Biology subjects

Harding, J.

Publications and source records attributed to Harding, J..

7 recordsLinked to original sources

bioRxiv2026

Delusions Emerge from Generative Model Reorganisation rather than Faulty Inference: Insights from Hybrid Predictive Coding

Predictive coding has influenced many conceptual accounts of delusions, the bizarre and distressing beliefs that accompany a range of neuropsychiatric conditions. However, these explanations remain incomplete and have rarely been tested directly using formal modelling. Here, we present a formal account of delusional beliefs based on hybrid predictive coding, which sheds light on the computational mechanisms underpinning the core features of delusions: thematic recurrence and imperviousness to contradictory evidence. In simulation experiments, we demonstrate that a combination of contextually inadequate initialisation of beliefs and excessive certainty (a hallmark of psychosis), triggers a reorganisation of the generative model relating observed events to hidden causes. This reorganisation enables the maintenance of delusional beliefs that are thematically stable, internally consistent with external inputs, and impervious to contradictory evidence, all without an increase in prediction error. Overall, our results suggest that delusions may arise not from faulty inference, as previously argued, but as an adaptive consequence of generative models learned under atypical conditions. These findings provide mechanistic insights into the computations underpinning delusions and have important implications for a novel therapeutic strategy in terms of re-training generative models.

neuroscience↗

bioRxiv2025

A Novel Glia-immune humanized mouse model for investigation of HIV CNS infection and neuroinflammation.

Dysregulation in neuroimmune interactions drives pathology in diverse neurological disorders. However, human cell-based in vivo models are limited for clinically relevant mechanistic studies and drug testing. To address this, we developed a novel humanized mouse model integrating all four major types of human glia - astrocytes, oligodendrocyte precursor cells (OPCs), oligodendrocytes, and microglia - in the brain, alongside donor-matched human immune system in peripheral blood and lymphoid tissues. We applied this model to study HIV-associated neurocognitive disorders, which can persist in tissue reservoirs including in the brain despite viral suppression by antiretroviral therapy. These glia-immune humanized mice supported robust HIV-1 replication in the peripheral blood, lymphoid tissues, and the brain, and recapitulated the synapse loss observed in patients. Furthermore, HIV-infected mice exhibited heightened inflammation in both peripheral and brain tissues. Notably, OPCs and oligodendrocytes in HIV-infected brains adopted an immune activated phenotype, upregulating interferon-stimulated genes, highlighting understudied roles of oligodendroglia in HIV infection. RNA-sequencing of human glia identified the upregulation of inflammasome-associated genes and the downregulation of genes involved in transcriptional, epigenetic, and metabolic regulation. Overall, this model provides a powerful in vivo platform to investigate human neuroimmune interactions relevant to diverse neurological disorders, offering critical insights into HIV CNS infection, pathology, and potential therapeutic strategies targeting CNS reservoirs and neuroinflammatory pathways.

immunology↗

bioRxiv2024

The impact of wild-boar derived microbiota transplantation on piglet microbiota, metabolite profile and gut proinflammatory cytokine production differs from sow-derived microbiota

Colonization of co-evolved, species-specific microbes in early life plays a crucial role in gastrointestinal development and immune function. This study hypothesized modern pig production practices have resulted in the loss of co-evolved species and critical symbiotic host- microbe interactions. To test this, we reintroduced microbes from wild boars (WB) into conventional piglets to explore their colonization dynamics and effects on gut microbial communities, metabolite profiles, and immune responses. At postnatal day (PND) 21, 48 piglets were assigned to four treatment groups: 1) WB-derived mixed microbial community (MMC), 2) sow-derived MMC, 3) a combination of WB and sow MMC (Mix), or 4) Control (PBS). Post- transplantation analyses at PND 48 revealed distinct microbial communities in WB-inoculated piglets compared to Controls, with trends toward differentiation from Sow but not Mix groups. WB-derived microbes were more successful in colonizing piglets, particularly in the Mix group, where they competed with sow-derived microbes. WB group cecal digesta enriched with Lactobacillus helveticus, Lactobacillus mucosae, and Lactobacillus pontis. Cecal metabolite analysis showed that WB piglets were enriched in histamine, acetyl-ornithine, ornithine, citrulline, and other metabolites, with higher histamine levels linked to Lactobacillus abundance. WB piglets exhibited lower cecal IL-1{beta} and IL-6 levels compared to Controls and Sow groups, while the Mix group showed reduced IFN-{gamma}, IL-2, and IL-6 compared to the Sow group. No differences in weight gain, fecal scores, or plasma cytokines were observed, indicating no adverse effects. These findings support that missing WB microbes effectively colonize domestic piglets and may positively impact metabolite production and immune responses. ImportanceThis study addresses the growing concern over losing co-evolved, species-specific microbes in modern agricultural practices, particularly in pig production. The implementation of strict biosecurity measures and widespread antibiotic use in conventional farming systems may disrupt crucial host-microbe interactions that are essential for gastrointestinal development and immune function. Our research demonstrates that by reintroducing wild boar-derived microbes into domestic piglets, these co-evolved microbes can successfully colonize the gut, influence microbial community composition, and alter metabolite profiles and immune responses without causing adverse effects. These findings also suggest that these co-evolved microbes can fill an intestinal niche, positively impacting immune activation. This research lays the groundwork for future strategies to enhance livestock health and performance by restoring natural microbial populations that produce immune-modulating metabolites. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/623678v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@6ec5c2org.highwire.dtl.DTLVardef@79804corg.highwire.dtl.DTLVardef@d63016org.highwire.dtl.DTLVardef@1ef0010_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Rapamycin Enhances CAR-T Control of HIV Replication and Reservoir Elimination in vivo.

Chimeric Antigen Receptor (CAR) T cell therapy has emerged as a powerful immune therapy for various diseases. Our studies in humanized mice and non-human primates (NHPs) demonstrate that hematopoietic stem cell (HSCs) modified with anti-HIV CAR leads to lifelong engraftment and supply of functional anti-viral CAR-T cells, leading to significantly reduced viral rebound after ART withdrawal. However, T cell exhaustion, driven by chronic immune activation, remains a major challenge for the continuous efficacy of CAR-T therapy, necessitating additional measures to achieve functional cure. We recently showed that in vivo treatment with low dose rapamycin reduced chronic inflammation and improved anti-HIV T cell function in HIV-infected humanized mice. Here, we report that rapamycin significantly improved CAR-T cell function both in vitro and in vivo. In vitro treatment with rapamycin improved CAR-T cell mitochondria respiration and cytotoxicity. In vivo treatment with low-dose rapamycin in HIV-infected, CAR-HSC treated mice reduced chronic inflammation, prevented exhaustion of CAR-T cells and improved CAR-T control of viral replication compared to CAR-HSCs treatment alone. RNAseq analysis of sorted CAR-T cells from humanized mice showed that rapamycin significantly modified the CAR-T cell transcriptome, including the downregulation of multiple check point inhibitors and the upregulation of key genes related to cell survival. We also observed significantly delayed viral rebound after ART withdrawal and diminished HIV reservoir in mice that were treated with rapamycin and CAR-HSCs as compared to CAR-HSCs treatment alone. Taken together, our data indicate that HSCs-based anti-HIV CAR-T combined with rapamycin treatment is a promising approach for treating persistent inflammation and improving immune control of HIV replication.

immunology↗

bioRxiv2024

Role of the CTCF Binding Site in Human T-Cell Leukemia Virus-1 Pathogenesis

During HTLV-1 infection, the virus integrates into the host cell genome as a provirus with a single CCCTC binding protein (CTCF) binding site (vCTCF-BS), which acts as an insulator between transcriptionally active and inactive regions. Previous studies have shown that the vCTCF-BS is important for maintenance of chromatin structure, regulation of viral expression, and DNA and histone methylation. Here, we show that the vCTCF-BS also regulates viral infection and pathogenesis in vivo in a humanized (Hu) mouse model of adult T-cell leukemia/lymphoma. Three cell lines were used to initiate infection of the Hu-mice, i) HTLV-1-WT which carries an intact HTLV-1 provirus genome, ii) HTLV-1-CTCF, which contains a provirus with a mutated vCTCF-BS which abolishes CTCF binding, and a stop codon immediate upstream of the mutated vCTCF-BS which deletes the last 23 amino acids of p12, and iii) HTLV-1-p12stop that contains the intact vCTCF-BS, but retains the same stop codon in p12 as in the HTLV-1-CTCF cell line. Hu-mice were infected with mitomycin treated or irradiated HTLV-1 producing cell lines. There was a delay in pathogenicity when Hu-mice were infected with the CTCF virus compared to mice infected with either p12 stop or WT virus. Proviral load (PVL), spleen weights, and CD4 T cell counts were significantly lower in HTLV-1-CTCF infected mice compared to HTLV-1-p12stop infected mice. Furthermore, we found a direct correlation between the PVL in peripheral blood and death of HTLV-1-CTCF infected mice. In cell lines, we found that the vCTCF-BS regulates Tax expression in a time-dependent manner. The scRNAseq analysis of splenocytes from infected mice suggests that the vCTCF-BS plays an important role in activation and expansion of T lymphocytes in vivo. Overall, these findings indicate that the vCTCF-BS regulates Tax expression, proviral load, and HTLV pathogenicity in vivo. Author SummaryHuman T-cell leukemia virus type 1 (HTLV-1) is a cause of leukemia and lymphoma, and several inflammatory medical disorders. The virus integrates in the host cell DNA, and it includes a single binding site for a cellular protein designated CTCF. This protein is important in regulation of many viruses, as well as properties of normal and malignant cells. In order to define the role of CTCF in HTLV-1 pathogenesis in vivo, we analyzed a mutant virus lacking the binding site in humanized mice. We found that this mutation slowed virus spread and attenuated the development of disease. Gene expression studies demonstrated a dynamic role of CTCF in regulating viral gene expression and T lymphocyte activation.

microbiology↗

bioRxiv2024

Single-Cell Transcriptomic Analysis of Kaposi Sarcoma

Kaposi Sarcoma (KS) is a complex tumor caused by KS-associated herpesvirus 8 (KSHV). Histological analysis reveals a mixture of "spindle cells", vascular-like spaces, extravasated erythrocytes, and immune cells. In order to elucidate the infected and uninfected cell types in KS tumors, we examined skin and blood samples from twelve subjects by single cell RNA sequence analyses. Two populations of KSHV-infected cells were identified, one of which represented a proliferative fraction of lymphatic endothelial cells, and the second represented an angiogenic population of vascular endothelial tip cells. Both infected clusters contained cells expressing lytic and latent KSHV genes. Novel cellular biomarkers were identified in the KSHV infected cells, including the sodium channel SCN9A. The number of KSHV positive tumor cells was found to be in the 6% range in HIV-associated KS, correlated inversely with tumor-infiltrating immune cells, and was reduced in biopsies from HIV-negative individuals. T-cell receptor clones were expanded in KS tumors and blood, although in differing magnitudes. Changes in cellular composition in KS tumors were identified in subjects treated with antiretroviral therapy alone, or immunotherapy. These studies demonstrate the feasibility of single cell analyses to identify prognostic and predictive biomarkers. Author SummaryKaposi sarcoma (KS) is a malignancy caused by the KS-associated herpesvirus (KSHV) that causes skin lesions, and may also be found in lymph nodes, lungs, gastrointestinal tract, and other organs in immunosuppressed individuals more commonly than immunocompetent subjects. The current study examined gene expression in single cells from the tumor and blood of these subjects, and identified the characteristics of the complex mixtures of cells in the tumor. This method also identified differences in KSHV gene expression in different cell types and associated cellular genes expressed in KSHV infected cells. In addition, changes in the cellular composition could be elucidated with therapeutic interventions.

cancer biology↗

bioRxiv2019

Induction of long-term allogeneic cell acceptance and formation of immune privileged tissue in immunocompetent Hosts

A vast number of diseases could be treated with therapeutic cells derived from pluripotent stem cells (PSCs). However, cell products that come from non-autologous sources can be immune rejected by the recipients immune system. Here, we show that forced expression of eight immunomodulatory transgenes, including Ccl21, Pdl1, Fasl, Serpinb9, H2-M3, Cd47, Cd200, and Mfge8, allows mouse embryonic stem cells (mESCs) and their derivatives to escape immune rejection in fully immunocompetent, allogeneic recipients. Despite no genetic alterations to major histocompatibility complex (MHC) genes, immune-modified C57BL/6 mESCs could generate long-term, allogeneic tissues in inbred FVB/N, C3H, and BALB/c, as well as outbred CD-1 recipients. Due to the tandem incorporation of our safe-cell suicide system, which allows tight and drug-inducible control over proliferation in vivo, these allotolerated cells can generate safe and dormant ectopic tissues in the host. We show that these ectopic tissues maintain high expression of all eight immunomodulatory transgenes and are immune-privileged sites that can host and protect unmodified mouse and human cells from rejection in allogeneic and xenogeneic settings, respectively. If translated to human clinical settings, we envision the development of a single pluripotent cell line that can be used to generate allo-tolerated, off-the-shelf cell products to serve all humankind, as well as immune-privileged ectopic tissues to host and immune-protect any kind of therapeutic cell product.

bioengineering↗