Biology subjects

Wan, A.

Publications and source records attributed to Wan, A..

4 recordsLinked to original sources

bioRxiv2025

Focal adhesion prevention on nanoparticle substrates upregulates stemness gene expression in primary melanocytes

HypothesisCell focal adhesions are initiated by interactions of cell surface integrins with extracellular matrix (ECM) proteins, and cells which lack focal adhesions have been associated with an intermediate adhesive state, which is more labile towards cell reprogramming. We hypothesized that cells cultured under conditions where they exhibit reduced focal adhesions will assume an intermediate adhesive state with a more stem cell-like transcriptional profile. ExperimentsTo recreate culture conditions for cells to exhibit reduced focal adhesions, we synthesized PMMA nanoparticles by evaporation-induced self-assembly (EISA), employing varying conditions of surfactant concentrations, and allowed them to self-assemble into nanoparticle substrates. Following guidelines from previous work, we selected nanoparticle substrates of dimensions [~]70nm, suitable for the prevention of focal adhesion formation. Primary human melanocytes were cultured on these substrates to verify the reduction of their focal adhesions; following that the cultures were characterized in terms of their expression of distinct sets of genes related to stemness and differentiation. FindingsThe melanocytes showed reduced focal adhesions on both non-coated and fibronectin-coated nanoparticle substrates, when compared to melanocytes cultured on TCPs. Accompanying the reduction in focal adhesions, the cells exhibited an increase in the expression of general as well as melanocyte-specific stemness related genes such as OCT4, LIN28, NANOG and PAX6 and a concurrent downregulation of genes expressed by differentiated melanocytes, such as TYR, TRP1 and MITF. These observations support our hypothesis.

bioengineering↗

bioRxiv2025

Age-dependent tumor-immune interactions underlie immunotherapy response in pediatric cancer

Pediatric cancers originate in rapidly growing tissues within the context of a developing host. However, the interactions between cancer cells and the developing immune system are incompletely understood. Here, we established a suite of pediatric syngeneic mouse cancer models across diverse anatomical sites and compared their tumor immune microenvironment with that in adult mice. Tumors in pediatric mice exhibited significantly accelerated growth and diminished leukocyte infiltration, dominated by naive-like PD-1low/CD8+ T cells, and proliferative MHCIIlow/PD-L1hi/CD86low macrophages. Tumor-infiltrating leukocytes in pediatric mice were enriched for MYC targets, which was also observed in pediatric patient samples. Furthermore, pediatric mice displayed poor responses to anti-PD-1/PD-L1 or bispecific T cell engager antibodies, which could be reversed by inducing a proinflammatory microenvironment via MYC inhibition or inducing macrophage polarization to an MHCIIhi phenotype. These findings underscore the significant influence of young age on cancer immune responses and reveal potential new therapeutic opportunities for pediatric cancers. HIGHLIGHTSO_LIAllograft tumors exhibit markedly accelerated growth in pediatric hosts compared to adults. C_LIO_LITumors growing in pediatric mice have reduced leukocyte infiltration, dominated by naive-like PD-1low/CD8+ T cells, and MHCIIlow/M2-like macrophages. C_LIO_LIEnrichment of MYC target genes is observed in pediatric mouse tumors and confirmed in primary patient tumor samples. C_LIO_LIPediatric mice display reduced response to anti-PD-1/PD-L1 and BiTE immunotherapy, which can be reversed by remodeling the TIME, using either MYC inhibition or macrophage polarization. C_LI

cancer biology↗

bioRxiv2023

Mussels on the move: new records of the invasive non-native quagga mussel (Dreissena rostriformis bugensis) in Great Britain using eDNA and a new probe-based qPCR assay

Invasive non-native species (INNS) pose a worldwide environmental threat, negatively impacting invaded ecosystems on an ecological and economical scale. In recent decades, quagga mussels (Dreissena rostriformis bugensis) have successfully invaded several countries in Western Europe from the Ponto-Caspian region, being recorded for the first time in Great Britain (GB) in 2014, in Wraysbury, near London. In recent years, environmental DNA (eDNA) analysis has proven to be a sensitive and effective method for early detection and monitoring of a number of INNS. Previously, a dye-based quantitative PCR (qPCR) assay was developed for the detection of quagga mussels from eDNA samples. Here, a target-specific probe was designed to further increase the specificity of this assay and used to obtain an updated distribution of this species in GB. Twenty-four sites were sampled, including sites with established populations near London and sites spread across the East Midlands and East Anglia regions. Positive detections were obtained for 11 of the 24 sites, and these were widely spread, as far as Nottingham (East Midlands) and Norfolk (East Anglia). Detection rates were 100% at the three sites with known established populations, while rates were lower (3-50% of positive replicates) in the eight newly-identified sites, consistent with an early stage of invasion. Of particular concern was the detection of quagga mussels in major waterways and in popular recreational sites, highlighting urgent measures are needed to control pathways and spread. Our study demonstrates that quagga mussels are considerably more widespread in GB than previously thought and provides a much-needed step towards operational use of eDNA for monitoring quagga mussels.

ecology↗

bioRxiv2019

Characterizing variants of unknown significance inrhodopsin: a functional genomics approach

Characterizing the pathogenicity of DNA sequence variants of unknown significance (VUS) is a major bottleneck in human genetics, and is increasingly important in determining which patients with inherited retinal diseases could benefit from gene therapy. A library of 210 rhodopsin (RHO) variants from literature and in-house genetic diagnostic testing was created to efficiently detect pathogenic RHO variants that fail to express on the cell surface. This study, while focused on RHO, demonstrates a streamlined, generalizable method for detecting pathogenic VUS. A relatively simple next generation sequencing (NGS)-based readout was developed so that a flow cytometry-based assay could be performed simultaneously on all variants in a pooled format, without the need for barcodes or viral transduction. The resulting dataset characterized surface expression of every RHO library variant with a high degree of reproducibility (Z=0.94, R2=0.92-0.95), recategorizing 37 variants. For example, three retinitis pigmentosa pedigrees were solved by identifying VUS which showed low expression levels (G18D, G101V, P180T). Results were validated across multiple assays and correlated with clinical disease severity. This study presents a parallelized, higher-throughput cell-based assay for the functional characterization of VUS in rhodopsin, and can be applied more broadly to other inherited retinal disease genes and other disorders.

genetics↗