bluuebunny/crossref_metadata_2025_split huggingface dataset:
AxSpA joint tissue is characterised by HLA-DR+tissue resident memory (TRM) and killer cell immunoglobulin-like receptor (KIR)+CD8+T cell subsets
Authors: Liu Feng , Shi Hui , Chen Jiewei , Kendrick Ben , Du Dajiang , Bowness Paul , Tong Qiang , Chen Liye 
Published: October 2024

ObjectiveAxial Spondyloarthritis (AxSpA) is a common inflammatory arthritis withHLA-B*27as the major genetic risk. Recent discoveries of AxSpA-specific T cell receptor (TCR) motifs and the self and bacterial peptides that they recognize support a pathogenic role of CD8+T cells. Despite of previous work on synovial fluid, the characteristics of CD8 cells in joint tissue are currently unknown.MethodSynovial tissues from 5 AxSpA patients were used for single cell RNA sequencing (scRNA-seq). Paired TCR sequencing was carried out for 2. The abundance of KIR+CD8+T cells in the blood from 9 AxSpA patients and 10 healthy controls was measured using flow cytometry. The expression of naïve and memory T cell markers (CCR7, CD45RA and CD45RO) were compared between KIR+and KIR-CD8 cells.ResultsWe observed conventional,TRAV1-2+mucosal-associated invariant T (MAIT) cell andMKI67+proliferating cell populations in synovium. Following sub-clustering of conventional CD8+T cells,HLA-DR+tissue resident memory (TRM), circulating,KIR+andFCGR3A+(encoding CD16) cell subsets were observed.HLA-DR+TRM andKIR+cells were clonally expanded and exhibited distinct transcriptional features, enriched for T cell activation pathways and natural killer (NK) cell-mediated cytotoxicity pathway respectively. Lastly, KIR+CD8+T cells were increased in AxSpA blood and enriched for CD45RA+CCR7-TEMRAcells.ConclusionHere we present the very first transcriptomic profiling of CD8+T cells in synovium tissue and highlight potential roles ofHLA-DR+TRM andKIR+cells in AxSpA pathology. This study adds novel insights to the disease mechanisms and offers new therapeutic opportunities.
RNA sequencing depth guidelines for the study of alternative splicing
Authors: Tsoy Olga , Ameling Sabine , Franzenburg Sören , Hoffmann Markus , Liv-Willuth Lina , Lee Hye Kyung , Knabl Ludwig , Furth Priscilla A. , Völker Uwe , Hennighausen Lothar , Baumbach Jan , Kacprowski Tim , List Markus 
Published: October 2024

ABSTRACTA key parameter in the experimental design of RNA-seq projects is the choice of sequencing depth. Considering a limited budget, one needs to find a tradeoff between the number of samples and the sensitivity of the analysis, particularly concerning lowly expressed genes. While previous studies have proposed a lower bound for the comprehensive analysis of differential gene expression, for the analysis of alternative splicing, it has only been proposed for human adipose tissue. However, alternative splicing differs across tissues and conditions. We analyzed publicly available and newly generated deep-sequenced paired-end RNA-seq samples (between 150 and >500 million reads, read length 50-150 bp) from human buffy coat cells and diverse sets of tissues, including gluteal subcutaneous fat, heart, and hypothalamus. Our results show that the sequencing depth typically used in published cohorts is not sufficient to comprehensively capture the landscape of alternative splicing. This motivates the use of deeper sequencing or long-read technologies in future studies. Toward this goal, we offer guidelines for choosing a suitable sequencing depth.GRAPHICAL ABSTRACT
Fibrous Network Nature of Plant Cell Walls Enables Tunable Mechanics for Development
Authors: Chen Si , Burda Isabella , Jani Purvil , Pendrak Bex , Silberstein Meredith N. , Roeder Adrienne H.K. 
Published: October 2024

AbstractDuring plant development, the mechanical properties of the cell walls must be tuned to regulate the growth of the cells. Cell growth involves significant stretching of the cell walls, yet little is known about the mechanical properties of cell walls under such substantial deformation, or how these mechanical properties change to regulate development. Here, we investigated the mechanical behavior of the Arabidopsis leaf epidermal cells being stretched. We found that the mechanical properties arise from the cell wall, which behaves as a fibrous network material. The epidermis exhibited a non-linear stiffening behavior that fell into three regimes. Each regime corresponded to distinct nonlinear behaviors in terms of transverse deformation (i.e., Poisson effect) and unrecoverable deformation (i.e., plasticity). Using a model, we demonstrated that the transition from reorientation and bending-dominated to stretch-dominated deformation modes of cellulose microfibrils cause these nonlinear behaviors. We found the stiffening behavior is more pronounced at later developmental stages. Finally, we show thespiral2-2mutant has anisotropic mechanical properties, likely contributing to the spiraling of leaves. Our findings reveal the fibrous network nature of cell walls gives a high degree of tunability in mechanical properties, which allows cells to adjust these properties to support proper development.
Structural and evolutionary determinants of Argonaute function
Authors: Wallmann Arndt , Van de Pette Mathew 
Published: October 2024

AbstractMembers of the Argonaute protein superfamily adopt functions ranging from host-defense to mediating elaborate and multi-component post-transcriptional and epigenetic systems of control. Despite this diversity of biological roles, the Argonaute structural fold is highly conserved throughout all domains of life. This raises questions about how Argonautes evolved to adapt to this increasing complexity of function, while conserving features that are broadly shared across the phylogenetic tree.Integrating structural, sequence, phylogenetic data and disease-related mutational data, we compiled a comprehensive study of the Argonaute evolutionary trajectory. By comparing Argonaute proteins across a diverse set of lineages and extensive evolutionary timescale, we identified universal and clade-specific sequence signatures and intra-protein contact networks that underlie the Argonaute structural fold, nucleic acid interface and protein-protein binding sites. We analyze how these features are affected by disease-related mutations and are fundamentally altered in the case of the Argonaute-like Med13 protein. With this work we gain better insights into how Argonaute function diversified in eAgos by redrawing the emergence of conserved molecular features that are associated with new biological functions.
Reverse engineering of the pattern recognition receptor FLS2 reveals key design principles of broader recognition spectra against evading flg22 epitopes
Authors: Zhang Songyuan , Liu Songyuan , Lai Hung-Fei , Caflisch Amedeo , Zipfel Cyril 
Published: October 2024

AbstractIn the ongoing plant-pathogen arms race, plants employ pattern recognition receptors (PRRs) to recognize pathogen-associated molecular patterns (PAMPs), while in successful pathogens, PAMPs can evolve to evade detection. Engineering PRRs to recognize evading PAMPs could potentially generate broad-spectrum and durable disease resistance. In this study, we reverse-engineered two natural FLAGELLIN SENSING 2 (FLS2) variants, VrFLS2XL and GmFLS2b, with extended recognition specificities towards evading flg22 variants. We identified minimal gain-of-function residues enabling blind FLS2s to recognize otherwise evading flg22 variants. We uncovered two strategies: (i) enhancing FLS2-flg22 interaction around flg22’s key evasion sites, and (ii) strengthening direct interaction between FLS2 and its co-receptor BAK1 to overcome weak agonistic and antagonistic flg22s, respectively. Additionally, we leveraged polymorphisms that enhance recognition through unknown mechanisms to engineer superior recognition capability. These findings offer basic design principles for PRRs with broader recognition spectra, paving the way for PRR engineering using precise gene-editing to increase disease resistance in crops.
Wax bloom dynamics onSorghum bicolorunder different environmental stresses reveal signaling modules associated with wax production
Authors: Larson Madison , Hampton Marshall , Busta Lucas 
Published: October 2024

Epicuticular wax blooms are associated with improved drought resistance in many species, includingSorghum bicolor. While the role of wax in drought resistance is well known, we report new insights into how light and drought dynamically influence wax production. We investigated how wax quantity and composition are modulated over time and in response to different environmental stressors, as well as the molecular and genetic mechanisms involved in such. Gas chromatography-mass spectrometry and photographic results showed that sorghum leaf sheath wax load and composition were altered in mature plants grown under drought and simulated shade, though this phenomenon appears to vary by sorghum cultivar. We combined anin vitrowax induction protocol with GC-MS and RNA-seq measurements to identify a draft signaling pathway for wax bloom induction in sorghum. We also explored the potential of spectrophotometry to aid in monitoring wax bloom dynamics. Spec-trophotometric analysis showed primary differences in reflectance between bloom-rich and bloomless tissue surfaces in the 230-500nm range of the spectrum, corresponding to the blue color channel of photographic data. Our smartphone-based system detected significant differences in wax production between control and shade treatment groups, demonstrating its potential for candidate screening. Overall, our data suggest that wax extrusion can be rapidly modulated in response to light, occurring within days compared to the months required for the changes observed under greenhouse drought/simulated shade conditions. These results highlight the dynamic nature of wax modulation in response to varying environmental stimuli, especially light and water availability.Significance StatementAgricultural crops require significant freshwater for irrigation, making food security vulnerable to drought. Epicuticular wax blooms are associated with drought tolerance in many plants, includingSorghum bicolor. We investigated how environmental factors like light and drought influence wax production in sorghum. Wax production, composition, and gene expression were compared between sorghum exposed to different environmental stressors, reavealing dynamic modulation of wax production in response to environmental stress as well as signaling genes potentially involved in regulating wax production. These findings broaden our understanding of wax-related drought tolerance mechanisms, providing a foundation for future efforts to enginner crops with improved climate resilience.
Exploring the Efficiency of Deep Graph Neural Networks for RNA Secondary Structure Prediction
Authors: Saon Md. Sharear , Boehm Kevin , Fu Grace , Hou Ian , Yu Jerry , Znosko Brent M. , Hou Jie 
Published: October 2024

ABSTRACTRibonucleic acid (RNA) plays a vital role in various biological processes and forms intricate secondary and tertiary structures associated with its functions. Predicting RNA secondary structures is essential for understanding the functional and regulatory roles of RNA molecules in biological processes. Traditional free-energy-based methods for predicting these structures often fail to capture complex interactions and long-range dependencies within RNA sequences. Recent advancements in machine learning, particularly with graph neural networks (GNNs), have shown promise in enhancing the ability to model the relationships between molecular sequences and their structures. This work specifically explores the efficacy of various GNN architectures in modeling RNA secondary structure. Through benchmarking the GNN methods against traditional energy-based models on standard datasets, our analysis demonstrates that GNN models improves traditional methods, offering a robust framework for accurate RNA structure prediction.
Real-time genomic characterization of pediatric acute leukemia using adaptive sampling
Authors: Geyer Julie , Opoku Kofi B. , Lin John , Ramkissoon Lori , Mullighan Charles , Bhakta Nickhill , Alexander Thomas B. , Wang Jeremy R. 
Published: October 2024

AbstractEffective treatment of pediatric acute leukemia is dependent on accurate genomic classification, typically derived from a combination of multiple time-consuming and costly techniques such as flow cytometry, fluorescencein situhybridization (FISH), karyotype analysis, targeted PCR, and microarrays (Arber et al., 2016; Iacobucci & Mullighan, 2017; Narayanan & Weinberg, 2020). We investigated the feasibility of a comprehensive single-assay classification approach using long-read sequencing, with real-time genome target enrichment, to classify chromosomal abnormalities and structural variants characteristic of acute leukemia. We performed whole genome sequencing on DNA from diagnostic peripheral blood or bone marrow for 57 pediatric acute leukemia cases with diverse genomic subtypes. We demonstrated the characterization of known, clinically relevant karyotype abnormalities and structural variants concordant with standard-of-care clinical testing. Subtype-defining genomic alterations were identified in all cases following a maximum of forty-eight hours of sequencing. In 18 cases, we performed real-time analysis – concurrent with sequencing – and identified the driving alteration in as little as fifteen minutes (for karyotype) or up to six hours (for complex structural variants). Whole genome nanopore sequencing with adaptive sampling has the potential to provide genomic classification of acute leukemia specimens with reduced cost and turnaround time compared to the current standard of care.
New insights into past and future invasion ofDrosophila suzukiiusing novel genomic resources and statistical methods to combine individual and pool sequencing data
Authors: Camus Louise , Rode Nicolas , Serga Svitlana , Loiseau Anne , Chen Xiao , Iampietro Carole , Kenis Marc , Marande William , Mensch Julián , Parinello Hugues , Savić Veselinović Marija , Valière Sophie , Zhang Jinping , Estoup Arnaud , Boitard Simon , Gautier Mathieu 
Published: October 2024

AbstractClimate change and globalization are accelerating biological invasions, highlighting the urgent need to understand adaptation mechanisms in invaded environments to improve management strategies. Genomic data can provide insights into the adaptation of invasive species through Genotype-Environment Association (GEA) studies, identifying genes and biological processes associated with invasion success, and more globally to estimate genetic (mal)adaptation to new environments by calculating Genomic Offset (GO) statistics. In this study, we investigate genetic adaptation in the invasive crop pestDrosophila suzukiiusing novel genomic resources and statistical methods. We rely on a new chromosome-level genome assembly and a dataset representing 36 populations, combining both publicly available and newly generated pooled and individual sequencing data, which are analyzed using an enhanced version of the BayPasssoftware, tailored for such hybrid datasets. We identify a limited number of genomic regions associated with invasion success, supporting the hypothesis of a polygenic architecture of the underlying adaptive traits. Using a GEA incorporating 28 environmental covariates, we further estimate GO between source environments and invaded areas to gain insight into the adaptive challenges faced byD. suzukiiduring past invasions. Reciprocally, we estimate GO between putative source environments and geographic areas that have not yet been invaded to predict regions at risk for potential future invasions. Finally, we used GO calculation to identify high risk regions from which pre-adapted populations could likely originate. Our results suggest that the adaptive challenge forD. suzukiipopulations to invade their current major invasion range was limited. We also identified uninvaded regions (in Africa, South America, and Australia) as being at high risk of future invasion. While further sampling and more extensive individual sequencing could refine these conclusions, our study provides important insights intoD. suzukiiadaptation and offers a generic and operational population genomics framework for studying and predicting biological invasions that can be applied to diverse species.
Knockdown proteomics reveals USP7 as a regulator of cell-cell adhesion in colorectal cancer via AJUBA
Authors: Al-Eidan Ahood , Draper Ben , Wang Siyuan , Coke Brandon , Skipp Paul , Wang Yihua , Ewing Rob M. 
Published: October 2024

ABSTRACTUbiquitin-specific protease 7 (USP7) is implicated in many cancers including colorectal cancer in which it regulates cellular pathways such as Wnt signalling and the P53-MDM2 pathway. With the discovery of small-molecule inhibitors, USP7 has also become a promising target for cancer therapy, and therefore systematically identifying USP7 deubiquitinase interaction partners and substrates has become an important goal. In this study, we selected a colorectal cancer cell model that is highly dependent on USP7 and in which USP7 knockdown significantly inhibited colorectal cancer cell viability, colony formation, and cell-cell adhesion. We then used inducible knockdown of USP7 followed by LC-MS/MS to quantify USP7 dependent proteins. We identified the Ajuba LIM domain protein as an interacting partner of USP7 through co-IP, its substantially reduced protein levels in response to USP7 knockdown, and its sensitivity to the specific USP7 inhibitor FT671. The Ajuba protein has been shown to have oncogenic functions in colorectal and other tumours, including regulation of cell-cell adhesion. We show that both knockdown of USP7 or Ajuba results in a substantial reduction of cell-cell adhesion, with concomitant effects on other proteins associated with adherens junctions. Our findings underlie the role of USP7 in colorectal cancer through its protein interaction networks and show that the Ajuba protein is a component of USP7 protein networks present in colorectal cancer.
EphA2 and Phosphoantigen-Mediated Selective Killing of Medulloblastoma by γδT Cells Preserves Neuronal and Stem Cell Integrity
Authors: Boutin Lola , Liu Mingzhi , Merville Julie Déchanet , Bedoya-Reina Oscar , Wilhelm Margareta T 
Published: October 2024

AbstractMedulloblastoma (MB) is a pediatric brain tumor that develops in the cerebellum, representing one of the most common malignant brain cancers in children. Standard treatment includes surgery, chemotherapy, and radiation, but despite a 5-year survival rate of approximately 70%, these therapies often lead to significant neurological damage in the developing brain. This underscores the urgent need for less toxic, more effective therapeutic alternatives. Recent advancements in cancer immunotherapy, including immune checkpoint inhibitors and CAR-T cell therapy, have revolutionized cancer treatment. One promising avenue is the use of Gamma Delta (γδ)T cells, a unique T cell population with potential advantages such as non-alloreactivity, potent tumor cell lysis, and broad antigen recognition. However, their capacity to recognize and target MB cells remains underexplored. To investigate the therapeutic potential of γδT cells against MB, we analyzed the proportion and status of MB-infiltrated γδT cells within patient datasets. We next investigated the expression of γδT cell ligands on MB cells and identified EphA2 receptor and the phosphoantigen/Butyrophilin complex as key ligands, activating Vγ9Vδ1 and Vγ9Vδ2 T cells, respectively, leading to significant MB cell lysis in both monolayer and spheroid models. Importantly, preliminary safety data showed that γδT cells did not target differentiated neurons or neuroepithelial stem cells derived from induced pluripotent stem cells, underscoring the selectivity and safety of this approach. In conclusion, γδT cells trigger an efficient and specific killing of MB, and would offer a promising novel therapeutic strategy.Key messagesMedulloblastoma patients often experience significant long-term side effects from current standard treatments. Immunotherapy has emerged as a promising alternative to conventional therapeutic approaches. In our study, we demonstrated that γδT cells can efficiently and specifically target medulloblastoma cells without causing harm to healthy neuronal tissue. These findings suggest that γδ T cell therapy may provide therapeutic benefits while potentially reducing treatment-related toxicity in medulloblastoma patients.
Essential tremor with tau pathology features seeds indistinguishable in conformation from Alzheimer’s disease and primary age-related tauopathy
Authors: Saez-Calveras Nil , Vaquer-Alicea Jaime , White Charles L. , Tak Yogesh , Cosentino Stephanie , Faust Phyllis L. , Louis Elan D. , Diamond Marc I. 
Published: October 2024

AbstractNeurodegenerative tauopathies are characterized by the deposition of distinct fibrillar tau assemblies whose rigid core structures correlate with defined neuropathological phenotypes. Essential tremor (ET) is a progressive neurological disease disease that, in some cases, is associated with cognitive impairment and tau accumulation.. Consequently, we explored the tau assembly conformation in ET patients with tau pathology using cytometry-based tau biosensor assays. These assays quantify tau prion seeding activity present in brain homogenates based on conversion of intracellular tau-fluorescent protein fusions from a soluble to an aggregated state. Prions exhibit seeding barriers, whereby a specific assembly structure cannot serve as a template for a native monomer if the amino acids are not compatible. We recently exploited the tau prion species barrier to define tauopathies by systematically substituting alanine (Ala) in the tau monomer and measuring its incorporation into seeded aggregates within biosensor cells. The Ala scan precisely classified the conformation of tau seeds from diverse tauopathies. We next studied 18 ET patient brains with tau pathology. Only one case had concurrent high amyloid-β plaque pathology consistent with Alzheimer’s disease (AD). We detected robust tau seeding activity in 9 (50%) of the patients. This predominantly localized to the temporal pole and temporal cortex. We examined 8 ET cases with the Ala scan and determined that the amino acid requirements for tau monomer incorporation into aggregates seeded from these ET brain homogenates were identical to those of AD and primary age-related tauopathy (PART), and completely distinct from other tauopathies such as corticobasal degeneration, chronic traumatic encephalopathy, and progressive supranuclear palsy. Based on these studies, tau assembly cores in a pathologically confined subset of ET cases with high tau pathology are identical to AD and PART. This could facilitate more precise diagnosis and therapy for ET patients with cognitive impairment.