Biology subjects

Gloss, B.

Publications and source records attributed to Gloss, B..

6 recordsLinked to original sources

bioRxiv2026

Single-cell multi-omics maps clonal IEL expansion and epithelial remodelling in refractory coeliac disease

Background Refractory coeliac disease type 1 (RCD1) lacks defining molecular markers, and the immune and epithelial mechanisms sustaining intestinal injury remain poorly understood. Objective To define the clonal immune and epithelial states that distinguish RCD1 from active coeliac disease (ACD) and determine their spatial organisation in the duodenal mucosa. Design We integrated single-cell RNA sequencing, CITE-seq surface proteomics and paired T-cell receptor sequencing of duodenal immune and epithelial compartments from Healthy controls (n = 6), ACD (n = 7), RCD1 (n = 9) and RCD2 (n = 2), with spatial transcriptomics in a subset of biopsies. Results RCD1 showed widespread TCR{beta} and TCR{gamma}{delta} clonal expansion across multiple IEL states, extending beyond previously defined mutation-bearing aberrant clones. Distinct IEL populations converged on a shared programme of adaptive persistence, innate-like signalling, metabolic fitness and cytoskeletal remodelling; GZMK expression marked both clonally expanded and non-clonal disease-associated states. In parallel, RCD1 epithelium showed loss of mature absorptive cell states and expansion of stress-associated, immune-interacting and regenerative programmes. Transit-amplifying cells acquired differentiation and tissue-remodelling signatures, while enteroendocrine cells expanded and developed a sensory-neurosecretory programme involving TRPA1, TRPV1, vesicle trafficking and NEUROD1 regulon activity. Spatial transcriptomics localised regenerative and enteroendocrine-associated epithelial programmes adjacent to immune-visible epithelial regions and KLRK1/GZMK-expressing IEL-rich niches in refractory tissue. Conclusion RCD1 represents a distinct mucosal state characterised by coordinated clonal IEL adaptation and epithelial remodelling, rather than simple amplification of ACD, providing a cellular framework for persistent tissue injury and disease stratification.

immunology↗

bioRxiv2025

Spatially resolved transcriptomics reveals a unique disease signature and potential biomarkers for chronic traumatic encephalopathy

Chronic traumatic encephalopathy (CTE) is a poorly understood environmental tauopathy uniquely associated with repetitive head injury. It is clinically ambiguous, and at present can only be diagnosed post-mortem. There is a pressing need to understand CTE pathophysiology in order to identify targets for possible intervention and biomarkers for in-life diagnosis, however molecular characterisation of the disease is hampered by the stochastic distribution of CTE lesions. Here we have taken advantage of Visium spatial transcriptomics to map gene expression in discrete CTE lesions and matched normal tissue from the same individuals. In doing so we derived a common 21-gene "signature" of CTE lesions that highlights astrocytic activation, neuroinflammation, blood-brain barrier function, and extracellular matrix remodeling as key in situ features of CTE lesions. Almost all CTE signature genes were strongly expressed in astrocytes, and ontological and protein association analyses implicated extracellular matrix functions as drivers of the disease. These findings provide the first glimpse into the intricate molecular dynamics underlying CTE lesions in situ, and present 21 candidate molecules for the development of in-life CTE diagnostics.

neuroscience↗

bioRxiv2023

The immunosuppressive Tuberculosis-associated microenvironment inhibits viral replication and promotes HIV-1 latency in CD4+ T cells

Author SummaryMycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is the most common coinfection among people living with HIV-1. This coinfection alters the efficacy of the immune response against both HIV-1 and Mtb, and is associated with accelerated HIV-1 disease progression and reduced survival. Enhanced HIV-1 replication in macrophages induced by Mtb coinfection may contribute to the worsened clinical outcomes observed in HIV-1/TB coinfected individuals. However, the impact of the HIV-1/TB coinfection on HIV-1 replication and latency in CD4+ T cells remains poorly studied. In this study, we used the acellular fraction of tuberculous pleural effusion (TB-PE) as a proxy for the microenvironment generated by Mtb infection. Using this physiologically relevant fluid, we investigated whether viral replication and HIV-1 latency in CD4+ T cells are affected by a TB-associated microenvironment. Interestingly, our results revealed that TB-PE shaped the transcriptional profile of CD4+ T cells impairing T cell receptor-dependent cell activation and decreased HIV-1 replication. Moreover, this immunosuppressive TB microenvironment promoted viral latency and inhibited HIV-1 reactivation in CD4+ T cells from people living with HIV-1. This study indicates that the immune response induced by TB may contribute to the persistence of the viral reservoir by silencing HIV-1 expression in individuals coinfected with both pathogens, allowing the virus to persist undetected by the immune system and increasing the size of the HIV-1 latent reservoir in cells at the site of the coinfection.

pathology↗

bioRxiv2023

Systematic comparison of high throughput Single-Cell RNA-Seq platforms in complex tissues

Single-cell transcriptomics has emerged as the preferred tool to define cell identity through the analysis of gene expression signatures. However, there are limited studies that have comprehensively compared the performance of different scRNAseq systems in complex tissues. Here, we present a systematic comparison of two well-established high throughput 3-scRNAseq platforms: 10x Chromium and BD Rhapsody, using tumours that present high cell diversity. Our experimental design includes both fresh and artificially damaged samples from the same tumours, which also provides a comparable dataset to examine their performance under challenging conditions. The performance metrics used in this study consist of gene sensitivity, mitochondrial content, reproducibility, clustering capabilities, cell type representation and ambient RNA contamination. These analyses showed that BD Rhapsody and 10x Chromium have similar gene sensitivity, while BD Rhapsody has the highest mitochondrial content. Interestingly, we found cell type detection biases between platforms, including a lower proportion of endothelial and myofibroblast cells in BD Rhapsody and lower gene sensitivity in granulocytes for 10x Chromium. Moreover, the source of the ambient noise was different between plate-based and droplet-based platforms. In conclusion, our reported platform differential performance should be considered for the selection of the scRNAseq method during the study experimental designs.

genomics↗

bioRxiv2022

Human genomic DNA is widely interspersed with i-motif structures

DNA i-motif structures are formed in the nucleus of human cells and are believed to provide critical genomic regulation. While the existence of i-motif structures in human cells has been demonstrated by immunofluorescent staining and by characterisation of select model genes, the abundance and distribution of such structures in the human genome has remained unclear. Here we utilize high affinity i-motif immunoprecipitation followed by sequencing to map i-motifs in human genomic DNA. Validated by biolayer interferometry and circular dichroism spectroscopy, our approach identified over 650,000 i-motif structures in human genomic DNA. The i-motif structures are widely distributed throughout the human genome and are common among highly expressed genes and in genes upregulated in G0/G1 cell cycle phase. Our findings provide experimental evidence for the widespread formation of i-motif structures in human genomic DNA.

genetics↗

bioRxiv2017

CA2 Neuronal Activity Controls Hippocampal Oscillations and Social Behavior

Hippocampal oscillations arise from coordinated activity among distinct populations of neurons and are associated with cognitive functions and behaviors. Although much progress has been made toward identifying the relative contribution of specific neuronal populations in hippocampal oscillations, far less is known about the role of hippocampal area CA2, which is thought to support social aspects of episodic memory. Furthermore, the little existing evidence on the role of CA2 in oscillations has led to conflicting conclusions. Therefore, we sought to identify the specific contribution of CA2 pyramidal neurons to brain oscillations using a controlled experimental system. We used excitatory and inhibitory DREADDs in transgenic mice to acutely and reversibly manipulate CA2 pyramidal cell activity. Here, we report on the role of CA2 in hippocampal-prefrontal cortical network oscillations and social behavior. We found that excitation or inhibition of CA2 pyramidal cells bidirectionally regulated hippocampal and prefrontal cortical low gamma oscillations and inversely modulated hippocampal ripple oscillations. Further, CA2 inhibition impaired social approach behavior. These findings support a role for CA2 in low gamma generation and ripple modulation within the hippocampus and underscore the importance of CA2 neuronal activity in extrahippocampal oscillations and social behavior.

neuroscience↗