Biology subjects

Shin, S. J.

Publications and source records attributed to Shin, S. J..

9 recordsLinked to original sources

bioRxiv2025

Bispecific Targeting of CHI3L1 and PD-1/PD-L1 Axis as a Novel Therapeutic Strategy for Idiopathic Pulmonary Fibrosis

CHI3L1, a chitinase-like protein, plays a key role in the pathogenesis of pulmonary fibrosis, though the precise mechanisms remain unclear. This study explores how CHI3L1 regulates profibrotic macrophage activation and invasive myofibroblast differentiation and their interactions. In vitro, CHI3L1 induced profibrotic M2 macrophage activation and differentiation marked by increased expression of CD163, CD206, and PD-L1. CHI3L1 also enhanced TGF-{beta}1 effects on lung fibroblasts including myofibroblast transformation, migration and tissue invasion. Mechanistically, CHI3L1 increased TGF-{beta}1-stimulation of Smad, Akt and Erk signaling and PD-L1 played a significant role in TGF-{beta}1/CHI3L1-stimulated myofibroblast transformation. Coculture experiment further confirmed the ability of CHI3L1 to induce profibrotic macrophage activation that enhanced myofibroblast transformation mediated via a CD44-PD-L1 axis. Following in vivo bleomycin challenge, CHI3L1 transgenic mice exhibited significantly higher levels of PD-L1+ M2 macrophages, PD-L1+/PDGFR+ fibroblasts and increased numbers of PD-1+ and CD45+/PD-1+ cells compared to wild-type controls. Notably, combined treatment with anti-CHI3L1 and anti-PD-1 antibodies, or a bispecific anti-CHI3L1-anti-PD-1 antibody, resulted in greater inhibition of bleomycin-induced fibrosis than either antibody alone. These findings suggest that there is a stimulatory interaction between CHI3L1 and the PD-1/PD-L1 axis in promoting profibrotic macrophage activation and invasive fibroblast differentiation. The results also highlight the potential of bispecific targeting of CHI3L1 and the PD-1/PD-L1 pathway as an effective therapeutic approach for pulmonary fibrosis.

immunology↗

bioRxiv2025

Kasugamycin inhibits melanoma lung metastasis and regulates CHI3L1-driven M2-like tumor-associated macrophage differentiation

CHI3L1, a chitinase-like protein, is a potent immune modulator involved in various diseases, including lung cancer. While recent studies have demonstrated that kasugamycin (KSM) is a pan-chitinase inhibitor with strong anti-fibrotic activity, its effects on specific chitinase-like proteins remain undefined. This study shows that KSM effectively abrogates CHI3L1-stimulated cellular signaling and bioactivities. In a B16/F10 melanoma lung metastasis model, where CHI3L1 plays a critical role, KSM treatment significantly reduced melanoma lung metastasis dose-dependently. The anti-tumor effect of KSM was found to be CHI3L1-specific, as CHI3L1 overexpression enhanced melanoma lung colony formation, which was effectively blocked by KSM. In melanoma-challenged lungs, KSM treatment significantly reduced the elevation of M2 macrophages expressing CD206, CD163, and PD-L1. In studies using human monocytic THP-1 cells, CHI3L1 promoted M2 macrophage differentiation, which KSM significantly suppressed. Bulk RNA sequencing of differentiated macrophages revealed that CHI3L1 highly induced the expression of epidermal growth factor receptor (EGFR), and this induction was counter-regulated by KSM, and CHI3L1-driven M2 macrophage activation was reduced with EGFR blocker treatment. These findings reveal a novel anti-tumor mechanism of KSM, which inhibits M2-like tumor-associated macrophage differentiation, potentially through the CHI3L1-EGFR axis.

immunology↗

bioRxiv2024

Type I interferon signaling enhances kainic acid-induced seizure severity

Epilepsy is a chronic neurological disorder characterized by recurrent seizures, yet the role and mechanisms of type I interferon (IFN) signaling in seizure conditions remain elusive. In this study, we demonstrate that type I IFN signaling exacerbates seizure phenotypes in a kainic acid-induced seizure mouse model. We found that the absence of type I IFN signaling in Ifnar1-/- mice led to decreased neuronal excitability and microglial activation in response to kainic acid stimulation. Conversely, intracerebroventricular injection of IFN-{beta} heightened the severity of kainic acid-induced seizures. In vitro calcium imaging revealed that IFN-{beta} treatment amplified both basal and kainic acid-induced neuronal excitability, though no significant difference was observed in basal neuronal excitability between wild-type and Ifnar1-/- neurons. Furthermore, Ifnar1-/- mice exhibited reduced mTOR activation in the brain following kainic acid administration. Consistent with this finding, IFN-{beta} treatment induced mTOR activation, as indicated by S6 phosphorylation in in vitro mixed glial cultures. Taken together, these results demonstrate the critical role of type I IFN signaling in seizure pathogenesis and suggest that targeting type I IFNs could be a promising therapeutic strategy for reducing seizure severity and mitigating epilepsy.

neuroscience↗

bioRxiv2024

Pan-cancer subclonal mutation analysis of 7,827 tumors predicts clinical outcome

Intra-tumor heterogeneity is characterized by a diverse population of tumor clones and subclones which are important drivers of tumor evolution and therapeutic response. However, accurate subclonal reconstruction at scale remains challenging. We developed a machine learning tool, CliPP, and surveyed 9,972 tumors from 32 cancer types. We found that high subclonal mutation load (sML), the fraction of subclonal single nucleotide variants (SNVs) to all SNVs in the coding region, was prognostic of survival (progression free survival or overall survival) in 18 cancer types. In 14 cancers with low to moderate tumor mutation burden (TMB), high sML was associated with better prognosis. In immunotherapy trials for 42 metastatic prostate cancer (mCRPC), high sML was predictive of favorable response to ipilimumab and associated with increased CD8+ T-cell infiltration and decreased macrophage population. A validation using 613 whole-genomes of esophageal adenocarcinoma confirms the favorable effect of high sML and the observed tumor-associated macrophage. Our study identifies sML as a key feature of cancer, suggesting a biphasic relationship between evolutionary dynamics and differential immune environments. Finally, sML may serve as an orthogonal approach to identify likely responders of immune checkpoint blockade in low to moderate TMB tumors.

genomics↗

bioRxiv2023

Personalized Risk Prediction for Cancer Survivors: A Bayesian Semi-parametric Recurrent Event Model with Competing Outcomes

Multiple primary cancers are increasingly more frequent due to improved survival of cancer patients. Characteristics of the first primary cancer largely impact the risk of developing subsequent primary cancers. Hence, model-based risk characterization of cancer survivors that captures patient-specific variables is needed for healthcare policy making. We propose a Bayesian semi-parametric framework, where the occurrence processes of the competing cancer types follow independent non-homogeneous Poisson processes and adjust for covariates including the type and age at diagnosis of the first primary. Applying this framework to a historically collected cohort with families presenting a highly enriched history of multiple primary tumors and diverse cancer types, we have derived a suite of age-to-onset penetrance curves for cancer survivors. This includes penetrance estimates for second primary lung cancer, potentially impactful to ongoing cancer screening decisions. Using Receiver Operating Characteristic (ROC) curves, we have validated the good predictive performance of our models in predicting second primary lung cancer, sarcoma, breast cancer, and all other cancers combined, with areas under the curves (AUCs) at 0.89, 0.91, 0.76 and 0.68, respectively. In conclusion, our framework provides covariate-adjusted quantitative risk assessment for cancer survivors, hence moving a step closer to personalized health management for this unique population.

genetics↗

bioRxiv2021

CliP: subclonal architecture reconstruction of cancer cells in DNA sequencing data using a penalized likelihood model

Tumor subclonal architecture shapes cancer evolution, yet subclonal reconstruction from bulk sequencing remains difficult to scale due to computational cost and model complexity. We present CliPP, a penalized-likelihood framework that jointly estimates cellular prevalence with pairwise fusion penalties, automatically identifying subclones without requiring extensive priors. Across simulations and 2,778 whole-genome tumors with external consensus reconstructions, CliPP achieves consistently good performances when compared to state-of-the-art approaches while providing substantial runtime reductions. Applied to 7,000+ tumors across >30 cancer types, CliPP quantifies pervasive subclonality and delineates cohort-level subclone landscapes. CliPP enables fast, reproducible large-scale subclonal analysis and is freely available to the community through GitHub and a shiny app.

bioinformatics↗

bioRxiv2019

Matrix mechanotransduction mediated by thrombospondin-1/integrin/YAP signaling pathway in the remodeling of blood vessels

RationaleThe extracellular matrix (ECM) initiates mechanical cues and transduces intracellular signaling through matrix-cell interactions. In the blood vessels, additional mechanical cues derived from the pulsatile blood flow and pressure play a pivotal role in homeostasis and disease development. Currently, the nature of the cues from ECM and how they coordinate with a mechanical microenvironment in large blood vessels to maintain the integrity of the vessel wall are not fully understood.\n\nObjectiveThe aim of this study was to elucidate the crucial mediator(s) and molecular signaling pathway(s) involved in matrix mechanotransduction during remodeling of the vessel wall.\n\nMethods and ResultsWe performed secretome analysis using rat vascular smooth muscle cells (SMCs) under cyclic stretch and examined matrix-cell interactions and cell behavior. We found that the matricellular protein thrombospondin-1 (Thbs1) was secreted upon cyclic stretch and bound to integrin v{beta}1, thereby recruiting vinculin and establishing focal adhesions. RNA-sequence (RNA-seq) analysis revealed that deletion of Thbs1 in vitro markedly affected the target gene expression of Yes-associated protein (YAP). Consistently, we found that Thbs1 promotes nuclear shuttling of YAP in response to cyclic stretch, which depends on the small GTPase Rap2 and Hippo pathway, and is not influenced by alteration of actin fibers. Deletion of Thbs1 in mice inhibited Thbs1/integrin/YAP signaling, leading to maladaptive remodeling of the aorta in response to pressure overload by transverse aortic constriction (TAC), whereas it suppressed neointima formation upon carotid artery ligation, exerting context-dependent effects on the vessel wall.\n\nConclusionsThbs1 serves as a mechanical stress-triggered extracellular mediator of mechanotransduction that acts via integrin v{beta}1 to establish focal adhesions and promotes nuclear shuttling of YAP. We thus propose a novel mechanism of matrix mechanotransduction centered on Thbs1, connecting mechanical stimuli to YAP signaling during vascular remodeling in vivo.\n\nSubject codesO_LIVascular Disease\nC_LIO_LIGenetically Altered and Transgenic Models\nC_LIO_LIVascular Biology\nC_LIO_LICell Signaling/Signal Transduction\nC_LI

molecular biology↗

bioRxiv2019

Risk of multiple primary cancer diagnosis over age in families of Li-Fraumeni syndrome: a single institution perspective

Li-Fraumeni syndrome (LFS) is a rare autosomal dominant disorder associated with TP53 germline mutations and an increased lifetime risk of multiple primary cancers (MPC). Penetrance estimation of time to first and second primary cancer within LFS remains challenging due to limited data availability and the difficulty of accounting for the characteristic effects of a primary cancer on the penetrance of a second primary cancer. Using a recurrent events survival modeling approach, we estimated penetrance for both first and second primary cancer diagnosis from a pediatric sarcoma cohort (number families=189; Single primary cancer, or SPC=771; MPC=87). We then validated the risk prediction performance using an independent clinical cohort of TP53 tested individuals from MD Anderson (SPC=102; MPC=58). Our penetrance estimates are dependent on TP53 genotype, sex, and, importantly, age of diagnosis (AoD) for the first PC. We observed the later the AoD is, the shorter the gap time is for this person to be diagnosed with a second PC. We achieved an Area under the ROC curve (AUC) of 0.77 for predicting individual outcomes of MPC vs. SPC. In summary, we have provided the first set of penetrance estimates for SPC and MPC for TP53 mutation carriers, and demonstrated its accuracy for cancer risk assessment. Our open-source R package, LFSPRO, provides future risk estimates for SPC and MPC among TP53 germline mutation carriers.\n\nSignificanceOur tool can be used to support clinical counseling of LFS cancer survivors for better health management.

genetics↗

bioRxiv2019

Risk of differential cancer types over age in families with Li-Fraumeni syndrome: a validation study using multi-center cohorts

Li-Fraumeni syndrome (LFS) is a rare hereditary cancer syndrome associated with an autosomal dominant mutation inheritance in the TP53 tumor suppressor gene and a wide spectrum of cancer diagnoses. An accurate estimation of the penetrance of different cancer types in LFS is crucial to improve the clinical characterization and management of high-risk individuals of LFS. Our competing risk-based statistical model incorporates the pedigree structure efficiently into the penetrance estimation and corrects for the ascertainment bias. A set of TP53 penetrance for three cancer types (breast, BR/sarcoma, SA/others, OT) involved in LFS is then estimated from 186 pediatric-sarcoma families collected at MD Anderson Cancer Center. The penetrance was then validated on a mixed cohort of clinically ascertained families with cancer (total number of families=668). The age-dependent onset probability distributions of specific cancer types are different. For breast cancer, the TP53 penetrance goes up at an earlier age than the reported BRCA1/2 penetrance. We validated the prediction performance of the penetrance estimates via two independent cohorts combined (BR=85, SA=540, OT=158). We obtained areas under the ROC curves (AUCs) of 0.92 (BR), 0.75 (SA), and 0.81 (OT). Our R package, LFSPRO, provides risk estimates for the diagnosis of breast cancer, sarcoma, other cancers or death before cancer diagnosis in future.\n\nSignificanceCancer-specific penetrance can facilitate clinical characterization of LFS and will contribute to the management of families at high risk of LFS.

genetics↗