ORCID Profile
0000-0001-9053-9138
Current Organisation
Peter MacCallum Cancer Centre
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Publisher: BMJ
Date: 06-2022
Abstract: Aberrations in homologous recombination repair (HRR) genes are emerging as important biomarkers for personalized treatment in prostate cancer (PCa). HRR deficiency (HRD) could affect the tumor immune microenvironment (TIME), potentially contributing to differential responses to poly ADP-ribose polymerase (PARP) inhibitors and immune checkpoint inhibitors. Spatial distribution of immune cells in a range of cancers identifies novel disease subtypes and is related to prognosis. In this study we aimed to determine the differences in the TIME of PCa with and without germline ( g ) HRR mutations. We performed gene expression analysis, multiplex immunohistochemistry of T and B cells and quantitative spatial analysis of PCa s les from 36 patients with g HRD and 26 patients with sporadic PCa. S les were archival tumor tissue from radical prostatectomies with the exception of one biopsy. Results were validated in several independent cohorts. Although the composition of the T cell and B cells was similar in the tumor areas of g HRD-mutated and sporadic tumors, the spatial profiles differed between these cohorts. We describe two T-cell spatial profiles across primary PCa, a clustered immune spatial (CIS) profile characterized by dense clusters of CD4 + T cells closely interacting with PD-L1 + cells, and a free immune spatial (FIS) profile of CD8 + cells in close proximity to tumor cells. g HRD tumors had a more T-cell inflamed microenvironment than sporadic tumors. The CIS profile was mainly observed in sporadic tumors, whereas a FIS profile was enriched in g HRD tumors. A FIS profile was associated with lower Gleason scores, smaller tumors and longer time to biochemical recurrence and metastasis. g HRD-mutated tumors have a distinct immune microenvironment compared with sporadic tumors. Spatial profiling of T-cells provides additional information beyond T-cell density and is associated with time to biochemical recurrence, time to metastasis, tumor size and Gleason scores.
Publisher: Wiley
Date: 09-03-2018
DOI: 10.1002/PROS.23500
Abstract: The development of radioresistance in prostate cancer (PCa) is an important clinical issue and is still largely uninformed by personalized molecular characteristics. The aim of this study was to establish a platform that describes the early oncoproteomic response of human prostate tissue to radiation therapy (RT) using a prospective human tissue cohort. Fresh and fixed transperineal biopsies from eight men with clinically localized tumors were taken prior to and 14 days following a single fraction of high-dose-rate brachytherapy. Quantitative protein analysis was achieved using an optimized protein extraction pipeline and subsequent data-independent acquisition mass spectroscopy (DIA-MS). Ontology analyses were used to identify enriched functional pathways, with the candidates further interrogated in formalin-fixed paraffin-embedded tissue biopsies from five additional patients. We obtained a mean coverage of 5660 proteins from fresh tissue biopsies with the principal post-radiation change observed being an increase in levels amongst a total of 49 proteins exhibiting abundance changes. Many of these changes in abundance varied between patients and, typically to prostate cancer tissue, exhibited a high level of heterogeneity. Ontological analysis revealed the enrichment of the protein activation cascades of three immunological pathways: humoral immune response, leukocyte mediated immunity and complement activation. These were predominantly associated with the extracellular space. We validated significant expression differences in between 20% and 61% of these candidates using the separate fixed-tissue cohort and established their feasibility as an experimental tissue resource by acquiring quantitative data for a mean of 5152 proteins per patient. In this prospective study, we have established a sensitive and reliable oncoproteomic pipeline for the analysis of both fresh and formalin-fixed human PCa tissue. We identified multiple pathways known to be radiation-responsive and have established a powerful database of candidates and pathways with no current association with RT. This information may be beneficial in the advancement of personalized therapies and potentially, predictive biomarkers.
Publisher: Cold Spring Harbor Laboratory
Date: 02-06-2020
DOI: 10.1101/2020.06.01.20115345
Abstract: Understanding the drivers of recurrence in aggressive prostate cancers requires detailed molecu-lar and genomic understanding in order to aid therapeutic interventions. Here we present a case study of a 70 year old male with high-grade clinically-localised acinar adenocarcinoma treated with definitive hormone therapy and radiotherapy. The patient progressed rapidly with rising PSA and succumbed without metastasis 52 months after diagnosis. We provide here a descrip-tion of histological, transcriptional, proteomic, immunological, and genomic features associated with this disease - identifying hallmarks of canonical neuroendocrine PC disease and other nov-el molecular features.
Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.TRECAN.2019.10.008
Abstract: Cancer cells devouring their neighbours to survive drug treatment is an abhorrent concept. Yet it holds hope for exploring new anticancer treatments. Tonnessen-Murray et al. adopted elegant cell-labelling methods using real-time microscopy to observe 'cellular gorging' by drug-treated cells. They discovered that in response to drug treatment, cells that became 'cannibals' were able to outlive their unindulged neighbours.
Publisher: Wiley
Date: 2019
DOI: 10.1002/CTI2.1094
Publisher: MDPI AG
Date: 27-11-2015
DOI: 10.3390/LIFE5041638
Publisher: Springer US
Date: 2021
Publisher: Cold Spring Harbor Laboratory
Date: 06-03-2020
DOI: 10.1101/2020.03.02.20030346
Abstract: Prostate cancer (PCa) has a profoundly immunosuppressive microenvironment, we hypothesized that radiation therapy would break this immune suppression. To investigate this, we performed high-throughput immune cell subset analysis, and gene expression profiling of pre-versus post-radiation tissue in a cohort of patients with localized disease that received high dose-rate brachytherapy (HDRBT). We resolved tumor and non-tumor zones in our spatial analysis to explore what drives the immunological response. Nanostring immune profiling revealed numerous immune checkpoint molecules were stimulated in response to HDRBT (e.g. B7-H3, CTLA4, PDL1 and PDL2). A published 16-gene tumor inflammation signature (TIS) gene profiling of immune activation states (high: hot , intermediate and low: cold ) showed that most tissues possessed a low TIS pre-HDRBT. Crucially, HDRBT converted 80% of these ‘cold’-phenotype tumors into an ‘intermediate’ or ‘hot’ class. We used digital spatial profiling to show these HDRBT-induced changes in prostate TIS scores were derived from the non-tumor regions. Furthermore, these changes in TIS were also associated with pervasive changes in immune cell density and spatial relationships – in particularly between T cell subsets and antigen presenting cells. We identified increased density of CD4 + FOXP3 + T cells, CD68 + macrophages and CD68 + CD11c + dendritic cells in response to HDRBT. The only subset change in tumor zones was PDL1 + macrophages. While these immune responses were heterogeneous, HDRBT induced significant changes in immune cell associations, including a gained T cell and HMWCK + PDL1 + interaction in tumor zones. In conclusion, we showed HDRBT has a clear impact in converting “cold” prostate tumors into more immunologically activated “hot” tissues, with accompanying spatially-organized immune infiltrates and signaling changes. Understanding and potentially harnessing these changes will have widespread implications for the future treatment of localized PCa and the possible use of combination immunotherapies.
Publisher: Oxford University Press (OUP)
Date: 18-07-2014
DOI: 10.1093/NAR/GKU620
Publisher: Elsevier BV
Date: 06-2018
Publisher: Springer New York
Date: 2014
DOI: 10.1007/978-1-4939-0931-5_14
Abstract: The rapidly growing list of small RNA species generated by next-generation sequencing technologies has accelerated the development of new bioinformatics tools for their detection. Small RNAs generated from tRNAs, transfer RNA-derived fragments (tRFs), represent a novel challenge in accurately identifying and distinguishing them from random degradation products of tRNAs. Here, we describe a bioinformatics approach to detect tRFs in next-generation sequencing libraries. We also present a biochemical purification protocol for enriching 5' tRFs and separating them from miRNAs. And finally, we suggest reliable methods for detecting and quantifying tRFs.
Publisher: American Chemical Society (ACS)
Date: 12-12-2017
DOI: 10.1021/ACS.JPROTEOME.6B00267
Abstract: The functionality of small RNAs from abundant species of "housekeeping" noncoding RNAs (e.g., rRNA, tRNA, snRNA, snoRNA, etc.) remains a highly studied topic. The current state of research on short RNAs derived from transfer RNA (tRNA), called tRNA-derived fragments (tRFs), has been restricted largely to expression studies and limited functional studies. 5' tRFs are known translational inhibitors in mammalian cells, yet little is known about their functionality. Here we report on the first experimental evidence of the tRF protein interactome, identifying the mammalian multisynthetase complex as the primary interactor of the 5' tRF Gln19. We also present proteome-wide SILAC evidence that 5' tRFs increase ribosomal and poly(A)-binding protein translation.
Publisher: Oxford University Press (OUP)
Date: 03-2019
DOI: 10.1093/JMCB/MJZ007
Publisher: Cold Spring Harbor Laboratory
Date: 30-05-2020
DOI: 10.1101/2020.05.28.122614
Abstract: Spatial technologies that query the location of cells in tissues at single-cell resolution are gaining popularity and are likely to become commonplace. The resulting data includes the X, Y coordinates of millions of cells, cell phenotypes and marker or gene expression levels. However, to date, the tools for the analysis of this data are largely underdeveloped, making us severely underpowered in our ability to extract quantifiable information. We have developed SPIAT ( Sp atial I mage A nalysis of T issues), an R package with a suite of data processing, quality control, visualization, data handling and data analysis tools. SPIAT includes our novel algorithms for the identification of cell clusters, cell margins and cell gradients, the calculation of neighbourhood proportions, and algorithms for the prediction of cell phenotypes. SPIAT also includes speedy implementations of the calculation of cell distances and detection of cell communities. This version of SPIAT is directly compatible with Opal multiplex immunohistochemistry images analysed through the HALO and InForm analysis software, but its intuitive implementation allows use with a ersity of platforms. We expect SPIAT to become a user-friendly and speedy go-to package for the spatial analysis of cells in tissues. SPIAT is available on Github: ancer-evolution/SPIAT
Publisher: Springer Science and Business Media LLC
Date: 08-09-2022
DOI: 10.1038/S41419-022-05211-Y
Abstract: Understanding prostate cancer onset and progression in order to rationally treat this disease has been critically limited by a dire lack of relevant pre-clinical animal models. We have generated a set of genetically engineered mice that mimic human prostate cancer, initiated from the gland epithelia. We chose driver gene mutations that are specifically relevant to cancers of young men, where aggressive disease poses accentuated survival risks. An outstanding advantage of our models are their intact repertoires of immune cells. These mice provide invaluable insight into the importance of immune responses in prostate cancer and offer scope for studying treatments, including immunotherapies. Our prostate cancer models strongly support the role of tumour suppressor p53 in functioning to critically restrain the emergence of cancer pathways that drive cell cycle progression alter metabolism and vasculature to fuel tumour growth and mediate epithelial to mesenchymal-transition, as vital to invasion. Importantly, we also discovered that the type of p53 alteration dictates the specific immune cell profiles most significantly disrupted, in a temporal manner, with ramifications for disease progression. These new orthotopic mouse models demonstrate that each of the isogenic hotspot p53 amino acid mutations studied (R172H and R245W, the mouse equivalents of human R175H and R248W respectively), drive unique cellular changes affecting pathways of proliferation and immunity. Our findings support the hypothesis that in idual p53 mutations confer their own particular oncogenic gain of function in prostate cancer.
Publisher: British Institute of Radiology
Date: 12-2019
DOI: 10.1259/BJR.20190373
Abstract: To investigate the association between multiparametric MRI (mpMRI) imaging features and hypoxia-related genetic profiles in prostate cancer. In vivo mpMRI was acquired from six patients prior to radical prostatectomy. Sequences included T 2 weighted (T 2 W) imaging, diffusion-weighted imaging, dynamic contrast enhanced MRI and blood oxygen-level dependent imaging. Imaging data were co-registered with histology using three-dimensional deformable registration methods. Texture features were extracted from T 2 W images and parametric maps from functional MRI. Full transcriptome genetic profiles were obtained using next generation sequencing from the prostate specimens. Pearson correlation coefficients were calculated between mpMRI data and hypoxia-related gene expression levels. Results were validated using glucose transporter one immunohistochemistry (IHC). Correlation analysis identified 34 candidate imaging features (six from the mpMRI data and 28 from T 2 W texture features). The IHC validation showed that 16 out of the 28 T 2 W texture features achieved weak but significant correlations (p 0.05). Weak associations between mpMRI features and hypoxia gene expressions were found. This indicates the potential use of MRI in assessing hypoxia status in prostate cancer. Further validation is required due to the low correlation levels. This is a pilot study using radiogenomics approaches to address hypoxia within the prostate, which provides an opportunity for hypoxia-guided selective treatment techniques.
Publisher: Elsevier BV
Date: 12-2019
Publisher: BMJ
Date: 06-2020
Abstract: Prostate cancer (PCa) has a profoundly immunosuppressive microenvironment and is commonly immune excluded with few infiltrative lymphocytes and low levels of immune activation. High-dose radiation has been demonstrated to stimulate the immune system in various human solid tumors. We hypothesized that localized radiation therapy, in the form of high dose-rate brachytherapy (HDRBT), would overcome immune suppression in PCa. To investigate whether HDRBT altered prostate immune context, we analyzed preradiation versus postradiation human tissue from a cohort of 24 patients with localized PCa that received HDRBT as primary treatment (RadBank cohort). We performed Nanostring immune gene expression profiling, digital spatial profiling, and high-throughput immune cell multiplex immunohistochemistry analysis. We also resolved tumor and nontumor zones in spatial and bioinformatic analyses to explore the immunological response. Nanostring immune profiling revealed numerous immune checkpoint molecules (eg, B7-H3, CTLA4, PDL1, and PDL2) and TGFβ levels were increased in response to HDRBT. We used a published 16-gene tumor inflammation signature (TIS) to ide tumors into distinct immune activation states (high: hot , intermediate and low: cold ) and showed that most localized PCa are cold tumors pre-HDRBT. Crucially, HDRBT converted 80% of these ‘cold’-phenotype tumors into an ‘intermediate’ or ‘hot’ class. We used digital spatial profiling to show these HDRBT-induced changes in prostate TIS scores were derived from the nontumor regions. Furthermore, these changes in TIS were also associated with pervasive changes in immune cell density and spatial relationships—in particular, between T cell subsets and antigen presenting cells. We identified an increased density of CD4 + FOXP3 + T cells, CD68 + macrophages and CD68 + CD11c + dendritic cells in response to HDRBT. The only subset change specific to tumor zones was PDL1 - macrophages. While these immune responses were heterogeneous, HDRBT induced significant changes in immune cell associations, including a gained T cell and HMWCK + PDL1 + interaction in tumor zones. In conclusion, we showed HDRBT converted “cold” prostate tumors into more immunologically activated “hot” tissues, with accompanying spatially organized immune infiltrates and signaling changes. Understanding and potentially harnessing these changes will have widespread implications for the future treatment of localized PCa, including rational use of combination radio-immunotherapy.
Publisher: BMJ
Date: 05-2022
Abstract: Vaginal melanoma (VM) is a rare cancer and has a poor response to immune checkpoint blockade (ICB). CD8 + Tissue Resident Memory (TRM) T cells proliferate in response to ICB and correlate with longer survival in metastatic cutaneous melanoma. However, their capacity to respond to VM and their neoantigens is not known. Using longitudinal s les, we explored the evolution of VM mutations by whole-exome sequencing and RNAseq, we also defined the immune context using multiplex immunohistochemistry and nanostring pan cancer immune profile. Then using fresh single cell suspensions of the metastatic s les, we explored VM T cells via mass cytometry and single cell RNAseq and T cell receptor sequencing (TCRseq). Finally, we investigated TRM, pre-TRM and exhausted T cell function against melanoma neo-antigens and melanoma differentiation antigens in vitro. Primary VM was non-inflamed and devoid of CD8 + TRM cells. In contrast, both metastases showed proliferating CD8 + TRM were clustered at the tumor margin, with increased numbers in the second ICB-refractory metastasis. The first metastasis showed dense infiltration of CD8 + T cells, the second showed immune exclusion with loss of melanoma cell Major histocompatibility complex (MHC)-I expression associated with downregulation of antigen presentation pathway gene expression. CD8 + TRM from both metastases responded to autologous melanoma cells more robustly than all other CD8 + T cell subsets. In addition, CD8 + TRM shared TCR clones across metastases, suggesting a response to common antigens, which was supported by recognition of the same neoantigen by expanded tumor infiltrating lymphocytes. In this study, we identified TRM clusters in VM metastases from a patient, but not primary disease. We showed TRM location at the tumor margin, and their superior functional response to autologous tumor cells, predicted neoantigens and melanoma differentiation antigens. These CD8 + TRM exhibited the highest tumor-responsive potential and shared their TCR with tumor-infiltrating effector memory T cells. This suggests VM metastases from this patient retain strong antitumor T cell functional responses however, this response is suppressed in vivo. The loss of VG MHC-I expression is a common immune escape mechanism which was not addressed by anti-PD-1 monotherapy rather an additional targeted approach to upregulate MHC-I expression is required.
Publisher: Elsevier BV
Date: 04-2020
DOI: 10.1016/J.JID.2019.07.725
Abstract: Lentigo maligna (LM) is a common subtype of in situ melanoma on chronically sun-exposed skin, particularly the head and neck of older patients. Although surgery is the standard treatment, there is associated morbidity, and options such as imiquimod cream or radiotherapy may be used if surgery is refused or inappropriate. Complete response rates following imiquimod treatment are variable in the literature. The aim of this study was to evaluate the host immune response both before and following treatment with imiquimod to better identify likely responders. Paired pre- and post-imiquimod treatment specimens were available for 27 patients. Patients were treated with imiquimod 5 days per week for 12 weeks at 16 weeks, lesions were excised for histological assessment. Of the 27 patients, 16 were responders and 11 failed to clear the disease. PDL1 protein expression was increased, accompanied by a unique gene signature in lesions from patients that subsequently histologically cleared LM by 16 weeks. This comprised 57 upregulated immune genes in signaling networks for antigen presentation, type I interferon signaling, and T-cell activation. This may represent an early responder group to imiquimod, and this unique gene signature potentially can be used as a biomarker of LM response to imiquimod.
Publisher: Springer Science and Business Media LLC
Date: 30-05-2018
DOI: 10.1007/S00411-018-0746-5
Abstract: Transcriptional dosimetry is an emergent field of radiobiology aimed at developing robust methods for detecting and quantifying absorbed doses using radiation-induced fluctuations in gene expression. A combination of RNA sequencing, array-based and quantitative PCR transcriptomics in cellular, murine and various ex vivo human models has led to a comprehensive description of a fundamental set of genes with demonstrable dosimetric qualities. However, these are yet to be validated in human tissue due to the scarcity of in situ-irradiated source material. This represents a major hurdle to the continued development of transcriptional dosimetry. In this study, we present a novel evaluation of a previously reported set of dosimetric genes in human tissue exposed to a large therapeutic dose of radiation. To do this, we evaluated the quantitative changes of a set of dosimetric transcripts consisting of FDXR, BAX, BCL2, CDKN1A, DDB2, BBC3, GADD45A, GDF15, MDM2, SERPINE1, TNFRSF10B, PLK3, SESN2 and VWCE in guided pre- and post-radiation (2 weeks) prostate cancer biopsies from seven patients. We confirmed the prolonged dose-responsivity of most of these transcripts in in situ-irradiated tissue. BCL2, GDF15, and to some extent TNFRSF10B, were markedly unreliable single markers of radiation exposure. Nevertheless, as a full set, these genes reliably segregated non-irradiated and irradiated tissues and predicted radiation absorption on a patient-specific basis. We also confirmed changes in the translated protein product for a small subset of these dosimeters. This study provides the first confirmatory evidence of an existing dosimetric gene set in less-accessible tissues-ensuring peripheral responses reflect tissue-specific effects. Further work will be required to determine if these changes are conserved in different tissue types, post-radiation times and doses.
Publisher: Oxford University Press (OUP)
Date: 10-04-2019
Abstract: Since its discovery, the E3 ubiquitin ligase E6-associated protein (E6AP) has been studied extensively in two pathological contexts: infection by the human papillomavirus (HPV), and the neurodevelopmental disorder, Angelman syndrome. Vital biological links between E6AP and other viruses, namely hepatitis C virus and encephalomyocarditis virus, have been recently uncovered. Critically, oncogenic E6AP activities have been demonstrated to contribute to cancers of both viral and non-viral origins. HPV-associated cancers serve as the primary ex le of E6AP involvement in cancers driven by viruses. Studies over the past few years have exposed a role for E6AP in non-viral-related cancers. This has been demonstrated in B-cell lymphoma and prostate cancers, where oncogenic E6AP functions drive these cancers by acting on key tumour suppressors. In this review we discuss the role of E6AP in viral infection, viral propagation and viral-related cancer. We discuss processes affected by oncogenic E6AP, which promote cancers of viral and non-viral aetiology. Overall, recent findings support the role of oncogenic E6AP in disrupting key cellular processes, including tumour suppression and the immune response. E6AP is consequently emerging as an attractive therapeutic target for a number of specific cancers.
Publisher: Research Square Platform LLC
Date: 12-08-2020
DOI: 10.21203/RS.3.RS-50207/V1
Abstract: MR1-restricted mucosal-associated invariant T (MAIT) cells recognize microbial metabolites and play an important role in immunity to infection, however, the role they play in tumor immunity is unclear. Here we show that MAIT cell-deficient mice are more resistant to subcutaneous and lung metastasis B16F10 tumor growth compared to control mice, an effect that was associated with enhanced NK cell numbers and was NK cell-dependent. Analysis of this interplay in cancer patients also revealed that a high expression of a novel MAIT gene signature negatively impacted the prognostic significance of NK cells. Paradoxically, pre-pulsing tumors with MAIT cell antigens, or antigen-mediated MAIT cell activation in vivo, enhanced immunity against B16F10 and E0771 lung tumor metastasis. Furthermore, MAIT cell activation effectively reduced metastatic burden in a more stringent model of established lung metastases in mice. These effects were associated with enhanced NK cell responses and increased expression of both IFNγ-dependent and inflammatory genes in NK cells, which was neutralized by IFNγ blockade. Importantly, activated human MAIT cells also enhanced the function of NK cells isolated from patient tumor s les. These findings provide insight into the contrasting roles that MAIT cells can play in controlling anti-tumor immune responses depending on their activation status, in both mice and humans, and suggest potential therapeutic avenues for exploiting their potential anti-tumor properties for cancer treatment.
Publisher: Elsevier BV
Date: 03-2021
DOI: 10.1016/J.EUF.2020.09.021
Abstract: LuTectomy is an open-label phase 1/2 nonrandomised clinical trial evaluating the dosimetry, efficacy, and toxicity of the lutetium-177-radiolabelled small molecule PSMA-617 in men with high-risk localised/locoregional advanced prostate cancer with high prostate-specific membrane antigen expression who are undergoing radical prostatectomy and pelvic lymph node dissection.
Publisher: Cold Spring Harbor Laboratory
Date: 16-03-2020
DOI: 10.1101/2020.03.16.993162
Abstract: Prostate cancer is caused by genomic aberrations in normal epithelial cells, however clinical translation of findings from analyses of cancer cells alone has been very limited. A deeper understanding of the tumour microenvironment is needed to identify the key drivers of disease progression and reveal novel therapeutic opportunities. In this study, the experimental enrichment of selected cell-types and the development of a Bayesian inference model for continuous differential transcript abundance permitted us to define the transcriptional landscape of the prostate cancer microenvironment along the disease progression axis. An important role of monocytes and macrophages in prostate cancer progression and disease recurrence was uncovered, supported by both transcriptional landscape findings and by differential tissue composition analyses. These findings were corroborated and validated by spatial analyses at the single-cell level using multiplex immunohistochemistry. This study advances our knowledge concerning the role of monocyte-derived recruitment in primary prostate cancer, and supports their key role in disease progression, patient survival and prostate microenvironment immune modulation.
Publisher: MDPI AG
Date: 11-06-2020
Abstract: Lung cancer poses the greatest cancer-related death risk and males have poorer outcomes than females, for unknown reasons. Patient sex is not a biological variable considered in lung cancer standard of care. Correlating patient genetics with outcomes is predicted to open avenues for improved management. Using a bioinformatics approach across non-small cell lung cancer (NSCLC) subtypes, we identified where patient sex, mutation of the major tumor suppressor gene, Tumour protein P53 (TP53), and immune signatures stratified outcomes in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), among datasets of The Cancer Genome Atlas (TCGA). We exposed sex and TP53 gene mutations as prognostic for LUAD survival. Longest survival in LUAD occurred among females with wild-type (wt) TP53 genes, high levels of immune infiltration and enrichment for pathway signatures of Interferon Gamma (INF-γ), Tumour Necrosis Factor (TNF) and macrophages-monocytes. In contrast, poor survival in men with LUAD and wt TP53 genes corresponded with enrichment of Transforming Growth Factor Beta 1 (TGFB1, hereafter TGF-β) and wound healing signatures. In LUAD with wt TP53 genes, elevated gene expression of immune checkpoint CD274 (hereafter: PD-L1) and also protein 53 (p53) negative-regulators of the Mouse Double Minute (MDM)-family predict novel avenues for combined immunotherapies. LUSC is dominated by male smokers with TP53 gene mutations, while a minor population of TCGA LC patients with wt TP53 genes unexpectedly had the poorest survival, suggestive of a separate etiology. We conclude that advanced approaches to LUAD and LUSC therapy lie in the consideration of patient sex, TP53 gene mutation status and immune signatures.
Publisher: Cold Spring Harbor Laboratory
Date: 10-03-2016
DOI: 10.1101/042101
Abstract: Parental exposure to an environmental challenge can induce phenotypes in offspring independent of the inherited DNA sequence. Whether such acquired traits can be inherited, i.e., can manifest in a generation beyond that exposed to the precipitating insult as germ cells, is unclear. Here we report a latent metabolic phenotype induced by paternal obesity that is inherited into a second generation, without germ cell exposure. Sons of obese male mice exhibit defects in glucose and lipid metabolism that are only unmasked by post-weaning dietary challenge, yet they transmit these defects to their own progeny (F2) in the absence of the challenge. F1 sperm exhibit changes in the abundance of several small RNA species, including diet responsive tRNA-derived fragments. These data suggest that induced metabolic phenotypes may be propagated for multiple generations through the actions of noncoding RNA.
Publisher: Informa UK Limited
Date: 2020
Publisher: Elsevier BV
Date: 09-2001
DOI: 10.1086/323123
Publisher: Springer Science and Business Media LLC
Date: 28-10-2020
DOI: 10.1186/S12894-020-00738-8
Abstract: Understanding the drivers of recurrence in aggressive prostate cancer requires detailed molecular and genomic understanding in order to aid therapeutic interventions. We provide here a case report of histological, transcriptional, proteomic, immunological, and genomic features in a longitudinal study of multiple biopsies from diagnosis, through treatment, and subsequent recurrence. Here we present a case study of a male in 70 s with high-grade clinically-localised acinar adenocarcinoma treated with definitive hormone therapy and radiotherapy. The patient progressed rapidly with rising PSA and succumbed without metastasis 52 months after diagnosis. We identified the expression of canonical histological markers of neuroendocrine PC (NEPC) including synaptophysin, neuron-specific enolase and thyroid transcription factor 1, as well as intact AR expression, in the recurrent disease only. The resistant disease was also marked by an extremely low immune infiltrate, extensive genomic chromosomal aberrations, and overactivity in molecular hallmarks of NEPC disease including Aurora kinase and E2F, as well as novel alterations in the cMYB pathway. We also observed that responses to both primary treatments (high dose-rate brachytherapy and androgen deprivation therapies) were consistent with known optimal responses—ruling out treatment inefficacy as a factor in relapse. These data provide novel insights into a case of locally recurrent aggressive prostate cancer harbouring NEPC pathology, in the absence of detected metastasis.
Publisher: Springer Science and Business Media LLC
Date: 15-05-2023
DOI: 10.1038/S41467-023-37822-0
Abstract: Spatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and clinical features, but there is significant lag in the development of downstream analysis methods and benchmarking tools. Here we present SPIAT (spatial image analysis of tissues), a spatial-platform agnostic toolkit with a suite of spatial analysis algorithms, and spaSim (spatial simulator), a simulator of tissue spatial data. SPIAT includes multiple colocalization, neighborhood and spatial heterogeneity metrics to characterize the spatial patterns of cells. Ten spatial metrics of SPIAT are benchmarked using simulated data generated with spaSim. We show how SPIAT can uncover cancer immune subtypes correlated with prognosis in cancer and characterize cell dysfunction in diabetes. Our results suggest SPIAT and spaSim as useful tools for quantifying spatial patterns, identifying and validating correlates of clinical outcomes and supporting method development.
No related grants have been discovered for Simon Keam.