Biology subjects

Nicholson, B.

Publications and source records attributed to Nicholson, B..

8 recordsLinked to original sources

bioRxiv2026

Integrated analysis of stemness-associated immune modulatory circuits in squamous cell carcinomas

Emerging evidence indicates that a subset of cancer cells enriched for stemness-related gene signatures possess distinct immunomodulatory capacities, enabling these tumor-initiating stem cells (tSCs) to more effectively evade or resist anti-tumor immunity. Despite these advances, the tSC-specific molecular circuits orchestrating their specialized immune privilege program are not well defined. Here, in squamous cell carcinomas of the skin and oral cavity, we comprehensively delineate the unique immune-evasive properties of tSCs and dissect the transcriptional regulation shaping their immunomodulatory programs. By integrating transcriptome profiling, chromatin landscape mapping, genetic perturbation, and single-cell RNA sequencing, we found that the tSC-specific immune program is broadly governed by SOX2, a stemness-associated transcription factor. We demonstrate that SOX2 enables tSCs to sustain immature tumor-associated neutrophils (TANs) and subsequently trigger these myeloid cells to foster the development of tumor-associated macrophages (TAMs). This SOX2-directed tSC-TAN-TAM axis establishes a localized immunosuppressive niche for protecting tSC. SIGNIFICANCEHere, we uncover SOX2 as a master regulator that orchestrates conserved immune modulatory circuits in tSCs to sustain pro-tumor myeloid cell states. These findings place tSCs at the apex of immune landscape remodeling, asserting a central role of stemness-associated program in organizing the immunosuppressive tumor microenvironment.

cancer biology↗

bioRxiv2026

Comparative single cell analysis of wound and cancer identifies the metabolic dialogues between tumor initiating stem cells and macrophages

Macrophages are pivotal mediators of wound healing, yet the cellular programs they employ can be hijacked by cancers to drive tumorigenesis. Although similar macrophage programs support both physiological tissue regeneration and pathological cell growth, the molecular and functional difference between wound-associated macrophages (WAMs) and tumor-associated macrophages (TAMs) remain poorly defined. Here, we perform comparative single-cell RNA sequencing to delineate the dynamic cell states of macrophages during skin wound healing and the progression of cutaneous squamous cell carcinoma. Our analyses reveal that aberrantly regulated lipid metabolism is a distinct feature of TAMs. Critically, our genetic manipulations allow us to identify SOX2High tumor-initiating stem cells as key orchestrators that modulate the lipid metabolism of TAMs and shape their cell states. These findings suggest that disrupting the metabolic crosstalk between tumor-initiating stem cells and TAMs represents a promising strategy to normalize myeloid cell function and enhance cancer immunotherapy efficacy.

cancer biology↗

bioRxiv2025

Tumor-Initiating Cells Fine-tune the Plasticity of Neutrophils to Sculpt a Protective Niche

The abundant accumulation of neutrophils in various solid cancers has been well recognized, but the functions of tumor-associated neutrophils (TANs) remain controversial. TANs have long been believed to be immune suppressive and have thus been referred to as "myeloid-derived suppressor cells". However, effective tumor control induced by immunotherapy was recently found to be associated with strong neutrophil signatures. These seemingly contradictory findings highlight the unexpected degree of plasticity and heterogeneity unique to TANs. How the cellular plasticity and functional heterogeneity of TANs are regulated remains unknown. Here, we show that, while anti-PDL1/CD40 agonist immunotherapy can induce interferon responses to reprogram many TANs, allowing them to become plastic and regain anti-tumor activities in squamous cell carcinomas, a subset of TANs residing at the tumor-stroma interface can preserve their immune suppressive state. Importantly, by designing a reverse genetic screening, we identified a group of Sox2Hi tumor-initiating cells (TICs) at the tumor-stroma interface that could upregulate Fatty Acid Desaturase 1 (Fads1) to produce arachidonic acid. This TIC-specific pathway can disrupt the interferon responsive potentials of TANs, preventing the interferon-mediated reprogramming. Thus, by fine-tuning the plasticity of neutrophils, TICs shape neutrophil heterogeneity and sculpt a protective micro-niche to survive from immunotherapy and drive cancer relapse.

cancer biology↗

bioRxiv2023

Temporal Dynamics of Normalization Reweighting

1For decades, neural suppression in early visual cortex has been thought to be fixed. But recent work has challenged this assumption by showing that suppression can be reweighted based on recent history; when pairs of stimuli are repeatedly presented together, suppression between them strengthens. Here we investigate the temporal dynamics of this process using a steady-state visual evoked potential (SSVEP) paradigm that provides a time-resolved, direct index of suppression between pairs of stimuli flickering at different frequencies (5 and 7Hz). Our initial analysis of an existing EEG dataset (N=100) indicated that suppression increases substantially during the first 2-5 seconds of stimulus presentation (with some variation across stimulation frequency). We then collected new EEG data (N=100) replicating this finding for both monocular and dichoptic mask arrangements in a preregistered study designed to measure reweighting. A third experiment (N=20) used source localized MEG, and found that these effects are apparent in primary visual cortex (V1), consistent with results from neurophysiological work. Because long-standing theories propose inhibition/excitation differences in autism, we also compared reweighting between individuals with high vs low autistic traits, and with and without an autism diagnosis, across our 3 data sets (total N=220). We find no compelling differences in reweighting that are associated with autism. Our results support the normalization reweighting model, and indicate that for prolonged stimulation, increases in suppression occur on the order of 2-5 seconds after stimulus onset.

neuroscience↗

bioRxiv2021

Mobile element integration reveals an atypical chromosome dimer resolution system in Legionella pneumophila.

In bacteria, the mechanisms used to repair DNA lesions during genome replication include homologous recombination between sister chromosomes. This can lead to the formation of chromosome dimers if an odd number of crossover events occurs. The concatenated DNA must be resolved before cell separation to ensure genomic stability and cell viability. The broadly conserved dif/Xer system counteracts the formation of dimers by catalyzing one additional crossover event immediately prior to cell separation. While dif/Xer systems have been characterized or predicted in the vast majority of proteobacteria, no homologs to dif or xer have been identified in the order Legionellales. Here we report the discovery of a distinct single-recombinase dif/Xer system in the intracellular pathogen Legionella pneumophila. The dif site was uncovered by our analysis of Legionella mobile element-1 (LME-1), which harbors a dif site-mimic and integrates into the L. pneumophila genome via site-specific recombination. We demonstrate that lpg1867 (herein named xerL) encodes a tyrosine recombinase that is necessary and sufficient for catalyzing recombination at the dif site, and that deletion of dif or xerL causes filamentation along with extracellular and intracellular growth defects. We show that the dif/XerL system is present throughout Legionellales and that Coxiella burnetii XerL and its cognate dif site can functionally substitute for the native system in L. pneumophila. Lastly, we describe an unexpected link between C. burnetii dif/Xer and the maintenance of its virulence plasmids. Significance StatementThe maintenance of circular chromosomes depends on the ability to resolve aberrant chromosome dimers as they form. In most proteobacteria, broadly conserved Xer recombinases catalyze single crossovers at short, species-specific dif sites located near the replication terminus. Chromosomal dimerization leads to the formation of two copies of dif, leading to rapid site-specific recombination and elimination of the duplicated intervening sequence. The apparent absence of chromosome-dimer resolution mechanisms in Legionellales has been a mystery to date. By studying a phage-like mobile genetic element, LME-1, we have identified a previously unknown single-recombinase dif/Xer system that is not only widespread across Legionellales but whose activity is linked to virulence in two important human pathogens.

microbiology↗

bioRxiv2021

Legionella pneumophila CRISPR-Cas suggests recurrent encounters with Gokushovirinae

Legionella pneumophila is a ubiquitous freshwater pathogen and the causative agent of Legionnaires disease. This pathogen and its ability to cause disease is closely tied to its environmental encounters. From phagocytic protists, L. pneumophila has "learned" how to avoid predation and exploit conserved eukaryotic processes to establish an intracellular replicative niche. Legionnaires disease is a product of these evolutionary pressures as L. pneumophila uses the same molecular mechanisms to replicate in grazing protists and in macrophages of the human lung. L. pneumophila growth within protists also provides a refuge from desiccation, disinfection, and other remediation strategies. One outstanding question has been whether this protection extends to phages. L. pneumophila isolates are remarkably devoid of prophages and to date no Legionella phages have been identified. Nevertheless, many L. pneumophila isolates maintain active CRISPR-Cas defenses. So far, the only known target of these systems has been an episomal element that we previously named Legionella Mobile Element-1 (LME-1). In this study, we have identified over 150 CRISPR-Cas systems across 600 isolates, to establish the clearest picture yet of L. pneumophilas adaptive defenses. By leveraging the sequence of 1,500 unique spacers, we can make two main conclusions: current data argue against CRISPR-Cas targeted integrative elements beyond LME-1 and the heretofore "missing" L. pneumophila phages are most likely lytic gokushoviruses. IMPORTANCEThe causative agent of Legionnaires disease, an often-fatal pneumonia, is an intracellular bacterium, Legionella pneumophila, that normally grows inside amoebae and other freshwater protists. Unfortunately for us, this has two major consequences: the bacterium can take what it has learned in amoebae and use similar strategies to grow inside our lungs; and these amoebae can protect Legionella from various forms of chemical and physical disinfection regimes. Legionella are ubiquitous in the environment and frequently found in man-made water systems. Understanding the challenges to Legionella survival before it reaches the human lung is critical to preventing disease. We have leveraged our earlier discovery that L. pneumophila CRISPR-Cas systems are active and adaptive - meaning that they respond to contemporary threats encountered in the environment. In this way, CRISPR arrays can be considered genomic diaries of past encounters, with spacer sequences used to identify elements that may impinge on the pathogens survival. One outstanding question in the field is whether L. pneumophila is susceptible to phage, given the presumptive protection provided by intracellular replication within its eukaryotic hosts. In this work, we use CRISPR spacer sequences to suggest that the heretofore "missing" L. pneumophila phage are most likely lytic gokushoviruses. Such information is critical to the long-term goal of developing of new strategies for preventing colonization of our water systems by Legionella and subsequent human exposure to the pathogen.

microbiology↗

bioRxiv2021

Endometrial Gap Junction Expression - Early Indicators of Endometriosis and Integral to Invasiveness

Endometriosis is an invasive disease, and a leading cause of pain, infertility and disability among women, with an incidence 10 fold that of cancer. A more complete understanding of disease pathogenesis is essential for the development of non-surgical diagnostic assays and non-hormonal therapeutics. Avoidance of immune clearance and implantation of endometrial tissue on peritoneal surfaces are features of endometriosis lesion formation that overlap with cancer metastasis. Connexins, and the gap junctions they form, have been implicated in cancer progression, and may be associated endometriosis pathophysiology. Single cell transcriptomic profiling of endometrial epithelial and stromal cells from women with endometriosis reveals a striking and progressive shift in expression of connexins and related regulatory and junctional genes. We demonstrate that gap junction coupling between endometrial cells and the peritoneal mesothelium is dramatically induced, specifically in endometriosis patients, and is required for invasion by inducing breakdown of the mesothelial barrier function.

cell biology↗

bioRxiv2017

DRUID: A pipeline for reproducible transcriptome-wide measurements of mRNA stability

Control of messenger RNA (mRNA) stability is an important aspect of gene regulation. The gold standard for measuring mRNA stability transcriptome-wide uses metabolic labeling, biochemical isolation of labeled RNA populations, and high-throughput sequencing. However, difficult normalization procedures and complex computational algorithms have inhibited widespread adoption of this approach. Here, we present DRUID (for Determination of Rates Using Intron Dynamics), a computational pipeline that is robust, easy to use, and freely available. Our pipeline uses endogenous introns to normalize time course data and yields more reproducible half-lives than other methods, even with datasets that were otherwise unusable. DRUID can handle datasets from a variety of organisms, spanning yeast to humans, and we even applied it retroactively on published datasets. We anticipate that DRUID will allow broad application of metabolic labeling for studies of mRNA stability.

molecular biology↗