Biology subjects

Kuang, C.

Publications and source records attributed to Kuang, C..

13 recordsLinked to original sources

bioRxiv2026

A direct, MFRN-independent Fe(II) transfer pathway at mitochondria-lysosome contacts

Mitochondrial iron homeostasis is fundamental to respiration and redox balance, and its dysregulation is implicated in neurodegeneration, cardiomyopathy, and metabolic diseases. Although lysosomes harbor the major cellular iron reservoir, the prevailing model holds that mitochondria acquire Fe(II) directly from the cytosolic labile iron pool (LIP) via MFRN transporters. Here, we challenge the canonical view by identifying a direct, MFRN-independent Fe(II) transfer pathway at mitochondria-lysosome contacts (MLCs). This VPS39/TOMM22/SFXN1-coordinated pathway enables lysosome-to-mitochondria Fe(II) flux bypassing the cytosolic LIP. Using live-cell structured illumination microscopy (SIM), we visualize direct Fe(II) transfer specifically occurring at MLCs. Multiple lines of evidence confirm that VPS39 and TOMM22 stabilize MLCs, while SFXN1 serves as the core effector protein for this MLC-dependent Fe(II) transport. Notably, SFXN1 knockdown markedly reduces mitochondrial Fe(II) levels independent of its established serine transport function. This pathway reveals a major route for mitochondrial Fe(II) acquisition to support redox homeostasis.

cell biology↗

bioRxiv2025

Cyclin-dependent kinase 9 inhibitors as oncogene signaling modulators in combination with targeted therapy for the treatment of colorectal cancer

BackgroundColorectal cancer (CRC) is the second deadliest cancer worldwide and new treatment options are urgently needed. Cyclin dependent kinase 9 (CDK9) promotes aberrant RNA transcription in cancer and is a promising target for cancer therapies. MethodsUsing CRC cell lines as well as newly established patient-derived organoid models of CRC, we studied the clinically promising CDK9 inhibitors (AZD4573, BAY1125152/VIP152/enitociclib, and NVP2) to determine their therapeutic potential. We investigated the efficacy and mechanisms of action through cell growth and cytotoxicity assays, RNAseq, immunoblotting, and IHC. ResultsWe found CDK9 inhibitors to be highly potent against CRC, through suppression of proliferation and induction of apoptosis. Our results demonstrated CDK9 inhibitors to be broadly active against a set of CRC models derived from a diverse patient population. Our mechanistic studies showed significant suppression of the Mitogen-active protein kinase (MAPK) signaling pathway due to CDK9 inhibitor treatment, suggesting that CDK9 inhibitor efficacy could be enhanced when combined with MAPK pathway inhibitors. As proof-of-concept, we found that CDK9 inhibitors and MEK inhibitors could be combined to synergistically suppress CRC growth and survival. ConclusionsCDK9 inhibitors show promising activity against patient-derived models of CRC. MAPK signaling is particularly suppressed by CDK9 inhibitors. Combining CDK9 inhibitors and targeted therapy against MAPK signaling pathway may be a viable strategy worthy of further investigation preclinically and clinically. State of translational relevanceNovel therapies for chemotherapy-refractory CRC remain urgently needed. Rapid validation of efficacy in appropriate translational models can provide the necessary rationale to test new therapies in clinical trials. Using newly established patient-derived organoids, we validate the preclinical efficacy of transcriptional CDK9 inhibitors against CRC. This is a therapeutic class that has been scarcely evaluated for efficacy against CRC. We found that CDK9 inhibitors potently inhibit patient-derived organoid models of CRC. Our mechanistic work also reveals that clinically achievable concentrations of CDK9 inhibitor treatment results in suppression of MAPK signaling. As proof-of-concept of the potential actionability of our findings, we demonstrate that CDK9 inhibitors can be combined with MEK inhibitors to synergistically suppress CRC growth. Our study provides new patient-derived CRC models as a resource available to others for therapeutic testing, as well as a roadmap for novel hypotheses about synergistic combination treatments using CDK9 inhibitors.

cancer biology↗

bioRxiv2025

High Throughput Screening Identifies Small Molecules that Synergize with MRTX1133 Against Acquired Resistant KRAS G12D Mutated CRC

Colorectal cancer (CRC) remains a significant clinical challenge, with a 5-year survival rate of 10%. Over half of all CRCs harbor mutations in the KRAS gene, leading to poor response to standard therapy. This underscores the crucial need for novel therapeutics targeting KRAS and overcoming the growing barrier of resistance. To address these critical challenges, we conducted a high-throughput screen to identify small molecules that synergize with KRAS G12D inhibitor MRTX1133 against CRC. Through screening a 2,652 kinase inhibitor library, we discovered that Osimertinib and its analogs strongly synergize with MRTX1133 against both parental and MRTX1133-resistant cells. The top compound from the screen, NT-1, is a chemical analog of Osimertinib. NT-1 strongly synergized with MRTX1133 to suppress EGFR/MAPK signaling and induce apoptosis in an MRTX1133-resistant patient-derived organoid model of CRC. We present novel small molecule combinations with the potential to overcome the limitations of MRTX1133 with direct clinical translational applications. One Sentence SummaryHigh throughput screening and validation in colon cancer PDOs identifies novel KRAS inhibitor combinations with potential for clinical translation.

cancer biology↗

bioRxiv2024

I2SIM: Boosting High-Fidelity Isotropic Super-Resolution with Image Interference and Spatial-Spectrum Optimization

Spatial resolution is crucial for imaging subcellular structures. The advent of three-dimensional structured illumination microscopy (3D-SIM) greatly benefits the biology community, providing a powerful tool for imaging organelles with a two-fold resolution enhancement in all three dimensions. However, the axial resolution of 3D-SIM is limited to around 300 nm, which is inferior to its lateral resolution. Here, a novel method called image interference SIM (I2SIM) is reported, which utilizes two oppositely positioned objectives to detect fluorescence emission interference under three-beam excitation. By incorporating spectral modulation and spatial domain Frobenius-Hessian optimization, I2SIM achieves an axial resolution approximately twice that of 3D-SIM, reaching around 130 nm. Furthermore, the potential of I2SIM for imaging subcellular structures is demonstrated on various biological samples, including microtubules, actin filaments, and mitochondrial outer membranes. The enhanced optical sectioning capability can be utilized to resolve axial structures that are challenging to discern using ordinary 3D-SIM.

biophysics↗

bioRxiv2024

ERVcancer: a web resource designed for querying activation of human endogenous retroviruses across major cancer types

Human endogenous retroviruses (HERVs) compose approximately 8% of the human genome, co-opted into the dynamic regulatory network of cellular potency in early embryonic development. In recent studies, resurgent HERVs transcriptional activity has been frequently observed in many types of human cancers, suggesting their potential functions in the occurrence and progression of malignancy. However, a web resource dedicated to querying the relationship between activation of HERVs and cancer development is lacking. Here, we have constructed a database to explore the sequence information, expression profiles, survival prognosis, and genetic interactions of HERVs in diverse cancer types. Our database currently incorporates RNA sequencing (RNA-seq) data of 580 HERVs across 16246 samples, comprising 151 early embryonic data from the Gene Expression Omnibus (GEO) database, 8051 human adult tissues data from the Genotype-Tissue Expression (GTEx) project, 932 cancer cell lines data from the Cancer Cell Line Encyclopedia (CCLE) project, 6478 tumoral and 634 normal tissue samples data from The Cancer Genome Atlas (TCGA) project. The primary goal is to provide an easily accessible and user-friendly database for professionals in the fields of bioinformatics, pathology, pharmacology, and related areas, enabling them to efficiently screen the activity of HERVs of interest in normal and cancerous tissues and evaluate the clinical relevance. The ERVcancer database is available at http://kyuanlab.com/ervcancer/.

genomics↗

bioRxiv2024

Senescent fibroblasts in the tumor stroma rewire lung cancer metabolism and plasticity

Senescence has been demonstrated to either inhibit or promote tumorigenesis. Resolving this paradox requires spatial mapping and functional characterization of senescent cells in the native tumor niche. Here, we identified senescent p16Ink4a+ cancer-associated fibroblasts with a secretory phenotype that promotes fatty acid uptake and utilization by aggressive lung adenocarcinoma driven by Kras and p53 mutations. Furthermore, rewiring of lung cancer metabolism by p16Ink4a+ cancer- associated fibroblasts also altered tumor cell identity to a highly plastic/dedifferentiated state associated with progression in murine and human LUAD. Our ex vivo senolytic screening platform identified XL888, a HSP90 inhibitor, that cleared p16Ink4a+ cancer- associated fibroblasts in vivo. XL888 administration after establishment of advanced lung adenocarcinoma significantly reduced tumor burden concurrent with the loss of plastic tumor cells. Our study identified a druggable component of the tumor stroma that fulfills the metabolic requirement of tumor cells to acquire a more aggressive phenotype.

cancer biology↗

bioRxiv2024

CD74+ fibroblasts proliferate upon mechanical stretching to promote angiogenesis in keloid

The healing of human skin wounds is susceptible to perturbation caused by excessive mechanical stretching, resulting in enlarged scars, hypertrophic scars, or even keloids in predisposed individuals. Keloids are fibro-proliferative scar tissues that extend beyond the initial wound boundary, consisting of the actively progressing leading edge and the quiescent center. The stretch-associated outgrowth and enhanced angiogenesis are two features of the leading edge of keloids. However, which cell population is responsible for transducing the mechanical stimulation to the pathological alterations of keloid tissues remains unclear. Herein, through joint analysis of single-cell RNA sequencing of keloid specimens and RNA sequencing of stretched keloid fibroblasts, we identified CD74+ fibroblasts, a previously unappreciated subset of fibroblasts, as a key player in stretch-induced keloid progression. Examination of macrophage markers suggested a possible myeloid origin of the CD74+ fibroblasts. Immunostaining of keloid cryosections depicted a predominant distribution of CD74+ fibroblasts in the leading edge, interacting with vasculature. CD74+ fibroblasts possessed pro-angiogenic and migratory capacities, as revealed by in vitro transwell and tube formation assays on purified CD74+ fibroblasts. Additionally, these cells underwent proliferation upon stretching, through PIEZO1-mediated calcium influx and the downstream ERK and AKT signaling. Collectively, our findings propose a model wherein CD74+ fibroblasts serve as pivotal drivers of stretch-induced keloid progression, fueled by their proliferative, pro-angiogenic, and migratory capacities. Targeting the attributes of CD74+ fibroblasts hold promise as a therapeutic strategy for keloid management. Significance statementKeloids are fibro-proliferative scars resulting from aberrant skin wound healing processes, consisting of the actively progressing leading edge and the quiescent center. Mechanical stretching and neo-vascularization have both been implicated in keloid progression, yet little is known about whether they are interconnected. Herein, we demonstrated that CD74+ fibroblasts, a previously undiscovered fibroblast subset, possessed heightened pro-angiogenic and migratory capacities, and underwent proliferation upon mechanical stretching, thereby facilitating the progression of the leading edge of keloids. Examination of macrophage markers suggested a possible myeloid origin of CD74+ fibroblasts. Our findings uncover the connection between stretch-induced keloid progression and neo-vascularization through CD74+ fibroblasts and provide valuable insights into potential therapeutic interventions.

cell biology↗

bioRxiv2023

Accurate 3D SMLM localization via Vectorial In-situ PSF Retrieval and Aberration Assessment

In single-molecule localization microscopy (SMLM), achieving precise localization hinges on obtaining an authentic point spread function (PSF) influenced by system and sample-induced aberrations. Here, we introduce VISPR (Vectorial in-situ PSF retrieval) retrieving precise 3D PSF models considering both system and sample-induced aberrations under SMLM conditions. By employing the theory of vectorial PSF model and maximum likelihood estimation (MLE) phase retrieval, VISPR is capable of reconstructing an accurate 3D PSF model achieving the theoretically minimum uncertainty and accurately reflecting three-dimensional information of single molecules. This capability empowers accurate 3D super-resolution reconstruction in 3D SMLM. Additionally, VISPR applies to low signal-to-noise ratio circumstances and is adept at retrieving high-frequency details of the experimental PSF across an extensive depth range--a challenging feat for alternative approaches. As an effective tool, VISPR enables the quantitative assessment of aberrations induced by the system and sample environment. From the simulations and experiments, we verified the superiority and effectiveness of VISPR. It is essential to highlight that VISPR applies to various SMLM microscope modalities.

molecular biology↗

bioRxiv2023

Multi-color live-cell optical nanoscopy using phasor analysis

Stimulated emission depletion microscopy (STED) is a powerful tool for studying nanoscale cell structure and activity, but the difficulties it encounters in multicolor imaging limit its application in biological research. To overcome the disadvantages of limited number of channels and high cost of multicolor STED imaging based on spectral identity, we introduced lifetime into live-cell multicolor STED imaging by separating selected dyes of the same spectrum by phasor analysis. Experimental results show that our method enables live-cell STED imaging with at least 4 colors, enabling observation of cellular activity beyond the diffraction limit.

cell biology↗

bioRxiv2022

Accurate background reduction in adaptive optical 3D-STED nanoscopy by dynamic phase switching

Stimulated emission depletion (STED) fluorescence nanoscopy allows the three-dimensional (3D) visualization of nanoscale subcellular structures, providing unique insights into their spatial organization. However, 3D-STED imaging and quantification of dense features are obstructed by the low signal-to-background ratio (SBR), resulting from optical aberrations and out-of-focus background. Here, combining with adaptive optics, we present an easy-to-implement and flexible method to improve SBR by dynamic phase switching. By switching to a counterclockwise vortex phase mask and a top-hat one with an incorrect inner radius, the depletion pattern features a nonzero-intensity center, enabling accurate background recordings. When the recorded background is subtracted from the aberration-corrected 3D-STED image, the SBR in dense sample areas can be improved by a factor of 3-6 times. We demonstrate our method on various dense subcellular structures, showing more advantages than the software-based background subtraction algorithms. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/497623v2_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@7aacd6org.highwire.dtl.DTLVardef@1e91f14org.highwire.dtl.DTLVardef@1f774acorg.highwire.dtl.DTLVardef@10ccf5d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

FIB-SEM analysis on three-dimensional structures of growing organelles in wild Chlorella pyrenoidosa cells

To clarify dynamic changes of organelle microstructures in Chlorella pyrenoidosa cells during photosynthetic growth with CO2 fixation, three-dimensional organelle microstructures in three growth periods of meristem, elongation and maturity were quantitatively determined and comprehensively reconstructed with focused ion beam scanning electron microscopy (FIB-SEM). The single round-pancake mitochondria in each cell split into a dumbbell and then into a circular ring, while barycenter distance of mitochondria to chloroplast and nucleus was reduced to 45.5% and 88.3% to strengthen energy transfer, respectively. The single pyrenoid consisting of a large part and another small part in each chloroplast gradually developed to a mature state in which the two parts were nearly equal in size. The nucleolus progressively became larger with euchromatin replication. The number of starch grains gradually increased, but average grain volume remained nearly unchanged.

cell biology↗

bioRxiv2020

Labeling subcellular structures in living specimens using live-cell incompatible dyes with excellent optical properties

Despite the urgent needs of imaging living specimens for cutting-edge biological research, most of the existing fluorescent labeling methods suffer from either poor optical properties or complicated operations to realize cell-permeability and specificity. Here, we introduce a method to overcome this tradeoff by incubating living cells and tissues with fluorescent dyes, no matter if they are cell-permeable or not, at particular conditions (concentration and temperature) without physical cell-penetration or chemical modifications. Based on this method, the mitochondrial labeling capability of Atto dyes, especially Atto 647N with extraordinary optical properties, together with interesting interactions between organelles is revealed. These results indicate the great potential of using dyes, which are normally considered "live-cell incompatible", to capture the morphology and dynamics of subcellular structures in living specimens.

cell biology↗

bioRxiv2019

Zebrafish Dscaml1 is Essential for Retinal Patterning and Function of Oculomotor Subcircuits

Down Syndrome Cell Adhesion Molecules (dscam and dscaml1) are essential regulators of neural circuit assembly, but their roles in vertebrate neural circuit function are still mostly unexplored. We investigated the role of dscaml1 in the zebrafish oculomotor system, where behavior, circuit function, and neuronal activity can be precisely quantified. Loss of zebrafish dscaml1 resulted in deficits in retinal patterning and light adaptation, consistent with its known roles in mammals. Oculomotor analyses showed that mutants have abnormal gaze stabilization, impaired fixation, disconjugation, and faster fatigue. Notably, the saccade and fatigue phenotypes in dscaml1 mutants are reminiscent of human ocular motor apraxia, for which no animal model exists. Two-photon calcium imaging showed that loss of dscaml1 leads to impairment in the saccadic premotor pathway but not the pretectum-vestibular premotor pathway, indicating a subcircuit requirement for dscaml1. Together, we show that dscaml1 has both broad and specific roles in oculomotor circuit function, providing a new animal model to investigate the development of premotor pathways and their associated human ocular disorders.

neuroscience↗