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Biology subjects

Yuan, Y.-C.

Publications and source records attributed to Yuan, Y.-C..

8 recordsLinked to original sources

Therapeutic Targeting of the TGFβ Pathway Augments CAR T cell Efficacy in Glioblastoma

Chimeric Antigen Receptor (CAR) T therapy represents a promising approach to improve outcomes for patients with high-grade gliomas (HGG). Recently, we reported on a phase I trial assessing the local delivery of CAR T cells for HGG. Despite notable clinical benefits to CAR T treatment, clinical responses were highly variable between patients. Here we report that TGF{beta} levels in the tumor cavity fluid (TCF) decreased following CAR T treatment and that lower TGF{beta} levels positively correlated with improved patient responses to CAR T therapy. Patients were stratified based on baseline TGF{beta} levels in the TCF before CAR T therapy. Single-cell RNA sequencing of patient tumor tissues identified significant upregulation of genes associated with angiogenesis and epithelial-to-mesenchymal transition, and IL6 and SLRP pathways in TGF{beta} high patients, while IL2, chemokine signaling and NK-mediated cytotoxicity pathways were significantly upregulated in TGF{beta} low patients. Preclinically, we demonstrated that systemic treatment with a TGF{beta}R1 inhibitor markedly improved CAR T efficacy in syngeneic murine glioma models, correlating with changes in the tumor microenvironment (TME) that benefited both endogenous and CAR T cell phenotype and trafficking. Further studies demonstrated that inhibition of the TGF{beta} pathway in CAR T cells, through either TGF{beta}R1 inhibitor or CRISPR/Cas9 knockout of TGF{beta}R2 (TGF{beta}R2-KO), significantly enhanced CAR T cell expansion and antitumor activity. Collectively, our clinical and preclinical findings strongly indicate that targeting the TGF{beta} pathway could significantly enhance CAR T therapy for patients with high-grade gliomas.

cancer biology↗

Intranasal L-MYC Neural Stem Cells Restore Neurovascular and Neuroimmune Homeostasis After TBI via CX3CL1 Upregulation and ICAM-1 Downregulation

Traumatic brain injury (TBI) triggers persistent neuroimmune and neurovascular dysfunction that contributes to secondary brain injury and limits recovery. Here, we investigated whether a single intranasal dose of LMNSC01 could reprogram neuroinflammatory and neurovascular responses post TBI and whether these effects were conserved across biological sex. Immunocompetent male and female rats underwent a controlled cortical impact (CCI) or Sham surgery and 7 days later received a single bolus dose of LMNSC01 (6 x10^6 cells/dose) or vehicle. Integrated histological and transcriptomic analyses and multiplex tissue ELISA were used to characterize injury- and treatment-associated responses. CCI induced persistent but sex-dependent transcriptional changes. Male rats exhibited prominent innate immune, adhesion, extracellular matrix, and tissue remodeling responses, whereas females demonstrated broader activation of microglial, interferon, complement, MHC/antigen presentation, and humoral/adaptive immune pathways. LMNSC01 treatment reprogrammed these distinct injury states through partially sex-specific mechanisms. In males, LMNSC01 increased endogenous immune-regulatory mediators, including Il1rn, and reduced pathways associated with adhesion and immune cell trafficking. In females, treatment decreased expression of genes related to microglial, leukocyte, MHC/antigen presentation, cytokine, and adhesion pathways, and reduced macrophage- and CD45 positive cell signatures. Despite these sex-dependent transcriptional changes, LMNSC01 produced conserved protein changes in both sexes, reducing injury associated ICAM-1 and restoring CX3CL1 proteins, proposing a novel molecular mechanism of LMNSCs modulating endothelial activation and neuron-microglia communication post injury. Our study provides further insight into sex differences in responses to injury and treatment after TBI and highlights candidate repair mechanisms, supporting further development of LMNSC01 as a minimally invasive therapy for TBI.

neuroscience↗

Proinflammatory circulating extracellular vesicles from type 1 diabetes patients contribute to beta cell cytotoxicity and disease pathogenicity

In Type 1 diabetes (T1D), {beta}-cell loss and autoimmunity initiate years before disease diagnosis. However, the mechanisms remain unknown. Here, we investigated the role and mechanisms of circulating extracellular vesicles (cEVs) on T1D pathogenesis and {beta}-cell cytotoxicity. We used cEVs isolated from healthy donors (HD), T1D, multiple autoantibody-positive (AAb+), pre- and post-islet transplantation T1D subjects, NOD-T1D mice, and T1D PBMCs. Patient T1D-cEVs significantly induced apoptosis in vitro in human {beta}-cells but not -cells compared to HD-cEVs. cEVs from AAb+ subjects and pre-diabetic mice were cytotoxic, demonstrating that cEV-induced {beta}-cell cytotoxicity precedes T1D onset and diagnosis. cEV reduction in prediabetic NOD-T1D mice improved {beta}-cell health implying cEV contribution to T1D development. Proteomic analysis of patient T1D-cEVs found several proinflammatory proteins, including interferon gamma, which induced {beta}-cell cytotoxicity. Our data using cEVs from pre- and post-islet transplant and PBMC-EVs from T1D patients implicated immune cells as a potential cellular source of cytotoxic cEVs in T1D. Collectively, our data using T1D patient samples coupled with studies in mice demonstrate that cEVs contribute to {beta}-cell cytotoxicity and to the progression of T1D pathogenicity. Our study is one of the first to demonstrate a functional role of the proinflammatory cEV protein cargo on glucose homeostasis, {beta}-cell health, and insulitis. Our studies on T1D-cEVs may lead to discovery of novel biomarkers and therapeutic targets for T1D.

cell biology↗

Combining Scalable Organ Chip Platform with Deep Learning-Based Imaging Analysis for Cancer Therapeutic Screening

Functional precision oncology represents an emerging approach to genomic approaches by testing treatment options directly on patient-derived models. Current assays, including the use of patient-derived xenograft (PDX) and patient-derived organoid (PDOs), faces major barriers in clinical use due to technical challenges, such as standardization, cost, assay time, scalability, and faithful mimicry of patient tumor microenvironment (TME). Here, we introduce an Organ Chip (OC) device constructed entirely from thermoplastic materials, free of porous membrane or other barrier structures, and optimized for high-content imaging (HCI). This automation-compatible device supports tissue-specific extracellular matrices and coculture for a wide spectrum of organ and disease types, including the TME. As a proof-of-concept, we demonstrate the growth of pancreatic, lung, and colon cancer cell lines and primary lung cancer cells and the testing of cancer drugs in these models. HCI-based phenotypic profiling enabled accurate quantification of drug response, with better performance than traditional biochemical assays. Moreover, we developed a deep-learning method for assessing drug responses using bright field images. The integration of a low-cost, scalable, and faithful OC models with automatic high-content image analysis represents a significant stride towards functional precision oncology and cancer drug discovery.

bioengineering↗

LGR4 is essential for maintaining beta-cell homeostasis through suppression of RANK

Pancreatic {beta}-cell stress contributes to diabetes progression. This study demonstrates that Leucine-rich repeat-containing G-protein-coupled-receptor-4 (LGR4) is critical for maintaining {beta}-cell health and is modulated by stressors. In vitro, Lgr4 knockdown decreases proliferation and survival in rodent {beta}-cells, while overexpression protects against cytokine-induced cell death in rodent and human {beta}-cells. Mechanistically, LGR4 suppresses Receptor Activator of Nuclear Factor Kappa B (NF{kappa}B) (RANK) and its subsequent activation of NF{kappa}B to protect {beta}-cells. {beta}-cell-specific Lgr4-conditional knockout (cko) mice exhibit normal glucose homeostasis but increased {beta}-cell death in both sexes and decreased proliferation only in females. Male Lgr4cko mice under stress display reduced {beta}-cell proliferation and a further increase in {beta}-cell death. Upon aging, both male and female Lgr4cko mice display impaired {beta}-cell homeostasis, however, only female mice are glucose intolerant with decreased plasma insulin. We show that LGR4 is required for maintaining {beta}-cell health under basal and stress-induced conditions, through suppression of RANK. TeaserLGR4 receptor is critical for maintaining {beta}-cell health under basal and stressed conditions, through suppression of RANK.

physiology↗

Rapid Prototyping of Thermoplastic Microfluidic 3D Cell Culture Devices by Creating Regional Hydrophilicity Discrepancy

Microfluidic three-dimensional cell culture devices that enable the recapitulation of key aspects of organ structures and functions in vivo represent a promising preclinical platform to improve translational success during drug discovery. Essential to these engineered devices is the spatial patterning of cells from different tissue types within a confined microenvironment. Traditional fabrication strategies lack the scalability, cost-effectiveness, and rapid prototyping capabilities required for industrial applications, especially for processes involving thermoplastic materials. Here, we introduce an approach to pattern fluid guides inside microchannels by establishing differential hydrophilicity using pressure-sensitive adhesives as masks and a subsequent selective coating with a biocompatible polymer. We identified optimal coating conditions using polyvinylpyrrolidone, which resulted in rapid and consistent hydrogel flow in both the open-chip prototype and the fully bonded device containing additional features for medium perfusion. We tested the suitability of our device for dynamic 3D cell culture by growing human hepatocytes in the device under controlled fluid flow for a 14-day period. Additionally, we demonstrated the potential of using our device for pharmaceutical high-throughput screening applications, such as predicting drug-induced liver injury. Our approach offers a facile strategy of rapid prototyping thermoplastic microfluidic organ chips with varying geometries, microstructures, and substrate materials.

bioengineering↗

Molecular profiling of innate immune response mechanisms in ventilator-associated pneumonia

Ventilator-associated pneumonia (VAP) is a common hospital-acquired infection, leading to high morbidity and mortality. Currently, bronchoalveolar lavage (BAL) is utilized in hospitals for VAP diagnosis and guiding treatment options. While BAL collection procedures are invasive, alternatives such as endotracheal aspirates (ETA) may be of diagnostic value, however, their utility has not been thoroughly explored. Longitudinal ETA and BAL were collected from 16 intubated patients up to 15 days, of which 11 developed VAP. We conducted a comprehensive LC-MS/MS based proteome and metabolome characterization of longitudinal ETA and BAL to detect host and pathogen responses to VAP infection. We discovered a diverse ETA proteome of the upper airways reflective of a rich and dynamic host-microbe interface. Prior to VAP diagnosis by microbial cultures from BAL, patient ETA presented characteristic signatures of reactive oxygen species and neutrophil degranulation, indicative of neutrophil mediated pathogen processing as a key host response to the VAP infection. Along with an increase in amino acids, this is suggestive of extracellular membrane degradation resulting from proteolytic activity of neutrophil proteases. Days prior to VAP diagnosis, detection of pathogen peptides with species level specificity in ETA may increase specificity over culture-based diagnosis. Our findings suggest that ETA may provide early mechanistic insights into host-pathogen interactions associated with VAP infection and therefore facilitate its diagnosis and treatment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/899294v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1ae626dorg.highwire.dtl.DTLVardef@1bff675org.highwire.dtl.DTLVardef@1cd90bcorg.highwire.dtl.DTLVardef@d9651d_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Transcriptome dynamics describe and predict state transition from health to leukemia

Temporal dynamics of gene expression are informative of changes associated with disease development and evolution. Given the complexity of high-dimensional temporal datasets, an analytical framework guided by a robust theory is needed to interpret time-sequential changes and to predict system dynamics. Herein, we use acute myeloid leukemia as a proof-of-principle to model gene expression dynamics in a transcriptome state-space constructed based on time-sequential RNA-sequencing data. We describe the construction of a state-transition model to identify state-transition critical points which accurately predicts leukemia development. We show an analytical approach based on state-transition critical points identified step-wise transcriptomic perturbations driving leukemia progression. Furthermore, the gene(s) trajectory and geometry of the transcriptome state-space provides biologically-relevant gene expression signals that are not synchronized in time, and allows quantification of gene(s) contribution to leukemia development. Therefore, our state-transition model can synthesize information, identify critical points to guide interpretation of transcriptome trajectories and predict disease development.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC=\"FIGDIR/small/238923v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (55K):\norg.highwire.dtl.DTLVardef@12eeaccorg.highwire.dtl.DTLVardef@1392af9org.highwire.dtl.DTLVardef@34786dorg.highwire.dtl.DTLVardef@ce78bb_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefThe theory of state-transition is applied to acute myeloid leukemia (AML) to model transcriptome dynamics and trajectories in a state-space, and is used to identify critical points corresponding to critical transcriptomic perturbations that predict leukemia development.\n\nHighlightsO_LILeukemia transcriptome dynamics are modeled as movement in transcriptome state-space\nC_LIO_LIState-transition model and critical points accurately predicts leukemia development\nC_LIO_LICritical point-based approach identifies step-wise transcriptome events in leukemia\nC_LIO_LIState-based geometric analysis provides quantification of leukemogenic contribution\nC_LI

cancer biology↗