Biology subjects

Hall, C. N.

Publications and source records attributed to Hall, C. N..

9 recordsLinked to original sources

bioRxiv2023

Spheroid architecture strongly induces miR-221/222 expression and promotes oxidative phosphorylation and survival of mobile tumor cells through a mechanism that includes restriction of miR-9 expression

Tumor cell spheroids are three dimensional multicellular structures that form during the expansive growth of carcinoma cells. Spheroids support tumor metastasis as vehicles of dissemination, promoting growth and survival of bulk tumor and cancer stem cells within the mobile tumor cell population. Deciphering how spheroid architecture affects tumor cell phenotype will be essential for the development of therapeutics to inhibit transperitoneal metastasis and the development of peritoneal carcinomatosis by ovarian cancers. We investigated how spheroid formation directly affects OXPHOS activity and microRNA expression in a cultured ovarian carcinoma cell system. The rate of oxidative phosphorylation/respiration per cell in spheroids was nearly double that of the same cell type growing in suspension as single cells. Cells growing as spheroids showed greatly enhanced expression of miR-221/222, an oncomiR that targets multiple tumor suppressor genes, promotes invasion, as well as reduced expression of miR-9, which targets mitochondrial tRNA-modification enzymes and inhibits OXPHOS. Consistent with the greater efficiency of ATP generation afforded by OXPHOS phosphorylation, tumor cells growing as spheroids injected into the nutrient-poor environment of the murine peritoneum survived longer than the cells growing in suspension as loosely associated aggregates. The data suggest that in addition to the reported effects of spheroid formation on cancer cell growth and phenotype, including promotion of stem cell generation, spheroid architecture increases the OXPHOS activity of constituent tumor cells. During the mobile phase of metastasis, when ovarian tumor cells disperse through nutrient-poor environments such as the peritoneum, enhanced OXPHOS activity afforded by spheroid architecture would enhance survival and thereby contribute to metastatic potential.

cancer biology↗

bioRxiv2023

Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma

High expression of MYC and its target genes define a subset of germinal center B-cell diffuse large B-cell lymphoma (GCB-DLBCL) associated with poor outcomes. Half of these high-grade cases show chromosomal rearrangements between the MYC locus and heterologous enhancer-bearing loci, while focal deletions of the adjacent non-coding gene PVT1 are enriched in MYC-intact cases. To identify genomic drivers of MYC activation, we used high-throughput CRISPR-interference (CRISPRi) profiling of candidate enhancers in the MYC locus and rearrangement partner loci in GCB-DLBCL cell lines and mantle cell lymphoma (MCL) comparators that lacked common rearrangements between MYC and immunoglobulin (Ig) loci. Rearrangements between MYC and non-Ig loci were associated with unique dependencies on specific enhancer subunits within those partner loci. Notably, fitness dependency on enhancer modules within the BCL6 super-enhancer (BCL6-SE) cluster regulated by a transcription factor complex of MEF2B, POU2F2, and POU2AF1 was higher in cell lines bearing a recurrent MYC::BCL6-SE rearrangement. In contrast, GCB-DLBCL cell lines without MYC rearrangement were highly dependent on a previously uncharacterized 3 enhancer within the MYC locus itself (GCBME-1), that is regulated in part by the same triad of factors. GCBME-1 is evolutionarily conserved and active in normal germinal center B cells in humans and mice, suggesting a key role in normal germinal center B cell biology. Finally, we show that the PVT1 promoter limits MYC activation by either native or heterologous enhancers and demonstrate that this limitation is bypassed by 3 rearrangements that remove PVT1 from its position in cis with the rearranged MYC gene. Key pointsO_LICRISPR-interference screens identify a conserved germinal center B cell MYC enhancer that is essential for GCB-DLBCL lacking MYC rearrangements. C_LIO_LIFunctional profiling of MYC partner loci reveals principles of MYC enhancer-hijacking activation by non-immunoglobulin rearrangements. C_LI

cancer biology↗

bioRxiv2023

Distinct neurochemical influences on fMRI response polarity in the striatum

The striatum is the primary input nucleus of the basal ganglia, widely studied for its complex roles in health and disease. Functional magnetic resonance imaging (fMRI) studies are essential for discerning striatal function, however the relationship between neuronal and hemodynamic activity, critical for interpreting fMRI signals, has not been rigorously examined in striatum. We find that optogenetic stimulation of striatal neurons or afferents evokes negative striatal fMRI responses in rats that can occur despite broad increases in local neuronal activity. Intra-striatal pharmacological manipulations suggest that opioidergic, but not dopaminergic transmission contributes to negative striatal fMRI signals (the latter instead associated with positive signals). Striatal neuronal activity peaks are also associated with negative hemodynamic signals in behaving rats. Negative fMRI responses are observed in human striatum under conditions of anticipated neuronal activity increases. Our results prompt consideration of local cellular and neurochemical environments along with neuronal activity in fMRI signal interpretation.

neuroscience↗

bioRxiv2022

ETV6 Deficiency and Microsatellite Enhancers Drive Transcriptional Dysregulation in B-Lymphoblastic Leukemia

Distal enhancers play critical roles in sustaining oncogenic gene expression programs. We identify aberrant enhancer-like activation of GGAA tandem repeats as a characteristic feature of B-cell acute lymphoblastic leukemia (B-ALL) with genetic defects of the ETV6 transcriptional repressor, including ETV6-RUNX1+ and ETV6-null B-ALL. We show that GGAA repeat enhancers are direct activators of previously identified ETV6-RUNX1+ B-ALL "signature" genes, including likely oncogenic drivers. When restored to ETV6-deficient B-ALL cells, ETV6 directly binds to GGAA repeat enhancers, represses their acetylation, downregulates adjacent genes, and inhibits B-ALL growth. In ETV6-deficient B-ALL cells, we find that the ETS transcription factor ERG directly binds to GGAA microsatellite enhancers and is required for sustained activation of many repeat enhancer-activated genes. Together, our findings reveal a novel epigenetic gatekeeper function of the ETV6 tumor suppressor gene and establish microsatellite enhancers as a key mechanism underlying the unique gene expression program of ETV6-RUNX1+ B-ALL. SignificanceWe show that the oncogenic gene expression program of a common pediatric leukemia relies on repetitive noncoding elements that are not conserved between humans and rodents, placing important limitations on animal models for this disease. Our findings may present new opportunities for targeting cancer-specific chromatin dysregulation in leukemia.

cancer biology↗

bioRxiv2021

SARS-CoV-2 variants of concern Alpha, Beta, Gamma and Delta have extended ACE2 receptor host-ranges

Following the emergence of SARS-CoV-2 in China in late 2019 a number of variants have emerged, with two of these - Alpha and Delta - subsequently growing to global prevalence. One characteristic of these variants are changes within the Spike protein, in particular the receptor binding domain (RBD). From a public health perspective these changes have important implications for increased transmissibility and immune escape; however, their presence could also modify the intrinsic host-range of the virus. Using viral pseudotyping we examined whether the variants of concern (VOCs) Alpha, Beta, Gamma and Delta have differing host ACE2 receptor usage patterns, focusing on a range of relevant mammalian ACE2 proteins. All four VOCs were able to overcome a previous restriction for mouse ACE2, with demonstrable differences also seen for individual VOCs with rat, ferret or civet ACE2 receptors, changes which we subsequently attribute to N501Y and E484K substitutions within the Spike RBD.

microbiology↗

bioRxiv2021

APOE4 genotype increases neuronal calcium signals and decreases pial arteriole responsivity and vasomotion in visual cortex of awake mice

Young mice possessing the e4 allele of the Apolipoprotein (APOE) gene (a risk factor for Alzheimers disease (AD)) have previously been shown to have dramatic decreases in vascular function, suggesting APOE4 may confer its risk via the vasculature. However, in human carriers, vascular and cognitive function decrease later in life. Mouse data may be confounded by an increased impact of anaesthesia and surgery in APOE4 animals, and has also focused on sensory cortices, ignoring medial lobe structures more sensitive to AD. To clarify how APOE4 expression alters neurovascular function, we studied the visual cortex and hippocampus of awake APOE3 and APOE4 targeted replacement mice, using 2-photon microscopy of neurons and blood vessels. We found milder vascular deficits than studies using anaesthetised preparations: functional hyperaemia was unaffected in APOE4 mice and neuronal or vascular function did not decrease with age. Instead, vascular responsiveness was lower at all ages, arteriole vasomotion was reduced and neuronal calcium signals during visual stimulation were increased. This suggests that, independently, APOE4 expression is not catastrophic but alters neurovascular physiology towards a state more sensitive to insults such as surgery or beta amyloid accumulation. Understanding how APOE4 expression interacts with these insults will be critical for understanding the emergence of AD in APOE4 carriers.

neuroscience↗

bioRxiv2021

Choice of method of place cell classification determines the population of cells identified.

Place cells, spatially responsive hippocampal cells, provide the neural substrate supporting navigation and spatial memory. Historically most studies of these neurons have used electrophysiological recordings from implanted electrodes but optical methods, measuring intracellular calcium, are becoming increasingly common. Several methods have been proposed as a means to identify place cells based on their calcium activity but there is no common standard and it is unclear how reliable different approaches are. Here we tested three methods that have previously been applied to two-photon hippocampal imaging or electrophysiological data, using both model datasets and real imaging data. These methods use different parameters to identify place cells, including the peak activity in the place field, compared to other locations (the Peak method); the stability of cells activity over repeated traversals of an environment (Stability method); and a combination of these parameters with the size of the place field (Combination method). The three methods performed differently from each other on both model and real data. The Peak method showed high sensitivity and specificity for detecting model place cells and was the most robust to variations in place field width, reliability and field location. In real datasets, vastly different numbers of place cells were identified using the three methods, with little overlap between the populations identified as place cells. Therefore, choice of place cell detection method dramatically affects the number and properties of identified cells. We recommend the Peak method be used in future studies to identify place cell populations, unless there is an explicit theoretical reason for detecting cells with more narrowly defined properties. Author SummaryPlace cells are hippocampal cells that have spatially constrained receptive fields, the place field. These cells have been widely studied in the context of navigation, more recently using virtual reality environments in combination with optical methods of recording neuronal activity. However, there is a lack of consensus regarding how to identify place cells in these data. In this study we tested the sensitivity and specificity of three methods of identifying place cells. By comparing these methods and quantifying the populations of place cells they identify, we aimed to increase our understanding of exactly the populations that are currently being studied under the name "place cells". Although the appropriate method may depend on the experimental design, we generally recommend a single method going forward, which will increase consensus within the field about what should be included in a place cell population, and allow us to better compare results between studies.

neuroscience↗

bioRxiv2021

An Open-Source Pipeline for Analyzing Changes In Microglial Morphology

Changes in microglial morphology are powerful indicators of the inflammatory state of the brain. Here we provide an open-source microglia morphology analysis pipeline that first cleans and registers images of microglia, before extracting 62 parameters describing microglial morphology. It then compares control and "inflammation" training data and uses dimensionality reduction to generate a single metric of morphological change (an inflammation index). This index can then be calculated for test data to assess inflammation, as we demonstrate by investigating the effect of short-term high fat diet consumption in heterozygous Cx3CR1-GFP mice, finding no significant effects of diet. Our pipeline represents the first open-source microglia morphology pipeline combining semi-automated image processing and dimensionality reduction. It uses free software (ImageJ and R) and can be applied to a wide variety of experimental paradigms. We anticipate it will enable others to more easily take advantage of the powerful insights microglial morphology analysis provides.

neuroscience↗

bioRxiv2019

Hippocampus has lower oxygenation and weaker control of brain blood flow than cortex, due to microvascular differences

The hippocampus is essential for spatial and episodic memory but is damaged early in Alzheimers disease and is very sensitive to hypoxia. Understanding how it regulates its oxygen supply is therefore key for designing interventions to preserve its function. However, studies of neurovascular function in the hippocampus in vivo have been limited by its relative inaccessibility. Here we compared hippocampal and visual cortical neurovascular function in awake mice, using two photon imaging of individual neurons and vessels and measures of regional blood flow and haemoglobin oxygenation. We show that blood flow, blood oxygenation and neurovascular coupling were decreased in the hippocampus compared to neocortex, because of differences in both the vascular network and pericyte and endothelial cell function. Modelling oxygen diffusion indicates that these features of the hippocampal vasculature could explain its sensitivity to damage during neurological conditions, including Alzheimers disease, where the brains energy supply is decreased.

neuroscience↗