Biology subjects

Kendirli, A.

Publications and source records attributed to Kendirli, A..

4 recordsLinked to original sources

bioRxiv2025

Truncating RELA variants drive autoinflammation and autoimmunity by impairing the negative feedback control of NF-kB

The NF-{kappa}B signaling pathway coordinates inflammation, cell survival, and proliferation, while restraining excessive cell death to maintain immune homeostasis. Truncating mutations in RELA, encoding the NF-{kappa}B subunit p65, have been linked to autoinflammation and autoimmunity, but the underlying mechanisms remain incompletely defined. We investigated six patients from five unrelated families carrying novel heterozygous truncating RELA variants. Despite reduced p65 expression, patients exhibited a broad spectrum of inflammatory manifestations alongside elevated baseline and stimulus-induced pro-inflammatory cytokines. Functional analyses in patient-derived cells and mutant RELA knock-in models showed that upstream NF-{kappa}B signaling was intact, but induction of inhibitory regulators such as I{kappa}B and A20 was impaired. This defective feedback control shifted immune homeostasis toward amplified inflammatory responses that depended on the residual activity of the remaining functional RELA allele. Single-cell transcriptomics revealed distinct cell type-specific consequences: monocytes displayed constitutive type I interferon and NF-{kappa}B activation, B cells retained partial compensatory signaling, whereas T and NK cells exhibited transcriptional signatures of cell death pathways. Patient fibroblasts and mutant RELA knock-in cells further confirmed enhanced TNF-induced inflammatory gene expression and hypersensitivity to apoptosis and necroptosis. These findings establish RELA haploinsufficiency as a cause of systemic immune dysregulation, and link defective NF-{kappa}B feedback control to unchecked inflammation and inflammatory cell death. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/687461v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1f0bfe6org.highwire.dtl.DTLVardef@c6cb60org.highwire.dtl.DTLVardef@1522accorg.highwire.dtl.DTLVardef@177c724_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Sample-multiplexed FACS-preprocessing of PBMCs enables scalable scRNA-seq without compromising transcriptomic or cellular integrity

Efficient preprocessing of peripheral blood mononuclear cells (PBMCs) for single-cell RNA-Sequencing (scRNA-seq) is crucial to ensure high sample throughput while maintaining sample integrity. In particular, when enrichment of rare immune cell populations is necessary to enable their representative profiling among more common PBMCs, sample preprocessing may become a detrimental bottleneck. Here, we present an optimized fluorescence-activated cell sorting (FACS)-based preprocessing workflow designed to enrich rare immune cells while conserving overall PBMC composition. The protocol integrates dead cell removal, targeted rare cell enrichment, channel splitting, and hash-based sample multiplexing together with a new powerful yet lightweight demultiplexing tool (YAHD), improving throughput and cell yield, reducing batch effects, and preserving biological context. Validation across cryopreserved human PBMCs obtained from different scientifically relevant sources (clinical routine and laboratory setting) demonstrated improved sample viability and representation of rare subsets in the final scRNA-seq data. Thorough transcriptomic assessment confirmed non-concerning levels of stress induction and T cell activation as well as low technical variability, removing concerns around FACS-processing, cross-donor multiplexing and channel splitting. The presented approach enables scalable and biologically faithful PBMC preprocessing for scRNA-seq, advancing the study of immune heterogeneity in health and disease.

genomics↗

bioRxiv2023

Targeting the TCA cycle can ameliorate widespread axonal energy deficiency in neuroinflammatory lesions

Inflammation in the central nervous system (CNS) can impair the function of neuronal mitochondria and contributes to axon degeneration in the common neuroinflammatory disease multiple sclerosis (MS). Here we combine cell type-specific mitochondrial proteomics with in vivo biosensor imaging to dissect how inflammation alters the molecular composition and functional capacity of neuronal mitochondria. We show that neuroinflammatory lesions in the mouse spinal cord cause widespread and persisting axonal ATP deficiency, which precedes mitochondrial oxidation and calcium overload. This axonal energy deficiency is associated with impaired electron transport chain function, but also an upstream imbalance of tricarboxylic acid (TCA) cycle enzymes, with several, including key rate-limiting, enzymes being depleted in neuronal mitochondria in experimental models and in MS lesions. Notably, viral overexpression of individual TCA enzymes can ameliorate the axonal energy deficits in neuroinflammatory lesions, suggesting that TCA cycle dysfunction in MS may be amendable to therapy.

neuroscience↗

bioRxiv2022

Identification of essential modules regulating T cell migration to the central nervous system in multiple sclerosis

Multiple sclerosis (MS) is a neuroinflammatory disease initiated by the infiltration of autoreactive T cells into the central nervous system (CNS). Several molecules that modulate T cell CNS infiltration in MS have been identified, but how the components of cell adhesion, migration and signalling pathways interact to execute this fundamental step in MS pathogenesis is unknown. We conducted a genome-wide in vivo CRISPR screen in an experimental autoimmune encephalomyelitis model of MS and identified 18 essential facilitators of T cell migration that include known targets of MS therapies. Combining in vitro studies with in vivo cell transfer and multiphoton microscopy enabled us to reveal three functional modules, centred around the adhesion molecule 4-integrin, the chemokine receptor CXCR3, and the GRK2 kinase, that are required for the migration of autoreactive CD4+ T cells into the CNS. Single-cell analysis of T cells from patients with MS confirmed that the expression of the essential regulators correlates with the propensity of CD4+ T cells to reach the CNS. Taken together, our data reveal the identity and functions of key modules that govern the critical step in the induction of MS lesions.

immunology↗