug discovery and gene therapy. Naïve hPSC have been suggested to be superior for gene editing compared to conventional 'primed' hPSC. Using droplet digital PCR, we uncover the kinetics of Cas9-induced double strand break repair in conventional hPSC. Cut but unrepaired alleles reach their maximum after 12-24 h. Homology directed repair plateaus after 24 h, whereas repair by non-homologous end joining continues until 48 h after Cas9 introduction. Using this method, we demonstrate that the rate of homology directed repair to resolve Cas9-induced double strand breaks is 40% lower in naïve hPSC compared to conventional hPSC, correlating with, and feasibly explained by, a higher number of cells in G 1 phase of the cell cycle in naïve hPSC. Therefore, naïve hPSC are less efficient for CRISPR/Cas9-mediated homology directed repair., Competing Interests: Declaration of interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Naïve human pluripotent stem cells (hPSC) resemble the embryonic epiblast at an earlier time-point in development than conventional, 'primed' hPSC. We present a comprehensive miRNA profiling of naïve-to-primed transition in hPSC, a process recapitulating aspects of early in vivo embryogenesis. We identify miR-143-3p and miR-22-3p as markers of the naïve state and miR-363-5p, several members of the miR-17 family, miR-302 family as primed markers. We uncover that miR-371-373 are highly expressed in naïve hPSC. MiR-371-373 are the human homologs of the mouse miR-290 family, which are the most highly expressed miRNAs in naïve mouse PSC. This aligns with the consensus that naïve hPSC resemble mouse naive PSC, showing that the absence of miR-371-373 in conventional hPSC is due to cell state rather than a species difference.

Characterization of the genomic distances over which transcription factor (TF) binding influences gene expression is important for inferring target genes from TF chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here we systematically examine the relationship between thousands of TF and histone modification ChIP-seq data sets with thousands of gene expression profiles. We develop a model for integrating these data, which reveals two classes of TFs with distinct ranges of regulatory influence, chromatin-binding preferences, and auto-regulatory properties. We find that the regulatory range of the same TF bound within different topologically associating domains (TADs) depend on intrinsic TAD properties such as local gene density and G/C content, but also on the TAD chromatin states. Our results suggest that considering TF type, binding distance to gene locus, as well as chromatin context is important in identifying implicated TFs from GWAS SNPs.

Endothelial cells (ECs) display remarkable plasticity during development before becoming quiescent and functionally mature. EC maturation is directed by several known transcription factors (TFs), but the specific set of TFs responsible for promoting high-resistance barriers, such as the blood-brain barrier (BBB), have not yet been fully defined. Using expression mRNA data from published studies on ex vivo ECs from the central nervous system (CNS), we predicted TFs that induce high-resistance barrier properties of ECs as in the BBB. We used our previously established method to  generate ECs from human pluripotent stem cells (hPSCs), and then we overexpressed the candidate TFs in hPSC-ECs and measured barrier resistance and integrity using electric cell-substrate impedance sensing, trans-endothelial electrical resistance and FITC-dextran permeability assays. SOX18 and TAL1 were the strongest EC barrier-inducing TFs, upregulating Wnt-related signaling and EC junctional gene expression, respectively, and downregulating EC proliferation-related genes. These TFs were combined with SOX7 and ETS1 that together effectively induced EC barrier resistance, decreased paracellular transport and increased protein expression of tight junctions and induce mRNA expression of several genes involved in the formation of EC barrier and transport. Our data shows identification of a transcriptional network that controls barrier resistance in ECs. Collectively this data may lead to novel approaches for generation of in vitro models of the BBB.

We developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes and outperformed alternative methods in identifying the perturbed TRs.

The kinase AKT2 (PKB) is an important mediator of insulin signaling, for which loss-of-function knockout (KO) mutants lead to early onset diabetes mellitus, and dominant active mutations lead to early development of obesity and endothelial cell (EC) dysfunction. To model EC dysfunction, we used edited human pluripotent stem cells (hPSCs) that carried either a homozygous deletion of AKT2 (AKT2 KO) or a dominant active mutation (AKT2 E17K), which, along with the parental wild type (WT), were differentiated into ECs. Profiling of EC lines indicated an increase in proinflammatory and a reduction in anti-inflammatory fatty acids, an increase in inflammatory chemokines in cell supernatants, increased expression of proinflammatory genes, and increased binding to the EC monolayer in a functional leukocyte adhesion assay for both AKT2 KO and AKT2 E17K. Collectively, these findings suggest that vascular endothelial inflammation that results from dysregulated insulin signaling (homeostasis) may contribute to coronary artery disease, and that either downregulation or upregulation of the insulin pathway may lead to inflammation of endothelial cells. This suggests that the standard of care for patients must be expanded from control of metabolic parameters to include control of inflammation, such that endothelial dysfunction and cardiovascular disorders can ultimately be prevented.