Biology subjects

Gibbs, S. L.

Publications and source records attributed to Gibbs, S. L..

10 recordsLinked to original sources

bioRxiv2026

Deep learning-based identification and quantification of rare circulating hybrid cells in orthotopic pancreatic cancer models

SignificanceRare-cell identification in fluorescence microscopy remains challenging because targets are sparse and background varies between specimens. Combining specimen-specific fluorescence enrichment with image classification may enable efficient and more specific automated detection of rare cells. AimWe developed a two-stage framework to identify and quantify candidate rare circulating hybrid neoplastic cells (CHCs, ECAD+/CD45+) in peripheral blood mononuclear cell (PBMC) preparations from tumor-bearing and tumor-naive mice. ApproachPBMCs from 28 mice were imaged by multichannel fluorescence microscopy. Matched unstained samples established animal-specific ECAD and CD45 background distributions for candidate cell enrichment. Blinded multi-annotator consensus labels were used to train a convolutional neural network (CNN) from DAPI, ECAD, and CD45 image crops. Generalization was evaluated by leave-one-animal-out validation across 10 random initializations. Final classification used a 10-model ensemble, and rare-cell burden was compared between groups using negative-binomial regression with total segmented-cell count as an exposure. ResultsOf the 1,065,512 segmented cells, enrichment retained 10,176 candidates (0.96%), reducing the search space by >99%. Four of five evaluable tumor-bearing animals showed reproducible held-out discrimination, with median quantified area under the receiver operator characteristic curve (AUROCs) of 0.918-0.951; one animal was a reproducible outlier (median AUROC, 0.338). Ensemble deployment identified 157.94 positive-consensus cells per 50,000 segmented cells in tumor-bearing animals versus 49.55 in controls. The estimated rare-cell rate was 3.15-fold higher in tumor-bearing animals (95% CI, 0.91-10.99; two-sided p=0.071; prespecified one-sided p=0.036). ConclusionsSpecimen-specific fluorescence enrichment combined with supervised image classification reduced the cellular search space and enabled automated quantification of a rare CHC (ECAD+/CD45+) phenotypes. Cross-animal validation also identified specimen-specific generalization failure, highlighting the importance of biological-specimen-level validation.

cancer biology↗

bioRxiv2026

Cyclic immunofluorescence platform using photocleavable linkers for direct antibody labeling enables cancer phenotyping

Advances in spatial proteomics through the development of multiplexed immunostaining platforms have facilitated analyses with increasing cellular and molecular granularity. However, currently available approaches are limited by harsh conditions for signal removal, restricting the number of antigens that can be probed in a single specimen without significant alterations to sample quality and structure. Here we present an approach for direct labeling of primary antibodies with fluorophores using a photocleavable linker (PCL) with a polyethylene glycol spacer (PEG) to enable cyclic immunofluorescence (cyCIF) with gentle signal removal conditions. Our innovative approach uses directly labeled primary antibodies to enhance staining specificity and cyclic immunostaining efficiency, while minimizing nonspecific background signal. Additionally, through integration of the PCL, this approach facilitates gentle cleavage of antibody conjugated fluorophore, preserving sample integrity over multiple rounds of staining. Direct PEG-PCL antibody labeling will promote greater multiplexing by minimizing specimen damage and allow for quantitative analyses of cyCIF spatial data. We demonstrate that cyCIF with PEG-PCL conjugated antibodies can be applied across a variety of cancer subtypes to identify and characterize rare neoplastic cell populations in both tumor tissue and fragile peripheral blood specimens.

biochemistry↗

bioRxiv2026

BBB-Permeable Near-Infrared Oxazine Fluorophores for White Matter Tract Imaging

Preserving critical functional tissue remains a major challenge in fluorescence-guided surgery (FGS), particularly in neurosurgery where injury to white matter tracts can lead to lasting neurological deficits. Probes for preventing iatrogenic injury of the peripheral nervous system have highlighted the potential of real-time intraoperative guidance for nerve-sparing surgery, supporting improved preservation of critical functional tissue, but analogous tools for the central nervous system remain limited. While there are some awake mapping and MRI based techniques that try to minimize the resection of white matter tracts (WMTs), they do not provide surgeons with real-time visualization. To address this gap, we rationally translated a peripheral nerve targeted oxazine fluorophore platform into a library of novel oxazine dyes that can penetrate the blood-brain barrier (BBB), exhibit specificity for white matter tissue and maintain spectral compatibility with clinically relevant imaging systems. Guided by our fluorophore medicinal chemistry platform, this work includes library design, photophysical property characterization, in vivo WMTs specificity screening, and in vivo imaging window assessment of the lead candidates to evaluate neurosurgical workflow compatibility. The lead candidate identified from this library demonstrated strong in vivo WMTs-specific fluorescence intensity, contrast and imaging window compatible with neurosurgical workflows, establishing BBB-permeable oxazine fluorophores as a promising scaffold for future structure-sparing neurosurgical FGS.

bioengineering↗

bioRxiv2026

Cell fusion reprograms tumor cells and promotes RUNX1-mediated invasion and dissemination in colorectal cancer

Metastasis remains the primary cause of cancer-related morbidity and mortality, despite significant advances in targeted therapies. Although metastatic dissemination requires tumor cells to escape the primary lesion and colonize distant organs, the mechanisms by which primary tumor cells gain metastatic competence remain poorly understood. Increasing evidence demonstrates that fusion of tumor (i.e., neoplastic) and immune (e.g., macrophages) cells generate a distinct population of tumor-immune hybrid cells with enhanced functional ability to migrate and disseminate into peripheral blood. Herein, our study investigates tumor-macrophage hybrid cells, an underexplored population of disseminated tumor cells, and their inherent heterogeneity and acquisition of molecular mechanisms underlying their dissemination as metastatic effectors in colorectal cancer (CRC). Through hybrid cell phenotyping utilizing integrative single-cell RNA sequencing (scRNA-seq), cyclic immunofluorescence (cyCIF) and functional assays with an in vitro model of CRC hybrid cells, we identify Runt-related transcription factor 1 (Runx1) as a central regulator of hybrid cell motility and invasion. Runx1 depletion in hybrid cells suppressed functional protease expression, chemotactic activity and extracellular matrix (ECM) invasion. Furthermore, pharmacologic inhibition of RUNX1 in an in vivo model reduced hybrid tumor growth and dissemination into peripheral blood, key attributes of metastatic spread of disease. In patients with CRC, RUNX1+ hybrid cells were identified in both primary tumor and peripheral blood, where circulating hybrid cells (CHCs) exhibited enriched migratory and epithelial-to-mesenchymal transition (EMT) phenotypes. Taken together, these findings reveal a mechanistic role for RUNX1 in driving invasive behavior of tumor-immune hybrids and highlight disseminated CHCs as an under-recognized contributor to metastatic spread and a promising noninvasive biomarker for tumor progression.

cancer biology↗

bioRxiv2025

Engineering NIR probes to enhance affinity and clinical workflow compatibility for prostate cancer imaging

Positive surgical margins following radical prostatectomy increase the risk of biochemical recurrence and subsequent disease progression. Fluorescence guided surgery (FGS) using targeted contrast agents has shown clinical benefits for several cancer types. However, current prostate cancer targeted imaging probes exhibit long pharmacokinetic (PK) profiles, necessitating extended waiting periods or repeated hospital visits, limiting their integration into standard clinical workflow. To overcome this critical clinical compatibility challenge, we developed an innovative tri-compartment, chemistry-driven probe design strategy. Specifically, we developed a congeneric library of near infrared (NIR) water soluble fluorescent probes incorporating: (1) a glutamic acid-urea-lysine (EuK) ligand targeting prostate specific membrane antigen (PSMA); (2) a NIR heptamethine cyanine fluorophore optimized for enhanced PSMA binding via secondary binding sites interactions; and (3) distinct PK modulators residing outside the PSMA binding pocket to promote rapid off-target tissue clearance. While molecular docking scores, photophysical properties and live-cell staining results showed similar overall performance, probes bearing PK modulators produced stronger tumor-specific fluorescence in vivo than the control lacking a PK modulator. This effort enabled identification of a lead probe with robust tumor targeting and accelerated off-target clearance, providing optimal tumor-specific signal and contrast in a timeframe, fully compatible with robotic-assisted radical prostatectomy (RARP) timelines.

pharmacology and toxicology↗

bioRxiv2025

Considerations for the use of contrast agents with diffuse in vivo flow cytometry to detect circulating cancer cell populations

SignificanceMetastasis is a leading cause of cancer-related deaths. Disseminated circulating tumor cells (CTCs) through the bloodstream seed metastatic tumors at distant sites. Most methods for enumerating CTCs in humans clinically rely on drawing and analyzing small blood samples, but these may yield inaccurate estimates of CTC burden and cannot measure CTC changes over time. Identification and enumeration of CTCs for experimental or clinical purposes largely rely on marker-driven analyses by flow cytometry. AimIn principle, non-invasive fluorescence enumeration of CTCs directly in vivo could provide a more accurate method for enumerating CTCs. However, this will require specific contrast agent for CTCs. The goal of this work is to define characteristics of useful CTC contrast agents and perform preliminary testing of candidate contrast agents used for fluorescence guided surgery (FGS). ApproachWe evaluated a clinical small-molecule folate receptor targeted contrast agent (OTL38, pafolacianine), a fluorogenic pan-cathepsin contrast agent (VGT-309, abenacianine), and a set of custom designed, small-molecule prostate specific membrane antigen (PSMA) targeted contrast agents. We tested these contrast agents using in vitro cell culture models and in in vivo murine models. ResultsAll tested contrast agents showed high uptake and labeling by target cell lines, but also small but significant labeling of non-cancer blood cells. Contrast agents that exhibited rapid clearance from circulation and the fluorogenic approach resulted in significantly reduced non-specific interfering background fluorescence signals. ConclusionsAlthough the fluorescence contrast agents tested have properties useful for labeling of CTCs, as yet none exhibited the required high specificity. This resulted in some labeling of non-cancer blood cells which presented false-positive CTC counts. Improved contrast agent design and multiplexed use of more than one contrast agent may improve this specificity.

bioengineering↗

bioRxiv2023

Analysis of uveal melanoma scRNA sequencing data identifies neoplastic-immune hybrid cells that exhibit metastatic potential

Uveal melanoma (UM) is the most common non-cutaneous melanoma and is an intraocular malignancy that affects nearly 7,000 individuals per year worldwide. Of these, nearly 50% will progress to metastatic disease for which there are currently no effective therapies. Despite advances in the molecular profiling and metastatic stratification of class 1 and 2 UM tumors, little is known regarding the underlying biology of UM metastasis. Our group has identified a disseminated tumor cell population characterized by co-expression of immune and melanoma proteins, (circulating hybrid cells (CHCs), in patients with UM. Compared to circulating tumor cells, CHCs are detected at an increased prevalence in peripheral blood and can be used as a non-invasive biomarker to predict metastatic progression. To identify mechanisms underlying enhanced hybrid cell dissemination we sought to identify hybrid cells within a primary UM single cell RNA-seq dataset. Using rigorous doublet discrimination approaches, we identified UM hybrids and evaluated their gene expression, predicted ligand-receptor status, and cell-cell communication state in relation to other melanoma and immune cells within the primary tumor. We identified several genes and pathways upregulated in hybrid cells, including those involved in enhancing cell motility and cytoskeleton rearrangement, evading immune detection, and altering cellular metabolism. In addition, we identified that hybrid cells express ligand-receptor signaling pathways implicated in promoting cancer metastasis including IGF1-IGFR1, GAS6-AXL, LGALS9-P4HB, APP-CD74 and CXCL12-CXCR4. These results contribute to our understanding of tumor progression and interactions between tumor cells and immune cells in the UM microenvironment that may promote metastasis.

cancer biology↗

bioRxiv2023

Robust biomarker discovery through multiplatform multiplex image analysis of breast cancer clinical cohorts

AO_SCPLOWBSTRACTC_SCPLOWSpatial profiling of tissues promises to elucidate tumor-microenvironment interactions and enable development of spatial biomarkers to predict patient response to immunotherapy and other therapeutics. However, spatial biomarker discovery is often carried out on a single patient cohort or imaging technology, limiting statistical power and increasing the likelihood of technical artifacts. In order to analyze multiple patient cohorts profiled on different platforms, we developed methods for comparative data analysis from three disparate multiplex imaging technologies: 1) cyclic immunofluorescence data we generated from 102 breast cancer patients with clinical follow-up, in addition to publicly available 2) imaging mass cytometry and 3) multiplex ion-beam imaging data. We demonstrate similar single-cell phenotyping results across breast cancer patient cohorts imaged with these three technologies and identify cellular abundance and proximity-based biomarkers with prognostic value across platforms. In multiple platforms, we identified lymphocyte infiltration as independently associated with longer survival in triple negative and high-proliferation breast tumors. Then, a comparison of nine spatial analysis methods revealed robust spatial biomarkers. In estrogen receptor-positive disease, quiescent stromal cells close to tumor were more abundant in good prognosis tumors while tumor neighborhoods of mixed fibroblast phenotypes were enriched in poor prognosis tumors. In triple-negative breast cancer (TNBC), macrophage proximity to tumor and B cell proximity to T cells were greater in good prognosis tumors, while tumor neighborhoods of vimentin-positive fibroblasts were enriched in poor prognosis tumors. We also tested previously published spatial biomarkers in our ensemble cohort, reproducing the positive prognostic value of isolated lymphocytes and lymphocyte occupancy and failing to reproduce the prognostic value of tumor-immune mixing score in TNBC. In conclusion, we demonstrate assembly of larger clinical cohorts from diverse platforms to aid in prognostic spatial biomarker identification and validation. SO_SCPLOWTATEMENTC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWOFC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSIGNIFICANCEC_SCPLOWOur single-cell spatial analysis of multiple clinical cohorts uncovered novel biomarkers of patient outcome in breast cancer. Additionally, our data, software, and methods will help advance spatial characterization of the tumor microenvironment.

cancer biology↗

bioRxiv2020

In Situ Optical Quantification of Extracellular Electron Transfer from Shewanella oneidensis using Plasmonic Metal Oxide Nanocrystals

Extracellular electron transfer (EET) is a critical form of microbial metabolism that enables respiration on a variety of inorganic substrates, including metal oxides. However, quantifying current generated by electroactive bacteria has been predominately limited to biofilms formed on electrodes. To address this, we developed a platform for quantifying EET flux from cell suspensions using aqueous dispersions of infrared plasmonic tin-doped indium oxide nanocrystals. Tracking the change in optical extinction during electron transfer enabled quantification of current generated by planktonic Shewanella oneidensis cultures. Using this method, we differentiated between starved and actively respiring cells, between cells of varying genotype, and between cells engineered to differentially express a key EET gene using an inducible genetic circuit. Overall, our results validate the utility of colloidally stable plasmonic metal oxide nanocrystals as quantitative biosensors in native biological environments and contribute to a fundamental understanding of planktonic S. oneidensis electrophysiology using simple in situ spectroscopy.

microbiology↗

bioRxiv2020

Crosstalk between invadopodia and the extracellular matrix

The scaffold protein Tks5 is required for invadopodia-mediated cancer invasion both in vitro and in vivo. We have previously also revealed a role for Tks5 in tumor cell growth using three-dimensional (3D) culture model systems and mouse transplantation experiments. Here we use both 3D and high-density fibrillar collagen (HDFC) culture to demonstrate that native type I collagen, but not a form lacking the telopeptides, stimulated Tks5-dependent growth, which was dependent on the DDR collagen receptors. We used microenvironmental microarray (MEMA) technology to determine that laminin, collagen I, fibronectin and tropoelastin also stimulated invadopodia formation. A Tks5-specific monoclonal antibody revealed its expression both on microtubules and at invadopodia. High- and super-resolution microscopy of cells in and on collagen was then used to place Tks5 at the base of invadopodia, separated from much of the actin and cortactin, but coincident with both matrix metalloprotease and cathepsin proteolytic activity. Inhibition of the Src family kinases, cathepsins or metalloproteases all reduced invadopodia length but each had distinct effects on Tks5 localization. These studies highlight the crosstalk between invadopodia and extracellular matrix components, and reveal the invadopodium to be a spatially complex structure.

cancer biology↗