Biology subjects

Sekine, S.

Publications and source records attributed to Sekine, S..

9 recordsLinked to original sources

bioRxiv2026

Senolytic targeting of CAF-induced KRT17+ colon cancer cells inhibits metastatic invasion

Metastasis remains the leading cause of cancer mortality, yet effective strategies to eliminate metastasis-initiating cells are lacking. Here, we dissected intratumoral heterogeneity in colon cancer using single-cell analyses and identified a KRT17+ slow-cycling cancer cell population that exhibits features of metastasis-initiating cells (L1CAM) and senescent-like cells (CDKN2A, BCL2L1). Spatial transcriptomics and immunostaining revealed that these cells localize at tumor-stroma interfaces, where they are closely associated with TGF-{beta}1-producing subset of cancer-associated fibroblasts (CAFs) and exhibit SMAD3 activation. Mechanistically, TGF-{beta}1 induces KRT17 expression in patient-derived cancer cells, while co-culture with CAFs drives the emergence of KRT17 migratory cells in a KRT17-dependent manner. Functionally, genetic ablation of KRT17 or senolytic targeting of BCL2L1 suppresses peritumoral invasion and liver metastasis in xenograft models. Clinically, KRT17 cells co-localize with TGF-{beta}1 CAFs, and their co-expression with L1CAM correlates with advanced disease stage. These findings support a model in which stromal TGF-{beta} signaling promotes the emergence of a KRT17 invasive cancer cell state with senescence-associated features and suggest that senolytic strategies may represent a potential approach to limit metastatic progression in colon cancer.

cancer biology↗

bioRxiv2025

Novel reporter of the PINK1-Parkin mitophagy pathway identifies its damage sensor in the import gate

Damaged mitochondria can be cleared from the cell by mitophagy, using a pathway formed by the recessive Parkinsons disease genes PINK1 and Parkin. How mitochondrial damage is sensed by the PINK1-Parkin pathway, however, remains uncertain. Here, using a Parkin substrate-based reporter in genome-wide screens, we identified that diverse forms of mitochondrial damage converge on loss of mitochondrial membrane potential (MMP) to activate PINK1. Consistently, the MMP but not the presequence translocase-associated motor (PAM) import motor provided the essential driving force for endogenous PINK1 import through the inner membrane translocase TIM23. In the absence of TIM23, PINK1 arrested in the translocase of the outer membrane (TOM) during import. The energy-state outside of the mitochondria further modulated the pathway by controlling the rate of new PINK1 synthesis. Our results identify separation of PINK1 from TOM by the MMP, as the key damage-sensing switch in the PINK1-Parkin mitophagy pathway. HighlightsO_LIMFN2-Halo is a quantitative single-cell reporter of PINK1-Parkin activation. C_LIO_LIDiverse forms of mitochondrial damage, identified in whole-genome screens, activate the PINK1-Parkin pathway by disrupting the mitochondrial membrane potential (MMP). C_LIO_LIThe primary driving force for endogenous PINK1 import through the TIM23 translocase is the MMP with the PAM import motor playing a supporting role. C_LIO_LILoss of TIM23 is sufficient to stabilize PINK1 in the TOM complex and activate Parkin. C_LI

cell biology↗

bioRxiv2022

A mitochondrial iron-sensing pathway regulated by DELE1

The heme-regulated kinase HRI is activated under heme/iron deficient conditions; however, the underlying molecular mechanism is incompletely understood. Here, we show that iron deficiency-induced HRI activation involves a heme-independent mechanism that requires the mitochondrial protein DELE1. Notably, mitochondrial import of DELE1 and its subsequent protein stability are regulated by iron availability. Under steady state conditions, DELE1 is degraded by the mitochondrial matrix-resident protease LONP1 soon after mitochondrial import. Upon iron chelation, DELE1 import is arrested, thereby stabilizing DELE1 on the mitochondrial surface to activate the HRI-mediated integrated stress response (ISR). Moreover, depletion of the mitochondrial ABC transporter ABCB7 that is involved in iron-sulfur cluster (ISC) metabolism markedly abrogates iron deficiency-induced ISR activation, suggesting the possible involvement of ISC-related molecules in this activation. Our findings highlight mitochondrial import regulation of DELE1 as the core component of a previously unrecognized iron monitoring system that connects the mitochondria to the cytosol.

cell biology↗

bioRxiv2021

Prediction of broad chemical toxicities using induced pluripotent stem cells and gene networks by transfer learning from embryonic stem cell data

The assessment of toxic chemicals using animals has limited applicability to humans. Moreover, from the perspective of animal protection, effective alternatives are also desired. Previously, we developed a method that combines developmental toxicity testing based on undifferentiated human embryonic stem (ES) cells (KhES-3) and gene networks. We showed that [≥] 95% accurate predictions could be achieved for neurotoxins, genotoxic carcinogens, and non-genotoxic carcinogens. Here, we expanded this method to predict broad toxicities and predicted the toxicity of 24 chemicals in six categories (neurotoxins, cardiotoxins, hepatotoxins, nephrotoxins [glomerular nephrotoxins/tubular nephrotoxins], and non-genotoxic carcinogens) and achieved high prediction accuracy (AUC = 0.90-1.00) in all categories. Moreover, to develop a testing system with fewer ethical issues, we screened for an induced pluripotent stem (iPS) cell line on the basis of cytotoxic sensitivity and used this line to predict toxicity in the six categories based on the gene networks of iPS cells using transfer learning from the ES cell gene networks. We successfully predicted toxicities in four toxin categories (neurotoxins, hepatotoxins, glomerular nephrotoxins, and non-genotoxic carcinogens) at high accuracy (AUC = 0.82-0.99). These results demonstrate that the prediction of chemical toxicity is possible even with iPS cells by transfer learning once a gene expression database has been developed from an ES cell line. This method holds promise for tailor-made safety evaluations using individual iPS cells.

pharmacology and toxicology↗

bioRxiv2021

Discovery of bactericides as an acute mitochondrial membrane damage inducer

Mitochondria evolved from endosymbiotic bacteria to become essential organelles of eukaryotic cells. The defined lipid composition and structure of mitochondrial membranes are critical for the proper functioning of mitochondria. However, mitochondrial stress responses that help maintain the integrity of mitochondrial membranes against internal or external insults are not well understood. One reason for this lack of insight is the absence of efficient tools to specifically damage mitochondrial membranes. Here, through a compound screen originally aimed at identifying inhibitors of the inner mitochondrial membrane (IMM)-resident protease OMA1, we found that two bis-biguanide compounds, Chlorhexidine and Alexidine, modified OMA1 activity by altering the integrity of the IMM. Interestingly, these compounds are well-known bactericides whose mechanism of action has centered on their damage-inducing activity on bacterial membranes. We found Alexidine binds to the IMM likely through the electrostatic interaction driven by the membrane potential as well as an affinity for anionic phospholipids. Electron microscopic analysis revealed that Alexidine severely perturbated the IMM, especially the cristae structure. Along with this, we observed the altered localization of IMM-resident membrane-shaping proteins, including Mic60. Notably, Alexidine evoked a specific transcriptional/proteostasis signature that was not induced by other typical mitochondrial stressors, highlighting the unique property of Alexidine as a novel mitochondrial membrane stressor. Our findings provide a chemical-biological tool that can induce acute and selective perturbation of the IMM integrity, which should enable the delineation of mitochondrial stress-signaling pathways required to maintain the mitochondrial membrane homeostasis.

cell biology↗

bioRxiv2020

Acetylation-mediated phase control of the nucleolus regulates cellular acetyl-CoA responses

The metabolite acetyl-CoA serves as an essential element for a wide range of cellular functions including ATP production, lipid synthesis and protein acetylation. Intracellular acetyl-CoA concentrations are associated with nutrient availability, but the mechanisms by which a cell responds to fluctuations in acetyl-CoA levels remain elusive. Here, we generate a cell system to selectively manipulate the nucleo-cytoplasmic levels of acetyl-CoA using CRISPR-mediated gene editing and acetate supplementation of the culture media. Using this system and quantitative omics analyses, we demonstrate that acetyl-CoA depletion alters the integrity of the nucleolus, impairing ribosomal RNA synthesis and evoking the ribosomal protein-dependent activation of p53. This nucleolar remodeling appears to be mediated through the class IIa HDAC deacetylases regulating the phase state of the nucleolus. Our findings highlight acetylation-mediated control of the nucleolus as an important hub linking acetyl-CoA fluctuations to cellular stress responses.

cell biology↗

bioRxiv2019

Loss of CHCHD2 and CHCHD10 activates OMA1 peptidase to disrupt mitochondrial cristae phenocopying patient mutations in vivo

Dominant mutations in the mitochondrial paralogs CHCHD2 (C2) and CHCHD10 (C10) were recently identified as causing Parkinsons disease and ALS/FTD/myopathy, respectively. Disruption of mitochondrial cristae has been observed in mutant C10 patient tissues and animal models, but the mechanism for this disruption remains controversial. Additionally, C10 patient mutant knock-in (KI) mice were recently reported to activate a mitochondrial integrated stress response (mt-ISR) and develop cardiomyopathy not seen in C10 knockout (KO) mice, calling into question whether mutant C10 pathogenesis is related to C2/C10 normal function or purely toxic gain of function. Here, using the first C2/10 double knockout (DKO) mice, we report that C10 pathogenesis and the normal function of C2/10 are intimately linked. Similar to patients with C10 mutations, we found that C2/10 DKO mice (but not either single KO mice) have disrupted mitochondrial cristae, due to cleavage of the mitochondrial shaping protein L-OPA1 by the stress-induced peptidase OMA1. OMA1 was found to be activated similarly in affected tissues of mutant C10 KI mice, demonstrating that L-OPA1 cleavage is a novel mechanism for cristae abnormalities due to both C10 mutation and C2/C10 loss, and that OMA1, a driver of neurodegeneration in other contexts, may be a therapeutic target. Finally, C2/10 DKO mice partially phenocopied mutant C10 KI mice with the development of cardiomyopathy and activation of the mt-ISR in affected tissues, tying mutant C10 pathogenesis to C2/C10 function.

cell biology↗

bioRxiv2018

Nanopore formation in the cuticle of the insect olfactory sensillum

Insects sense odorants through small (50-200-nm diameter) pores in the cuticle covering the olfactory sensilla. These nanopores serve as a filter, preventing the entry of larger airborne particles and limiting water loss. Here we show that the nanopores in Drosophila originate from a curved ultrathin film formed in the outermost layer of the cuticle, secreted from specialized plasma membrane protrusions. The gore-tex/Osiris23 gene, encoding an endosomal protein, is required for nanopore formation and odor receptivity, and is expressed specifically in developing olfactory shaft cells. The 24-member Osiris gene family is expressed in various cuticle-secreting cells, and is found only in insect genomes. Some Osiris mutants show defective cuticle-associated functions, suggesting that Osiris genes may provide a platform for investigating functional surface nano-fabrication in insects.\n\nOne Sentence SummaryAn insect-specific endosomal protein promotes the formation of nano-scale pore structures of the apical extracellular matrix.

developmental biology↗

bioRxiv2017

Improved Split Fluorescent Proteins For Endogenous Protein Labeling

Self-complementing split fluorescent proteins (FPs) have been widely used for protein labeling, visualization of subcellular protein localization, and detection of cell-cell contact. To expand this toolset, we have developed a screening strategy for the direct engineering of self-complementing split FPs. Via this strategy, we have generated a yellow-green split-mNeonGreen21-10/11 that improves the ratio of complemented signal to the background of FP1-10-expressing cells compared to the commonly used split-GFP1-10/11, as well as a 10-fold brighter red-colored split-sfCherry21-10/11. Based on split-sfCherry2, we have engineered a photoactivatable variant that enables single-molecule localization-based super-resolution microscopy. We have demonstrated dual-color endogenous protein tagging with sfCherry211 and GFP11, revealing that endoplasmic reticulum translocon complex Sec61B has reduced abundance in certain peripheral tubules. These new split FPs not only offer multiple colors for imaging interaction networks of endogenous proteins, but also hold the potential to provide orthogonal handles for biochemical isolation of native protein complexes.

bioengineering↗