Biology subjects

Kitamura, S.

Publications and source records attributed to Kitamura, S..

14 recordsLinked to original sources

bioRxiv2025

Claudin-1 Inhibitor PDS-0330 Ameliorates Diabetic Kidney Disease by Suppressing Src/Akt/mTOR Signaling Pathway in Podocytes

IntroductionRecent studies have reported that claudin-1, which is reactively expressed in malignant tumors and inflammatory diseases, plays an important role in disease progression. In diabetic kidney disease (DKD), upregulated expression of claudin-1 in podocytes has also been shown to contribute to disease progression. However, it remains unclear whether claudin-1 itself could be a therapeutic target in DKD. In this study, we investigated whether the claudin-1 inhibitor PDS-0330 could ameliorate DKD. MethodsFive-week-old male C57BL/6J mice were fed either a high-fat diet (HFD) or a normal diet (ND). At 15 weeks of age, PDS-0330 (Inh) or vehicle as control (Ctrl) was administered orally once per week for 4 weeks. At the end of the treatment period, blood, urine, and kidney samples were collected. In in vitro study, immortalized podocytes were treated with Inh or Ctrl and cultured for 48 hours in either normal glucose medium (5.5 mM; NG) or high glucose medium (25 mM; HG), after which proteins were extracted for analysis. ResultsMice fed an HFD showed significant increases in body weight and serum glucose levels compared with ND mice, and these parameters were not significantly affected by Inh treatment. HFD mice treated with Ctrl (HFD-Ctrl) exhibited significantly higher urinary albumin excretion than ND mice treated with Ctrl (ND-Ctrl), whereas the Inh-treated HFD mice (HFD-Inh) showed a significant reduction. Transmission electron microscopy revealed foot process effacement in HFD-Ctrl podocytes, which was markedly improved in HFD-Inh mice. Immunofluorescence staining demonstrated claudin-1 expression in podocytes of HFD mice. Furthermore, phospho-mTOR staining in podocytes was significantly increased in HFD-Ctrl compared with ND-Ctrl and was significantly attenuated in HFD-Inh. Western blot analysis of kidney samples revealed activation of the Src/Akt/mTOR signaling pathway in HFD-Ctrl mice, which was significantly reduced in HFD-Inh mice. In in vitro study, Ctrl-treated podocytes cultured in HG (HG-Ctrl) showed significant activation of Src/Akt/mTOR signaling compared with those in NG (NG-Ctrl). This activation was significantly suppressed in Inh-treated podocytes (HG-Inh). ConclusionThese findings suggest that podocyte claudin-1 could be a potential therapeutic target in DKD.

physiology↗

bioRxiv2025

Inactivation of peptidoglycan remodeling promotes antibiotic susceptibility in vancomycin-resistant Enterococcus faecium

Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of healthcare-associated infections globally and demands new approaches for treatment. Here we show that genetic and pharmacological inactivation of a highly conserved NlpC/P60 peptidoglycan hydrolase, secreted antigen A (SagA), enhanced vancomycin susceptibility of VREfm ex vivo and in vivo. Notably, genetic deletion of sagA impaired VREfm peptidoglycan remodeling, growth and increased the activity of vancomycin. We then identified first-in-class covalent NlpC/P60 peptidoglycan hydrolase inhibitors and demonstrated that pharmacological inactivation of SagA activity also impaired peptidoglycan remodeling and increased the efficacy of vancomycin across genetically distinct VREfm clinical isolates. Our study reveals peptidoglycan hydrolases are druggable targets whose inactivation improves the efficacy of vancomycin against VREfm.

microbiology↗

bioRxiv2025

Exploiting an Epigenetic Resistance Mechanism to PI3 Kinase Inhibition in Leukemic Stem Cells

Acquired non-genetic resistance mechanisms to existing therapies contribute to poor outcomes for acute myeloid leukemia (AML) patients, and inability to target leukemic stem cells (LSCs) can lead to relapse. To overcome these challenges, we tested whether LSCs have dependencies on PI3 kinase (PI3K). We found that LSCs are susceptible to isoform-selective targeting of PI3K and are particularly dependent on the P110 alpha isoform of PI3K. We discovered that PI3K inactivation leads to dynamic changes in EZH2/PRC2 function in leukemic cells, and we uncovered downregulation of EZH2 protein levels as a resistance mechanism in response to PI3K inhibition. We found that PI3K inhibition in AML cells can lead to compensatory upregulation of EZH1, and that EZH1 knockdown can sensitize AML cells to PI3K inhibition. We leveraged this resistance mechanism by combining a PI3K inhibitor with an EZH1/2 dual inhibitor, which successfully overcomes the acquired resistance and leads to sustained targeting of AML cells ex vivo and in murine AML and PDX models in vivo. This study identifies a promising novel therapeutic regimen for targeting LSCs in AML.

cancer biology↗

bioRxiv2025

Light stimulation system for measuring pupillary light responses based on Maxwellian view optical system using a retina presentation type viewfinder

BackgroundMelanopsin-expressing intrinsically photosensitive retinal ganglion cells (ipRGC) contribute predominantly to non-image-forming effects of light, such as light-induced circadian phase shift, melatonin suppression, and pupillary light reflex. Post-illumination pupil response (PIPR) has been well-used for the evaluation of ipRGC sensitivity for humans since it is able to detect ipRGC function independently from conventional cones. However, pharmacological mydriasis or a specialized light stimulation system, such as the Maxwellian view (MV) optical system, is required to avoid dynamic pupil constriction in the stimulated eye for effective PIPR measurements, which makes these approaches less practical and difficult to implement in standard experimental settings. In this context, we propose the application of a retinal projection viewfinder based on the MV system as a practical approach for measuring PIPR, and evaluate the feasibility of this approach by comparing its performance with a typical LED-based optical system. MethodsTwenty-two healthy participants underwent pupillometry using both the MV-based viewfinder and a typical LED-based system. Monochromatic red and blue light stimuli were presented for durations of 1 and 10 seconds. Pupil responses, including maximum constriction, PIPR amplitude after 6 seconds from the light offset, area under the curve (AUC) values of PIPR, and sustained slopes, were analyzed using a linear mixed-effects model to assess the differences between the two systems. ResultsThe MV-based viewfinder significantly enhanced net PIPR amplitude (p < 0.05) and sustained slope (p < 0.01) during 10-second light stimulation compared to the LED system, demonstrating its capability to effectively measure ipRGC-driven responses. In contrast, no significant differences were observed in the net AUC values. These results highlight that the MV-based viewfinder enables effective PIPR measurements by delivering constant and controlled light stimulation directly to the retina, minimizing the effects of dynamic pupil constriction during light stimulation. ConclusionsThe MV-based viewfinder showed feasibility as an effective method for measuring PIPR without requiring pharmacological dilation or complex optical instrumentation. This approach has strong potential for advancing the assessment of human ipRGC function using pupillary responses.

neuroscience↗

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↗

bioRxiv2025

Development and Validation of a Stem Cell-Based Kidney Organoid Platform for Nephrotoxicity Assessment

Background and hypothesisRecent cases of acute kidney injury (AKI) in Japan have been linked to the Beni-koji CholesteHelp supplement. Renal biopsies from affected patients revealed tubular damage, and puberulic acid was subsequently identified as a potential nephrotoxic contaminant. Recognizing the urgent need for a reliable in vitro nephrotoxicity testing platform, we hypothesized that a kidney organoid-based system could replicate nephrotoxic injury and help identify novel nephrotoxicants. In this study, we developed a screening model using kidney organoids derived from adult rat kidney stem (KS) cells and applied it to evaluate the toxicity of puberulic acid. MethodsKidney organoids were generated from KS cells and exposed to established nephrotoxicants, including cisplatin and gentamicin, to validate the model. The nephrotoxicity of puberulic acid was evaluated using both KS cell-derived organoids and wild-type mice. Nephrotoxicity was assessed by morphological changes, Kim-1 mRNA expression, transmission electron microscopy (TEM), and analysis of markers related to mitochondrial injury, oxidative stress, and apoptosis. ResultsThe kidney organoids reproduced morphological features of injury induced by known nephrotoxins and showed significant upregulation of Kim-1 mRNA. Puberulic acid-treated organoids displayed ultrastructural features consistent with acute tubular necrosis (ATN) and increased Kim-1 expression. In vivo, puberulic acid-exposed mice exhibited impaired renal function and histological findings consistent with ATN. Both in vitro and in vivo models revealed mitochondrial structural abnormalities and reduced expression of cytochrome c oxidase subunit IV (COX-IV). Additionally, oxidative stress and apoptotic markers, including 8-hydroxy-2-deoxyguanosine (8-OHdG) and cleaved caspase-3, were significantly elevated, suggesting that puberulic acid induces mitochondrial dysfunction and oxidative stress, leading to tubular cell death. ConclusionPuberulic acid-induced nephrotoxicity was demonstrated using our kidney organoid model. KS cell-derived kidney organoids provide a simple, reproducible, and rapid platform for nephrotoxicity assessment, which contribute to a reduction of animal use in toxicology research.

pharmacology and toxicology↗

bioRxiv2025

TTLL4 glutamyltransferase is a therapeutic target for NPM1-mutated acute myeloid leukemia

NPM1-mutated acute myeloid leukemia (AML) is defined by aberrant cytoplasmic localization of the mutant NPM1c protein, and therapeutic strategies targeting this specific disease remain limited. Here, we identify TTLL4, a mono-glutamate glutamyltransferase, as a selective vulnerability in NPM1c AML. TTLL4 catalyzes post-translational hyper-glutamylation of NPM1c at E126, stabilizes its cytoplasmic localization and promotes a differentiation block in leukemic cells. Multiple genetic TTLL4 inactivation approaches in human NPM1c-mutant cell lines reduce NPM1c glutamylation, trigger myeloid differentiation, and impair proliferation. Transcriptomic analyses show that TTLL4 knockdown pheno-copies NPM1c degradation and aligns with KMT2A and XPO1-targeted gene expression programs. Furthermore, Ttll4 knockout significantly prolonged survival in an NPM1c/NRAS-driven mouse AML model and promoted differentiation. We identify a small molecule, EN7, that selectively inhibits TTLL4 and recapitulates these phenotypes in NPM1c+ cells. These findings identify glutamylation as a new axis of leukemic regulation and highlight TTLL4 as a druggable epigenetic regulator in NPM1c AML.

cancer biology↗

bioRxiv2024

High-throughput diversification of protein-ligand surfaces to discover chemical inducers of proximity

Chemical inducers of proximity (CIPs) stabilize biomolecular interactions, often causing an emergent rewiring of cellular biochemistry1,2. While rational design strategies can expedite the discovery of heterobifunctional CIPs, monovalent, molecular glue-like CIPs have relied predominantly on serendipity3. Envisioning a prospective approach to discover molecular glues for a pre-selected target, we hypothesized that pre-existing ligands could be systematically decorated with chemical modifications to empirically discover protein-ligand surfaces that are tuned to cooperatively engage another protein interface. Here, we used sulfur(VI)-fluoride exchange (SuFEx)-based high-throughput chemistry (HTC) to install 3,163 structurally diverse chemical building blocks onto ENL and BRD4 ligands and then screened the crude products for degrader activity. This revealed dHTC1, a potent, selective, and stereochemistry-dependent degrader of ENL. It recruits CRL4CRBN to ENL through an extended interface of protein-protein and protein-ligand contacts, but only after pre-forming the ENL:dHTC1 complex. We also characterized two structurally distinct BRD4 degraders, including dHTC3, a molecular glue that selectively dimerizes the first bromodomain of BRD4 to SCFFBXO3, an E3 ligase not previously accessible for chemical rewiring. Altogether, this study introduces HTC as a facile tool to discover new CIPs and actionable cellular effectors of proximity pharmacology.

biochemistry↗

bioRxiv2024

In vivo-Active Soluble Epoxide Hydrolase-targeting PROTACs with Improved Potency and Stability

Soluble epoxide hydrolase (sEH) is a bifunctional enzyme involved in fatty acid metabolism and promising drug target. We previously reported first-generation sEH proteolysis-targeting chimeras (PROTACs) with limited degradation potency and low aqueous and metabolic stability. Herein, we report the development of next-generation sEH PROTAC molecules with improved stability and degradation potency. One of the most potent molecules (compound 8) exhibits a half-maximal degradation concentration in the sub-nM range, is stable in vivo, and effectively degrades sEH in mouse livers and brown adipose tissues. Given the role played by sEH in many metabolic and nonmetabolic diseases, the presented molecules provide useful chemical probes for the study of sEH biology. They also hold potential for therapeutic development against a range of disease conditions, including diabetes, inflammation, and metabolic disorders.

biochemistry↗

bioRxiv2022

PROTAC-mediated selective degradation of cytosolic soluble epoxide hydrolase enhances ER-stress reduction

Soluble epoxide hydrolase (sEH) is a bifunctional enzyme responsible for lipid metabolism and is a promising drug target. Here, we report the first-in-class PROTACs small molecule degraders of sEH. Our optimized PROTAC selectively targets the degradation of cytosolic but not peroxisomal sEH, resulting in exquisite spatiotemporal control. Remarkably, our sEH PROTAC molecule has higher potency in cellular assays compared to the parent sEH inhibitor as measured by significantly reduced ER stress. Interestingly, our mechanistic data indicate that our PROTAC directs degradation of cytosolic sEH via the lysosome, not through the proteasome. The molecules presented here are useful chemical probes to study the biology of sEH with the potential for therapeutic development. Broadly, our results represent a proof-of-concept for the superior cellular potency of sEH degradation over sEH enzymatic inhibition, as well as subcellular compartment-selective modulation of a protein by PROTACs. HighlightsO_LIFirst-in-class soluble epoxide hydrolase (sEH) small-molecule degraders. C_LIO_LISelective degradation of cytosolic but not peroxisomal sEH. C_LIO_LISignificant and stable reduction in sEH protein levels, leading to enhanced cellular efficacy in ER stress reduction relative to the parent inhibitor. C_LI

biochemistry↗

bioRxiv2020

Chemical inhibition of ENL/AF9 YEATS domains in acute leukemia

Transcriptional co-regulators, which mediate chromatin-dependent transcriptional signaling, represent tractable targets to modulate tumorigenic gene expression programs with small molecules. Genetic loss-of-function studies have recently implicated the transcriptional co-activator, ENL, as a selective requirement for the survival of acute leukemia and highlighted an essential role for its chromatin reader YEATS domain. Motivated by these discoveries, we executed a screen of nearly 300,000 small molecules and identified an amido-imidazopyridine inhibitor of the ENL YEATS domain (IC50 = 7 {micro}M). Leveraging a SuFEx-based high-throughput approach to medicinal chemistry optimization, we discovered SR-0813 (IC50 = 25 nM), a potent and selective ENL/AF9 YEATS domain inhibitor that exclusively inhibits the growth of ENL-dependent leukemia cell lines. Armed with this tool and a first-in-class ENL PROTAC, SR-1114, we detailed the response of AML cells to pharmacological ENL disruption for the first time. Most notably, displacement of ENL from chromatin by SR-0813 elicited a strikingly selective suppression of ENL target genes, including HOXA9/10, MYB, MYC and a number of other leukemia proto-oncogenes. Our study reproduces a number of key observations previously made by CRISPR/Cas9 loss of function and dTAG-mediated degradation, and therefore, both reinforces ENL as an emerging leukemia target and validates SR-0813 as a high-quality chemical probe.

cancer biology↗

bioRxiv2020

An influenza A hemagglutinin small-molecule fusion inhibitor identified by a new high-throughput fluorescence polarization screen.

Influenza hemagglutinin (HA) glycoprotein is the primary surface antigen targeted by the host immune response and a focus for development of novel vaccines, broadly neutralizing antibodies (bnAbs) and therapeutics. HA enables viral entry into host cells via receptor binding and membrane fusion and is a validated target for drug discovery. However, to date, only a very few bona fide small molecules have been reported against the HA. To identity new antiviral lead candidates against the highly conserved fusion machinery in the HA stem, we synthesized a fluorescence-polarization probe based on a recently described neutralizing cyclic peptide P7 derived from the complementarity-determining region loops of human bnAbs FI6v3 and CR9114 against the HA stem. We then designed a robust binding assay compatible with high-throughput screening to identify molecules with low M to nM affinity to influenza A group 1 HAs. Our simple, low-cost, and efficient in vitro assay was used to screen H1/Puerto Rico/8/1934 HA trimer against approximately 72,000 compounds. The crystal structure of H1/Puerto Rico/8/1934 HA in complex with our best hit compound F0045(S) confirmed that it binds to pockets in the HA stem similar to bnAbs FI6v3 and CR9114, cyclic peptide P7, and small molecule inhibitor JNJ4796. F0045 is enantioselective against a panel of group 1 HAs and F0045(S) exhibits in vitro neutralization activity against multiple H1N1 and H5N1 strains. Our assay, compound characterization, and small-molecule candidate should further stimulate the discovery and development of new compounds with unique chemical scaffolds and enhanced influenza antiviral capabilities. SummaryInfluenza hemagglutinin (HA) glycoprotein enables viral entry into host cells and is the main target for antibodies in our immune system. While HA has now been established as a validated target for drug discovery, no FDA-approved small molecules are available that specifically prevent HA from binding host receptors or inhibit its membrane fusion activity and thus prevent infection. We therefore designed a fluorescence polarization probe to enable rapid identification of small molecules that bind to the stem fusion machinery of group 1 HAs. Application of our assay yielded a small molecule to the influenza A group 1 HA stem with antiviral efficacy.

biophysics↗

bioRxiv2019

Transcriptome stability profiling identifies novel and functional MIRNA targets in melanoma cells

RNA half-life is closely related to its cellular physiological function, so stability determinants may have regulatory functions. Micro(mi)RNAs have primarily been studied with respect to post-transcriptional mRNA regulation and target degradation. Here we study the impact of the tumor suppressive melanoma miRNA miR-211 on transcriptome stability and phenotype in the non-pigmented melanoma cell line, A375. Using 5-bromouridine IP chase (BRIC)-seq, transcriptome-wide RNA stability profiles revealed highly regulated genes and pathways important in this melanoma cell line. By combining BRIC-seq, RNA-seq and in silico predictions, we identified both existing and novel direct miR-211 targets. We validated DUSP3 as one such novel miR-211 target, which itself sustains colony formation and invasion in A375 cells via MAPK/PI3K signaling. miRNAs have the capacity to control RNA turnover as a gene expression mechanism, and RNA stability profiling is an excellent tool for interrogating functionally relevant gene regulatory pathways and miRNA targets when combined with other high-throughput and in silico approaches.

cancer biology↗

bioRxiv2018

The Genetic Basis for the Cooperative Bioactivation of Plant Lignans by a Human Gut Bacterial Consortium

Plant-derived lignans, consumed daily by most individuals, are inversely associated with breast cancer; however, their bioactivity is only exerted following gut bacterial conversion to enterolignans. Here, we dissect a four-species bacterial consortium sufficient for all four chemical reactions in this pathway. Comparative genomics and heterologous expression experiments identified the first enzyme in the pathway. Transcriptional profiling (RNAseq) independently identified the same gene and linked a single genomic locus to each of the remaining biotransformations. Remarkably, we detected the complete bacterial lignan metabolism pathway in the majority of human gut microbiomes. Together, these results are an important step towards a molecular genetic understanding of the gut bacterial bioactivation of lignans and other plant secondary metabolites to downstream metabolites relevant to human disease.\n\nOne Sentence SummaryBess et al. provide a first step towards elucidating the molecular genetic basis for the cooperative gut bacterial bioactivation of plant lignans, consumed daily by most individuals, to phytoestrogenic enterolignans.

microbiology↗