Biology subjects

Shin, S.-J.

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

4 recordsLinked to original sources

bioRxiv2024

Genomic and single-cell characterization of patient-derived tumor organoid models of head and neck squamous cell carcinoma

Head and Neck Squamous Cell Carcinoma (HNSCC) remains a significant health burden due to tumor heterogeneity and treatment resistance, emphasizing the need for improved biological understanding and tailored therapies. This study enrolled 31 HNSCC patients for the establishment of patient-derived tumor organoids (PDOs), which faithfully maintained genomic features and histopathological traits of primary tumors. Long-term culture preserved key characteristics, affirming PDOs as robust representative models. PDOs demonstrated predictive capability for cisplatin treatment responses, correlating ex vivo drug sensitivity with patient outcomes. Bulk and single-cell RNA sequencing unveiled molecular subtypes and intratumor heterogeneity (ITH) in PDOs, paralleling patient tumors. Notably, a hybrid epithelial-mesenchymal transition (hEMT)-like ITH program is associated with cisplatin resistance and poor patient survival. Functional analyses identified amphiregulin (AREG) as a potential regulator of the hybrid epithelial/mesenchymal state. Moreover, AREG contributes to cisplatin resistance via EGFR pathway activation, corroborated by clinical samples. In summary, HNSCC PDOs serve as reliable and versatile models, offer predictive insights into ITH programs and treatment responses, and uncover potential therapeutic targets for personalized medicine. One Sentence SummaryThis study establishes patient-derived tumor organoids (PDOs) from 31 Head and Neck Squamous Cell Carcinoma (HNSCC) patients, faithfully recapitulating characteristics of primary tumors and accurately predicting clinical responses to cisplatin treatment. We reveal intertumoral heterogeneity within PDOs and a hybrid epithelial-mesenchymal transition (hEMT) program conferring cisplatin resistance, highlighting amphiregulin (AREG) as a regulator of cellular plasticity and potential therapeutic target for HNSCC treatment.

cancer biology↗

bioRxiv2024

Matrix-rigidity cooperates with biochemical cues in M2 macrophage activation through increased nuclear deformation and chromatin accessibility

Macrophages encounter a myriad of biochemical and mechanical stimuli across various tissues and pathological contexts. Notably, matrix rigidity has emerged as a pivotal regulator of macrophage activation through mechanotransduction. However, the precise mechanisms underlying the interplay between mechanical and biochemical cues within the nuclear milieu remain elusive. Here we elucidate how the increased matrix rigidity drives macrophages to amplify alternatively-activated (M2 phenotype) signalings cooperatively with biochemical cues (e.g., IL4/13) through altered nuclear mechanics. Notably, we found that reconstructed podosome-like F-actins and contractility induced nucleus deformation, opening nuclear pores, which facilitates nuclear translocation of the key transcription factor STAT6. Furthermore, the altered nuclear mechanics increased chromatin accessibility induced by H3K9 methylation, particularly of M2-associated gene promoters. These cooperative events of the mechano-chemical signaling at the cytoskeletal-to-nuclear domains facilitated M2 transcriptional activation and cellular functions. We further evidenced the rigidity-primed M2 macrophages were immunosuppressive and accumulated in stiffened tumor tissues. This study proposes a mechanism by which matrix mechanics crosstalks with biochemical signals to potentiate macrophage activation through nuclear mechanosensing and chromatin modifications, offering insights into macrophage mechanobiology and its therapeutic modulations.

bioengineering↗

bioRxiv2023

Three-dimensional virtual H&E staining of label-free colon cancer tissue using holotomography and deep learning

In standard histopathology, hematoxylin and eosin (H&E) staining stands as a pivotal tool for cancer tissue analysis. However, this method is limited to two-dimensional (2D) analysis or requires labor-intensive preparation for three-dimensional (3D) inspection of cancer tissues. In this study, we present a method for 3D virtual H&E staining of label-free cancer tissues, employing holotomography and deep learning. Holotomography is used to measure the 3D refractive index (RI) distribution of the label-free cancer slides. A deep learning-based image-to-image translation framework is integrated into the resulting 3D RI distribution, enabling virtual H&E staining in 3D. Our method has been applied to colon cancer tissue slides with thicknesses up to 20 m, with conventional chemical H&E staining providing a direct validation for the method. This framework not only bypasses the conventional staining process but also provides 3D structures of glands, lumens, and individual nuclei. The results demonstrate enhancement in histopathological efficiency and the extension of the standard histopathology into the 3D realm. To validate the repeatability and scalability of the approach, we applied the framework to the gastric cancer slides obtained from different institute and imaging devices.

cancer biology↗

bioRxiv2018

Optimization of Tenocyte Lineage-related Factors from Tonsil-derived Mesenchymal Stem Cells using Response Surface Methodology

Researchers should consider various potential factors that affect tenogenic differentiation of mesenchymal stem cells (MSCs); however, this requires numerous experimental settings, which are associated with high cost and time. We aimed to assess the differential effects of transforming growth factor beta 3 (TGF-{beta}3) on the tenogenesis of tonsil-derived MSCs (T-MSCs) and bone marrow-derived MSCs (BM-MSCs) using design of experiments (DoE). Bone marrow and tonsillar tissue was collected from four patients; mononuclear cells were separated and treated with 5 and 10 ng/mL of TGF-{beta}3 with vehicle control. A full-factorial experimental design with a categorical factor of 0 was employed to study the effect of tension based on T-MSCs. Eighty-four trials were utilized, fitted with RSM, and then used to obtain mathematical prediction models. Exposure of T-MSCs and BM-MSCs to TGF-{beta}3 increased the expression of scleraxis (SCX), tenomodulin (TNMD), decorin, collagen I, and tenascin C. Expression of most of these factors reached a maxima after 2-3 days of treatment. Considering all of the tenocyte lineage-related factors that were assessed, the predicted value of the factors from T-MSCs was significantly induced at 2.7 ng/mL of TGF-{beta}3 during 2.5-day culture, whereas the predicted value of the factors from BM-MSCs was significantly induced during 2.3-day culture, regardless of TGF-{beta}3 concentration. This study demonstrated that tenogenic differentiation of T-MSCs and BM-MSCs under TGF-{beta}3 stimulation showed a similar culture time for peak expression of tenocyte-related mRNAs using RSM. This study suggests the potential of using the DoE approach for optimization of the culture protocol for tenogenesis of MSCs.

bioengineering↗