Biology subjects

Williamson, S.

Publications and source records attributed to Williamson, S..

6 recordsLinked to original sources

bioRxiv2025

Mapping Molecular Diversity in Prostate Cancer with a Combined Multiplex IHC and RNA-ISH Assay

Combining multiplex Immunohistochemistry (mIHC) and RNA in situ hybridization (RNA-ISH) in a single assay allows for the simultaneous detection of multiple markers in tissue sections. This approach can be a powerful tool for understanding the molecular landscape of tumors, such as prostate cancer, by providing information in the same tissue context. Studying the expression of multiple genes in the same tissue is often necessary. ERG, SPINK1, ETV1, and ETV4 are all relevant genes in the context of prostate cancer. ERG is a transcription factor, and its fusion with the TMPRSS2 gene is one of the most common genetic alterations in prostate cancer. Overexpression of the ERG protein due to this gene, involved in gene fusion with TMPRSS2 and rarely with other 5 partner genes, can be detected using Immunohistochemistry (IHC) due to the availability of a characterized antibody. SPINK1 (serine peptidase inhibitor, Kazal type 1) is an overexpressed protein in a subset of prostate cancers that do not harbor ERG rearrangements. High SPINK1 expression is known to be associated with a more aggressive tumor phenotype in some studies. SPINK1 expression can be detected using a well-characterized antibody by IHC. ETV1 and ETV4 are transcription factors that can also be involved in gene fusions in prostate cancer, albeit less frequently than ERG. There are no well-characterized antibodies for ETV1 and ETV4. Due to the mutually exclusive expression of ERG, SPINK1, ETV1, and ETV4, simultaneous evaluation of these genes can provide valuable information on the molecular subtype of prostate cancer, which can have implications for the assessment of inter- and intra-tumor heterogeneity, prognosis, and potential treatment. We describe a novel approach for the simultaneous evaluation of all four markers in prostate cancer tissues using a combined dual IHC and dual RNA-ISH method using validated antibodies for ERG, SPINK1, and RNAscope probes for ETV1 and ETV4.

pathology↗

bioRxiv2025

Diverse Genomic Landscape of Swine Influenza A Virus in England (2014 - 2021)

Surveillance of influenza A viruses in pigs (SwIAV) is critical for identification of novel genetic groups that pose a risk to pig health and might have zoonotic potential. SwIAVs circulating in pigs in England between 2014 and 2021 were characterised using whole genome sequencing (WGS). Haemagglutinin (HA) and neuraminidase (NA) sequencing data from 82 of 368 influenza A positive samples (71 submissions) were determined, identifying H1N1 and H1N2 subtypes from the 1A classical swine and 1B human-seasonal lineages respectively. The 1B lineage viruses were predominant, accounting for 68.29% of sequenced viruses, with 1A lineage viruses comprising 31.71%, primarily from the 1A.3.3.2 clade (2009 H1N1 pandemic origin). This study characterised previously undefined diversity within the 1B lineage which led to the designation of new HA clades 1B.1.1.1, 1B.1.1.2 and 1B.1.1.3. Complete genome data were obtained from 64/82 viruses thereby updating the definition of genetic diversity thresholds and leading to the identification of 24 unique genotypes. All these 64 viruses contained PB2, PB1, PA, NP, MP, and NS gene segments of 2009 H1N1 pandemic origin. These data highlight the increasing divergence of SwIAV within pig populations England and emphasise the requirement for continued genomic surveillance to improve animal health and monitor zoonotic risk.

genomics↗

bioRxiv2023

Replicated Functional Evolution in Cichlid Adaptive Radiations

Adaptive radiations highlight the mechanisms by which species and traits diversify and the extent to which these patterns are predictable. We used 1,110 high-speed videos of suction feeding to study functional and morphological diversification in 300 cichlid species from three African Great Lake radiations of varying ages (Tanganyika, Malawi and Victoria) and an older, spatially dispersed continental radiation in the Neotropics. Among African radiations, standing diversity was reflective of time. Morphological and functional variance in Lake Victoria, the youngest radiation, was a subset of that within Lake Malawi, which itself was nested within the older Tanganyikan radiation. However, functional diversity in Neotropical cichlids was often lower than in Lake Tanganyika, despite being at least 25 My older. These two radiations broadly overlapped, but each diversified into novel trait spaces not found in the youngest lake radiations. Evolutionary rates across radiations were inversely related to age, suggesting, at least for lake radiations, extremely rapid trait evolution at early stages. Despite this support for early bursts, other patterns of trait diversity were inconsistent with expectations of adaptive radiations. This work suggests that cichlid functional evolution has played out in strikingly similar fashion in different radiations, with contingencies eventually resulting in lineage-specific novelties.

evolutionary biology↗

bioRxiv2022

Multi-omic profiling of breast cancer cells uncovers stress MAPK-associated sensitivity to AKT degradation

Over 50% of human tumors display hyperactivation of the serine/threonine kinase AKT. Despite evidence of clinical efficacy, there remains scope to improve upon the therapeutic window of the current generation of AKT inhibitors. Here we report the development of a second-generation AKT degrader, INY-05-040, which outperformed catalytic AKT inhibition with respect to cellular suppression of AKT-driven phenotypes in breast cancer cell lines. A systematic growth inhibition screen across 288 cancer cell lines confirmed a substantially higher potency for INY-05-040 (median GI50adj = 1.1 {micro}M) compared to our first-generation AKT degrader (INY-03-041; median GI50adj = 3.1 {micro}M), with both compounds outperforming catalytic AKT inhibition with GDC-0068 (median GI50adj > 10 {micro}M). Using multi-omic profiling and causal network integration in breast cancer cells, we demonstrate that the enhanced efficacy of INY-05-040 is associated with sustained suppression of AKT signaling, followed by a potent induction of the stress mitogen activated protein kinase (MAPK) c-Jun N-terminal kinase (JNK). Further integration of growth inhibition assays with publicly available transcriptomic, proteomic, and reverse phase protein array (RPPA) measurements established low baseline JNK signaling as a biomarker for breast cancer sensitivity to AKT degradation. Collectively, our study presents a systematic framework for mapping the network-wide signaling effects of therapeutically relevant compounds, and identifies INY-05-040 as a potent pharmacological suppressor of AKT signaling.

cancer biology↗

bioRxiv2021

Characterising the Photoplethysmography Pulse Waveform for Use in Human Neuroscience: The Hybrid Excess and Decay (HED) Model

Photoplethysmography (PPG) offers a widely-used, convenient and non-invasive approach to monitoring basic indices of cardiovascular function such as heart rate and blood oxygenation. However, while the pulse waveform, generated by PPG comprises features that are shaped by physiological and psychological factors, it is frequently overlooked in analyses of such data. We suggest that studies could be enriched by exploiting the possibilities afforded by a systematic analysis of PPG waveforms. To do this we initially require a robust and automated means of characterising it, thereby allowing us to examine variations across individuals and between different physiological and psychological contexts. We present a psychophysiologically-relevant model, the Hybrid Excess and Decay (HED) Model, which characterises pulse wave morphology in terms of three underlying pressure waves and a decay function. We show that these parameters capture PPG data with a high degree of precision and, moreover, are sensitive to specific, physiologically-relevant changes within individuals. We present the theoretical and practical basis for the model and demonstrate its performance when applied to a pharmacological dataset of 105 participants receiving intravenous administrations of the sympathomimetic drug isoproterenol (Isoprenaline). We conclude by discussing the possible value in using the HED model to complement standard measures of PPG outputs.

neuroscience↗

bioRxiv2019

Clonal evaluation of early onset prostate cancer by expression profiling of ERG, SPINK1, ETV1, and ETV4 on whole mount radical prostatectomy tissue

Expression profiles of ETS related genes and SPINK1 in early onset prostate cancer have not been thoroughly explored. We retrieved 151 radical prostatectomy specimens from young men with prostate cancer (<55yrs) and characterized the expression of ERG, SPINK1, ETV1 and ETV4 by dual immunohistochemistry and dual RNA in-situ hybridization. Age, race, family history, preoperative prostate-specific antigen, biochemical recurrence and pathological variables using whole mount radical prostatectomy tissue were collected. 313 tumor nodules from 151 men including 68 (45%) Caucasians and 61 (40%) African Americans. Positive family history of prostate cancer was observed in 65 (43%) patients. Preoperative prostate-specific antigen ranged from 0.3 to 52.7 ng/ml (mean 7.04). Follow-up period ranged from 1 to 123.7 months (Mean 30.3). Biochemical recurrence was encountered in 8/151 (5%). ERG overexpression was observed in 85/151 (56%) cases, followed by SPINK1 in 61/151 (40%), ETV1 in 9/149 (6%), and ETV4 in 4/141 (3%). There were 25/151 (17%) cases showing both ERG and SPINK1 overexpression within different regions of either the same tumor focus or different foci. Higher frequency of ERG overexpression was seen in younger patients ([≤] 45 years old) (76% vs. 49%, p = 0.002213), Caucasian men (71% vs. 41% p = 0.000707), organ-confined tumors (64% vs. 33%, p = 0.00079), and tumors of Grade Groups 1 and 2 (62% vs. 26%, p = 0.008794). SPINK1 overexpression was more in African American men (68% vs. 26%, p = 0.00008), in tumors with high tumor volume (> 20%) and with anterior located tumors. ETV1 and ETV4 demonstrated rare overexpression in these tumors, particularly in the higher-grade tumors. This study expands the knowledge of the clonal evolution of multifocal cancer in young patients and support differences in relation to racial background and genetics of prostate cancer.

pathology↗