Biology subjects

Lamb, A. D.

Publications and source records attributed to Lamb, A. D..

10 recordsLinked to original sources

bioRxiv2025

IRE1 activity regulates tumour and microenvironment cell lineage states while stratifying localised and metastatic prostate cancer.

Prostate cancer (PCa) is an androgen receptor (AR) driven, high-incidence disease significantly contributing to cancer mortality. PCa is in need of better risk stratification at diagnosis and treatment outcomes in patients at high risk of metastasis. The unfolded protein response (UPR) is an AR-dependent process. However, the impact of the UPR transducer IRE1 on AR-dependent biology and treatment resistance has not been defined. We use diverse pre-clinical models of stress response to describe IRE1 activity impact on multiple disease stages and demonstrate its involvement with poor prognosis (RB1 loss), and cell lineage determination (club phenotypes). Integrating clinical transcriptomic datasets, we chart IRE1 activity throughout PCa evolution by developing a PCa-specific, IRE1 activity gene set (IRE1_18) reflecting both tumoral and micro-environmental niches. IRE1_18 can determine tumoral identity, inform androgen deprivation treatment suitability, prognosticate localised and metastatic disease independently from AR activity, and guide IRE1 modulation as a novel combination therapeutic. Graphical Abstract created using Biorender.com O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/643042v3_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@18edd6aorg.highwire.dtl.DTLVardef@6a759eorg.highwire.dtl.DTLVardef@14ff3fborg.highwire.dtl.DTLVardef@1ae77d_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

ECM-free patient-derived organoids preserve diverse prostate cancer lineages and uncover in vitro-enriched cell types

Patient-derived organoids (PDOs) offer new opportunities to model various cancers. However, their application in prostate cancer (PCa) has been hampered by poor success rates and overgrowth of cell types which are not representative of the patient samples. By exploiting a cohort of 164 PCa patient samples and tuning several culture parameters, we show that an extracellular matrix-free (ECM)-free culture system increases the take-rate of PDOs with luminal-like and PCa features. Single-cell RNA sequencing (scRNA-seq) reveals that ECM-free PDOs comprise cell populations associated with known PCa signatures and exhibit transcriptomic resemblance with their respective parental tumors. In addition, we define organoid-associated cell type signatures and identify markers discriminating tumors versus benign cells ex vivo and in situ. Furthermore, we generate the first prostate PDO single-cell atlas integrating previously-published scRNA-seq datasets and our newly- generated data. We show that Matrigel-based organoid cultures derived from primary PCa are essentially composed of benign-like epithelial cells, irrespective of the dataset or the malignant nature of the tissue of origin. In contrast, ECM-free conditions maintain heterogenous patient-specific luminal tumor cell populations and enrich in intermediate cell types. Ultimately, our work will significantly enhance the potential of PDOs in basic and translational PCa research.

cancer biology↗

bioRxiv2023

Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post-radiotherapy, and those with de novo metastatic disease.

PurposeIt is important to identify molecular features that improve prostate cancer (PCa) risk stratification before radical treatment with curative intent. Molecular analysis of historical diagnostic formalin-fixed paraffin-embedded (FFPE) prostate biopsies from cohorts with post-radiotherapy (RT) long-term clinical follow-up has been limited. Utilizing parallel sequencing modalities, we performed a proof-of-principle sequencing analysis of historical diagnostic FFPE prostate biopsies. We compared patients with i) stable PCa post-primary or salvage RT (sPCa), ii) progressing PCa post-RT (pPCa), and iii) de novo metastatic PCa (mPCa). Experimental DesignA cohort of 19 patients with diagnostic prostate biopsies (n=6 sPCa, n=5 pPCa, n=8 mPCa) and mean 4 years 10 months follow-up (diagnosed 2009-2016) underwent nucleic acid extraction from demarcated malignancy. Samples underwent 3RNA sequencing (3RNAseq) (n=19), nanoString analysis (n=12) and Illumina 850k methylation (n=8) sequencing. Bioinformatic analysis was performed to coherently identify differentially expressed genes (DEGs) and methylated genomic regions (MGRs). Results18 of 19 samples provided useable 3RNAseq data. Principal Component Analysis (PCA) demonstrated similar expression profiles between pPCa and mPCa cases, versus sPCa. Coherently differentially methylated probes between these groups identified [~]600 differentially MGRs. The top 50 genes with increased expression in pPCa patients were associated with reduced progression-free survival post-RT (p<0.0001) in an external cohort. Conclusions3RNAseq, nanoString and 850K-methylation analyses are each achievable from historical FFPE diagnostic pre-treatment prostate biopsies, unlocking the potential to utilize large cohorts of historic clinical samples. Profiling similarities between individuals with pPCa and mPCa suggests biological similarities and historical radiological staging limitations, which warrant further investigation.

genomics↗

bioRxiv2023

Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of heterogeneity on genomic signature scoring

Genetic signatures have added a molecular dimension to prognostics and therapeutic decision-making. However, tumour heterogeneity in prostate cancer and current sampling methods could confound accurate assessment. Based on previously published spatial transcriptomic data from multifocal prostate cancer, we created virtual biopsy models that mimic conventional biopsy placement and core size. We then analysed the gene expression of different prognostic signatures (OncotypeDx(R), Decipher(R), Prostadiag(R)) using a step-wise approach increasing resolution from pseudo-bulk analysis of the whole biopsy, to differentiation by tissue subtype (benign, stroma, tumour), followed by distinct tumour grade and finally clonal resolution. The gene expression profile of virtual tumour biopsies revealed clear differences between grade groups and tumour clones, compared to a benign control, which were not reflected in bulk analyses. This suggests that bulk analyses of whole biopsies or tumour-only areas, as used in clinical practice, may provide an inaccurate assessment of gene profiles. The type of tissue, the grade of the tumour and the clonal composition all influence the gene expression in a biopsy. Clinical decision making based on biopsy genomics should be made with caution while we await more precise targeting and cost-effective spatial analyses. Patient summaryProstate cancers are very variable, including within a single tumour. Current genetic scoring systems, which are sometimes used to make decisions for how to treat patients with prostate cancer, are based on sampling methods which do not reflect these variations. We found, using state-of-the-art spatial genetic technology to simulate accurate assessment of variation in biopsies, that the current approaches miss important details which could negatively impact clinical decisions. Take home messageVirtual biopsies from spatial transcriptomic analysis of a whole prostate reveal that current genomic risk scores potentially deliver misleading results as they are based on bulk analysis of prostate biopsies and ignore tumour heterogeneity.

genomics↗

bioRxiv2023

Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of cancer

Epithelial cancers are typically heterogeneous with primary prostate cancer being a typical example of histological and genomic variation. Prostate cancer is the second most common male cancer in western industrialized countries. Prior studies of primary prostate cancer tumor genetics revealed extensive inter and intra-patient tumor heterogeneity. Recent advances have enabled extensive single-cell and spatial transcriptomic profiling of tissue specimens. The ability to resolve accurate prostate cancer tumor phylogenies at high spatial resolution would provide tools to address questions in tumorigenesis, disease progression, and metastasis. Recent advances in machine learning have enabled the inference of ground-truth genomic single-nucleotide and copy number variant status from transcript data. The inferred SNV and CNV states can be used to resolve clonal phylogenies, however, it is still unknown how faithfully transcript-based tumor phylogenies reconstruct ground truth DNA-based tumor phylogenies. We sought to study the accuracy of inferred-transcript to recapitulate DNA-based tumor phylogenies. We first performed in-silico comparisons of inferred and directly resolved SNV and CNV status, from single cancer cells, from three different cell lines. We found that inferred SNV phylogenies accurately recapitulate DNA phylogenies (entanglement = 0.097). We observed similar results in iCNV and CNV based phylogenies (entanglement = 0.11). Analysis of published prostate cancer DNA phylogenies and inferred CNV, SNV and transcript based phylogenies demonstrated phylogenetic concordance. Finally, a comparison of pseudo-bulked spatial transcriptomic data to adjacent sections with WGS data also demonstrated recapitulation of ground truth (entanglement = 0.35). These results suggest that transcript-based inferred phylogenies recapitulate conventional genomic phylogenies. Further work will need to be done to increase accuracy, genomic, and spatial resolution.

bioinformatics↗

bioRxiv2023

Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole genome sequencing with histopathological features

Extension of prostate cancer beyond the primary site into the surrounding organs by local invasion or nodal metastasis is associated with poor prognosis. The emergence and evolution of cancer clones at this early stage of expansion and spread has not been studied in detail. We performed whole genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and regional lymph nodes of five treatment-naive patients with locally advanced disease who underwent radical prostatectomy. Using cancer cell fractions computed from single nucleotide variants and copy number alterations, we reconstructed the tumour phylogenies, which in turn allowed us to infer key molecular steps in the progression of prostate cancer in these individuals. We mapped the clonal composition of cancer sampled across the prostate in each individual and inferred the routes of spread of cancer cells within the prostate and to seminal vesicles and lymph nodes. Based on these data, we delineated the route of tumour progression and metastasis following the transformation of adenocarcinoma to amphicrine morphology, the molecular events leading to whole genome duplication associated with a single clonal expansion and identified putative driver events associated with local invasion and lymph node metastasis. We also correlated genomic changes associated with differences in morphology and identified putative driver events associated with spread to seminal vesicle invasion and lymph node metastasis. Taken together, these findings have implications for diagnosis and risk stratification, in addition to providing a rationale for further studies to characterise the genetic changes associated with morphological transformation. Our results demonstrate the value of integrating multi-region sequencing with histopathological data to study tumour evolution and identify mechanisms of prostate cancer spread.

cancer biology↗

bioRxiv2021

The spatial landscape of clonal somatic mutations in benign and malignant tissue

Defining the transition from benign to malignant tissue is fundamental to improve early diagnosis of cancer. Here, we provide an unsupervised approach to study spatial genome integrity in situ to gain molecular insight into clonal relationships. We employed spatially resolved transcriptomics to infer spatial copy number variations in >120 000 regions across multiple organs, in benign and malignant tissues. We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue. Our results suggest a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution. We highlight the power of an unsupervised approach to capture the molecular and spatial continuums in a tissue context and challenge the rationale for treatment paradigms, including focal therapy.

genomics↗

bioRxiv2020

Tumor irradiation combined with vascular-targeted photodynamic therapy enhances anti-tumor effects in preclinical prostate cancer.

RationaleThere is an important clinical need to improve the treatment of high risk localized and locally advanced prostate cancer (PCa), and to reduce the side effects of these treatments. We hypothesized that multi-modality therapy combining radiotherapy and vascular-targeted photodynamic therapy (VTP) could PCa tumour control compared against monotherapy with each of these treatments alone. This could provide proof-of-concept to take to the clinic. VTP is a focal therapy for localized PCa, which rapidly destroys targeted tumors through vascular disruption. Tumor vasculature is characterized by vessel immaturity, increased permeability, aberrant branching and inefficient flow. Fractionated radiotherapy (FRT) alters the tumor microenvironment and promotes transient vascular normalization. ObjectiveWe investigated whether sequential delivery of FRT followed by VTP 7 days later improves PCa tumor control compared to monotherapy with FRT or VTP alone. FindingsFRT induced vascular normalization changes in PCa flank tumor allografts, improving vascular function as demonstrated using dynamic contrast enhanced magnetic resonance imaging. FRT followed by VTP significantly delayed tumor growth in flank PCa allograft pre-clinical models, compared with monotherapy with FRT or VTP alone, and improved overall survival. ConclusionTaken together, these results suggest that combining FRT and VTP could become a promising multimodal clinical strategy in PCa therapy. This provides proof-of-concept for this multi-modality therapy approach to take forward to early phase clinical trials.

cancer biology↗

bioRxiv2020

What makes Hemidactylus invasions successful? A case study on the island of Curacao.

Hemidactylus spp. (House geckos) rank among the most successful invasive reptile species worldwide. Hemidactylus mabouia in particular has become ubiquitous across tropical urban settings in the Western Hemisphere. H. mabouia’s ability to thrive in close proximity to humans has led to the rapid displacement of native geckos in urban areas, however the mechanisms driving this displacement remain understudied. Here we combine data from nitrogen and carbon stable isotopes, stomach contents, and morphometric analyses of traits associated with feeding and locomotion to test alternate hypotheses of displacement between H. mabouia and a native gecko, Phyllodactylus martini, on the island of Curaçao. Consistent with expectations of direct food resource competition, we demonstrate substantial overlap of invertebrate prey resources between the species. Additionally, we found strong evidence from both diet content and stable isotope analyses that H. mabouia acts as a vertebrate predator, preying upon P. martini as well as other native and non-native reptiles. Finally, we show that H. mabouia possesses several morphological advantages, including larger sizes in feeding-associated traits and limb proportions that could offer a propulsive locomotor advantage on vertical surfaces. Together, these findings suggest the successful establishment of H. mabouia likely involves a combination of both exploitative interspecific competition and predation. Given the ubiquity of H. mabouia, illuminating the role of this species as both a competitor and a predator casts new concerns on the ecological and demographic impacts of this widespread urban invader.Competing Interest StatementThe authors have declared no competing interest.View Full Text

zoology↗

bioRxiv2017

Mining human prostate cancer datasets: The "camcAPP" shiny app

Obtaining access to robust, well-annotated human genomic datasets is an important step in demonstrating relevance of experimental findings and, often, in generating the hypotheses that led to those experiments being conducted in the first place. We recently published data from two cohorts of men with prostate cancer who had undergone prostatectomy, men from Cambridge, UK and Stockholm, Sweden.1 We considered how we might best share our output with those who wish to interrogate the data with their own ideas, gene lists and clinical questions. We recognised that finding, down-loading, processing and assimilating any such dataset into a usable format is daunting and may put off even the more persistent researcher. We also felt that interrogation tools generated to date (e.g. cBioPortal) lack functionality as they either cover too many organ types, or fall short in terms of clinical annotation. We therefore determined to produce an accessible web-based platform ...

cancer biology↗