Biology subjects

Chan, B.

Publications and source records attributed to Chan, B..

10 recordsLinked to original sources

bioRxiv2026

Murine cytomegalovirus m119-118 encodes a new viral Fc receptor antagonizing host Fc receptor activation

Cytomegaloviruses (CMVs) encode numerous immunomodulatory proteins to counteract innate and adaptive immunity. One class of immune evasion proteins is viral Fc receptors (vFcRs), which bind to the Fc region of IgG antibodies and interfere with antibody-mediated effector functions crucial for antiviral defense. Despite the established role of vFcRs in modulating antibody-mediated immunity, their contribution to viral pathogenesis in vivo remains incompletely understood. Although human CMV (HCMV) encodes four vFcRs, only a single vFcR, fcr-1 encoded by gene m138, has been identified in murine CMV (MCMV). By comparing and cloning the genomes of MCMV strains v70, K181+, and K181Perth, we identified a frameshift mutation affecting the spliced m119-118 transcript in K181Perth. This finding prompted us to investigate the function of the m119-118 gene. We show that it encodes a second MCMV vFcR, which we named fcr-2. It is structurally similar to its positional homolog in HCMV, UL119-118/gp68, and binds specifically to the Fc part of murine IgG. Deletion of both vFcRs genes from the MCMV genome resulted in substantially reduced Fc-binding to the surface of infected cells, indicating a complementary function of the vFcRs. Functional assays with viral deletion mutants further demonstrated that both proteins inhibit host Fc receptor activation in a cooperative fashion. Although an m119-118-deficient MCMV was only marginally attenuated in infected BALB/c mice, an m119-118 and m138 double mutant attained significantly lower organ titers than the m138-deficient mutant. These data suggest an important cooperative function of the two MCMV vFcRs for viral dissemination and pathogenesis in vivo.

microbiology↗

bioRxiv2026

Large-scale cerebrospinal fluid proteomics identifies diagnostic biomarker candidates across the clinico-pathological continuum of frontotemporal lobar degeneration

Frontotemporal lobar degeneration (FTLD), predominantly comprised of tau and TDP-43 proteinopathies, is a common cause of early-onset dementia. Biomarkers that reliably classify FTLD subtypes are limited, thereby hindering in-vivo diagnosis and clinical trial stratification. We conducted large-scale, multi-platform cerebrospinal fluid proteomics in 566 individuals, including 274 FTLD-spectrum (48 autopsy-confirmed FTLD-TDP, 90 autopsy-confirmed FTLD-tau), 171 Alzheimers disease, and 95 controls. In neuropathological subtype contrasts, elevated matrix metalloproteinase MMP10 classified Picks disease (PiD) versus other subtypes with near-perfect accuracy across proteomic platforms. We further validated CSF MMP10 as a potential PiD diagnostic biomarker via a targeted immunoassay in an independent, autopsy-confirmed FTLD cohort. Post-synaptic proteins HOMER1 and DLG4 exhibited elevations across FTLD-TDP subtypes (A, B, and C) versus FTLD-tau. Network analysis identified RNA metabolism and pro-inflammatory signatures in FTLD-TDP, and cytoskeletal and heat shock signatures in progressive supranuclear palsy. These findings reveal candidate diagnostic biomarkers and proteomic pathways underlying FTLD clinico-pathological heterogeneity.

neuroscience↗

bioRxiv2026

Entanglement dilution and high fractal dimension mediated by loop extrusion revealed in simulations of active polymer melts

In the active loop extrusion model, the cohesin protein complex creates chromatin loops in eukaryotic cells. Extrusion maintains topologically associated domains (TADs), which are contiguous segments of chromatin that preferentially colocalize in space and are typically bounded by CTCF proteins that pause cohesin translocation. Here, we model active loop extrusion with hybrid molecular dynamics - Monte Carlo simulations in entangled flexible linear polymer melts. Intra-chain contact probabilities of polymers with active loop extrusion are enhanced compared to their equilibrium, passive counterparts. Extrusion causes the size of chain segments to be much smaller than in passive melts. While the overlap parameter in passive melts without extrusion monotonically increases with segment length, it is nonmonotonic in active melts and on the order of unity within the parameters of this study. Active loop extrusion suppresses contacts between TADs in favor of intra-TAD contacts. Reduction of overlaps between chain segments dilutes entanglements in active melts. Depending on parameters, active extrusion without TADs may induce more compact conformations than with TADs, due in part to fractal loopy globule-like dynamics. This work suggests that active loop extrusion reduces overlaps between TADs, contributing to effective gene regulation by cis-regulatory elements.

biophysics↗

bioRxiv2026

The regulatory landscape of optic fissure closure in the vertebrate eye

PurposeOptic fissure closure (OFC) is a critical tissue fusion event in normal eye development and its failure results in ocular coloboma (OC), an inferonasal ocular tissue defect that persists throughout life. Most OC cases lack a genetic diagnosis, reflecting limited understanding of the genes and pathways that regulate OFC. We aimed to determine if OFC gene expression is regulated by the non-coding genome and identify novel candidate loci for OFC/OC. MethodsUsing the embryonic chicken eye, we performed integrated profiling of accessible chromatin and gene expression patterns during OFC. Matched RNA-seq and ATAC-seq from distinct spatial and temporal eye tissues were utilised with bioinformatic tools to identify regulatory genomic elements and infer gene regulatory networks, and to map synonymous loci in the human genome. ResultsWe revealed domains of accessible chromatin during active fusion and the broader ventral retina that were distinct from those in the dorsal retina, implicating these loci for gene regulation during development and fusion of the optic fissure. In silico analysis using de novo motif enrichment and transcription factor (TF) foot-printing revealed TEAD, ZIC, and SOX TF activity during OFC, and retinoic acid signalling related TF activity in the dorsal eye. A subset of chicken OFC-specific peaks mapped to human cis-regulatory elements near known coloboma genes and OFC candidate genes identified in this study. ConclusionsThis provides the first evidence for dynamic cis-regulatory activity during OFC, identifies candidate loci for future mutational analysis, and offers new genetic leads for OC cases without a genetic diagnosis.

developmental biology↗

bioRxiv2024

Control of alveolar bone development, homeostasis, and socket healing by salt inducible kinases

Alveolar bone supports and anchors teeth. The parathyroid hormone-related protein (PTHrP) pathway plays a key role in alveolar bone biology. Salt inducible kinases (SIKs) are important downstream regulators of PTH/PTHrP signaling in the appendicular skeleton where SIK inhibition increases bone formation and trabecular bone mass. However, the function of these kinases in alveolar bone remains unknown. Here, we report a critical role for SIK2/SIK3 in alveolar bone development, homeostasis, and socket healing after tooth extraction. Inducible SIK2/SIK3 deletion led to dramatic alveolar bone defects without changes in tooth eruption. Ablating these kinases impairs alveolar bone formation due to disrupted osteoblast maturation, a finding associated with ectopic periostin expression by fibrous cells in regions of absent alveolar bone at steady state and following molar extraction. Distinct phenotypic consequences of SIK2/SIK3 deletion in appendicular versus craniofacial bones prompted us to identify a specific transcriptomic signature in alveolar versus long bone osteoblasts. Thus, SIK2/SIK3 deletion illuminates a key role for these kinases in alveolar bone biology and highlights the emerging concept that different osteoblast subsets utilize unique genetic programs. Summary statementSIK2/SIK3 deletion in alveolar bone reduces bone formation and mass by impairing osteoblast maturation, unlike in long bones, where it increases bone formation and mass.

developmental biology↗

bioRxiv2024

SARM1 orthosteric base exchange inhibitors cause subinhibitory SARM1 activation

SARM1, an octameric NADase, is a key regulator of axon degeneration and an emerging target in small molecule drug discovery to treat a wide range of neurodegenerative diseases. Recently, a structurally diverse series of adduct-forming, orthosteric SARM1 inhibitors have been discovered. Here, we show that subinhibitory concentrations of these orthosteric inhibitors, under mildly SARM1 activating conditions, cause sustained SARM1 activation. This synergistic adverse effect leads to increased nicotinamide adenine dinucleotide (NAD) consumption, neurodegeneration and release of the biomarker neurofilament-light (NfL) in cultured cortical neurons. In two distinct animal models, we found that low-dose treatment with these orthosteric SARM1 inhibitors results in increased plasma NfL and adverse events when combined with cellular stress or injury conditions. This may present a critical liability for orthosteric SARM1 inhibitors in certain patient populations.

neuroscience↗

bioRxiv2024

Activity-driven chromatin organization during interphase: compaction, segregation, and entanglement suppression

In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross over between two and four at contour lengths on the order of 30 kilo-base pairs (kbp). The anomalously high fractal dimension D = 4 is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times ({Delta}t) longer than tens of minutes to be proportional to {Delta}t1/3. We validate our results with hybrid molecular dynamics - Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation. SIGNIFICANCE STATEMENTDuring interphase, cells must compact chromatin such that gene promoters and their regulatory elements frequently contact each other in space. However, cells also need to insulate promoters from regulatory elements in other genomic sections. Using polymer physics theory and computer simulations, we propose that the cohesin protein complex actively extrudes chromatin into topologically associated domains (TADs) with an anomalously high fractal dimension of D {approx} 4 while suppressing spatial overlap between different TADs. Our model suggests that the fast kinetics of active loop extrusion compared to the slow relaxation of chromatin loops maintains a dense chromatin organization. This work presents a physical framework explaining how cohesin contributes to effective transcriptional regulation.

biophysics↗

bioRxiv2023

The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes

Heteromorphic sex chromosomes are usually thought to have originated from a pair of autosomes that acquired a sex-determining locus and subsequently stopped recombining, leading to degeneration of the sex-limited chromosome. In contrast, in rhabditid nematodes, sex is determined by an X-chromosome counting mechanism and males are hemizygous for one or more X chromosomes (XX/X0). Some species of filarial nematodes, including important parasites of humans, have heteromorphic XX/XY systems. It has been assumed that sex is determined by a Y-linked locus in these species. However, karyotypic analyses suggested that filarial Y chromosomes are derived from the unfused autosome following an X-to-autosome fusion. Here, we generated a chromosome-level reference genome for Litomosoides sigmodontis, a filarial nematode with the ancestral filarial karyotype and sex determination mechanism (XX/X0). We mapped the assembled chromosomes to the rhabditid nematode ancestral linkage (or Nigon) elements. We found that the L. sigmodontis X chromosome was formed from a fusion of NigonX (the ancestrally X-linked element) and NigonD (ancestrally autosomal) that occurred in the last common ancestor of all filarial nematodes. In the two filarial lineages with XY systems, the X chromosomes were formed from two recent and independent fusions of the ancestral X chromosome with different autosomal Nigon elements. In both lineages, the region shared by the neo-X and neo-Y chromosomes is within the ancestrally autosomal portion of the X, confirming that the filarial Y chromosomes are derived from unfused autosomes. Sex determination in XY filarial nematodes therefore likely continues to operate via the ancestral X-chromosome counting mechanism, rather than via a neo-Y-linked sex-determining locus.

evolutionary biology↗

bioRxiv2022

Realtime morphological characterization and sorting of unlabeled viable cells using deep learning

Phenotyping of single cells has dramatically lagged advances in molecular characterization and remains a manual, subjective, and destructive process. We introduce COSMOS, a platform for phenotyping and enrichment of cells based on deep learning interpretation of high-content morphology data in realtime. By training models on an atlas of >1.5 billion images, we demonstrate enrichment of unlabeled cells up to 33,000 fold. We apply COSMOS to multicellular tissue biopsy samples demonstrating that it can identify malignant cells with similar accuracy to molecular approaches while enriching viable cells for functional evaluation. We show high-dimensional embedding vectors of morphology generated by COSMOS without any need for complex sample pre-processing, gating, or bioinformatics capabilities, which enables discovery of cellular phenotypes, and integration of morphology into multi-dimensional analyses. One sentence summaryA novel platform capable of high-throughput imaging and gently sorting cells using deep morphological assessment.

cell biology↗

bioRxiv2021

Rapid screening of pest resistance genes in maize using a sugarcane mosaic virus vector

Spodoptera frugiperda (fall armyworm) is a notorious pest that threatens maize production world-wide. Current control measures involve the use of chemical insecticides and transgenic maize expressing Bacillus thuringiensis (Bt) toxins. Although several additional transgenes have confirmed insecticidal activity in other plants, limited research has been conducted in maize, at least partially due to the technical difficulty of maize transformation. Here, we describe implementation of a sugarcane mosaic virus (SCMV) vector for rapidly testing the efficacy of transgenes for the control of S. frugiperda in maize. Four categories of proteins were tested using the SCMV vector: (i) maize defense signaling proteins: peptide elicitors (Pep1 and Pep3) and jasmonate acid conjugating enzymes (JAR1a and JAR1b); (ii) maize defensive proteins: the previously identified ribosome-inactivating protein (RIP2) and maize proteinase inhibitor (MPI), and two proteins with predicted but unconfirmed anti-insect activities, an antimicrobial peptide (AMP) and a lectin (JAC1); (iii) lectins from other plant species: Allium cepa agglutinin (ACA) and Galanthus nivalis agglutinin (GNA); and (iv) spider and scorpion toxins: peptides from Urodacus yaschenkoi (UyCT3 and UyCT5) and Hadronyche versuta (Hvt). In most cases, S. frugiperda larval growth on maize was reduced by transient SCMV-mediated overexpression of genes encoding these proteins. Additionally, experiments with some of the SCMV-expressed genes showed effectiveness against two aphid species, Rhopalosiphum maidis (corn leaf aphid) and Myzus persicae (green peach aphid). Together, these results demonstrate that SCMV vectors can be exploited as a rapid screening method for testing the efficacy and insecticidal activity of candidate genes in maize.

plant biology↗