Biology subjects

Thomas, G. J.

Publications and source records attributed to Thomas, G. J..

8 recordsLinked to original sources

bioRxiv2026

Histopathology-inferred spatial transcriptomics characterizes the tumor microenvironment in 1,500 head and neck tumors and predicts clinical outcomes

Head and neck squamous cell carcinoma (HNSC) is a prevalent malignancy associated with poor prognosis despite recent therapeutic advances. We hypothesized that a comprehensive understanding of the spatial heterogeneity and organization of the tumor microenvironment (TME) can substantially improve risk stratification and prediction of treatment response in HNSC. As spatial transcriptomics (ST) remains labor-intensive and costly, we developed HEiST (H&E-Inferred Spatial Transcriptomics), a deep learning framework that predicts spatially resolved gene expression profiles directly from routine hematoxylin and eosin (H&E)-stained histology slides. After rigorous validation across two independent external ST cohorts, we applied HEiST to infer spatial transcriptomes across 1,500 HNSC patient tumors spanning two publicly available datasets and two newly generated cohorts, one treated with concurrent chemoradiotherapy (CCRT) and one with immunotherapy. This large-scale analysis uncovered reproducible spatial clusters characterizing the HNSC TME, defining two distinct prognostic Spatiotypes, Immune-Exhausted and Immune-Activated, with significantly distinct survival outcomes. Critically, spatial cluster composition accurately predicts HPV status and yields treatment response predictors for both CCRT/radiotherapy and immunotherapy that outperform costly gene-expression and direct image-based approaches. Notably, the ST cluster-based predictor of immunotherapy response markedly surpasses the performance of commonly used FDA-approved biomarkers, including CPS, TPS, and their combination. To the best of our knowledge, this represents the first virtual spatial profiling effort and the most comprehensive large-scale spatial TME analysis in HNSC to date. HEiST thus introduces a scalable, low-cost, and spatially grounded biomarker discovery for precision oncology in HNSC.

cancer biology↗

bioRxiv2025

Pancreatic cancer metastasis is regulated by an eleven amino-acid sequence

Pancreatic ductal adenocarcinoma (PDAC) has a very poor prognosis with a 5-year survival rate less than 5% because of its ability to metastasise, its late detection and the lack of effective therapies. The Integrin v{beta}6 is highly overexpressed in PDAC and correlates with poor prognosis. The integrin {beta}6 subunit contains a unique C-terminal tail of 11 amino acids (aa) that regulates downstream signals, although the mechanism remains unclear. Here, using integrin {beta}6-deficient cells lines, we have developed two PDAC mouse models overexpressing the full-length {beta}6 and a mutant {beta}6 lacking the C-terminal 11aa (v{Delta}{beta}6). In vitro, v{beta}6 overexpression increased cell proliferation, migration and invasion in a 3D spheroid model. The elimination of the C-terminal 11aa decreased proliferation and totally impaired cell migration and invasion. v{Delta}{beta}6 cells also expressed reduced MMPs in vitro. In vivo, orthotopic implantation of v{beta}6 overexpressing cells showed decreased overall survival and more spontaneous metastasis compared to v{Delta}{beta}6 and v{beta}6-null cells. Therefore, the C-terminal 11aa of the integrin {beta}6 subunit regulates PDAC progression and metastasis.

cancer biology↗

bioRxiv2024

Developmental programmes drive cellular plasticity, disease progression and therapy resistance in lung adenocarcinoma

BackgroundCellular plasticity, involving loss of lineage determination and emergence of hybrid cell states, plays a pivotal role in non-small cell lung cancer (NSCLC) disease progression and therapy resistance. However, the full spectrum of atypical states generated in human NSCLC and the pathways that regulate them are yet to be fully elucidated. Here we examine the role of developmental programmes, alveogenesis and branching morphogenesis (BM), in regulating phenotypic diversity in NSCLC. MethodsTranscriptomic analysis of epithelial cells isolated from murine lungs at different stages of organogenesis were used to derive gene signatures for developmental programmes. Bulk tissue transcriptomic datasets from human NSCLC and non-neoplastic control samples were used to identify whether developmental programmes were associated with molecular, morphological, and clinical parameters. Single-cell RNA-sequencing was used to identify malignant cell states in human NSCLC (n = 16,621 epithelial cells from 72 samples) and protein level validation of these states was carried out using multiplexed immunohistochemistry (n = 40). ResultsMutually antagonistic regulation of alveogenesis and BM was found to account for a significant proportion of transcriptomic variance in human NSCLC bulk tissue datasets. BM activation was associated with poor overall survival rates in five independent lung adenocarcinoma (LUAD) cohorts (p=2.04e-13); and was significantly prognostic for resistance to tyrosine kinase inhibitors (TKIs; p=0.003) and immune checkpoint blockade (ICBs; p=0.014), in pre-treatment biopsies. Single-cell RNA-sequencing analysis revealed that malignant LUAD cells with loss of alveolar lineage fidelity predominantly acquired inflamed or basal-like cellular states, which were variably persistent in samples from TKI and ICB recurrence. ConclusionsOur results show LUAD tumours undergo reversion from an alveogenic to branching morphogenic phenotype during disease progression, generating inflamed or basal-like cell states that are variably persistent following TKI or ICB treatments. These findings identify prognostic biomarkers for therapy response and underscore the role of different cell states in resistance to multiple treatment modalities.

cancer biology↗

bioRxiv2024

Human-like APOBEC3 gene expression and anti-viral responses following replacement of mouse Apobec3 with the 7-gene human APOBEC3 locus

The seven human APOBEC3 (hA3) genes encode polynucleotide cytidine deaminases that play vital roles in restricting replication of viruses and retrotransposons. However, off-target A3 deamination of the cellular genome is a major source of somatic mutations in human cancer. The ability to study A3 biology in vivo is hindered by the fact that the solitary murine Apobec3 gene (mA3) encodes a cytoplasmic enzyme, with no apparent mutagenic activity. Transgenic expression of individual hA3 genes in mice has helped to confirm their oncogenic potential but important questions including which hA3 genes are active in different tissue contexts and how they function in concert when under control of their cognate promoters cannot be addressed using these models. Here we describe humanization of the mouse mA3 locus by integration of a modified BAC clone encompassing the entire 7-gene hA3 locus from human chromosome 22 replacing mA3 on mouse chromosome 15. APOBEC3 mice are viable and fertile and hA3 gene expression in cells and tissues correlates strongly with expression in corresponding human cells and tissues, indicating human-like regulation of hA3 gene expression in the mice. Splenocytes from this line display a functional human A3 response to Friend Murine Leukaemia Virus (F-MLV) infection. We propose that the Hs-APOBEC3 mouse will uniquely model the function of the complete hA3 locus in a living organism and that it will serve as a useful background upon which to model human cancer, as well as assisting drug discovery efforts.

cancer biology↗

bioRxiv2020

Spatially discrete signalling niches regulate fibroblast heterogeneity in human lung cancer

Fibroblasts are functionally heterogeneous cells, capable of promoting and suppressing tumour progression. Across cancer types, the extent and cause of this phenotypic diversity remains unknown. We used single-cell RNA sequencing and multiplexed immunohistochemistry to examine fibroblast heterogeneity in human lung and non-small cell lung cancer (NSCLC) samples. This identified seven fibroblast subpopulations: including inflammatory fibroblasts and myofibroblasts (representing terminal differentiation states), quiescent fibroblasts, proto-myofibroblasts (x2) and proto-inflammatory fibroblasts (x2). Fibroblast subpopulations were variably distributed throughout tissues but accumulated at discrete niches associated with differentiation status. Bioinformatics analyses suggested TGF-{beta}1 and IL-1 as key regulators of myofibroblastic and inflammatory differentiation respectively. However, in vitro analyses showed that whilst TGF-{beta}1 stimulation in combination with increased tissue tension could induce myofibroblast marker expression, it failed to fully re-capitulate ex-vivo phenotypes. Similarly, IL-1{beta} treatment only induced upregulation of a subset of inflammatory fibroblast marker genes. In silico modelling of ligand-receptor signalling identified additional pathways and cell interactions likely to be involved in fibroblast activation, which can be examined using publicly available R shiny applications (at the following links: myofibroblast activation and inflammatory fibroblast activation). This highlighted a potential role for IL-11 and IL-6 (among other ligands) in myofibroblast and inflammatory fibroblast activation respectively. This analysis provides valuable insight into fibroblast subtypes and differentiation mechanisms in NSCLC.

cancer biology↗

bioRxiv2019

Parallel evolution of multiple mechanisms for demethylase inhibitor fungicide resistance in the barley pathogen Pyrenophora teres f. sp. maculata

The demethylase inhibitor (DMI) or group 3 fungicides are the most important class of compounds for the control both of plant and human fungal pathogens. The necrotrophic fungal pathogen Pyrenophora teres f. sp. maculata (Ptm), responsible for spot form of net blotch (SFNB), is currently the most significant disease of barley in Australia, and a disease of increasing concern worldwide. The main basis for management of SFNB is by fungicide application, and in Australia the DMIs predominate. Although reduced sensitivity to DMI fungicides has recently been described in the closely related pathogen P. teres f. sp. teres (Ptt), the mechanisms of DMI resistance have not thus far been described for Ptm. In this study, several different levels of sensitivity to DMI fungicides were identified in Western Australian strains of Ptm from 2016 onwards, and reduced sensitivity phenotypes were correlated with a number of distinct mutations in both the promoter region and coding sequence of the DMI target gene encoding cytochrome P450 sterol 14-demethylase (Cyp51A). Five insertions elements of 134-base pairs in length were found at different positions within the upstream regulatory region of Cyp51A in both highly DMI-resistant (HR) and select moderately DMI-resistant (MR1) Ptm isolates. The five insertion elements had at least 95% sequence identity and were determined to be Solo-LTR (Long Terminal Repeat) elements, all deriving from Ty1/Copia-family LTR Retrotransposons. The 134-bp elements contained a predicted promoter sequence and several predicted transcription factor binding sites, and the presence of an insertion element was correlated with constitutive overexpression of Cyp51A. The substitution of phenylalanine by leucine at position 489 of the predicted amino acid sequence of CYP51A was found in both HR and select moderately DMI-resistant (MR2) Ptm isolates. The same F489L amino acid substitution has been previously reported in Western Australian strains of Ptt, where it has also been associated with reduced sensitivity to DMI fungicides. In Ptm, the F489L amino acid change was associated with either of three different single nucleotide polymorphisms in codon 489. This suggests that, in contrast to Ptt, in Ptm the F489L mutation has emerged as a result of three distinct mutational events. Moderately DMI-resistant isolates had one or the other of the F489L substitution or a promoter insertion mutation, whereas highly DMI-resistant isolates were found to have combinations of both mechanisms together. Therefore, multiple mechanisms acting both alone and in concert were found to contribute to the observed phenomena of DMI fungicide resistance in Ptm. Moreover, these mutations have apparently emerged repeatedly and independently in Western Australian Ptm populations, by a process of convergent or parallel evolution.

plant biology↗

bioRxiv2018

Integrin αVβ6-EGFR crosstalk regulates bidirectional force transmission and controls breast cancer invasion

The mechanical properties of the extracellular matrix within tumours control multiple cellular functions that drive cancer invasion and metastasis. However, the mechanisms controlling microenvironmental force sensation and transmission, and how these regulate transcriptional reprogramming and invasion, are unclear. Our aim was to understand how mechanical inputs are transmitted bidirectionally and translated into biochemical and transcriptional outputs to drive breast cancer progression. We reveal that adhesion receptor and growth factor receptor crosstalk regulates a bidirectional feedback mechanism co-ordinating force-dependent transcriptional regulation and invasion.\n\nIntegrin V{beta}6 drives invasion in a range of carcinomas and is a potential therapeutic target. V{beta}6 exhibits unique biophysical properties that promote force-generation and increase matrix rigidity. We employed an inter-disciplinary approach incorporating proteomics, biophysical techniques and multi-modal live-cell imaging to dissect the role of V{beta}6-EGFR crosstalk on transmission of mechanical signals bidirectionally between the extracellular matrix and nucleus.\n\nWe show that V{beta}6 expression correlates with poor prognosis in triple-negative breast cancer (TNBC) and drives invasion of TNBC cells. Moreover, our data show that a complex regulatory mechanism exists involving crosstalk between V{beta}6 integrin and EGFR that impacts matrix stiffness, force transmission to the nucleus, transcriptional reprogramming and microenvironment rigidity. V{beta}6 engagement triggers EGFR & MAPK signalling and V{beta}6-EGFR crosstalk regulates mutual receptor trafficking mechanisms. Consequently, EGF stimulation suppresses V{beta}6-mediated force-application on the matrix and nuclear shuttling of force-dependent transcriptional co-activators YAP/TAZ. Finally, we show that crosstalk between V{beta}6 & EGFR regulates TNBC invasion.\n\nWe propose a model whereby V{beta}6-EGFR crosstalk regulates matrix stiffening, but also the transmission of extracellular forces into the cell in order to co-ordinate transcriptional reprogramming and invasion. To exploit adhesion receptors and receptor tyrosine kinases therapeutically, it will be essential to understand the integration of their signalling functions and how crosstalk mechanisms influence invasion and the response of tumours to molecular therapeutics.

cancer biology↗

bioRxiv2018

Pan-cancer deconvolution of cellular composition identifies molecular correlates of antitumour immunity and checkpoint blockade response

The nature and extent of immune cell infiltration into solid tumours are key determinants of therapeutic response. Here, using a novel DNA methylation-based approach to tumour cell fraction deconvolution, we report the integrated analysis of tumour composition and genomics across a wide spectrum of solid cancers. Initially studying head and neck squamous cell carcinoma, we identify two distinct tumour subgroups: immune hot and immune cold, which display differing prognosis, mutation burden, cytokine signalling, cytolytic activity, and oncogenic driver events. We demonstrate the existence of such tumour subgroups pan-cancer, link clonal-neoantigen burden to hot tumours, and show that transcriptional signatures of hot tumours are selectively engaged in immunotherapy responders. We also find that treatment-naive hot tumours are markedly enriched for known immune-resistance genomic alterations and define a catalogue of novel and known mediators of active antitumour immunity, deriving biomarkers and potential targets for precision immunotherapy.

cancer biology↗