Biology subjects

Falk, C. S.

Publications and source records attributed to Falk, C. S..

9 recordsLinked to original sources

bioRxiv2025

Probiotic-conditioned microbiota from preterm infants modulate immune response to pathogen challenge in a humanized mouse model

AbstractEarly-life host-microbe interactions critically shape immune development, lifelong homeostasis, and disease susceptibility. The PRIMAL trial (Priming Immunity at the Beginning of Life) demonstrated that multistrain probiotics shifted the gut microbiota of very preterm infants toward eubiosis without affecting sepsis incidence, yet the immunological consequences remained unresolved. To explore this, we colonized germ-free female mice with fecal samples from probiotic- or placebo-treated preterm infants from the PRIMAL trial. Microbiota composition was vertically transmitted and stable across generations. At steady-state, 3-week-old pups colonized with probiotic-conditioned microbiota exhibited markedly reduced populations of innate immune cells, particularly in the colon, with subtler effects in the small intestine and spleen, while adaptive immune subsets were less affected. Upon enteropathogenic Escherichia coli challenge at day 5, pups harboring probiotic-conditioned microbiota displayed reduced growth and impaired bacterial clearance, correlating with diminished numbers of key innate immune cell populations. These findings demonstrate that probiotic-driven shifts in human-derived microbial communities can attenuate immune cell development in mice and alter early-life infection outcomes. Our study underscores the complex, context-dependent effects of probiotics on the neonatal microbiota-immune axis and provides mechanistic insight into how interventions in preterm infants may influence susceptibility to infection.

immunology↗

bioRxiv2025

Cerebrospinal fluid inflammome analysis identifies host-and pathogen-specific inflammatory profiles and signaling pathways in meningitis and predicts clinical outcome

Increasing evidence indicate that individual host immune response to pathogens may be as important as virulence factors in determining the severity of infection. However, most available data on pathogen-host interactions are based on in vitro findings, neglecting the genetic complexity of the immune response. We conducted a comparative observational study of bacterial and viral meningitis to identify pathogen-specific and host-dependent inflammatory pathways that may predict the severity of infection by analysing 54 inflammatory factors using plexing technology. Infection severity and neurological disability were assessed using the modified RANKIN scale. To identify pathogen-specific and host-dependent pathways, plex data were entered into EMBiology(R) software and gene set enrichment analysis (GSEA) was performed. We also investigated pathogen- and host-dependent regulatory effects on blood-brain barrier function using human iPSC-derived endothelial cells as a model. BBB function was characterised at the level of transendothelial electrical resistance (TEER), endothelial apoptosis and drug transporter activity. We identified 36 factors that are highly differentially regulated in either bacterial or viral meningoencephalitis compared to healthy subjects, 15 of which have not been previously described. GSEA identified previously unknown pathogen-specific pathways including neurotrophin, NOTCH, immune tolerance, antiviral defence and tight junction signalling. As a key finding, we identified 15 host-dependent factors that correlated with the grade of disability and with blood-CSF barrier dysfunction. GSEA revealed stronger responses of neuroprotective (AKT/ERK), anti-apoptotic (Bcl-2/p53) and anti-inflammatory (JAK1/STAT1) pathways in patients with favourable course, whereas patients with severe infection show stronger pro-inflammatory STAT-activation, NKC/CTL-responses and NF{kappa}-B-associated neurotoxicity. BBB analysis supports these findings with dysregulation of TEER, drug transporter activity and induction of endothelial cell death in patients with severe infection. Our data highlight the need for future approaches to personalised medicine that go beyond traditional anti-infective therapy to target the individual immune response. Author SummeryInfections often cause personal suffering, but also high economic costs. Brain infections such as bacterial or viral meningitis are particularly serious and carry a high risk of death or permanent disability. At the same time, resistance to anti-infective drugs is increasing and fewer new antibiotics are being developed. As a result, there is a great need for translational research to develop new treatments beyond conventional anti-infectives. Due to its strict compartmentalisation, the brain is well suited to identify specific pathogen-dependent, but also host (patient) dependent inflammatory patterns in infections. Using a cohort of patients with a defined group of pathogen-specific meningitis, we investigated the inflammatory patterns in the cerebrospinal fluid and were able to describe new specific pathogen-dependent and new host-dependent immune responses and identify associated signalling pathways. We were also able to show how and at what cellular and molecular level the blood-brain barrier is disrupted by infection. The degree of damage to the blood-brain barrier is an important aspect and has major implications for the course and prognosis of brain infections. Once the pathogen- and host-specific aspects of the immune response are understood, new personalised therapeutic approaches can be developed that directly target the regulation of the individual immune response.

immunology↗

bioRxiv2024

Aberrant and Ectopic Cell Populations of the Fibrotic Pushing Border in Restrictive Allograft Syndrome after Lung Transplantation

RationaleRestrictive allograft syndrome (RAS) is a major cause of mortality in patients following lung transplantation due to rapid progressive fibrosis in the pulmonary graft. We have only limited knowledge of the cellular and molecular mechanisms that characterize the fibrosis in the RAS lung. ObjectiveTo elucidate cellularly-resolved transcriptomic and histologic characteristics of the structural cells in human RAS lungs. MethodsSingle-nuclei RNA-sequencing was performed in peripheral lung tissues from 15 RAS patients undergoing lung re-transplantation, and from 9 healthy control lungs. Findings were validated and complemented by various histologic techniques, including immunofluorescence, RNAscope, combined Elastica van Gieson-immunohistochemistry stains, and micro-CT scans. Measurement and Main resultsDifferential gene expression analysis of our single-nuclei RNA-sequencing data revealed in human RAS lungs previously undescribed and uniquely distributed aberrant basaloid cells, ectopic COL15A1+ vascular endothelial cells, and CTHRC1+ fibrotic fibroblasts, all first characterized in idiopathic pulmonary fibrosis (IPF). In contrast to IPF, RAS lacks the cellular equivalent of bronchiolization. Histologic stains confirmed our transcriptomic discoveries and disclosed distinctive distribution patterns: Aberrant basaloid cells are primarily localized at the edge of the fibrotic pushing border, forming together with the juxtaposed CTHRC1+ fibrotic fibroblasts the fibrotic niche of alveolar fibroelastosis (AFE), the histopathological hallmark in RAS lungs. On the endothelial side, PRX+ alveolar microvasculature is lost in AFE areas. Micro-CT scans revealed that blood supply, now facilitated by expanded and ectopic COL15A1+ VE cells, changes from pulmonary to systemic perfusion. Last, our data reveals potential therapeutically-modifiable expression patterns in RAS, including genes coding for the integrin subunits v{beta}6, activators of TGF{beta}. ConclusionConsidering the marked clinical, histologic and etiologic dissimilarities of RAS and IPF, our snRNAseq study revealed a surprising general principle of cellular and molecular pathogenesis in the fibrosing lung: the entity-spanning composition of the fibrotic niche by a) aberrant basaloid cells localized at the fibrotic pushing border, b) ectopic COL15A1+ vascular ECs and c) effector CTHRC1+ fibrotic fibroblasts. This general principle justifies a flexible but cellular pathogenesis-guided transferability of potential therapeutic approaches between progressive fibrotic lung diseases.

cell biology↗

bioRxiv2023

DNA methylation profiling identifies TBKBP1 as potent amplifier of cytotoxic activity in CMV-specific human CD8+ T cells

Epigenetic mechanisms stabilize gene expression patterns during CD8+ T cell differentiation. However, although adoptive transfer of virus-specific T cells is clinically applied to reduce the risk of virus infection or reactivation in immunocompromised individuals, the DNA methylation pattern of virus-specific CD8+ T cells is largely unknown. Hence, we here performed whole-genome bisulfite sequencing of cytomegalovirus-specific human CD8+ T cells and found that they display a unique DNA methylation pattern consisting of 79 differentially methylated regions when compared to bulk memory CD8+ T cells. Among them was TBKBP1, coding for TBK-binding protein 1 that can interact with TANK-binding kinase 1 (TBK1) and mediate pro-inflammatory responses in innate immune cells downstream of intracellular virus sensing. Since TBKBP1 has not yet been reported in T cells, we aimed to unravel its role in virus-specific CD8+ T cells. TBKBP1 demethylation in terminal effector CD8+ T cells correlated with TBKBP1 expression and was stable upon long-term in vitro culture. TBKBP1 overexpression resulted in enhanced TBK1 phosphorylation upon stimulation of CD8+ T cells and significantly improved their virus neutralization capacity. Collectively, our data demonstrate that TBKBP1 modulates virus-specific CD8+ T cell responses and could be exploited as therapeutic target to improve adoptive T cell therapies.

immunology↗

bioRxiv2023

Donor tissue-resident memory-like T and NK cells generate a transient peripheral chimerism in lung transplant recipients, potentially protective from chronic lung allograft dysfunction

Lung transplantation (LTx) is the only definite treatment option of patients suffering from end- stage lung disease. Long-term outcome is hampered by chronic allograft dysfunction resulting from poorly defined immune mechanisms. In this study of 97 lung recipients, we demonstrate dynamic changes of T, B and NK cell subsets early after lung transplantation with a selective decrease in memory CD4+ and CD8+ T cells accompanied by a relative increase in NK cells. Simultaneously, donor-derived T and NK cells were detected in recipient blood (n=44) immediately after LTx, persisting for three weeks. Donor T and NK cells displayed a CD69+ but CD103-CD49a- CD25- phenotype, which was shared by T and NK cells in lung perfusion solutions. In order to uncover the origin of these donor T and NK cells, the immune compartment of human lung explant tissue, i.e. trachea and parenchyma, was analyzed and it revealed three major subsets: classical circulating CD69-CD103-CD49a- T and NK cells, CD69+CD103+CD49a+ tissue-resident memory (TRM) T and NK cells and CD69+CD103-CD49a- TRM-like T and NK cells. Single-cell RNA sequencing confirmed the presence of TRM-like subsets with unique features, which reflected the phenotypes of donor T and NK cells and created a transient chimerism in recipient blood. Higher frequencies of donor T cells within the first three weeks showed a tendency for protection from chronic lung allograft dysfunction (CLAD) two years after transplantation although the correlation analyses did not reach statistical significance. To the best of our knowledge, we show for the first time that a transient chimerism is established within the first weeks after lung transplantation by donor TRM- like T and NK cells, which may contribute to protection from chronic lung allograft dysfunction (CLAD) development. Single Sentence SummaryDonor TRM-like T and NK cells cause a transient chimerism in lung recipients and potentially contribute to protection from CLAD.

immunology↗

bioRxiv2022

Triple COVID-19 vaccination induces humoral and cellular immunity to SARS-CoV-2 with cross-recognition of the Omicron variant and IgA secretion

COVID-19 vaccination is the leading strategy to prevent severe courses after SARS-CoV-2 infection. In our study, we analyzed humoral and cellular immune responses in detail to three consecutive homologous or heterologous COVID-19 vaccinations. All individuals (n=20) responded to vaccination with increasing S1- /RBD-/S2-specific IgG levels, whereas specific plasma IgA displayed individual variability. The third dose increased antibody inhibitory capacity (AIC) against immune-escape variants Beta and Omicron independently from age. The mRNA-primed vaccination induced IgG and IgA immunity more efficiently, whereas vector-primed individuals displayed higher levels of memory T and B cells. Vaccinees showed a SARS-CoV-2-specific T cell responses, which were further improved and specified after Omicron breakthrough infections in parallel to appearance of new variant-specific antibodies. In conclusion, the third vaccination was essential to increase IgG levels, mandatory to boost AIC against immune-escape variants and induced SARS-CoV-2-specific T cells. Breakthrough infection with Omicron generates additional spike specificities covering all known variants.

immunology↗

bioRxiv2021

Langerhans islets induce anti-tumor immunity at the expense of glycemic control and predict chemotherapy response in pancreatic cancer

Induction of anti-tumor immunity in pancreatic ductal adenocarcinoma (PDA) is an unresolved challenge. Systematic investigation of the microenvironment of primary pancreatic tumors revealed a role of endocrine Langerhans islets in the coordination of immune activation. We found that intratumoral {beta}-cells, regulated via STAT3, secrete C-C motif chemokine ligand 27 (CCL27) and thereby promote a TH1 phenotype in the microenvironment resulting in an enhanced T cell infiltration and prolonged patient survival. The local effect can be abrogated in a patient-based human explant model by inhibition of the CCL27 receptor CCR10. This defense mechanism is paralleled by an impaired metabolic function of Langerhans islets with reduced insulin levels resulting in a dysregulation of glycemic control in patients. Based on these findings, screening of PDA cases (n= 2264) led to the identification of type 2 diabetes mellitus (T2DM) and extractable glycated haemoglobin (HbA1c) levels as response markers for neoadjuvant chemotherapy with fluorouracil, leucovorin, irinotecan and oxaliplatin (FOLFIRINOX). Collectively these data provide insights into the interconnection of T2DM and PDA, and link declining glycemic control to therapeutic efficacy, which can be utilized as a tool for clinical decision-making and improve patient management.

cancer biology↗

bioRxiv2020

Influenza A virus-induced thymus atrophy differentially affects dynamics of conventional and regulatory T cell development

Foxp3+regulatory T (Treg) cells, which are crucial for maintenance of self-tolerance, mainly develop within the thymus, where they arise from CD25+Foxp3-or CD25-Foxp3+ Treg cell precursors. Although it is known that infections can cause transient thymic involution, the impact of infection-induced thymus atrophy on thymic Treg (tTreg) cell development is unknown. Here, we infected mice with influenza A virus (IAV) and studied thymocyte population dynamics post infection. IAV infection caused a massive, but transient thymic involution, dominated by a loss of CD4+CD8+ double-positive (DP) thymocytes, which was accompanied by a significant increase in the frequency of CD25+Foxp3+ tTreg cells. Differential apoptosis susceptibility could be experimentally excluded as a reason for the relative tTreg cell increase, and mathematical modeling suggested that enhanced tTreg cell generation cannot explain the increased frequency of tTreg cells. Yet, an increased death of DP thymocytes and augmented exit of single-positive (SP) thymocytes was suggested to be causative. Interestingly, IAV-induced thymus atrophy resulted in a significantly reduced T cell receptor (TCR) repertoire diversity of newly produced tTreg cells. Taken together, IAV-induced thymus atrophy is substantially altering the dynamics of major thymocyte populations, finally resulting in a relative increase of tTreg cells with an altered TCR repertoire.

immunology↗

bioRxiv2017

Cellular reprogramming of human monocytes is regulated by time-dependent IL4 signalling and NCOR2

The clinical and therapeutic value of human in vitro generated monocyte-derived dendritic cell (moDC) and macrophages is well established. However, in line with recent findings regarding myeloid cell ontogeny and due to our limited understanding of their physiological counterparts, transcriptional regulation and heterogeneity, the full potential of these important cellular systems is still underestimated.\n\nIn this study, we use cutting edge high-dimensional analysis methods to better understand the transcriptional organization, phenotypic heterogeneity and functional differences between human ex vivo isolated and in vitro generated mononuclear phagocytes with the aim to better realize their full potential in the clinic.\n\nWe demonstrate that human monocytes activated by MCSF or GMCSF most closely resemble inflammatory macrophages identified in vivo, while IL4 signalling in the presence of GMCSF generates moDCs resembling inflammatory DCs in vivo, but not steady state cDC1 or cDC2. Moreover, these reprogramming regimes lead to activated monocytes that present with profoundly different transcriptomic, metabolic, phenotypic and functional profiles. Furthermore, we demonstrate that CD14+ monocytes are integrating multiple exogenous activation signals such as GMCSF and IL4 in a combinatorial and temporal fashion, resulting in a high-dimensional cellular continuum of reprogrammed monocytes dependent on the mode and timing of cytokine exposure. Utilizing nanostraw-based knockdown technology, we demonstrate that the IL4-dependent generation of moDCs relies on the induction, nuclear localization and function of the transcriptional regulator NCOR2.\n\nFinally, we unravel unappreciated heterogeneity within the clinically moDCs population and propose a novel high-dimensional phenotyping strategy to better tailor clinical quality control strategies for patient need and culture conditions to enhance therapeutic outcome.

immunology↗