Biology subjects

Bishop, K.

Publications and source records attributed to Bishop, K..

10 recordsLinked to original sources

bioRxiv2026

A conserved vesicular circuit enables metabolic adaptation and maintains systemic heme homeostasis

Metabolic homeostasis depends on adaptive control of intracellular metabolite flux, yet how such control is reconfigured when canonical transport pathways fail is unknown. Here we define a conserved vesicular circuit that preserves systemic heme balance by rerouting intracellular heme flux. We show that loss of the intestinal heme exporter MRP-5 in Caenorhabditis elegans causes lethal heme sequestration within endolysosomal compartments. This defect is bypassed by disabling the vesicular adaptor AP-3, which stabilizes and reroutes the heme importer HRG-1, restoring heme export without increasing cytosolic heme. Unbiased genetics and transcriptomics identify two previously uncharacterized SLC49A family members, HRG-13 and HRG-14, as heme exporters with distinct affinities that engage in a vesicular importer-exporter handoff. Live imaging reveals heme-enhanced contacts between HRG-1 and SLC49A-containing vesicles, consistent with direct vesicular transfer. This circuitry extends to vertebrates as disruption of the SLC49A3 homolog impairs erythropoiesis in zebrafish and causes intracellular heme overload, premature hemoglobinization and apoptosis in differentiating human erythroid cells. Together, these findings establish SLC49A3 proteins as conserved heme exporters and uncover a general principle of metabolic adaptation in which reprogramming intracellular compartmentalization, rather than increasing nutrient supply, restores systemic homeostasis.

cell biology↗

bioRxiv2026

Age dependent collective trafficking of tissue resident T cells in zebrafish

How tissue-resident T cells are organized to provide immune surveillance in healthy peripheral tissues and how this organization changes with age remains largely unknown. Here we use intravital imaging in zebrafish to identify a previously undescribed, appendage-specific mode of adaptive immune organization: fin-resident T cells undergo coordinated collective "streaming" migration within connective tissue compartments. T cells colonize the developing fin prior to lymphatic or blood vessel formation, indicating that initial residency can be established independently of classical immune conduits. However, collective streaming is not immediate; it emerges during juvenile maturation, coincident with maturation of fin architecture, and is restricted to T cells rather than other leukocyte populations. After fin amputation, young adults restore streaming within regenerated tissue once spatial compartments are re-established, whereas middle-aged fish following thymic involution repopulate the fin yet fail to promptly recover coordinated streaming and show broader tissue dispersion and altered motility in comparable times. Transcriptomic profiling across ages, regenerative states, and immune-altered microenvironments reveals coupled regulation of stromal remodeling programs and antigen presentation pathways, including differential expression of MHC class I and II components with strong microenvironmental dependence. These data define an age-regulated, tissue-instructed program that organizes resident T cell dynamics and immune potential in situ, providing a framework for understanding how tissue specific stromal environments constrain immune surveillance. Significance StatementT cells patrol most organs, but we know surprisingly little about how they are arranged inside healthy tissues over an animals lifetime. By imaging zebrafish in vivo, we discovered that fin-resident T cells do not move independently: they organize into coordinated "streams" that migrate collectively through fin connective tissue. This collective behavior appears during juvenile maturation, re-forms after regeneration in young adults, and is delayed or disrupted in older fish as age-related thymus decline reduces new T cell production. In parallel, aging and the tissue microenvironment reshape the expression of genes involved in antigen presentation. These results reveal a tissue-specific, age-regulated architecture for adaptive immune surveillance that links aging to impaired immune organization during regeneration.

developmental biology↗

bioRxiv2023

Organ specific microenvironmental MR1 expression in cutaneous melanoma

The microenvironment is an important regulator of intertumoral trafficking and activity of immune cells. Understanding how the immune system can be tailored to maintain anti-tumor killing responses in metastatic disease remains an important goal. Thus, immune mediated eradication of metastasis requires the consideration of organ specific microenvironmental cues. Using a xenograft model of melanoma metastasis in adult zebrafish, we perturbed the dynamic balance between the infiltrating immune cells in the metastatic setting using a suite of different transgenic zebrafish. We employed intravital imaging coupled with metabolism imaging (FLIM) to visualize and map the organ specific metabolism with near simultaneity in multiple metastatic lesions. Of all the MHC complexes examined for brain and skeletal metastases, we determined that there is an organ specific expression of mhc1uba (human ortholog, MR1) for both the melanoma cells and the resident and infiltrating immune cells. Specifically, immune clusters did not express mhc1uba in brain metastatic lesions in immune competent fish. Finally, the differential immune response drove organ specific metabolism where tumor glycolysis was increased in brain metastases compared to skeletal and parental lines as measured using fluorescence lifetime imaging microscopy (FLIM). As MR1 belongs to the MHC class I molecules and is a target of immunotherapeutic drugs, we believe that our data presents an opportunity to understand the relationship between organ specific tumor metabolism and drug efficacy in the metastatic setting.

cancer biology↗

bioRxiv2021

Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development

RUNX1 is essential for the generation of hematopoietic stem cells (HSCs). Runx1 null mouse embryos lack definitive hematopoiesis and die in mid-gestation. However, even though zebrafish embryos with a runx1 W84X mutation have defects in early definitive hematopoiesis, some runx1W84X/W84X embryos can develop to fertile adults with blood cells of multi-lineages, raising the possibility that HSCs can emerge without RUNX1. Here, using three new zebrafish runx1-/- lines we uncovered the compensatory mechanism for runx1-independent hematopoiesis. We show that, in the absence of a functional runx1, a cd41-GFP+ population of hematopoietic precursors still emerge from the hemogenic endothelium and can colonize the hematopoietic tissues of the mutant embryos. Single-cell RNA sequencing of the cd41-GFP+ cells identified a set of runx1-/--specific signature genes during hematopoiesis. Significantly, gata2b, which normally acts upstream of runx1 for the generation of HSCs, was increased in the cd41-GFP+ cells in runx1- /- embryos. Interestingly, genetic inactivation of both gata2b and its paralog, gata2a, did not affect hematopoiesis. However, knocking out runx1 and any three of the four alleles of gata2a and gata2b abolished definitive hematopoiesis. Gata2 expression was also upregulated in hematopoietic cells in Runx1-/- mice, suggesting the compensatory mechanism is conserved. Our findings indicate that RUNX1 and GATA2 serve redundant roles for HSC production, acting as each others safeguard. Key pointsO_LIExistence of RUNX1-independent mechanisms for the generation of HSCs and the development of functional definitive hematopoietic cells C_LIO_LIGATA2 and RUNX1 functionally complement each other for their respective roles during hematopoiesis C_LI

genetics↗

bioRxiv2020

A metabolic shift to glycolysis promotes zebrafish tail regeneration through TGF-β dependent dedifferentiation of notochord cells to form the blastema

Mammals are generally poor at tissue regeneration, in contrast, fish maintain a high capacity for regenerating complex tissues after injury. Using larval zebrafish, we show that tail amputation triggers an metabolic shift to glycolysis in cells surrounding the notochord as they reposition to the amputation site. Blocking glycolysis prevents the fin from regenerating after amputation due to the failure to form a normal, pluripotent blastema. We performed a time series of scRNA-sequencing on regenerating tails under normal conditions or in the absence of glycolysis. Strikingly, we detected a transient cell population in the single cell analysis that represents notochord sheath cells undergoing a TGF-{beta} dependent dedifferentiation and epithelium-to-mesenchyme transition to become pluripotent blastema cells. We further demonstrated that the metabolic switch to glycolysis is required for TGF-{beta} signaling and blocking either glycolysis or TGF-{beta} receptors results in aberrant blastema formation through the suppression of essential EMT mediators such as snai1.

developmental biology↗

bioRxiv2019

A model for reticular dysgenesis shows impaired sensory organ development and hair cell regeneration linked to cellular stress

Mutations in the gene AK2 are responsible for Reticular Dysgenesis (RD), a rare and severe form of primary immunodeficiency in children. RD patients have a severely shortened life expectancy and without treatment die a few weeks after birth. The only available therapeutic option for RD is bone marrow transplantation. To gain insight into the pathophysiology of RD, we previously created zebrafish models for an AK2 deficiency. One of the clinical features of RD is hearing loss, but its pathology and causes have not been determined. In adult mammals, sensory hair cells of the inner ear do not regenerate; however, their regeneration has been observed in several non-mammalian vertebrates, including zebrafish. Therefore, we use our RD zebrafish models to determine if AK2 deficiency affects sensory organ development and/or hair cell regeneration. Our studies indicated that AK2 is required for the correct development, survival and regeneration of sensory hair cells. Interestingly, AK2 deficiency induces the expression of several oxidative stress markers and it triggers an increased level of cell death in the hair cells. Finally, we show that glutathione treatment can partially rescue hair cell development in the sensory organs in our RD models, pointing to the potential use of antioxidants as a supportive therapeutic modality for RD patients, not only to increase their chances of survival, but to prevent or ameliorate their sensorineural hearing deficits.

developmental biology↗

bioRxiv2018

Mercury methylating microbial communities of boreal forest soils

The formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase, hgcA, combined with geochemical characterisation of soils, were used to determine the microbial populations contributing to MeHg formation in forest soils across Sweden. The hgcA sequences obtained were distributed among diverse clades, including Proteobacteria, Firmicutes, and Methanomicrobia, with Deltaproteobacteria, particularly Geobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is linked to the composition of also non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for the hgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.\n\nImportanceDespite a global state of awareness that mercury, and methylmercury in particular, is a neurotoxin that millions of people continue to be exposed to, there are sizable gaps in our fundamental understanding of the processes and organisms involved in methylmercury formation. In the present study we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal forest soils. All the microorganisms identified have a relevant role on the processing of organic matter in soils. Moreover, our results show that the formation of methylation formation is not only linked to mercury methylating microorganisms but also to the presence of non-mercury methylating bacterial communities that contribute to methylmercury formation by the appropriate substrate to the microorganisms responsible for the actual methylation process. This study improves current knowledge on the diversity of organisms involved in methylmercury formation in soils.

microbiology↗

bioRxiv2017

Tissue architectural cues drive the emergence of non-random trafficking of human tumor cells in the larval zebrafish

Sites of metastasis are non-random, with certain types of cancers showing organ preference during distal colonization. Using multiple brain- and bone marrow-seeking human and murine breast cancer subclones, we determined that tumor cells that home to specific murine organs (brain and bone marrow) ultimately colonized analogous tissues (brain and caudal vein plexus [CVP]) in larval zebrafish. We then exploited the zebrafish model to delineate factors leading to differential cell homing and extravasation. Bone marrow-tropic clones showed higher expression of integrins and focal adhesions associated with mechanosensing machinery than brain-tropic clones and were more sensitive to vessel topography during extravasation. Knockdown of {beta}1 integrin reduced extravasation and redistributed organ targeting from disordered vessels in the CVP to the brain. Our results show that organ selectivity is driven by topography- and cell type-dependent extravasation at the tumor-endothelial interface in the larval zebrafish and provide important insights into the early stages of metastasis.

biophysics↗

bioRxiv2017

Human macrophages survive and adopt activated genotypes in living zebrafish

The inflammatory response, modulated both by tissue resident macrophages and recruited monocytes from peripheral blood, plays a critical role in human diseases such as cancer and neurodegenerative disorders. Here, we sought a model to interrogate human immune behavior in vivo. We determined that primary human monocytes and macrophages survive in zebrafish for up to two weeks. Flow cytometry revealed that human monocytes cultured at the physiological temperature of the zebrafish survive and differentiate comparable to cohorts cultured at human physiological temperature. Moreover, key genes that encode for proteins that play a role in tissue remodeling were also expressed. Human cells migrated within multiple tissues at speeds comparable to zebrafish macrophages. Analysis of gene expression of in vivo educated human macrophages confirmed expression of activated macrophage phenotypes. Here, human cells adopted phenotypes relevant to cancer progression, suggesting that we can define the real time immune modulation of human tumor cells during the establishment of a metastatic lesion in zebrafish.

developmental biology↗

bioRxiv2016

Highly-efficient Cpf1-mediated gene targeting in mice following high concentration pronuclear injection

Cpf1 has emerged as an alternative to the Cas9 RNA-guided nuclease. Here we show that gene targeting rates in mice using Cpf1 can meet or even surpass Cas9 targeting rates (approaching 100% targeting) but require higher concentrations of mRNA and guide. We also demonstrate that co-injecting two guides with close targeting sites can result in synergistic genomic cutting, even if one of the guides has minimal cutting activity.

genetics↗