Biology subjects

Yu, J.

Publications and source records attributed to Yu, J..

At least 199 records · Page 11Linked to original sources

bioRxiv2024

Genome-wide mapping of EBV-induced genomic variationsidentifies the role of MUC19 in EBV latency

Epstein-Barr virus (EBV) infects over 95% of the worlds population and is tightly associated with multiple human malignant diseases. As the first discovered human oncovirus, EBV is known to induce genomic instability by promoting various types of genomic modifications in host chromosomes. However, the mechanisms through which EBV interacts with the host genome and regulates cellular gene expression in genomic modifications are not yet fully elucidated. In this study, we conducted primary EBV infection in B cells and performed the analyses of copy number variants using whole genome sequencing. After comparing to other distinct B cells with varying EBV infection backgrounds, we identified susceptible regions and unveiled critical host factors induced by EBV infection on chromosomes. Combined with the genome-wide transcriptomic analyses, we found that the mucin gene MUC19 is distinctively activated by EBV infection and MUC19 promotes oncogenesis through the activation of mTOR signaling in lymphoblastoid cell lines (LCLs). Further results indicate that EBV nuclear antigen 1 (EBNA1) binds to multiple regions within MUC19 and enhances the expression of MUC19. Moreover, sequence alignment has shown intriguing motif homology between the basic repeat unit of MUC19 and EBV genome, suggesting the potential of EBV-specific integration. To conclude, our study maps the genomic perturbations induced by EBV primary infection and offers new insights into the oncogenic roles of MUC19 during EBV latency.

microbiology↗

bioRxiv2024

Bacterial lipoate protein ligases rescue lipoylation and respiration deficiency in mammals

Human lipoylation pathway deficiencies caused by LIPT2/LIAS/LIPT1 gene mutations lead to inherited metabolic disorders characterized by severe defects of mitochondrial energy and amino acids metabolism. Patients with such mutations suffer from hyperlactic acidemia, encephalopathy, hypotonia and early death. So far there is no effective treatment. Here we introduced the bacteria salvage lipoylation pathway, which is absent in eukaryotes, into lipoylation defective human cells and mouse models. Both E. coli-derived LplA and B. subtilis-derived LplJ restored the phenotypes of LIPT2/LIAS/LIPT1 gene knockout cells to those of wildtype cells with lipoic acid supplementation. Biochemical and isotope tracing analysis demonstrated LplA and LplJ function through direct lipoylation of the H protein of glycine cleavage system and the E2 subunits of 2-oxoacid dehydrogenases, thereby reactivating the short-circuited TCA cycle and amino acids metabolism. This strategy is further extended to treat lipoyl precursor supply defects caused by MECR and FDX1 mutations and its efficacy and safety are validated in Lipt1-/- and LplAOE/+ mouse models. This study provides systematic characterization of lipoylation deficiency and paves the way to gene therapy for treatment of lipoylation-deficient patients.

cell biology↗

bioRxiv2024

Limited involvement of Ca2+/calmodulin-dependent kinase II alpha and beta in mammalian sleep

While sleep is important, our understanding of its molecular mechanisms is limited. Over the last two decades, protein kinases have been implicated in sleep regulation, with a prominent role for Ca++/calmodulin-dependent kinase II (CaMKII) {beta}. Of all the known mouse genetic mutants, the biggest changes in sleep was reported to be observed in Camk2b gene knockout mice: sleep was reduced by approximately 120 minutes (mins) over 24 hours (hrs). We have reexamined the sleep phenotype in Camk2a and Camk2b knockout mice, and while we have observed sleep reduction in Camk2a knockout mice, we did not find sleep reduction in Camk2b mutants.We did find both Camk2a and Camk2b participated in homeostatic sleep rebound, though. Because CamKII and {beta} are widely known to be crucial kinases with interesting properties, it is worthwhile to keep our results in record for a general service to the field.

animal behavior and cognition↗

bioRxiv2024

Spotiphy enables single-cell spatial whole transcriptomics across the entire section

Spatial transcriptomics (ST) has advanced our understanding of tissue regionalization by enabling the visualization of gene expression within whole tissue sections1, but the approach remains dogged by the challenge of achieving single-cell resolution without sacrificing whole genome coverage2,3. Here we present Spotiphy (Spot imager with pseudo single-cell resolution histology), a novel computational toolkit that transforms sequencing-based ST data into single-cell-resolved whole-transcriptome images. In evaluations with Alzheimers disease (AD) and normal mouse brains, Spotiphy delivers the most precise cellular compositions. For the first time, Spotiphy reveals novel astrocyte regional specification in mouse brains. It distinguishes sub-populations of DAM (Disease-Associated Microglia) located in different AD mouse brain regions. Spotiphy also identifies multiple spatial domains as well as changes in the patterns of tumor-tumor microenvironment interactions using human breast ST data. Spotiphy enables visualization of cell localization and gene expression in tissue sections, offering key insights into the function of complex biological systems.

systems biology↗

bioRxiv2024

Peptide-Based Complex Coacervates Stabilized by Cation-π Interactions for Cell Engineering

Complex coacervation is a form of liquid-liquid phase separation (LLPS), whereby two types of macromolecules, usually bearing opposite net charges, self-assemble into dense microdroplets driven by weak molecular interactions. Peptide-based coacervates have recently emerged as promising carriers to deliver large macromolecules (nucleic acids, proteins and complex thereof) inside cells. Thus, it is essential to understand their assembly/disassembly mechanisms at the molecular level in order to tune the thermodynamics of coacervates formation and the kinetics of cargo release upon entering the cell. In this study, we design histidine-rich peptides consisting of modular sequences in which we systematically incorporate cationic, anionic, or aromatic residues at specific positions along the sequence in order to modulate intermolecular interactions and the resulting coacervation stability. We show that cation-{pi} interactions between arginine and aromatic side chains are particularly efficient in stabilizing complex coacervates, and these interactions can be disrupted in the protein-rich intracellular environment, triggering the disassembly of complex coacervates followed by cargo release. With the additional grafting of a disulfide-based self-immolative sidechain, these complex coacervates exhibit enhanced stability and can deliver proteins, mRNA, and CRISPR/Cas9 genome editing tools with tunable release kinetics into cells. This capability extends to challenging cell types, such as macrophages. Our study highlights the critical role of cation-{pi} interactions in the design of peptide-based coacervates, expanding the biomedical and biotechnology potential of this emerging innovative intracellular delivery platform. Table of ContentTandem peptides designed from histidine-rich beak proteins are modified with either negative, positive, or aromatic residues that can undergo complex coacervation through cation-{pi} rather than electrostatic interactions. These complex coacervates can effectively recruit various macromolecular cargos and deliver them intracellularly with controlled release kinetics, including in hard-to-transfect macrophages. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=183 SRC="FIGDIR/small/619264v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@1e92628org.highwire.dtl.DTLVardef@1c80e19org.highwire.dtl.DTLVardef@115ac05org.highwire.dtl.DTLVardef@1d0b122_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Connectomic Organization of the Suprachiasmatic Nucleus

The suprachiasmatic nucleus (SCN), the mammalian master clock, is a special structure dedicated to the time computation. However, a connectomic understanding of the nucleus as a whole is lacking. Using serial section electron microscopy, we reconstructed multiscale and multimodal SCN communication networks. Intra-SCN synaptic network consists of 9,566 morphologically similar neurons and 4.3 million synapses, organized into multiscale circuitries that interact with SCN-traversing axon fascicles. Strikingly, SCN neurons engage in unique soma-soma ephaptic interaction, forming 2,038 electrotonic integrative units with the largest overlapping the light-responsive area (LRA). SCNs paracrine modality contains 47,396 m3 dense core vesicles, with notable scarcity in the LRA, suggesting cross-modal coordination and functional integration. These distinct network features provide comprehensive insights into the system architecture of the mammalian circadian clock.

neuroscience↗

bioRxiv2024

Exploring the Efficiency of Deep Graph Neural Networks for RNA Secondary Structure Prediction

Ribonucleic acid (RNA) plays a vital role in various biological processes and forms intricate secondary and tertiary structures associated with its functions. Predicting RNA secondary structures is essential for understanding the functional and regulatory roles of RNA molecules in biological processes. Traditional free-energy-based methods for predicting these structures often fail to capture complex interactions and long-range dependencies within RNA sequences. Recent advancements in machine learning, particularly with graph neural networks (GNNs), have shown promise in enhancing the ability to model the relationships between molecular sequences and their structures. This work specifically explores the efficacy of various GNN architectures in modeling RNA secondary structure. Through benchmarking the GNN methods against traditional energy-based models on standard datasets, our analysis demonstrates that GNN models improves traditional methods, offering a robust framework for accurate RNA structure prediction.

bioinformatics↗

bioRxiv2024

Cryo-EM of native membranes reveals an intimate connection between the Krebs cycle and respiration in mycobacteria

Imaging of endogenous protein complexes in their native membranes can reveal protein-protein interactions that are lost upon detergent solubilization. To investigate interactions in the mycobacterial oxidative phosphorylation machinery, we prepared inverted membrane vesicles from Mycobacterium smegmatis and enriched for vesicles containing complexes of interest by affinity chromatography. Electron cryomicroscopy (cryo-EM) of these vesicles revealed that malate-quinone oxidoreductase (Mqo), an enzyme from the Krebs cycle, physically associates with the electron transport chain Complex III2IV2 (CIII2CIV2) supercomplex. Analysis of the Mqo:CIII2CIV2 interaction shows that CIII2CIV2 is necessary for malate-driven, but not NADH- driven, electron transport chain activity and oxygen consumption. Further, the association of Mqo with CIII2CIV2 enables electron transfer from malate to CIII2CIV2 with millisecond kinetics. Together, these findings indicate a connection between the Krebs cycle and respiration that directs electrons along a single branch of the mycobacterial electron transport chain.

biochemistry↗

bioRxiv2024

Genetically-encoded markers for confocal visualization of single dense core vesicles

Neuronal dense core vesicles (DCVs) store and release a diverse array of neuromodulators, trophic factors and bioamines. The analysis of single DCVs has largely been possible only using electron microscopy, which makes understanding cargo segregation and DCV heterogeneity difficult. To address these limitations, we developed genetically-encoded markers for DCVs that can be used in combination with standard immunohistochemistry and expansion microscopy, to enable single-vesicle resolution with confocal microscopy.

neuroscience↗

bioRxiv2024

Ectonucleotidases and Purinergic Receptors in Mouse Prostate Gland

Extracellular ATP/ADP and its metabolite adenosine are important signaling molecules that regulate cellular function by binding to P2 and P1/adenosine receptors. The kinetics of these signaling molecules are critically modulated by ectonucleotidases, enzymes that convert ATP/ADP to adenosine. Although the expression and function of these enzymes and relevant purinergic receptors in the prostate gland are not well understood, recent reports indicate impaired ATP hydrolysis activity in the aging prostate. Purinergic signaling is known for its role in inflammation, muscle contraction, pain sensation, and cell proliferation in many systems, suggesting its potential importance in normal prostate function and pathological conditions such as benign prostatic hyperplasia and prostatitis. To better understand purine-converting enzymes and purinergic receptors in the prostate, we isolated mouse prostate glands for immunofluorescent staining and microscopy imaging using specific antibodies. Our study identified a differential expression profile of purinergic enzymes and receptors in the prostate: ENTPD1 and P2x1 receptors predominantly in prostate smooth muscle cells, ENTPD2 and NT5E in prostate interstitial cells, and ALPL in prostate epithelial cells. Functionally, in addition to the P2x1-mediated prostate smooth muscle contraction induced by agonist ,{beta}-meATP, we observed an ATP{gamma}S-induced contraction force after P2x1 desensitization. This led to the identification of multiple P2Y receptors in mouse prostate smooth muscle, including P2Y1, P2Y2, and P2Y11 receptors, which potentially mediate the ATP{gamma}S-induced contraction force. These discoveries lay the foundation for further mechanistic understanding of how purinergic signaling regulates prostate function and dysfunction in both rodents and potentially humans.

physiology↗

bioRxiv2024

Bimodal cell mass distribution separates CD8+ T cells into two distinct types with divergentdifferentiation dynamics

T cells are central to immune defense, yet existing molecular and phenotypic assays do not fully capture a cells intrinsic immune potential. Here we show that a single physical property, buoyant mass, reveals hidden heterogeneity within phenotypically similar, resting CD8+ T cells. Using suspended microchannel resonator measurements, we identify two distinct populations: "light" cells, enriched for mitochondrial content but prone to delayed activation and exhaustion, and "heavy" cells, biosynthetically poised for proliferation and memory formation. In patients with melanoma receiving immune checkpoint blockade, pre-treatment buoyant mass profiling of circulating T cells predicted therapeutic response with an accuracy comparable with standard tumor-derived biomarkers. Our findings establish buoyant mass as a label-free, stimulation-independent measure of systemic T cell fitness, providing a rapid and broadly applicable framework for immune profiling and response prediction in cancer and beyond.

biophysics↗

bioRxiv2024

Naturally occurring variation in a cytochrome P450 modifies thiabendazole responses independent of beta-tubulin

Widespread anthelmintic resistance has complicated the management of parasitic nematodes. Resistance to the benzimidazole (BZ) drug class is nearly ubiquitous in many species and is associated with mutations in beta-tubulin genes. However, mutations in beta-tubulin alone do not fully explain all BZ resistance. We performed a genome-wide association study using a genetically diverse panel of Caenorhabditis elegans strains to identify loci that contribute to resistance to the BZ drug thiabendazole (TBZ). We identified a quantitative trait locus (QTL) on chromosome V independent of all beta-tubulin genes and overlapping with two promising candidate genes, the cytochrome P450 gene cyp-35d1 and the nuclear hormone receptor nhr-176, identified by another mapping technique. Both genes were previously demonstrated to play a role in TBZ metabolism. NHR-176 binds TBZ and induces the expression of CYP-35D1, which metabolizes TBZ. We generated single gene deletions of nhr-176 and cyp-35d1 and found that both genes play a role in TBZ response. A predicted high-impact lysine-to-glutamate substitution at position 267 (K267E) in CYP-35D1 was identified in a sensitive parental strain, and reciprocal allele replacement strains in both genetic backgrounds were used to show that the lysine allele conferred increased TBZ resistance. Using competitive fitness assays, we found that neither allele is deleterious, but the lysine allele is selected in the presence of TBZ. Additionally, we found that the lysine allele significantly increased the rate of TBZ metabolism compared to the glutamate allele. Moreover, yeast expression assays showed that the lysine version of CYP-35D1 had twice the enzymatic activity of the glutamate allele. To connect our results to parasitic nematodes, we analyzed four Haemonchus contortus cytochrome P450 orthologs but did not find variation at the 267 position in fenbendazole-resistant populations. Overall, we confirmed that variation in this cytochrome P450 gene is the first locus independent of beta-tubulin to play a role in BZ resistance. Author SummaryBenzimidazoles (BZs) are the most common drug class used to control parasitic nematodes, but because of overuse, resistance is widespread. The known genetic causes of BZ resistance are associated with mutations in beta-tubulin and are the most well understood of any anthelmintic class. However, BZ response varies significantly and differential levels of resistance likely require mutations in genes independent of beta-tubulin. We used the free-living model nematode Caenorhabditis elegans to identify and characterize a novel cytochrome P450 gene, cyp-35d1, associated with natural resistance to the BZ drug thiabendazole (TBZ). We demonstrated that a lysine at position 267 confers TBZ resistance and is selected over multiple generations after TBZ treatment. This allele significantly increased the rate of TBZ metabolism in both C. elegans and yeast. In conclusion, we have characterized the role of variation in a cytochrome P450 that contributes to TBZ resistance, independent of mutations in beta-tubulin.

genetics↗

bioRxiv2024

Identification of the orphan GPR25 as a receptor of the chemokine CXCL17

C-X-C motif chemokine ligand 17 (CXCL17) is a small secretory protein primarily expressed in mucosal tissues and likely functions as a chemoattractant, but its receptor is still controversial. In the present study, we identified the rarely studied orphan G protein-coupled receptor 25 (GPR25) as a receptor of CXCL17 via prediction by the newly developed AlphaFold 3 algorithm and validation by the NanoBiT-based {beta}-arrestin recruitment assay. In the {beta}-arrestin recruitment assay, recombinant human CXCL17 could activate human GPR25 in transfected human embryonic kidney (HEK) 293T cells with an EC50 value around 100 nM, but it had no activation effect on 17 other tested G protein-coupled receptors (GPCRs). Deletion of three conserved C-terminal residues of human CXCL17 almost abolished its activity, and alanine replacement of W95 or R178 of human GPR25, two conserved residues in the predicted orthosteric ligand binding pocket, almost abolished its response towards CXCL17. These results are consistent with the AlphaFold 3-predicted binding model in which the highly conserved C-terminal fragment of CXCL17 inserts into the orthosteric ligand binding pocket of the receptor GPR25. According to the expression pattern of CXCL17 and GPR25 shown at the Human Protein Atlas, CXCL17 might be an endogenous agonist of GPR25 in human and other mammals, but this hypothesis needs to be tested in future studies via more assays. The present deorphanization paves the way for further functional characterization of the orphan receptor GPR25 and the orphan ligand CXCL17.

biochemistry↗

bioRxiv2024

Human iPSC-derived brain pericytes exhibit differences in inflammatory activation compared to primary human brain pericytes

BackgroundiPSC-derived cells are increasingly used to model complex diseases in vitro because they can be patient derived and can differentiate into any cell in the adult human body. Recent studies have demonstrated the generation of brain pericytes using a neural crest-based differentiation protocol. However, the inflammatory response of these iPSC-derived brain pericytes has not been investigated. We aimed to investigate the response of iPSC-derived brain pericytes to common inflammatory stimuli, thereby assessing the suitability of these cells to study inflammatory disease. MethodsBrain pericytes were differentiated from iPSCs for 42 days. The expression of brain pericyte markers was assessed by RT-qPCR and immunofluorescent staining at days 0, 15, 21, and 42 of differentiation to validate the brain pericyte-like phenotype. Nuclear localisation of NF{kappa}B and STAT1 was assessed by immunofluorescence following IL-1{beta}- and TNF-treatment in day 21 and day 42 iPSC-derived pericytes, and primary human pericytes. Cytometric bead array assessed the concentration of secreted inflammatory factors in the cell medium and phagocytosis was investigated using fluorescent carboxylated beads and flow cytometry. ResultsAt day 42 of differentiation, but not at day 21, cells expressed brain pericyte markers. Generally, iPSC-derived pericytes lacked consistent responses to inflammatory treatment compared to primary human pericytes. Day 21 and 42 iPSC-derived pericytes exhibited a NF{kappa}B response to IL-1{beta} treatment comparable to primary human pericytes. Day 21 iPSC-derived pericytes exhibited a STAT1 response with IL-1{beta} treatment which was absent in day 42 cells, but present in a subset of primary human pericytes. TNF treatment presented similar NF{kappa}B responses between day 21 and 42 iPSC-derived and primary human pericytes, but a STAT1 response was again present in a subset of primary human pericytes which was absent in both day 21 and day 42 iPSC-derived pericytes. Numerous differences were observed in the secretion of cytokines and chemokines following treatment of iPSC-derived and primary human pericytes with IL-1{beta} and TNF. iPSC-derived pericytes exhibited greater rates of phagocytosis than primary human pericytes. ConclusionsWith the increase in iPSC-derived cells in research, labs should undertake validation of lineage specificity when adapting an iPSC-derived differentiation protocol. In our hands, the inflammatory response of iPSC-derived pericytes was different to that of primary human pericytes, raising concern regarding the use of iPSC-derived pericytes to study neuroinflammatory disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/613375v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1e3612eorg.highwire.dtl.DTLVardef@1014537org.highwire.dtl.DTLVardef@6729adorg.highwire.dtl.DTLVardef@e14825_HPS_FORMAT_FIGEXP M_FIG C_FIG Brain pericytes can be generated from iPSCs. The work presented here shows the generation of phenotypically distinct pericytes from the original protocol, demonstrating the significant variability present within some iPSC differentiation protocols. Furthermore, functional differences are demonstrated between iPSC-derived brain pericytes and primary brain pericytes, revealing limitations in the use of iPSC-derived brain pericytes to model brain pericyte biology. Key PointsO_ST_ABSWhat is already known about this topic?C_ST_ABSBrain pericyte-like cells can be generated from induced pluripotent stem cells, however their responses to inflammatory stimuli has not been assessed. What does this study add?iPSC-derived brain pericytes exhibit different inflammatory responses compared to primary brain pericytes, showing that some iPSC-derived cell models are not appropriate for modelling all aspects of a cells biology. Furthermore, the iPSC-derived pericytes generated here were markedly different to those generated from the original article. It is therefore important for each lab to optimise the generation of iPSC-derived cell in their own hands to account for potential inter-lab variability.

cell biology↗

bioRxiv2024

Screening activity of brain cancer-derived factors on primary human brain pericytes

Brain cancers offer poor prognoses to patients accompanied by symptoms that drastically impact the patient and their family. Brain tumours recruit local non-transformed cells to provide trophic support and immunosuppression within the tumour microenvironment, supporting tumour progression. Given the localization and supportive role of pericytes at the brain vasculature, we explored the potential for brain pericytes to contribute to the brain cancer microenvironment. To investigate this, primary brain pericytes were treated with factors commonly upregulated in brain cancers. Changes to brain pericyte cell signalling, inflammatory secretion, and phagocytosis were investigated. The TGF{beta} superfamily cytokines TGF{beta} and GDF-15 activated SMAD2/3 and inhibited C/EBP-{delta}, revealing a potential mechanism behind the pleiotropic action of TGF{beta} on brain pericytes. IL-17 induced secretion of IL-6 without activating NF{kappa}B, STAT1, SMAD2/3, or C/EBP-{delta} signalling pathways. IL-27 and IFN{gamma} induced STAT1 signalling and significantly reduced pericyte phagocytosis. The remaining brain cancer-derived factors did not induce a measured response, indicating that these factors may act on other cell types or require co-stimulation with other factors to produce significant effects. Together, these findings show potential mechanisms by which brain pericytes contribute to aspects of inflammation and starts to uncover the supportive role brain pericytes may play in brain cancers.

cancer biology↗

bioRxiv2024

Unveiling multi-scale architectural features in single-cell Hi-C data using scCAFE

Single-cell Hi-C (scHi-C) has provided unprecedented insights into the heterogeneity of 3D genome organization. However, its sparse and noisy nature poses challenges for computational analyses, such as chromatin architectural feature identification. Here, we introduce scCAFE, a deep learning model for the multi-scale detection of architectural features at the single-cell level. scCAFE provides a unified framework for annotating chromatin loops, TAD-like domains (TLDs), and compartments across individual cells. Our model outperforms previous scHi-C loop calling methods and delivers accurate predictions of TLDs and compartments that are biologically consistent with previous studies. The resulting single-cell annotations also offer a measure to characterize the heterogeneity of different levels of architectural features across cell types. We leverage this heterogeneity and identify a series of marker loop anchors, which demonstrate the potential of the 3D genome data to annotate cell identities without the aid of simultaneously sequenced omics data. Overall, scCAFE not only serves as a useful tool for analyzing single-cell genomic architecture, but also paves the way for precise cell-type annotations solely based on 3D genome features.

bioinformatics↗

bioRxiv2024

Divergent response to radio-immunotherapy is defined by intrinsic features of the tumor microenvironment

BackgroundTreatment with immunotherapy can elicit varying responses across cancer types, and the mechanistic underpinnings that contribute to response vs. progression remain poorly understood. However, to date there are few preclinical models that accurately represent these disparate disease scenarios. MethodsUsing combinatorial radio-immunotherapy consisting of PD-1 blockade, IL2R{beta}{gamma} biased signaling, and OX40 agonism we were able to generate preclinical tumor models with conflicting responses, where head and neck squamous cell carcinoma (HNSCC) models responds and pancreatic ductal adenocarcinoma (PDAC) progresses. ResultsBy modeling these disparate states, we find that regulatory T cells (Tregs) are expanded in PDAC tumors undergoing treatment, constraining tumor reactive CD8 T cell activity. Consequently, the depletion of Tregs restores the therapeutic efficacy of our treatment and abrogates the disparity between models. Moreover, we show that through heterotopic implantations that the site of tumor development defines the response to therapy, as implantation of HNSCC tumors into the pancreas resulted in comparable levels of tumor progression. ConclusionsThis work highlights complexity of combining immunotherapies within the tumor microenvironment and further defines the immune and non-immune components of the tumor microenvironment as an intrinsic feature of immune suppression. What is already known on this topicO_LIIn Head and neck squamous cell carcinomas (HNSCC) and pancreatic ductal adenocarcinoma (PDAC), targeting PD-1 and IL2R{beta}{gamma} simultaneously (PD1-IL2v) has been shown to be effective when combined with radiation therapy (RT), yet complete response is still limited. The T cell co-stimulatory receptor OX40 (TNFRSF4) has pleiotropic effects, promoting T cell survival, expansion, and memory differentiation in conventional effector T cells, while subsequently limiting regulatory T cell (Treg) suppression by constraining induction and expression of Foxp3. Expression of OX40 is highly upregulated after treatment with PD1-IL2v, and we postulated that combining OX40 agonism with PD1-IL2v and RT would provide additional benefit. C_LI What this study addsO_LIUsing orthotopic models of HNSCC and PDAC, we found that the addition of OX40 agonism unexpectedly drives tumor progression in PDAC, but not HNSCC. Intriguingly, this effect dependent on the tumor microenvironment as the effect is reversed by swapping the location of tumor implantation. This progression was also abrogated by the depletion of regulatory T cells (Tregs), a known mediator of resistance in these models. C_LI How this study might affect research, practice or policyO_LIOur data demonstrate that unexpected and deleterious effects can stem from combining multiple immunotherapies. These findings hold particular translational relevance as the use of combination immunotherapies is increasingly common on trial. C_LI

immunology↗

bioRxiv2024

Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences

Proteins including transcription factors (TFs) and regulating enzymes search DNA for specific sites by alternating 3D diffusion in cell nucleus space and 1D diffusion on DNA. The search dynamics and free energy landscape of the protein along DNA depend essentially on the protein-DNA interactions, which simultaneously determine the protein-DNA association strength and relative population profiling along DNA, e.g., measured from protein binding microarray (PBM) to genome-wide mapping. Here we present a minimal structure-based model of protein diffusional search along DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along DNA can be physically derived to be consistent with experimental measurements. We also show that the sequence-dependent protein sliding or stepping patterns along DNA are regulated by collective interfacial HB dynamics, which also determines the ruggedness of the 1D diffusion free energy landscape. In comparison, protein association or binding with DNA are generically dictated by the protein-DNA electrostatic interactions, with an interaction zone of nanometers around DNA. Extra degrees of freedom (DOFs) of the protein such as rotations and conformational fluctuations can be well accommodated within the electrostatic interaction zone. As such we demonstrate that the protein binding or association free energy profiling along DNA smoothens over the 1D diffusion free energy landscape, which leads to population variations for an order of magnitude upon a marginal free energetic smoothening around the specific or consensus sites. We further show that the protein unbinding or dissociation from a comparatively high-binding affinity DNA site is dominated by lateral diffusion to the flanking low-affinity sites. The results suggest that experimental characterizations on the relative protein-DNA binding affinities or population profiling on the DNA are systematically and physically impacted by the extra DOFs of protein motions aside from translation as well as from flanking DNA sequences due to protein 1D diffusion and non-specific binding/unbinding.

biophysics↗