Biology subjects

Richmond, J.

Publications and source records attributed to Richmond, J..

5 recordsLinked to original sources

bioRxiv2026

Multi-omic Longitudinal Analysis of Canine Osteosarcoma Identifies Inter-Patient Heterogeneity and Immune Enrichment in Metastatic Lesions

Osteosarcoma (OS) exhibits substantial genomic complexity and inter-patient heterogeneity, necessitating longitudinal, patient-matched analyses to understand acquired features of tumor evolution. However, most published OS data is limited to primary tumor samples, limiting insight into patient-specific resistance mechanisms. To address this, we characterized the genomic landscape of paired primary and metastatic tumor samples from dogs with spontaneous OS. Whole-genome and single-cell RNA sequencing reveal mutation and gene expression profiles that are predominantly organized by patient identity. Mutational burden and pathway alterations such as those involving PI3K, NOTCH, TP53, MAPK, RAS and epigenetic regulation differ between primary and metastatic samples. Variants present in tumor tissue are readily detectable in paired cfDNA samples, demonstrating the utility of this assay for identifying tumor-specific alterations associated with treatment resistance. Analysis of bulk RNA-seq data to estimate cell-type composition shows greater immune cell representation in metastases, underscoring the importance of immune signaling pathways in OS. These findings exemplify the presence of patient-specific alterations in genomic architecture over the course of tumor progression, linking CNV amplification, pathway reprogramming, and immune evasion in metastatic OS.

genomics↗

bioRxiv2025

Evolutionarily Conserved and Divergent Mechanisms of Dual Ca2+ Sensors in Synaptic Vesicle Exocytosis

Neurotransmitter release at the C. elegans neuromuscular junction is governed by a dual Ca{superscript 2} sensor system composed of SNT-1 and SNT-3, which are functional analogs of synaptotagmin-1 and -7 (Syt1/Syt7) in mammalian central synapses. In this study, we investigated how SNT-1 and SNT-3 mediate fast and slow neurotransmitter release through their potential interactions with the SNARE complex and their polybasic motifs. AlphaFold 3 models of SNT-1-SNARE and SNT-3-SNARE complexes accurately recapitulated the canonical Syt1 C2B-SNARE primary interface (Zhou et al., 2015, Nature) and precisely identified conserved binding residues within the C2B domains, as well as in SNAP-25 and Syntaxin, highlighting the evolutionary conservation of this interaction. Electrophysiological analyses using targeted mutagenesis demonstrated that both SNT-1 and SNT-3 require C2B-SNARE interactions and polybasic motifs within their C2 domains to drive evoked fast and slow neurotransmitter release. Notably, SNT-1 and SNT-3 exhibited differential dependence on distinct regions of the C2B-SNARE interface and their respective polybasic motifs, suggesting that Ca{superscript 2}-triggered fast and slow release operate via distinct mechanistic strategies. Furthermore, we found that SNT-1 mediates spontaneous neurotransmitter release through multiple pathways, involving not only the primary C2B-SNARE interface but also additional putative SNARE-binding interactions. Together, our findings uncover both conserved and divergent mechanisms for synaptic exocytosis regulated by the dual Ca2+ sensors in C. elegans.

neuroscience↗

bioRxiv2025

Comparative spatial transcriptomics of hair follicle-T cell interactions in mouse, dog and human reveals conserved drivers of primary cicatricial alopecia

Primary cicatricial alopecias (PCA) encompass several autoimmune disorders characterized by scarring hair loss. Many of these conditions are lymphocytic and are thought to be driven by T cell populations. Here, we sought to characterize potential T cell-hair follicle communication pathways in the microanatomical niche using spatial transcriptomics across 3 mammalian species including a novel mouse model, spontaneous disease in companion dogs and human archival diagnostic biopsies. Flow cytometry of mouse model skin confirmed loss of CD34+ bulge cells and keratinocytes, and bulk microarray and histology revealed expression of collagens and development of fibrosis. In vivo ear imaging in mice engrafted with Kikume photoconvertible OT1 CD8+ T cells confirmed long-lived RFP+ T cells in skin arrest near hair follicles and recruit other GFP+ T cells. OT1 T cells expressed CD69, CD103, CD122 and CD62L, which is a binding partner of CD34. Digital spatial profiling using CD3, CD8 and CD45 cell masking identified CXCR3 ligands and IFN response genes in hair follicles, and "metabolic" pathways in T cells, which were also recapitulated in dog and human biopsies. Bulk human RNA as well as spatial analysis of perifollicular T cells confirmed enrichment of CD69 and SELL/CD62L. Different pathways predominated in other CD3+ regions of interest in CD4+ driven conditions including mucocutaneous lupus erythematosus and subacute cutaneous lupus erythematosus. Last, we identify novel drug-targetable pathways, namely CFD and S100A8/9, that could be further explored to disrupt processes in these conditions through veterinary and human trials.

immunology↗

bioRxiv2020

Microglia Stimulate Zebrafish Brain Repair Via a Specific Inflammatory Cascade

The adult zebrafish brain, unlike mammals, has a remarkable regenerative capacity. Although inflammation inhibits regeneration in mammals, it is necessary for zebrafish brain repair. Microglia are resident brain immune cells that regulate the inflammatory response. To explore the microglial role in repair, we used liposomal clodronate, colony stimulating factor-1 receptor (csf1r) inhibition to ablate microglia and two genetic mutants that lacks microglia during brain injury. We found that microglial ablation inhibited injury-induced neurogenesis and regeneration. Microglial suppression specifically attenuated cell proliferation at the progenitor cell amplification stage of neurogenesis. Notably, the loss of microglia impaired phospho-stat3 (signal transducer and activator of transcription 3) and {beta}-catenin signaling by dynamic regulation of tumor necrosis factor-a after injury, and the ectopic activation of stat3 and {beta}-catenin rescued neurogenesis defects caused by microglial loss. Microglial absence leads to neutrophil accumulation, hindering the resolution of inflammation and macrophages are not sufficient for regeneration. These findings reveal specific roles of microglia and inflammatory signaling during zebrafish telencephalic regeneration that should provide strategies to improve mammalian brain repair.

neuroscience↗

bioRxiv2019

The development of methodology and techniques for crop disease identification

In India, an estimated 15-25% of potential crop production is lost due pest and diseases (Roy and Bezbaruah, 2002). The country needs not only to raise production but also ensure food security for its growing consumption needs while curbing excessive pesticide usage. Detection of pests and diseases at an early stage plays a significant role in addressing the above-mentioned concerns and image classification offers a cost-effective and scalable solution to the disease detection problem (A. Ramcharan et al. 2017). Here, the principles of transfer learning are implemented with pretrained model - Resnet34 (K. He et al. 2015), and test its effectiveness in image classification using a dataset of tea leaves. The novelty of this work is that the images used are not curated, individual leaves with controlled backgrounds but of plants in-situ. The effect of the level of zoom and background is examined and class activation maps are used to validate that the basis of classification is indeed the disease and not an artificial bias from factors such as background, lighting etc.

plant biology↗