Biology subjects

Harris, K. S.

Publications and source records attributed to Harris, K. S..

4 recordsLinked to original sources

bioRxiv2026

MaCADEMIA: a software toolbox for single-molecule fluorescence image quantification

Single-molecule localisation microscopy (SMLM) is a powerful tool in molecular and cellular biology and part of the broad umbrella of super-resolution microscopy. A distinct feature of SMLM, is its capacity for deep quantification, beyond just spatial information, to copy number, stoichiometry, molecular interaction and dynamics in living cells. The hardware required is increasingly straightforward to implement. However, complexity remains in the image analysis where much remains fragmented across specialised software tools. Here, we present MaCADEMIA (Matlab Computational Analysis of Diffusion, Emitter Molecular Intensity and Abundance), a simple yet powerful toolbox of MATLAB functions and associated documentation to enable straightforward extraction of quantitative single-molecule information. MaCADEMIA performs ensemble particle detection achieving localisation accuracies down to 0.5 pixels Root mean squared error (RMSE) across wide signal-to-noise (SNR) ranges on standardised particle tracking benchmarks, consistently matching or exceeding the performance of 14 leading methods. Our integrated workflow enables molecular counting and stoichiometry determination through stepwise photobleaching analysis, mobility measurement via mean squared displacement, colocalisaton analysis and absolute protein copy number quantification using three-dimensional cellular models.

bioinformatics↗

bioRxiv2023

Inflammation and autophagy dysfunction in metachromatic leukodystrophy: a central role for mTOR?

Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder typically resulting from biallelic loss-of-function variants in the ARSA gene which encodes the lysosomal enzyme, arylsulphatase A, leading to the accumulation of its substrate, sulphatide, and widespread demyelination. Although gene therapy is available for MLD, it is limited by high cost and a narrow window for intervention, which means the development of therapies for MLD remains a key goal. The aim of the present study was to explore disease mechanisms in MLD with a view to identifying novel targets for therapeutic intervention for patients who cannot avail of gene therapy. Postmortem globus pallidus and dentate nucleus tissue was obtained from MLD cases (N=5; age 2-33 years old) and compared to age-, sex and ethnicity matched controls (N=5) and studied using discovery proteomics which demonstrated a marked inflammatory response, activation of the mTOR pathway, oxidative stress and metabolic remodelling in MLD cases. Histological analysis of inflammatory markers, including the terminal fragment of complement pathway activation, C3d, and the secreted glycoprotein YKL-40, a commonly used biomarker for inflammation, demonstrated their enrichment in MLD cases. Given that the mTOR pathway plays a key role in supressing autophagy, we next investigated autophagy and identified the accumulation of autophagosomes in MLD cases, consistent with deficient autophagy. Taken together, these findings suggest inflammation and autophagy dysfunction are key processes involved in MLD and that the mTOR pathway could be a novel therapeutic target for MLD.

neuroscience↗

bioRxiv2023

Phenotypic screen-based discovery of a small molecule that can increase adult neurogenesis and improve memory

Stem cells and neurogenesis persist in the postnatal and adult brain. Adult brain stem cells can be neuroprotective in disease and augment hippocampal-dependent cognitive function and thus are an important therapeutic target. Although many molecules have been discovered that regulate neurogenesis, few studies have attempted to amplify the process pharmacologically as a therapeutic goal. To address this gap, we used murine neurosphere cultures from the two major stem cell niches: the subventricular zone (SVZ) and the subgranular zone (SGZ). We screened compounds sharing pharmacophores with known inducers of neurogenesis and found several dozen proneurogenic compounds in an in vitro phenotypic screen. One, OXS-N1 was stable, and had acceptable absorption, distribution, metabolism, and excretion profiles in animal studies. OXS-N1 could increase neurogenesis in the SVZ and SGZ in WT mice after both intraperitoneal and oral administration. The number of newborn neurons (BrdU+/NeuN+) was increased; however, the number of activated stem cells (BrdU+/GFAP+) was not, suggesting an effect on neurogenesis independent of stem cell activation. This was supported by OXS-N1 increasing neurosphere differentiation but not proliferation. OXS-N1 also increased neurogenesis and improved performance in a Y maze cognitive task in PDGF-APPSw,Ind mice, a model of Alzheimers disease. RNAseq of SVZ and SGZ neurospheres in turn showed that genes associated with synaptic function were significantly increased by OXS-N1. Our study demonstrates the utility of phenotypic screening for the identification of molecules that increase neurogenesis and might be of therapeutic relevance.

neuroscience↗

bioRxiv2020

Platelet TSP-1 Controls Prostate Cancer-Induced Osteoclast Differentiation and Bone Marrow-Derived Cell Mobilization through TGFβ-1

The development of distant metastasis is the main cause of prostate cancer (CaP)-related death with the skeleton being the primary site of metastasis. While the progression of primary tumors and the growth of bone metastatic tumors are well described, the mechanisms controlling pre-metastatic niche formation and homing of CaP to bone remain unclear. Through prior studies, we demonstrated that platelet secretion was required for ongoing tumor growth and pre-metastatic tumor-induce bone formation and bone marrow-derived cell mobilization to cancers supporting angiogenesis. We hypothesized that proteins released by the platelet granules were responsible for inducing changes in the pre-metastatic bone niche. We found that the classically anti-angiogenic protein thrombospondin (TSP)-1 was significantly increased in the platelets of mice bearing tumors. To determine the role of increased TSP-1, we implanted tumors in TSP-1 null animals and assessed changes in tumor growth and pre-metastatic niche formation. TSP-1 loss resulted in increased tumor size and enhanced angiogenesis but reduced bone marrow-derived cell mobilization and tumor-induced bone formation with enhanced osteoclast formation. We hypothesized that these changes in the pre-metastatic niche were due to the retention of TGF-{beta}1 in the platelets of mice with TSP-1 deleted. To assess the importance of platelet-derived TGF-{beta}1, we implanted CaP tumors in mice with platelet-specific deletion of TGF-{beta}1. Similar to TSP-1 deletion, loss of platelet TGF-{beta}1 resulted in increased angiogenesis with a milder effect on tumor size and BMDC release. Within the bone microenvironment, platelet TGF-{beta}1 deletion prevented tumor-induced bone formation due to increased osteoclastogenesis. Thus, we demonstrate that the TSP-1/TGF-{beta}1 axis regulates pre-metastatic niche formation and tumor-induced bone turnover. Targeting the platelet release of TSP-1 or TGF-{beta}1 represents a potential method to interfere with the process of CaP metastasis to bone.

cancer biology↗