Biology subjects

Lambie, N.

Publications and source records attributed to Lambie, N..

6 recordsLinked to original sources

bioRxiv2026

A microbiota-responsive polyfunctional cytotoxic CD4⁺ T-cell state promotes mucosal inflammation in ulcerative colitis

Ulcerative colitis (UC) is characterised by chronic colonic inflammation with marked heterogeneity in disease severity and therapeutic outcomes. Here, we define a spatially organised, polyfunctional cytotoxic CD4 T-cell state associated with mucosal inflammation and adverse therapeutic outcomes in UC. Integrating ex vivo T-cell receptor stimulation with multi-cohort bulk and single-cell transcriptomics and multiparameter flow cytometry, we show that GZMB CD4 T cells are preferentially enriched in inflamed UC mucosa, but not peripheral blood, and co-express cytotoxic molecules, Th1- and Th17-associated cytokines and chemokines, and immunoregulatory receptors. Single-cell analyses implicate inflammatory cytokine and antigen-presentation signals in the acquisition or maintenance of this state. High-resolution spatial profiling localised this programme predominantly to Th17 cells, which were preferentially enriched within multicellular inflammatory and tertiary lymphoid structure-associated niches. Across independent patient cohorts, a transcriptional signature derived from this state increased with endoscopic disease severity and was associated with reduced response to anti-TNF and anti-IL-12/23p40 therapies. Adoptive transfer of Gzma/Gzmb-deficient rather than wild-type CD4 T cells into Rag2-deficient recipient mice markedly attenuated experimental colitis and abrogated the polyfunctional cytokine phenotype, demonstrating that granzyme-dependent effector activity is a key mechanism driving CD4+ T-cell-mediated intestinal inflammation. Finally, human host-microbiome analysis linked this programme to intestinal dysbiosis, while transfer of dysbiotic microbiota promoted the emergence of a corresponding state in vivo. Collectively, these findings define a microbiota-responsive, spatially organised polyfunctional cytotoxic CD4 T-cell programme that contributes to intestinal inflammation and is associated with disease severity and treatment resistance in UC.

immunology↗

bioRxiv2026

A dysregulated stromal remodelling programme characterises prior anti-TNF failure in ulcerative colitis

Prior anti-tumour necrosis factor (TNF) failure is associated with reduced efficacy of subsequent advanced therapies in ulcerative colitis (UC), but the biological basis of this treatment-refractory state remains unclear. We integrated clinical outcomes and baseline colonic transcriptomic data from UC patients in the UNIFI phase III trial programme with regulatory and signalling network inference, connectivity mapping, and single-cell-resolution spatial transcriptomics. Colonic transcriptomic analyses identified coordinated enrichment of extracellular matrix organisation, collagen remodelling and integrin-associated programmes, increased stromal cell representation and elevated inferred MAPK/EGFR activity in UC patients with prior anti-TNF failure. Causal network inference prioritised MAPK3 as a candidate regulator of this state, while connectivity mapping identified MEK/EGFR inhibitors as candidate perturbagens. MEK inhibition suppressed stromal pathways and reduced inferred MAPK/EGFR activity ex vivo. Spatial profiling of active UC and non-IBD colonic tissues localised these programmes to UC-enriched stromal niches. Ligand-receptor inference further identified reciprocal stromal-myeloid communication within these niches. Collectively, these findings define a stromal remodelling programme associated with prior anti-TNF failure and nominate MAPK/EGFR signalling as a potentially tractable component of treatment-refractory UC.

systems biology↗

bioRxiv2026

Spatial transcriptomic analysis reveals coordinated gene expression in ovarian clear cell carcinoma and adjacent endometriosis in UK and Japanese patients

PurposeOvarian clear cell carcinoma (OCCC) is strongly associated with endometriosis and shows geographic variation in incidence. We investigated whether OCCC and adjacent endometriosis exhibit distinct transcriptional states and whether these patterns differ between United Kingdom (UK) and Japanese cohorts. Experimental DesignWe performed whole-transcriptome spatial profiling on specimens from 16 OCCC cases (8 UK, 8 Japan) in which tumor and endometriosis were both present. Gene expression was analyzed in tumor, endometriosis and stroma. ARID1A status was assessed by immunohistochemistry. ResultsMedian age was 59 years (range 26-82). 13/16 cases (81.3%) had early-stage disease. Tissue compartment rather than cohort of origin was the dominant source of variation across endometriosis and tumor regions. Endometriosis was enriched for inflammatory and immune-related pathways compared to tumor, whilst there was greater representation of chromatin and protein-DNA complex assembly pathways in tumor regions. These patterns were conserved across both cohorts and after stratification by ARID1A status. Mesenchymal-associated gene expression scores also significantly differed across stroma, endometriosis and tumor with clear compartmental separation. Cell type deconvolution analyses showed clear compositional differences between stromal and epithelial disease compartments. ConclusionsOCCC and coexisting endometriosis are transcriptionally distinct, with the dominant contrast being compartmental rather than geographic. ARID1A alone is unlikely to account for the principal spatial transcriptional states identified here. Further analyses will be required to ascertain whether these differences reflect genuine biological differences between OCCC and coexisting endometriosis or represent different stages of endometriosis-associated tumorigenesis. Translational RelevanceOvarian clear cell carcinoma often arises in association with endometriosis, yet the biological transition between these lesions remains poorly understood. Using spatial transcriptomics in matched tumor and adjacent endometriosis from Japanese and UK cohorts, we showed that endometriosis is characterized by inflammatory and antigen-presentation features, whereas tumor regions showed chromatin-organization and oncogenic transcriptional states. These patterns were largely maintained irrespective of ARID1A status and geographic background. In addition, spatial deconvolution suggested differences in local immune composition, with tumor regions showing relatively greater neutrophil- and T cell-associated signals. Together, our data suggest that OCCC and coexisting endometriosis share a spatially linked tissue context, but that tumor regions have distinct transcriptional profile and microenvironment that may be involved in the malignant transformation and inform interpretation of molecular classification in endometriosis-associated OCCC.

pathology↗

bioRxiv2025

Multimodal imaging reveals a lysosomal drug reservoir that drives heterogeneous distribution of PARP inhibitors

For all drugs, effective target engagement requires sufficient intracellular concentrations of drug to be reached, but whether tumour heterogeneity impacts drug distribution and efficacy is poorly studied. PARP inhibitors have transformed treatment of high-grade serous ovarian carcinoma (HGSOC), but resistance remains a clinical hurdle in this highly heterogeneous tumour type. We developed a patient-derived explant multi-modal imaging pipeline, which demonstrated that cell-intrinsic PARP inhibitor accumulation is highly variable, both between patients and within tumours. Spatial transcriptomics revealed enrichment of apoptotic and lysosomal signatures in high-drug regions. Rucaparib, an intrinsically fluorescent PARP inhibitor, accumulates heterogeneously at the single-cell level, with rucaparib-high cells demonstrating increased drug response relative to rucaparib low. Mechanistically, lysosomal sequestration creates a rucaparib reservoir that determines drug levels in the nucleus. Perturbation of lysosomal content altered intracellular levels of weak base PARP inhibitors rucaparib and niraparib, but not olaparib. Together these data suggest that lysosomes act as a reservoir for a subset of PARP inhibitor drugs to improve drug response.

cancer biology↗

bioRxiv2024

Multiscale single-cell assessment of the fibrotic niche in idiopathic pulmonary fibrosis

BackgroundIdiopathic pulmonary fibrosis (IPF) is a progressive, fatal disease characterised by excessive extracellular matrix deposition within the lung. Recent advances in single-cell RNA sequencing have identified distinct fibrotic populations, yet their origins and spatial relationships remain incompletely understood. MethodsUsing spatial transcriptomics and Hyperion imaging mass cytometry we compared the cellular composition in formalin fixed paraffin embedded fibrotic lesions (n=9 patients) with control lung (n=9), and cellular interactions were inferred using CellChat V2 ligand-receptor analysis. Monolayers of airway epithelial cells were used to identify changes in keratin (KRT) expression following cell detachment and cyclical mechanical stretch. ResultsSpatial multiomics profiling of human lung cells confirmed the in situ localisation of previously described IPF-enriched populations, and identified a previously unrecognized KRT5low/KRT17 epithelial population derived from airway basal cells that progressively acquiring molecular features of aberrant basaloid cells, forming a unique fibrotic niche enriched with the Secreted Phosphoprotein 1 (SPP1) positive macrophages. Functional studies demonstrated that epithelial detachment and cyclical mechanical stretch drive KRT5 reduction, providing a mechanism for the emergence of this transitional state. In addition, we also identified distinct immune-stromal niches enriched in lymphocytes and alveolar fibroblasts. ConclusionThese findings delineate distinct fibrotic epithelial niches in IPF and support a model in which epithelial loss induces aberrant basaloid differentiation and fibroblast activation, with subsequent airway traction and epithelial detachment generating a secondary niche enriched in basal-derived KRT5low/KRT17 cells and SPP1 macrophages.

molecular biology↗

bioRxiv2024

KLF6 in Pulmonary Hypertension: The Dual Role of Friend and Foe

BackgroundPulmonary arterial hypertension (PAH) is a severe lung condition with unmet clinical needs, marked by endothelial damage, excessive repair, and arterial narrowing, though mechanisms remain unclear. MethodsThis study investigates Kruppel-like transcription factor 6 (KLF6), known for its role in tissue injury response and cancer onset, in PAH through functional and expression analyses in human pulmonary artery endothelial cells (HPAECs) and human and rodent PAH lung tissues. FindingsKLF6 expression increased in early experimental PAH in response to hypoxia and inflammation, while the expression of endothelial homeostasis regulators KLF2 and KLF4, previously linked to PAH, decreased. KLF6 overexpression enhanced pulmonary endothelial survival and angiogenesis through broad transcriptomic remodelling, including changes in genes governing endothelial homeostasis and arterial identity (e.g., SOX17, ERG, BMPR2) and promoted human pulmonary artery smooth muscle cells (HPASMCs) proliferation, which was inhibited by bosentan and imatinib. KLF6 functional and transcriptomic responses differed from those of KLF2 and KLF4. Comparative analysis of RNA-seq PAH databases and spatial transcriptomic analysis of human idiopathic PAH (IPAH) tissues highlighted strong association of KLF6 with vascular remodelling, especially with the formation of angioproliferative (plexiform) lesions. High KLF6 expression was observed in IPAH vascular endothelium and IPAH blood-derived endothelial progenitor cells. Single nucleus RNA-seq in PAH associated with Alveolar Capillary Dysplasia confirmed disease-related elevated KLF6 expression in arterial endothelial cells. InterpretationAccumulation and reorganization of KLF6+ endothelial cells characterize human PAH. KLF6 drives endothelial repair and an apoptosis-resistant, angioproliferative endothelial phenotype. Targeting KLF6 could be a novel therapeutic approach for PAH. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPulmonary arterial hypertension (PAH) is a progressive and life-shortening lung disease with no cure. In PAH development, endothelial damage is believed to initiate an abnormal repair process, leading to extensive vascular remodelling and the formation of complex angio-proliferative (plexiform) lesions. We conducted a systematic search of the PubMed database to identify transcription factors potentially involved in driving endothelial repair and promoting an apoptosis-resistant, angio-proliferative vascular phenotype. Previous research has linked the loss of endothelial homeostasis in PAH to the inhibition of transcription factors KLF2 and KLF4. While KLF6 is known to play a vital role in vascular development and supports endothelial repair, its specific role in PAH remains unexplored. Added value of this studyThis study is the first to establish a connection between KLF6 and PAH pathogenesis. Our findings reveal that KLF6 activation is a key feature of an apoptosis-resistant, angio-proliferative endothelial phenotype characteristic of human PAH-associated plexogenic arteriopathy. Furthermore, we identify both overlapping and unique activation patterns and transcriptional programs regulated by KLF2, KLF4, and KLF6 in lung endothelial cells, highlighting KLF6s unique role in driving endothelial dysfunction in PAH. Implications of all the available evidenceTargeting KLF6 offers a promising therapeutic strategy to counteract excessive vascular repair and prevent the vascular remodelling in PAH. FUNDINGPhD studentship from the University of Hafr Al Batin, KSA, and the Saudi Cultural Bureau in London (UKSACB) (Rehab Alharbi). Spatial transcriptomic reagents were funded by the British Heart Foundation Centre of Research Excellence Award and Senior BHF Fellowship FS/18/52/33808 (Allan Lawrie). Human samples used in this research project were obtained from the Imperial College Healthcare Tissue Bank (ICHTB) supported by the National Institute for Health Research (NIHR) Biomedical Research Centre based at Imperial College Healthcare NHS Trust and Imperial College London.

cell biology↗