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Biology subjects

Lang, R.

Publications and source records attributed to Lang, R..

14 recordsLinked to original sources

A pro-inflammatory effector-memory T cell program links peripheral EBV priming to CNS autoimmunity

T and B cell-mediated immunosurveillance of the central nervous system (CNS) can become maladaptive in multiple sclerosis (MS). Epstein-Barr virus (EBV) is a likely driver of MS, yet how exactly EBV-specific T cells contribute remains unclear. We generated an antigen-resolved atlas of blood and cerebrospinal fluid (CSF) T cells from untreated MS patients and controls. T cell clones carrying a GZMK effector-memory program in blood were CSF-biased, particularly in MS, and associated with EBV reactivity. In CSF, EBV-reactive GZMK CD8 T cells engaged B lineage cells. Activated CD8 T cells promoted atypical B cell and plasmablast formation, whereas GZMK-enriched effector-memory cells induced IL-6 and IL-8 release from myeloid cells. Together, these findings identify an infection-imprinted, CNS-biased state and support a model in which EBV-specific CD8 T cells contribute to inflammation through a non-canonical mode of B cell and myeloid cell activation.

immunology↗

The lipid A acylation pattern of Coxiella burnetii prevents detection and clearance by the non-canonical inflammasome in primary murine macrophages

C. burnetii is a Gram-negative, obligate intracellular bacterium and the causative agent of Q fever. The disease is either asymptomatic or manifests as a mild flu-like illness, but pneumonia or hepatitis might also occur. In most cases, the infection is self-limiting and the pathogen is cleared. In a small percentage of patients, the host immune system fails to eliminate the pathogen, potentially allowing the development of chronic Q fever months or even years after primary infection. The elimination of the bacteria, and thereby prevention of disease onset, would require an inflammatory response. Inflammasomes are multimeric protein complexes that induce a pro-inflammatory response to combat pathogens. Here we show that C. burnetii fails to induce a strong activation of the non-canonical inflammasome, independently of its type IVB secretion system. However, the pathogen is unable to prevent external activation of the non-canonical inflammasome, which subsequently results in a reduction of the bacterial burden. Importantly, the acylation pattern of lipid A was identified to be involved in avoiding the activation of the non-canonical inflammasome. C. burnetii harbors a tetra-acylated lipid A. Modification of the C. burnetii lipid A to penta-/hexa-acylation resulted in increased secretion of IL1{beta} and reduced bacterial load. Together, these results suggest that the acylation pattern of lipid A constitutes an important immune evasion strategy of C. burnetii by failing to activate the non-canonical inflammasome. In addition, evidence was provided that oxygen limitation arrests activation of the NLRP3 inflammasome in murine BMDM, which might prevent efficient elimination of bacteria under hypoxic conditions, such as in granulomas or in inflamed tissue. AUTHOR SUMMARYSeveral pathogens have evolved mechanisms to persist in the human host, which allows reoccurring or late onset of infection. The human innate immune system has therefore established several pathways, including the inflammasome, to prevent bacterial survival. Here we show that the obligate intracellular pathogen Coxiella burnetii, the causative agent of Q fever, prevents detection by the non-canonical NLRP3 inflammasome. This is mediated by the acylation pattern of its lipid A. Altering this acylation pattern allows activation of the inflammasome and, consequently, improved clearance of the pathogen. This information opens new avenues to target the immune response to C. burnetii infection with the goal to eliminate the bacteria and thereby prevent disease.

immunology↗

Discovery of potent oligopeptides for various metabolic diseases using deep learning

Artificial intelligence (AI)-based methods are increasingly critical in peptide drug discovery, but their applications are limited in a narrow scope such as antimicrobial peptides. For indications where peptide therapy inherently excels, such as metabolism, endocrinology, and tissue regeneration, AI-based pipeline for therapeutic peptide discovery is long awaited but still unmet. Here, we propose a deep learning-based pipeline, Deepeptide, capable of identifying therapeutic oligopeptides for various metabolism-related indications. Leveraging the intrinsical relationship of disease indication -- biological processes -- molecular functions, Deepeptide discovers oligopeptides with indication-ameliorating-related molecular functions as lead candidates for indication of interest. Deepeptide was applied in five representative indications of metabolism, endocrinology, and tissue regeneration: angiogenesis, lipid metabolism, osteogenesis, glucose metabolism, and anti-angiogenesis. Overall, 62% of the identified oligopeptide candidates demonstrated significant bioactivity in vitro, with most of them showing comparable potency to the first-line drugs. Notably, the heptapeptide AP7 exhibited angiogenic potency comparable to VEGF in excisional wound splinting mouse model by promoting cell migration rather than proliferation, and hexapeptide TP6 showed significant dual-efficacy against hyperlipidemia and obesity in high-fat diet mice by inhibiting lipid synthesis and regulating gut microbiota. These findings highlight the potential and generalizability of Deepeptide in therapeutic oligopeptide discovery for metabolic diseases.

bioinformatics↗

LRP8 is a Receptor for Yellow Fever Virus

Yellow fever virus (YFV), an arbovirus causing substantial human morbidity and mortality, was the first human virus discovered over a century ago. The live-attenuated 17D vaccine is among the most successful vaccines in medicine. Despite the importance of YFV, its receptor has remained unknown. Here, we performed a barcoded, genome-wide human ORF library screen and identified LRP8 (also named APOER2) as a receptor for YFV. We show that LRP8 expression specifically boosts YFV infection in cell lines by promoting entry. AAV-mediated expression of human LRP8 in mouse liver aggravates infection and pathology. LRP8 knockdown abolishes YFV infection in brain cells, primary human hepatocytes, and notably in mosquitoes. Biochemically, LRP8 directly interacts with YFV particles via the viral envelope protein. This function of LRP8 is conserved across species, particularly in mosquitoes and primates. A soluble LRP8 decoy protein can block YFV infection in vitro and in mice, providing a potential therapeutic or prophylactic strategy. Our findings provide groundwork for understanding YFV entry, tropism, and pathogenesis, and may enable development of novel therapeutics to treat YFV infection.

microbiology↗

Coxiella burnetii infects osteoclasts and alters their differentiation and function in a type IV secretion system-dependent manner

1Chronic Q fever is caused by persistent infection with the Gram-negative bacterium Coxiella burnetii. The mechanisms underlying this persistence remain elusive, but the presence of the bacteria in the bone marrow of C. burnetii-infected patients has been demonstrated. Therefore, we investigated the potential role of osteoclasts, the bone-resorbing cells, in harboring C. burnetii during the infection. The histological analysis of bones from a murine model of Q fever revealed the presence of C. burnetii inside osteoclasts. In vitro infection assays confirmed that osteoclasts can be infected with C. burnetii and supported bacterial replication in a type IVB secretion system (T4BSS)-dependent manner. Wild-type C. burnetii infection inhibited osteoclast differentiation and bone-resorbing activity, while the T4BSS mutant enhanced the differentiation and bone-degrading function of osteoclasts. Taken together, our findings identify osteoclasts as a potential host cell for C. burnetii, opening new perspectives on mechanisms that may underlie chronic Q fever. Additionally, infection-induced alterations in osteoclast function raise the possibility of alterations of the bone structure in affected patients.

immunology↗

CellSexID: Sex-Based Computational Tracking of Cellular Origins in Chimeric Models

Cell tracking in chimeric models is essential yet challenging, particularly in developmental biology, regenerative medicine, and transplantation research. Existing methods such as fluorescent labeling and genetic barcoding are technically demanding, costly, and often impractical for dynamic or heterogeneous tissues. Here, we introduce CellSexID, a computational framework that leverages sex as a surrogate marker for cell origin inference. Using a machine learning model trained on single-cell transcriptomic data, CellSexID accurately predicts the sex of individual cells, enabling in silico distinction between donor and recipient cells in sex-mismatched settings. The model identifies minimal sex-linked gene sets through ensemble feature selection and has been validated using both public datasets and experimental flow sorting, confirming the biological relevance of predicted populations. We further demonstrate CellSexIDs applicability beyond chimeric models, including organ transplantation and multiplexed sample demultiplexing. As a scalable and cost-effective alternative to physical labeling, CellSexID facilitates precise cell tracking and supports diverse biomedical applications involving mixed cellular origins.

bioinformatics↗

A marsh samphire (Salicornia europaea) extract induces a strictly sex-specific, Tor-signaling-dependent extension of lifespan and exhibits anti-obesogenic properties

We have studied the health-promoting properties of the marsh samphire Salicornia europaea by employing the fruit fly Drosophila melanogaster. Supplementing a standard diet with 0.2% of an aqueous extract of this halophilic plant (SEE), which grows in sandy and muddy habitats in intertidal zones, extended the lifespan of two different Drosophila strains by up to a third. This effect was strictly sex-specific and only affected females. When analyzing the body composition, we found that the body fat content of SEE-treated female flies was lower compared to controls. The extract also positively impacted the lifespan of flies fed a high-fat diet but not a high-sugar diet. It is of note in this context that SEE exhibited a lipase-inhibitory activity in vitro. Moreover, SEE counteracted ageing-associated loss of intestinal barrier integrity. The sex-specific lifespan extensions induced by the SEE were entirely dependent on functional Tor signaling in the flies. Tissue-specific silencing of the Tor signalling pathway in different cellular compartments of the intestine reduced, but did not completely abolish, the lifespan-prolonging effect in females. This suggests that other organs also contribute to this effect. In contrast to the observation that Tor signalling is necessary for the life-prolonging effect, Foxo deficiency led to a reduction in the effect, but not to its complete absence. In conclusion, the SEE is a promising candidate for a health-promoting intervention, and we laid the current groundwork for identifying the compounds that mediate this effect in future studies.

physiology↗

Regulatory Functional Landscape of the HMX1 Gene for Normal Ear Development

Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the spatial specificity and the levels of gene expression, and their aberrations can result in diseases. The association between HMX1 and its downstream enhancer with ear deformities has been previously documented. However, the pathogenic variations and molecular mechanisms underlying the bilateral constricted ear (BCE) malformations remain unclear. This study identifies a copy number variation (CNV) encompassing three enhancers that induces BCE. These enhancers, collectively termed the positional identity hierarchical enhancer cluster (PI-HEC), co-regulate spatiotemporal expression of the HMX1 gene in a coordinated and synergistic mode, each displaying unique activity-location-structure characteristics. A thorough exploration of this regulatory locus reveals that specific motif clusters within the PI-HEC variably modulate its activity and specificity, with the high mobility group (HMG) box combined with Coordinator and homeodomain (HD)-TFs notably influencing them respectively. Our findings based on various types of mouse models, reveal that both aberrant Hmx1 expression in the fibroblasts of the basal pinna, originating from neural crest cells, and ectopic expression in the distal pinna structures contribute to the abnormal development of the outer ear, including the cartilage, muscle, and epidermis tissues. This study deepens our understanding of mammalian ear morphogenesis and sheds light on the complexity of gene expression regulation by enhancers and specific sequence motifs.

developmental biology↗

Defining the SPCA2C interactome identifies unique links to store-operated calcium entry

Calcium (Ca2+) is critical for normal cell function and several protein networks are required for Ca2+ signaling. In the pancreas, regulated changes in cytosolic Ca2+ allow for the exocytosis of zymogen granules and altered Ca2+ signaling underlies pancreatic pathologies. Previously, our laboratory showed a pancreas-specific isoform of secretory pathway Ca2+-ATPase 2 (SPCA2C) affects multiple pathways involved in Ca2+ homeostasis. The goal of this study was to define the SPCA2C interactome that contributes to these processes. Using proximity-dependent biotin identification, BioID, we expressed SPCA2C-BirA*HA in HEK293 cells with constitutive Orai1 expression. In silico modeling of SPCA2C showed a highly dynamic cytosolic C-terminus, revealing a putative site for interactions and was selected for BirA* fusion. 150 candidate SPCA2C interactors were identified. Gene Ontology and KEGG Pathway analyses supported localization of SPCA2C to the endoplasmic reticulum as well as function in Ca2+ signaling and suggested roles in vesicular transport. SPCA2C interactions with stromal interaction molecule 1 (STIM1), extended synaptotagmin-1 (ESYT1), and aspartate beta-hydroxylase (ASPH) were validated. Coiled-coil domain containing protein 47 (CCDC47) ranked as a high confidence SPCA2C-interactor which was confirmed through immunoprecipitation and co-localization with SPCA2C. CCDC47 interactions with SPCA2C, STIM1 and Orai1 were maintained following deletion of the CCDC47 luminal and cytosolic domains while deletion of only the coiled-coil domain altered CCDC47 localization and decreased interactions with STIM1 and Orai1. Overall, this study defines several novel protein interactions for SPCA2C and suggests it may be involved in affecting CCDC47, STIM1 and Orai1 function.

cell biology↗

Macrophages inhibit Coxiella burnetii by the ACOD1-itaconate pathway for containment of Q fever

Infection with the intracellular bacterium Coxiella (C.) burnetii can cause chronic Q fever with severe complications and limited treatment options. Here, we identify the enzyme cis- aconitate decarboxylase 1 (ACOD1 or IRG1) and its product itaconate as protective host immune pathway in Q fever. Infection of mice with C. burnetii induced expression of several anti-microbial candidate genes, including Acod1. In macrophages, Acod1 was essential for restricting C. burnetii replication, while other antimicrobial pathways were dispensable. Intratracheal or intraperitoneal infection of Acod1-/- mice caused increased C. burnetii burden, significant weight loss and stronger inflammatory gene expression. Exogenously added itaconate restored pathogen control in Acod1-/- mouse macrophages and blocked replication in human macrophages. In axenic cultures, itaconate directly inhibited growth of C. burnetii. Finally, treatment of infected Acod1-/-mice with itaconate efficiently reduced the tissue pathogen load. Thus, ACOD1-derived itaconate is a key factor in the macrophage-mediated defense against C. burnetii and may be exploited for novel therapeutic approaches in chronic Q fever.

immunology↗

Preclinical establishment of a divalent vaccine against SARS-CoV-2

First-generation vaccines against SARS-CoV-2 have been administered to more than 60% of the population in developed countries. However, the monovalent vaccines currently available in Europe do not confer adequate and durable immune protection. To satisfy the need for a novel vaccine, we engineered a divalent gene construct consisting of the receptor binding domain (RBD, 300-685 aa) of the spike protein and the immunodominant region of the nucleocapsid (100-300 aa). This fusion protein was cloned into a pET-30a plasmid and expressed either in Escherichia coli or in a recombinant baculovirus in insect cells. Following purification via its His-tag, the fusion protein was mixed with adjuvant, and administered to mice in a prime-booster-mode. Upon testing for IgG antibody response against nucleocapsid and RBD, a titer of 10-4 - 10-5 was demonstrated 14 days after the first booster injection in 72% of the animals, which could be increased to 100% by a second booster. Notably, comparable IgG responses were detected against the delta, gamma and omicron variants of the RBD region. Durability testing revealed the presence of IgG beyond 90 days. In addition, granzyme A and perforin mRNA expression (cytolytic effector cell molecules) was increased in cytotoxic lymphocytes isolated from peripheral blood. Ex vivo stimulation of T-cells by nucleocapsid and RBD peptides showed antigen-specific upregulation of CD44 in vaccinated mice among their CD4+ and CD8+ T-cells. No side-effect was documented in the central nervous system, be it either endothelial inflammation or neuronal damage. Cumulatively, the combined induction of B-cell and T-cell response by a bivalent protein-based vaccine directed against two structural SARS-CoV-2 proteins represents a proof-of-principle approach alternative to existing mRNA vaccination strategies, which could confer long-lasting immunity against all known viral strains.

bioengineering↗

IL-4 and helminth infection downregulate MINCLE-dependent macrophage response to mycobacteria and Th17 adjuvanticity

The myeloid C-type lectin receptor (CLR) MINCLE senses the mycobacterial cell wall component trehalose-6,6-dimycolate (TDM). Recently, we found that IL-4 down-regulates MINCLE expression in macrophages. IL-4 is a hallmark cytokine in helminth infections, which appear to increase the risk for mycobacterial infection and active tuberculosis. Here, we investigated functional consequences of IL-4 and helminth infection on MINCLE-driven macrophage activation and Th1/Th17 adjuvanticity. IL-4 inhibited MINCLE and cytokine induction after macrophage infection with Mycobacterium bovis Bacille Calmette-Guerin (BCG). Infection of mice with BCG upregulated MINCLE on myeloid cells, which was inhibited by IL-4 plasmid injection and by infection with the nematode Nippostrongylus brasiliensis in monocytes. To determine the impact of helminth infection on MINCLE-dependent immune responses, we vaccinated mice with a recombinant protein together with the MINCLE ligand Trehalose-6,6-dibehenate (TDB) as adjuvant. Concurrent infection with N. brasiliensis or with Schistosoma mansoni promoted T cell-derived IL-4 production and suppressed Th1/Th17 differentiation in the spleen. In contrast, helminth infection did not reduce Th1/Th17 induction by TDB in draining peripheral lymph nodes, where IL-4 levels were unaltered. Upon use of the TLR4-dependent adjuvant G3D6A, N. brasiliensis infection impaired selectively the induction of splenic antigen-specific Th1 but not of Th17 cells. Thus, helminth infection attenuated the Th17 response to MINCLE-dependent immunization in an organ-specific manner. Taken together, our results demonstrate down-regulation of MINCLE expression on monocytes and macrophages by IL-4 as a possible mechanism of thwarted Th17 vaccination responses by underlying helminth infection.

immunology↗

Virtual-SMLM, a virtual environment for real-time interactive SMLM acquisition

Although single molecule localisation microscopy enables for the visualisation of cells nanoscale organisation, its dissemination remains limited mainly due to the complexity of the associated imaging acquisition, impacting on outputs reliability and reproducibility. We propose here the first all-in-one fully virtual environment for SMLM acquisition: Virtual-SMLM, including on-the-fly interactivity and real time display. It relies on a novel realistic approach to simulate fluorophores photo-physics based on independent pseudo-continuous emission traces. It also facilitates for user-specific experimental and optical environment design. As such, it constitutes a unique tool for the training of both users and machine learning approaches to automated SMLM, as well as for experimental validation, whilst providing realistic data sets for the development of image reconstruction algorithms and data analysis software.

biophysics↗

Light responses of melanopsin-expressing ganglion cells in the foetal mammalian retina

Sensory stimulation plays a critical role in the maturation of sensory organs and systems. For example, when deprived of light before birth, foetal mouse pups in utero exhibit altered ocular vascular development. Normal vascular development depends on light excitation of melanopsin, a non-rod, non-cone photopigment that is expressed in a subset of ganglion cells (mRGCs) in the retina. However, there is no direct evidence that mRGCs in foetal eyes are light-responsive. Very little is known about how light absorption leads to excitation in these foetal neurons. Using mRGC-specific expression of the calcium indicators GCaMP3 and GCaMP6, we report that foetal mouse mRGCs respond to light as early as 4 days before birth. Further, two distinct Gq/11-G protein family antagonists, FR9000359 and YM-254890, abolish these light responses. TTX, a blocker of voltage-activated sodium channels, reversibly represses light responses, and FPL6417 and L-cis-diltiazem, which modify L-type calcium channels, respectively increase and reduce light responses. Electrophysiological patch pipette recordings show that embryonic mRGCs respond to light of intensity as low as 2.9 x 1012 photons/cm2/s. The present findings demonstrate a heretofore unproven but postulated light sensitivity in the retinas of foetal mice and identify the transduction pathways involved. Surprisingly, mRGCs do not function as completely independent photoreceptors but are electrotonically coupled with other mRGCs. Given that melanopsin is expressed in foetal human retinas, these findings support the idea that the eyes of foetal and early preterm infants are likely to exhibit functional photosensitivity.\n\nKey pointsO_LIMelanopsin is a light-excitable photopigment expressed in a subset of ganglion cell neurons (mRGCs) in the retinas of many different species of vertebrates. In mature animals, light activation of mRGCs modulates many visual adaptive functions including pupil constriction, entrainment of circadian rhythms, mood and learning. In neonatal pups at ages prior to the developmental onset of visual signalling from rods and cones, melanopsin cells mediate photoaversive behaviour. In foetal pups, light activation of melanopsin cells accelerates maturation of the ocular vasculature. Here, we describe and physiologically characterize the light responses of melanopsin ganglion cells in the retinas of foetal pups.\nC_LIO_LIMRGCs in embryonic retinas respond to light at least four days prior to birth and exhibit responses to light of intensity as low as 3 x 1012 photons/cm2/s.\nC_LIO_LIPhototransduction mechanisms include melanopsin activation of Gq/11 - G proteins, voltage-activated sodium currents, and voltage-gated L-type calcium currents.\nC_LIO_LIMRGCs are electrotonically coupled to other mRGCs in foetal retinas.\nC_LIO_LIWe propose that melanopsin-expressing ganglion cells are excited by light while in utero and that this excitation relies, for the most part, on phototransduction pathways that have been described in postnatal retinas. Furthermore, we propose that foetal mRGCs have the requisite properties to modulate light-regulated maturation of the ocular vasculature and, perhaps, the development of visual pathways.\nC_LI

neuroscience↗