bluuebunny/crossref_metadata_2025 huggingface dataset:
TSniffer: Unbiasedde novoidentification of RNA editing sites and quantification of editing activity in RNA-seq data
Authors: Herrmann Maike , Krebs Yvonne , Acosta Francisco M , Parusel Sebastian , Siering Oliver , Andres Felix G. M. , Taye Biruhalem , Miskey Csaba , Pfaller Christian K.
Published: November 2024

RNA editing by adenosine deaminases acting on RNA (ADARs) is an evolutionarily conserved posttranscriptional modification essential for organismal development and normal cell function. Three catalytically active ADARs are conserved in mammals: two isoforms of ADAR1 referred to as ADAR1-p150 and ADAR1-p110, as well as ADAR2. All recognize and edit double-stranded RNA (dsRNA) structures but demonstrate target specificity and selectivity that dictate the unique essential biological functions of the three enzymes. The editing activity of ADAR1-p150 suppresses autoimmune responses against self-RNA structures, whereas ADAR1-p110 and ADAR2 have other primary functions. To better understand the mechanism of target selection by ADARs, we developedTSniffer, which allows accuratede novoidentification of edited transcripts and quantification of the extent of editing within each transcript. We found that 17-40% of protein coding transcripts in mice, ferrets, and humans are edited by ADARs. Individual transcripts can harbor hundreds and thousands of editing sites, mostly within inverted retrotransposable elements. For human transcripts, we found differential editing by ADAR1 and ADAR2, aligning with a supportive role for ADAR2, while some targets were dominantly edited by ADAR1. Relying only on RNA-seq data and reference genome,TSnifferrepresents a novel tool to decipher the role of ADAR editing in different physiological states including disease models. Its unbiased approach is suitable for any organism.
Nuclear partitioning by surface condensation on metaphase chromatids
Authors: Murugesan Vasanthanarayan , Quail Thomas , Elsner Maria , Brugues Jan
Published: November 2024

Protein partitioning between the nucleus and the cytoplasm is a defining feature of eukaryotic cells, and it is thought to be primarily regulated by transport across the nuclear envelope. However, during early vertebrate development, ensuring accurate nuclear composition is challenging due to dramatic changes in cell size and rapid cell division. Here, we show that the embryonic linker histone H1.8 is rapidly partitioned into the nucleus through a nuclear import-independent mechanism. In the cytoplasm of Xenopus laevis egg extracts, prior to nuclear assembly, H1.8 condenses on the surface of chromatids as droplets that partially wet them. Simultaneously, H1.8 also forms condensates in the cytoplasm that buffer the condensate nucleation rate on the chromatid surface, resulting in a nuclear partitioning that is independent of the DNA-to-cytoplasm ratio. To show the generality of the surface condensation mechanism, we extended our study to Nucleophosmin 1 (NPM1) in human cell culture. Similar to H1.8, NPM1 forms a layer around chromatids that breaks into droplets that subsequently are incorporated into the nucleus. Our findings show that the properties of condensate wetting and nucleation on chromatid surfaces provide an alternative and robust biophysical mechanism to regulate nuclear composition.
Benchmarking Peak Calling Methods for CUT&RUN
Authors: Nooranikhojasteh Amin , Tavallaee Ghazaleh , Orouji Elias
Published: November 2024

Cleavage Under Targets and Release Using Nuclease (CUT&RUN) has rapidly gained prominence as an effective approach for mapping protein-DNA interactions, especially histone modifications, offering substantial improvements over conventional chromatin immunoprecipitation sequencing (ChIP-seq). However, the effectiveness of this technique is contingent upon accurate peak identification, necessitating the use of optimal peak calling methods tailored to the unique characteristics of CUT&RUN data. Here, we benchmark four prominent peak calling tools, MACS2, SEACR, GoPeaks, and LanceOtron, evaluating their performance in identifying peaks from CUT&RUN datasets. Our analysis utilizes in-house data of three histone marks (H3K4me3, H3K27ac, and H3K27me3) from mouse brain tissue, as well as samples from the 4D Nucleome database. We systematically assess these tools based on parameters such as the number of peaks called, peak length distribution, signal enrichment, and reproducibility across biological replicates. Our findings reveal substantial variability in peak calling efficacy, with each method demonstrating distinct strengths in sensitivity, precision, and applicability depending on the histone mark in question. These insights provide a comprehensive evaluation that will assist in selecting the most suitable peak caller for high-confidence identification of regions of interest in CUT&RUN experiments, ultimately enhancing the study of chromatin dynamics and transcriptional regulation.
Development of a Tick-Borne Encephalitis Virus Nanoparticle Vaccine Utilizing Envelope Dimer
Authors: Wang Bingjie , Zhao Haiyan
Published: November 2024

Tick-borne encephalitis virus (TBEV) is primarily transmitted to humans through tick bites, leading to symptoms of encephalitis with a fatality rate ranging from 1% to 30%, depending on the virus subtype. Currently, only inactivated virus vaccines are available for human use, though break-through infections can still occur. Therefore, developing new vaccines against TBEV is crucial. In this study, we designed and characterized a novel nanoparticle-based TBEV envelope (E) dimer vaccine. We successfully expressed and purified the TBEV E dimer by engineering disulfide bond mutants, and animal experiments demonstrated that the E dimer protein elicited a stronger immunogenic responses compared to the E monomer protein. Further, antibody depletion experiment confirmed that the E dimer protein effectively mimics the virion surface structure, inducing robust humoral immunity targeted at neutralizing epitopes. We also presented the TBEV E dimer on the surface of the nanoparticle Mi3 using the SpyCatcher-SpyTag system, with animal experiment showing that this TBEV E dimer nanoparticle vaccine elicited a potent humoral immune response. These findings offer new insights into the immunogenicity of the TBEV E dimer and suggest that the nanoparticle-based TBEV E dimer vaccine represents a promising and highly effective candidate for TBEV immunization.
Should elephants graze or browse? The nutritional and functional consequences of dietary variation in a mixed-feeding megaherbivore
Authors: Gautam Hansraj , Berzaghi Fabio , Thanikodi M , Ravichandran Abhirami , Sreeman Sheshshayee M. , Sankaran Mahesh
Published: November 2024

Unlike specialist browsers and grazers, the diets of mixed-feeding megaherbivores like elephants are complex and broad, comprising numerous plant species of variable nutritional quality. Here, we revisit an unresolved debate on whether browse is more nutritious than grasses for elephants, as browse is thought to have greater crude protein content. We first analyzed carbon isotopes in 102 fecal samples of Asian elephants to quantify the contribution of browsing and grazing to their diet in Nagarahole National Park, southern India. We show that elephants are predominantly browsers in the grass-scarce Nagarahole forests, in contrast with predominant grazing reported in the nearby grass-abundant savannas of the Nilgiri Biosphere Reserve. We then compared the forage quality of high-browsing and high-grazing diets by analyzing these samples for two proxies of crude protein content (CP): nitrogen content (N%) and Carbon-to-Nitrogen ratio (C:N). Interestingly, high-browsing diets did not have higher N% or lower C:N (proxies for high CP) than low-browsing (high-grazing) diets. To explore the generality of this finding, we analyzed nutritional differences (i.e., CP and fibre content values) between browse and grass across 141 plant species consumed by Asian elephants. We show that woody browse and non-legume browse, which are major components of elephant browse, do not have appreciably higher CP than grasses. Our findings suggest that browsing and grazing broadly have similar nutritional value for such bulk-feeding mixed feeders. Finally, based on the observed habitat-wide variation in browsing, we provide a new framework for assessing how elephants shape woody vegetation across the forests and savannas of Asia, with important implications for conservation and carbon cycling.
Unbiased discovery of antibody therapies that stimulate macrophage-mediated destruction of B-cell lymphoma
Authors: Ribeiro Juliano , Pagès-Geli Carlota , Meglan Anna , Velarde Jose , Blandin Jasmine , Vaccaro Kyle , Wienclaw Thomas , Fernández-Guzmán Patricia , Hahn Cynthia K. , Crespo Marta , Weiskopf Kipp
Published: November 2024

Macrophages are critical effectors of antibody therapies for lymphoma, but the best targets for this purpose remain unknown. Here, we sought to define a comprehensive repertoire of cell surface antigens that can be targeted to stimulate macrophage-mediated destruction of B-cell lymphoma. We developed a high-throughput assay to screen hundreds of antibodies for their ability to provoke macrophages to attack B-cell lymphoma cells. Across both mouse and human systems, we identified multiple unappreciated targets of opsonization as well as putative immune checkpoints. We used this information to engineer a compendium of 156 bispecific antibodies, and we identified dozens of bispecifics that dramatically stimulate macrophage-mediated cytotoxicity of lymphoma cells. Among these, a bispecific comprising a SIRPα decoy domain and a CD38-targeting arm (WTa2d1xCD38) exhibited maximal efficacy while minimizing the risk of hematologic toxicity. This bispecific stimulated robust anti-tumor responses in multiple xenograft models of aggressive B-cell lymphoma. Our approach can be directly applied to other cancers to rapidly discover bispecific antibodies that leverage anti-tumor responses by macrophages or other innate immune cells.
High fitness paths can connect proteins with low sequence overlap
Authors: Kantroo Pranav , Wagner Günter P. , Machta Benjamin B.
Published: November 2024

The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein’s sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral networks can connect a local region of sequence space by single residue mutations that preserve viability. However, the larger-scale connectedness of protein morphospace remains poorly understood. Recent advances in artificial intelligence have enabled us to computationally predict a protein’s structure and quantify its functional plausibility. Here we build on these tools to develop an algorithm that generates viable paths between distantly related extant protein pairs. The intermediate sequences in these paths differ by single residue changes over subsequent steps – substitutions, insertions and deletions are admissible moves. Their fitness is evaluated using the protein language model ESM2, and maintained as high as possible subject to the constraints of the traversal. We document the qualitative variation across paths generated between progressively divergent protein pairs, some of which do not even acquire the same structural fold. The ease of interpolating between two sequences could be used as a proxy for the likelihood of homology between them.
Epigenetic modulation of NLRP6 inflammasome sensor as a therapeutic modality to reduce necroptosis-driven gastrointestinal mucosal dysfunction in HIV/SIV infection
Authors: Premadasa Lakmini S. , McDew-White Marina , Romero Luis , Gondo Beverly , Drawec Jade A. , Ling Binhua , Okeoma Chioma M. , Mohan Mahesh
Published: November 2024

The epigenetic mechanisms driving persistent gastrointestinal mucosal dysfunction in HIV/SIV infection is an understudied topic. Using reduced-representation bisulfite sequencing, we identified HIV/SIV infection in combination anti-retroviral therapy (cART)-naive rhesus macaques (RMs) to induce marked hypomethylation throughout promoter-associated CpG islands (paCGIs) in genes related to inflammatory response (NLRP6, cGAS), cellular adhesion and proliferation in colonic epithelial cells (CEs). Moreover, low-dose delta-9-tetrahydrocannabinol (THC) administration reduced NLRP6 protein expression in CE by hypermethylating theNLRP6paCGI and blocked polyI:C induced NLRP6 upregulation in vitro. In cART suppressed SIV-infected RMs, NLRP6 protein upregulation associated with significantly increased expression of necroptosis-driving proteins; phosphorylated-RIPK3(Ser199), phosphorylated-MLKL(Thr357/Ser358), and HMGB1. Most strikingly, supplementing cART with THC effectively reduced NLRP6 and necroptosis-driving protein expression to pre-infection levels. These findings for the first time demonstrate that NLRP6 upregulation and ensuing activation of necroptosis promote HIV/SIV-induced gastrointestinal mucosal dysfunction and that epigenetic modulation using phytocannabinoids represents a feasible therapeutic modality for alleviating HIV/SIV-induced gastrointestinal inflammation and associated comorbidities.
Comprehensive Mosquito Wing Image Repository for Advancing Research on Geometric Morphometric- and AI-Based Identification
Authors: Nolte Kristopher , Agboli Eric , Azambuja Garcia Gabriela , Badolo Athanase , Becker Norbert , Loc Do Huy , Dworrak Tarja Viviane , Eguchi Jacqueline , Eisenbarth Albert , de Freitas Rafael Maciel , Doumna-Ndalembouly Ange Gatien , Heitmann Anna , Jansen Stephanie , Jöst Artur , Jöst Hanna , Kiel Ellen , Meyer Alexandra , Pfitzner Wolf-Peter , Saathoff Joy , Schmidt-Chanasit Jonas , Sulesco Tatiana , Tokatlian Artin , Velavan Thirumalaisamy P. , de Castro Carmen Villacañas , Wehmeyer Magdalena Laura , Zahouli Julien , Sauer Felix Gregor , Lühken Renke
Published: November 2024

Accurate identification of mosquito species is essential for effective vector control and mitigation of mosquito-borne disease outbreaks. Traditional morphological identification requires highly specialized personnel and is time-consuming, while molecular techniques can be cost-effective and dependent on comprehensive genetic information. Wing geometric morphometry has emerged as a promising alternative, leveraging detailed geometric measurements of wing shapes and vein patterns to distinguish between species and detect intraspecies variations. This paper presents a curated dataset of 18,104 mosquito wing images, collected from 10,500 mosquito specimens, annotated with extensive meta-information, designed to support research in wing geometric morphometry and the development of machine learning models, ultimately supporting efforts in vector surveillance and research.
Delineation of Single-cell Altas Provides New Insights for Development of Coronary Artery Lesions in Kawasaki Disease: Bad and Good Signaling Molecules
Authors: Lin Qiuping , Lv Xin , Qiu Qingzhu , Mei Lianni , Chen Liqin , Song Sirui , Liu Wei , Jiang Xunwei , Huang Min , Shen Libing , Xiao Tingting , Xie Lijian
Published: November 2024

Background

Kawasaki Disease (KD) is a vasculitis syndrome featured with a high and persistent fever and mainly affects children under 5 years of age. It is the leading cause of acquired heart disease in the form of coronary artery lesions (CALs) for children in developed countries. Most KD can be relieved with the high-dosage Intravenous immunoglobulin (IVIG) therapy, but a small proportion develop CALs after IVIG treatment.

Methods

We performed the single-cell RNA sequencing for the peripheral blood mononuclear cells (PBMCs) from three KD non-CAL patients whose samples were acquired before and after IVIG treatment and three KD CAL patients whose samples were acquired only after IVIG treatment. Cell-to-cell communication patterns were also analyzed in KD CAL and non-CAL patients

Results

Overall cell expression feature analyses show immunoglobulin and adaptive immunity related genes are upregulated in KD CAL patients while B cell activation related genes are downregulated in them. Pseudo-time analyses demonstrate that both KD non-CAL patients before treatment and KD CAL patients after treatment have a dysregulated B cell developmental trajectory while the former has a mixed T and B lineage and the latter has a mixed monocyte and B lineage. The early elevated expression of SPI1 could partly explain the dysregulated B cell development in KD CAL patients. Cell communication analyses propose a disorder cell communication pattern in KD non-CAL patients before treatment and some persistent bad cell-to-cell signals in KD CAL patients after treatment. There are four signaling molecules, APP, CCL, and MCH-II, whose expression is significantly increased in the CD14 and CD16 monocytes of KD CAL patients, where the expression of RESISTIN is significantly increased in those KD non-CAL patients.

Conclusions

Our results suggest that APP, CCL, and MCH-II might be the bad signals for indicating the possible development of CAL while RESISTIN is a good one for protecting from CAL.
Acute Myeloid Leukemia with deletion 5q is an epigenetically distinct subgroup defined by heterozygous loss ofKDM3B
Authors: Kelly Katherine , Welte Linda , Sollier Etienne , Riedel Anna , Brown-Burke Fiona , Scherer Michael , Keer Harold N. , Azab Mohammad , Jahn Ekaterina , Döhner Hartmut , Döhner Konstanze , Lutsik Pavlo , Plass Christoph
Published: November 2024

Acute myeloid leukemia (AML) is a hematological malignancy characterized by a block in differentiation and accelerated proliferation of myeloid progenitor cells. Genes encoding for epigenetic regulators are among the most frequent targets for mutations and structural variations in AML, giving rise to profound epigenetic heterogeneity between and within tumors. Deletions of chromosome 5q [del(5q)] are among the most common copy number alterations in AML and are associated with extremely poor clinical outcome and therapy resistance, however the mechanisms linking del(5q) to leukemic progression are not understood. Analyzing DNA methylation profiles from 477 elderly AML patients using DNA methylome deconvolution, we discovered that del(5q) AML is an epigenetically distinct subgroup characterized by a signature of DNA hypermethylation, which we propose may be linked to dysregulation of H3K9me1/2 and overexpression of the leukemic stem cell marker,DNMT3B. Interrogation of the minimally deleted 5q region highlighted the H3K9me1/2 demethylase KDM3B as a likely target for haploinsufficiency in this subgroup. Our data suggest that del(5q) AML should be reconsidered as an epigenetically dysregulated subgroup, driven by heterozygous loss ofKDM3B, and that the resulting imbalance of H3K9me1/2 may contribute to the progression of these aggressive leukemias.
A Robust Computational Framework for the Optimization of CDK7 Inhibitors as Promising Cancer Therapy
Authors: Shi Zhaoqi , Gao Xufan , Buratto Damiano , Zhou Ruhong
Published: November 2024

Cyclin-dependent kinase 7 (CDK7) plays a crucial role in cell cycle regulation and transcription, establishing it as a promising target for cancer therapy. Although the covalent inhibitor THZ1 effectively targets CDK7, it presents risks such as short half-life and potential off-target side effects. To address these limitations, we employed a computational workflow integrating virtual screening, molecular dynamics (MD) simulations, and free energy perturbation (FEP) method to design non-covalent CDK7 inhibitors with enhanced selectivity and safety profiles. MD simulations elucidated THZ1’s inhibitory mechanism and identified key molecular fragments within its structure. By incorporating fragments from known inhibitors, we introduced extensive non-covalent interactions within the binding pocket, leading to the identification of three novel non-covalent inhibitors with binding affinities comparable to or higher than that of THZ1. Our findings not only introduce promising CDK7 inhibitors but also present a robust computational framework that could accelerate the discovery of kinase-targeted therapeutics.
A Multi-Property Optimizing Generative Adversarial Network for de novo Antimicrobial Peptide Design
Authors: Liu Jiaming , Cui Tao , Wang Tao , Zeng Xi , Niu Yinbo , Jiao Shaoqing , Lu Dazhi , Wang Jun , Xiao Shuyuan , Xie Dongna , Wang Xuecheng , Wang Yongtian , Shang Xuequn , Wei Zhongyu , Peng Jiajie
Published: November 2024

Antimicrobial peptides (AMPs) play a crucial role in developing novel antiinfective drugs due to their broad-spectrum antimicrobial activity and lower likelihood of causing bacterial resistance. However, laboratory synthesis of AMPs is tedious and time-consuming. Existing computational methods have limited capability in optimizing multiple desired properties simultaneously. Here, we propose a Multi-Property Optimizing Generative Adversarial Network (MPOGAN), a feedback-loop framework that iteratively learns from data with multiple desired properties. This approach enables de novo design of AMPs with potent antimicrobial activity, reduced cytotoxicity, and diversity. Through extensive computational tests, MPOGAN exhibits superior performance in optimizing multiple desired properties of generated AMPs. Ten of the most promising candidates are chemically synthesized, with nine showing potent antimicrobial activity against three bacterial strains and low cytotoxicity against eukaryotic cells. MPOGAN offers a powerful computational approach for effective multi-property optimization of AMPs, thereby advancing the field of AI-aided drug discovery.
Shading does not lower thermal tolerance in the coralMontipora capitata: implications for conservation intervention
Authors: Ducret Hugo , Suchocki Christopher R. , Bardin Claire E. , Lewis Claire J. , Permentier Tristan , Hardt Madeleine , Toonen Robert J. , Kochzius Marc , Flot Jean-François
Published: November 2024

Marine heatwaves trigger severe coral bleaching events that result in dramatic losses of coral reefs worldwide. An increasingly common method used to mitigate coral bleaching is to shade portions of reefs. However, as shaded corals become less exposed to environmental stress, shading has also been hypothesized to lower their thermal tolerance, which would be detrimental for their survival. Here, we investigated how long-term shading modifies the response ofMontipora capitatato both light and temperature stressors. After two years of growth, we used the Coral Bleaching Automated Stress System (CBASS) to compare responses of 73% shaded and unshaded corals during 1) temperature stress under ambient light, 2) temperature stress under low light, and 3) ambient temperature with light stress. Results show that shaded corals are less resistant than control ones to light stress and to heat stress under high light, but not to heat stress under low light, where no difference was detected. We further demonstrate that low light intensity during heat stress reduces the decline of photosynthetic efficiency when compared to heat stress at ambient light, regardless of the light history of the coral colonies. Our data support light-mediated stress, both independent of and synergistic with heat-induced stress, and suggest that light and heat stresses trigger different molecular and cellular pathways. We hereby confirm the benefits of coral shading under both short– and long-term temperature stress, and underline the importance of light acclimation in the conservation and restoration of coral reefs.
T cell receptor sharing in hypersensitivity pneumonitis
Authors: Sendama Wezi , Funston Wendy , Davidson Richard CH , Rostron Anthony J , Simpson A John
Published: November 2024

Hypersensitivity pneumonitis (HP) is characterised by an excessive pulmonary T cell response in susceptible individuals after exposure to inhaled antigens. The most effective treatment for the condition is antigen avoidance, but in most cases an antigen cannot be identified. Profiling antigen-specific T cell responses may form the basis of a strategy to identify causative antigens of the disease. We used public RNA sequencing data and reconstructed T cell receptor (TCR) repertoires from blood and bronchoalveolar lavage samples from patients with HP, idiopathic pulmonary fibrosis and healthy controls. After excluding TCR sequences likely to be related to common microbial exposures in patients with HP, we identified TCRs shared between patients with shared human leukocyte antigen alleles, indicating patients likely to have a common causative antigen. We also identified clusters of TCRs containing identical and similar TCR clones in individual patients that are plausibly related to the causative antigens in those patients. These results establish the feasibility of profiling TCR repertoires to identify antigens in HP.
DDA-BERT: leveraging transformer architecture pre-training for data-dependent acquisition mass spectrometry-based proteomics
Authors: Jun A , Liu Pu , Sun Yingying , Lin Jiaying , Zhang Xiaofan , Nie Zongxiang , Zhang Yuqi , Xing Ziyuan , Chen Yi , Guo Tiannan
Published: November 2024

In data-dependent acquisition mass spectrometry (DDA-MS)-based proteomics, machine learning based rescoring methods are often employed to integrate multiple scores measuring quality of peptide-spectrum matches (PSMs) from different aspects. Existing rescoring tools face limitations incurred by manual feature extraction, shallow machine learning models, and limited training data. Here, we introduce DDA-BERT, a transformer-based end-to-end deep learning model trained with 95 million human spectra for PSM rescoring. DDA-BERT demonstrates superior performance across various sample types, mass spectrometer platforms, trace sample proteomics, and multiple species proteome data. It consistently outperforms state-of-the-art methods of its kind for DDA-MS spectra analysis with up to 103.5% increased protein group identifications. For single cell proteomics, DDA-BERT identifies up to 85.6% more protein groups compared to existing tools. In addition, DDA-BERT can be effectively extended to proteome of non-human species. DDA-BERT offers a robust and scalable solution for enhancing PSM rescoring in proteomics.
Building a single cell transcriptome-based coordinate system for cell ID with SURE
Authors: Zeng Feng , Han Jiahuai
Published: November 2024

The surge in single-cell transcriptome data necessitates a unified cell identification system. We propose a strategy that uses metacells as landmarks, coupled with a data-driven method called SURE, to create a cell ID coordinate system. This system streamlines cell atlases, enhances molecular signals, and ensures accurate cell identification while mitigating sequencing noise. We demonstrated the effectiveness of SURE by assembling similar cell types from datasets with cell type imbalance issues. We employed SURE to establish a unified coordinate system for the human hematopoietic system (HBMCA), which enables the direct, zero-shot mapping of single-cell datasets from 13 different diseases, showcasing its value as a common foundation for investigating the diverse disease effects on human blood cells. SURE has successfully addressed the long-standing challenge of positioning cells within a common multidimensional space, paving the way for a convergent understanding of cell identity across diverse experimental landscapes.
The firstde novoHiFi genome assemblies for three clownfish-hosting sea anemone species (Anthozoa: Actiniaria)
Authors: De Jode Aurélien , Titus Benjamin M.
Published: November 2024

The symbiosis between clownfish and giant tropical sea anemones (Order Actiniaria) is one of the most iconic on the planet. Distributed on tropical reefs, 28 species of clownfishes form obligate mutualistic relationships with 10 nominal species of venomous sea anemones. Our understanding of the symbiosis is limited by the fact that most research has been focused on the clownfishes. Chromosome scale reference genomes are available for all clownfish species, yet there are no published reference genomes for the host sea anemones. Recent studies have shown that the clownfish-hosting sea anemones belong to three distinct clades of sea anemones that have evolved symbiosis with clownfishes independently. Here we present the first high quality long read assemblies for three species of clownfish hosting sea anemones belonging to each of these clades:Entacmaea quadricolor, Stichodactyla haddoni, Radianthus doreensis. PacBio HiFi sequencing yielded 1,597,562, 3,101,773, and 1,918,148 million reads forE. quadricolor, S. haddoni, andR. doreensis, respectively. All three assemblies were highly contiguous and complete with N50 values above 4Mb and BUSCO completeness above 95% on the Metazoa dataset. Genome structural annotation with BRAKER3 predicted 20,454, 18,948 and 17,056 protein coding genes inE. quadricolor, S. haddoniandR. doreeensisgenome, respectively. These new resources will form the basis of comparative genomic analyses that will allow us to deepen our understanding of this mutualism from the host perspective.

Significance

Chromosome-scale genomes are available for all 28 clownfish species yet there are no high-quality reference genomes published for the clownfish-hosting sea anemones. The lack of genomic resources impedes our ability to understand evolution of this iconic symbiosis from the host perspective. The clownfish-hosting sea anemones belong to three clades of sea anemones that have evolved mutualism with clownfish independently. Here we assembled the first high-quality long-read genomes for three species of host sea anemones each belonging to a different host clade:Entacmaea quadricolor, Stichodactyla haddoni, Radianthus doreensis. These resources will enable in depth comparative genomics of clownfish-hosting sea anemones providing a critical perspective for understanding how the symbiosis has evolved. Finally, these reference genomes present a significant increase in the number of high-quality long-read genome assemblies for sea anemones (11 currently published) and double the number of high-quality reference genomes for the sea anemone superfamily Actinoidea.
Companion to: A molecular basis for milk allergen immune recognition in eosinophilic esophagitis
Authors: Dilollo Julianna , Hu Alex , Qu Huiqi , Canziani Karina E. , Clement Rachel L. , McCright Sam J. , Shreffler Wayne G. , Hakonarson Hakon , Spergel Jonathan M. , Cerosaletti Karen , Hill David A.
Published: November 2024

Background

Eosinophilic esophagitis (EoE) is a chronic, type 2 inflammatory disease that is increasing in incidence and has substantial morbidity. Despite being clinically defined as a food allergy, the molecular details of food antigen presentation and recognition by the immune system are unknown.

Objective

The objective of this study was to identify and characterize the molecular basis of milk antigen presentation and T cell recognition in a patient with EoE milk allergy.

Methods

Milk-expanded TCR clonotypes were identified usingex vivostimulation followed by single cell RNA with linked, pairedTRAandTRBsequencing. HLA restriction and antigen specificity of TCRs were identified using a combination of lentiviral expression, HLA sequencing, antibody blockade, and a peptide library screen.

Results

We isolated a β-casein specific TCR clonotype (eoeTCR-4) and determined its HLA restriction (HLA-DRB1*07:01) and cognate antigen (β-casein AA 59-78). EoeTCR-4 was not detected among a larger group of subjects and is likely private to EoE Subject 1.

Conclusion

In conjunction with the parent manuscript, this companion article provides the first molecular identity of food antigen presentation and immune recognition in EoE.

This manuscript is a companion to the parent manuscript “A molecular basis for milk allergen immune recognition in eosinophilic esophagitis”. It provides additional data and detailed methods not provided in the parent manuscript. It is designed to supplement and support the findings and conclusions of the parent manuscript.
Impact of a Cancer-Associated Mutation on Poly(ADP-ribose) Polymerase1 Inhibition
Authors: Shanmugam Neel , Chatterjee Shubham , Cisneros G. Andres
Published: November 2024

Poly(ADP-ribose) polymerase1 (PARP1) plays a vital role in DNA repair and its inhibition in cancer cells may cause cell apoptosis. In this study, we investigated the effects of a PARP1 variant, V762A, which is strongly associated with several cancers in humans, on the inhibition of PARP1 by three FDA approved inhibitors: niraparib, rucaparib and talazoparib. Our work suggests that these inhibitors bind to the V762A mutant more effectively than to the wild-type (WT), with similar binding free energies between them. Talazoparib inhibition uniquely lowers the average residue fluctuations in the mutant than the WT including lower fluctuations of mutants N- and C-terminal residues, conserved H-Y-E traid residues and donor loop (D-loop) residues which important for catalysis more effectively than other inhibitions. However, talazoparib also enhances destabilizing interactions between the mutation site in the HD domain in the mutant than WT. Further, talazoparib inhibition significantly disrupts the functional fluctuations of terminal regions in the mutant, which are otherwise present in the WT. Lastly, the mutation and inhibition do not significantly affect PARP1s essential dynamics.
Lipid Nanoparticles fromL. meyeniiWalp Mitigate Sepsis through Multimodal Protein Corona Formation
Authors: Sung Junsik J. , Shaw Jacob R. , Rezende Josie D. , Dharmaraj Shruti , Cottingham Andrea L. , Weldemariam Mehari M. , Jones Jace W. , Kane Maureen A. , Pearson Ryan M.
Published: November 2024

Background

Plant-derived nanoparticles (PDNP) are nano-sized particles isolated from various edible plants that contain bioactive components involved in regulating cellular immune responses against pathogenic intrusion and inflammation.

Purpose

This study describes a novel PDNP derived fromLepidium meyeniiWalp (maca) that efficiently captures pro-inflammatory cytokines and acute phase proteins in its protein corona to enhance survival in two representative lethal models of sepsis.

Methods

Lipid nanoparticles were isolated from maca (MDNP) and triacylglycerols and phytoceramides were identified as major constituents using lipidomics. The physicochemical properties of MDNPs were determined, anti-inflammatory effects of MDNP were evaluated usingin vitromodels andin vivousing endotoxemia and cecal ligation and puncture (CLP) polymicrobial sepsis models. Proteomic analysis of MDNP in healthy or LPS-induced inflammatory plasma was used to determine the composition and inflammatory pathways modulated due to the MDNP protein corona.

Results

In vitrostudies showed that MDNP were non-toxic, reduced macrophage activation, and effectively sequestered pro-inflammatory cytokines to mitigate NF-κB activity under lipopolysaccharide (LPS) stimulation. In a pre-established LPS-induced endotoxemia model, MDNP-treated mice showed significantly reduced systemic pro-inflammatory cytokines and enhanced survival. Untargeted proteomics and pathway analysis of the MDNP protein corona identified an enrichment in acute phase proteins in MDNP-LPS plasma coronas. MDNP treatment also significantly improved survival in the CLP sepsis model in the absence of antibiotics.

Conclusion

This work identified MDNP as an efficient, plant-derived lipid NP that broadly sequesters and neutralizes a compilation of inflammatory mediators in their coronas, offering multimodal therapeutic potential for treating inflammatory diseases.
Physiologic Regulation of Lipid Oxidation and Ferroptosis By Vitamin E, High-Density Lipoprotein, and Scavenger Receptor Class B Type 1
Authors: Rink Jonathan S. , Calvert Andrea E. , Moxley Alexandra , Lin Adam Yuh , Nguyen SonBinh T. , Gordon Leo I , Thaxton C. Shad
Published: November 2024

Ferroptosis is a form of cell death caused by oxidative (-OOH) damage to phospholipids (PL) that comprise the cell membrane. Understanding mechanisms of ferroptosis is important because of the role it plays in human disease, including cancer and neurodegeneration. Previous work has focused on the intracellular antioxidant enzyme glutathione peroxidase 4 (GPx4), which detoxifies PL-peroxides (PL-OOH) and prevents ferroptosis. Studies also show that alpha-tocopherol (α-toc), the active form of Vitamin E, is an exogenous lipophilic antioxidant that inhibits ferroptosis in cancer cells in vitro and in neurons and hematopoietic stem cells in vivo. The mechanisms by which α-toc engages cells to manipulate PL redox balance and ferroptosis are unknown. Lipoproteins, like high- and low-density lipoproteins (HDL and LDL), carry α-toc in the circulation, which compelled our investigation of their role in α-toc delivery and ferroptosis. Using cancer and neuronal cell models, here we show that lipoproteins, particularly HDL, deliver α-toc by binding the cell membrane receptor scavenger receptor class B type 1 (SR-B1) to prevent ferroptosis. Additionally, we synthesized SR-B1 targeted HDL-like particles that contained α-toc to validate data obtained with native lipoproteins. We reveal here a tunable cellular redox axis whereby native and synthetic HDLs containing α-toc target SR-B1 to reduce PL-OOH and prevent ferroptosis.
Evolution of pineal non-visual opsins in lizards and the tuatara (Lepidosauria)
Authors: Romero Ricardo , de Souza Flávio S J
Published: November 2024

Many lizards (Squamata), as well as the tuatara (Rhynchocephalia), are distinguished among vertebrate groups for the presence of the parietal eye - also called “third eye” - a structure derived from the pineal complex that develops from the roof of the diencephalon and resembles a simplified retina. The parietal eye is located near the dorsal surface of the head and possesses photoreceptor cells expressing an array of nonvisual opsins that differs from the visual opsin repertoire of the lateral eyes. These pineal opsins are pinopsin (OPNP), parapinopsin (OPNPP) and parietopsin (OPNPT), all being evolutionary close to the visual opsins. A fourth member of the group, vertebrate-ancient opsin (OPNVA), is expressed in the brain. Here, we have searched over 50 lepidosaurian genomes (tuatara + lizards) for pineal non-visual opsins to check for the evolutionary trajectory of these genes during reptile evolution. Unexpectedly, we identified a novel opsin gene, which we termed “lepidopsin” (OPNLEP), that is present in the tuatara and most lizards but absent from the genomes of other reptiles. Phylogenetic analyses indicate that OPNLEP proteins are grouped in a clade distinct from nonvisual and visual opsins. Remnants of the gene are found in the coelacanth and some ray-finned fishes like gars and sturgeons, implying that OPNLEP is an ancient opsin that has been repeatedly lost during vertebrate evolution. As for the survey, we found that the tuatara and most lizards of the Iguania, Anguimorpha, Scincoidea and Lacertidae clades, which possess a parietal eye, harbour all five non-visual opsin genes analysed. Lizards missing the parietal eye, like geckos (Gekkota), the fossorialRhineura floridana(Amphisbaenia) and lacertoids of the Teiidae and Gymnophthalmidae families lack most or all pineal nonvisual opsins. In summary, our survey of reptile pineal non-visual opsins has revealed i) the persistence of a previously unknown ancient opsin gene – OPNLEP - in lepidosaurians; ii) losses of non-visual opsins in specific lizard clades and iii) a correlation between the presence of a parietal eye and the genomic repertoire of pineal non-visual opsins.
Inhibition of acid ceramidase as a therapeutic strategy for Niemann-Pick C disease
Authors: Haynes Isabelle , Ward Simon E. , Jones D. Heulyn , Lloyd-Evans Emyr , Waller-Evans Helen
Published: November 2024

Lysosomal storage disorders (LSDs) are a group of individually rare diseases that as a group constitute the most common forms of childhood neurodegeneration. These life limiting and life shortening diseases have the largest economic burden per patient of any rare disease with the majority being orphan diseases with no disease modifying therapy. Whilst there is significant development in the area of gene therapies for LSDs, these can only be used to treat individual diseases, are expensive, and in recent times many companies have abandoned their gene therapy pipelines. Small molecules on the other hand can be developed to target common mechanisms of pathogenesis or common central disease phenotypes providing therapies that can treat multiple diseases. In this study we report acid ceramidase as a novel therapeutic target for treating Niemann-Pick type C (NPC) disease. Using siRNA, and the literature tool compound carmofur, we observed a reduction in lysosomal area and reduced accumulation of the lipids cholesterol and LBPA in an NPC cellular model. These lipids are known to accumulate as secondary storage molecules across many lysosomal diseases, particularly primary sphingolipid storage disorders where lyso-sphingolipids are known to accumulate via the action of acid ceramidase. As acid ceramidase has also been shown to be a therapeutic target for Krabbe disease, our findings indicate that this is a novel target for the potential treatment of multiple LSDs with primary or secondary storage of sphingolipids.
Semaglutide-induced weight loss improves mitochondrial energy efficiency in skeletal muscle
Authors: Choi Ran Hee , Karasawa Takuya , Meza Cesar A. , Maschek J. Alan , Manuel Allison , Nikolova Linda S. , Fisher-Wellmen Kelsey H. , Cox James E. , Chaix Amandine , Funai Katsuhiko
Published: November 2024

Objective

Glucagon-like peptide 1 receptor agonists (e.g. semaglutide) potently induce weight loss and thereby reducing obesity-related complications. However, weight regain occurs when treatment is discontinued. An increase in skeletal muscle oxidative phosphorylation (OXPHOS) efficiency upon diet-mediated weight loss has been described, which may contribute to reduced systemic energy expenditure and weight regain. We set out to determine the unknown effect of semaglutide on muscle OXPHOS efficiency.

Methods

C57BL/6J mice were fed a high-fat diet for 12 weeks before receiving semaglutide or vehicle for 1 or 3 weeks. The rate of ATP production and O2consumption were measured by a high-resolution respirometry and fluorometry to determine OXPHOS efficiency in skeletal muscle at these 2 timepoints.

Results

Semaglutide treatment led to significant reductions in fat and lean mass. Semaglutide improved skeletal muscle OXPHOS efficiency, measured as ATP produced per O2consumed (P/O) in permeabilized muscle fibers. Mitochondrial proteomic analysis revealed changes restricted to two proteins linked to complex III assembly (Lyrm7 and Ttc1, p <0.05 without multiple corrections) without substantial changes in the abundance of OXPHOS subunits.

Conclusions

These data indicate that weight loss with semaglutide treatment increases skeletal muscle mitochondrial efficiency. Future studies could test whether it contributes to weight regain.
Metabolic reprogramming and synergistic cytotoxicity of genistein and chemotherapy in human breast cancer cells
Authors: Tobón-Cornejo Sandra , Vargas-Castillo Ariana , Juarez Mandy , Acevedo-Carabantes Joshua Ayork , Noriega Lilia G. , Granados-Portillo Omar , Chávez-Blanco Alma , Morales-Bárcenas Rocío , Torres Nimbe , Tovar Armando R. , Schcolnik-Cabrera Alejandro
Published: November 2024

Breast cancer (BCa) is a heterogeneous disease, initially responsive to hormone therapy but often developing resistance to both hormonal and chemotherapy treatments. Novel therapeutic strategies are needed for drug-resistant BCa. Genistein, a phytoestrogen structurally similar to estrogen, competes with estrogen for receptor binding and exhibits anti-cancer effects. In this study, we investigated the cellular and metabolic impacts of genistein, alone or in combination with chemotherapy, in two human BCa cell lines—one estrogen receptor-positive (ER+) and one estrogen receptor-negative (ER−). We observed a strong synergistic effect on cell viability at low concentrations of genistein and chemotherapy, resulting in reduced clonogenic capacity and impaired cell migration. Genistein alone modulated cellular energy metabolism, notably reducing ATP production in MCF7 (ER+) cells. This metabolic shift was linked to a decreased dependence on fatty acids for energy, coupled with a decrease in the rate-limiting mitochondrial translocase CPT1 required for fatty acid oxidation, alongside with an increase in intracellular fatty acid levels. While the most significant changes occurred in ER+ cells, ER− cells also showed responses to genistein treatment. Collectively, our findings suggest that low dose genistein, in combination with conventional chemotherapy, induces synergistic anti-cancer effects, promoting cellular senescence. This effect may be partly mediated by a reduced reliance on fatty acid metabolism in BCa cells.
Structure Characterization of Bacterial Microcompartment Shells via X-ray Scattering and Coordinate Modeling: Evidence for adventitious capture of cytoplasmic proteins
Authors: Zuo Xiaobing , Jussupow Alexander , Ponomarenko Nina S. , Tefft Nicholas M. , Yadav Neetu Singh , Range Kyleigh L. , Ralston Corie Y. , TerAvest Michaela A. , Sutter Markus , Kerfeld Cheryl A. , Vermaas Josh V. , Feig Michael , Tiede David M.
Published: November 2024

Bacterial microcompartments (BMCs) are self-assembling, protein shell structures that are widely investigated across a broad range of biological and abiotic chemistry applications. A central challenge in BMC research is the targeted capture of enzymes during shell assembly. While crystallography and cryo-EM techniques have been successful in determining BMC shell structures, there has been only limited success in visualizing the location of BMC-captured enzyme cargo. Here, we demonstrate the opportunity to use small angle X-ray scattering (SAXS) and pair density distribution function (PDDF) measurements combined with quantitative comparison to coordinate structure models as an approach to characterize BMC shell structures in solution conditions directly relevant to biochemical function. Using this approach, we analyzed BMC shells fromHaliangium ochraceumthat were isolated following expression inE. coli. The analysis allowed BMC shell structures and the extent of encapsulated enzyme cargo to be identified. Notably, the results demonstrate that HO-BMC shells adventitiously capture significant amounts of cytoplasmic cargo during assembly inE. coli. Our findings highlight the utility of SAXS/PDDF analysis for evaluating BMC architectures and enzyme encapsulation, offering valuable insights for designing BMC shells as platforms for biological and abiotic catalyst capture within confined environments.
Atomic elementary flux modes explain the steady state flow of metabolites in large-scale flux networks
Authors: Chitpin Justin G. , Perkins Theodore J.
Published: November 2024

Steady state fluxes are a measure of cellular activity under metabolic homoeostasis, but understanding how individual substrates are metabolized remains a challenge in large-scale networks. Pathway-based approaches such as elementary flux mode (EFM) analysis are limited to small networks due to the combinatorial explosion of pathways and the ambiguity of decomposing fluxes onto EFMs. Here, we present an alternative approach to explain metabolic fluxes in terms of the steady state flow of their atomic constituents. We refer to these pathways as atomic elementary flux modes (AEFMs) and show that computations involving AEFMs are orders of magnitude faster than standard EFMs. Using our approach, we enumerate carbon and nitrogen AEFMs in five genome-scale metabolic models and compute the AEFM decomposition of fluxes estimated in a HepG2 liver cancer cell line. Our results systematically characterize carbon and nitrogen remodelling and, on the HepG2 network, predict glutamine metabolism through a recently discovered non-canonical TCA cycle.