Biology subjects

Burden, S.

Publications and source records attributed to Burden, S..

3 recordsLinked to original sources

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↗