Biology subjects

Strong, C.

Publications and source records attributed to Strong, C..

7 recordsLinked to original sources

bioRxiv2026

CalFluxTools: An R package for analysis of high-throughput calcium oscillation screening data

Whole plate detection of calcium flux signals using fluorescence is a powerful technology for monitoring oscillatory activity of excitable cells in a high throughput fashion that sees broad applications in neurotoxicity and cardiotoxicity research. However, analysis of calcium oscillation profiles can output more than 60 peak kinetic parameters, which makes manual data analysis challenging. We have created the CalFluxTools R package, an automated pipeline for parsing plate data for 384 well plates, generating quality control metrics and plots, and performing data analysis, including T-tests, Z-score analysis, and machine learning prediction of compound toxicity values. CalFluxTools requires a plate map and experimental manifest that includes parameter filtration specifications, as well as data in the ".statall" format. CalFluxTools runs in less than a minute on a Macbook Pro with a 2.6 GHz 6-Core Intel Core i7 processor.

bioinformatics↗

bioRxiv2026

Multifractal Fluctuations in Electrogram Dynamics Distinguish Atrial Fibrillation Phenotype, Drug Response, and Imminent Termination: Implications for Mechanism and Treatment.

Structured AbstractO_ST_ABSBackgroundC_ST_ABSAtrial fibrillation (AF) is maintained by complex dynamics, clinically characterised by bursting periods of organization and disorganization in intracardiac electrograms. We have previously postulated that cardiac conduction behaves like a critical system, where phase shift from organised rhythm to AF is a phase transition at the critical point. We thus hypothesized that using multifractal analysis of AF electrograms could potentially quantify non-stationary fluctuations, revealing novel mechanistic insights into the cardiac critical system and examine potential clinically relevant markers of AF dynamics, phenotype and treatment response. ObjectivesTo determine whether multifractal analysis of AF electrograms can (i) Distinguish paroxysmal (PAF0 and non-paroxysmal AF (NPAF), (ii) predict response to pharmacologic modulation, and (iii) identify imminent spontaneous termination, thereby acting as marker of proximity to criticality along complex system phase spectrum. MethodsWe analysed >1.4 million seconds of high-density bipolar electrograms from 106 patients (paroxysmal n{approx}52, non-paroxysmal n{approx}54) undergoing left atrial mapping with a 24-bipole HD-Grid catheter at standardized sites (RENEWAL AF-ANZCTR ACTRN12619001172190)). Multifractal analysis using the Wavelet Transform Modulus Maxima Method (WTMM) was applied to a burst-energy observable to derive log-normal multifractal parameters c (support dimension), c (spectrum location), and c2 (fluctuations). Hierarchical mixed-effects models accounted for channels nested within locations within patients. A flecainide sub-study (n=15) provided paired pre-/post-infusion recordings, and 27 spontaneous termination events in 15 patients were analysed using 60-s pre-termination windows. Spatial texture of c2 was quantified by variogram-derived correlation length and sill. ResultsAF electrograms exhibited robust multifractality confirming multifractal fluctuations as an intrinsic property of AF. Non-paroxysmal AF showed significantly reduced fluctuations versus paroxysmal AF (c2: {beta}=-0.01, p=0.001), indicating a paradoxical loss of fluctuations with disease progression. Flecainide selectively increased fluctuations in paroxysmal AF ({Delta}c2 = +0.04, p<0.01; {Delta}c = +0.06, p<0.01) but had no significant effect on fluctuations (c2) in non-paroxysmal AF, revealing phenotype-dependent drug response. Immediately prior to spontaneous AF termination, fluctuations increased significantly compared with sustained AF (c2: 0.198 vs 0.181, p=0.024). Spatial variogram analysis revealed heterogenous patterns in paroxysmal AF, whereas non-paroxysmal AF displayed a homogenised, flattened fluctuations landscape. ConclusionsAtrial fibrillation exhibits robust multifractal dynamics rather than random electrical activity. Reduced fluctuations characterizes non-paroxysmal AF, whereas higher fluctuations is observed in paroxysmal AF, during flecainide modulation, and immediately prior to spontaneous termination. These findings suggest that multifractal fluctuations (c2) reflects the dynamical state of AF and may serve as a quantitative biomarker of disease progression, pharmacologic responsiveness, and proximity to termination. CONDENSED ABSTRACTTAtrial fibrillation (AF) exhibits multifractal electrogram fluctuations that vary with disease stage, pharmacologic responsiveness, and proximity to spontaneous termination. In this study, multifractal fluctuations (c2) was higher in paroxysmal than non-paroxysmal AF, increased selectively with flecainide in paroxysmal AF, and rose immediately before spontaneous termination. These findings identify c2 as a quantitative marker of AF progression, and imminent reorganization. Clinically, multifractal analysis may enhance intra-procedural assessment of AF phenotype, guide drug selection, and improve recognition of transitions toward sinus rhythm, and connects AF with concepts of criticality and phase transitions.

biophysics↗

bioRxiv2025

Multidimensional characterization of cellular ecosystems in Hodgkin lymphoma

The tissue architecture of classic Hodgkin Lymphoma (CHL) is unique among cancers and characterized by rare malignant Hodgkin and Reed-Sternberg cells that co-evolve with a complex ecosystem of immune cells in the tumor microenvironment (TME). The lack of a comprehensive systems-level interrogation has hindered the description of disease heterogeneity and clinically relevant molecular subtypes. Here, we employed an integrative, multimodal approach to characterize CHL tumors using malignant cell sequencing, spatial transcriptomics and imaging mass cytometry. We identified four molecular subtypes (CST, CN913, STB, and CN2P), each characterized by distinct clinical features, mutational patterns, malignant cell gene expression profiles, and spatial architecture involving immune cell populations. Functional modeling of CSF2RB mutations, a characteristic feature of the CST subtype, revealed dysregulated oncogenic signaling and unique TME crosstalk. These findings highlight the significance of multi-dimensional profiling in elucidating patterns of molecular alterations that drive immune ecosystems and underlie therapeutically exploitable vulnerabilities.

cancer biology↗

bioRxiv2023

The spatially resolved tumor microenvironment predicts treatment outcome in relapsed/refractory Hodgkin lymphoma

PURPOSEAbout a third of relapsed or refractory classic Hodgkin lymphoma (r/r CHL) patients succumb to their disease after high-dose chemotherapy followed by autologous stem cell transplantation (HDC/ASCT). Here, we aimed to describe spatially resolved tumor microenvironment (TME) ecosystems to establish novel biomarkers associated with treatment failure in r/r CHL. METHODSWe performed imaging mass cytometry (IMC) on 169 paired primary diagnostic and relapse biopsies using a marker panel specific for CHL biology. For each cell type in the TME, we calculated a spatial score measuring the distance of nearest neighbor cells to the malignant Hodgkin Reed Sternberg cells within close interaction range. Spatial scores were used as features in prognostic model development for post-ASCT outcomes. RESULTSHighly multiplexed IMC data revealed shared TME patterns in paired diagnostic and early relapse/refractory CHL samples, whereas TME patterns were more divergent in pairs of diagnostic and late relapse samples. Integrated analysis of IMC and single cell RNA sequencing data identified unique architecture defined by CXCR5+ HRS cells and their strong spatial relationship with CXCL13+ macrophages in the TME. We developed a prognostic assay ( RHL4S) using four spatially resolved parameters, CXCR5+ HRS cells, PD1+CD4+ T cells, tumor-associated macrophages, and CXCR5+ B cells, which effectively separated patients into high-risk vs low-risk groups with significantly different post-ASCT outcomes. The RHL4S assay was validated in an independent r/r CHL cohort using a multicolor immunofluorescence assay. CONCLUSIONSWe identified the interaction of CXCR5+ HRS cells with ligand-expressing CXCL13+ macrophages as a prominent crosstalk axis in relapsed CHL. Harnessing this TME biology, we developed a novel prognostic model applicable to r/r CHL biopsies, RHL4S, opening new avenues for spatial biomarker development.

cancer biology↗

bioRxiv2022

Integrated single cell analysis reveals co-evolution of malignant B cells and the tumor microenvironment in transformed follicular lymphoma

Follicular lymphoma (FL) is the most common indolent form of non-Hodgkin lymphoma. Histological transformation of FL to a more aggressive form of lymphoma occurs with a linear incidence of 2-3% per year and is associated with poor outcome. Divergent clonal evolution and an altered tumour microenvironment (TME) have both been implicated in the transformation process. However, the phenotypic consequences of this evolution and its implication in reshaping the TME remain unknown. To address this knowledge gap we performed single cell whole genome (scWGS) and single cell whole transcriptome sequencing (scWTS) of paired pre/post transformation samples of 11 FL patients. We further performed scWTS analysis of additional 11 FL samples from patients that had not undergone transformation within 7 years. Our comprehensive single cell analysis revealed the evolutionary dynamics of transformation at unprecedented resolution. Computational integration of scWGS and scWTS allowed us to identify gene programs upregulated and positively selected during evolution. Furthermore, our scWTS analysis revealed a shifting TME landscape, with an exhausted CD8 T cell signature emerging during transformation. Using multi-color immunofluorescence we transferred these findings to a novel TME based biomarker of transformation, subsequently validated in 2 independent cohorts of pretreatment FL samples. Taken together, our results provide a comprehensive view of the combined genomic and phenotypic evolution of malignant cells during transformation, and the shifting cross-talk between malignant cells and the TME. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/516951v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@92abf7org.highwire.dtl.DTLVardef@157f2c2org.highwire.dtl.DTLVardef@102a879org.highwire.dtl.DTLVardef@182daec_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

Functional brain region-specific neural spheroids for modeling neurological diseases and therapeutics screening

3D spheroids have emerged as powerful drug discovery tools given their high-throughput screening (HTS) compatibility. Here, we established a method for generating functional neural spheroids with differentiated human induced pluripotent stem cell (hiPSC)-derived neurons and astrocytes at cell type compositions mimicking specific regions of the human brain. Recordings of intracellular calcium oscillations were used as functional assays, and the utility of this spheroids system was shown through disease modelling, drug testing, and formation of assembloids to model neurocircuitry. We developed disease models for Alzheimers and Parkinsons Disease through incorporating genetically engineered cells into spheroids, and Opioid Use Disorder by chronically treating spheroids with DAMGO. We reversed baseline functional deficits in each disease model with clinically approved treatments and showed that assembloid activity can be chemogenetically manipulated. Here, we lay the groundwork for brain region-specific spheroids as a robust functional assay platform for HTS studies.

bioengineering↗

bioRxiv2020

Nanoscape, a data-driven 3D real-time interactive virtual cell environment

Knowledge of cellular and structural biology has reached unprecedented levels of detail. In conjunction with advances in 3D computer visualisation techniques this has allowed exploration of cellular ultrastructure and environments by a virtual user. The extraction and integration of relevant scientific information, along with consideration of the best representation of data, is often a bottleneck in the visualisation process for many 3D biomedical artists. Here we introduce Nanoscape, a collaborative project between 3D computer artists, computer graphics developers, and cell biologists that enables a user to navigate a cell in a complex 3D computer visualised environment. We combine actual data from various scientific disciplines (including structural biology, cell biology and multiple microscopic techniques) and apply artistic expression and design aesthetics to create a unique new experience where a real-time virtual explorer can traverse a cell surface, observe and interact with a more scientifically accurate cell surface environment.

scientific communication and education↗