Biology subjects

Kan, E.

Publications and source records attributed to Kan, E..

6 recordsLinked to original sources

bioRxiv2025

Single-cell, Spatially-Resolved TCR Profiling Links T Cell Phenotype and Clonality in Human Tumors

Despite remarkable success in melanoma and other cancers, immune checkpoint blockade has shown limited efficacy in head and neck squamous cell carcinoma (HNSCC), with durable responses in only [~]10% of patients. This is paradoxical given the abundant infiltration of CD8 T cells in HNSCC, suggesting that current T cell profiling methods fail to fully capture functional anti-tumor immunity and that key immunosuppressive mechanisms remain poorly understood. To uncover mechanisms regulating T cell function in situ, we developed a multimodal profiling framework integrating high-dimensional flow cytometry, single-cell RNA- and TCR-sequencing, and spatial transcriptomics, including spatially-resolved TCR profiling at single-cell resolution. Applying this approach to paired blood and tumor samples from 27 HNSCC patients enabled single-cell resolution mapping of T cell clonality, transcriptional state, and spatial localization within intact tumors. Tumors with similar clinical features and immune profiles by flow cytometry and scRNA-seq exhibited markedly different spatial immune architectures. Within the T cell compartment, stem- and memory-like T cells localized within immune-rich niches, while exhausted cells were broadly dispersed in tumor-rich regions. Targeted spatial TCR mapping revealed that tumor-enriched TCR clones were distributed throughout the tumor yet adopted distinct, location-dependent phenotypes, indicating that both antigen specificity and spatial cues shape T cell differentiation and function in human tumors. These findings reveal fundamental principles of T cell organization in solid tumors and establish a versatile platform for spatially-resolved, antigen-specific T cell profiling.

immunology↗

bioRxiv2025

Bypassing cisplatin resistance in Nrf2 hyperactivated head and neck cancer through effective PI3Kinase targeting

BackgroundFor patients with head and neck squamous cell carcinoma (HNSCC), failure of definitive radiation combined with cisplatin nearly universally results in death. Although hyperactivation of the Nrf2 pathway can drive radiation and cisplatin resistance along with suppressed anti-tumor immunity, treatment-refractory HNSCC tumors may retain sensitivity to targeted agents secondary to synergistic lethality with other oncogenic drivers (e.g., NOTCH1 mutations). PurposeWe evaluated the efficacy of PI3K inhibitors (PI3Ki) in bypassing Nrf2-mediated cisplatin resistance in HNSCC. MethodsWe measured transcriptomic, metabolomic and signaling changes driven by PI3Kis in cisplatin-resistant HNSCCs in vitro and tested efficacy in vivo in subcutaneous, orthotopic and metastatic xenograft models using immunodeficient and humanized murine models of HNSCC coupled with spatial transcriptomics. ResultsThe PI3K pathway is activated in Nrf2-driven cisplatin-resistant HNSCC and is suitable for blockade as demonstrated in an in vivo shRNA screen. The PI3Ki gedatolisib inhibits cisplatin-resistant HNSCC proliferation, induces G2M arrest and potentiates cisplatin effectiveness through activation of autophagy, senescence and disruption of fatty acid metabolism. Gedatolisib suppresses HNSCC tumor growth in orthotopic and metastatic settings and demonstrates profound anti-tumor activity in humanized murine models of HNSCC, coupled with a reduction in hypoxia-rich regions and reduced infiltration by regulatory T lymphocytes. ConclusionOur findings emphasize the critical role of the PI3K-AKT-mTOR pathway in cisplatin-resistant HNSCC and highlight the therapeutic potential of PI3K inhibitors. Gedatolisib induced metabolic regulation and substantial re-sensitization of resistant cells to cisplatin, positioning it as a promising candidate for combination therapies aimed at overcoming primary chemo-radiation failure in HNSCC. Statement of translational relevanceCisplatin resistance, whether intrinsic or acquired, translates to treatment failure and nearly universal death in head and neck squamous cell carcinoma (HNSCC). However, the development of effective systemic regimens for cisplatin-resistant HNSCC has not yet been successful. Here, we present, for the first time, a mechanistic, biomarker-informed strategy for effective targeting of the PI3Kinase pathway in cisplatin-resistant HNSCC with substantial anti-tumor activity in both orthotopic and metastatic models, which may be capable of bypassing or reversing cisplatin resistance in this disease.

cancer biology↗

bioRxiv2024

Longitudinal mapping of cortical change during early adolescence associated with prenatal tobacco and/or alcohol exposure in the Adolescent Brain Cognitive DevelopmentSM Study

ImportanceThe effects of prenatal alcohol (PAE) and tobacco exposure (PTE) on adolescent neuroanatomical development are typically evaluated cross-sectionally. It is unclear if observed effects persist throughout life or reflect different developmental trajectories. ObjectiveTo determine how PAE and PTE are associated with cortical structure and development across two timepoints in early adolescence. DesignObservational, longitudinal analyses of data within the Adolescent Brain Cognitive Development{square} Study Setting21 study sites in the United States Participants5,417 youth participants, aged [~]9-12 years old ExposuresPAE and PTE based on caregiver (self) reports of alcohol/tobacco use during pregnancy, before and after pregnancy recognition. Main Outcomes and MeasuresCortical thickness (mm) and cortical surface area (mm2) measured approximately 2 years apart in early adolescence, across 68 bilateral cortical regions. ResultsAt baseline data collection, youth participants were [~]9.9 years old (SD=0.6). At the second neuroimaging appointment, youth participants were [~]11.9 years old (SD=0.6). When modelling cortical thickness, we controlled for individuals whole-brain volume; when modelling cortical surface area, individuals total surface area. Cortical thickness generally declined with age. Cortical surface area either expanded or contracted with age, depending on region. PAE had minimal effects on cortical structure (main effects) and development (PAExAge interactions). PTE had robust effects on cortical thickness and was associated with faster rates of cortical thinning in several regions within the frontal lobe. Post hoc analyses on (1) the effects of PTE for those who continued tobacco use after pregnancy recognition and (2) the effects of PTE in those who did not also use alcohol revealed weaker effects. Conclusions and RelevancePTE had robust effects on neuroanatomical structure and longitudinal development, particularly cortical thickness. Analyzing developmental cortical trajectories informs how PTE and/or PAE not only affects cortical structure but how it develops long after those prenatal exposures occurred. Future analyses involving cotinine biomarkers of PTE would enhance the temporal resolution of the ABCD Study(R)s PTE-related queries of tobacco use before and after learning of the pregnancy. Key Points- How does prenatal tobacco and/or alcohol exposure affect brain structure and longitudinal development in early adolescence? - Prenatal tobacco exposure was robustly associated with faster rates of cortical thinning in the frontal lobe; prenatal alcohol exposure had more minimal effects. - Prenatal substance exposure, especially prenatal tobacco exposure, not only affects cortical structure but how it develops long after those prenatal exposures occurred.

neuroscience↗

bioRxiv2024

Longitudinal sex-at-birth and age analyses of cortical structure in the ABCD Study

While the brain continues to develop during adolescence, such development may depend on sex-at-birth. However, the elucidation of such differences may be hindered by analytical decisions (e.g., covariate selection to address body/brain-size differences) and the typical reporting of cross-sectional data. To further evaluate adolescent cortical development, we analyzed data from the Adolescent Brain Cognitive Development StudySM, whose cohort of 11,000+ youth participants with biannual neuroimaging data collection can facilitate understanding neuroanatomical change during a critical developmental window. Doubly considering individual differences in the context of group-level effects, we analyzed regional changes in cortical thickness, sulcal depth, surface area, and volume between two timepoints ([~]2 years apart) in 9-to 12-year-olds assigned male or female sex-at-birth. First, we conducted linear mixed-effects models to gauge how controlling for intracranial volume, whole-brain volume (WBV), or a summary metric (e.g., mean cortical thickness) influenced interpretations of age-dependent cortical change. Next, we evaluated the relative changes in thickness and surface area as a function of sex-at-birth and age. Here, we showed that WBV (thickness, sulcal depth, volume) and total cortical surface area were more optimal covariates; controlling for different covariates would have substantially altered our interpretations of overall and sex-at-birth-specific neuroanatomical development. Further, we provided evidence to suggest that aggregate change in how cortical thickness is changing relative to surface area is generally comparable across those assigned male or female sex-at-birth, with corresponding change happening at slightly older ages in those assigned male sex-at-birth. Overall, these results help elucidate neuroanatomical developmental trajectories in early adolescence. Significance StatementWhile most of our brains development happens early in life, much of it still happens in adolescence. Because many factors can alter those developmental trajectories, it is important to evaluate the shape/timing of those trajectories (i.e., what generally constitutes typical brain development). Here, we showed that our understanding of those trajectories can be affected by how we choose to analyze them. First, we showed that the way researchers address differences in brain/body size affects how we interpret regional variation in brain change over time. Further, we showed that it is important to consider how similar patterns of development may simply be happening at different ages in different groups. These results support a relatively novel way of analyzing adolescent brain development.

neuroscience↗

bioRxiv2022

Relating neighborhood deprivation to childhood obesity in the ABCD Study(R): evidence for theories of neuroinflammation and neuronal stress

ObjectiveWe evaluated whether the relationships between area deprivation (ADI), body mass index (BMI) and brain structure (e.g., cortical thickness, subcortical volume) during pre-adolescence supported the neuroinflammation (NI) and/or neuronal stress (NS) theories of overeating. The NI theory proposes that ADI causes structural alteration in the brain due to the neuroinflammatory effects of overeating unhealthy foods. The NS theory proposes that ADI-related stress negatively impacts brain structure, which causes stress-related overeating and subsequent obesity. MethodsData were gathered from the Adolescent Brain Cognitive DevelopmentSM Study(R) (9-12-years-old; n=2872, 51.3% female). Linear mixed-effects models identified brain regions that were associated with both ADI and BMI; longitudinal mediation models assessed potential causal pathways. The NI model included ADI and BMI at 9/10-years-old and brain data at 11/12-years-old. The NS model included ADI and brain data at 9/10-years-old and BMI at 11/12-years-old. ResultsIn the NI model, BMI at 9/10-years-old positively mediated the relationship between AD and cortical thinning in the cuneus, lingual, and paracentral gyrus and larger volume of the Ventral DC at 11/12-years-old. In the NS model, cortical thinning in the lateral orbitofrontal cortex, lingual gyrus and larger volume of the Ventral DC at 9/10-years-old partially mediated the relationship between ADI and BMI at 11/12-years-old. ConclusionGreater area deprivation may indicate fewer access to resources that support healthy development, like nutritious food and non-stressful environments. Our findings provide evidence in support of the neuroinflammation and stress theories of overeating, specifically, with greater ADI influencing health outcomes of obesity via brain structure alterations.

neuroscience↗

bioRxiv2022

Longitudinal assessment of brain structure and behavior in youth with rapid weight gain: Potential contributing causes and consequences

ObjectiveIndependent of weight status, rapid weight gain has been associated with underlying brain structure variation in regions associated with food intake and impulsivity among pre-adolescents. Yet, we lack clarity on how developmental maturation coincides with rapid weight gain and weight stability. MethodsWe identified brain predictors of two-year rapid weight gain and its longitudinal effects on brain structure and impulsivity in the Adolescent Brain Cognitive DevelopmentSM Study(R). Youth were categorized as Healthy Weight/Weight Stable (WSHW, n=225) or Weight Gainers (WG, n=221, >38lbs); 63% of the WG group were healthy weight at 9-to-10-years-old. ResultsA five-fold cross-validated logistic elastic-net regression revealed that rapid weight gain was associated with structural variation amongst 39 brain features at 9-to-10-years-old in regions involved with executive functioning, appetitive control, and reward sensitivity. Two years later, WG youth showed differences in change over time in several of these regions and performed worse on measures of impulsivity. ConclusionsThese findings suggest that brain structure in pre-adolescence may predispose some to rapid weight gain and that weight gain itself may alter maturational brain change in regions important for food intake and impulsivity. Behavioral interventions that target inhibitory control may improve trajectories of brain maturation and facilitate healthier behaviors.

neuroscience↗