Biology subjects

Matsuda, R.

Publications and source records attributed to Matsuda, R..

8 recordsLinked to original sources

bioRxiv2026

Branch extension and pruning share the same regulatory module in the developing Drosophila airways

Branched tubular organs represent a common solution to the problem of fluid transport in large animals. The growth of new branches has been extensively studied but the regulation of branch pruning remains underexplored. Here, we investigate branch removal in the stereotyped branching patterns of the developing Drosophila airways. After progenitor invagination, the tips of the distal airways generate a stereotyped branching pattern in each central metameric unit. An intriguing exception in the repeating patterns is the lack of branches targeting the visceral mesoderm (visceral primary branch, VB) in the third and nineth metameres. We show that these branches initially form but the localized expression of the pro-apoptotic gene reaper and resultant apoptosis prune them. We reveal that VB3/9 pruning entails four sequential programs. First, a common distal outgrowth program promotes budding and extension of the primary branches, including VB3 and 9. Second, a VB identity program is established representing the ground state of all primary branches. Third, the Bithorax-Complex transcription factors define metameric identities and interfere with the VB program to induce reaper and apoptosis specifically in VB3/9 in a concentration dependent manner. Finally, the default VB cell identity is transformed by extrinsic BMP/Decapentaplegic and WNT/Wingless into more derived primary branch identities and spared from pruning in metamers 3 and 9. Our results demonstrate that molecular and genetic circuits promoting branch emergence and extension can be regionally modified and deployed also for branch pruning. Author summaryMany of our internal organs like the lung, kidney and various glands are composed of epithelial tubes. The function of these organs is sustained by the morphologies of the constituting tubes. The formation of distinct branching patterns in tubular networks including regional variegations can be accomplished by branch ramification and branch pruning. Extensive studies of tube ramification and extension showed that they are typically regulated by extrinsic guidance cues. In contrast to branch extension, branch maintenance and removal is much less understood. Here, we identify a program that intrinsically promotes apoptosis to prune specific branches in the developing Drosophila airways. Intriguingly, the branch extension program is diverted to a branch pruning program. Activation of the branch outgrowth program is prerequisite for both branch extension and pruning. The Hox gene expression code that characterizes regional cell identities along the body axes intrinsically interferes with the branch extension program of visceral primary branches (VB) targeting the visceral muscles. This results in VB pruning only in metameres 3 and 9, where extrinsic WNT and BMP guidance cues direct towards distal branch identities that are spared from apoptotic pruning. Similar interplay of branching and pruning programs may operate in sculpting our lung and vasculature.

developmental biology↗

bioRxiv2026

Functional definition of the Drosophila airway progenitor field through overlapping compensatory regulators

Tubular organs present a common solution to fluid transport in multicellular organisms. They often arise by an initial bulging of flat epithelial progenitor cells, which then undergo branching morphogenesis. Here, we present 3 cooperative programs fully defining the Drosophila airway progenitor field and their roles in early morphogenesis linking the radial pattern of the 2-dimensional (2D) field to the proximo-distally patterning of the 3D tubes. We previously showed that extrinsic Hedgehog (Hh) and intrinsic POU-Homeobox TF Ventral-veinless (Vvl)/Drifter/U-turn dominantly drive the transcriptional program toward the distal airway cell identity at the expense of a proximal program specified by the GATA TF grain (grn). Both programs require the basic-HLH-POU TF trachealess (trh) (Matsuda et. al, 2015). Whereas trh is not essential for primordia invagination, we show that in hh vvl double mutants, the oval-shaped primordia frequently remain at the 2D plane, retaining trh expression in a grn dependent manner. Therefore, hh and vvl are the principal regulators of progenitor invagination independent of trh. Each of the 3 regulators, Trh, Vvl and Grn fulfills only complementary or compensatory functions in transcription and morphogenesis but their combinations functionally define the airway progenitor field. We further provide a comprehensive description for allocating the airway progenitors on the body coordinates, involving dorsal Decapentaplegic/BMP signaling along the dorso-ventral axis and subsequent radial EGFR signaling along the proximo-distal axis. The presence of 3 complementary, regulatory programs in early gene expression and morphogenesis of the simple Drosophila airways may reflect the vital needs for respiration, and their influence on the evolution of various strategies in tubular organ development.

developmental biology↗

bioRxiv2025

TNF signaling maintains local restriction of bacterial founder populations in intestinal and systemic sites during oral Yersinia infection

Enteroinvasive bacterial pathogens are responsible for an enormous worldwide disease burden that critically affects the young and immunocompromised. Yersinia pseudotuberculosis is a Gram-negative enteric pathogen, closely related to the plague agent Y. pestis, that colonizes intestinal tissues, induces the formation of pyogranulomas along the intestinal tract, and disseminates to systemic organs following oral infection of experimental rodents. Prior studies proposed that systemic tissues were colonized by a pool of intestinal replicating bacteria distinct from populations within Peyers patches and mesenteric lymph nodes. Whether bacteria within intestinal pyogranulomas serve as the source for systemic dissemination, and the relationship between bacterial populations within different tissue sites is poorly defined. Moreover, the factors that regulate Yersinia colonization and dissemination are not well understood. Here, we demonstrate, using Sequence Tag-based Analysis of Microbial Populations in R (STAMPR), that remarkably small founder populations independently colonize intestinal and systemic tissues. Notably, intestinal pyogranulomas contain clonal populations of bacteria that are restricted and do not spread to other tissues. However, populations of Yersinia are shared among systemic organs and the blood, suggesting that systemic dissemination occurs via hematogenous spread. Finally, we demonstrate that TNF signaling is a key contributor to the bottlenecks limiting both tissue colonization and lymphatic dissemination of intestinal bacterial populations. Altogether, this study reveals previously undescribed aspects of infection dynamics of enteric bacterial pathogens. ImportanceBacterial escape from the intestine can lead to severe disease, including sepsis, organ damage, and death. However, the intestinal bacterial population dynamics governing the colonization of mucosal and systemic tissues and the intestinal sites that seed systemic spread are not clear. Yersinia pseudotuberculosis is a rodent and human intestinal pathogen closely related to the plague agent and provides a natural rodent-adapted model to study systemic bacterial dissemination. Our findings define the infection dynamics of enteric Yersinia and the impact of the innate immune system on Yersinia colonization of the intestine and systemic organs.

microbiology↗

bioRxiv2023

Forward genetic screening in engineered colorectal cancer organoids identifies novel regulators of metastasis

Cancer is the second leading cause of death globally, due primarily to metastatic dissemination and colonization of distal sites. Recurrent genetic drivers of metastasis are elusive, suggesting that, unlike the stereotyped mutations promoting primary tumor development, drivers of metastasis may be variable. Here, we interrogate pathways governing metastasis through CRISPR/Cas9-based forward genetic screening in a genetically defined colorectal adenocarcinoma tumor organoid (tumoroid) model using ex vivo invasion screens and orthotopic, in vivo screens for gain of metastatic potential. We identify Ctnna1 and Bcl2l13 as bona fide metastasis suppressors. CTNNA1 loss promotes carcinoma cell invasion and migration through an atypical EMT-like mechanism, whereas BCL2L13 loss promotes cell survival after extracellular matrix detachment and non-cell-autonomous macrophage polarization. Ultimately, this study provides a proof-of-principle that high-content forward genetic screening can be performed in tumor-organoid models in vivo and identifies novel regulators of colon cancer metastasis.

cancer biology↗

bioRxiv2023

A TNF-IL-1 circuit controls Yersinia within intestinal granulomas

SummaryMonocytes restrict Yersinia infection within intestinal granulomas. Here, we report that monocyte-intrinsic TNF signaling drives production of IL-1 that signals to non-hematopoietic cells to control intestinal Yersinia infection within granulomas. Tumor necrosis factor (TNF) is a pleiotropic inflammatory cytokine that mediates antimicrobial defense and granuloma formation in response to infection by numerous pathogens. Yersinia pseudotuberculosis colonizes the intestinal mucosa and induces recruitment of neutrophils and inflammatory monocytes into organized immune structures termed pyogranulomas that control the bacterial infection. Inflammatory monocytes are essential for control and clearance of Yersinia within intestinal pyogranulomas, but how monocytes mediate Yersinia restriction is poorly understood. Here, we demonstrate that TNF signaling in monocytes is required for bacterial containment following enteric Yersinia infection. We further show that monocyte-intrinsic TNFR1 signaling drives production of monocyte-derived interleukin-1 (IL-1), which signals through IL-1 receptor on non-hematopoietic cells to enable pyogranuloma-mediated control of Yersinia infection. Altogether, our work reveals a monocyte-intrinsic TNF-IL-1 collaborative circuit as a crucial driver of intestinal granuloma function, and defines the cellular target of TNF signaling that restricts intestinal Yersinia infection.

immunology↗

bioRxiv2023

METTL3 is essential for small intestinal epithelial proliferation via regulation of growth factor signaling including KRAS

Intestinal epithelial transit amplifying cells are essential stem progenitors required for intestinal homeostasis, but their rapid proliferation renders them vulnerable to DNA damage from radiation and chemotherapy. Despite their critical roles in intestinal homeostasis and disease, few studies have described genes that are essential to transit amplifying cell function. We report that the RNA methyltransferase, METTL3, is required for survival of transit amplifying cells in the murine small intestine. Transit amplifying cell death after METTL3 deletion was associated with crypt and villus atrophy, loss of absorptive enterocytes, and uniform wasting and death in METTL3-depleted mice. Ribosome profiling and sequencing of methylated RNAs in enteroids and in vivo demonstrated decreased translation of hundreds of unique methylated transcripts after METTL3 deletion, particularly transcripts involved in growth factor signal transduction such as Kras. Further investigation confirmed a novel relationship between METTL3 and Kras methylation and protein levels in vivo. Our study identifies METTL3 as an essential factor supporting the homeostasis of small intestinal tissue via direct maintenance of transit amplifying cell survival. We highlight the crucial role of RNA modifications in regulating growth factor signaling in the intestine, with important implications for both homeostatic tissue renewal and epithelial regeneration.

cell biology↗

bioRxiv2022

Inflammatory monocytes promote pyogranuloma formation to counteract Yersinia blockade of host defense

Granulomas are organized immune cell aggregates that form in response to chronic infection or antigen persistence. Yersinia pseudotuberculosis (Yp) blocks innate inflammatory signaling and phagocytosis, inducing formation of neutrophil-rich pyogranulomas within lymphoid tissues. Here, we uncover that Yp triggers pyogranuloma formation within the murine intestinal mucosa, a site not known to contain such structures. Mice lacking circulating monocytes fail to form defined pyogranulomas, have defects in neutrophil activation, and succumb to Yp infection. Yersinia lacking the virulence factors that block phagocytosis did not induce pyogranulomas, indicating that intestinal pyogranulomas form in response to Yp disruption of phagocytosis. Notably, mutation of a single anti-phagocytic virulence factor, YopH, restored pyogranuloma formation and control of Yp infection in monocyte-deficient mice, demonstrating that monocytes override YopH-dependent blockade of innate immune defense. This work reveals an unappreciated site of Yersinia intestinal invasion, and defines host and pathogen drivers of intestinal granuloma formation.

microbiology↗

bioRxiv2021

The Card19 locus of murine chromosome 13 regulates terminal cell lysis downstream of caspase activation and Gasdermin-D cleavage

Cell death plays a critical role in inflammatory responses. During pyroptosis, inflammatory caspases cleave Gasdermin D (GSDMD) to release an N-terminal fragment that generates plasma membrane pores that mediate cell lysis and IL-1 cytokine release. Terminal cell lysis and IL-1{beta} release following caspase activation can be uncoupled in certain cell types or in response to particular stimuli, a state termed hyperactivation. However, the factors and mechanisms that regulate terminal cell lysis downstream of GSDMD cleavage remain poorly understood. In the course of studies to define regulation of pyroptosis during Yersinia infection, we identified a line of Card19-deficient mice (Card19lxcn) whose macrophages were protected from cell lysis and showed reduced apoptosis and pyroptosis, yet had wild-type levels of caspase activation, IL-1 secretion, and GSDMD cleavage. Unexpectedly, CARD19, a mitochondrial CARD-containing protein, was not directly responsible for this, as two independently-generated CRISPR/Cas9 Card19 knockout mice showed no defect in macrophage cell lysis, and expression of CARD19 in Card19lxcn macrophages did not restore cell lysis. Card19 is located on chromosome 13, adjacent to Ninj1, which was recently reported to regulate cell lysis downstream of GSDMD activation. Intriguingly, RNA-seq and western blotting revealed that Card19lxcn BMDMs are hypomorphic for NINJ1 expression, and reconstitution of Ninj1 in Card19lxcn immortalized BMDMs restored cell lysis. Card19lxcn mice exhibited significantly increased susceptibility to Yersinia infection, demonstrating that cell lysis itself plays a key role in protection against bacterial infection. Our findings identify genetic targeting of Card19 being responsible for off-target effects on the adjacent Ninj1 gene, thereby disrupting the ability of macrophages to undergo plasma membrane rupture downstream of gasdermin cleavage and impacting host survival and bacterial control during Yersinia infection. Author SummaryProgrammed cell death is critical for regulating tissue homeostasis and host defense against infection. Pyroptosis is an inflammatory form of programmed cell death that couples cell lysis with release of inflammatory cytokines. Cell lysis is triggered by activation of particular intracellular pore forming proteins, but how regulation of cell lysis occurs is not well understood. Genetic targeting of Card19 on chromosome 13 resulted in decreased expression of the adjacent gene, Ninj1 which was recently found to regulate terminal lysis events in response to cell death-inducing stimuli. We found that macrophages from Card19-deficient mice were resistant to multiple forms of cell death in response to a variety of inflammatory stimuli, including canonical and non-canonical inflammasome activation, as well as triggers of cell-extrinsic apoptosis. Notably, Card19-deficient mice were more susceptible to Yersinia infection, indicating that cell lysis contributes to control of bacterial infections. Our data provide new insight into the impact of terminal cell lysis on control of bacterial infection and highlight the role of additional factors that regulate lytic cell death downstream of gasdermin cleavage.

immunology↗