Biology subjects

Burden, S.

Publications and source records attributed to Burden, S..

5 recordsLinked to original sources

bioRxiv2026

Glucocorticoid receptor activation reorganizes Wnt/LEF1 regulatory circuitry associated with therapeutic response in B-cell acute lymphoblastic leukemia

Glucocorticoids (GCs) are foundational to B-cell acute lymphoblastic leukemia (B-ALL) therapy, yet how glucocorticoid receptor (GR) activation interacts with lineage regulatory circuitry to shape therapeutic response remains incompletely understood. Using LEF1 to interrogate canonical Wnt regulatory circuitry, we show that GR activation reorganizes GR+LEF1 elements into recruitment, retention, and dissociation states. LEF1 dissociates from Wnt-responsive regulatory elements while being recruited to GRE-rich GR-associated elements that progressively acquire chromatin accessibility, H3K27ac, BRD4 and BRG1. RUNX1 and AP-1 show class-dependent redistribution across LEF1-defined states, extending organization beyond LEF1. GR+LEF1 reorganization is observed in patient-derived B-ALL. GR+LEF1 elements lose accessibility in GC-resistant B-ALL and during diagnosis-to-relapse evolution, with recruitment elements enriched for remodeling. Perturbation of resistance-associated GR+LEF1 elements at BIM and BMF alters GC-induced apoptotic signaling. Together, these findings identify Wnt/LEF1 circuitry as an interface through which therapeutic GR activation reorganizes the B-ALL regulatory landscape into states associated with glucocorticoid response and resistance.

cancer biology↗

bioRxiv2026

zFISHer: Automated 3D Registration, Detection, and Colocalization with Interactive Curation for Sequential Multiplexed FISH

SummarySequential multiplexed fluorescence in situ hybridization (FISH) enables spatially resolved molecular profiling in cell monolayers, but analyzing puncta colocalization across three-dimensional (3D) datasets remains a labor-intensive bottleneck. zFISHer is an open-source application built on the napari viewer that provides complete automation of sequential FISH image processing in conjunction with interactive user-curation tools. zFISHer provides end-to-end analysis of paired FISH datasets, encompassing nuclear segmentation, automated puncta detection on unaligned z-stacks, multi-round image registration via translation-constrained RANSAC with optional B-spline deformable warping, precise transformation of puncta coordinates into aligned space, consensus nuclei generation, interactive editing with real-time collision detection, and pairwise and tri-channel colocalization analysis with statistics. This includes a "Fishing Hook" raycasting algorithm that enables users to locate puncta at their true 3D centroids by identifying intensity maxima along the camera ray, eliminating manual z-slice navigation, complemented by a sub-voxel volume optimization. The included batch processing mode enables high-throughput unattended analysis of multiple experimental datasets. Availability and ImplementationzFISHer is open source under the MIT license, freely available on GitHub: https://github.com/stjude/zFISHer. The example dataset (deconvolved ND2 image stacks) is archived on Zenodo at https://doi.org/10.5281/zenodo.20288536. zFISHer is developed in Python utilizing the napari viewer for the interface. Documentation and expected test outputs for the sample dataset are available on the GitHub: https://github.com/stjude/zFISHer. To report an issue using zFISHer or contributing to it, please file an issue in the GitHub repository: https://github.com/stjude/zFISHer/issues. ContactSeth.Staller@STJUDE.ORG Supplementary InformationSupplementary data are available online.

bioinformatics↗

bioRxiv2025

Gene-specific response to MuSK agonist antibody in the treatment of Congenital Myasthenic Syndromes

Congenital myasthenic syndromes (CMS) are a group of rare disorders characterized by fatigable muscle weakness and caused by impaired neuromuscular junction (NMJ) function. CMS symptoms are highly variable, but can be detrimental and lead to death. There are over 40 different genetic subtypes, including Agrn-CMS and ColQ-CMS. Agrn encodes for neural AGRIN, which is released from the nerve terminal and triggers muscle-specific kinase phosphorylation (pMuSK). pMuSK is essential for NMJ development and maintenance, thus AGRIN deficiency causes NMJ impairment. ColQ encodes for collagenous subunit Q (ColQ), which anchors acetylcholinesterase and stabilizes MuSK. As a result, ColQ deficiency results in NMJ degeneration from prolonged transmission signals and decreased pMuSK. Current treatments for Agrn-CMS and ColQ-CMS are limited, highlighting the importance of finding more efficient therapies. Recently, a MuSK agonist antibody with high affinity for the Frizzled-like domain showed remarkable rescue of a Dok7-CMS mouse model. We hypothesized a similar antibody could benefit Agrn- and ColQ-CMS mouse models. Agrn-CMS mice were treated at postnatal day 5 (P5), P15 and P35, and ColQ-CMS mice were treated weekly from P22 to P57. In Agrn-CMS mice, 3B2 treatment rescued survival, bodyweight, fibre type switching and pMuSK levels, and improved grip strength and NMJ morphology. In ColQ-CMS mice, 3B2 treatment was unable to rescue deficits observed. Our findings suggest that MuSK agonists may benefit patients with Agrn-CMS, which should be tested in clinical trials. Our study emphasizes that effective CMS treatment is gene-dependent and relies on an accurate genetic diagnosis.

molecular biology↗

bioRxiv2025

Seq2Karyotype (S2K): A Method for in-silico Karyotyping Using Single-Sample Whole-Genome Sequencing Data

DNA abnormalities characterized by cytogenetic imaging at the single cell resolution, i.e. karyotyping, have long served as cancer diagnostic and prognostic biomarkers. To enable in-silico karyotyping using unpaired whole-genome sequencing data, we developed Seq2Karyotype (S2K), a tool that fits karyotype models with clonality estimation based on read-depth and allelic imbalance in a bulk sample and supports visualization-guided refinement. Analysis on 19 adult and pediatric cancer cell lines revealed unexpected intratumoral heterogeneity involving multiple copy number variation (CNV) states including whole-genome duplication, which were validated by imaging and single-cell omics profiling. Analyses on patient samples showed high concordance with clinical cytogenetic reports for acute myeloid leukemia, and revealed evolutionary trajectories from multi-region metastatic neuroblastomas implicating reversion. These findings highlight extensive and dynamic intratumoral heterogeneity contributed by CNV in both cell line models and patient samples, which may inform future research on tumor evolution under selective pressure such as drug exposure.

bioinformatics↗

bioRxiv2024

Topology-informed regulatory element collections coordinate cell identity gene expression programs

Transcription proteins are concentrated at nuclear transcriptional condensates. These condensates contain cis-regulatory elements (CREs), including enhancers and promoters, that are thought to regulate genes in the same condensate. The roles of condensates are of great current interest, but research into their function is limited by an inability to comprehensively identify their associated CREs. Here, we present a conceptual framework and algorithm, BOUQUET, for integrating genome topology, chromatin occupancy, and graph theory to associate CREs and transcription protein machinery with target genes and identify exceptionally protein-rich communities that interact with condensates. BOUQUET uncovers surprising quantitative correlations between community protein accumulation and gene expression phenotypes by combining accurate CRE-gene assignment with co-activator binding profiles. A small subset of communities, which we call "3D-super-enhancers," is exceptionally protein-rich. BOUQUET-predicted 3D-SEs are comparable in number to co-activator nuclear puncta, and all genes known to interact with co-activator condensates in embryonic stem cells are within 3D-SEs. 3D-SEs are enriched for association with cell identity genes across mammalian tissues. Microscopy analyses show frequent co-localization and co-expression of genes from the same 3D-SE within a single co-activator punctum, suggesting 3D-SE components interact with co-activator condensates. Thus 3D-SEs correspond to co-activator puncta, which nominates additional condensate-associated genes and CREs.

molecular biology↗