Deshpande, S. A. | Search bioRxiv

bioRxiv2026

Multiomic Spatial Imaging Assay (MSIA) -- A High-plex In Situ Detection Method for mRNAs, Proteins, and Protein-Protein Interactions using Manual And Semi-Automated Workflows

We report Multiomics Spatial Image Analysis (MSIA), a suite of technologies that include streamlined manual and semi-automated workflows to image 100s of RNAs from fresh frozen and formalin-fixed paraffin-embedded (FFPE) samples, contextualize RNAs with select protein markers including imaging synaptic protein interactions, a data analysis pipeline that includes corrections for chromatic aberration, algorithms for image stitching, deep learning models for image analysis (cell segmentation and RNA dot detection using hundreds of RNAscope images) from multiple stain-image cycles and proof of concept for a language model trained on extensive Parkinsons Disease (PD) literature. We used the language model to identify potential new biomarkers that were confirmed in MPTP-treated mouse model of PD. Furthermore, by incorporating more stain-image cycles alongside an additional fluorescent channel and advanced error-correcting decoding schemes, the MSIA workflow demonstrates the scalability to potentially quantify over 1,000 genes.

neuroscience↗

bioRxiv2023

Drosophila cells that express octopamine receptors can either inhibit or promote oviposition

Adrenergic signaling is known to play a critical role in regulating female reproductive processes in both mammals and insects. In Drosophila, the ortholog of noradrenaline, octopamine (Oa), is required for ovulation as well as several other female reproductive processes. Loss of function studies using mutant alleles of receptors, transporters, and biosynthetic enzymes for Oa have led to a model in which disruption of octopaminergic pathways reduces egg laying. However, neither the complete expression pattern in the reproductive tract nor the role of most octopamine receptors in oviposition is known. We show that all six known Oa receptors are expressed in peripheral neurons at multiple sites within in the female fly reproductive tract as well as in non-neuronal cells within the sperm storage organs. The complex pattern of Oa receptor expression in the reproductive tract suggests the potential for influencing multiple regulatory pathways, including those known to inhibit egg-laying in unmated flies. Indeed, activation of some neurons that express Oa receptors inhibits oviposition, and neurons that express different subtypes of Oa receptor can affect different stages of egg laying. Stimulation of some Oa receptor expressing neurons (OaRNs) also induces contractions in lateral oviduct muscle and activation of non-neuronal cells in the sperm storage organs by Oa generates OAMB-dependent intracellular calcium release. Our results are consistent with a model in which adrenergic pathways play a variety of complex roles in the fly reproductive tract that includes both the stimulation and inhibition of oviposition.

neuroscience↗