Biology subjects

Kim, M. H.

Publications and source records attributed to Kim, M. H..

12 recordsLinked to original sources

bioRxiv2026

Thal-Kak: unifying biomolecular structure predictors reveals a sampling-selection gap

Complementary all-atom structure predictors sample different solutions, but how to allocate a fixed sampling budget across them and select the best output remains unclear. Thal-Kak unifies five released predictors under shared upstream inputs and a common schema. Across FoldBench and CASP16, model mixing improves oracle sampling over single-model runs, but selection remains a bottleneck because confidence scores do not transfer across models and existing quality-assessment methods cannot resolve this gap.

bioinformatics↗

bioRxiv2026

Circulating miR-10b-5p drives Kawasaki vasculitis through endothelial reprogramming and nominates CXCL8 as an early diagnostic biomarker

BackgroundKawasaki disease (KD) is an acute systemic vasculitis of unknown etiology and the leading cause of acquired heart disease in children. Coronary artery aneurysm formation represents its most serious complication, yet no specific biomarker exists for early diagnosis at emergency department (ED) presentation. We sought to define the molecular mechanisms driving KD vasculitis and to identify a clinically actionable early diagnostic marker. MethodsWhole microRNA sequencing was performed on buffy coat specimens from KD patients and febrile controls presenting to the ED. Disease-associated miRNA candidates were validated in two independent murine KD-like vasculitis models: Lactobacillus casei cell wall extract (LCWE; n=12-20) and Candida albicans water-soluble fraction (CAWS; n=12). The functional role of miR-10b-5p was assessed by antagomir-mediated inhibition in the LCWE model. Transcriptomic and chromatin-level reprogramming were characterized by single-cell RNA sequencing (scRNA-seq), bulk RNA-seq, and assay for transposase-accessible chromatin with sequencing (ATAC-seq) in human coronary artery endothelial cells (HCAECs). Transcription factor binding was validated by in vitro binding assays and chromatin immunoprecipitation. Serum chemokine (C-X-C motif) ligand 8 (CXCL8) was quantified by enzyme-linked immunosorbent assay. ResultsForty miRNAs were upregulated in KD patients and fourteen miRNAs were prioritized for further analysis. miR-10b-5p was consistently elevated across both vasculitis models, and its antagomir-mediated inhibition attenuated aortic root inflammation in vivo. In HCAECs, miR-10b-5p suppressed its direct targets marker of proliferation Ki-67 (MKI67)/Chromobox5 (CBX5), driving a cell-state transition from proliferative/metabolic programs toward a pro-inflammatory phenotype. Consistently, analyses of bulk RNA-seq supported cell-cycle arrest and altered chromatin remodeling. ATAC-seq revealed increased chromatin accessibility at the CXCL8 and Matrix metalloproteinases 10 (MMP10) promoters, and motif analysis identified CCAAT/enhancer-binding protein alpha (CEBPA) as the key transcriptional activator; CEBPA knockdown abrogated miR-10b-5p-induced CXCL8 and MMP10 upregulation. Serum CXCL8 was markedly elevated in KD patients relative to febrile controls at first ED presentation, prior to definitive diagnosis, and declined significantly at 8-week follow-up. ConclusionsWe define a miR-10b-5p-MKI67/CBX5-CEBPA-CXCL8 axis as a mechanistic driver of endothelial reprogramming and neutrophil-recruiting inflammation in KD. Serum CXCL8 emerges as a candidate early diagnostic biomarker that may facilitate timely KD recognition at ED presentation.

molecular biology↗

bioRxiv2025

Modeling viral and bacterial infections in human lung organotypic systems reveals strain specific host responses

In this study, we developed novel lung organoid-on-chip models that elucidate differential human tissue response to various strains of respiratory pathogens: Streptococcus pneumoniae and SARS-CoV-2. We show that human fetal-derived distal lung epithelial cells are readily expandable in 3D as organoids, thereby providing a highly sustainable source of lung progenitor cells. These 3D organoid progenitors can then be induced to produce airway and alveolar organoids on microfluidic devices. Upon challenge with Streptococcus pneumoniae, a bacterium known to cause pneumonia, a rapid and strain-dependent colonization was observed at the epithelial surface of alveolar chips. We also assessed SARS-CoV-2 infection in the alveoli-on-chip system and observed that the Delta variant exhibited greater infectivity as compared to the Omicron BA.5. Both SARS-CoV-2 variants induced potent interferon responses and triggered the expression of different interferon-stimulated genes. Our results demonstrate that strain-specific host defense mechanisms can be recapitulated in human-organoid-based microfluidic systems, paving the way for the use of such platforms for more targeted assessments of human response to novel emergent pathogen strains. HighlightsO_LIHuman fetal epithelial lung stem cells can be expanded as multipotent organoids and differentiated into both airway or alveolar organoids C_LIO_LIMultipotent lung organoids efficiently produce functional epithelia of small airway or alveoli when grown on-chip. C_LIO_LIStreptococcus pneumoniae inoculation in alveoli-on-chip mimics the early stages of bacterial colonization in lung epithelia C_LIO_LIAlveoli on-chip system recapitulates variant-specific interactions. SARS-CoV-2 Delta replicates but not Omicron BA.5. C_LIO_LIRobust interferon response upon SARS-CoV-2 infection shows Alveoli on-chip can model innate immune responses. C_LI

bioengineering↗

bioRxiv2024

High-Throughput Bioprinting of Spheroids for Scalable Tissue Fabrication

Tissue biofabrication that replicates an organ-specific architecture and function requires physiologically-relevant cell densities. Bioprinting using spheroids has the potential to create constructs with native cell densities, but its application is limited due to the lack of practical, scalable techniques. This study presents HITS-Bio (High-throughput Integrated Tissue Fabrication System for Bioprinting), a novel multiarray spheroid bioprinting technology enabling scalable tissue fabrication by rapidly positioning a number of spheroids simultaneously using a digitally-controlled nozzle array (DCNA) platform. HITS-Bio achieves an unprecedented speed, an order of magnitude faster compared to existing techniques while maintaining high cell viability (>90%). The platforms ability to pattern multiple spheroids simultaneously enhances fabrication rates proportionally to the size of DCNA used. The utility of HITS-Bio was exemplified in multiple applications, including intraoperative bioprinting with microRNA transfected spheroids for calvarial bone regeneration ([~]30 mm3) in a rat model achieving a near-complete defect closure ([~]91% in 3 weeks and [~]96% in 6 weeks). Additionally, the successful fabrication of scalable cartilage constructs (1 cm3) containing [~]600 chondrogenic spheroids highlights its high-throughput efficiency (under 40 min per construct) and potential for repairing volumetric tissue defects.

bioengineering↗

bioRxiv2023

Nested biofabrication: Matryoshka-inspired Intra-embedded Bioprinting

Engineering functional tissues and organs remains a fundamental pursuit in biofabrication. However, the accurate constitution of complex shapes and internal anatomical features of specific organs, including their intricate blood vessels and nerves, remains a significant challenge. Inspired by the Matryoshka doll, we here introduce a new method called Intra-Embedded Bioprinting (IEB), building upon existing embedded bioprinting methods. We used a xanthan gum-based material, which served a dual role as both a bioprintable ink and a support bath, due to its unique shear-thinning and self-healing properties. We demonstrated IEBs capabilities in organ modelling, creating a miniaturized replica of a pancreas using a photocrosslinkable silicone composite. Further, a head phantom and a Matryoshka doll were 3D printed, exemplifying IEBs capability to manufacture intricate, nested structures. Towards the use case of IEB and employing innovative coupling strategy between extrusion-based and aspiration-assisted bioprinting, we developed a breast tumor model that included a central channel mimicking a blood vessel, with tumor spheroids bioprinted in proximity. Validation using a clinically-available chemotherapeutic drug illustrated its efficacy in reducing the tumor volume via perfusion over time. This method opens a new way of bioprinting enabling the creation of complex-shaped organs with internal anatomical features.

bioengineering↗

bioRxiv2022

High-throughput microgel biofabrication via air-assisted co-axial jetting for cell encapsulation, 3D bioprinting, and scaffolding applications

Microgels have recently received widespread attention for their applications in a wide array of domains such as tissue engineering, regenerative medicine, and cell and tissue transplantation because of their properties like injectability, modularity, porosity, and the ability to be customized in terms of size, form, and mechanical properties. However, it is still challenging to mass produce microgels with diverse sizes and tunable properties. Herein, we developed an air-assisted co-axial device (ACAD) for continuous production of microgels in a high-throughput manner. To test its robustness, microgels of multiple hydrogels and their combination, including alginate (Alg), gelatin methacrylate (GelMA) and Alg-GelMA, were formed at a maximum production rate of 65,000 microgels per sec while retaining circularity and a size range of 50-500 m based on varying air pressure levels. The ACAD platform allowed single and multiple cell encapsulation with around 75% efficiency. These microgels illustrated appealing rheological properties such as yield stress, viscosity, and shear modulus for bioprinting applications. Specifically, Alg microgels have the potential to be used as a sacrificial support bath while GelMA microgels have potential for direct extrusion both on their own or when loaded in a bulk GelMA hydrogel. Generated microgels showed high cell viability (>90%) and proliferation over 7 days with their increased interactions with cells, particularly for GelMA microgels. The developed strategy provides a facile and rapid approach without any complex or expensive consumables and accessories for scalable high-throughput microgel production for cell therapy, tissue regeneration and 3D bioprinting applications.

bioengineering↗

bioRxiv2022

SARS-CoV-2 variants show temperature-dependent enhancedpolymerase activity in the upper respiratory tract and high transmissibility

With the convergent global emergence of SARS-CoV-2 variants of concern (VOC), a precise comparison study of viral fitness and transmission characteristics is necessary for the prediction of dominant VOCs and the development of suitable countermeasures. While airway temperature plays important roles in the fitness and transmissibility of respiratory tract viruses, it has not been well studied with SARS-CoV-2. Here we demonstrate that natural temperature differences between the upper (33{degrees}C) and lower (37{degrees}C) respiratory tract have profound effects on SARS-CoV-2 replication and transmission. Specifically, SARS-COV-2 variants containing the P323L or P323L/G671S mutation in the NSP12 RNA-dependent RNA polymerase (RdRp) exhibited enhanced RdRp enzymatic activity at 33{degrees}C compared to 37{degrees}C and high transmissibility in ferrets. MicroScale Thermophoresis demonstrated that the NSP12 P323L or P323L/G671S mutation stabilized the NSP12-NSP7-NSP8 complex interaction. Furthermore, reverse genetics-derived SARS-CoV-2 variants containing the NSP12 P323L or P323L/G671S mutation displayed enhanced replication at 33{degrees}C, and high transmission in ferrets. This suggests that the evolutionarily forced NSP12 P323L and P323L/G671S mutations of recent SARS-CoV-2 VOC strains are associated with increases of the RdRp complex stability and enzymatic activity, promoting the high transmissibility.

microbiology↗

bioRxiv2022

3D Bioprinted perfusable and vascularized breast tumor model for dynamic screening of chemotherapeutics and CAR-T cells

Despite substantial advancements in development of cancer treatments, lack of standardized and physiologically-relevant in vitro testing platforms limit the rapid and early screening of anti-cancer agents. A major barrier in this endeavor, is the complex interplay between the tumor microenvironment and host immune response and lack of predictive biomarkers for clinical benefit. To tackle this challenge, we have developed a dynamic-flow based three-dimensionally (3D) bioprinted vascularized breast tumor model, responding to chemo and immunotherapeutic treatments. Heterotypic tumor spheroids, comprising metastatic breast cancer cells (MDA-MB-231), human umbilical vein endothelial cells (HUVECs) and human dermal fibroblasts (HDFs), precisely bioprinted at pre-defined distances from a perfused vasculature, exhibited tumor angiogenesis and cancer invasion. Proximally bioprinted tumors ([~]100 m) exhibited enhanced capillary sprouting, anastomosis to perfused vasculature and increased cancer cell migration as compared to distally bioprinted spheroids ([~]500 m). Proximally bioprinted tumors treated with varying dosages of doxorubicin for 72 h enabled functional analysis of drug response, wherein, tumors portrayed a dose-dependent drug response behavior with [~]70% decrease in tumor volume for 1 M dose. Additionally, a cell based immune therapy approach was explored by perfusing HER2-targeting chimeric antigen receptor (CAR) modified CD8+ T cells for 24 or 72 h through the central vasculature. Extensive CAR-T cell recruitment to the endothelium and substantial T cell activation and infiltration in the tumor site, resulted in [~]70% reduction in tumor growth for high CAR treatment densities, after 72 h of treatment. The presented 3D model paves the way for a robust, precisely fabricated and physiologically-relevant 3D tumor microenvironment platform for future translation of anti-cancer therapies to personalized medicine for cancer patients. One Sentence SummaryA physiologically-relevant 3D bioprinted perfusable vascularized tumor model capable of dynamic screening of chemo and immunotherapeutics.

bioengineering↗

bioRxiv2022

Development of 3D breast cancer models with human T cells expressing engineered MAIT cell receptors

Immunotherapy has revolutionized cancer treatment with the advent of advanced cell engineering techniques aimed at targeted therapy with reduced systemic toxicity. However, understanding the underlying immune-cancer interactions require development of advanced three-dimensional (3D) models of human tissues. In this study, we developed proof-of-concept 3D tumor models with increasing complexity to study the cytotoxic responses of CD8+ T cells, genetically engineered to express mucosal-associated invariant T (MAIT) cell receptors, towards MDA-MB-231 breast cancer cells. Homotypic MDA-MB-231 and heterotypic MDA-MB-231/human dermal fibroblast (HDF) tumor spheroids were primed with precursor MAIT cell ligand 5-amino-6-D-ribitylaminouracil (5-ARU). Engineered T cells effectively eliminated tumors after a 3-day culture period, demonstrating that the engineered TCR recognized MR1 expressing tumor cells in the presence of 5-ARU. Tumor cell killing efficiency of engineered T cells were also assessed by encapsulating these cells in fibrin, mimicking a tumor extracellular matrix microenvironment. Expression of proinflammatory cytokines such as IFN{gamma}, IL-13, CCL-3 indicated immune cell activation in all tumor models, post immunotherapy. Further, in corroborating the cytotoxic activity, we found that granzymes A and B were also upregulated, in homotypic as well as heterotypic tumors. Finally, a 3D bioprinted tumor model was employed to study the effect of localization of T cells with respect to tumors. T cells bioprinted proximal to the tumor had reduced invasion index and increased cytokine secretion, which indicated a paracrine mode of immune-cancer interaction. Development of 3D tumor-T cell platforms may enable studying the complex immune-cancer interactions and engineering MAIT cells for cell-based cancer immunotherapies.

immunology↗

bioRxiv2021

Aspiration-assisted freeform bioprinting of mesenchymal stem cell spheroids within alginate microgels

Aspiration-assisted freeform bioprinting (AAfB) has emerged as a promising technique for precise placement of tissue spheroids in three-dimensional (3D) space for fabrication of tissues. For successful embedded bioprinting using AAfB, an ideal support bath should possess shear-thinning behavior and yield-stress to obtain tightly fused assembly of bioprinted spheroids. Several studies have demonstrated support baths for embedded bioprinting, but these materials pose major challenges due to their low biocompatibility, opaqueness, complex and prolonged preparation procedures, and limited spheroid fusion efficacy. In this study, to circumvent the aforementioned limitations, we present the feasibility of AAfB of human mesenchymal stem cell (hMSC) spheroids in alginate microgels as a support bath. First, alginate microgels were prepared with different particle sizes modulated by blending time and concentration, followed by determination of the optimal bioprinting conditions by the assessment of rheological properties, bioprintability, and spheroid fusion efficiency. The bioprinted and consequently self-assembled tissue structures made of hMSC spheroids were osteogenically induced for bone tissue formation. Alongside, we investigated the effects of peripheral blood monocyte-derived osteoclast incorporation into the hMSC spheroids in heterotypic bone tissue formation. We demonstrated that alginate microgels enabled unprecedented positional accuracy (~5%), transparency for visualization, and improved fusion efficiency (~97%) of bioprinted hMSC spheroids for bone fabrication. This study demonstrates the feasibility of using alginate microgels as a support bath for many different applications including but not limited to freeform bioprinting of spheroids, cell-laden hydrogels, and fugitive inks to form viable tissue constructs.

bioengineering↗

bioRxiv2019

Heterogeneous loop model to infer 3D chromosome structures from Hi-C

Adapting a well-established formalism in polymer physics, we develop a minimalist approach to infer threedimensional (3D) folding of chromatin from Hi-C data. The 3D chromosome structures generated from our heterogeneous loop model (HLM) are used to visualize chromosome organizations that can substantiate the measurements from FISH, ChIA-PET, and RNA-Seq signals. We demonstrate the utility of HLM with several case studies. Specifically, the HLM-generated chromosome structures, which reproduce the spatial distribution of topologically associated domains (TADs) from FISH measurement, show the phase segregation between two types of TADs explicitly. We discuss the origin of cell-type dependent gene expression level by modeling the chromatin globules of -globin and SOX2 gene loci for two different cell lines. We also use HLM to discuss how the chromatin folding and gene expression level of Pax6 loci, associated with mouse neural development, is modulated by interactions with two enhancers. Finally, HLM-generated structures of chromosome 19 of mouse embryonic stem cells (mESCs), based on single-cell Hi-C data collected over each cell cycle phase, visualize changes in chromosome conformation along the cell cycle. Given a contact frequency map between chromatic loci supplied from Hi-C, HLM is a computationally efficient and versatile modeling tool to generate chromosome structures, which can complement interpreting other experimental data.

biophysics↗

bioRxiv2019

Multi-CD: Multi-scale discovery of Chromatin Domains

Identifying chromatin domains (CDs) from high-throughput chromosome conformation capture (Hi-C) data is currently a central problem in genome research. Here we present a unified algorithm, Multi-CD, which infers CDs at various genomic scales by leveraging the information from Hi-C. By integrating a model of the chromosome from polymer physics, statistical physics-based clustering analysis, and Bayesian inference, Multi-CD identifies the CDs that best represent the global pattern of correlation manifested in Hi-C. The multi-scale intra-chromosomal structures compared across different cell types allow us to glean the principles of chromatin organization: (i) Sub-TADs, TADs, and meta-TADs constitute a robust hierarchical structure. (ii) The assemblies of compartments and TAD-based domains are governed by different organizational principles. (iii) Sub-TADs are the common building blocks of chromosome architecture. CDs obtained from Multi-CD applied to Hi-C data enable a quantitative and comparative analysis of chromosome organization in different cell types, providing glimpses into structure-function relationship in genome.

biophysics↗