Biology subjects

Nicholson, S.

Publications and source records attributed to Nicholson, S..

10 recordsLinked to original sources

bioRxiv2026

Minimally invasive monitoring of clonal evolution through integrated single cell and ctDNA analysis

Circulating cell-free DNA (cfDNA) offers a minimally invasive lens into tumor evolution. However, the accurate quantification of clonal composition from cfDNA remains challenging. Existing methods for clone tracking using liquid biopsies are constrained by issues such as their reliance on bulk tissue references, incomplete representations of clonal architecture or limited breadth of mutation panels. To address these limitations, we developed cfClone, a Bayesian framework that integrates single-cell whole-genome sequencing (scWGS) derived clonal structures with cfDNA whole-genome sequencing (cfDNA-WGS) data to enable high-resolution tissue-informed clonal tracking. By jointly modeling local copy-number alterations and haplotype-specific signals via Bayesian model selection and Markov chain Monte Carlo (MCMC) sampling, the algorithm yields uncertainty-aware estimates of clonal prevalence and tumour fraction (TF). Applied to longitudinal clinical cohorts, cfClone can be used to reconstruct evolutionary trajectories and uncovers clonal selection driving therapeutic resistance, including the de novo detection of emergent clonal populations. We demonstrate that cfClone achieves accurate TF estimates and circulating tumor DNA (ctDNA) detection in malignancies with varying degrees of copy-number variant (CNV) burden using semi-synthetic data. We then compare to the state of the art scWGS informed panel based approach, and demonstrate cfClone provides comparable accuracy while allowing for the tracking of more clones and detection of novel clones. Finally, we show how cfClone can be used to quantitatively track clonal dynamics in response to treatment in high grade serous ovarian cancer. Github link: https://github.com/Roth-Lab/cfclone

cancer biology↗

bioRxiv2026

Utanos: A general-purpose shallow whole-genome sequencing analysis workflow identifies interpretable copy number signatures

SummaryA modular FASTQ-to-figures solution for analyzing low-depth or shallow whole-genome sequencing (sWGS) data. Shallow WGS can be used to detect copy number (CN) aberrations, Homologous Recombination Deficiency (HRD), and to detect and create CN signatures. Growing in popularity, this sequencing type is used for neonatal diagnostics and studying cancer. One of the major benefits is the reduced cost compared with deeper sequencing modalities such as Whole Genome Sequencing (WGS). With just 15 million reads often targeted, and sample substrate options like Formalin-Fixed, Paraffin-Embedded (FFPE) blocks widely available, this approach enables an affordable study to be performed at scale. Our pipeline and R package are an end-to-end solution implemented with reusability and modularity in mind. It makes entry and exit from the ecosystem easy, providing regular standardized output formats throughout execution. The pipeline is written in the well-supported and cross-platform Nextflow framework and has been submitted for inclusion in nf-core. Additionally, a Docker image for the utanos R package has been created to improve modularity. Availability and ImplementationThe latest version of all software is freely available on GitHub. For the full processing pipeline, visit: https://github.com/Huntsmanlab/swgs-processing-pipeline. For just the utanos R package, visit: https://github.com/Huntsmanlab/utanos.

bioinformatics↗

bioRxiv2026

Brief report on the development of patient-derived lung cancer organoids with keratinizing squamous cell carcinoma morphology

IntroductionNovel therapeutic options are urgently required to improve outcomes and survival for patients with lung squamous cell carcinoma (LUSC). In particular, understanding the unique histological features that define LUSC is essential to improving lung cancer mortality. Many pre-clinical models fail to accurately represent intratumour heterogeneity and recapitulate the tumour microenvironment. This is partly responsible for the poor translation of clinical findings to approved therapies. Our objective was to investigate whether patient-derived organoids, replicate the histological morphological, and structural features of keratinizing LUSC, a poor prognostic subtype of lung cancer. MethodsOrganoid cultures were established and maintained from two patients presenting with keratinizing lung squamous cell carcinomas. Immunofluorescent staining of individual organoids and confocal microscopy was performed to confirm expression of tumour markers. Whole organoid domes were fixed, and immunofluorescent staining and imaging was performed to investigate the structural features of the organoid cultures. Findings were compared with histopathological features of the original tumour tissue. ResultsPatient-derived organoids expressed tumour markers specific to the squamous cell carcinoma subtype of non-small cell lung cancer, which were confirmed to be expressed in the parent tissue. Within organoid cultures, keratin pearl structures spontaneously developed, matching the keratinizing pattern demonstrated by hematoxylin and eosin staining of the original tumour. ConclusionsPatient-derived organoids have the capability to replicate key histological features of their parent tumour. This high degree of fidelity makes these 3D models an important and valuable tool for understanding complex tumour biology and as a platform for preclinical drug testing to advance novel therapies into the clinic.

cancer biology↗

bioRxiv2026

A Modular In-Incubator Microscope for Longitudinal Live Cell Microscopy

Longitudinal live cell imaging is valuable for characterizing dynamic morphological and phenotypic changes in biological systems. However, conventional approaches rely on manual microscope operation, which is labor-intensive, limits imaging frequency, and disrupts the cellular environment. These constraints reduce scalability, increase experimental variability, and restrict both the duration and temporal resolution of continuous imaging. Although automated imaging platforms partially address these limitations, existing solutions are often constrained by the cost, footprint, and inflexibility of in-incubator microscopes or stage-top incubators. Here, we present an automated in-incubator epifluorescence microscope designed for long-term operation. The system features a modular architecture with optional multi-fluorescence imaging, automated plate scanning, configurable light sources, and compatibility with multiple plate formats, including integration with fluidic automation devices. By positioning the light sources and control electronics outside the incubator, the platform improves thermal stability and long-term operational reliability. This approach enables continuous, high-frequency imaging over extended durations, providing a source of rich data for quantifying time-dependent tissue phenotypes, morphological remodeling, and transient biological processes.

bioengineering↗

bioRxiv2025

A comprehensive view of somatic mosaicism by single-cell DNA analysis

Single-cell DNA sequencing offers a powerful means of studying somatic mosaicism but requires careful analysis to mitigate DNA amplification-related artifacts. We performed primary template-directed amplification (PTA) and sequencing of 102 nuclei from postmortem lung and colon tissues of a 74-year-old male. Single-cell mutation burdens and spectra were validated by duplex sequencing and revealed heterogeneity across organs and cells, including signatures of APOBEC activity and tobacco exposure. Cells from both tissues exhibited chromosomal aneuploidies, loss of chromosome Y, and chromosomal rearrangements including rearrangements of the T-cell receptor loci indicative of T-cells. Shared embryonic mutations between cells enabled reconstruction of cellular ancestries from the zygote, which were validated by bulk sequencing. Collectively, we demonstrate a comprehensive approach for single-cell genomics that yields an expansive view of diverse somatic mutation types from development through aging across diverse tissues--insights that are obscured in bulk sequencing and only partially captured by other single-cell methods.

genomics↗

bioRxiv2025

Prenatal anti-oxidant treatment suppresses maternal immune activation induced increases in alcohol self-administration in a sex-specific manner

Prenatal exposure to infection is a risk factor in the development of several neuropsychiatric disorders, including schizophrenia and depression, which often co-occur with alcohol misuse, exacerbating adverse outcomes. Despite these consequences, little is understood regarding the mechanisms by which early exposure to infection might increase the risk of alcohol misuse. We have previously demonstrated that maternal immune activation (MIA) combined with adolescent alcohol exposure (AA) increases home-cage drinking and disrupts neural circuit function in adulthood. The current project aims to determine whether these findings extend to the motivation to work for alcohol, and whether prenatal anti-oxidant treatment can prevent the effects of MIA on self-administration. Pregnant Sprague-Dawley rats were exposed to poly(I:C) (4mg/kg) or saline on gestational day 15, and the anti-oxidant n-acetylcysteine (NAC; 100 mg/kg) or saline 24 hours before and after MIA. Offspring were given 24-hour home cage access to 10% ethanol and water dur adolescence. In adulthood, offspring were trained to self-administer 10% ethanol and tested on escalating schedules of reinforcement: fixed ratio (FR)1, FR2, FR4, and progressive ratios (PR). MIA and NAC independently led to an increased willingness to work for alcohol in males, compared to saline-treated rats. NAC treatment suppressed the effect of MIA on self-administration behavior. These data support the hypothesis that oxidative stress caused by MIA negatively influences development, priming the brain to be more susceptible to the negative effects of AA, leading to an increased risk of alcohol misuse in adulthood, particularly in males.

pharmacology and toxicology↗

bioRxiv2025

GPR68, a proton-sensing GPCR, mediates acid-induced visceral nociception

Background & AimsLocalised acidification from immune cell infiltration and heightened glycolysis contributes to colitis pathology by activating acid-sensing receptors such as GPR68, a proton-sensing GPCR expressed on immune and stromal cells. Single-cell RNAseq analysis revealed GPR68 is also expressed in colonic sensory neurons, prompting us to investigate its role in acid-induced colonic nociception. MethodsExpression of GPR68 in colonic nociceptors and tissue from people with colitis was confirmed by in silico analysis of our RNAseq databases. Its contribution to disease activity was assessed using the acute dextran sulphate sodium (DSS) model of colitis. Acid-evoked sensory signalling was evaluated via colonic afferent recordings and Ca{superscript 2} imaging in DRG neurons from wild-type and GPR68-/- mice, supported by pharmacological studies using Ogerin (a GPR68 positive allosteric modulator) and Ogremorphin (a GPR68 antagonist). ResultsRNAseq analysis showed GPR68 is robustly expressed in Trpv1 colonic nociceptors and upregulated in tissue from people with inflammatory bowel disease, consistent with reduced disease activity in DSS-treated GPR68-/- mice. Genetic deletion of GPR68 abolished colonic afferent responses to acid, which were also attenuated by Ogremorphin and enhanced by Ogerin. In Ca{superscript 2}-free buffer, DRG neurons from GPR68-/- mice or those pre-treated with Ogremorphin showed significantly reduced acid-evoked intracellular Ca{superscript 2} responses. By contrast the colonic afferent and DRG Ca2+ response (in Ca2+-containing buffer) to capsaicin was comparable between tissue from wild-type and GPR68-/- mice highlighting the involvement of divergent proton-dependent cellular signalling cascades. ConclusionsThese findings identify GPR68 as a key mediator of acid-induced colonic nociception and highlight its potential as a therapeutic target for the treatment of pain in colitis. SynopsisWe demonstrate that the proton-sensing receptor GPR68 mediates acid-induced signalling in colonic sensory neurons. Genetic and pharmacological modulation confirms GPR68s role in visceral nociception and supports its potential as a therapeutic target for pain management in colitis.

neuroscience↗

bioRxiv2025

ARAP2 regulates responses to interferon-gamma by restricting SOCS1

Interferon-gamma (IFN{gamma}) is critical for immunity against intra-macrophagic pathogens, signaling through the JAK-STAT pathway to induce a tyrosine-phosphorylation cascade that ensures a potent immune response. Excessive JAK-STAT signaling can drive hyperinflammation and autoimmunity, and thus signaling is tightly and selectively regulated by the IFN{gamma}-inducible protein, Suppressor of Cytokine Signaling 1 (SOCS1). SOCS1 inhibits signaling by directly blocking JAK kinase activity. Here we identified a SOCS1-interacting partner, ARAP2 that fine-tunes SOCS1 function. We report that tyrosine 415 in ARAP2 binds the SOCS1-Src Homology 2 (SH2) domain and limits the ability of SOCS1 to inhibit IFN{gamma} signaling. Our findings show that ARAP2 promotes the IFN{gamma} response through a phosphorylation dependent interaction with the negative regulator SOCS1.

cell biology↗

bioRxiv2024

Chronic intermittent alcohol yields sex-specific disruptions in cortical-striatal-limbic oscillations

BackgroundWhile the neurobiology of alcohol use disorder (AUD) has been extensively researched, the vast majority of these studies included only male organisms. However, there are significant sex differences in both the causes and consequences of alcohol misuse and dependence, suggesting sex-specific neurobiological mechanisms. The current study used a rodent model to determine whether chronic alcohol exposure impacts sex-specific neural circuits, and whether these changes contribute to the development of alcohol misuse. MethodsMale and female Sprague-Dawley rats were trained to self-administer 10% alcohol before implanting bilateral electrodes into the infralimbic medial prefrontal cortex (IL), nucleus accumbens shell (NAcSh), and central nucleus of the amygdala (CeA). Half of the rats were then exposed to four weeks of chronic intermittent alcohol (CIA) vapor (14 hours on/10 hours off). During acute withdrawal (6-8 after the vapor turns off), local field potentials (LFPs) were recorded from the IL, NAcSh, and CeA during 30-minute self-administration sessions. Using an unbiased machine learning approach, we built predictive models to determine whether/which LFP features could distinguish CIA-exposed from control rats in each sex, as well as if any of these LFP features correlated with rates of alcohol self-administration. ResultsFemale rats self-administered more alcohol in general compared to males, but only males exposed to CIA showed increased alcohol intake during acute withdrawal. LFPs predicted CIA exposure in both sexes better than chance estimates, but models built on IL and NAcSh oscillations performed the best in males, while models built on IL and CeA LFPs performed best in females. High {gamma} LFPs recorded in the NAcSh correlated with rates of alcohol self-administration in males exposed to CIA, while only left-right NAcSh {beta} coherence correlated with drinking in control females. ConclusionsThese data provide support for the hypothesis that the neural circuits driving alcohol dependence development are sex-specific, and that high frequency oscillations in the NAcSh may be related to the increased drinking observed in males exposed to CIA. Overall, these data add to our understanding of the neurobiological underpinnings behind the sex differences observed in AUD and offer promising biomarkers for future therapeutic research.

neuroscience↗

bioRxiv2023

CD45 limits Natural Killer cell development from common lymphoid progenitors

The clinical development of Natural Killer (NK) cell-mediated immunotherapy marks a milestone in the development of new cancer therapies and has gained traction due to the intrinsic ability of the NK cell to target and kill tumour cells. To fully harness the tumour killing ability of NK cells, we need to improve NK cell persistence and overcome suppression of NK cell activation in the tumour microenvironment. The trans-membrane, protein tyrosine phosphatase CD45, regulates NK cell homeostasis, with genetic loss of CD45 in mice resulting in increased numbers of mature NK cells [1-3]. This suggests that CD45-deficient NK cells might display enhanced persistence following adoptive transfer. However, here we demonstrated that adoptive transfer of CD45-deficiency did not enhance NK cell persistence in mice, and instead, the homeostatic disturbance of NK cells in CD45-deficient mice stemmed from a developmental defect in the common lymphoid progenitor population. The enhanced maturation within the CD45-deficient NK cell compartment was intrinsic to the NK cell lineage, and independent of the developmental defect. CD45 is not a conventional immune checkpoint candidate, as systemic loss is detrimental to T and B cell development [4-6], compromising the adaptive immune system. Nonetheless, this study suggests that inhibition of CD45 in progenitor or stem cell populations may improve the yield of in vitro generated NK cells for adoptive therapy.

cell biology↗