Biology subjects

Leedham, S.

Publications and source records attributed to Leedham, S..

12 recordsLinked to original sources

bioRxiv2026

Stromal Prostaglandin is a Dominant Spatial Regulator of Cell-fate Plasticity in Colorectal Cancer

Colorectal cancer (CRC) tumours with high stromal content have a worse outcome, but the mechanisms governing this are unclear. Using high-throughput single-cell perturbation analysis of CRC patient-derived organoids (PDOs) and cancer-associated fibroblasts (CAFs) we find that epithelial cells with high stromal-communication potential are marked by the transcriptional co-repressor DACH1. To define the causal regulators of stromal-epithelial signalling, we developed a novel CRISPR screening platform to perturb the CAF secretome and measure epithelial stem cell responses at single-cell resolution. Intercellular CRISPR screening and full factorial ligand analysis revealed that stromal Prostaglandin E2 (PGE2) is a dominant regulator of CRC cell-fate plasticity. Stromal PGE2 converts DACH1+ epithelia from a chemosensitive proliferative colonic stem cell (proCSC) fate into a chemorefractory and prometastatic revival colonic stem cell (revCSC) fate. PGE2-driven epithelial transdetermination is rapid and reversible, providing an acute mechanism for stromal-driven plasticity in CRC tumours. Genetic and pharmacological inhibition of stromal COX2 inhibits epithelial plasticity, trapping CRC epithelia in an anti-metastatic and chemosensitive proCSC fate. PTGS2+ CAFs support a spatially resolved revCSC to proCSC plasticity gradient in human CRC tumours marked by increasing DACH1 expression. These results reveal that stromal prostaglandin is a dominant spatial regulator of poor-prognosis cell-fates and may explain the benefit of anti-COX therapies in both preventing and treating CRC.

cancer biology↗

bioRxiv2025

Hallmarks of adaptive immunity in a metastatic clear cell renal cell carcinoma (ccRCC) long-term elite survivor

Clear cell renal cell carcinoma (ccRCC) presents with metastatic disease in nearly one-third of patients, with a 5-year survival of only [~]10%. Although anti-angiogenic therapies and immune checkpoint inhibitors (ICIs) have improved outcomes, therapeutic resistance and immune-related adverse events limit durable responses. Exceptional long-term survivors provide a unique opportunity to uncover mechanisms of sustained anti-tumour immunity and guide therapeutic strategies. Here, we present a spatial and temporal dissection of adaptive immunity in an extraordinary 16-year ccRCC survivor, integrating single-cell sequencing, multiplex immunofluorescence, B and T cell receptor (BCR/TCR) repertoire analysis, and antibody profiling. We reveal persistent and spatially coordinated B and T cell clones over 16 years, indicating long-term immune memory and surveillance throughout tumour evolution. B cell analysis identified pronounced clonal expansions involving intrinsically autoreactive IGHV4-34 B cells undergoing ongoing germinal centre (GC) maturation in tumour-draining lymph nodes (dLNs) and spleen. These clones progressively lost autoreactivity while acquiring tumour-specificity through somatic hypermutation (SHM), consistent with clonal redemption. Redeemed B cells displayed enhanced antigen-presenting functions and localised to tertiary lymphoid structures (TLS), where they interacted with CD8 T cells, as inferred from doublet analysis. In parallel, persistent CD8+ effector T cell clones highlighted the contribution of long-lived lymphocytes to tumour control. Comparison of the primary tumour and pancreatic metastatic with paired tumour-free dLNs showed that TLS mirrored GC functionality, particularly for PD-1+ CD8+ T cells, while TLS maturation was stroma-dependent and impaired at the metastatic site. Finally, tumour-derived BCRs revealed antibody binding to tumour specific "public" antigens without cross-reactivity to normal tissue. Together, these findings establish clonal persistence, TLS engagement, and coordinated B-T cell immune surveillance as hallmarks of durable tumour control, providing a framework for next-generation antibody therapeutics and patient stratification in metastatic ccRCC. What is already known on this topic.Tertiary lymphoid structures within the tumour microenvironment (TME) and clonal expansions of CD8+ T cells are associated with better survival and improved response to immunotherapies in ccRCC. However, identifying markers of prolonged survival is challenging due to the rarity of long-term survivors (LTS), and the predominance of studies focused on T cell immunity, leaving B cell contribution almost unexplored. What this study adds.This study provides an integrated analysis of B and T cell responses in an exceptional 16-year LTS with metastatic ccRCC, revealing key immunologic features of sustained anti-tumour immunity. Beyond T cell dynamics, it highlights the multifaceted role of B cells as antigen presenting cells, antibody producers, and modulators of CD8+ T cell effector functions through direct interactions within TLS. Importantly, it reveals potential tumour-specific antigens driving humoral responses. How this study might affect research, practice or policy.By uncovering mechanisms of sustained tumour control, this work establishes a framework for identifying adaptive immune biomarkers of long-term survival and refining patient stratification in metastatic ccRCC. Multimodal assessment of B cell specificity and spatial interactions between re-educated B cells and CD8+ T cells within TLS introduces a new paradigm for understanding coordinated B and T cell responses. These insights have direct implications for antibody-based drug discovery and development of immunotherapies that harness the B-T cell axis.

cancer biology↗

bioRxiv2025

Climate Shaped the Global Population Structure of Leopards and their Extinction in Europe

Environmental change is often invoked as a key force shaping species evolution and demography, but quantifying its role is challenging. Leopards (Panthera pardus), a widely distributed generalist species, provide an ideal case for studying the role of the environment. The population dynamics of African and Asian leopards differ dramatically, with near panmixia in Africa versus a strong structure and eight subspecies in Asia. Fossil records show that a population in Europe disappeared after the Last Glacial Maximum (LGM), further pointing to complex range dynamics in Eurasia. In this study, we explicitly test the role of climate in shaping leopards population dynamics across the continents, by quantitatively combining paleoclimatic, demographic, and genetic simulations over the last 450 thousand years. Using an Approximate Bayesian Computational framework, we show that the genetic structure differences between Africa and Asia can be explained by distinct historical climatic conditions in these two continents: most of sub-Saharan Africa and parts of Southeast Asia exhibited a stable range without geographical barriers, while other areas such as Morocco, Afghanistan and Northeast Asia showed expansion and extinction cycles during glacial and interglacials. We further model population dynamics in Europe and validate it against fossil and radiocarbon dates records. We find that European populations were likely fragile, with extinctions repeatedly predicted over multiple glacial cycles, indicating that climate change possibly led to the extinction of the European subspecies following the LGM. Notably, we found that climate during the Holocene should have allowed a more recent recolonisation that did not happen, indicating other factors such as human presence might have blocked it.

zoology↗

bioRxiv2024

Viral mimicry redirects immunosuppressed colorectal tumour landscapes towards a proinflammatory and CMS1-like regenerative state

In colorectal cancer (CRC), tumours classifier as consensus molecular subtype 4 (CMS4) have the worst prognosis and derive negligible benefit from chemotherapy. We previously described how repressed interferon-related signalling is associated with increased relapse in CMS4 tumours. Although the viral mimetic poly(I:C) can reduce liver metastasis in vivo, the initial phenotypic changes that underpin its anti-metastatic response remain poorly described, particularly in the immunosuppressed CMS4 tumour microenvironment. Here we characterise lineage-specific anti-metastatic responses induced by poly(I:C), including acute macrophage polarisation and a novel CMS1-like regenerative stem cell state, which drive pro-inflammatory microenvironmental changes in CRC. These insights enabled the development of tractable biomarkers that identify an "immune-warm" patient subset most likely to respond to poly(I:C), enriched for mismatch-repair proficient (pMMR), anti-inflammatory macrophages and CMS4-like features. The viral mimetic poly(I:C) offers a tailored treatment option for CMS4 tumours, by reprogramming stem cell states and activation of an innate-adaptive anti-metastatic response.

cancer biology↗

bioRxiv2023

Niche conservatism in a generalist felid: low differentiation of the climatic niche among subspecies of the leopard (Panthera pardus)

AimSpecies distribution modelling can be used to reveal if the ecology of a species varies across its range, to investigate if range expansions entailed niche shifts, and to help assess ecological differentiation: the answers to such questions are vital for effective conservation. The leopard (Panthera pardus spp.) is a generalist species composed of one African and eight Asian subspecies, reflecting dispersal from an ancestral African range. This study uses species distribution models to compare the niches of leopard subspecies, to investigate if they conserved their niches when moving into new territories or adapted to local conditions and shifted niche. LocationAfrica and Eurasia MethodsWe assembled a database of P. pardus spp. presences. We then associated them with bioclimatic variables to identify which are relevant in predicting the distribution of the leopard. We then constructed a species distribution model and compared the distribution predicted from models based on presences from all subspecies versus the ones built only using African leopards. Finally, we used multivariate analysis to visualise the niche occupied by each subspecies in the climate space, and to compare niche overlaps to assess ecological differentiation. ResultsNiche comparisons and model predictions suggest a general lack of niche separation between all subspecies. Most Asian subspecies have overlapping niches and occupy subsets of the niche of the African leopard. Nevertheless, we found the Persian leopard Panthera pardus saxicolor to have the most distinct niche, giving some evidence for niche expansion in more Northern Asian subspecies. Main conclusionsThese results suggest little ecological differentiation among leopard subspecies and a lack of adaptation to novel climates after dispersal from Africa. This finding complements recent genetic studies in implying that the taxonomy of Asian leopards may not reflect biological differentiation, an issue that is important to resolve due to its relevance for the conservation of the species.

ecology↗

bioRxiv2022

Biological misinterpretation of transcriptional signatures in tumour samples can unknowingly undermine mechanistic understanding and faithful alignment with preclinical data

Precise mechanism-based gene expression signatures (GESs) have been developed in appropriate in vitro and in vivo model systems, to identify important cancer-related signalling processes. However, some GESs originally developed to represent specific disease processes, primarily with an epithelial cell focus, are being applied to heterogeneous tumour samples where the expression of the genes in the signature may no longer be epithelial-specific. Therefore, unknowingly, even small changes in tumour stroma percentage can directly influence GESs, undermining the intended mechanistic signalling. Using colorectal cancer as an exemplar, we deployed numerous orthogonal profiling methodologies, including laser capture microdissection, flow cytometry, bulk and multiregional biopsy clinical samples, single cell RNAseq and finally spatial transcriptomics, to perform a comprehensive assessment of the potential for the most widely-used GESs to be influenced, or confounded, by stromal content in tumour tissue. To complement this work, we generated a freely-available resource, ConfoundR; https://confoundr.qub.ac.uk/, that enables users to test the extent of stromal influence on an unlimited number of the genes/signatures simultaneously across colorectal, breast, pancreatic, ovarian and prostate cancer datasets. Findings presented here demonstrate the clear potential for misinterpretation of the meaning of GESs, due to widespread stromal influences, which in-turn can undermine faithful alignment between clinical samples and preclinical data/models, particularly cell lines and organoids, or tumour models not fully recapitulating the stromal and immune microenvironment. As such, efforts to faithfully align preclinical models of disease using phenotypically-designed GESs must ensure that the signatures themselves remain representative of the same biology when applied to clinical samples.

cancer biology↗

bioRxiv2021

Gattaca: Base pair resolution mutation tracking for somatic evolution studies using agent-based models

Gattaca provides the first base-pair resolution artificial genomes for tracking somatic mutations within agent based modeling. Through the incorporation of human reference genomes, mutational context, sequence coverage/error information Gattaca is able to realistically provide comparable sequence data for in-silico comparative evolution studies with human somatic evolution studies. This user-friendly method, incorporated into each in-silico cell, allows us to fully capture somatic mutation spectra and evolution.

evolutionary biology↗

bioRxiv2021

VALIS: Virtual Alignment of pathoLogy Image Series

Spatial analyses can reveal important interactions between and among cells and their microenvironment. However, most existing staining methods are limited to a handful of markers per slice, thereby limiting the number of interactions that can be studied. This limitation is frequently overcome by registering multiple images to create a single composite image containing many markers. While there are several existing image registration methods for whole slide images (WSI), most have specific use cases. Here, we present the Virtual Alignment of pathoLogy Image Series (VALIS), a fully automated pipeline that opens, registers (rigid and/or non-rigid), and saves aligned slides in the ome.tiff format. VALIS has been tested with 273 immunohistochemistry (IHC) samples and 340 immunofluorescence (IF) samples, each of which contained between 2-69 images per sample. The registered WSI tend to have low error and are completed within a matter of minutes. In addition to registering slides, VALIS can also using the registration parameters to warp point data, such as cell centroids previously determined via cell segmentation and phenotyping. VALIS is written in Python and requires only few lines of code for execution. VALIS therefore provides a free, opensource, flexible, and simple pipeline for rigid and non-rigid registration of IF and/or IHC that can facilitate spatial analyses of WSI from novel and existing datasets.

cancer biology↗

bioRxiv2021

The Molecular Subtyping Resource (MouSR): a user-friendly tool for rapid biological discovery from human or mouse transcriptional data

Generation of transcriptional data has dramatically increased in the last decade, driving the development of analytical algorithms that enable interrogation of the biology underpinning the profiled samples. However, these resources require users to have expertise in data wrangling and analytics, reducing opportunities for biological discovery by "wet-lab" users with a limited programming skillset. Although commercial solutions exist, costs for software access can be prohibitive for academic research groups. To address these challenges, we have developed an open source and user-friendly data analysis platform for on-the-fly bioinformatic interrogation of transcriptional data derived from human or mouse tissue, called "MouSR". This internet-accessible analytical tool, https://mousr.qub.ac.uk/, enables users to easily interrogate their data using an intuitive "point and click" interface, which includes a suite of molecular characterisation options including QC, differential gene expression, gene set enrichment and microenvironmental cell population analyses from RNA-Seq. Users are provided with adjustable options for analysis parameters to generate results that can be saved as publication-quality images. To highlight its ability to perform high quality data analysis, we utilise the MouSR tool to interrogate our recently published tumour dataset, derived from genetically engineered mouse models and matched organoids, where we rapidly reproduced the key transcriptional findings. The MouSR online tool provides a unique freely-available option for users to perform rapid transcriptomic analyses and comprehensive interrogation of the signalling underpinning transcriptional datasets, which alleviates a major bottleneck for biological discovery.

bioinformatics↗

bioRxiv2020

Stabilising selection causes grossly altered but stable karyotypes in metastatic colorectal cancer

Aneuploidy, the loss and gain of whole and part chromosomes, is near-ubiquitous in cancer genomes and likely defines cancer cell biology. However, the temporal evolutionary dynamics that select for aneuploidy remain uncharacterised. Here we perform longitudinal genomic analysis of 755 samples from a total of 167 patients with colorectal-derived neoplastic lesions that represent distinct stages of tumour evolution through metastasis and treatment. Adenomas typically had few copy number alterations (CNAs) and most were subclonal, whereas cancers had many clonal CNAs, suggesting that progression goes through a CNA bottleneck. Individual CRC glands from the same tumour typically had very similar karyotypes, despite evidence of ongoing instability at the cell level in patient tumours, cell lines and organoids. CNAs in metastatic lesions sampled from liver and other organs, after chemotherapy or targeted therapies, and in late recurrences were typically similar to the primary tumour. Mathematical modelling and statistical inference indicated that these data are consistent with the action of negative selection on CNAs that traps cancer cell genomes on a fitness peak defined by the specific pattern of chromosomal aberrations. These data suggest that the initial progression of colorectal cancer requires the traversal of a rugged fitness landscape and subsequent CNA evolution, including metastatic dissemination and therapeutic resistance, is constrained by negative selection.

cancer biology↗

bioRxiv2019

Niche engineering drives early passage through an immune bottleneck in progression to colorectal cancer

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/623959v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (55K):\norg.highwire.dtl.DTLVardef@1c48cf5org.highwire.dtl.DTLVardef@1026747org.highwire.dtl.DTLVardef@ca92f1org.highwire.dtl.DTLVardef@1753cd5_HPS_FORMAT_FIGEXP M_FIG C_FIG Colorectal cancer develops from its precursor lesion, the adenoma. The immune system is hypothesized to be key in modulating progression, but tumor-immune eco-evolutionary dynamics remain uncharacterized. Here, we demonstrate a key role for immune evasion in the progression of human benign disease to colorectal cancer. We constructed a mathematical model of tumor-immune eco-evolutionary dynamics that predicted ecological succession, from an \"immune-hot\" adenoma immune ecology rich in T cells to an \"immune-cold\" carcinoma ecology, deficient in T cells and rich in immunosuppressive cells. Using a cross-sectional cohort of adenomas and carcinomas, we validated this prediction by direct measurement of the tumor-immune ecology using whole-slide 10-marker immunohistochemistry (IHC), and analysis of neoantigen clonal architecture multi-region exome sequencing data. Changes in immune ecology relax selection against antigens with high recognition potentials. This study indicates that immune surveillance represents a key evolutionary bottleneck in the evolution of colon cancer.

cancer biology↗

bioRxiv2019

Clonal Architecture of the Epidermis: Homeostasis Limits Keratinocyte Evolution

The skin is the largest human organ, functioning to serve as the protective barrier to the harsh, outside world. Recent studies have revealed that large numbers of somatic mutations accumulate in normal tissue, which can be used to infer skin cell dynamics1-5. Here we present the first realistic, cell-genome mechanistic epidermal model that shows homeostasis imposes a characteristic log-linear subclone size distribution for both neutral and oncogenic driver mutations, where the largest skin subclones are the oldest subclones. Because homeostasis inherently limits proliferation and therefore clonal sweeps, selection for driver mutations (NOTCH1 and TP53) in normal epidermis is instead conferred by greater persistence, which leads to larger subclone sizes. These results highlight how the integration of mechanistic modeling with genomic data provide novel insights into the evolutionary cell dynamics of normal human homeostatic tissues.

evolutionary biology↗