Biology subjects

Cope, A.

Publications and source records attributed to Cope, A..

7 recordsLinked to original sources

bioRxiv2026

Persistent circulating autoreactive PD1⁺TIGIT⁺ peripheral helper T cells reflect synovial lymphoid activity and poor response to conventional disease-modifying anti-rheumatic drugs in early rheumatoid arthritis

ObjectiveIn the first year after onset of the autoimmune disease RA (RA), 40-60% do not achieve remission on conventional synthetic disease-modifying anti-rheumatic drugs (csDMARDs). To understand how autoreactive T cells may contribute to unstable or non-remission, we studied CD4+ T cells, including those recognising citrullinated (Cit) vimentin in participants with RA. MethodsTwo cohorts of drug-naive new-onset participants with RA were treated with csDMARDs. Disease activity score (DAS28-CRP) and peripheral blood (PB) mononuclear cells were collected longitudinally. In HLA-DR-shared epitope+ cohort 1 (n=21), T cells were assessed with a 17-marker spectral flow panel, incorporating HLA-DRB1*04:01/01:01- VimentinCit6459-71 or HLA-DRB1*04:04-VimentinCit7166-78 tetramers. Changes in T cell subsets over time were assessed in remitting and non-remitting participants using a generalized linear mixed model with a negative binomial distribution. In cohort 2 (n=26), the transcriptome of disaggregated synovial tissue (ST) and PB CD4+ T cells were analysed at baseline, and ST biopsy spatial proteomics at baseline and 6 months. ResultsCD4CXCR5-PD1+ peripheral helper T cells (Tph), including Cit-vimentin-reactive Tph, CD4CCR7+CXCR5-PD1+ stem-like Tph and TIGIT+PD1+ Tph were increased with moderate/high DAS28-CRP at any time point. Remission outcome was associated with low CD4 follicular helper T cell (Tfh) and Cit-vimentin-reactive Tfh. In non-remitting participants, Tph/fh infiltrated germinal-centre-like ST aggregates. This decreased in remission. Circulating TIGIT+ Tph genes reflected B lymphoid activation and lymph node egress, while in ST they reflected local differentiation. ConclusionPersistently high circulating TIGIT+ Tph and Tfh, including Cit-vimentin specificities, reflecting antigen-presenting B-cell interactions, are associated with reduced response to csDMARDs in recent-onset RA. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LITph and Tfh cells interacting with B cells are implicated in active ACPA+ RA C_LIO_LICitrullinated (Cit)-vimentin is an important neutrophil extracellular trap-derived target of ACPA C_LI What this study addsO_LIHigh circulating TIGIT+ Tph, Cit-vimentin-autoreactive Tph and Tfh associate with failure to reach remission on conventional synthetic DMARDs within the first year in early HLA-DR shared-epitope+ RA C_LIO_LITph/Tfh and adjacent regulatory T cells surround follicular B-cells in lymphoid aggregates in synovial tissue in non-remission C_LIO_LICirculating TIGIT+ Tph bear a transcriptional signature of lymphoid tissue expansion and lymph node egress as compared to functional differentiation and antigen experience in synovial tissue C_LI How this study might affect research, practice or policyO_LIWhen a remission target is not achieved in HLA-DR shared-epitope+ RA patients during the first year of treatment, high circulating TIGIT+ Tph implicate autoreactive T-B-lymphoid expansion in synovial tissue. C_LI

immunology↗

bioRxiv2025

PTPN22 Regulates T Cell Synapse Formation through PSTPIP1-Dependent Actin Remodeling

Protein tyrosine phosphatase non-receptor type 22 (PTPN22) is a critical regulator of T cell signaling, working in concert with C-terminal SRC kinase (Csk) to dephosphorylate key signaling proteins and suppress lymphocyte activation. The R620W variant of PTPN22, one of the most prevalent mutations associated with autoimmune diseases, has been implicated in altered T cell responses, although its broader effects on T cell activation are not fully understood. Recent studies have uncovered a novel interaction between PTPN22 and proline-serine-threonine phosphatase interacting protein 1 (PSTPIP-1), a cytoskeletal adaptor protein involved in F-actin remodeling. PSTPIP-1 recruits Wiskott-Aldrich Syndrome Protein (WASp) to facilitate actin foci formation, a process integral to stabilizing TCR microclusters and amplifying downstream signaling. Given that mutations in PSTPIP-1 impair actin remodeling and localize within the PTPN22 binding domain, we hypothesized that PTPN22 modulates actin dynamics through its interaction with PSTPIP-1. Using live and fixed multi-color super-resolution fluorescence imaging, we demonstrate that PTPN22 deficiency or inhibition of its phosphatase activity leads to aberrant Arp2/3-dependent actin remodeling and exaggerated calcium signaling, particularly under low- affinity TCR stimulation. Single-protein resolution imaging via DNA-PAINT further revealed disrupted nanoscale clustering of PSTPIP-1 and TCR in PTPN22-deficient T cells, uncovering a previously unrecognized PSTPIP-1-TCR interaction in the absence of PTPN22. These findings highlight a novel PTPN22-PSTPIP-1 signaling axis, offering new insights into the molecular mechanisms that may contribute to autoimmune disease susceptibility. One Sentence SummaryPTPN22 and PSTPIP-1 control actin remodeling upon T cell synapse formation, modulating TCR clustering and activation.

immunology↗

bioRxiv2021

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

Chemical modifications of RNA 5' ends enable "epitranscriptomic" regulation, influencing multiple aspects of RNA fate. In transcription initiation, a large inventory of substrates compete with nucleoside triphosphates (NTPs) for use as initiating entities, providing an ab initio mechanism for altering the RNA 5' end. In Escherichia coli cells, RNAs with a 5'-end hydroxyl are generated by use of dinucleotide RNAs as primers for transcription initiation, "primer-dependent initiation." Here we use massively systematic transcript end readout ("MASTER") to detect and quantify RNA 5' ends generated by primer-dependent initiation for ~410 (~1,000,000) promoter sequences in E. coli. The results show primer-dependent initiation in E. coli involves any of the 16 possible dinucleotide primers and depends on promoter sequences in, upstream, and downstream of the primer binding site. The results yield a consensus sequence for primer-dependent initiation, YTSS-2NTSS-1NTSSWTSS+1, where TSS is the transcription start site, NTSS-1NTSS is the primer binding site, Y is pyrimidine, and W is A or T. Biochemical and structure-determination studies show that the base pair (nontemplate-strand base:template-strand base) immediately upstream of the primer binding site (Y:RTSS-2, where R is purine) exerts its effect through the base on the DNA template strand (RTSS-2) through inter-chain base stacking with the RNA primer. Results from analysis of a large set of natural, chromosomally-encoded E. coli promoters support the conclusions from MASTER. Our findings provide a mechanistic and structural description of how TSS-region sequence hard-codes not only the TSS position, but also the potential for epitranscriptomic regulation through primer-dependent transcription initiation.

biochemistry↗

bioRxiv2021

Altered Sub-Genomic RNA Expression in SARS-CoV-2 B.1.1.7 Infections

SARS-CoV-2 lineage B.1.1.7 viruses are more transmissible, may lead to greater clinical severity, and result in modest reductions in antibody neutralization. subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome and is a crucial step in the SARS-CoV-2 life cycle. Applying our tool (periscope) to ARTIC Network Oxford Nanopore genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA expression profiles are significantly increased in B.1.1.7 infections (n=879). This increase is seen over the previous dominant circulating lineage in the UK, B.1.177 (n=943), which is independent of genomic reads, E gene cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median expression. We hypothesise that this is a direct consequence of a triple nucleotide mutation in nucleocapsid (28280:GAT>CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3 of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles in sequence data to evaluate emerging potential variants of concern. One Sentence SummaryThe recently emerged and more transmissible SARS-CoV-2 lineage B.1.1.7 shows greater subgenomic RNA expression in clinical infections and enhanced expression of a noncanonical subgenomic RNA near ORF9b.

genomics↗

bioRxiv2020

Cholesterol metabolism drives regulatory B cell function

Regulatory B cells restrict immune and inflammatory responses across a number of contexts. This capacity is mediated primarily through the production of IL-10. Here we demonstrate that the induction of a regulatory program in human B cells is dependent on a metabolic priming event driven by cholesterol metabolism. Synthesis of the metabolic intermediate geranylgeranyl pyrophosphate (GGPP) was required to specifically drive IL-10 production, and to attenuate Th1 responses. Furthermore, GGPP-dependent protein modifications controlled signaling through PI3K{delta}-AKT-GSK3, which in turn promoted BLIMP1-dependent IL-10 production. Inherited gene mutations in cholesterol metabolism result in a severe autoinflammatory syndrome, termed mevalonate kinase deficiency (MKD). Consistent with our findings, B cells from MKD patients induced poor IL-10 responses and were functionally impaired. Moreover, metabolic supplementation with GGPP was able to reverse this defect. Collectively, our data define cholesterol metabolism as an integral metabolic pathway for the optimal functioning of human IL-10 producing regulatory B cells. Graphical abstractMKD = Mevalonate kinase deficiency O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/893982v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@e23fd0org.highwire.dtl.DTLVardef@1cb9611org.highwire.dtl.DTLVardef@e9769corg.highwire.dtl.DTLVardef@16a1d0f_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2019

Differential nanoscale organisation of LFA-1 modulates T cell migration

Effector T-cells rely on integrins to drive adhesion and migration to facilitate their immune function. Heterodimeric transmembrane integrin LFA-1 (L{beta}2) regulates adhesion and migration through linkage of the extracellular matrix with the intracellular actin treadmill machinery. We quantitated the velocity and direction of F-actin flow in migrating T-cells alongside single molecule localisation of transmembrane and intracellular LFA-1. Our results show that retrograde actin flow positively correlated and immobile actin negatively correlated with T-cell velocity. Plasma membrane localised LFA-1 forms unique nano-clustering patterns in the leading edge, compared to the mid-focal zone, in migrating T-cells. Deleting the cytosolic phosphatase PTPN22, a negative regulator of integrin signaling, increased T-cell velocity, and leading-edge cluster co-localisation of pY397 FAK, pY416 Src family kinases and LFA-1. These data suggest that differential nanoclustering patterns of LFA-1 in migrating T-cells can instruct intracellular signalling linked with the actin treadmill. Our data presents a paradigm where T cells modulate the nanoscale organisation of adhesion and signalling molecules to fine tune their migration speed. This has implications for the regulation of immune and inflammatory responses.

immunology↗

bioRxiv2017

Basal Ganglia Control Of Reflexive Saccades: A Computational Model Integrating Physiology Anatomy And Behaviour

It is hypothesised that the basal ganglia play a key role in solving the problem of action selection. Here we investigate this hypothesis through computational modelling of the primate saccadic oculomotor system. This system is an excellent target for computational modelling because it is supported by a reasonably well understood functional anatomy, has limited degrees of freedom, and there is a wealth of behavioural and electrophysiological data for model comparison. Here, we describe a computational model of the reflexive saccadic oculomotor system incorporating the basal ganglia, key structures in motor control and competition between possible actions. To restrict the likelihood of overfitting the model it is structured and parameterised by the known anatomy and neurophysiology along with data from a single experimental behavioural paradigm, then validated by testing against several additional behavioural experimental data without modification of the parameters. With this model we reproduce a range of fundamental reflexive saccadic results both qualitatively and quantitatively, comprising: the distribution of saccadic latencies; the effect of eccentricity, luminance and fixation-target interactions on saccadic latencies; and the effect of competing targets on saccadic endpoint. By investigating the model dynamics we are able to provide mechanistic explanations for the sources of these behaviours. Further, because of its accesibility, the oculomotor system has also been used to study general principle of sensorimotor control. We interpret the ability of the basal ganglia to successfully control saccade selection in our model as further evidence for the action selection hypothesis.

neuroscience↗