Biology subjects

Hata, A.

Publications and source records attributed to Hata, A..

12 recordsLinked to original sources

bioRxiv2026

Oxidized protein states define metastatic fitness in lung cancer

AbstractReactive oxygen species (ROS) are a pervasive feature of human cancers, yet the protein targets through which ROS-regulated cell states shape tumor biology remains poorly understood. Here, using cysteine chemical proteomics, we define signatures of protein states under distinct cellular ROS environments that capture protein oxidation and conformational changes. Quantifying these signatures in primary lung tumors and brain metastases revealed a surprising enrichment of oxidative states in metastasis. To determine how these states support fitness, we performed genome-wide CRISPR screens and identified the mitochondrial Complex I subunit NDUFA10 as a key oxidation-dependent vulnerability. Oxidation of NDUFA10*Cys253 supports Complex I function through a previously unrecognized nucleotide kinase activity that maintains mitochondrial DNA levels. Enforcing a reduced conformation in NDUFA10 disrupts brain metastatic colonization in vivo. These findings establish ROS regulated protein states as a functional layer of tumor fitness, providing a framework for identifying redox-dependent mechanisms that support cancer progression.

Cancer Biology↗

bioRxiv2025

Antibody peptide epitope conjugates for αPD-1 therapy-resistant head and neck squamous cell carcinoma

Poor tumor antigenicity is an important cause of non-response to immune checkpoint blockade (ICB)-therapy in many cancer patients and mandates new treatment strategies. Here we explore the use of proteolytically activated antibody-peptide epitope conjugates (APECs) to redirect the immunological effector activities of tumor-infiltrating antiviral bystander CTLs against head and neck squamous cell carcinoma (HNSCC) by loading cancer cell surface MHC I proteins with viral peptides. We find that inflationary T cell memory responses against common viral pathogens such as CMV and EBV unfold superior anti-tumor activity compared to conventional memory responses under APEC therapy in an ICB-resistant preclinical model of HNSCC. Mechanistically, APEC activation required cancer cell-intrinsic protease activity, even for proteases expressed by cells of the tumor stroma. Data mining and functional screening identified the protease activity of plasminogen activator urokinase (PLAU) as widely shared between human HNSCC cancers and as a highly efficient proteolytic activator of APECs. Furthermore, peripheral blood analysis in HNSCC patients reliably predicts the specificity, magnitude, and quality of intratumoral bystander CTL, thus allowing for the screening of HNSCC patients who may benefit most from APEC therapy.

immunology↗

bioRxiv2025

Suppression of PP2A-B56α Drives EMT in EGFR Mutant Non-Small Cell Lung Cancer

Lung cancer is the leading cause of cancer-related deaths in the United States and [~]50% of these patients present with metastatic disease at diagnosis. Epithelial-to-Mesenchymal Transition (EMT) is an important initiating step in the metastatic cascade that allows cells to acquire the migratory and invasive phenotypes necessary for dissemination. The transcriptional reprogramming that takes place during EMT has been well described in multiple cancer types; however, the posttranslational regulatory mechanisms that govern EMT are poorly understood. Protein Phosphatase 2A (PP2A) is serine/threonine (ser/thr) phosphatase that accounts for 50% of cellular ser/thr phosphatase activity and is critically important in regulating signaling homeostasis. PP2A dysregulation has been implicated in cell state regulation, EMT, and metastasis, but the roles of individual PP2A complexes are poorly understood. Our data indicate that suppression of the specific PP2A complex, PP2A-B56, results in decreased expression of epithelial markers and increased expression of mesenchymal markers consistent with EMT. These molecular changes are associated with migratory and invasive phenotypes both in vitro and in vivo. Furthermore, these migratory phenotypes can be rescued with B56 overexpression. Together, these findings implicate B56 as a key regulator of cellular plasticity and highlight the dynamic nature by which PP2A-B56 posttranslationally regulates NSCLC EMT.

cancer biology↗

bioRxiv2025

Essential Role of Protein Kinase R in the Pathogenesis of Pulmonary Veno-occlusive Disease

Pulmonary veno-occlusive disease (PVOD) is a rare and severe subtype of pulmonary arterial hypertension, marked by progressive remodeling of small pulmonary arteries and veins with no therapies. Using a mitomycin C (MMC)-induced rat model, we previously demonstrated that protein kinase R (PKR)-mediated integrated stress response (ISR) drives endothelial dysfunction and vascular remodeling. To determine if PKR is the sole mediator of ISR and the pathogenesis, we treated control (Ctrl) and PKR knockout (KO) mice with the same dose of MMC. Consistent with rat data, Ctrl mice displayed ISR activation, vascular remodeling, and pulmonary hypertension after MMC treatment, while KO mice showed none of these phenotypes. Proteomic analysis revealed that MMC-mediated ISR activation attenuates protein synthesis in Ctrl but not in KO mice. These findings underscore the significance of PKR-dependent ISR activation and subsequent perturbation of proteostasis as central mechanisms driving PVOD pathogenesis and identifying PKR as a promising therapeutic target.

cell biology↗

bioRxiv2024

Systematic Targeting of Protein Complexes with Molecular COUPLrs

Molecular glues that engage protein complexes have transformed the study of cell biology and have had a direct impact on clinical oncology. However, the identification of new glue classes and their corresponding protein complexes has remained largely serendipitous. To overcome this challenge, we report the development of molecular COUPLrs, elaborated small molecules flanked by two cysteine-reactive warheads, as well as CONNECT, an integrated chemical proteomic platform for target deconvolution. By profiling a library of molecular COUPLrs across 13 cancer cell lines, we uncovered hundreds of proteins that can be coupled together, including in some cases in mutant selective fashions. We develop an advanced COUPLr for the oncogene EML4-ALK, which engages the fusion outside of its kinase domain, restricts protein dynamics, and disrupts EML4-ALK signaling. Collectively, molecular COUPLrs substantially expand the scope of proteins that can be chemically connected, providing an unbiased approach to identify small molecules that target protein complexes.

systems biology↗

bioRxiv2024

Depletion of Protein Phosphatase 1 Results in Persistent Activation of the Integrated Stress Response and Age-Associated Exacerbation of Pulmonary Veno-Occlusive Disease

Pulmonary veno-occlusive disease (PVOD) is a form of pulmonary hypertension that affects individuals across the age spectrum. PVOD is characterized by the obstruction of small pulmonary vessels, causing increased pulmonary artery (PA) pressure and leading to right ventricular heart (RV) failure. Previous research showed that the administration of Mitomycin-C (MMC) in rats mediates PVOD through the activation of the eukaryotic initiation factor 2 (eIF2) kinase PKR and the integrated stress response (ISR), resulting in the impairment of vascular endothelial junctional structure and barrier function. In this study, we reveal that older rats experience more severe pulmonary vascular remodeling and RV hypertrophy than younger rats after MMC treatment due to lower levels of protein phosphatase 1, leading to prolonged eIF2 phosphorylation and ISR activation. We demonstrate that pharmacological blocking of the PKR-ISR pathway mitigates PVOD symptoms in both age groups, suggesting targeting the PKR-ISR axis as a potential PVOD therapeutic strategy.

cell biology↗

bioRxiv2023

Reversal of pulmonary veno-occlusive disease phenotypes by inhibition of the integrated stress response

Pulmonary veno-occlusive disease (PVOD) is a rare form of pulmonary hypertension arising from EIF2AK4 gene mutations or mitomycin C (MMC) administration. The lack of effective PVOD therapies is compounded by a limited understanding of the mechanisms driving the vascular remodeling in PVOD. We show that the administration of MMC in rats mediates the activation of protein kinase R (PKR) and the integrated stress response (ISR), which lead to the release of the endothelial adhesion molecule VE-Cadherin in the complex with Rad51 to the circulation, disruption of endothelial barrier, and vascular remodeling. Pharmacological inhibition of PKR or ISR attenuates the depletion of VE-Cadherin, elevation of vascular permeability, and vascular remodeling instigated by MMC, suggesting potential clinical intervention for PVOD. Finally, the severity of PVOD phenotypes was increased by a heterozygous BMPR2 mutation that truncates the carboxyl tail of BMPR2, underscoring the role of deregulated BMP signal in the development of PVOD.

cell biology↗

bioRxiv2023

In vivo metabolomics identifies CD38 as an emergent vulnerability in LKB1-mutant lung cancer

LKB1/STK11 is a serine/threonine kinase that plays a major role in controlling cell metabolism, resulting in potential therapeutic vulnerabilities in LKB1-mutant cancers. Here, we identify the NAD+ degrading ectoenzyme, CD38, as a new target in LKB1-mutant NSCLC. Metabolic profiling of genetically engineered mouse models (GEMMs) revealed that LKB1 mutant lung cancers have a striking increase in ADP-ribose, a breakdown product of the critical redox co-factor, NAD+. Surprisingly, compared with other genetic subsets, murine and human LKB1-mutant NSCLC show marked overexpression of the NAD+-catabolizing ectoenzyme, CD38 on the surface of tumor cells. Loss of LKB1 or inactivation of Salt-Inducible Kinases (SIKs)--key downstream effectors of LKB1-- induces CD38 transcription induction via a CREB binding site in the CD38 promoter. Treatment with the FDA-approved anti-CD38 antibody, daratumumab, inhibited growth of LKB1-mutant NSCLC xenografts. Together, these results reveal CD38 as a promising therapeutic target in patients with LKB1 mutant lung cancer. SIGNIFICANCELoss-of-function mutations in the LKB1 tumor suppressor of lung adenocarcinoma patients and are associated with resistance to current treatments. Our study identified CD38 as a potential therapeutic target that is highly overexpressed in this specific subtype of cancer, associated with a shift in NAD homeostasis.

cancer biology↗

bioRxiv2022

Essential role of the amino-terminal region of Drosha for the Microprocessor function

The ribonuclease (RNase) III enzyme Drosha enables processing of microRNA (miRNA) primary transcripts (pri-miRNAs) and control of ribosomal protein (RP) biogenesis by the Microprocessor. The extensively studied carboxyl-terminal half of Drosha is sufficient to crop pri-miRNAs in vitro, but the function of the evolutionarily conserved Drosha amino-terminal region (NTR) is unknown, despite it harboring mutations linked to a hereditary vascular disorder. Here, we provide evidence that, when replacing the endogenous Drosha, a mutant missing the NTR ({Delta}N-Drosha) fails to associate with endogenous pri-miRNAs and to support the expression of all miRNAs, except the miR-183 cluster. Surprisingly, Argonaute2 (Ago2) associates with and cleaves pri-miR-183 in {Delta}N-Drosha cells and in Drosha-depleted cells. {Delta}N-Drosha is also unable to inhibit RP biogenesis upon serum starvation. Thus, Drosha NTR is essential for pri-miRNA processing and RP biogenesis in vivo, and Ago2 can process the miR-183 cluster in the absence of Drosha.

molecular biology↗

bioRxiv2020

Cycling cancer persister cells arise from lineages with distinct transcriptional and metabolic programs

Non-genetic mechanisms have recently emerged as important drivers of therapy failure in cancer (Salgia and Kulkarni, 2018), where some cancer cells can enter a reversible drug-tolerant persister state in response to treatment (Vallette et al., 2019). While most cancer persisters, like their bacterial counterparts, remain arrested in the presence of drug, a rare subset of cancer persisters can re-enter the cell cycle under constitutive drug treatment (Sharma et al., 2010). Little is known about the non-genetic mechanisms that enable cancer persisters to maintain proliferative capacity in the presence of drug. Here, using time-lapse imaging, we found that cycling persisters emerge early in the course of treatment of EGFR-mutant lung cancer cells with the EGFR inhibitor osimertinib. To study this rare, transiently-resistant, proliferative persister population we developed Watermelon, a new high-complexity expressed barcode lentiviral library for simultaneous tracing each cells clonal origin, proliferative state, and transcriptional state. Analysis of Watermelon-transduced PC9 cells demonstrated that cycling and non-cycling persisters arise from different pre-existing cell lineages with distinct transcriptional and metabolic programs. The proliferative capacity of persisters is associated with an upregulation of antioxidant gene programs and a metabolic shift to fatty acid oxidation in specific subpopulations of tumor cells. Mitigating oxidative stress or blocking metabolic reprograming significantly alters the fraction of cycling persister cells. In human tumors, programs associated with cycling persisters were induced in malignant cells in response to multiple tyrosine kinase inhibitors. The Watermelon system enabled the identification of rare persister lineages, that are preferentially poised through specific gene programs to proliferate under drug pressure, thus exposing new vulnerabilities that can be targeted to delay or even prevent disease recurrence.

cancer biology↗

bioRxiv2020

Control of ribosomal protein synthesis by Microprocessor complex

Ribosome biogenesis in eukaryotes requires stoichiometric production and assembly of 80 ribosomal proteins (RPs) and 4 ribosomal RNAs, and its rate must be coordinated with cellular growth. The indispensable regulator of RP biosynthesis is the 5-terminal oligopyrimidine (TOP) motif, spanning the transcription start site of all RP genes. Here we show that the Microprocessor complex, previously linked to the first step of processing microRNAs (miRNAs), coregulates RP expression by binding the TOP motif of nascent RP mRNAs and stimulating transcription elongation via resolution of DNA/RNA hybrids. Cell growth arrest triggers nuclear export and degradation of the Microprocessor protein Drosha by the E3 ubiquitin ligase Nedd4, accumulation of DNA/RNA hybrids at RP gene loci, decreased RP synthesis, and ribosome deficiency, hence synchronizing ribosome production with cell growth. Conditional deletion of Drosha in erythroid progenitors phenocopies human ribosomopathies, in which ribosomal insufficiency leads to anemia. Outlining a miRNA-independent role of the Microprocessor complex at the interphase between cell growth and ribosome biogenesis offers a new paradigm by which cells alter their protein biosynthetic capacity and cellular metabolism.

molecular biology↗

bioRxiv2019

Tissue-specific 3 prime end-adenylation of miR-125b mediates cell survival

Next-generation sequencing has uncovered microRNAs (miRNAs) that undergo sequence modifications, known as isomiRs. Their physiological significance, however, remains uncertain, partly because they generally comprise a small fraction of total miRNAs. Here we report that more than 60% of miR-125b, one of the most abundant miRNAs in vascular smooth muscle cells (vSMC), exists as an edited isoform containing a non-templated adenosine residue at the 3 prime-end (miR-125b+A). The properties of miR-125b+A, such as stability and subcellular localization, are similar to those of canonical miR-125b, but miR-125b+A more potently inhibits the expression of a subgroup of targets, including the apoptosis effector Caspase-6 (CASP6). In the CASP6 transcript, adenylated miR125b preferentially targets a conserved, atypical site, with an unusual 36 nucleotides loop between seed sequence and 3 prime-end supplementary site. PAP associated domain containing 2 (PAPD2) is responsible for monoadenylation of miR-125b. Downregulation of PAPD2 results in the conversion of miR-125b+A to miR-125b, derepression of CASP6, and sensitization of vSMC to apoptotic stimuli. Thus, atypical site recognition by a tissue-specific isomiR fulfills a pro-survival role.

molecular biology↗