Biology subjects

Coffer, P.

Publications and source records attributed to Coffer, P..

3 recordsLinked to original sources

bioRxiv2024

Basement membrane hydrogels dampen CAR-T cell activation: nanofibrillar cellulose gels as alternative to preserve T cell function in 3D cell cultures.

BackgroundHydrogel-based 3D culture systems are emerging as a valuable tool for preclinical screening of cell-based immunotherapies against solid and hematological malignancies, such as chimeric antigen receptor T (CAR-T) cells. Hydrogels can influence T cell function in a non-desired manner due to their mechanical properties and chemical composition, potentially skewing results in preclinical testing of novel immunotherapeutic compounds. MethodsIn this study, we assess CD4+ T and CAR-T cell activation and proliferation in chemically-undefined matrices (Matrigel and basement membrane extract, BME) and compare them to a synthetic nanofibrillar cellulose (NFC) hydrogel. ResultsRheometric analyses show that NFC is more rigid than Matrigel and BME. Murine CD4+ T cells acquire a regulatory T cell (Treg) phenotype in Matrigel and BME, while this is not observed in NFC. Proliferation and activation of human T cells are higher in NFC than in Matrigel or BME. Similarly, we show that CAR-T cell activation and proliferation is significantly impaired in Matrigel and BME, in contrast to NFC. ConclusionsOur findings highlight the impact of hydrogel choice on (CAR-)T cell behavior, with direct implications for preclinical immunotherapy testing. In contrast to Matrigel and BME, NFC offers a chemically-defined 3D environment where T cell function is preserved. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSIn 3D (preclinical) tumor-killing assays for evaluating engineered T cell cytotoxicity, the surrounding matrix can influence immune cell phenotype and function, potentially skewing T cell activity. Basement membrane hydrogels such as Matrigel and basement membrane extract (BME), widely used as scaffolds for 3D culture, are inherently heterogeneous and contain extracellular matrix components that can influence lymphocyte function. What this study addsHere, we show that (CAR-)T cell function is significantly reduced in Matrigel and BME as compared to standard (2D) culture conditions. In contrast, (CAR-)T cell activity is preserved in synthetic nanofibrillar cellulose (NFC) gels. Importantly, murine T cells spontaneously acquire a Treg phenotype in Matrigel and BME. T cell proliferation and cytokine secretion are >10-fold lower in Matrigel than in NFC. Similarly, CAR-T cell survival and expansion are 10-fold higher in NFC than in Matrigel or BME. How this study might affect research, practice or policyWe report that the intrinsic cytotoxic and proliferative potential of (CAR-)T cells can be underestimated when performing assays in 3D cultures based on Matrigel or BME. As an alternative, we suggest the use of chemically defined synthetic gels, and we show that nanofibrillar cellulose hydrogels are suitable 3D matrices for preserving T cell phenotype and activation.

immunology↗

bioRxiv2024

Glycolytic reprogramming shapes the epigenetic landscape of activated CD4+ T Cells in Juvenile Idiopathic Arthritis

Juvenile Idiopathic Arthritis (JIA) describes a heterogeneous group of autoimmune conditions with an unknown cause and childhood onset. It is characterized by the accumulation of mononuclear cells, notably activated CD4+ memory/effector T (Tmem/Teff) cells, within the synovial fluid of affected joints. JIA CD4+ T cells exhibit a unique epigenomic signature linked to inflammation, however, the molecular mechanisms driving this remain unclear. Here we show that CD4+ T cells isolated from JIA synovial fluid (SF) exhibit abnormal intracellular metabolism marked by heightened glycolysis after activation driving transcriptional reprogramming. Epigenetic profiling between activated healthy controls and JIA patients allowed the definition of specific disease-related enhancers upregulated in SF-derived JIA CD4+ T cells. Pharmacological inhibition of glycolytic flux affected the expression of genes associated with these enhancers. When activated in the presence of JIA SF, CD4+ T cells obtained from healthy control (HC) subjects, displayed heightened glycolytic activity compared to paired plasma. Moreover, this also led to increased H3K27ac at JIA-specific genes. Increased H3K27ac was dependent on glycolytic flux, but not oxidative phosphorylation. Inhibition of glycolysis also specifically affected the transcription of genes upregulated during T cell activation in the presence of SF. Inhibiting the glycolytic enzyme pyruvate dehydrogenase (PDH) reduced JIA-associated gene expression. Taken together, these findings demonstrate that for JIA, the inflammatory microenvironment can modulate T cell activation-driven transcriptional programs through a glycolysis-mediated pathway. Specific targeting of this T cell metabolism-epigenetic axis may provide avenues for intervention during the development of autoinflammatory disease.

immunology↗

bioRxiv2021

Epigenetic changes in autoimmune monocytes contribute to disease and can be targeted by JAKinhibition

How the local inflammatory environment regulates epigenetic changes in the context of autoimmune diseases remains unclear. Here we assessed the transcriptional and active enhancer profile of monocytes derived from the inflamed joints of Juvenile Idiopathic Arthritis (JIA) patients, a model well-suited for studying autoimmune diseases. RNA-sequencing analysis demonstrated that synovial-derived monocytes display an activated phenotype, characterized by increased expression of surface activation markers and multiple chemokines and cytokines. This increased expression is regulated on the epigenetic level, as ChIP-sequencing indicated increased H3K27 acetylation of genes upregulated in synovial monocytes. IFN signaling-associated genes are increased and epigenetically altered in synovial monocytes, suggesting a role for IFN in establishing the inflammatory phenotype. Treatment of human synovial monocytes with the Janus-associated kinase (JAK) inhibitor Ruxolitinib, which inhibits IFN signaling, transformed the activated enhancer landscape and reduced disease-associated gene expression, thereby inhibiting the inflammatory phenotype. Taken together, these data provide novel insight into epigenetic regulation of autoimmune disease-patient derived monocytes and suggest that altering the epigenetic profile can be a therapeutic approach for the treatment of autoimmune diseases.

immunology↗