bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes
Authors: Ewald Jessica D. , Titterton Katherine L. , Bäuerle Alex , Beatson Alex , Boiko Daniil A. , Cabrera Ángel A. , Cheah Jaime , Cimini Beth A. , Gorissen Bram , Jones Thouis , Karczewski Konrad J. , Rouquie David , Seal Srijit , Weisbart Erin , White Brandon , Carpenter Anne E. , Singh Shantanu 
Published: January 2025

AbstractHigh-throughput, human-relevant approaches for predicting chemical toxicity are urgently needed for better decision-making in human health. Here, we apply image-based profiling (the Cell Painting assay) and two cytotoxicity assays (metabolic and membrane damage readouts) to primary human hepatocytes after exposure to eight concentrations of 1085 compounds that include pharmaceuticals, pesticides, and industrial chemicals with known liver toxicity-related outcomes. Three computational methods (CellProfiler, a Cell Painting-specific convolutional neural network, and a pretrained vision transformer) were compared to extract morphology features from single cells or entire images. We used these morphology features to predict activity in the measured cytotoxicity assays, as well as in 412 curated ToxCast assays that span cytotoxicity, cell-based, and cell-free categories. We found that the morphological profiles detect compound bioactivity at lower concentrations than standard cytotoxicity assays. In supervised analyses, they predict cytotoxicity and targeted cell-based assay readouts, but not cell-free assay readouts. We also found that the various feature extraction methods performed relatively similarly and that filtering out non-bioactive or cytotoxic concentrations did not boost supervised assay prediction performance for any assay endpoint category, although it did have a large influence on unsupervised cluster analysis. We envision that image-based profiling could serve as a key component of modern safety assessment.
Evolution of chronic lymphocytic leukemia after allogeneic stem cell transplant
Authors: Garber Haven R. , Wang Danwei , Kerros Celine , Beird Hannah C. , Mao Xizeng , Howard Nina G. , Zhang Jianhua , Roszik Jason , Miller John P. , Leonard Paul , Cao Yu , Zhao Li , Song Xingzhi , Seth Sahil , Lin Pei , Sun Huandong , St John Lisa S. , Lu Sijie , Wierda William , Khouri Issa F. , Clise-Dwyer Karen , Im Jin S. , Alatrash Gheath , Futreal P. Andrew , Liang Shoudan , Koppikar Priya , Gu Shengqing (Stan) , Molldrem Jeffrey J. 
Published: January 2025

ABSTRACTAllogeneic stem cell transplant (alloSCT) for patients with relapsed/refractory chronic lymphocytic leukemia (CLL) can result in cure in some patients. Analogous to chemotherapy and targeted therapy, we hypothesized that allogeneic cellular immunotherapies, including alloSCT and donor lymphocyte infusion (DLI), would impact malignant evolution through the application of selective immunologic pressure with reciprocal changes in the T cell compartment. We tested a cohort of 24 patients treated with HLA-matched alloSCT +/− DLI, two mediators of the graft versus leukemia (GVL) effect. Comparison of pre-alloSCT samples revealed that a key difference between responders (n=13) and non-responders (n=11) is the cellularity of leukemic cells. We further mapped mutational trajectories of tumor cells by whole exome sequencing (WES) of sort-purified CLL in 11 post-transplant relapsed patients and found evidence of subclonal leukemic evolution in 8/11 patients after nonmyeloablative human leukocyte antigen (HLA)-matched alloSCT. Different patterns of CLL evolution were observed, and these changes included putative CLL drivers in every case. To investigate the presence of immune-related variants in patients, we collected 19 T cell co-culture CRISPR datasets and identified the top positive and negative regulators of cancer cell’s response to T-cell-dependent killing. We found that most mutations linked to T-cell killing emerged after allo-SCT treatment, suggesting that selective pressures from the GVL effect may drive the evolution of these mutations. Together, these data identify cellular homogeneity as a key biomarker for susceptibility to GVL-driven immunity in CLL and illustrate how the leukemic cells further evolve to evade immunosurveillance.SIGNIFICANCEThe impact of allogeneic stem cell transplant (alloSCT) on subclonal leukemia evolution remains poorly understood. By performing whole exome sequencing (WES) on pre- and post-alloSCT patient samples, we reveal different patterns of CLL evolution and potential immune-related driver genes influencing CLL relapse and refractory disease post-alloSCT.
JNK regulates GABAAR expression at the cell surface via the receptor clustering protein GIT1 (ArfGAP1)
Authors: Varidaki Artemis , Deshpande Prasannakumar , Nagaeva Elina , Sino Valentina , Schäfer Annika , Sourander Christel , Lagerholm Christoffer , James Peter , Korpi Esa R. , Coffey Eleanor 
Published: January 2025

ABSTRACTGABA type A receptors (GABAARs) receive inhibitory neurotransmitter input and control excitatory/inhibitory balance in the nervous system. Loss of GABAergic function leads to maladaptive changes in circuit dynamics associated with neuropsychiatric disorders, yet the adaptive mechanisms used by cells to regulate GABAAR availability are poorly understood. Previously, we identified that the stress-sensing kinase JNK1 promotes anxiety-like behaviours in mice. Here, we show that genetic deletion or inhibition of JNK1 increases GABAAR β3 subunit surface expression at extrasynaptic sites and at excitatory synapses. We also identify that JNK1 phosphorylates the signalling scaffold GIT1 on S371. Accordingly, GIT1 enriches in dendritic spines inJnk1-/-mice or JNK inhibitor-treated neurons, and GIT1-S371D is excluded. Furthermore, GIT1 is required for JNK-dependent regulation of GABAAR β3 surface expression. Consistent with these findings, the amplitude of spontaneous inhibitory post-synaptic potentials and tonic inhibitory currents are increased in neurons fromJnk1-/-mice. These results suggest that JNK1 activity represses GABAAR complex stability and function.Significance statementIn this study we identify that the stress-sensing kinase JNK1 regulates the amount of GABAARs that are at the plasma membrane both at synapses and at extrasynaptic sites. When JNK activity is blocked, there is more GABAAR detected at the cell surface and GABAAR current is increased. The mechanism involves the receptor clustering protein GIT1 (ArfGAP1), which when dephosphorylated on S371 is enriched at dendritic spines and its binding to a receptor complex including β3-GABAAR, paxillin and 14-3-3ζ also increases. These results are significant because they provide a mechanism whereby cells can rapidly regulate GABAAR availability in response to stress.
Root Cap-Specific Transcriptomics Identify the NAC Transcription Factor SOMBRERO as a Versatile Regulator of Auxin Gradients
Authors: Wang Pengfei , Liu Zhongyuan , Zhou Yuling , He Junxian , Kang Byung-Ho 
Published: January 2025

SUMMARYAuxin gradients in the root cap play a crucial role in the root cap development and root tropism. In the central root cap, meristematic cells in the columella initial differentiate into gravity-sensing columella cell, and mature into border-like cells that eventually separate from the root cap. Golgi stacks exhibit distinct ultrastructural features in each cell type across the central root cap, serving as effective cell markers. This cell type-specific Golgi remodeling was inhibited insmb-3mutant root cap. When we carried out transcriptomic analyses of isolated root cap from Col-0 andsmb-3, transcript levels of numerous auxin-related genes, including those involved in auxin synthesis, transport, and signaling, were significantly altered insmb-3mutant root caps. The auxin gradient was suppressed within the central root cap ofsmb-3mutant lines and they displayed decreased sensitivity to N-1-naphthylphthalamic acid (NPA) in comparison to Col-0. Furthermore, we demonstrated that the SMB binds to the promoter regions of auxin-related genes displaying large changes insmb-3root cap cells. Our findings suggest that SMB functions as a versatile transcription factor that regulates the expression of genes critical for local auxin distribution and responses in the root cap, thereby coordinating root cap cell differentiation and controlling root growth directions in response to external stimuli.
Chemistry-based vectors map the chemical space of natural biomes from untargeted mass spectrometry data
Authors: Peets Pilleriin , Litos Aristeidis , Dührkop Kai , Garza Daniel R. , van der Hooft Justin J.J. , Böcker Sebastian , Dutilh Bas E. 
Published: January 2025

AbstractUntargeted metabolomics can comprehensively map the chemical space of a biome, but is limited by low annotation rates (<10%). We used chemistry-based vectors, consisting of molecular fingerprints or chemical compound classes, predicted from mass spectrometry data, to characterize compounds and samples. These chemical characteristics vectors (CCVs) estimate the fraction of compounds with specific chemical properties in a sample. Unlike the aligned MS1 data with intensity information, CCVs incorporate actual chemical properties of compounds, offering deeper insights into sample comparisons. Thus, we identified key compound classes differentiating biomes, such as ethers which are enriched in environmental biomes, while steroids enriched in animal host-related biomes. In biomes with greater variability, CCVs revealed key clustering compound classes, such as organonitrogen compounds in animal distal gut and lipids in animal secretions. CCVs thus enhance the interpretation of untargeted metabolomic data, providing a quantifiable and generalizable understanding of the chemical space of natural biomes.
In Silico Analysis of Non-Coding RNA Regulation in Human Gene Expression: A Systematic Computational Approach to Understanding Regulatory Networks
Authors: Akbar Arshiya 
Published: January 2025

AbstractThe regulatory networks of miRNAs, lncRNAs, and their target genes play a crucial role in controlling various cellular processes, including cell growth, apoptosis, and immune responses. In this study, we performed an in silico analysis to explore the interactions between miRNAs, lncRNAs, and their target genes in the context of disease mechanisms. We utilized multiple computational approaches, including miRNA-target interaction prediction, lncRNA-target network analysis, differential expression analysis using RNA-seq data, and validation of interactions using miRNA target prediction tools. Our results highlight key genes involved in apoptosis, cell cycle regulation, and tumorigenesis, providing valuable insights into the molecular mechanisms underlying disease progression.Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), have emerged as pivotal regulators of gene expression in human cells. Despite substantial research into their roles, there remains a critical gap in understanding how these molecules interact within complex regulatory networks. In this study, we employed a comprehensive bioinformatics approach to systematically identify and analyze ncRNA-mediated gene regulation in human cells. We utilized publicly available datasets from the ENCODE and GEO repositories, combined with computational tools such as miRBase, LNCipedia, TargetScan, and Cytoscape, to predict ncRNA-gene interactions and construct regulatory networks. Our analysis reveals several novel ncRNA regulators and their associated gene targets, which were further explored through pathway enrichment analysis. This study provides new insights into the regulatory networks of ncRNAs in human gene expression, offering a foundation for future functional studies and potential therapeutic applications.
Detection of low pre-existing humoral immunity against influenza virus H5N1 clade 2.3.4.4b in unexposed individuals
Authors: Daniel Katharina , Ullrich Leon , Ruchnewitz Denis , Meijers Matthijs , Halwe Nico Joel , Wild Ursula , Eberhardt Jan , Stumpf Ricarda , Schlotz Maike , Wunsch Marie , Lessa Luana Girao , Dietrich Christopher , Pinger Andreas , Schumacher Anna-Lena , Germer Maximilian , Rohde Malena , Kukat Christian , Gieselmann Lutz , Gruell Henning , Hoffmann Donata , Beer Martin , Erren Thomas , Lässig Michael , Kreer Christoph , Klein Florian 
Published: January 2025

AbstractThe repeated spill-over of Influenza A virus H5N1 clade 2.3.4.4b from cattle to humans highlights the risk of a human H5N1 pandemic. Given the impact of pre-existing immunity on the course and severity of viral infections, we assessed in detail the humoral immunity against the H5N1 A/Texas/37/2024 isolate in H5N1-naïve individuals. To this end, we performed complementary binding and neutralization assays on 66 subjects and ranked activities among a panel of 76 influenza A virus isolates. We detected low but distinct cross-neutralizing titers against A/Texas/37/2024 with a 3.9 to 15.6-fold reduction compared to selected H1N1 or H3N2 strains. Moreover, by cloning and evaluating 136 monoclonal antibodies from single memory B cells, we identified potent A/Texas/37/2024-neutralizing monoclonal antibodies in five out of six investigated individuals. These antibodies predominantly utilize VH1-69 gene segments, cross-neutralize H1, and compete with antibodies targeting the HA stem. Our findings demonstrate partial pre-existing humoral immunity to A/Texas/37/2024 in H5N1-naïve individuals.
CD226 identifies effector CD8+T cells during tuberculosis and costimulates recognition ofMycobacterium tuberculosis-infected macrophages
Authors: Shinkawa Tomoyo , Chang Evelyn , Rakib Tasfia , Cavallo Kelly , Lai Rocky , Behar Samuel M. 
Published: January 2025

AbstractCD8+T cells defend againstMycobacterium tuberculosis(Mtb) infection but variably recognize Mtb-infected macrophages. To define how the diversity of lung parenchymal CD8+T cells changes during chronic infection, cells from C57BL/6J mice infected for 6- and 41-weeks were analyzed by scRNA-seq. We identified an effector lineage, including a cluster that expresses high levels of cytotoxic effectors and cytokines, and dysfunctional lineage that transcriptionally resembles exhausted T cells. The most significant differentially expressed gene between two distinct CD8+T cell lineages is CD226. Mtb-infected IFNγ-eYFP reporter mice revealed IFNγ production is enriched in CD226+CD8+T cells, confirming these as functional T cells in vivo. Purified CD226+but not CD226−CD8+T cells recognize Mtb-infected macrophages, and CD226 blockade inhibits IFNγ and granzyme B production. Thus, CD226 costimulation is required for efficient CD8+T cell recognition of Mtb-infected macrophages, and its expression identifies CD8+T cells that recognize Mtb-infected macrophages.One Sentence SummaryShinkawa et al. discover that CD226 is a functional marker that distinguishes effector from dysfunctional CD8+T cells in theMycobacterium tuberculosis(Mtb)-infected lung and has a crucial role in costimulating CD8+T cell recognition of Mtb-infected macrophages.
Exploring Genomic Signatures of Selection in Guineafowl and Chicken Populations Across Diverse Climatic Zones: A Comparative Analysis of Africa, Asia, and Europe Research Article
Authors: Moraa Grace , Ogada Stephen , Kuria Stephen , Lichoti Jacqueline , Ommeh Sheila 
Published: January 2025

AbstractThis study aimed to investigate the signatures of selection in guineafowl and chicken genomes adapted to divergent climatic conditions across Africa, Asia, and Europe. We used whole genome sequence data of guineafowls and chicken from selected countries in these continents. To identify the signatures of selection, we employed three population genomics methods: FST,integrated Haplotype Score (iHS), and Cross-Population Extended Haplotype Homozygosity (XP-EHH). Our findings revealed enriched terms related to metabolic processes, response to stimulus, signaling, and developmental processes, all of which play a role in the stress response for both guineafowls and chickens. Several candidate genes such asCRYGN,BRAF,MAP3K2,ANGPT2,COL1A1,ATP13A4, andSLC66A1, were among the positively selected candidate genes. Most of the candidate genes selected and the significant pathways identified play various roles in stress response in these two poultry species. Examination of divergent populations has provided new insights into genes potentially under selection for tolerance to the population’s indigenous environment, serving as a baseline for examining the genomic contributions to tolerance adaption. The knowledge gained from this research establishes a valuable foundation and guide for molecular breeding and conservation.
CAR T-cell and oncolytic virus dynamics and determinants of combination therapy success for glioblastoma
Authors: Conte Martina , Xella Agata , Woodall Ryan T. , Cassady Kevin A. , Branciamore Sergio , Brown Christine E. , Rockne Russell C. 
Published: January 2025

AbstractGlioblastoma is a highly aggressive and treatment-resistant primary brain cancer. While chimeric antigen receptor (CAR) T-cell therapy has demonstrated promising results in targeting these tumors, it has not yet been curative. An innovative approach to improve CAR T-cell efficacy is to combine them with other immune modulating therapies. In this study, we investigatein vitrocombination of IL-13Rα2 targeted CAR T-cells with an oncolytic virus (OV) and study the complex interplay between tumor cells, CAR T-cells, and OV dynamics with a novel mathematical model. We fit the model to data collected from experiments with each therapy individually and in combination to reveal determinants of therapy synergy and improved efficacy. Our analysis reveals that the virus bursting size is a critical parameter in determining the net tumor infection rate and overall combination treatment efficacy. Moreover, the model predicts that administering the oncolytic virus simultaneously with, or prior to, CAR T-cells could maximize therapeutic efficacy.
Characterization of nuclear genome size and variation in a freshwater snail model system featuring a recent whole-genome duplication
Authors: Neiman Maurine , Pichler Maria , Haase Martin , Lamatsch Dunja K. 
Published: January 2025

AbstractSpecies are defined by unique nuclear genome characteristics like nucleotide composition, genomic structure, and genome size. These fundamental aspects of the nuclear genome can themselves be the object of natural selection. We here provide the first high-quality direct measurements of nuclear genome DNA content in a representative diverse sample ofPotamopyrgus antipodarum, an Aotearoa New Zealand freshwater snail that is a textbook example of the maintenance of sexual reproduction in nature and is invasive worldwide. We used propidium-iodide-based flow cytometry to characterize nuclear DNA content, and its variation, in nearly 100P. antipodarumfrom multiple populations representing both sexual and asexual individuals. We also estimated nuclear DNA content in multipleP. estuarinus, a closely related obligately sexual species. These data confirmed and extended earlier lines of evidence for polyploidy and variable genome size within asexualP. antipodarumand provided the first direct evidence for distinctly higher nuclear genome content in diploid (sexual)P. antipodarumrelative to diploid sexualP. estuarinus. These data are consistent with genomic evidence for a recent whole-genome duplication (WGD) and subsequent and in-process rediploidization inP. antipodarum, setting the stage for use ofPotamopyrgusas a model for WGD and its consequences.
ANDROGENS PROTECT ILC2S FROM FUNCTIONAL SUPPRESSION DURING INFLUENZA VIRUS INFECTION
Authors: Kadel Sapana , Miller Reegan A. J. , Karlik Anna , Turner Sean , Williams Abigael P. , Ainsua-Enrich Erola , Hatipoglu Ibrahim , Bagavant Harini , Alberola-Ila José , Garton Joshua W. , Pelikan Richard , Kovats Susan 
Published: January 2025

AbstractBiological sex differences in morbidity upon influenza A virus (IAV) infection are linked to stronger IFN-centered immune responses in females, yet the regulatory role of sex hormone receptors in immune cell subsets is incompletely understood. Lung-resident group 2 innate lymphoid cells (ILC2s) express notably high levels of androgen receptors (AR). In IAV infection, ILC2s produce type 2 cytokines and facilitate tissue repair, but they also may be functionally suppressed by type 1 cytokines. Here we report sex differences in the magnitude of lung ILC2 functional suppression at the peak of sublethal IAV infection. Relative to males, ILC2s in females show attenuated proliferation, decreased propensity for IL-5 and amphiregulin production and reduced expression of GATA3 and IL-33R, features supported by divergent transcriptomes. Equivalent inflammatory cytokine levels and viral load suggested sex differences in ILC2-intrinsic factors. Indeed, naïve female ILC2s showed elevated IFNGR expression and higher phospho-STAT1 levels following IFNγ stimulation, and lymphocyte-restricted STAT1 deficiency reversed IAV-induced suppression of female ILC2s. Lymphocyte-restricted AR deficiency or loss of androgens via orchiectomy led to increased IFNGR expression and suppression of male ILC2s. These data support the hypothesis that intrinsic AR activity regulates IFNGR-STAT1 signaling pathways to preserve canonical ILC2 function in males during IAV infection.
7β-hydroxysteroid dehydratase Hsh3 eliminates the 7-hydroxy group of the bile salt ursodeoxycholate during degradation bySphingobiumsp. strain Chol11 and otherSphingomonadaceae
Authors: Richtsmeier Phil , Nedielkov Ruslan , Haring Malte , Yücel Onur , Elsner Lea , Lülf Rebekka Herdis , Wöhlbrand Lars , Rabus Ralf , Moeller Heiko , Philipp Bodo , Mueller Franziska Maria 
Published: January 2025

AbstractBile salts are steroids with distinctive hydroxylation patterns that are produced and excreted by vertebrates. In contrast to common human bile salts, ursodeoxycholate (UDCA) has a 7-hydroxy group in β-configuration and is used in large amounts for treatment of diverse gastrointestinal diseases. We isolated the 7β-hydroxysteroid dehydratase Hsh3 that is involved in UDCA degradation bySphingobiumsp. strain Chol11. Hsh3 eliminates the 7β-hydroxy group as water, leading to a double bond in the B-ring. This is similar to 7α-hydroxysteroid dehydratases in this and other strains, but Hsh3 is evolutionary different from these. Purified Hsh3 accepted steroids with and without side chain as substrates and had minor activity with 7α-hydroxy groups. The deletion mutant strain Chol11 Δhsh3had impacted growth with UDCA and accumulated a novel compound. The compound was identified as 3’,5-dihydroxy-H-methyl-hexahydro-5-indene-1-one-propanoate, consisting of steroid rings C and D with a C3-side chain carrying the former 7β-hydroxy group, indicating that Hsh3 activity is important especially for the later stages of bile salt-degradation. Hsh3 homologs were found in other sphingomonads that were also able to degrade UDCA as well as in environmental metagenomes. Thus, Hsh3 adds to the bacterial enzyme repertoire for degrading a variety of differently hydroxylated bile-salts.ImportanceThe bacterial degradation of different bile salts is not only important for the removal of these steroidal compounds from the environment but also harbors interesting enzymes for steroid biotechnology. The 7β-hydroxy bile salt UDCA naturally occurs in high concentration in the feces of black bears and has important pharmaceutical relevance for the treatment of different liver-related diseases, for which it is administered in high and increasing amounts. Additionally, it is present in the bile salt pool of humans in trace amounts. While ursodeoxycholate degradation is environmentally important, the enzyme Hsh3 modifies the hydroxy group that confers the medically relevant properties and thus might be interesting for microbiome analyses and biotechnological applications.