Biology subjects

Tsubouchi, K.

Publications and source records attributed to Tsubouchi, K..

5 recordsLinked to original sources

bioRxiv2026

Inflammatory signaling drives SQSTM1-dependent suppression of interferon-γ-induced MHC class I

An immune-inflamed tumor microenvironment features interferon-{gamma} (IFN-{gamma}) and inflammatory cytokines, yet how cancer cells integrate these opposing signals to regulate immunogenicity remains poorly understood. Here, we investigated the effect of interleukin-1{beta} (IL-1{beta}) on IFN-{gamma}-induced major histocompatibility complex class I (MHC-I) expression in non-small cell lung cancer (NSCLC) cells. IL-1{beta} suppressed IFN-{gamma}-induced surface MHC-I expression despite preserved or enhanced expression of antigen presentation-related genes, indicating post-transcriptional regulation. This effect emerged 12-24 h after stimulation and accompanied accelerated MHC-I turnover without altering total protein abundance. RNA sequencing identified selective induction of autophagy-related genes under combined IFN-{gamma} and IL-1{beta} stimulation. Immunofluorescence and biochemical analyses demonstrated MHC-I redistribution to autophagosome-lysosome compartments. Mechanistically, the selective autophagy receptor SQSTM1 associated with MHC-I and was required for its surface downregulation, whereas NBR1 depletion and autophagy or lysosomal inhibition failed to restore MHC-I expression, indicating a nonredundant role for SQSTM1. These findings identify post-translational MHC-I trafficking as an underappreciated regulatory layer linking inflammatory signaling to the canonical IFN-{gamma}-MHC-I axis and reveal an SQSTM1-dependent mechanism controlling MHC-I surface availability in immune-inflamed tumors.

immunology↗

bioRxiv2026

Trajectory inference of epithelial-centered neighborhood profiles reconstructs a pseudo-temporal continuum in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is characterized by complex lung architecture and spatially heterogeneous remodeling, which have hindered integrated analysis of cell-intrinsic activity and intercellular communication during disease progression. Here we profiled six IPF lung specimens comprising more than 630,000 cells using the Xenium 5k panel and developed an epithelial-centered neighborhood profiling framework based on the local cellular composition around each epithelial cell. This approach captured fibrosis-associated variation in epithelial niches without requiring predefined histological regions. Pseudo-temporal continuum inference of these profiles reconstructed a continuous axis that reflected the spatial progression of fibrotic remodeling from relatively preserved alveolar regions to fibrotic and airway-like remodeled regions. Within this spatial dataset, we mapped coordinated changes in epithelial states, local microenvironments, epithelial intracellular pathway activities, and directional interactions with neighboring cell types along the same axis. Our findings provide a spatial framework that generates testable hypotheses for progressive epithelial niche remodeling in IPF.

bioinformatics↗

bioRxiv2023

Exploratory mass cytometry analysis reveals immunophenotypes of cancer treatment-related pneumonitis

Anti-cancer treatments can result in various adverse effects, including infections due to immune suppression/dysregulation and drug-induced toxicity in the lung. One of the major opportunistic infections is Pneumocystis jirovecii pneumonia (PCP), which can cause severe respiratory complications and high mortality rates. Cytotoxic drugs and immune-checkpoint inhibitors (ICIs) can induce interstitial lung diseases (ILDs). Nonetheless, the differentiation of these diseases can be difficult, and the pathogenic mechanisms of such diseases are not yet fully understood. To better comprehend the immunophenotypes, we conducted an exploratory mass cytometry analysis of immune cell subsets in bronchoalveolar lavage fluid from patients with PCP, cytotoxic drug-induced ILD (DI-ILD), and ICI-associated ILD (ICI-ILD) using two panels containing 64 markers. In PCP, we observed an expansion of the CD16+ T cell population, with the highest CD16+ T proportion in a fatal case. In ICI-ILD, we found an increase in CD57+ CD8+ T cells expressing immune checkpoints (TIGIT+ LAG3+ TIM-3+ PD-1+), FCRL5+ B cells, and CCR2+ CCR5+ CD14+ monocytes. These findings uncover the diverse immunophenotypes and possible pathomechanisms of cancer treatment-related pneumonitis.

immunology↗

bioRxiv2023

Mass cytometry identifies characteristic immune cell subsets in bronchoalveolar lavage fluid from interstitial lung diseases

Immune cells have been implicated in interstitial lung diseases (ILDs), although their phenotypes and effector mechanisms remain poorly understood. To better understand these cells, we conducted an exploratory mass cytometry analysis of immune cell subsets in bronchoalveolar lavage fluid (BALF) from patients with idiopathic pulmonary fibrosis (IPF), connective-tissue disease (CTD)-related ILD, and sarcoidosis, using two panels including 64 markers. Among myeloid cells, we observed the expansion of CD14+ CD36hi CD84hi monocyte populations in IPF. These CD14+ CD36hi CD84hi subsets were also increased in ILDs with a progressive phenotype, particularly in a case of acute exacerbation (AEx) of IPF. Analysis of B cells revealed the presence of cells at various stages of differentiation in BALF, with a higher percentage of IgG memory B cells in CTD-ILDs and a trend toward more FCRL5+ B cells. These FCRL5+B cells were also present in the patient with AEx-IPF and sarcoidosis with advanced lung lesions. Among T cells, we found increased levels of IL-2R+TIGIT+ LAG3+ CD4+T cells in IPF, increased levels of CXCR3+ CD226+ CD4+ T cells in sarcoidosis, and increased levels of PD1+ TIGIT+ CD57+ CD8+ T cells in CTD-ILDs. Together, these findings underscore the diverse immunopathogenesis of ILDs.

immunology↗

bioRxiv2022

Intrinsic BMP inhibitor Gremlin regulates lung alveolar progenitor cell proliferation and differentiation

Type 1 alveolar epithelial cells (AT1s) and type 2 alveolar epithelial cells (AT2s) regulate the structural integrity and function of alveoli. AT1s mediate gas exchange, whereas AT2s serve multiple functions, including surfactant secretion and alveolar repair through proliferation and differentiation into AT1s as progenitors. However, mechanisms regulating AT2 proliferation and differentiation remain unclear. Here we demonstrate that Gremlin, an intrinsic inhibitor of bone morphogenetic protein (BMP), induces AT2 proliferation and differentiation. Transient overexpression of Gremlin in rat lungs by adenovirus vector delivery suppressed BMP signaling, induced proliferation of AT2s and the production of Bmp2, which in turn led to the recovery of BMP signaling and induced AT2 differentiation into AT1s. Gremlin was upregulated in a bleomycin-induced lung injury model. TGF-{beta} and IL-1{beta} induced Gremlin expression in fibroblasts. Taken together, our findings implicate that Gremlin expression during lung injury leads to precisely timed inhibition of BMP signaling and activates AT2s, leading to alveolar repair.

molecular biology↗