bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compensatory Mechanisms in γδ T Cell-Deficient Chickens FollowingSalmonellainfection
Authors: Tetzlaff Felix , Methner Ulrich , von Heyl Theresa , Menge Christian , Schusser Benjamin , Berndt Angela 
Published: February 2025

AbstractAvian γδ T lymphocytes are highly abundant in the intestinal mucosa and play a critical role in immune defense against infectious diseases in chickens. However, their specific contributions to infection control remain poorly understood. To investigate the role of γδ T cells and their possible compensation, we studied wild-type and γδ T cell knockout chickens following infection withSalmonellaEnteritidis. Bacterial loads in the liver, cecal content, and cecal wall were quantified. Immune cell populations in blood, spleen, and cecum were analyzed using flow cytometry. Immune gene transcription in sorted T cell subsets and cecal tissue was measured by RT-qPCR.Strikingly, chickens lacking γδ T cells had significantly higher bacterial loads in the liver and more extensiveSalmonellainvasion in the cecal wall during the early stages of infection compared to wild-type birds. In the blood, infected γδ T cell knockout chickens displayed a significantly increased percentage of CD25+NK-like cells. In both blood and tissue, infected wild-type chickens demonstrated an increased absolute number of CD8αα++γδ T cells. Conversely, γδ T cell knockout chickens exhibited an augmented cell count of a CD8αα++CD4-non-γδ T cell population after infection, which might include αβ T cells. At 7 days post infection (dpi), gene expression analysis revealed elevated transcription of the activation marker IL-2Rα and proinflammatory cytokines (IL-17A, IFN-γ) in CD8αα++CD4-non-γδ T cells from γδ T cell knockout chickens compared to CD8αα++γδ T cells from wild-type birds. By 12 dpi, these differences diminished as transcription levels increased in γδ T cells of wild-type animals.Our findings demonstrate that γδ T cells play a role in early immune protection againstSalmonellaEnteritidis infection in chickens. In later stages of the infection, the γδ T cells and their functions appear to be replaced by other cells.
Splenic MARCO+marginal zone macrophages regulate rapid production of MCP-1 and KC but are dispensable for alloantibody generation in response to stored RBCs in a murine model
Authors: Arneja Abhinav , Salazar Juan E. , Medved Jelena , Ratcliffe Sarah J. , Smolkin Mark E. , Santhanakrishnan Manjula , Stowell Sean R. , Hudson Krystalyn E. , Zimring James C. , Hendrickson Jeanne E. , Luckey Chance John 
Published: February 2025

ABSTRACTBACKGROUNDAlloimmunization to transfused red blood cells (RBCs) remains a significant clinical problem. However, the cells that initiate immune responses to transfused RBCs remain incompletely characterized.Recently published work has identified splenic marginal zone B (MZB) cells as being critically required for the production of anti-RBC alloantibodies in response to RBCs. In infectious models, MZB cell activation has been shown to depend on a unique population of marginal zone macrophages (MZMs). We hypothesized that MZMs would capture stored RBCs and present them to MZBs, and ultimately MZMs would be required for generation of anti-RBC alloantibodies in response to stored RBC transfusion.STUDY DESIGN AND METHODSStored GFP+murine RBCs were utilized to determine the splenic localization and erythrophagocytosis by splenic macrophage populations. To determine the functional impact of MZMs, we compared LXRα-KO mice, which have been reported to lack MZMs, with wild type mice. Both innate and adaptive immune responses to stored HOD allogenic RBC transfusion were measured in LXRα-KO and wild type mice.RESULTSRBC storage leads to a significant increase in the phagocytosis of transfused RBCs by splenic MZMs. LXRα-KO mice demonstrated a lack of MZMs and had significantly decreased rapid phase production of cytokines MCP-1 and KC, but similar levels of IL-6. Surprisingly, anti-RBC alloantibody levels were unaffected by the absence of splenic MZMs.CONCLUSIONSSplenic MZMs are involved in the innate response to transfused stored HOD RBCs, contributing to both MCP-1 and KC cytokine production. However, MZMs are dispensable for anti-RBC alloantibody production.
Swiprosin-1/EFhd2 promotes mitochondrial spare capacity in response to immobilized antigen in B cells via microtubule stabilization
Authors: Weckwerth Leonie , Tripal Philipp , Schmid Benjamin , Thomas Jana , Himmelreich Ann-Kathrin , Pracht Katharina , Urbanczyk Sophia , Allnach Hannah , Gottwald Anna , Palmisano Ralph , Mielenz Dirk 
Published: February 2025

AbstractB cells can recognize soluble and membrane bound antigens, enabling them to initiate and execute versatile immune responses. This study examines Swiprosin-1/EFhd2 (EFhd2) in regulating mitochondrial function and organization in B cells during B cell receptor (BCR) activation and immune synapse formation. Using EFhd2 knockout (KO) and wild-type (WT) murine B cells, we assessed mitochondrial abundance, membrane potential, and respiratory capacity using soluble anti-IgM and anti-CD40/IL-4 stimulation. EFhd2KO B cells exhibit more functional mitochondria and mitochondrial spare capacity selectively in activated but not in resting cells. This phenotype changed absolutely upon BCR synapse formation: While activated WT B cells enhance basal mitochondrial respiration, ATP production and maximal respiration, with large increments of spare capacity, EFhd2KO B cells fail completely to do so. Actin depolymerization and microtubule destabilization impair functional mitochondrial upregulation in WT but not in EFhd2KO B cells, while microtubule stabilization restores full spare capacity in EFhd2KO B cells at the BCR synapse. Live-cell imaging reveals that EFhd2KO B cells fail to organize mitochondria, microtubules, and BCRs symmetrically. Super-resolution 3D imaging shows that WT B cells condense mitochondria at the synapse, whereas EFhd2KO B cells display dispersed, unorganized mitochondria and BCR clusters. EFhd2 re-expression restores mitochondrial polarization in EFhd2KO B cells, confirming its role in coordinating mitochondrial positioning. These findings highlight EFhd2 as a key integrator of cytoskeletal and mitochondrial functions for optimal B cell responses to membrane bound antigens.Graphical Abstract
Refining sequence-to-expression modelling with chromatin accessibility
Authors: Lapohos Orsolya , Fonseca Gregory J. , Emad Amin 
Published: February 2025

AbstractSequence-to-expression models have gained popularity in the past decade, enabling prediction of gene expression from genomic sequence alone. However, these models typically do not take into account chromatin accessibility, a major factor limiting gene regulation. We hypothesized that supplying accessibility as an input feature would allow a sequence-to-expression model to focus on important open regions of the genome. Using single-nucleus multiome RNA- and ATAC-sequencing data, we found that the predictive performance of such an augmented model was significantly greater than that of sequence-only or accessibility-only models with similar architectures. Specifically, its ability to predict the expression of highly variable genes and gene expression in other cell types improved, which we attribute to a reduction in bias originating from lowly variable genes. Moreover, post-hoc analyses revealed that higher attribution scores in the input DNA sequences of the augmented model conformed to accessibility, whereas those in the sequence-only model were scattered. Additionally, we show that fine-tuning a pre-trained sequence-only model with both sequence and accessibility can boost performance even further. We also highlight the importance of sequencing depth in sequence-to-expression prediction. Altogether, the results of this study provide a compelling argument for the inclusion of chromatin accessibility in sequence-to-expression models, as this strategy can be implemented easily and may improve downstream applications.
Neutrophil KLF2 regulates inflammasome-dependent neonatal mortality from endotoxemia
Authors: Mukherjee Devashis , Satyavolu Sriram , Thomas Asha , Cioffi Sarah , Li Yuexin , Chan E. Ricky , Wen Katherine , Huang Alex Y. , Jain Mukesh K. , Dubyak George R. , Nayak Lalitha 
Published: February 2025

ABSTRACTPreterm neonates die at a significantly higher rate from sepsis than full-term neonates, attributable to their dysregulated immune response. In addition to tissue destruction caused directly by bacterial invasion, an overwhelming cytokine response by the immune cells to bacterial antigens also results in collateral damage. Sepsis leads to decreased gene expression of a critical transcription factor, Krüppel-like factor-2 (KLF2), a tonic repressor of myeloid cell activation. Using a murine model of myeloid-Klf2deletion, we show that loss of KLF2 is associated with decreased survival after endotoxemia in a developmentally dependent manner, with increased mortality at postnatal day 4 (P4) compared to P12 pups. This survival is significantly increased by neutrophil depletion. P4 knockout pups have increased pro-inflammatory cytokine levels after endotoxemia compared to P4 controls or P12 pups, with significantly increased levels of IL-1β, a product of the activation of the NLRP3 inflammasome complex. Loss of myeloid-KLF2 at an earlier postnatal age leads to a greater increase in NLRP3 priming and activation and greater IL-1β release by BMNs. Inhibition of NLRP3 inflammasome activation by MCC950 significantly increased survival after endotoxemia in P4 pups. Transcriptomic analysis of bone marrow neutrophils showed that loss of myeloid-KLF2 is associated with gene enrichment of pro-inflammatory pathways in a developmentally dependent manner. These data suggest that targeting KLF2 could be a novel strategy to decrease the pro-inflammatory cytokine storm in neonatal sepsis and improve survival in neonates with sepsis.Summary sentenceKLF2 regulates the developmental response to endotoxin in neonatal mice through the NLRP3 inflammasome signaling pathway.
Beyond the Hype: The Complexity of Automated Cell Type Annotations with GPT-4
Authors: Kazmi Arman , Singh Deepshikha , Jatav Shashank , Luthra Soumya 
Published: February 2025

AbstractRecent research has shown the impressive capability of large language models like GPT-4 in various downstream tasks in single-cell data analysis. Among these tasks, cell type annotation remains particularly challenging, with researchers exploring various methods to improve accuracy and efficiency. While recent studies on GPT-like models have demonstrated annotation performance comparable to manual annotations, a significant gap remains in understanding their limitations and generalizability. In this work, we compare and evaluate the annotation performance of the GPT-4 model against traditional methods on nine randomly selected public single-cell RNA seq datasets from cellxgene, covering diverse tissue types. Our evaluation highlights the complexity of annotating cell types in single-cell data, revealing key differences between automated and manual approaches. We found specific cases where GPT-4 underperforms, demonstrating its limitations in certain contexts. We further introduce an automated approach to incorporate literature search using a RAG approach which enhances and outperforms GPT-4 cell type annotation when compared to traditional methods. We also introduce metrics based on taxonomic distance in the ontology tree to evaluate the granularity of the cell type annotations. To support future research, we also release an open-source Python package1that enables fully automated cell-type annotation of single-cell data using GPT-4 alongside other methods. The pipeline can take paper as an input and do cell type annotations on its own.
ABCG5 ABCG8-independent mechanisms fail to maintain sterol balance in mice fed a high cholesterol diet
Authors: Anspach Garrett B. , Chauhan Isha , Savage Erika L. , Poole Brittney , Noffsinger Victoria P. , Fu Xiaoming , Wang Zeneng , Temel Ryan E. , Gordon Scott R. , Helsley Robert N. , Graf Gregory A. 
Published: February 2025

AbstractThe ABCG5 ABCG8 (G5G8) sterol transporter opposes the accumulation of dietary xenosterols, but is also the primary mediator of biliary cholesterol secretion in the cholesterol elimination pathway. In humans and in mouse models of disrupted biliary cholesterol secretion, fecal neutral sterols remain constant, indicating the presence of a G5G8-independent mechanism for cholesterol excretion. Transintestinal cholesterol elimination (TICE) is thought to compensate for biliary G5G8 insufficiency. We sought to measure the compensatory increase in intestinal cholesterol secretion and provide mechanistic insight for how TICE maintains sterol balance in the absence of G5G8. Differences were not observed in fecal neutral sterols between control, acute, and chronic liver-specific G5G8 deficient mice (G5G8LKO). Cholesterol content did not differ at any point along the intestinal tract between genotypes. We also observed no change in the expression of apical or basolateral sterol transporting enzymes in the proximal small intestine. We then measured biliary and intestinal cholesterol secretion rates using cholesterol free and cholesterol enriched bile acid micelles as acceptors. While biliary cholesterol secretion was reduced, the intrinsic rate of intestinal cholesterol secretion did not differ between genotypes. G5G8LKOand whole-body G5G8-deficient mice were challenged with a cholesterol-containing diet. While control mice upregulate fecal neutral sterol excretion, G5G8LKOand G5G8-/-mice fail to do so and accumulate sterol in the liver and plasma. These studies indicate that while G5G8-independent mechanisms can mediate cholesterol excretion, TICE is not upregulated in response to a loss of hepatic G5G8 and is unable to compensate for hepatic or whole-body G5G8-deficiency in response to dietary cholesterol in mice.
Lymph nodes link sex-biased immune aging to compromised antigen recognition
Authors: Menzel Lutz , Zschummel Maria , O’Melia Meghan J. , Zhou Hengbo , Lei Pin-Ji , Liu Lingshan , Sen Debattama R. , Munn Lance L. , Padera Timothy P. 
Published: February 2025

AbstractA diverse naive CD8 T cell repertoire is essential to provide broad protection against infection and cancer. Aging diminishes naive T cells, reducing potential diversity and leading to lymph node contraction. Here, we revealed that this decline occurs earlier in males, resulting in significant sex differences in immunity during middle age. Earlier in life, naive CD8 T cells in males become virtual memory cells prone to premature senescence. Due to androgen-driven thymic atrophy in males, naïve CD8 T cells are insufficiently replenished. Therapeutic thymus rejuvenation via testosterone ablation restored naive CD8 T cells in lymph nodes of middle-aged male mice, leading to enhanced tumor recognition. These findings show the crucial role of sex and age on lymph node T cell repertoires and suggest potential strategies to restore immune function in males during aging.
Deconvolution of Sample Identity in Single-Cell RNA SequencingviaGenome Imputation
Authors: Ghosh Rohit , Hugh-White Rupert , Nassiri Farshad , Zadeh Gelareh , Boutros Paul C. 
Published: February 2025

AbstractBackgroundDroplet based single-cell RNA sequencing (scRNA-seq) is a powerful tool for measuring RNA abundance profiles at cell-specific resolution. Droplet-based barcoding technology allows sample multiplexing, thereby facilitating high-scale of single cell sequencing. The resulting processing complexity, sample contamination and the underlying chemistries can all contribute to cell mis-labelling and consequent spurious cell-to-sample assignment. Approaches for barcode-free de-multiplexing which leverage natural genetic variation have been developed, but generally require an external source of genotype information.ResultsWe propose a novel method to exploit genome imputation and clustering to assign cells to inferred donor groups in the absence of a priori genetic information. Using tumor-derived single-cell RNA-sequencing (scRNA-seq) data, our workflow successfully assigned individual cells to donor-of-origin with high concordance.ConclusionsThis imputation-clustering approach represents a quality-assessment and quality-control strategy for barcode-free single cell donor-origin deconvolution with the capacity to resolve cases of sample cross-contamination.
Peroxisome proliferator-activated receptor gamma (PPARG)-mediated myocardial salvage in acute myocardial infarction managed with left ventricular unloading and coronary reperfusion
Authors: Visker Joseph R. , Tseliou Eleni , Kyriakopoulos Christos P. , Hamouche Rana , Yin Michael , Ling Jing , Shankar Thirupura S. , Kwan Eugene , Cedeno-Rosaria Luis , Velasco-Silva Jesse N. , Sideris Konstantinos , Kwak Hyoin , Hillas Yanni , Yannias Eleni , Maneta Eleni , Srinivasan Harini , Padilla Laisha , Polishchuck Georgiy , Navankasattusas Sutip , Tandar Anwar , Ducker Gregory S. , Rutter Jared , Hong TingTing , Shaw Robin M. , Lui Charles , Welt Frederick G. , Drakos Stavros G. 
Published: February 2025

ABSTRACTIschemic heart disease and acute myocardial infarction (AMI) is a leading cause of morbidity and mortality. Improvements have been made in coronary interventions to restore blood flow, but ischemia/reperfusion (I/R) injury significantly impacts clinical outcomes. We previously reported that activation of percutaneous mechanical unloading of the left ventricle (LV) with a transvalvular axial-flow device simultaneously with reperfusion improves myocardial salvage. However, the underlying mechanisms, potential adjuvant pharmacological interventions and the timing of the use of LV unloading as a cardioprotective approach in AMI are not well understood. This study investigated a) the mechanisms associated with improved myocardial salvage, b) a pharmacological intervention, and c) the timing of LV unloading. Following 90 minutes of ischemia, adult swine were subjected to reperfusion alone, simultaneous unloading with reperfusion, upfront unloading with delayed reperfusion, upfront reperfusion with delayed unloading, or reperfusion with concurrent use of esmolol and milrinone. Compared to controls, the simultaneous group had a 47% increase in myocardial salvage following AMI. This was associated with increased expression of neutrophil degranulation, macrophage activation, iNOS signaling, wound healing, and PPAR signaling. From these pathways,PPARG(peroxisome proliferator-activated receptor gamma) emerged as a potential cardioprotective gene that was uniquely overexpressed in the simultaneously unloaded and reperfused myocardium. Next, we showedPPARGagonism with rosiglitazone reduces mitochondrial oxygen demand in cardiomyocytes and in vivo, improves myocardial salvage following I/R injury inC57BL6/Jmice. Thiazolidinediones (TZDs), such as rosiglitazone could be investigated as therapies combined with simultaneous LV unloading and coronary interventions to mitigate reperfusion injury.GRAPHICAL ABSTRACT
Reprogrammable 4D Tissue Engineering Hydrogel Scaffold via Reversible Ion Printing
Authors: Ding Aixiang , Tang Fang , Alsberg Eben 
Published: February 2025

AbstractShape changeable hydrogel scaffolds recapitulating morphological dynamism of native tissues have emerged as an elegant tool for future tissue engineering (TE) applications, due to their capability to create morphodynamical tissues with complex architectures. Hydrogel scaffolds capable of preprogrammable, reprogrammable and/or reversible shape transformations would widely expand the scope of possible temporal shape changes. Current morphable hydrogels are mostly based on multimaterial, multilayered structures, which involve complicated and time-consuming fabrication protocols, and are often limited to single unidirectional deformation. This work reports on the development of a transformable hydrogel system using a fast, simple, and robust fabrication approach for manipulating the shapes of soft tissues at defined maturation states. Simply by using an ion-transfer printing (ITP) technology (i.e., transferring Ca2+from an ion reservoir with filter paper and subsequent covering on a preformed alginate-derived hydrogel), a tunable Ca2+crosslinking density gradient across the hydrogel thickness has been incorporated, which enables preprogrammable deformations upon further swelling in cell culture media. Combining with a surface patterning technology, cell-laden constructs (bioconstructs) capable of morphing in multiple directions are deformed into sophisticated configurations. Not only can the deformed bioconstructs recover their original shapes by chemical treatment, but at user-defined times they can also be incorporated with new, different spatially controlled gradient crosslinking via the ITP process, conferring 3D bioconstruct shape reprogrammability. In this manner, unique “3D-to-3D” shape conversions have been realized. Finally, we demonstrated effective shape manipulation in engineered cartilage-like tissue constructs using this strategy. These morphable scaffolds may advance 4D TE by enabling more sophisticated spatiotemporal control over construct shape evolution.
Evolutionary Rescue Promotes Mutators
Authors: Tuffaha Marwa Z , Wahl Lindi M 
Published: February 2025

AbstractThe role of mutation rate in evolutionary rescue has been extensively explored, but little work has investigated how evolutionary rescue can promote mutators, lineages with higher mutation rates. We investigate the likelihood of evolutionary rescue on a mutator background that either emergesde novoor pre-exists in the population prior to a severe environmental change. If such an evolutionary rescue event occurs, the mutator lineage sweeps into the population, and thus the environmental stress has promoted mutators. Our findings indicate that mutation rate evolution can substantially boost rescue probabilities, but stronger mutators are most effective when the wildtype has a low mutation rate, while their advantage diminishes for higher wildtype mutation rates. Interestingly, at intermediate wildtype mutation rates, emerging mutators can be almost equally likely to sweep no matter how slowly or quickly the environment changes. However, at low wildtype mutation rates, mutators are only likely to sweep for very slow environmental changes due to the sequential nature of necessary mutations for such sweeps to occur. Finally, we show that pre-existing mutators can be significantly more likely to rescue the population compared to the wildtype, provided the wildtype’s mutation rate is relatively low. This research opens new avenues for investigating mutator dynamics in response to environmental stress.