Public Research Projects

How does the hypoxic, desmoplastic PDAC microenvironment recruit and reprogram myeloid-derived suppressor cells to exclude cytotoxic T cells? We combine multiplexed imaging (CODEX/IMC), spatial transcriptomics, and orthotopic KPC mouse models to map HIF-1alpha-driven chemokine gradients (CXCL1/CXCL8, CSF1) and metabolic crosstalk that polarize tumor-associated macrophages. Success means identifying a targetable node such as CXCR2 or adenosine-axis blockade that converts the microenvironment to an inflamed phenotype and restores response to checkpoint immunotherapy.

Why do many B-ALL and DLBCL patients relapse after CD19 CAR-T therapy, and can we anticipate the escape route? We track clonal dynamics with single-cell DNA/RNA sequencing and longitudinal flow on pre- and post-relapse patient samples to distinguish CD19 antigen loss, lineage switch, and T-cell exhaustion. Success is a predictive framework for relapse mode plus preclinical validation of dual-targeting (CD19/CD22) or armored CAR constructs that pre-empt the dominant escape mechanism in defined patient subsets.

Can lytic phages be deployed to steer extensively drug-resistant A. baumannii into evolutionary dead ends where escaping phage predation re-sensitizes cells to carbapenems? We isolate capsule-targeting phages, characterize receptor (K-locus) mutations driving resistance via whole-genome sequencing, and measure collateral antibiotic sensitivity in evolved escapees. Phage-antibiotic combinations are validated in Galleria mellonella and murine pneumonia models. Success is a rationally designed phage cocktail whose resistance cost predictably restores antibiotic susceptibility, with a defined steering protocol.

Does early hyperphosphorylated tau accumulation in the locus coeruleus drive noradrenergic dysfunction that precedes and accelerates cortical Alzheimer's pathology? Using fiber photometry and chemogenetic (DREADD) control of LC-NA neurons in TgF344-AD rats and PS19 mice, paired with 7T MRI neuromelanin imaging and single-nucleus RNA-seq of LC neurons, we test whether restoring phasic noradrenergic tone slows tau spread to entorhinal cortex. A successful outcome identifies LC activity as a modifiable upstream lever and validates neuromelanin-MRI plus pupillometry as a preclinical staging biomarker.

Which metabolic checkpoints sustain granulocytic MDSC-mediated T-cell suppression in the hypoxic, desmoplastic PDAC microenvironment, and can they be pharmacologically disarmed to license checkpoint therapy? Using the KPC autochthonous and orthotopic pancreatic models with Seahorse metabolic flux, arginase/iNOS reporters, and spatial transcriptomics, we dissect the arginine-depletion and lipid-uptake programs driving suppression. A successful outcome is a metabolic intervention that reverses local T-cell anergy and unlocks responsiveness to anti-PD-1 combination therapy.

We ask why P. aeruginosa biofilms on catheters and endotracheal tubes survive bactericidal antibiotics at 100-1000x planktonic MIC, and whether engineered dispersal converts tolerant persisters into killable cells before resistance fixes. Using flow-cell biofilm reactors, c-di-GMP biosensor reporters, confocal time-lapse of tobramycin penetration, and nitric-oxide/cis-2-decenoic-acid dispersal triggers, we quantify the tolerance-to-resistance pipeline. A successful outcome is a dispersal-plus-antibiotic regimen that clears mature biofilms in a CDC-bioreactor and ex vivo device model without selecting for resistant escape mutants.

Why do a subset of melanoma patients progress on anti-PD-1 despite initial T-cell infiltration, and which co-inhibitory axis dominates the adaptive resistance state? Using paired pre/post-treatment biopsies, CyTOF, and ex vivo tumor fragment cultures alongside B16-OVA and YUMMER1.7 syngeneic models, we profile LAG-3, TIM-3, and TIGIT upregulation on exhausted TCF7+ progenitor versus terminal CD8 subsets. A successful outcome is a biomarker-defined patient stratum and a validated dual-blockade sequencing schedule that reverts terminal exhaustion.

How do clinical K. pneumoniae populations evolve last-resort colistin resistance, and is plasmid-borne mcr-1 acquisition a one-way ratchet or a reversible, fitness-costly state? We combine experimental evolution in chemostats under sub-MIC colistin gradients, single-cell heteroresistance assays (PAP testing), and Oxford Nanopore long-read sequencing to track lipid-A modification (pmrAB/phoPQ) and plasmid dynamics across passages. Success means a predictive map of resistance trajectories and identification of evolutionary chokepoints where colistin-sparing or collateral-sensitivity drugs can re-sensitize the population.

Do forskolin-induced swelling responses in rectal-biopsy-derived intestinal organoids predict clinical CFTR-modulator efficacy for patients carrying rare or uncharacterized mutations excluded from registration trials? We expand Lgr5+ crypt organoids in Matrigel/WNT-RSPO1-Noggin medium, quantify forskolin-induced swelling by live confocal imaging across elexacaftor/tezacaftor/ivacaftor combinations, and correlate with sweat chloride and FEV1. Success is a validated theranostic assay that reclassifies non-eligible genotypes into treatable categories.

Why do distinct alpha-synuclein fibril conformers (strains) produce divergent clinical phenotypes across Parkinson's disease, multiple system atrophy, and dementia with Lewy bodies? We combine cryo-EM structural characterization of patient-derived fibrils, RT-QuIC seed amplification, and stereotaxic injection of conformationally defined preformed fibrils into the duodenal wall and olfactory bulb of M83 and wild-type mice to trace vagal and trans-synaptic spread. Success means a structure-to-spread map linking specific fibril folds to defined propagation routes and selective neuronal vulnerability, yielding strain-discriminating diagnostic seeds.

Can authentic A9-subtype midbrain dopaminergic neurons differentiated from human pluripotent stem cells survive, mature, and functionally reinnervate the striatum without graft overgrowth? We use floor-plate-based directed differentiation (SHH/FGF8/CHIR-WNT activation), single-cell RNA-seq to confirm FOXA2/LMX1A/NURR1 identity, and 6-OHDA-lesioned rat and athymic mouse xenografts with amphetamine-rotation behavioral readouts. Success means scalable, batch-consistent grafts with under 0.1% proliferative KI67+ contaminants and durable motor rescue at 6 months.

What epigenetic events lock CD8+ T cells into a terminally exhausted state, and which are reversible to restore antitumor function? Using whole-genome bisulfite sequencing, ATAC-seq, and CUT&RUN for TOX/TCF1 across an in vitro chronic-stimulation system plus the LCMV clone-13 mouse model, we map the methylation and chromatin trajectory and test TET2/DNMT3A perturbations. Success means identifying a defined epigenetic node whose editing durably reprograms exhausted cells toward a stem-like, treatment-responsive phenotype.

How do individual Lgr5+ crypt base columnar stem cells compete, fix, and repopulate the epithelium following irradiation or DSS-colitis injury, and what reserve populations (Bmi1+, Hopx+) contribute to regeneration? We use Lgr5-EGFP-CreERT2;R26R-Confetti mice for multicolor clonal tracking, intravital and whole-mount confocal imaging, and quantitative neutral-drift modeling of clone-size distributions. Success is a predictive model of niche succession and the dedifferentiation hierarchy driving repair.

Can B2M-knockout, HLA-E/CD47-engineered iPSC-derived pancreatic islet organoids evade allogeneic T-cell and NK-cell rejection while maintaining glucose-responsive insulin secretion, eliminating the need for immunosuppression or encapsulation? We use stepwise endoderm-to-endocrine differentiation (Activin/CHIR, then NKX6.1/PDX1 induction), CRISPR multiplex editing, in vitro co-culture cytotoxicity assays, and STZ-diabetic humanized-mouse transplants. Success is normoglycemia restoration with intact grafts and no detectable immune clearance at 90 days.

What governs the expansion and inter-species spread of antimicrobial resistance genes in the human gut after antibiotic exposure, and which commensals act as resistome reservoirs? We pair longitudinal shotgun metagenomics and functional metagenomic library screening of patient stool cohorts with anaerobic gut-on-a-chip and gnotobiotic mouse models to track conjugative HGT in situ using fluorescent transfer reporters. Success means identifying keystone reservoir taxa and transfer-permissive niches, plus a microbiome-recovery strategy (e.g., targeted probiotics or bile-acid modulation) that suppresses resistome amplification.

How do CD103+CD69+ tissue-resident memory CD8 T cells acquire and maintain their lung-resident program after respiratory infection, and can that program be deliberately induced by vaccination? We combine intranasal influenza and SARS-CoV-2 challenge in C57BL/6 and Hobit/Blimp1 reporter mice with parabiosis, single-cell ATAC/RNA-seq, and spectral flow to map the TGF-beta/Runx3-driven differentiation trajectory. Success is a defined adjuvant-route combination that durably seeds protective TRM in mucosa, validated by reduced viral titers on heterologous rechallenge.

How do hippocampal engram ensembles transfer to neocortex during systems consolidation, and what tips a precise memory into overgeneralized fear? We combine activity-dependent labeling (TRAP2/Fos-driven), dual-site Miniscope calcium imaging across CA1 and prefrontal cortex, and closed-loop optogenetic manipulation of sharp-wave-ripples during sleep in mice running a context-discrimination task. A successful program produces a quantitative model of engram drift and a ripple-timed intervention that rescues discrimination, with translational relevance to PTSD memory rigidity.

Does segmented-filamentous-bacteria-induced intestinal Th17 expansion drive the breach of self-tolerance that precedes joint inflammation in autoimmune arthritis? We use the collagen-induced and K/BxN arthritis models in gnotobiotic and SFB-monocolonized mice, paired with fecal-transplant from at-risk anti-CCP+ human cohorts, RORgt fate-mapping, and 16S/metabolomic profiling of short-chain fatty acids. A successful outcome identifies a microbial-metabolite intervention that restrains pathogenic Th17 conversion and delays clinical arthritis onset.

How does central-carbon flux rewire as disseminated triple-negative breast cancer cells enter and exit dormancy, and which flux nodes gate reawakening? We combine 13C-glucose/glutamine isotope-tracing LC-MS, 13C-MFA modeling, and Seahorse respirometry across organoid and dormant-PDX models, integrated with matched transcriptomics. A successful program delivers a quantitative flux map pinpointing rate-limiting reactions whose inhibition keeps cells dormant or selectively kills reawakening cells.

What circuit-level imbalance between D1 direct-pathway and D2 indirect-pathway spiny projection neurons underlies the aberrant plasticity of levodopa-induced dyskinesia in Parkinson's disease? Using 6-OHDA-lesioned mice with pathway-specific Cre lines, cell-type-resolved fiber photometry and in vivo electrophysiology during dyskinetic episodes, plus closed-loop optogenetic and focused-ultrasound modulation, we test whether normalizing direct-pathway burst firing abolishes dyskinesia without blunting the anti-parkinsonian benefit. A successful outcome yields a circuit-targeted stimulation protocol and a biomarker of the dyskinetic state for adaptive deep brain stimulation.

How do dynamic enhancer landscapes and transcription-factor circuits commit human pluripotent stem cells to definitive endoderm versus alternative fates? We pair 10x multiome (snRNA-seq + snATAC-seq) with CUT&Tag for FOXA2/GATA4/SOX17 and Perturb-ATAC across a differentiation time course to reconstruct gene-regulatory networks. A successful outcome is a validated enhancer-to-target-gene logic model that predicts, and lets us re-engineer, fate-commitment efficiency.

Can a perfusion-decellularized rodent and porcine lung extracellular-matrix scaffold be repopulated with iPSC-derived AT2 alveolar epithelial cells and endothelium to restore gas-exchange-competent, barrier-tight tissue? We optimize SDS/Triton decellularization preserving laminin/collagen-IV ultrastructure, seed via airway and vascular perfusion in a biomimetic bioreactor, and assess surfactant protein-C expression, barrier permeability, and orthotopic transplant viability. Success is a recellularized graft maintaining oxygenation for over 72h post-transplant.

Why do phenotypically tolerant, non-replicating M. tuberculosis subpopulations survive months of multidrug therapy, and can targeting efflux and the stringent response sterilize them faster? We use hypoxia (Wayne model) and nutrient-starvation persistence assays, single-cell microfluidic time-lapse with fluorescent replication reporters, RNA-seq of the DosR/Rel regulons, and efflux-pump inhibitor adjuvants under BSL-3 conditions. Success is a regimen-shortening adjuvant strategy that collapses the persister reservoir, validated against clinical MDR isolates and in a relapse-readout mouse model.

Why do non-small-cell lung cancers initially respond to covalent KRAS-G12C inhibitors (sotorasib, adagrasib) but rebound within months? We map adaptive resistance using barcoded PDX and cell-line panels under sustained inhibition, paired with phospho-proteomics and scRNA-seq to track RTK/SHP2/MAPK reactivation and the drug-tolerant persister state. Success is a validated vertical-blockade combination (G12C inhibitor + SHP2 or SOS1 inhibitor) that suppresses adaptive ERK rebound and durably collapses persister populations in vivo.

BRCA1/2-mutant high-grade serous ovarian cancers respond to PARP inhibitors but relapse through restored homologous recombination or stabilized replication forks. We interrogate fork-protection mechanisms (loss of PTIP/EZH2-MUS81, 53BP1/Shieldin pathway reversion) using DNA-fiber assays, olaparib-resistant organoid lines, and isogenic reversion models. Success is a validated combination of PARP inhibitor plus ATR or WEE1 inhibition that re-sensitizes resistant tumors by re-imposing replication stress, with a functional HR-deficiency assay predicting durable benefit.

How does loss of nuclear TDP-43 function unmask cryptic exons (e.g., in STMN2 and UNC13A) and feed back on nucleocytoplasmic transport collapse in C9orf72-expansion ALS/FTD? We use isogenic iPSC-derived motor neurons with CRISPR-corrected repeat expansions, long-read RNA-seq, and optogenetic clustering of TDP-43 to dissect the order of phase-separation, mislocalization, and splicing failure. Success delivers antisense oligonucleotides that rescue STMN2 full-length transcript and restore RanGAP1-gradient integrity, with a cryptic-splicing fluid biomarker for trial stratification.

MYC is a near-universal oncogenic driver yet remains undruggable directly, so we hunt for synthetic-lethal vulnerabilities its overexpression creates. Using genome-wide CRISPR-Cas9 dropout screens across isogenic MYC-high/MYC-low Burkitt lymphoma and triple-negative breast lines, we nominate dependencies in transcriptional CDKs (CDK7/CDK9), BET bromodomains, and spliceosome components, then validate with degrader tools. A successful outcome is a context-defined dependency that selectively kills MYC-addicted tumors while sparing normal proliferating cells, with a biomarker for patient stratification.

Can a logic-gated bispecific CD19/CD22 CAR construct prevent the antigen-loss relapse that follows single-target CAR-T therapy in B-cell ALL while constraining IL-6/IFN-gamma-driven cytokine release syndrome? We engineer and screen tandem and OR-gate CAR designs in primary human T cells, test cytotoxicity against patient-derived CD19-low/CD22-variable blasts, and model toxicity in NSG xenografts with humanized myeloid compartments. Success is a construct that clears antigen-heterogeneous tumor with a measurably lower cytokine burden and durable in vivo persistence.

Which gene dependencies allow acute myeloid leukemia cells to survive venetoclax/azacitidine therapy, and how does the protective bone-marrow microenvironment rewire them? We run dual genome-wide CRISPRi and CRISPRa screens in patient-derived AML lines and primary blasts, co-cultured on mesenchymal stromal feeders and in PDX models, with single-cell readout of selected hits. Success is a ranked, niche-context-dependent dependency map that nominates 3-5 combinatorial targets reversing resistance and validates at least one in vivo.

Can the nif gene cluster be refactored into orthogonal, host-controllable modules that enable robust nitrogen fixation in a cereal-associated diazotroph under field-relevant oxygen and ammonium conditions? We deconstruct and rebuild the Klebsiella/Azotobacter nif pathway with synthetic regulatory parts, characterize modules by acetylene-reduction and 15N2 incorporation assays, and colonize maize roots in gnotobiotic systems. A successful outcome is an engineered strain delivering quantifiable fixed nitrogen to the plant, reducing synthetic-fertilizer dependence.

How does Salmonella Typhimurium hijack host inflammatory responses to outcompete a protective gut microbiota and gain a colonization advantage? We dissect the tetrathionate/nitrate respiration axis and type-III secretion-driven inflammation using streptomycin-treated and gnotobiotic mouse models, intestinal organoid-derived monolayers, RNA-seq dual transcriptomics, and defined-community (Oligo-MM12) reconstitution. A successful outcome defines the metabolic and immune levers that restore colonization resistance, pointing to microbiota-based or anti-virulence interventions that block pathogen blooms without antibiotics.

Acquired ESR1 ligand-binding-domain mutations (Y537S, D538G) drive constitutive ER activity and resistance to aromatase inhibitors in metastatic ER+ breast cancer. We use CRISPR knock-in MCF7/T47D models and patient ctDNA longitudinal sampling to dissect how these mutations rewire the ER cistrome and bypass CDK4/6 blockade. A successful outcome is mechanistic evidence and preclinical proof that next-generation SERDs (elacestrant) combined with CDK4/6 or PI3K inhibition overcome ESR1-mutant resistance, plus a ctDNA assay to detect emergence early.

How does cyclic-dinucleotide STING activation shape germinal center output and the breadth of the neutralizing antibody response compared with conventional adjuvants? We immunize mice with stabilized HIV Env and influenza HA trimers formulated with CDN, MPLA, or AS01-like adjuvants, then quantify Tfh help, GC B-cell affinity maturation, and somatic hypermutation by photoactivatable fate-mapping and BCR repertoire sequencing. Success is an adjuvant formulation that measurably broadens cross-reactive neutralizing breadth without excess systemic type-I interferon toxicity.

Does the TREM2-APOE axis convert protective microglia into a synaptotoxic state that drives complement-mediated over-pruning in early Alzheimer's? We build iPSC-derived cortical organoids fused with isogenic microglia (assembloids) carrying TREM2 R47H and APOE4 variants, then apply live two-photon imaging of synapse engulfment, spatial transcriptomics, and C1q/C3 blockade to map the pruning cascade. Success defines a variant-specific microglial state that predicts synapse loss and nominates complement or TREM2-agonist intervention points testable in a human model.

Can the core enzymatic and circadian machinery of crassulacean acid metabolism be transplanted into a C3 crop to improve water-use efficiency under drought? We assemble and tune a multi-gene CAM module (PEPC, PPCK, malate transporters, stomatal-timing regulators) via Golden Gate cloning and stable transformation in tobacco and rice, screening with gas-exchange phenotyping and metabolite tracing. Success is a transgenic line showing measurable nocturnal CO2 fixation and improved water-use efficiency without major yield penalty under controlled drought.

Can in situ delivery of GMT (Gata4/Mef2c/Tbx5) plus Hand2 and miR combinations convert scar-resident cardiac fibroblasts into functional induced cardiomyocytes that electrically couple and reduce fibrosis after myocardial infarction? We screen reprogramming cocktails in mouse and human fibroblasts, validate sarcomere assembly and spontaneous calcium transients by patch-clamp and GCaMP imaging, and test AAV-delivered factors in a LAD-ligation mouse model with echocardiographic ejection-fraction readouts. Success is durable iCM conversion with measurable contractile recovery.