bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplex Base Editing to Protect from CD33-Directed Therapy: Implications for Immune and Gene Therapy
Authors: Borot Florence , Humbert Olivier , Newby Gregory A , Fields Emily , Kohli Sajeev , Radtke Stefan , Laszlo George S. , Mayuranathan Thiyagaraj , Ali Abdullah Mahmood , Weiss Mitchell J. , Yen Jonathan S. , Walter Roland B. , Liu David R. , Mukherjee Siddhartha , Kiem Hans-Peter 
Published: February 2023

AbstractOn-target toxicity to normal cells is a major safety concern with targeted immune and gene therapies. Here, we developed a base editing (BE) approach exploiting a naturally occurring CD33 single nucleotide polymorphism leading to removal of full-length CD33 surface expression on edited cells. CD33 editing in human and nonhuman primate (NHP) hematopoietic stem and progenitor cells (HSPCs) protects from CD33-targeted therapeutics without affecting normal hematopoiesisin vivo, thus demonstrating potential for novel immunotherapies with reduced off-leukemia toxicity. For broader applications to gene therapies, we demonstrated highly efficient (>70%) multiplexed adenine base editing of the CD33 and gamma globin genes, resulting in long-term persistence of dual gene-edited cells with HbF reactivation in NHPs.In vitro, dual gene-edited cells could be enriched via treatment with the CD33 antibody-drug conjugate, gemtuzumab ozogamicin (GO). Together, our results highlight the potential of adenine base editors for improved immune and gene therapies.Graphical abstract
Prior College Biology Coursework Increases Student Outcomes for Underrepresented Minority Students studying Anatomy and Physiology
Authors: Stephens Brian R. 
Published: February 2023

ABSTRACTStudent performance and achievement in anatomy and physiology (AP) are determining factors in admissions into medical and other health-allied programs. Madison College has had historically poor course retention and pass rates for underrepresented minorities in A&P. Course and enrollment data from 2013 – 2020 were examined to determine whether students who optionally took lab-based biology coursework had improved student outcomes. Underrepresented minority students who completed ≥ 1 lab-based college biology course before entering AP had improved student outcomes evidenced by an increased pass rate and a reduced failure rate. Statistical analysis uncovered a statistically significant association (p≤ 0.10) with prior lab-based college biology coursework and student outcomes in AP for underrepresented minority students.
High resolution cryo-EM and crystallographic snapshots of the large actinobacterial 2-oxoglutarate dehydrogenase: an all-in-one fusion with unique properties
Authors: Yang Lu , Wagner Tristan , Mechaly Ariel , Boyko Alexandra , Bruch Eduardo M. , Megrian Daniela , Gubellini Francesca , Alzari Pedro M. , Bellinzoni Marco 
Published: February 2023

AbstractActinobacteria possess unique ways to regulate the oxoglutarate node located in the central position of the tricarboxylic acid cycle, a crossroad between energy conservation and nitrogen metabolism. Here, we studied the decarboxylative oxidation route that leads, through the 2-oxoglutarate dehydrogenase (ODH) complex, to the generation of succinyl-CoA and reduced equivalents to feed the respiratory chain. Compared to most organisms in which the oxidative decarboxylation and reductive acylation steps are carried out by different enzymes within the ODH complex, actinobacteria rely on an all-in-one protein (OdhA) in which both activities are carried out by the same polypeptide. We describe high-resolution cryo-EM and X-ray crystallography snapshots of representative enzymes fromMycobacterium smegmatisandCorynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that folds into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the FHA (Fork-Head Associated) signalling protein OdhI, delivering new molecular details on how this actinobacterial-specific switching mechanism operates. Overall, the quaternary organization of OdhA represents a new piece of the fascinating puzzle of the synergistic, mixed pyruvate dehydrogenase/2-oxoglutarate dehydrogenase actinobacterial supercomplex.
Multi-view learning to unravel the different levels underlying hepatitis B vaccine response
Authors: Affaticati Fabio , Bartholomeus Esther , Mullan Kerry , Van Damme Pierre , Beutels Philippe , Ogunjimi Benson , Laukens Kris , Meysman Pieter 
Published: February 2023

AbstractThe immune system acts as the intricate apparatus dedicated to mounting a defence that ensures host survival from microbial threats. To engage this faceted immune response and provide protection against infectious diseases, vaccinations are the critical tool developed. However, vaccine responses are governed by levels that when interrogated separately only explain a fraction of the immune reaction. To address this knowledge gap, we conducted a feasibility study to determine if multi-view modelling can aid in gaining actionable insights on response markers shared across populations, capture the immune system diversity, and disentangle confounders. We thus sought to assess this multi-view modelling capacity on the responsiveness to Hepatitis B virus (HBV) vaccination.Seroconversion to vaccine induced antibodies against HBV surface antigen (anti-HBs) in early-converters (n=21; <2 month) and late-converters (n=9; <6 months), was defined based on the anti-HBs titres (>10IU/L). The multi-view data encompassed bulk RNA-seq, CD4+ T cell parameters (including T-cell receptor data), flow cytometry data, and clinical metadata (including age and gender). The modelling included testing single-view and multi-view joint dimensionality reductions. Multi-view joint dimensionality reduction out-performed single-view methods in terms of area under curve and balanced accuracy, confirming an increase in predictive power to be gained. The interpretation of the findings showed that age, gender, inflammation-related gene sets and pre-existing vaccine specific T-cells were associated with vaccination responsiveness.This multi-view dimensionality reduction approach complements the clinical seroconversion and all single modalities. Importantly, this modelling could identify what features predict HBV vaccine response. This methodology could be extended to other vaccination trials to identify key features regulating responsiveness.
GENEvaRX: A Novel AI-Driven Method and Web Tool Can Identify Critical Genes and Effective Drugs for Lichen Planus
Authors: Turki Turki , Taguchi Y-h. 
Published: February 2023

AbstractLichen planus (LP) is an autoimmune disorder diagnosed based on physical symptoms and lab tests. Examples of symptoms include flat bumps, and itchy and purplish skin, while lab tests include a shave biopsy of the lesion. When the pathology report shows consistency with LP and is negative for potential triggers for an allergy test and hepatitis C, a dermatologist typically prescribes corticosteroid in the form of pills or injection into the lesion to treat the symptoms. To understand the molecular mechanism of the disease and thereby overcome issues associated with disease treatment, there is a need to identify potential effective drugs, drug targets, and therapeutic targets associated the LP. Hence, we propose a novel computational framework based on new constrained optimization to support vector machines coupled with enrichment analysis. First, we downloaded three gene expression datasets (GSE63741, GSE193351, GSE52130) pertaining to healthy and LP patients from the gene expression omnibus (GEO) database. We then processed each dataset and entered it into our computational framework to select important genes. Finally, we performed enrichment analysis of selected genes, reporting the following results. Our methods outperformed baseline methods in terms of identifying disease and skin tissue. Moreover, we report 5 drugs (including, dexamethasone, retinoic acid, and quercetin), 45 unique genes (including PSMB8, KRT31, KRT16, KRT19, KRT17, COL3A1, LCE2D, LCE2A), and 23 unique TFs (including NFKB1, STAT1, STAT3) reportedly related to LP pathogenesis, treatments, and therapeutic targets. Our methods are publicly available in the GENEvaRX web server athttps://aibio.shinyapps.io/GENEvaRX/.
A novel human iPSC model of COL4A1/A2 small vessel disease unveils a key pathogenic role of matrix metalloproteinases in extracellular matrix abnormalities
Authors: Al-Thani Maha , Goodwin-Trotman Mary , Bell Steven , Patel Krushangi , Fleming Lauren K , Vilain Catheline , Abramowicz Marc , Allan Stuart M , Wang Tao , Cader Zameel , Horsburgh Karen , Van Agtmael Tom , Sinha Sanjay , Markus Hugh S , Granata Alessandra 
Published: February 2023

Abstract/SummaryCerebral small vessel disease (SVD) affects the small vessels in the brain and is a leading cause of stroke and dementia. Emerging evidence supports a role of the extracellular matrix (ECM), at the interface between blood and brain, in the progression of SVD pathology but this remains poorly characterized.To address ECM role in SVD, we developed a co-culture model of mural and endothelial cells using human induced pluripotent stem cells from patients withCOL4A1/A2SVD-related mutations. This model revealed that these mutations induce apoptosis, migration defects, ECM remodelling and transcriptome changes in mural cells. Importantly, these mural cell defects exert a detrimental effect on endothelial cells tight junctions through paracrine actions.COL4A1/A2models also express high levels of matrix metalloproteinases (MMP) and inhibiting MMP activity partially rescues the ECM abnormalities and mural cell phenotypic changes. These data provide a basis for targeting MMP as a therapeutic opportunity in SVD.HighlightsA novel human iPSC-derived model of genetic SVD due to collagen IV (COL4A1/A2) mutations is describedMural cells expressingCOL4A1/A2mutations have prominent ECM abnormalities as seen in patients and mouse models and contribute to endothelial cells defectsECM and endothelial cells abnormalities can be rescued by MMP inhibition in theCOL4A1/A2model
Statistical mining of triple-negative breast cancer-specific nanobodies among huge libraries from immunized alpacas
Authors: Maeda Ryota , Yamazaki Hiroyuki , Kobayashi Ryoga , Yamamoto Seishiro , Kasai Kazuki , Imura Akihiro 
Published: February 2023

AbstractBreast cancer can be classified into several types according to the expression patterns of human epidermal growth factor receptor 2 (Her2), oestrogen receptor (ER), and progesterone receptor (PgR) proteins. The prognosis of patients with tumors showing low Her2 expression and no ER and PgR expression—categorized as triple-negative breast cancer (TNBC)—is worst among these groups. Due to the lack of specific antibodies for TNBC, curative treatments for TNBC remain limited. Antibodies targeting TNBC have potential as diagnostic and therapeutic tools. Here, we generate a panel of nanobodies targeting TNBC cell lines by immunizing alpacas and subsequently panning the resulting phage libraries with TNBC cell lines. We show that several clones exclusively stain Her2-negative cells in tissues of breast cancer patients, and a few clones stain both Her2-positive and Her2-negative regions in these tissues. These clones can be applied to patient-specific therapies using drug-conjugated antibodies, radiolabelled antibodies, chimaera antigen receptor T cells, or drug delivery components, as well as to TNBC diagnosis.
HilE represses the activity of HilD via a mechanism distinct from that of intestinal long-chain fatty acids
Authors: Joiner Joe D. , Steinchen Wieland , Kronenberger Thales , Bange Gert , Poso Antti , Wagner Samuel , Hartmann Marcus D. 
Published: February 2023

AbstractThe expression of virulence factors essential for the invasion of host cells bySalmonella entericais tightly controlled by a network of transcription regulators. The AraC/XylS transcription factor HilD is the main integration point of environmental signals into this regulatory network, with many factors affecting HilD activity. Long chain fatty acids (LCFAs), which are highly abundant throughout the host intestine directly bind to, and repress HilD, acting as environmental cues to coordinate virulence gene expression. The regulatory protein HilE also negatively regulates HilD activity, through a protein-protein interaction. Both of these regulators inhibit HilD dimerisation, preventing HilD from binding to target DNA. We investigated the structural basis of these mechanisms of HilD repression. LCFAs bind to a conserved pocket in HilD, in a comparable manner to that reported for other AraC/XylS regulators, whereas HilE forms a stable heterodimer with HilD by binding to the HilD dimerisation interface. Our results highlight two distinct mechanisms by which HilD activity is repressed, which could be exploited for the development of new antivirulence leads.
Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation
Authors: Kim Eun Na , Chen Phyllis Zixuan , Bressan Dario , Tripathi Monika , Miremadi Ahmad , di Pietro Massimiliano , Coussens Lisa M , Hannon Gregory J , Fitzgerald Rebecca C , Zhuang Lizhe , Chang Young Hwan 
Published: February 2023

SummaryImaging mass cytometry (IMC) is a powerful multiplexed tissue imaging technology that allows simultaneous detection of more than 30 makers on a single slide. It has been increasingly used for singlecell-based spatial phenotyping in a wide range of samples. However, it only acquires a small, rectangle field of view (FOV) with a low image resolution that hinders downstream analysis. Here, we reported a highly practical dual-modality imaging method that combines high-resolution immunofluorescence (IF) and high-dimensional IMC on the same tissue slide. Our computational pipeline uses the whole slide image (WSI) of IF as a spatial reference and integrates small FOVs IMC into a WSI of IMC. The high-resolution IF images enable accurate single-cell segmentation to extract robust high-dimensional IMC features for downstream analysis. We applied this method in esophageal adenocarcinoma of different stages, identified the single-cell pathology landscape via reconstruction of WSI IMC images, and demonstrated the advantage of the dual-modality imaging strategy.MotivationHighly multiplexed tissue imaging allows visualization of the spatially resolved expression of multiple proteins at the single-cell level. Although imaging mass cytometry (IMC) using metal isotope-conjugated antibodies has a significant advantage of low background signal and absence of autofluorescence or batch effect, it has a low resolution that hampers accurate cell segmentation and results in inaccurate feature extraction. In addition, IMC only acquires mm2-sized rectangle regions, which limits its application and efficiency when studying larger clinical samples with non-rectangle shapes. To maximize the research output of IMC, we developed the dual-modality imaging method based on a highly practical and technical improvement requiring no extra specialized equipment or agents and proposed a comprehensive computational pipeline that combines IF and IMC. The proposed method greatly improves the accuracy of cell segmentation and downstream analysis and is able to obtain whole slide image IMC to capture the comprehensive cellular landscape of large tissue sections.
Insulin B peptide-MHC class II-specific chimeric antigen receptor-Tregs prevent autoimmune diabetes
Authors: Spanier Justin A. , Fung Vivian , Wardell Christine M. , Alkhatib Mohannad H. , Chen Yixin , Swanson Linnea A. , Dwyer Alexander J. , Weno Matthew E. , Silva Nubia , Mitchell Jason S. , Orban Paul C. , Mojibian Majid , Verchere C. Bruce , Fife Brian T. , Levings Megan K. 
Published: February 2023

AbstractAdoptive immunotherapy with Tregs is a promising approach for prevention or treatment of type 1 diabetes. Islet antigen-specific Tregs have more potent therapeutic effects than polyclonal cells, but their low frequency is a barrier for clinical application. To generate Tregs that recognize islet antigens, we engineered a chimeric antigen receptor (CAR) derived from a monoclonal antibody with specificity for the insulin B-chain 10-23 peptide presented in the context of the IAg7MHC class II allele present in NOD mice. Peptide specificity of the resulting InsB-g7 CAR was confirmed by tetramer staining and T cell proliferation in response to recombinant or islet-derived peptide. The InsB-g7 CAR re-directed NOD Treg specificity such that insulin B 10-23-peptide stimulation enhanced suppressive function, measured via reduction of proliferation and IL-2 production by BDC2.5 T cells and CD80 and CD86 expression on dendritic cells. Co-transfer of InsB-g7 CAR Tregs prevented adoptive transfer diabetes by BDC2.5 T cells in immunodeficient NOD mice. In wild type NOD mice, InsB-g7 CAR Tregs stably expressed Foxp3 and prevented spontaneous diabetes. These results show that engineering Treg specificity for islet antigens using a T cell receptor-like CAR is a promising new therapeutic approach for the prevention of autoimmune diabetes.Brief SummaryChimeric antigen receptor Tregs specific for an insulin B-chain peptide presented by MHC class II prevent autoimmune diabetes.
Human A2-CAR T cells reject HLA-A2+ human islets transplanted into mice without inducing graft versus host disease
Authors: Ellis Cara E. , Mojibian Majid , Ida Shogo , Fung Vivian C.W. , Skovsø Søs , McIver Emma , O’Dwyer Shannon , Webber Travis D. , Braam Mitchell J.S. , Saber Nelly , Kieffer Timothy J. , Levings Megan K. 
Published: February 2023

ABSTRACTBackgroundType 1 diabetes (T1D) is an autoimmune disease characterised by T cell mediated destruction of pancreatic beta-cells. Islet transplantation is an effective therapy, but its success is limited by islet quality and availability along with the need for immunosuppression. New approaches include use of stem cell-derived insulin-producing cells and immunomodulatory therapies, but a limitation is the paucity of reproducible animal models in which interactions between human immune cells and insulin-producing cells can be studied without the complication of xenogeneic graft-versus-host disease (xGVHD).MethodsWe expressed an HLA-A2-specific chimeric antigen receptor (A2-CAR) in human CD4+ and CD8+ T cells and tested their ability to reject HLA-A2+ islets transplanted under the kidney capsule or anterior chamber of the eye of immunodeficient mice. T cell engraftment, islet function and xGVHD were assessed longitudinally.ResultsThe speed and consistency of A2-CAR T cells-mediated islet rejection varied depending on the number of A2-CAR T cells and the absence/presence of co-injected peripheral blood mononuclear cells (PBMCs). When <3 million A2-CAR T cells were injected, co-injection of PBMCs accelerated islet rejection but also induced xGVHD. In the absence of PBMCs, injection of 3 million A2-CAR T cells caused synchronous rejection of A2+ human islets within 1 week and without xGVHD for 12 weeks.ConclusionsInjection of A2-CAR T cells can be used to study rejection of human insulin-producing cells without the complication of xGVHD. The rapidity and synchrony of rejection will facilitate in vivo screening of new therapies designed to improve the success of isletreplacement therapies.
Multiple sources of uncertainty confound inference of historical human generation times
Authors: Ragsdale Aaron P. , Thornton Kevin R. 
Published: February 2023

AbstractWanget al. (2023) recently proposed an approach to infer the history of human generation intervals from changes in mutation profiles over time. As the relative proportions of different mutation types depend on the ages of parents, binning variants by the time they arose allows for the inference of average paternal and maternal generation intervals over times. Applying this approach to published allele age estimates, Wanget al. (2023) inferred long-lasting sex differences in average generation times and surprisingly found that ancestral generation times of West African populations remained substantially higher than those of Eurasian populations extending tens of thousands of generations into the past. Here we argue that the results and interpretations in Wanget al. (2023) are primarily driven by noise and biases in input data and a lack of validation using independent approaches for estimating allele ages. With the recent development of methods to reconstruct genome-wide gene genealogies, coalescence times, and allele ages, we caution that downstream analyses may be strongly influenced by uncharacterized biases in their output.
Structural Analysis of Genomic and Proteomic Signatures Reveal Dynamic Expression of Intrinsically Disordered Regions in Breast Cancer and Tissue
Authors: Zatorski Nicole , Sun Yifei , Elmas Abdulkadir , Dallago Christian , Karl Timothy , Stein David , Rost Burkhard , Huang Kuan-Lin , Walsh Martin , Schlessinger Avner 
Published: February 2023

SummaryStructural features of proteins capture underlying information about protein evolution and function, which enhances the analysis of proteomic and transcriptomic data. Here we developStructuralAnalysis ofGene and proteinExpressionSignatures (SAGES), a method that describes expression data using features calculated from sequence-based prediction methods and 3D structural models. We used SAGES, along with machine learning, to characterize tissues from healthy individuals and those with breast cancer. We analyzed gene expression data from 23 breast cancer patients and genetic mutation data from the COSMIC database as well as 17 breast tumor protein expression profiles. We identified prominent expression of intrinsically disordered regions in breast cancer proteins as well as relationships between drug perturbation signatures and breast cancer disease signatures. Our results suggest that SAGES is generally applicable to describe diverse biological phenomena including disease states and drug effects.