Anna Kremer

VIB-UGent Center for Inflammation Research

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Saskia Lippens

VIB-UGent Center for Inflammation Research

Peter Borghgraef

VIB-UGent Center for Inflammation Research

Christopher J. Guérin

VIB-UGent Center for Inflammation Research

Fred Van Leuven

KU Leuven

Peter Borghgraef

KU Leuven

Bieke Vanslembrouck

Lawrence Berkeley National Laboratory

Jolanda van Hengel

Ghent University

Herman Devijver

KU Leuven

Ilse Dewachter

Hasselt University

Benoit Lechat

VIB-KU Leuven Center for Cancer Biology

Cooperative Institutions

Ghent University

Vlaams Instituut voor Biotechnologie

KU Leuven

VIB-UGent Center for Inflammation Research

Ghent University Hospital

VIB-UGent Center for Plant Systems Biology

VIB-KU Leuven Center for Brain & Disease Research

University of Antwerp

VIB-UGent Center for Medical Biotechnology

Cancer Research Institute Ghent

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A “Human-in-the-Loop” Approach for Semi-automated Image Restoration in Electron Microscopy

bioRxiv (Cold Spring Harbor Laboratory) (2019)

Joris Roels Frank Vernaillen Anna Kremer Amanda Gonçalves Jan Aelterman

ABSTRACT The recent advent of 3D in Electron Microscopy (EM) has allowed for detection of detailed sub-cellular nanometer resolution structures. While being a scientific breakthrough, this has also caused an explosion in dataset size, necessitating the development of automated workflows. Automated workflows typically benefit reproducibility and throughput compared to manual analysis. The risk of automation is that it ignores the expertise of the microscopy user that comes with manual analysis. To mitigate this risk, this paper presents a hybrid paradigm. We propose a ‘human-in-the-loop’ (HITL) approach that combines expert microscopy knowledge with the power of large-scale parallel computing to improve EM image quality through advanced image restoration algorithms. An interactive graphical user interface, publicly available as an ImageJ plugin, was developed to allow biologists to use our framework in an intuitive and user-friendly fashion. We show that this plugin improves visualization of EM ultrastructure and subsequent (semi-)automated segmentation and image analysis.

Plug-in

Graphical user interface

Human-in-the-loop

10.1101/644146

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Citations (3)

GSK3ß, a centre-staged kinase in neuropsychiatric disorders, modulates long term memory by inhibitory phosphorylation at Serine-9

Neurobiology of Disease (2009)

Ilse Dewachter Laurence Ris Tomasz Jaworski Claire M. Seymour Anna Kremer

Anisomycin

Cognitive Decline

10.1016/j.nbd.2009.04.003

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Citations (86)

Three-dimensional ultrastructure of the brain pericyte-endothelial interface

Journal of Cerebral Blood Flow & Metabolism (2021)

Sharon Ornelas Andrée‐Anne Berthiaume Stephanie Bonney Vanessa Coelho‐Santos Robert G. Underly

Pericytes and endothelial cells share membranous interdigitations called “peg-and-socket” interactions that facilitate their adhesion and biochemical crosstalk during vascular homeostasis. However, the morphology and distribution of these ultrastructures have remained elusive. Using a combination of 3D electron microscopy techniques, we examined peg-and-socket interactions in mouse brain capillaries. We found that pegs extending from pericytes to endothelial cells were morphologically diverse, exhibiting claw-like morphologies at the edge of the cell and bouton-shaped swellings away from the edge. Reciprocal endothelial pegs projecting into pericytes were less abundant and appeared as larger columnar protuberances. A large-scale 3D EM data set revealed enrichment of both pericyte and endothelial pegs around pericyte somata. The ratio of pericyte versus endothelial pegs was conserved among the pericytes examined, but total peg abundance was heterogeneous across cells. These data show considerable investment between pericytes and endothelial cells, and provide morphological evidence for pericyte somata as sites of enriched physical and biochemical interaction.

Pericyte

Crosstalk

10.1177/0271678x211012836

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Citations (50)

Sensory neuropathy-causing mutations in ATL3 cause aberrant ER membrane tethering

bioRxiv (Cold Spring Harbor Laboratory) (2017)

Michiel Krols Sammy Detry Bob Asselbergh Leonardo Almeida-Souza Anna Kremer

SUMMARY The ER is a complex network of sheets and tubules that is continuously being remodeled. The relevance of this membrane dynamics is underscored by the fact that mutations in Atlastins (ATL), the ER fusion proteins in mammals, cause neurodegeneration. How defects in this process disrupt neuronal homeostasis is largely unknown. Here we show by EM volume reconstruction of transfected cells, neurons and patient fibroblasts that the HSAN-causing ATL3 mutants promote aberrant ER tethering hallmarked by bundles of laterally attached ER tubules. In vitro , these mutants cause excessive liposome tethering, recapitulating the results in cells. Moreover, ATL3 variants retain their dimerization-dependent GTPase activity, but are unable to promote membrane fusion, suggesting a defect on an intermediate step of the ATL3 functional cycle. Our data therefore show that the effects of ATL3 mutations on ER network organization stretch beyond a loss of fusion, shedding a new light on neuropathies caused by atlastin defects.

10.1101/192484

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Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver

Immunity (2020)

Anneleen Remmerie Liesbet Martens Tinne Thoné Ângela Castoldi Ruth Seurinck

Metabolic-associated fatty liver disease (MAFLD) represents a spectrum of disease states ranging from simple steatosis to non-alcoholic steatohepatitis (NASH). Hepatic macrophages, specifically Kupffer cells (KCs), are suggested to play important roles in the pathogenesis of MAFLD through their activation, although the exact roles played by these cells remain unclear. Here, we demonstrated that KCs were reduced in MAFLD being replaced by macrophages originating from the bone marrow. Recruited macrophages existed in two subsets with distinct activation states, either closely resembling homeostatic KCs or lipid-associated macrophages (LAMs) from obese adipose tissue. Hepatic LAMs expressed Osteopontin, a biomarker for patients with NASH, linked with the development of fibrosis. Fitting with this, LAMs were found in regions of the liver with reduced numbers of KCs, characterized by increased Desmin expression. Together, our data highlight considerable heterogeneity within the macrophage pool and suggest a need for more specific macrophage targeting strategies in MAFLD.

Osteopontin

Steatohepatitis

Steatosis

Pathogenesis

Kupffer cell

10.1016/j.immuni.2020.08.004

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Citations (391)

Optimized protocol for the three-dimensional visualization and reconstruction of intercellular junctions in cardiac muscle using SBF-SEM and FIB-SEM

Bieke Vanslembrouck Anna Kremer Benjamin Pavie Frans van Roy Saskia Lippens

Cardiac muscle

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Cesarean Delivery and Operative Vaginal Delivery

Obstetrics and gynecology. (2020)

Francesco Callipari Anna Kremer Fahimeh Sasan Jian Jenny Tang

Cesarean delivery is safe and has significantly reduced both fetal and maternal morbidity and mortality. Compared to vaginal delivery, women undergoing cesarean delivery are at higher risk for short-term and long-term health consequences. This chapter provides information on the background of the procedure, including its incidence/prevalence and economic impact. Given the morbidity associated with cesarean deliveries, the American College of Obstetrics and Gynecologists and Society for Maternal-Fetal Medicine recently published a consensus statement in attempting to reduce the incidence of primary cesarean delivery. The chapter discusses the indications, delivery timing, precesarean antibiotics, laboratory testing, and delivery techniques, for primary cesarean delivery. It also describes operative vaginal delivery and its classification, as well as vacuum-assisted vaginal delivery.

Cesarean delivery

10.1002/9781119450047.ch11

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Systematic optimization of siRNA productive uptake into resting and activated T cellsex vivo

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Anna Kremer Tatyana Ryaykenen RA Haraszti

Abstract RNA-based medicines are ideally suited for precise modulation of T cell phenotypes in anti-cancer immunity, in autoimmune diseases and for ex vivo modulation of T-cell-based therapies. Therefore, understanding productive siRNA uptake to T cells is of particular importance. Most studies used unmodified siRNAs or commercially available siRNA with undisclosed chemical modifications patterns to show functionality in T cells. Despite being an active field of research, robust siRNA delivery to T cells still represents a formidable challenge. Therefore, a systematic approach is needed to further optimize and understand productive siRNA uptake pathways to T cells. Here we compared conjugate-mediated and nanoparticle-mediated delivery of siRNAs to T cells in the context of fully chemically modified RNA constructs. We showed that lipid-conjugate-mediated delivery outperforms lipid-nanoparticle-mediated and extracellular-vesicle-mediated delivery in activated T cells ex vivo . Yet, ex vivo manipulation of T cells without the need of activation is of great therapeutic interest for CAR-T, engineered TCR-T and allogeneic donor lymphocyte applications. We are first to report productive siRNA uptake into resting T cells using lipid-conjugate mediated delivery. Interestingly, we observed strong dependence of silencing activity on lipid-conjugate-identity in resting T cells but not in activated T cells. This phenomenon is consistent with our early uptake kinetics data. Lipid-conjugates also enabled delivery of siRNA to all mononuclear immune cell types, including both lymphoid and myeloid lineages. These findings are expected to be broadly applicable for ex vivo modulation of immune cell therapies.

Ex vivo

10.1101/2023.10.20.563275

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Glycogen synthase kinase‐3β, or a link between amyloid and tau pathology?

Genes Brain & Behavior (2008)

David Muyllaert Anna Kremer Tomasz Jaworski Peter Borghgraef Herman Devijver

Phosphorylation is the most common post‐translational modification of cellular proteins, essential for most physiological functions. Deregulation of phosphorylation has been invoked in disease mechanisms, and the case of Alzheimer’s disease (AD) is no exception: both in the amyloid pathology and in the tauopathy are kinases deeply implicated. The glycogen synthase kinase‐3 (GSK‐3) isozymes participate in diverse cellular processes and important signalling pathways and have been implicitly linked to diverse medical problems, i.e. from diabetes and cancer to mood disorders and schizophrenia, and in the neurodegeneration of AD. Here, we review specific aspects of GSK‐3 isozymes in the framework of recent data that we obtained in novel transgenic mouse models that robustly recapitulate the pathology and mechanistical problems of AD.

GSK3B

Amyloid (mycology)

10.1111/j.1601-183x.2007.00376.x

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Citations (130)

Intercalated discs : specialized cytoskeletal anchors in cardiac muscle

Jolanda van Hengel Maarten De Smet Anna Kremer Saskia Lippens Marjolijn Renard

Cardiac muscle

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