{"689822":{"#nid":"689822","#data":{"type":"event","title":"BioE PhD Defense Presentation- Nicholas Zhang","body":[{"value":"\u003Cp\u003E\u003Cstrong\u003EAdvisor:\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003EAhmet F. Coskun, Ph.D. (Biomedical Engineering, Georgia Institute of Technology)\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003ECommittee:\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003EPeng Qiu, Ph.D. (Department of Biomedical Engineering, Georgia Institute of Technology)\u003C\/p\u003E\u003Cp\u003ESaurabh Sinha, Ph.D. (Department of Biomedical Engineering, Georgia Institute of Technology)\u003C\/p\u003E\u003Cp\u003ERabindra Tirouvanziam, Ph.D. (Department of Biomedical Engineering, Georgia Institute of Technology)\u003C\/p\u003E\u003Cp\u003EMarcus Cicerone, Ph.D. (Department of Chemistry \u0026amp; Biochemistry, Georgia Institute of Technology)\u003C\/p\u003E\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003ETimeseries Spatial Omics of Immune Cell Signaling in Inflammation\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003ECystic fibrosis (CF) affects over 162,000 people worldwide. Although FDA-approved therapies have shown promising results, chronic inflammation and bacterial infections persist, causing tissue damage and worsening quality of life despite a large immune cell presence. This thesis investigates the spatiotemporal dynamics of NF-\u03baB signaling during inflammation by developing and applying spatial omics tools at the single-cell level across multiple biological contexts.\u003C\/p\u003E\u003Cp\u003EWe first introduce PRISMS, an open-sourced, automated multiplexing pipeline for spatial transcriptomic and proteomic imaging compatible with Nikon widefield and Cephla spinning disk confocal microscopy. Using PRISMS, we apply pSigOmics static fixation to profile over 100,000 mouse fibroblasts stimulated with TNF\u03b1 and IL-1\u03b2, revealing a novel asymmetric protein-RNA (APR) relationship between p65 RNA and protein. Graph neural network classification and PHATe trajectory analysis further delineate distinct APR subpopulations among stimulated fibroblasts.\u003C\/p\u003E\u003Cp\u003EWe next extend pSigOmics with programmable fixation via helical perfusion to create a continuous gradient of cell response, confirming the APR phenomenon with finer temporal resolution through cross-correlation, generalized additive model smoothing, and pseudotime analyses. Together, static and programmable fixation establish a comprehensive spatiotemporal framework for studying oscillatory translational regulation in single cells.\u003C\/p\u003E\u003Cp\u003EWe then develop graph-based super-resolution protein-protein interaction (GSR-PPI) analysis to predict cancer drug responses from spatial PPI networks in lung adenocarcinoma cells and patient-derived NSCLC tissues, and introduce multiplexed iterative sequential PLA (iseqPLA) to visualize 3D NF-\u03baB supercomplex dynamics. Upstream supercomplexes containing TRAF-5_TRADD and TRAF-5_TRAF-2 undergo rapid dissociation upon cytokine stimulation, inversely correlated with p65 nuclear translocation. Macrophage-fibroblast coculture experiments reveal that CF airway supernatant-exposed macrophages impart a hyperinflammatory phenotype to neighboring fibroblasts through paracrine NF-\u03baB activation. We additionally validate our NF-\u03baB gene panel using scGPT foundation models trained on multi-disease transcriptomic datasets, establishing a mechanistic link between protein-level supercomplex dynamics and transcriptional outputs.\u003C\/p\u003E\u003Cp\u003EThese contributions demonstrate the power of combining spatial multiplexing, temporal reconstruction, and computational modeling to decode immune signaling at single-cell and subcellular resolution, with implications for understanding chronic inflammation in CF and identifying opportune windows for therapeutic intervention.\u003C\/p\u003E","summary":"","format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EBioE PhD Defense Presentation- \u0022Timeseries Spatial Omics of Immune Cell Signaling in Inflammation\u0022 -Nicholas Zhang\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"\u0022Timeseries Spatial Omics of Immune Cell Signaling in Inflammation\u0022"}],"uid":"27917","created_gmt":"2026-04-17 13:09:05","changed_gmt":"2026-04-17 13:10:25","author":"Laura Paige","boilerplate_text":"","field_publication":"","field_article_url":"","field_event_time":{"event_time_start":"2026-05-01T12:00:00-04:00","event_time_end":"2026-05-01T14:00:00-04:00","event_time_end_last":"2026-05-01T14:00:00-04:00","gmt_time_start":"2026-05-01 16:00:00","gmt_time_end":"2026-05-01 18:00:00","gmt_time_end_last":"2026-05-01 18:00:00","rrule":null,"timezone":"America\/New_York"},"location":"1128 IBB","extras":[],"groups":[{"id":"65448","name":"Bioengineering Graduate Program"}],"categories":[],"keywords":[{"id":"172056","name":"go-BioE"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[],"email":[],"slides":[],"orientation":[],"userdata":""}}}