bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tuning the potency and therapeutic window of ImmTAC molecules by affinity modulation
Authors: Robertson Ian B , Mulvaney Rachel , Dieckmann Nele , Vantellini Alessio , Canestraro Martina , Amicarella Francesca , O’Dwyer Ronan , Cole David K. , Harper Stephen , Dushek Omer , Kirk Peter 
Published: November 2022

AbstractT cell engaging bispecifics have great clinical potential for the treatment of cancer and infectious diseases. The binding affinity and kinetics of a bispecific molecule for both target and T cell CD3 have substantial effects on potency and specificity, but the rules governing these relationships are not fully understood. Using ImmTAC (Immune mobilizing monoclonal TCRs Against Cancer) molecules as a model, we explored the impact of altering affinity for target and CD3 on the potency and specificity of the re-directed T cell response. This class of bispecifics, exemplified by tebentafusp which has recently shown survival benefit in a randomized phase 3 clinical trial1, bind specific target peptides presented by human leukocyte antigen (HLA) on the cell surfaceviaan affinity-enhanced T cell receptor and can redirect T cell activation with an anti-CD3 effector moiety. The data reveal that combining a strong affinity TCR with an intermediate affinity anti-CD3 results in optimal T cell activation, while strong affinity of both targeting and effector domains significantly reduces efficacy. Moreover, by optimising the affinity of both parts of the molecule, it is possible to improve the therapeutic window. These results could be effectively modelled based on kinetic proof-reading with limited signalling. This model explained the experimental observation that strong binding at both ends of the molecules leads to reduced activity, through very stable target-bispecific-effector complexes leading to CD3 entering a non-signalling dark-state. These findings have important implications for the design of anti-CD3 based bispecifics with optimal biophysical parameters for both activity and specificity.Graphical abstract
TCR_Explore: a novel webtool for T cell receptor repertoire analysis
Authors: Mullan Kerry A. , Zhang Justin B. , Jones Claerwen M. , Goh Shawn J. R. , Revote Jerico , Illing Patricia T. , Purcell Anthony W. , Gruta Nicole L. La , Li Chen , Mifsud Nicole A. 
Published: November 2022

AbstractT cells expressing either alpha-beta or gamma-delta T cell receptors (TCR) are critical sentinels of the adaptive immune system, with receptor diversity being essential for protective immunity against a broad array of pathogens and agents. Programs available to profile TCR clonotypic signatures can be limiting for users with no coding expertise. Current analytical pipelines can be inefficient due to manual processing steps, open to data transcription errors and have multiple analytical tools with unique inputs that require coding expertise. Here we present a bespoke webtool designed for users irrespective of coding expertise, coined ‘TCR_Explore’, incorporating automated quality control steps that generates a single output file for creation of flexible and publication ready figures. TCR_Explore will elevate a user’s capacity to undertake in-depth TCR repertoire analysis of both new and pre-existing datasets for identification of T cell clonotypes associated with health and disease. The web application is located athttps://tcr-explore.erc.monash.edufor users to interactively explore TCR repertoire datasets.Key PointsBespoke program for non-specialists in computerised methodologies for deep exploration of TCR repertoire analysisAutomated QC and analysis pipelines for Sanger based TCR sequencing coupled with immunophenotyping, with the capacity for integration of other sequencing platform outputsAutomated summary processes to aid data visualisation and generation of publication-ready graphical displays
A cellular and spatial map of salivary glands at single cell resolution reveals the functional basis of tertiary lymphoid structure formation in Sjogren’s syndrome
Authors: Nayar Saba , Turner Jason D. , Asam Saba , Fennell Eanna , Pugh Matthew , Colfrancesco Serena , Berardicurti Onorina , Smith Charlotte G. , Flint Joe , Teodosio Ana , Iannizzotto Valentina , Gardner David H. , van Roon Joel , Korsunsky Ilya ,   Roche Fibroblast Network Consortium, Bowman Simon J. , Ng Wan-Fai , Croft Adam P , Filer Andrew , Fisher Benjamin A. , Buckley Christopher D. , Barone Francesca 
Published: November 2022

AbstractThe key role of tertiary lymphoid structures in autoimmune and non-autoimmune conditions has been recently appreciated. While many of the molecular mechanisms involved in tertiary lymphoid structure (TLS) formation have been identified, their cellular sources and their temporal and spatial relationship to each other during the development of TLS remain unknown. Here we have constructed a cellular and functional map of key components involved in the formation of TLS in the minor salivary glands (SG) in humans. We have confirmed the presence of an immunofibroblast cell state and identified an undescribed immunopericyte cell state with potential immunological functions within TLS. The identification of TLS cellular and functional properties and their relevant modulators provided by this analysis provides key therapeutic cues for TLS associated conditions in autoimmunity and cancer.
Acetylation of fission yeast tropomyosin does not promote differential association with cognate formins
Authors: Tang Qing , Pollard Luther W. , Homa Kaitlin E. , Kovar David R. , Trybus Kathleen M. 
Published: November 2022

AbstractIt was proposed from cellular studies thatS. pombetropomyosin Cdc8 (Tpm) segregates into two populations due to the presence or absence of an amino-terminal acetylation that specifies which formin-mediated F-actin networks it binds, but with no supporting biochemistry. To address this mechanismin vitro, we developed methods forS. pombeactin expression in Sf9 cells. We then employed 3-color TIRF microscopy using all recombinantS. pombeproteins to probein vitromulticomponent mechanisms involving actin, acetylated and unacetylated Tpm, formins, and myosins. Acetyl-Tpm exhibits tight binding to actin in contrast to weaker binding by unacetylated Tpm. In disagreement with the differential recruitment model, Tpm showed no preferential binding to filaments assembled by the FH1-FH2-domains of twoS. pombeformins, nor did Tpm binding have any bias towards the growing formin-bound actin filament barbed end. Although ourin vitrofindings do not support a direct formin-tropomyosin interaction, it is possible that formins bias differential tropomyosin isoform recruitment through undiscovered mechanisms. Importantly, despite a 12% sequence divergence between skeletal andS. pombeactin,S. pombemyosins Myo2 and Myo51 exhibited similar motile behavior with these two actins, validating key prior findings with these myosins that used skeletal actin.
ASCARIS: Positional Feature Annotation and Protein Structure-Based Representation of Single Amino Acid Variations
Authors: Cankara Fatma , Doğan Tunca 
Published: November 2022

AbstractMotivationGenomic variations may cause deleterious effects on protein functionality and perturb biological processes. Elucidating the effects of variations is critical for developing novel treatment strategies for diseases of genetic origin. Computational approaches have been aiding the work in this field by modeling and analyzing the mutational landscape. However, new approaches are required, especially for accurate and comprehensive representation and data-centric analysis of sequence variations.ResultsIn this study, we propose ASCARIS (Annotation and StruCture-bAsed RepresentatIon of Single amino acid variations - SAVs), a method for the featurization (i.e., quantitative representation) of SAVs, which could be used for a variety of purposes, such as predicting their functional effects or building multi-omics-based integrative models. In ASCARIS representations, we incorporated the correspondence between the location of the SAV on the sequence and 30 different types of positional feature annotations (e.g., active/lipidation/glycosylation sites; calcium/metal/DNA binding, inter/transmembrane regions, etc.) from UniProt, along with structural features such as protein domains, the location of variation (e.g., core/interface/surface), and the change in physico-chemical properties using models from PDB and AlphaFold-DB. We also mapped the mutated and annotated residues to the 3-D plane and calculated the spatial distances between them in order to account for the functional changes caused by variations in positions close to the functionally essential ones. Finally, we constructed a 74-dimensional feature set to represent each SAV in a dataset composed of ∼100,000 data points.We statistically analyzed the relationship between each of these features and the consequences of variations, and found that each of them carries information in this regard. To investigate potential applications of ASCARIS, we trained variant effect predictor models that utilize our SAV representations as input. We carried out both an ablation study and a comparison against the state-of-the-art methods over well-known benchmark datasets. We observed that our method displays a competing performance against widely-used predictors. Also, our predictions were complementary to these methods which is probably due to fact that ASCARIS has a rather unique focus in modeling variations. ASCARIS can be used either alone or in combination with other approaches, to universally represent SAVs from a functional perspective.Availability and implementationThe source code, datasets, results, and user instructions of ASCARIS are available athttps://github.com/HUBioDataLab/ASCARIS.
BCL6 regulates the endothelial pro-immunogenic phenotype relevant to organ transplant rejection
Authors: Acevedo Adriana Franco , Valenzuela Nicole M 
Published: November 2022

AbstractBackgroundIFNγ induces an endothelial cell pro-immunogenic phenotype through the JAK/STAT1 pathway, which can influence alloreactive leukocytes in transplant rejection. Numerous endogenous suppressors of JAK and STAT activation have been described, but regulation of STAT1 at the level of transcription is not well-understood. In immune cells, the DNA binding protein BCL6 controls transcription of lineage and inflammatory genes, including STAT-dependent responses. The goal of this study was to determine if BCL6 also modulates the IFNγ-induced immunogenic phenotype in endothelium.MethodsBCL6 binding to target genes and similarity to STAT1 motifs was analyzedin silicousing public datasets.In vitro, primary human aortic endothelial cells were tested for expression of IFNγ-inducible costimulatory molecules, HLA and cytokines, under BCL6 overexpression, depletion and pharmacological targeting. Gene expression was measured by RNA-Seq and protein expression was confirmed by flow cytometry, Luminex and ELISA. Paired biopsies from stable and rejecting human cardiac allografts were compared for expression of BCL6, PD ligands, CXCL chemokines and HLA-DR in the vasculature.ResultsBCL6 expression is increased within human cardiac transplants during rejection, which is positively correlated with expression of interferon response gene HLA-DR in donor blood vessels. Further, BCL6 is IFNγ-inducible via JAK1/2 in endothelium. Next, the consensus DNA binding motif of BCL6 is highly similar to that of STAT1, and numerous interferon response genes harbor BCL6 DNA binding motifs. Depletion of BCL6 in endothelium results in augmentation, while overexpression causes suppression, of MHC class II, chemokine, and PD ligand expression. Unexpectedly, pharmacological targeting of the corepressor domain BTB domain of BCL6 also repressed many interferon response genes, particularly HLA class II, CXCR3 chemokines and PD-L2. On the other hand, BCL6 targeting did not impact inducible expression of any HLA class I genes, PD-L1 or CD40; and the effect is correlated with the presence of BCL6 binding motifs in or near affected genes.ConclusionOur results show for the first time that the transcriptional repressor BCL6 selectively controls the endothelial response to IFNγ. A better understanding of the endogenous mechanisms that regulate donor endothelial activation has the potential to discover new avenues to dampen transplant rejection, with broader relevance to other vascular inflammatory diseases.
RNA m6A and 5hmC regulate monocyte and macrophage gene expression programs
Authors: Pinello Natalia , Song Renhua , Lee Quintin , Calonne Emilie , Duan Kun-Long , Wong Emilie , Tieng Jessica , Mehravar Majid , Rong Bowen , Lan Fei , Roediger Ben , Ma Cheng-Jie , Yuan Bi-Feng , Rasko John E J , Larance Mark , Ye Dan , Fuks François , Wong Justin J. -L. 
Published: November 2022

AbstractBackgroundRNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications regulate the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear. To date, most studies have focused on m6A, while other RNA modifications, including 5hmC, remain poorly characterised. The interplay between different RNA modifications that may occur in specific cellular contexts remains similarly unexplored.ResultsWe profiled m6A and 5hmC epitranscriptomes, transcriptomes, translatomes and proteomes of monocytes and macrophages at rest and pro- and anti-inflammatory states. We observed that decreased expression of m6A and 5hmC writers, METTL3 and TET-enzymes respectively, facilitated monocyte-to-macrophage differentiation. Despite a global trend of m6A and 5hmC loss during macrophage differentiation, enrichment of m6A and/or 5hmC on specific categories of transcripts essential for macrophage differentiation positively correlated with their expression and translation. m6A and 5hmC mark and are associated with the expression of transcripts with critical functions in pro- and anti-inflammatory macrophages. Notably, we also discovered the coexistence of m6A and 5hmC marking alternatively-spliced isoforms and/or opposing ends of the untranslated regions (UTR) of transcripts with key roles in macrophage biology. In specific examples, RNA 5hmC controls the decay of transcripts independently of m6A.ConclusionsThis study: i) uncovers m6A, 5hmC and their writer enzymes as regulators of monocyte and macrophage gene expression programs and ii) provides a comprehensive dataset to interrogate the role of RNA modifications in a plastic system. Altogether, this work sheds light on the role of RNA modifications as central regulators of effector cells in innate immunity.
GSK-3484862 targets DNMT1 for degradation in cells
Authors: Chen Qin , Zeng Yang , Hwang Jee Won , Liu Bigang , Dai Nan , Corrêa Ivan R. , Estecio Marcos R. , Zhang Xing , Santos Margarida A. , Chen Taiping , Cheng Xiaodong 
Published: November 2022

ABSTRACTMaintenance of genomic methylation patterns at DNA replication forks by DNMT1 is the key to faithful mitotic inheritance. DNMT1 is often overexpressed in cancer cells and the DNA hypomethylating agents azacytidine and decitabine are currently used in the treatment of hematologic malignancies. However, the toxicity of these cytidine analogs and their ineffectiveness in treating solid tumors have limited wider clinical use. GSK-3484862 is a newly-developed, dicyanopyridine containing, non-nucleoside DNMT1-selective inhibitor with low cellular toxicity. Here, we show that GSK-3484862 targets DNMT1 for protein degradation in both cancer cell lines and murine embryonic stem cells (mESCs). DNMT1 depletion was rapid, taking effect within hours following GSK-3484862 treatment, leading to global hypomethylation. Inhibitor-induced DNMT1 degradation was proteasome-dependent, with no discernible loss ofDNMT1mRNA. In mESCs, GSK-3484862-induced Dnmt1 degradation requires Uhrf1, an accessory factor of Dnmt1 with E3 ubiquitin ligase activity. We also show that Dnmt1 depletion and DNA hypomethylation induced by the compound are reversible after its removal. Together, these results indicate that this DNMT1-selective degrader/inhibitor will be a valuable tool for dissecting both coordinated events linking DNA methylation to gene expression and identifying downstream effectors that ultimately regulate cellular response to altered DNA methylation patterns in a tissue/cell-specific manner.HighlightsGSK-3484862 targets DNMT1 for protein degradation in a wide-range of cancer cell lines, without a decrease inDNMT1mRNA levelsDNMT1 depletion leads to a >50% loss of global DNA methylation in cells within 2-days of treatment with GSK-3484862GSK-3484862-induced DNMT1 degradation is proteasome-dependentIn mESCs, Uhrf1 is required for GSK-3484862 to induce Dnmt1 degradation
Investigating the Zoonotic Origin of the Marburg Virus Outbreak in Guinea in 2021
Authors: Makenov Marat , Boumbaly Sanaba , Tolno Faya Raphael , Sacko Nouminy , N’Fatoma Leno Tamba , Mansare Oumar , Kolie Bonaventure , Stukolova Olga , Morozkin Evgeny , Kholodilov Ivan , Zhurenkova Olga , Fyodorova Marina , Akimkin Vasily , Popova Anna , Conde Namoudou , Boiro Mamadou Yero , Karan Lyudmila 
Published: November 2022

AbstractIn 2021, a patient died from Marburg virus (MARV) disease in Guinea, which was the first confirmed case in West Africa. The source of the outbreak has not been identified. It was revealed only that the patient had not traveled anywhere before the illness. Prior to this outbreak, MARV had been found in bats in the neighboring Sierra Leone. In Guinea, this virus has never been found before. Therefore, the question of the source of infection arose: was it an autochthonous case with spillover from a local population of bats or an imported case with spillover from fruit bats foraging/migrating from Sierra Leone?In this paper, we aimed to conduct a study ofRousettus aegyptiacusin Guinea and determine the source of the most likely infection of a patient who died from Marburg virus disease in 2021 in Guinea.We caught bats at 32 sites in Guéckédou prefecture, including seven caves and 25 locations on the flight path. A total of 501 fruit bats (Pteropodidae) were captured, including 66R. aegyptiacus. The subsequent screening showed three PCR-positive MARV bats. We have found and described two caves in Guéckédou prefecture where MARV-positiveR. aegyptiacusroost. Sequencing has shown that at least two different MARV genetic variants circulate inR. aegyptiacusin Guinea: an Angola-like strain and MARV strains of major marburgvirus lineages.
Liver type 1 innate lymphoid cells lacking IL-7 receptor are a native killer cell subset fostered by parenchymal niches
Authors: Asahi Takuma , Abe Shinya , Cui Guangwei , Shimba Akihiro , Nabekura Tsukasa , Miyachi Hitoshi , Kitano Satsuki , Ohira Keizo , Dijkstra Johannes M. , Miyazaki Masaki , Shibuya Akira , Ohno Hiroshi , Ikuta Koichi 
Published: November 2022

AbstractGroup 1 innate lymphoid cells (G1-ILCs), including circulating natural killer (NK) cells and tissue-resident type 1 ILCs (ILC1s), are innate immune sentinels critical for responses against infection and cancer. In contrast to relatively uniform NK cells through the body, diverse ILC1 subsets have been characterized across and within tissues in mice, but their developmental and functional heterogeneity remain unsolved. Here, using multimodalin vivoapproaches including fate-mapping and targeting of the interleukin 15 (IL-15)-producing microenvironment, we demonstrate that liver parenchymal niches support the development of a cytotoxic ILC1 subset lacking IL-7 receptor (7R−ILC1s). During ontogeny, fetal liver (FL) G1-ILCs arise perivascularly and then differentiate into 7R−ILC1s within sinusoids. Hepatocyte-derived IL-15 supports parenchymal development of FL G1-ILCs to maintain adult pool of 7R−ILC1s. IL-7R+(7R+) ILC1s in the liver, candidate precursors for 7R−ILC1s, are not essential for 7R−ILC1 development in physiological conditions. Functionally, 7R−ILC1s exhibit killing activity at steady state through granzyme B expression, which is underpinned by constitutive mTOR activity, unlike NK cells with exogenous stimulation-dependent cytotoxicity. Our study reveals the unique ontogeny and functions of liver-specific ILC1s, providing a detailed interpretation of ILC1 heterogeneity.
Assessment of infant outgrowth of cow’s milk allergy in relation to the faecal microbiome and metaproteome
Authors: Hendrickx Diana M. , An Ran , Boeren Sjef , Mutte Sumanth K ,   PRESTO study team, Lambert Jolanda M , Belzer Clara 
Published: November 2022

Previous studies provide evidence for an association between modifications of the gut microbiota in early life and the development of food allergies. We studied the faecal microbiota composition (16S rRNA gene amplicon sequencing) and faecal microbiome functionality (metaproteomics) in a cohort of 40 infants diagnosed with cow’s milk allergy (CMA) when entering the study. Some of the infants showed outgrowth of CMA after 12 months, while others did not. Faecal microbiota composition of infants was analysed directly after CMA diagnosis (baseline) as well as 6 and 12 months after entering the study. The aim was to gain insight on gut microbiome parameters in relation to outgrowth of CMA.The results of this study show that microbiome differences related to outgrowth of CMA can be mainly identified at the taxonomic level of the 16S rRNA gene, and to a lesser extent at the protein-based microbial taxonomy and functional protein level. At the 16S rRNA gene level outgrowth of CMA is characterized by lower relative abundance ofLachnospiraceaeat baseline and lowerBacteroidaceaeat visit 12 months.
Automated liquid-handling operations for robust, resilient, and efficient bio-based laboratory practices
Authors: Torres-Acosta Mario A. , Lye Gary J. , Dikicioglu Duygu 
Published: November 2022

AbstractIncrease in the adoption of liquid handling devices (LHD) can facilitate experimental activities. Initially adopted by businesses and industry-based laboratories, the practice has also moved to academic environments, where a wide range of non-standard/non-typical experiments can be performed. Current protocols or laboratory analyses require researchers to transfer liquids for the purpose of dilution, mixing, or inoculation, among other operations. LHD can render laboratories more efficient by performing more experiments per unit of time, by making operations robust and resilient against external factors and unforeseen events such as the COVID-19 pandemic, and by remote operation. The present work reviews literature that reported the adoption and utilisation of LHD available in the market and presents examples of their practical use. Applications demonstrate the critical role of automation in research development and its ability to reduce human intervention in the experimental workflow. Ultimately, this work will provide guidance to academic researchers to determine which LHD can fulfil their needs and how to exploit their use in both conventional and non-conventional applications. Furthermore, the breadth of applications and the scarcity of academic institutions involved in research and development that utilise these devices highlights an important area of opportunity for shift in technology to maximize research outcomes.