Biology subjects

Parker, R.

Publications and source records attributed to Parker, R..

At least 19 recordsLinked to original sources

bioRxiv2026

m6A depletion attenuates the macrophage type I interferon response

Macrophages play an important role in coordinating the antiviral response and post-transcriptional regulation of mRNA is an important element of the inflammatory gene expression required for defense against viral pathogens. N6-methyladenosine (m6A) deposition on mRNA by METTL3 constitutes one such post-transcriptional event which facilitates a cascade of downstream regulation via RNA decay and translation. We discovered that in THP1-derived and peripheral blood macrophages, m6A depletion with the METTL3 inhibitor STM2457 leads to enhanced proliferation of the human coronavirus OC43. Using TimeLapse-seq to comprehensively measure changes in abundance, RNA decay and transcription, we find that STM2457 downregulates the interferon response far upstream by reducing expression of both the type I interferon receptor and STAT1. We conclude that macrophages depend on m6A to support expression of interferon sensing machinery and in m6As absence, fail to mount as strong of a type I interferon response.

immunology↗

bioRxiv2026

Analysis of dRIF Composition Identifies ZNF346 as a Regulator of PKR Activation

Mammalian dsRNA sensors coordinate an array of cellular responses upon detection of dsRNA including translation repression, RNA degradation and interferon induction. Cytoplasmic endogenous or exogenous dsRNA can condense into cytosolic ribonucleoprotein assemblies in mammalian cells, referred to as dsRNA-induced foci (dRIFs), which enrich some dsRNA sensors including OAS3 and PKR. However, the protein composition of dRIFs, and their impact on dsRNA response regulation, are not well-understood. To determine other components of dRIFs, we reconstituted dRIFs in in vitro and analyzed their composition by mass spectrometry. We identified, and validated, multiple new dRIF components including dsRNA binding proteins and canonical RNA binding proteins with roles in innate immunity, transcription regulation, and proteostasis. Moreover, we identify dRIFs forming during mitosis with altered composition. Functional interrogation of dRIFs identified DHX9 as a limiting factor for dRIF formation, and the dRIF resident protein ZNF346 as a modulator of PKR signaling.

cell biology↗

bioRxiv2026

Nuclear tau aggregates inhibit RNA export and form by secondary seeding from cytosolic tau aggregates.

Tau aggregates contribute to multiple neurodegenerative diseases including frontotemporal dementia and Alzheimers disease (AD). In models of tauopathy and in patient tissue, tau aggregates can form in the cytoplasm, perinuclear region, and nucleus. Using a HEK293T tau biosensor system, we identified that cytoplasmic tau aggregates formed first, followed by perinuclear-ring-like tau assemblies, and then nuclear tau aggregates formed in nuclear speckles. Nuclear tau aggregates only form in cells with pre-existing cytoplasmic tau aggregates and mostly form independently of cells traversing mitosis. Finally, nuclear tau aggregates do not contain exogenous tau seeds and arise by a secondary seeding event dependent on VCP. Nuclear tau aggregates inhibit mRNA export and show a twofold increase in poly-adenylated mRNAs in the nucleus. Together, these findings indicate that nuclear tau aggregation alters RNA biogenesis and occurs by a secondary seeding event from cytoplasmic tau aggregates, which could contribute to tau pathology.

neuroscience↗

bioRxiv2026

Coxsackievirus B Escapes Antiviral CD8⁺ T Cells but Triggers Robust CD4⁺ Memory Responses

Coxsackieviruses B (CVBs) are plausible triggers of the pancreatic islet autoimmunity leading to type 1 diabetes. Islet autoantibody seroconversion correlates with persistent CVB infections in the gut and pancreas, suggesting defective antiviral control and the need to define immune mechanisms at the intestinal entry site. We investigated how CVB3 modulates antigen presentation, the viral immunopeptidome of enterocytes and antigen-presenting cells, and downstream T-cell immunity. CVB3-infected enterocytes escaped immune recognition by downregulating HLA Class I and viral peptide presentation, impairing CD8+ T-cell responses in vitro. In CVB-seropositive individuals, circulating CVB-reactive CD8+ T cells were stalled in naive-like and exhausted effector/memory states. In contrast, CVB3 induced HLA class II upregulation, promoting robust CD4 T-cell activation. Circulating CVB3-reactive CD4 T cells fully differentiated into polyfunctional T helper memory. These findings indicate that CVB3 antiviral control is predominantly CD4 T-cell-mediated and provide a rationale for mucosal vaccination strategies and immune monitoring tools to follow infection or vaccination. TeaserCoxsackievirus evades CD8+ T-cell immunity in the gut, leaving CD4+ T cells as the main line of antiviral defense.

immunology↗

bioRxiv2026

NetMHCIIphosPan: a machine learning tool for predictingHLA class II antigen presentation of phosphorylated peptides.

Phosphorylated peptides presented by human leukocyte antigen (HLA) class II molecules play pivotal roles in immune regulation, yet their characterization and prediction remain challenging due to data noise and limited HLA coverage. Here, we introduce NetMHCIIphosPan, a prediction method for HLA-II antigen presentation of phosphorylated peptides, developed using mass spectrometry (MS)-based immunopeptidomics datasets. Employing a refined peptide identification workflow, we reanalyzed earlier HLA-II phospholigand datasets and trained predictive models, achieving superior performance compared to models trained on original data. Binding motif analysis revealed that HLA-specific preferences for phospholigands closely aligned with those of unmodified ligands. Incorporating unmodified ligands into training further enhanced predictive accuracy, particularly for HLA-DP and HLA-DQ molecules. NetMHCIIphosPan outperformed existing tools, such as NetMHCIIpan-4.3 and MixMHC2pred-1.3, for prediction of HLA antigen presentation of phosphorylated peptides demonstrating robustness and utility. This work establishes NetMHCIIphosPan as a state-of-the-art tool for understanding the HLA-II phospholigandome, with potential applications in immunotherapy and vaccine design.

bioinformatics↗

bioRxiv2025

Base Composition Influences the Position andPrecision of RNA Polymerase II Disassociation inBasal and Perturbed Conditions.

RNA Polymerase II (Pol II) transcribes all protein-coding and many non-protein coding genes in the genome. Pol II transcription termination is crucial for mRNA maturation and, when disrupted, can lead to altered mRNA processing and mRNA export. Termination involves two intertwined processes: pre-mRNA cleavage and Pol II release from the DNA (disassociation). Despite its importance, the exact mechanisms underlying Pol II disassociation from the DNA remain poorly understood. Moreover, under certain cellular stress conditions, there is a partial failure of cleavage, leading to a shift of the position of disassociation further downstream, a phenomenon known as run-on transcription. We performed the first-ever systematic analysis of Pol II termination across cell types and species and provide novel insights into the mechanism of disassociation. Using a probabilistic mixture model to quantify Poll II dynamics across an entire gene body from nascent RNA sequencing data, we discovered that genes have two types of conserved regions near the disassociation site: one characterized by a T-rich region upstream of disassociation, and another characterized by a GC-rich region surrounding disassociation. Strikingly, the GC-rich disassociation regions have more accessible chromatin and higher levels of phospho-threonine 4 on the CTD of Pol II. Additionally, we find that upstream T-rich genes are preferentially affected by perturbations that alter disassociation, including heat-shock, viral infection, kinase inhibition, and arsenic treatment. Thus, our work has determined there are two types of Pol II disassociation regions, which are differentially affected by perturbation of cellular homeostasis.

genomics↗

bioRxiv2025

Impact of G-tract RNAs and the DHX36 helicase on stress granule composition and formation

Stress granules are RNA-protein condensates that form in response to an increase in untranslating mRNPs. Stress granules form by the condensation of mRNPs through a combination of protein-protein, protein-RNA, and RNA-RNA interactions. Several reports have suggested that G-rich RNA sequences capable of forming G-quadruplexes promote stress granule formation. Here, we provide three observations arguing that G-tracts capable of forming rG4s do not promote mRNAs partitioning into stress granules in human osteosarcoma cells. First, we observed no difference in the accumulation in stress granules of reporter mRNAs with and without G-tracts in their 3 UTRs. Second, in U-2 OS cell lines with reduced DHX36 expression, which is thought to unwind G-quadruplexes, the partitioning of endogenous mRNAs was independent of their predicted rG4-forming potential. Third, while mRNAs in stress granules initially appeared to have a higher probability of forming rG4s than bulk mRNAs, this effect disappeared when rG4 motif abundance was standardized by mRNA length. However, we observe that in a G3BP1/2 double knockout cell line, reducing DHX36 expression rescued stress granule-like foci formation. This indicates that DHX36 can limit stress granule formation, potentially by unwinding trans rG4s, or limiting other intermolecular RNA-RNA interactions that promote stress granule formation. Key Points- G-tract RNAs with quadruplex forming potential in an mRNA do not affect its partitioning into stress granules - mRNA partitioning to stress granules is dependent on mRNA length rather than rG4-forming potential - DHX36, a DEAH-box helicase that unwinds RNA G-quadruplexes, limits stress granule formation O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/659950v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@a24c58org.highwire.dtl.DTLVardef@1422ce9org.highwire.dtl.DTLVardef@1929677org.highwire.dtl.DTLVardef@d48fa6_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Polyserine-tau interactions modulate tau fibrilization

Tau aggregates are the defining feature of multiple neurodegenerative diseases and contribute to the pathology of disease. However, the molecules affecting tau aggregation in cells are unclear. We previously determined that polyserine-rich domain containing proteins enrich in tau aggregates, assemble into puncta that can serve as sites of tau aggregation, and exacerbate tau aggregation in cells and mice. Herein, we show that polyserine domains are sufficient to define assemblies as sites of tau aggregation, in part, through localization of tau seeds. Purified polyserine self-assembles and directly interacts with monomeric and fibrillar tau. Moreover, polyserine-tau assemblies recruit RNA, leading to faster rates of tau fibrillization in vitro. Using polyserine variants, we found that enrichment in tau aggregates and stimulation of tau aggregation are separable functions of polyserine domains, with polyserine self-assembly stimulating tau aggregation. Together, our results show that polyserine self-assembles and directly interacts with tau to form preferred sites of tau aggregation.

biochemistry↗

bioRxiv2024

Polyserine peptides are toxic and exacerbate tau pathology in mice

Polyserine domains mediate the association of nuclear RNA binding proteins with cytoplasmic tau aggregates that occurs across tauopathy models and patient samples. In cell lines, polyserine peptides co-localize with and promote formation of tau aggregates suggesting the cytoplasmic mislocalization of polyserine-containing proteins might contribute to human disease. Moreover, polyserine can be produced by repeat associated non-AUG translation in CAG repeat expansion diseases. However, whether polyserine expressed in a mammalian brain is toxic and/or can exacerbate tau pathology is unknown. Here, we used AAV9-mediated delivery to express a 42-repeat polyserine protein in wild-type and tau transgenic mouse models. We observe that polyserine expression has toxic effects in wild-type animals indicated by reduced weight, behavioral abnormalities and a striking loss of Purkinje cells. Moreover, in the presence of a pathogenic variant of human tau, polyserine exacerbates disease markers such as phosphorylated and insoluble tau levels and the seeding capacity of brain extracts. These findings demonstrate that polyserine domains can promote tau-mediated pathology in a mouse model and are consistent with the hypothesis that cytoplasmic mislocalization of polyserine containing proteins might contribute to the progression of human tauopathies.

neuroscience↗

bioRxiv2024

The molecular arsenal of the key coastal bioturbator Hediste diversicolor faced with changing oceans

The importance of infaunal bioturbators for the functioning of marine ecosystems cannot be overstated. Inhabitants of estuarine and coastal habitats are expected to show resilience to fluctuations in seawater temperature and pH, which adds complexity to our understanding of the effects of global change drivers. Further, stress responses may be propagated through chemical cues within and across species, which may amplify the costs of life and alter species interactions. Research into the molecular mechanisms underlying this resilience has been limited by a lack of annotated genomes and associated molecular tools. In this study, we present the first chromosome-level, annotated draft genome of the marine ragworm Hediste diversicolor, specifically mapping genes important for chemical communication, sensing and pH homeostasis. Using these resources, we then evaluate the transcriptomic and behavioural responses of two distinct populations -- one field-sampled from Portugal (Ria Formosa) and one laboratory-acclimated and -bred from the United Kingdom (Humber) -- to changes in seawater pH, temperature, and odour cues from a low pH-stressed predator. Both populations displayed adaptive responses to future oceanic conditions, with targeted acid-base regulation in the Ria Formosa population experiment, and broader changes in metabolism and growth genes in the Humber population experiment. Chemical cues from stressed fish predators induced genes related to Schreckstoff biosynthesis in ragworms. Additionally, under future ocean conditions including increased temperature, the Humber population exhibited signs of cellular stress and damage. Our findings using the new annotated genome offer novel insights into the molecular arsenal of acid-base regulation which aids in predicting the impacts of an increasingly acidified and unstable ocean, and to transfer this knowledge to investigate these mechanisms in species with less tolerance.

genomics↗

bioRxiv2024

IL-23 tunes inflammatory functions of human mucosal-associated invariant T (MAIT) cells

IL-23 signaling plays a key role in the pathogenesis of chronic inflammatory and infectious diseases, yet the cellular targets and signaling pathways affected by this cytokine remain poorly understood. We show that IL-23 receptors are expressed on the large majority of human MAIT, but not of conventional T cells. Protein and transcriptional profiling at the population and single cell level demonstrates that stimulation with IL-23 or the structurally related cytokine IL-12 drives distinct functional profiles, revealing a high level of plasticity of MAIT cells. IL-23, in particular, affects key molecules and pathways related to autoimmunity and cytotoxic functions. Integrated analysis of transcriptomic and chromatin accessibility, supported by CRISPR/Cas9 mediated deletion, shows that AP-1 transcription factors constitute a key regulatory node of the IL-23 pathway in MAIT cells. In conclusion, our findings indicate that MAIT cells are key mediators of IL-23 functions in immunity to infections and chronic inflammatory diseases.

immunology↗

bioRxiv2023

Shieldin and CST co-orchestrate DNA polymerase-dependent tailed-end joining reactions independently of 53BP1-governed repair pathway choice

53BP1 regulates DNA end-joining in lymphocytes, diversifying immune antigen receptors. This involves nucleosome-bound 53BP1 at DNA double-stranded breaks (DSBs) recruiting RIF1 and shieldin, a poorly understood DNA-binding complex. The 53BP1-RIF1-shieldin axis is pathological in BRCA1-mutated cancers, blocking homologous recombination (HR) and driving illegitimate non-homologous end-joining (NHEJ). However, how this axis regulates DNA end-joining and HR suppression remains unresolved. We investigated shieldin and its interplay with CST, a complex recently implicated in 53BP1-dependent activities. Immunophenotypically, mice lacking shieldin or CST are equivalent, with class-switch recombination co-reliant on both complexes. ATM-dependent DNA damage signalling underpins this cooperation, inducing physical interactions between these complexes that reveal shieldin as a DSB-responsive CST adaptor. Furthermore, DNA polymerase {zeta} functions downstream of shieldin, establishing DNA fill-in synthesis as the physiological function of shieldin-CST. Lastly, 53BP1 suppresses HR and promotes NHEJ in BRCA1-deficient mice and cells independently of shieldin. These findings showcase the resilience of the 53BP1 pathway, achieved through the collaboration of chromatin-bound 53BP1 complexes and DNA end-processing effector proteins.

molecular biology↗

bioRxiv2023

Human Heart Failure Alters Mitochondria and Fiber 3D Structure Triggering Metabolic Shifts

This study, utilizing SBF-SEM, reveals structural alterations in mitochondria and myofibrils in human heart failure (HF). Mitochondria in HF show changes in structure, while myofibrils exhibit increased cross-sectional area and branching. Metabolomic and lipidomic analyses indicate concomitant dysregulation in key pathways. The findings underscore the need for personalized treatments considering individualized structural changes in HF.

physiology↗

bioRxiv2023

Post-transcriptional control contributes to hypoxia induced tumorigenic phenotypes in macrophages

Macrophages are effector immune cells that experience substantial changes to oxygenation when transiting through tissues, especially when entering tumors or infected wounds. How the transition to hypoxia alters gene expression and macrophage effector function remains poorly understood, especially at the post-transcriptional level. Here we use TimeLapse-seq to measure how hypoxia modifies inflammatory activation of primary macrophages. Nucleoside recoding sequencing allowed us to derive steady-state transcript levels, degradation rates, and transcriptional synthesis rates from the same dataset. We find that inflammatory activation of macrophages is altered by hypoxia due to increased mRNA decay. Destabilized transcripts encode for proteins associated with phagocytosis and proteolysis of the extracellular matrix. Consistent with differential gene expression, we observed hypoxia alters the specificity of macrophage phagocytosis and reduces their invasion of extracellular matrix. Hypoxic gene expression bears similarity to tumorigenic macrophages in solid tumor biopsies suggesting post-transcriptional control contributes to the macrophage transition from tumoricidal to tumorigenic.

immunology↗

bioRxiv2023

Interferon-α promotes neo-antigen formation andpreferential HLA-B-restricted antigen presentation in pancreatic β-cells

Interferon (IFN)- is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but its effect on the repertoire of HLA Class I (HLA-I)-bound peptides presented by pancreatic {beta}-cells is unknown. Using immunopeptidomics, we characterized the peptide/HLA-I presentation in in-vitro resting and IFN--exposed {beta}-cells. IFN- increased HLA-I expression and peptide presentation, including neo-sequences derived from alternative mRNA splicing, post-translational modifications - notably glutathionylation - and protein cis-splicing. This antigenic landscape relied on processing by both the constitutive and immune proteasome. The resting {beta}-cell immunopeptidome was dominated by HLA-A-restricted ligands. However, IFN- only marginally upregulated HLA-A and largely favored HLA-B, translating into a major increase in HLA-B-restricted peptides and into an increased activation of HLA-B-restricted vs. HLA-A-restricted CD8+ T-cells. A preferential HLA-B hyper-expression was also observed in the islets of T1D vs. non-diabetic donors, and we identified islet-infiltrating CD8+ T-cells from T1D donors reactive to HLA-B-restricted granule peptides. Thus, the inflammatory milieu of insulitis may skew the autoimmune response toward epitopes presented by HLA-B, hence recruiting a distinct T-cell repertoire that may be relevant to T1D pathogenesis.

immunology↗

bioRxiv2022

Cytosolic condensates enriched in polyserine repeats are preferred sites of tau fiber propagation

Tau aggregates are a hallmark of multiple neurodegenerative diseases and can contain RNAs and RNA binding proteins, including SRRM2 and PNN. How these resident nuclear proteins mislocalize and their influence on the prion-like propagation of tau fibers remains unknown. We demonstrate that polyserine repeats in SRRM2 and PNN are necessary and sufficient for recruitment to tau aggregates. Moreover, we demonstrate tau fibers preferentially grow in association with endogenous cytoplasmic assemblies - mitotic interchromatin granules and cytoplasmic speckles - which contain SRRM2 and PNN. Polyserine undergoes self-assembly in vitro and in cells, where polyserine-assemblies are sites of tau fiber propagation. Modulating the levels of polyserine containing proteins results in a corresponding change in tau aggregation. These findings define a specific protein motif, and cellular condensates, that promote tau fiber propagation. As cytoplasmic speckles form in iPSC neurons under inflammatory or hyperosmolar stress, they may promote tau fiber propagation in various neurodegenerative diseases.

neuroscience↗

bioRxiv2022

Quantitative reconstitution of yeast RNA processing bodies

Many biomolecular condensates appear to form through liquid-liquid phase separation (LLPS). Individual condensate components can often undergo LLPS in vitro, capturing some features of the native structures. However, natural condensates contain dozens of components with different concentrations, dynamics, and contributions to compartment formation. Most biochemical reconstitutions of condensates have not benefitted from quantitative knowledge of these cellular features nor attempted to capture natural complexity. Here, we build on prior quantitative cellular studies to reconstitute yeast RNA processing bodies (P bodies) from purified components. Individually, five of the seven highly-concentrated P-body proteins form homotypic condensates at cellular protein and salt concentrations, using both structured domains and intrinsically disordered regions. Combining the seven proteins together at their cellular concentrations with RNA, yields phase separated droplets with partition coefficients and dynamics of most proteins in reasonable agreement with cellular values. The dynamics of most proteins in the reconstitution are also comparable to cellular values. RNA delays the maturation of proteins within, and promotes reversibility of, P bodies. Our ability to quantitatively recapitulate the composition and dynamics of a condensate from its most concentrated components suggests that simple interactions between these components carry much of the information that defines the physical properties of the cellular structure.

biophysics↗

bioRxiv2022

Identification of neoantigens in esophageal adenocarcinoma

Esophageal adenocarcinoma (EAC) has a relatively poor long-term survival and limited treatment options. Promising targets for immunotherapy are short peptide neoantigens containing tumor mutations, presented to cytotoxic T-cells by human leukocyte antigen molecules (HLA). Despite an association between putative neoantigen abundance and therapeutic response across cancers, immunogenic neoantigens are challenging to identify. Here we characterized the mutational and immunopeptidomic landscapes of tumors from a cohort of seven patients with EAC. We directly identified one HLA-I presented neoantigen from one patient, and report functional T-cell responses from a predicted HLA-II neoantigen in a second patient. The predicted class II neoantigen contains both HLA I and II binding motifs. Our exploratory observations are consistent with previous neoantigen studies in finding that neoantigens are rarely directly observed, and an identification success rate following prediction in the order of 10%. However, our identified putative neoantigen is capable of eliciting strong T-cell responses, emphasizing the need for improved strategies for neoantigen identification.

cancer biology↗