Biology subjects

Hocke, A. C.

Publications and source records attributed to Hocke, A. C..

8 recordsLinked to original sources

bioRxiv2025

An autologous human iPSC-derived 3D organoid infection model for preclinical testing of antiviral T cells

Immunocompromised patients, such as those undergoing hematopoietic stem cell or solid organ transplantation, are highly susceptible to viral complications. Given the limitations and side effects of available antiviral therapies, adoptive transfer of antiviral T cells offers a promising alternative by restoring immune defense. However, existing models for evaluating antiviral T cell therapies lack physiological relevance, limiting accurate predictions of efficacy and safety. There is a critical need for in vitro human infection platforms that support personalized assessment of therapeutic responses. To address this, we developed antiviral T cell products (TCPs) targeting Influenza A virus (IAV)-infected cells, alongside an autologous human induced pluripotent stem cell (iPSC)-derived 3D lung organoid infection platform. This model recapitulates key immunological responses and is compatible with a new 3D high-throughput, high-content imaging pipeline. Our study provides the first proof-of-concept for assessing T cell-mediated cytotoxicity in a 3D in vitro lung infection model, advancing personalized antiviral immunotherapy development.

immunology↗

bioRxiv2024

Phage-phage competition and biofilms reduce the efficacy of a combination of two virulent bacteriophages against Pseudomonas aeruginosa

Combined use of virulent bacteriophages (phages) and antibiotics reduces the severity of difficult-to-treat Pseudomonas aeruginosa infections in many patients. In vitro methods that attempt to reproduce more than one physiological state of the pathogens can provide a valuable assessment of antibacterials like phages. Here, by measuring bacterial killing kinetics and individual replication in different growth conditions, including biofilms and a human lung epithelial cell line, we elucidated factors influencing the efficacy of two virulent phages against P. aeruginosa PAO1. A single administration of phages effectively reduced the P. aeruginosa viability in planktonic conditions and infected human lung cell cultures, however, the emergence of phage-resistant variants occurred subsequently. In static biofilms, the phage combination displayed initial inhibition of biofilm dispersal, but sustained control was achieved only by combining phages and meropenem. In contrast, surface-attached biofilms exhibited tolerance to phage and/or meropenem, suggesting a spatiotemporal variation in the antibacterial effect. Moreover, the phage with the shorter lysis time lysed P. aeruginosa more rapidly and selected a specific nucleotide polymorphism that conferred a competitive disadvantage and cross-resistance to the second phage of the combination. The sequential addition of phages resulted in their unimpeded replication with no increase in bacteriolytic activity. These findings highlight biofilm developmental stages, phage-phage competition, and phage resistance as factors restricting the in vitro efficacy of a two-phage combination. Our findings provide a framework for selecting and optimizing phage combinations for enhanced efficacy against P. aeruginosa, a metabolically flexible pathogen that undergoes specific adaptation within the infected lung.

microbiology↗

bioRxiv2024

IGF1R is protective in pneumococcal pneumonia

BackgroundStreptococcus pneumoniae (S.pn) is the most prevalent causal bacterial pathogen in community-acquired pneumonia. Despite appropriate antimicrobial therapy, pneumococcal pneumonia can progress to acute respiratory distress syndrome where actual therapies are mainly supportive, and the discovery of new molecular targets is needed. ObjectiveTo investigate the role of IGF1R (Insulin-like Growth Factor 1 Receptor) in pneumococcal pneumonia. MethodsIgf1r-deficient (UBC-CreERT2; Igf1rfl/fl) and control (Igf1rfl/fl) mice were infected with 5x106 S.pn (PN36) or PBS (sham infected). Mice were sacrificed 48 h after infection. Pulmonary permeability, local inflammatory response, and pulmonary and extra-pulmonary bacterial loads were analyzed. Further, IGF1R protein expression was determined in human lung tissue after S.pn infection and IGF1 and IGF1R levels were determined serum of pneumonia patients. ResultsIn patients and mice infected with S.pn, IGF1 signaling was significantly altered. Igf1r-deficient mice had significantly increased pulmonary permeability after infection with increased pulmonary inflammatory cytokine levels, while inflammatory cell recruitment was not altered compared to infected Igf1rfl/fl control animals. Pulmonary bacterial load was significantly higher in Igf1r-deficient mice, and histological analysis confirmed increased alveolar edema and necrosis compared to infected Igf1rfl/fl control and sham-infected mice. Ex vivo, S.pn caused a decrease in IGF1R protein expression in human lung tissue. ConclusionOur results demonstrate a significant regulation of IGF1R in ex-vivo infected human lung tissue and in serum of S.pn pneumonia patients. Moreover, pneumonia severity was increased in Igf1r-deficient mice upon S.pn infection compared to Igf1rfl/fl control mice, suggesting that IGF1R plays a protective role in pneumococcal pneumonia.

molecular biology↗

bioRxiv2024

Inference of alveolar capillary network connectivity from blood flow dynamics

The intricate structure of the lungs is essential for the gas exchange within the alveolar region. Despite extensive research on the pulmonary vasculature, there are still unresolved questions regarding the connection between capillaries and the vascular tree. A major challenge is obtaining comprehensive experimental data that integrates morphological and physiological aspects. We propose a computational approach that combines data-driven 3D morphological modeling with computational fluid dynamics simulations. This method enables investigating the connectivity of the alveolar capillary network with the vascular tree based on the dynamics of blood flow. We developed 3D sheet-flow models to accurately represent the morphology of the alveolar capillary network and conducted computational fluid dynamics simulations to predict flow velocities and pressure distributions. Our approach focuses on leveraging functional features to identify the most plausible architecture of the system. For given capillary flow velocities and arteriole-to-venule pressure drops, we deduce details about arteriole connectivity. Preliminary connectivity analyses for non-human species indicate that their alveolar capillary network of a single alveolus is linked to at least two arterioles with diameters of 20 {micro}m or a single arteriole with a minimum diameter of 30 {micro}m. Our study provides insights into the structure of the pulmonary microvasculature by evaluating blood flow dynamics. This inverse approach represents a new strategy to exploit the intricate relationship between morphology and physiology, applicable to other tissues and organs. In the future, the availability of experimental data will play a pivotal role in validating and refining the hypotheses analyzed with our computational models. New and noteworthyThe alveolus is pivotal for gas exchange. Due to its complex morphology and dynamic nature, structural experimental studies are challenging. Computational modeling offers an alternative. We developed a databased 3D model of the alveolar capillary network and performed blood flow simulations within it. Choosing a novel perspective, we inferred structure from function. We systematically varied properties of vessels connected to our capillary network and compared simulation results with experimental data to obtain plausible vessel configurations.

physiology↗

bioRxiv2022

Tissue protective role of Ganetespib in SARS-CoV-2-infected Syrian golden hamsters

The emergence of new SARS-CoV-2 variants, capable of escaping the humoral immunity acquired by the available vaccines, together with waning immunity and vaccine hesitancy, challenges the efficacy of the vaccination strategy in fighting COVID-19. Improved therapeutic strategies are therefore urgently needed to better intervene particularly in severe cases of the disease. They should aim at controlling the hyper-inflammatory state generated upon infection, at reducing lung tissue pathology and endothelial damages, along with viral replication. Previous research has pointed a possible role for the chaperone HSP90 in SARS-CoV-2 replication and COVID-19 pathogenesis. Pharmacological intervention through HSP90 inhibitors was shown to be beneficial in the treatment of inflammatory diseases, infections and reducing replication of diverse viruses. In this study, we analyzed the effects of the potent HSP90 inhibitor Ganetespib in vitro on alveolar epithelial cells and alveolar macrophages to characterize its effects on cell activation and viral replication. Additionally, to evaluate its efficacy in controlling systemic inflammation and the viral burden after infection in vivo, a Syrian hamster model was used. In vitro, Ganetespib reduced viral replication on AECs in a dose-dependent manner and lowered significantly the expression of pro-inflammatory genes, in both AECs and alveolar macrophages. In vivo, administration of Ganetespib led to an overall improvement of the clinical condition of infected animals, with decreased systemic inflammation, reduced edema formation and lung tissue pathology. Altogether, we show that Ganetespib could be a potential medicine to treat moderate and severe cases of COVID-19.

microbiology↗

bioRxiv2021

Transcriptomic responses of the human kidney to acute injury at single cell resolution

BackgroundAcute kidney injury (AKI) occurs frequently in critically ill patients and is associated with adverse outcomes. Cellular mechanisms underlying AKI and kidney cell responses to injury remain incompletely understood. MethodsWe performed single-nuclei transcriptomics, bulk transcriptomics, molecular imaging studies, and conventional histology on kidney tissues from 8 individuals with severe AKI (stage 2 or 3 according to Kidney Disease: Improving Global Outcomes (KDIGO) criteria). Specimens were obtained within 1-2 hours after individuals had succumbed to critical illness associated with respiratory infections, with 4 of 8 individuals diagnosed with COVID-19. Control kidney tissues were obtained post-mortem or after nephrectomy from individuals without AKI. ResultsHigh-depth single cell-resolved gene expression data of human kidneys affected by AKI revealed enrichment of novel injury-associated cell states within the major cell types of the tubular epithelium, in particular in proximal tubules, thick ascending limbs and distal convoluted tubules. Four distinct, hierarchically interconnected injured cell states were distinguishable and characterized by transcriptome patterns associated with oxidative stress, hypoxia, interferon response, and epithelial-to-mesenchymal transition, respectively. Transcriptome differences between individuals with AKI were driven primarily by the cell type-specific abundance of these four injury subtypes rather than by private molecular responses. AKI-associated changes in gene expression between individuals with and without COVID-19 were similar. ConclusionThe study provides an extensive resource of the cell type-specific transcriptomic responses associated with critical illness-associated AKI in humans, highlighting recurrent disease-associated signatures and inter-individual heterogeneity. Personalized molecular disease assessment in human AKI may foster the development of tailored therapies.

molecular biology↗

bioRxiv2021

Post-entry, spike-dependent replication advantage of B.1.1.7 and B.1.617.2 over B.1 SARS-CoV-2 in an ACE2-deficient human lung cell line

Epidemiological data demonstrate that SARS-CoV-2 variants of concern (VOC) B.1.1.7 and B.1.617.2 are more transmissible and infections are associated with a higher mortality than non-VOC virus infections. Phenotypic properties underlying their enhanced spread in the human population remain unknown. B.1.1.7 virus isolates displayed inferior or equivalent spread in most cell lines and primary cells compared to an ancestral B.1 SARS-CoV-2, and were outcompeted by the latter. Lower infectivity and delayed entry kinetics of B.1.1.7 viruses were accompanied by inefficient proteolytic processing of spike. B.1.1.7 viruses failed to escape from neutralizing antibodies, but slightly dampened induction of innate immunity. The bronchial cell line NCI-H1299 supported 24- and 595-fold increased growth of B.1.1.7 and B.1.617.2 viruses, respectively, in the absence of detectable ACE2 expression and in a spike-determined fashion. Superior spread in NCI-H1299 cells suggests that VOCs employ a distinct set of cellular cofactors that may be unavailable in standard cell lines.

microbiology↗

bioRxiv2020

A SARS-CoV-2 neutralizing antibody protects from lung pathology in a COVID-19 hamster model

The emergence of SARS-CoV-2 led to pandemic spread of coronavirus disease 2019 (COVID-19), manifesting with respiratory symptoms and multi-organ dysfunction. Detailed characterization of virus-neutralizing antibodies and target epitopes is needed to understand COVID-19 pathophysiology and guide immunization strategies. Among 598 human monoclonal antibodies (mAbs) from ten COVID-19 patients, we identified 40 strongly neutralizing mAbs. The most potent mAb CV07-209 neutralized authentic SARS-CoV-2 with IC50 of 3.1 ng/ml. Crystal structures of two mAbs in complex with the SARS-CoV-2 receptor-binding domain at 2.55 and 2.70 [A] revealed a direct block of ACE2 attachment. Interestingly, some of the near-germline SARS-CoV-2 neutralizing mAbs reacted with mammalian self-antigens. Prophylactic and therapeutic application of CV07-209 protected hamsters from SARS-CoV-2 infection, weight loss and lung pathology. Our results show that non-self-reactive virus-neutralizing mAbs elicited during SARS-CoV-2 infection are a promising therapeutic strategy.

immunology↗