Biology subjects

Wabnitz, G.

Publications and source records attributed to Wabnitz, G..

6 recordsLinked to original sources

bioRxiv2025

THE IMMUNE RESPONSE AGAINST CANCER IS MODULATED BY STROMAL CELL FIBRONECTIN

Cancer-associated fibroblasts remain poorly understood, with some of them originating from the bone marrow. We therefore took advantage of the diversity of bone marrow stromal cells to shed light on how fibroblasts modulate cancer growth. In two murine cancer models, adding these fibroblasts to tumor cells resulted in smaller lesions. Suppression was enhanced by pretreatment with fibronectin, while genetic deletion of fibronectin in a small subpopulation of stromal cells expressing osterix/sp7 restored growth. The suppressive stromal population showed two more characteristics: the absence of CD31/pecam1 and CD105/endoglin. However, only a decrease in CD105/ENDOGLIN in melanoma patients translated in improved survival. Mechanistically, fibronectin or fibronectin fragments activate integrin 5{beta}1 and TLR4 and increase chemokine production by stromal cells ultimately leading to enhanced recruitment and activity of Ly6G+ myeloid cells without T-cell involvement. This work thus characterizes a beneficial interaction between stromal cells and neutrophils enhancing the immune response against early cancer. HighlightsO_LIStromal cells can be divided into two populations, a tumor supportive one with the potential to stimulate angiogenesis and an inhibitory one with the potential to enhance the immune response C_LIO_LIStromal fibronectin expressing the transduction factor osterix/sp7 produce fibronectin that acts on 5{beta}1 integrin and/or TLR4 on neighboring fibroblasts to modulate Ly6G+ immune cells and suppress tumor growth C_LI One sentence summaryTumor inhibitory fibroblasts have three characteristics and through production of fibronectin act on neighboring cells inducing signaling cascades that ultimately lead to a stronger immune response against early cancer.

cancer biology↗

bioRxiv2025

Modulation of collagen-binding integrins affects fibroblast activation and inhibits fibrosis

The extracellular matrix contributes to the progression of several diseases, sometimes by disrupting organ function such as in lung and liver fibrosis. Because integrin receptors mediate cell-matrix interactions, we conditionally deleted {beta}1 integrin in murine hepatocytes in vivo. Increased TGF-{beta} and matrix deposition ensued. Application of a cyclic peptide (GLQGE) that binds to both 10{beta}1 and 11{beta}1 diminished fibrosis in two murine models. In liver fibrosis, TGF-{beta} production was reduced. In lung fibrosis, however, the effect was exclusively due to suppressing fibroblast activation and hence collagen production without TGF-{beta} involvement. In summary, integrin manipulation successfully changed cell behavior, with effects differing depending on the cell type. Importantly, it is possible to directly suppress fibroblast activation and consequently diminish matrix production independent of disease pathogenesis. This underscores the importance of matrix composition in modifying the behavior of embedded cells and hence disease severity. Key findingsO_LILoss of 11{beta}1 integrin-mediated signal in hepatocytes increases TGF-{beta} and leads to fibrosis C_LIO_LIEngaging 10{beta}1 and/or 11{beta}1 with a cyclic peptide (GLQGE) inhibits fibroblast activation directly and, consequently matrix production and progression of fibrosis C_LI

cell biology↗

bioRxiv2024

Accurate, fast and memory efficient quantification of immune cell phenotypes in cytometry using machine learning

To achieve accurate and reproducible cytometry data analysis, we benchmarked 19 machine learning algorithms for supervised and unsupervised cell classification. The underlying data encompassed 138 million cells from seven independent datasets including conventional flow cytometry, spectral flow cytometry and mass cytometry. We found that tree-based classifiers and in particular Decision Trees, outperformed other approaches in classification accuracy, speed and memory use. High accuracy was achieved even for cell populations rarer than 1% using decision trees. We validated our decision tree-based approach in a clinical setting using diagnostic blood T cell phenotyping of 107 patients. Automatic quantification of CD4 helper T cell phenotypes achieved 99 % accuracy compared to manual expert assessment. Finally, we combined automated data transformation, supervised and unsupervised gating, an application program interface and a user-friendly desktop-application into FACSPy and FACSPyUI, a fast and scalable open-source toolbox for the analysis and visualization of cytometry data.

bioinformatics↗

bioRxiv2022

Human and murine neutrophils share core transcriptional programs in both homeostatic and inflamed contexts

Neutrophils are frequently studied in murine models, but the extent to which findings translate to humans remains poorly defined. Here, we performed an integrative transcriptomic analysis of 11 murine and 13 human datasets. In homeostasis, neutrophils exhibited the highest number of lineage-specific genes and the greatest degree of correlated expression among genes with one-to-one orthologs (r = 0.79, P < 2.2 x 10-16) compared to other leukocytes. In inflammation, neutrophils displayed considerable transcriptional diversity, but shared a core inflammation program across a broad range of conditions which was conserved between species. This core program included genes encoding IL-1 family members, CD14, IL-4R, CD69 and PD-L1. Chromatin accessibility of core inflammation genes increased significantly in blood compared to bone marrow and further with migration from blood to tissue. Transcription factor enrichment analysis nominated members of the NF-{kappa}B family and AP-1 complex as important drivers of the core inflammation program, and HoxB8 neutrophils with JUNB knockout showed a significantly reduced expression of core inflammation genes at baseline and upon stimulation. In vitro perturbations confirmed surface protein upregulation of core inflammation members in both species. Together, we demonstrate substantial transcriptional conservation in neutrophils in homeostasis and identify a core inflammation program conserved across species. This systems biology approach can be leveraged to improve transitions between the murine and human context. Key PointsO_LIThe transcriptome of resting neutrophils is substantially conserved between humans and mice C_LIO_LIA core inflammation program in neutrophils is shared across a broad range of conditions and conserved across humans and mice C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=52 SRC="FIGDIR/small/516246v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@1f6b40borg.highwire.dtl.DTLVardef@1a67bb4org.highwire.dtl.DTLVardef@1039a8forg.highwire.dtl.DTLVardef@1982d10_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2021

Aging and interferon gamma response drive the phenotype of neutrophils in the inflamed joint

ObjectivesNeutrophils are typically the most abundant leukocyte in arthritic synovial fluid. We sought to understand changes that occur in neutrophils as they migrate from blood to joint. MethodsWe performed RNA sequencing of neutrophils from healthy human blood, arthritic blood, and arthritic synovial fluid, comparing transcriptional signatures with those from murine K/BxN serum transfer arthritis. We employed mass cytometry to quantify protein expression and sought to reproduce the synovial fluid phenotype ex vivo in cultured healthy blood neutrophils. ResultsBlood neutrophils from healthy donors and patients with active arthritis exhibited largely similar transcriptional signatures. By contrast, synovial fluid neutrophils exhibited more than 1,600 differentially expressed genes. Gene signatures identified a prominent response to interferon gamma (IFN{gamma}), as well as to tumor necrosis factor, interleukin 6, and hypoxia, in both humans and mice. Mass cytometry also found healthy and arthritic donor blood neutrophils largely indistinguishable but revealed a range of neutrophil phenotypes in synovial fluid defined by downregulation of CXCR1 and upregulation of Fc{gamma}RI, HLA-DR, PD-L1, ICAM-1 and CXCR4. Reproduction of key elements of this signature in cultured blood neutrophils required both IFN{gamma} and prolonged culture. ConclusionsCirculating neutrophils from arthritis patients resemble those from healthy controls, but joint fluid cells exhibit a network of changes, conserved across species, that implicate IFN{gamma} response and aging as complementary drivers of the synovial neutrophil phenotype. KEY MESSAGESO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LINeutrophils are central in the effector phase of inflammatory arthritis but their phenotypic heterogeneity in inflamed synovial fluid is poorly understood. C_LI What does this study add?O_LIRNA-seq and mass cytometry identify a hallmark phenotype of neutrophils in synovial fluid consisting of upregulated ICAM-1, HLA-DR, PD-L1, Fc receptors and CXCR4. C_LIO_LITranscriptomics highlight an IFN{gamma} response signature conserved across humans and mice. C_LIO_LIIn vitro experiments implicate aging and IFN{gamma} as complementary factors orchestrating the synovial fluid neutrophil phenotype. C_LI How might this impact on clinical practice or future developments?O_LIUnderstanding the specific features of neutrophils in the arthritic joint may disclose opportunities for safe therapeutic targeting of this lineage. C_LI

immunology↗

bioRxiv2021

Inflammation induces pro-NETotic neutrophils via TNFR2 signaling

Cytokines released during chronic inflammatory diseases induce pro-inflammatory properties in polymorphonuclear neutrophils (PMN). Here we show that in vitro cytokine treatment leads to the development of a subgroup of human PMN expressing CCR5, termed CCR5+ cytokine-induced PMN (CCR5+ cPMN). Auto/paracrine TNF signaling increases intracellular neutrophil elastase (ELANE) abundance and induces NETosis in CCR5+ cPMN. Triggering of CCR5 amplifies NETosis. Membranous TNF (mTNF) outside-in signaling induces the formation of reactive oxygen species, a known activator of NETosis. In vivo, we find an increased number of CCR5+ cPMN in the peripheral blood and inflamed lamina propria of patients with ulcerative colitis (UC) but not Crohns disease (CD). Notably, failure of anti-TNF therapy is associated with higher frequencies of CCR5+ cPMN. In conclusion, we identify a phenotype of pro-NETotic, CCR5 positive PMN present in inflamed tissue in vivo and inducible in vitro. These cells may reflect an important component of tissue damage during chronic inflammation and could be of diagnostic value.

immunology↗