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Samakovlis, ChristosORCID iD iconorcid.org/0000-0002-9153-6040
Alternative names
Publications (10 of 39) Show all publications
Tsarouhas, V., Liu, D., Tsikala, G., Engström, Y., Strigini, M. & Samakovlis, C. (2023). A surfactant lipid layer of endosomal membranes facilitates airway gas filling in Drosophila. Current Biology, 33(23), 5132-5146, e1-e5
Open this publication in new window or tab >>A surfactant lipid layer of endosomal membranes facilitates airway gas filling in Drosophila
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2023 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 33, no 23, p. 5132-5146, e1-e5Article in journal (Refereed) Published
Abstract [en]

The mechanisms underlying the construction of an air-liquid interface in respiratory organs remain elusive. Here, we use live imaging and genetic analysis to describe the morphogenetic events generating an extracellular lipid lining of the Drosophila airways required for their gas filing and animal survival. We show that sequential Rab39/Syx1A/Syt1-mediated secretion of lysosomal acid sphingomyelinase (Drosophila ASM [dASM]) and Rab11/35/Syx1A/Rop-dependent exosomal secretion provides distinct components for lipid film assembly. Tracheal inactivation of Rab11 or Rab35 or loss of Rop results in intracellular accumulation of exosomal, multi-vesicular body (MVB)-derived vesicles. On the other hand, loss of dASM or Rab39 causes luminal bubble-like accumulations of exosomal membranes and liquid retention in the airways. Inactivation of the exosomal secretion in dASM mutants counteracts this phenotype, arguing that the exosomal secretion provides the lipid vesicles and that secreted lysosomal dASM organizes them into a continuous film. Our results reveal the coordinated functions of extracellular vesicle and lysosomal secretions in generating a lipid layer crucial for airway gas filling and survival.

National Category
Developmental Biology
Identifiers
urn:nbn:se:su:diva-225400 (URN)10.1016/j.cub.2023.10.058 (DOI)001131980100001 ()37992718 (PubMedID)2-s2.0-85177875658 (Scopus ID)
Available from: 2024-01-17 Created: 2024-01-17 Last updated: 2024-01-17Bibliographically approved
Sountoulidis, A., Marco Salas, S., Braun, E., Avenel, C., Bergenstråhle, J., Theelke, J., . . . Samakovlis, C. (2023). A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nature Cell Biology, 25(2), 351-365
Open this publication in new window or tab >>A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung
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2023 (English)In: Nature Cell Biology, ISSN 1465-7392, E-ISSN 1476-4679, Vol. 25, no 2, p. 351-365Article in journal (Refereed) Published
Abstract [en]

The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-215134 (URN)10.1038/s41556-022-01064-x (DOI)000916842700001 ()36646791 (PubMedID)2-s2.0-85146289982 (Scopus ID)
Available from: 2023-03-03 Created: 2023-03-03 Last updated: 2024-02-28Bibliographically approved
Kryvenko, V., Alberro-Brage, A., Fysikopoulos, A., Wessendorf, M., Tello, K., Morty, R. E., . . . Vadasz, I. (2023). Clathrin-Mediated Albumin Clearance in Alveolar Epithelial Cells of Murine Precision-Cut Lung Slices. International Journal of Molecular Sciences, 24(3), Article ID 2644.
Open this publication in new window or tab >>Clathrin-Mediated Albumin Clearance in Alveolar Epithelial Cells of Murine Precision-Cut Lung Slices
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2023 (English)In: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 24, no 3, article id 2644Article in journal (Refereed) Published
Abstract [en]

A hallmark of acute respiratory distress syndrome (ARDS) is an accumulation of protein-rich alveolar edema that impairs gas exchange and leads to worse outcomes. Thus, understanding the mechanisms of alveolar albumin clearance is of high clinical relevance. Here, we investigated the mechanisms of the cellular albumin uptake in a three-dimensional culture of precision-cut lung slices (PCLS). We found that up to 60% of PCLS cells incorporated labeled albumin in a time- and concentration-dependent manner, whereas virtually no uptake of labeled dextran was observed. Of note, at a low temperature (4 °C), saturating albumin receptors with unlabeled albumin and an inhibition of clathrin-mediated endocytosis markedly decreased the endocytic uptake of the labeled protein, implicating a receptor-driven internalization process. Importantly, uptake rates of albumin were comparable in alveolar epithelial type I (ATI) and type II (ATII) cells, as assessed in PCLS from a SftpcCreERT2/+: tdTomatoflox/flox mouse strain (defined as EpCAM+CD31CD45tdTomatoSPCT1α+ for ATI and EpCAM+CD31CD45tdTomatoSPC+T1α for ATII cells). Once internalized, albumin was found in the early and recycling endosomes of the alveolar epithelium as well as in endothelial, mesenchymal, and hematopoietic cell populations, which might indicate transcytosis of the protein. In summary, we characterize albumin uptake in alveolar epithelial cells in the complex setting of PCLS. These findings may open new possibilities for pulmonary drug delivery that may improve the outcomes for patients with respiratory failure.

Keywords
precision-cut lung slices, endocytosis, protein transport, albumin, alveolar epithelium, acute respiratory distress syndrome
National Category
Biological Sciences Chemical Sciences
Identifiers
urn:nbn:se:su:diva-215515 (URN)10.3390/ijms24032644 (DOI)000930425200001 ()36768968 (PubMedID)2-s2.0-85148074642 (Scopus ID)
Available from: 2023-03-16 Created: 2023-03-16 Last updated: 2023-03-17Bibliographically approved
Alberro-Brage, A., Kryvenko, V., Malainou, C., Guenther, S., Morty, R. E., Seeger, W., . . . Vadasz, I. (2023). Influenza virus decreases albumin uptake and megalin expression in alveolar epithelial cells. Frontiers in Immunology, 14, Article ID 1260973.
Open this publication in new window or tab >>Influenza virus decreases albumin uptake and megalin expression in alveolar epithelial cells
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2023 (English)In: Frontiers in Immunology, E-ISSN 1664-3224, Vol. 14, article id 1260973Article in journal (Refereed) Published
Abstract [en]

Introduction

Acute respiratory distress syndrome (ARDS) is a common complication of influenza virus (IV) infection. During ARDS, alveolar protein concentrations often reach 40-90% of plasma levels, causing severe impairment of gas exchange and promoting deleterious alveolar remodeling. Protein clearance from the alveolar space is at least in part facilitated by the multi-ligand receptor megalin through clathrin-mediated endocytosis.

Methods

To investigate whether IV infection impairs alveolar protein clearance, we examined albumin uptake and megalin expression in MLE-12 cells and alveolar epithelial cells (AEC) from murine precision-cut lung slices (PCLS) and in vivo, under IV infection conditions by flow cytometry and western blot. Transcriptional levels from AEC and broncho-alveolar lavage (BAL) cells were analyzed in an in-vivo mouse model by RNAseq.

Results

IV significantly downregulated albumin uptake, independently of activation of the TGF- β1/GSK3β axis that has been previously implicated in the regulation of megalin function. Decreased plasma membrane abundance, total protein levels, and mRNA expression of megalin were associated with this phenotype. In IV-infected mice, we identified a significant upregulation of matrix metalloproteinase (MMP)-14 in BAL fluid cells. Furthermore, the inhibition of this protease partially recovered total megalin levels and albumin uptake.

Discussion

Our results suggest that the previously described MMP-driven shedding mechanisms are potentially involved in downregulation of megalin cell surface abundance and clearance of excess alveolar protein. As lower alveolar edema protein concentrations are associated with better outcomes in respiratory failure, our findings highlight the therapeutic potential of a timely MMP inhibition in the treatment of IV-induced ARDS.

Keywords
influenza virus, albumin, epithelial cells, lungs, endocytosis
National Category
Cell and Molecular Biology Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:su:diva-223230 (URN)10.3389/fimmu.2023.1260973 (DOI)001067433400001 ()37727782 (PubMedID)2-s2.0-85171386198 (Scopus ID)
Available from: 2023-11-06 Created: 2023-11-06 Last updated: 2024-01-17Bibliographically approved
Pinheiro, A. S., Tsarouhas, V., Senti, K., Arefin, B. & Samakovlis, C. (2023). Scavenger receptor endocytosis controls apical membrane morphogenesis in the Drosophila airways. eLIFE, 12, Article ID e84974.
Open this publication in new window or tab >>Scavenger receptor endocytosis controls apical membrane morphogenesis in the Drosophila airways
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2023 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 12, article id e84974Article in journal (Refereed) Published
Abstract [en]

The acquisition of distinct branch sizes and shapes is a central aspect in tubular organ morphogenesis and function. In the Drosophila airway tree, the interplay of apical extracellular matrix (ECM) components with the underlying membrane and cytoskeleton controls tube elongation, but the link between ECM composition with apical membrane morphogenesis and tube size regulation is elusive. Here, we characterized Emp (epithelial membrane protein), a Drosophila CD36 homolog belonging to the scavenger receptor class B protein family. emp mutant embryos fail to internalize the luminal chitin deacetylases Serp and Verm at the final stages of airway maturation and die at hatching with liquid filled airways. Emp localizes in apical epithelial membranes and shows cargo selectivity for LDLr-domain containing proteins. emp mutants also display over elongated tracheal tubes with increased levels of the apical proteins Crb, DE-cad, and phosphorylated Src (p-Src). We show that Emp associates with and organizes the βH-Spectrin cytoskeleton and is itself confined by apical F-actin bundles. Overexpression or loss of its cargo protein Serp lead to abnormal apical accumulations of Emp and perturbations in p-Src levels. We propose that during morphogenesis, Emp senses and responds to luminal cargo levels by initiating apical membrane endocytosis along the longitudinal tube axis and thereby restricts airway elongation.

National Category
Developmental Biology
Identifiers
urn:nbn:se:su:diva-225396 (URN)10.7554/eLife.84974 (DOI)001134618100001 ()37706489 (PubMedID)2-s2.0-85171664401 (Scopus ID)
Available from: 2024-01-18 Created: 2024-01-18 Last updated: 2024-01-18Bibliographically approved
Mirzazadeh, R., Andrusivova, Z., Larsson, L., Newton, P. T., Galicia, L. A., Abalo, X. M., . . . Lundeberg, J. (2023). Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. Nature Communications, 14(1), Article ID 509.
Open this publication in new window or tab >>Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
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2023 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 509Article in journal (Refereed) Published
Abstract [en]

Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins. Spatial transcriptomics relies on RNA quality, which is variable and dependent on sample handling, storage, and/or intrinsic factors. Here, authors present a genome-wide spatial gene expression profiling method called RNA Rescue Spatial Transcriptomics (RRST), designed for the analysis of moderate to low quality fresh frozen tissue samples and demonstrate its robustness on 7 different tissue types.

National Category
Other Natural Sciences Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:su:diva-230433 (URN)10.1038/s41467-023-36071-5 (DOI)001026236800009 ()36720873 (PubMedID)2-s2.0-85147171092 (Scopus ID)
Available from: 2024-06-10 Created: 2024-06-10 Last updated: 2024-06-10Bibliographically approved
Yin, W., Liontos, A., Koepke, J., Ghoul, M., Mazzocchi, L., Liu, X., . . . Samakovlis, C. (2022). An essential function for autocrine hedgehog signaling in epithelial proliferation and differentiation in the trachea. Development, 149(3), Article ID dev199804.
Open this publication in new window or tab >>An essential function for autocrine hedgehog signaling in epithelial proliferation and differentiation in the trachea
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2022 (English)In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 149, no 3, article id dev199804Article in journal (Refereed) Published
Abstract [en]

The tracheal epithelium is a primary target for pulmonary diseases as it provides a conduit for air flow between the environment and the lung lobes. The cellular and molecular mechanisms underlying airway epithelial cell proliferation and differentiation remain poorly understood. Hedgehog (HH) signaling orchestrates communication between epithelial and mesenchymal cells in the lung, where it modulates stromal cell proliferation, differentiation and signaling back to the epithelium. Here, we reveal a previously unreported autocrine function of HH signaling in airway epithelial cells. Epithelial cell depletion of the ligand sonic hedgehog (SHH) or its effector smoothened (SMO) causes defects in both epithelial cell proliferation and differentiation. In cultured primary human airway epithelial cells, HH signaling inhibition also hampers cell proliferation and differentiation. Epithelial HH function is mediated, at least in part, through transcriptional activation, as HH signaling inhibition leads to downregulation of cell type-specific transcription factor genes in both the mouse trachea and human airway epithelial cells. These results provide new insights into the role of HH signaling in epithelial cell proliferation and differentiation during airway development.

Keywords
Sonic hedgehog, Smoothened, Trachea, Tracheomalacia, Airway epithelial cells
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-203222 (URN)10.1242/dev.199804 (DOI)000759117000011 ()35112129 (PubMedID)
Available from: 2022-03-24 Created: 2022-03-24 Last updated: 2022-09-16Bibliographically approved
Luecken, M. D., Zaragosi, L.-E., Madissoon, E., Sikkema, L., Firsova, A. B., De Domenico, E., . . . Nawijn, M. C. (2022). The discovAIR project: a roadmap towards the Human Lung Cell Atlas. European Respiratory Journal, 60(2), Article ID 2102057.
Open this publication in new window or tab >>The discovAIR project: a roadmap towards the Human Lung Cell Atlas
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2022 (English)In: European Respiratory Journal, ISSN 0903-1936, E-ISSN 1399-3003, Vol. 60, no 2, article id 2102057Article, review/survey (Refereed) Published
Abstract [en]

The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell-cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions.

National Category
Cell and Molecular Biology Respiratory Medicine and Allergy
Identifiers
urn:nbn:se:su:diva-212457 (URN)10.1183/13993003.02057-2021 (DOI)000886648200004 ()35086829 (PubMedID)2-s2.0-85128854167 (Scopus ID)
Available from: 2022-12-08 Created: 2022-12-08 Last updated: 2022-12-08Bibliographically approved
Liu, D., Tsarouhas, V. & Samakovlis, C. (2022). WASH activation controls endosomal recycling and EGFR and Hippo signaling during tumor-suppressive cell competition. Nature Communications, 13(1), Article ID 6243.
Open this publication in new window or tab >>WASH activation controls endosomal recycling and EGFR and Hippo signaling during tumor-suppressive cell competition
2022 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 6243Article in journal (Refereed) Published
Abstract [en]

Cell competition is a conserved homeostatic mechanism whereby epithelial cells eliminate neighbors with lower fitness. Cell communication at the interface of wild-type winner cells and polarity-deficient (scrib-/-) losers is established through Sas-mediated Ptp10D activation in polarity-deficient cells. This tumor-suppressive cell competition restrains EGFR and Hippo signaling and enables Eiger-JNK mediated apoptosis in scrib-/- clones. Here, we show that the activation state of the endosomal actin regulator WASH is a central node linking EGFR and Hippo signaling activation. The tyrosine kinase Btk29A and its substrate WASH are required downstream of Ptp10D for loser cell elimination. Constitutively active, phosphomimetic WASH is sufficient to induce both EGFR and Yki activation leading to overgrowth. On the mechanistic level we show that Ptp10D is recycled by the WASH/retromer complex, while EGFR is recycled by the WASH/retriever complex. Constitutive WASH activation selectively interferes with retromer function leading to Ptp10D mistargeting while promoting EGFR recycling and signaling activation. Phospho-WASH also activates aberrant Arp2/3 actin polymerization, leading to cytoskeletal imbalance, Yki activation and reduced apoptosis. Selective manipulation of WASH phosphorylation on sorting endosomes may restrict epithelial tumorous growth. 

National Category
Biological Sciences Cell and Molecular Biology
Identifiers
urn:nbn:se:su:diva-211074 (URN)10.1038/s41467-022-34067-1 (DOI)000871124000027 ()36271083 (PubMedID)2-s2.0-85140293577 (Scopus ID)
Available from: 2022-11-10 Created: 2022-11-10 Last updated: 2023-03-28Bibliographically approved
Moretti, C. H., Schiffer, T. A., Montenegro, M. F., Larsen, F. J., Tsarouhas, V., Carlström, M., . . . Lundberg, J. O. (2020). Dietary nitrite extends lifespan and prevents age-related locomotor decline in the fruit fly. Free Radical Biology & Medicine, 160, 860-870
Open this publication in new window or tab >>Dietary nitrite extends lifespan and prevents age-related locomotor decline in the fruit fly
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2020 (English)In: Free Radical Biology & Medicine, ISSN 0891-5849, E-ISSN 1873-4596, Vol. 160, p. 860-870Article in journal (Refereed) Published
Abstract [en]

Aging is associated with decreased nitric oxide (NO) bioavailability and signalling. Boosting of a dietary nitrate nitrite-NO pathway e.g. by ingestion of leafy green vegetables, improves cardiometabolic function, mitochondrial efficiency and reduces oxidative stress in humans and rodents, making dietary nitrate and nitrite an appealing intervention to address age-related disorders. On the other hand, these anions have long been implicated in detrimental health effects of our diet, particularly in formation of carcinogenic nitrosamines.

The aim of this study was to assess whether inorganic nitrite affects lifespan in Drosophila melanogaster and investigate possible mechanisms underlying any such effect.

In a survival assay, female flies fed a nitrite supplemented diet showed lifespan extension by 9 and 15% with 0.1 and 1 mu M nitrite respectively, with no impact of nitrite on reproductive output. Interestingly, nitrite could also protect female flies from age-dependent locomotor decline, indicating a protective effect on healthspan. NO generation from nitrite involved Drosophila commensal bacteria and was indicated by a fluorescent probe as well as direct measurements of NO gas formation with chemiluminescence.

Nutrient sensing pathways such as TOR and sirtuins, have been strongly implicated in lifespan extension. In aged flies, nitrite supplementation significantly downregulated dTOR and upregulated dSir2 gene expression. Total triglycerides and glucose were decreased, a described downstream effect of both TOR and sirtuin pathways.

In conclusion, we demonstrate that very low doses of dietary nitrite extend lifespan and favour healthspan in female flies. We propose modulation of nutrient sensing pathways as driving mechanisms for such effects.

Keywords
Lifespan, Longevity, Aging, Nitric oxide, Nitrate, Drosophila melanogaster
National Category
Biological Sciences Nutrition and Dietetics
Research subject
Nutrition
Identifiers
urn:nbn:se:su:diva-197268 (URN)10.1016/j.freeradbiomed.2020.09.018 (DOI)000595084100002 ()
Funder
Swedish Research Council
Available from: 2021-09-29 Created: 2021-09-29 Last updated: 2023-10-16Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-9153-6040

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