Biology subjects

Zielinski, C. E.

Publications and source records attributed to Zielinski, C. E..

5 recordsLinked to original sources

bioRxiv2026

Metabolic specialization structures gut bacterial niches and drives colorectal cancer progression

Despite the established association between the gut microbiome and colorectal cancer (CRC), the functional distinction between microbial passengers and drivers of CRC progression remains unresolved. Here, we collected stool, blood, as well as paired tumor, and normal mucosa tissues from seventy-seven CRC patients to characterize the systemic and localized impact of the gut microbiome on early- and late-stage CRC. By deep shotgun metagenomic sequencing, we identified distinct bacterial species and functions residing in tumor versus normal mucosa, highlighting an enrichment of oral-associated bacteria in tumor tissues. Several of these species remained undetected in the stool microbiome analysis. We further combined bacterial culturing with untargeted metabolomics of bacteria enriched in tumor and normal mucosa tissues, revealing distinct clusters of metabolic potential. Functional testing of multiple members from one cluster comprising both tumor- and mucosa-enriched species revealed Leptotrichia wadei as a pro-tumorigenic bacterium in a murine CRC model. Single-nucleus RNA sequencing and in vitro experiments further demonstrated that L. wadei and its secretome induces M2 macrophage polarization to promote tumor growth. Overall, our study shows that metabolic specialization structures microbial colonization niches, while species-specific metabolic outputs identify functional drivers of CRC progression, and uncovers L. wadei as an oncogenic bacterium in CRC.

microbiology↗

bioRxiv2025

An immunobiliary single-cell atlas resolves crosstalk of type 2 cDCs and γδT cells in cholangitis

Background and aimsThe immunobiliary niche serves as a reservoir of tissue-resident immune cells, yet the role of unconventional T cells during cholangitis remains poorly understood. Here, we connect cell state dynamics of type 2 conventional dendritic cells (cDC2) in cholangitis with site-specific{gamma}{delta} T17 responses in liver and draining lymph nodes (LN). MethodsThe 0.1% Diethoxycarbonyl-1,4-Dihydrocollidine (DDC) diet was used to generate an immunobiliary DC- and{gamma}{delta} T-enriched mouse liver and LN single-cell RNA-sequencing (scRNA-seq) atlas covering temporal disease dynamics, resolution and cDC2B depletion. cDC2 trajectories were inferred using VarID2 and{gamma}{delta} T cell transcription factor (TF) regulon activity was predicted by SCENIC. The human biliary niche was resolved by integrating human liver scRNA-seq data with available spatial transcriptomics data. Functional studies were conducted using Tcrd knockout, Il17a/f knockout and Tcrd reporter mice. ResultsA disease trajectory of Mgl2+ cDC2B was identified connecting DC maturation, homing and the expression of Il17-inducing genes. Disease progression was associated with numeric exhaustion of mature cDC2B and recruitment of DC precursors.{gamma}{delta} T cells were the main Il17 producers and were subtyped into Il17ahigh Scart1+ V{gamma}6+ and Il17low Scart2+ V{gamma}4+ populations exhibiting cDC2-directed communication and divergent TF regulon activity. Spatial proximity and conserved molecular interactions of cDC2 and{gamma}{delta} T cells were confirmed in human cholangitis. Il17-deficiency resulted in reduced liver fibrosis in mice, while cDC2B depletion attenuated{gamma}{delta} T17 cell states. ConclusionsIn cholangitis, a profibrogenic function of{gamma}{delta} T cells is contingent on the induction by peribiliary cDC2B, thereby highlighting relevant disease determinants within the immunobiliary and liver-draining LN niche. Impact and ImplicationsThe immunobiliary niche contains rare immune cells such as conventional dendritic cells and unconventional T cells, however, the function of these cell types in liver inflammation remains poorly understood. Mirroring human biliary diseases such as primary sclerosing cholangitis, we induced experimental cholangitis in a mouse model to generate a site-specific single-cell sequencing atlas resource resolving underexplored cell populations. Our data capture a profibrotic hepatic disease state trajectory of Mgl2+ cDC2B inducing a{gamma}{delta} T cell-specific Il17-response, which is attenuated upon cDC2B depletion and in DC precursors, which are characterized by reduced genomic accessibility of{gamma}{delta} T cell-interacting genes. These results highlight the importance of portal niche residing underexplored immune cell populations and the necessity to further resolve immunobiliary niche responses and crosstalk in inflammatory settings such as in cholangitis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/664083v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d21193org.highwire.dtl.DTLVardef@7ff3dcorg.highwire.dtl.DTLVardef@630c78org.highwire.dtl.DTLVardef@c79f9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Sodium chloride in the tumor microenvironment enhances T-cell metabolic fitness and cytotoxicity

Adoptive T-cell therapy has become a powerful weapon for cancer treatment. The efficacy of antitumor immunity is associated with the metabolic state of cytotoxic T cells, which is highly sensitive to the tumor microenvironment. It is therefore of considerable interest to bypass immunosuppressive signals in the tumor microenvironment and to identify factors that augment cytotoxic effector functions and ultimately tumor killing. Whether ionic signals serve as aberrant immune signals and influence the adaptive human antitumor immune response is still largely unexplored. We therefore investigated the effect of sodium on the phenotype, function and metabolic regulation of human CD8+ T cells using transcriptomic, metabolomic, high-dimensional flow cytometric and functional assays. We demonstrate a significant enrichment of sodium in solid tumors from patients with breast cancer, which leaves a transcriptomic imprint on intratumoral immune cells. Sodium chloride (NaCl) enhanced the activation state and effector functions of human CD8+ memory T cells. These functional alterations were associated with enhanced metabolic fitness, particularly increases in glycolysis, oxidative phosphorylation and overall nutrient uptake. These NaCl-induced effects translated into increased tumor cell killing in vitro and in a tumor mouse model in vivo. We therefore propose NaCl as a positive regulator of acute antitumor immunity that could be harnessed for ex vivo conditioning of adoptively transferred T cells, such as CAR T-cells.

immunology↗

bioRxiv2020

Transcriptional profiling and single-cell chimerism analysis identifies human tissue resident T cells in the human skin after allogeneic stem cell transplantation

Tissue resident memory T cells (TRM) have recently emerged as crucial cellular players for host defense in a wide variety of tissues and barrier sites. Mouse models revealed that they are maintained long-term in loco unlike recirculating effector memory T cells (TEM). Insights into the maintenance and regulatory checkpoints of human tissue resident T cells (TRM) remain scarce, especially due to the obstacles in tracking T cells over time and system-wide in humans. We present a clinical model that allowed us to overcome these limitations. We demonstrate that allogeneic stem cell transplantation resulted in compartmentalization of host T cells in the human skin despite complete donor T cell chimerism in the blood, thus unmasking long-term persistence of tissue resident T cell subsets of host origin within the diverse skin T cell community. Single-cell transcriptional profiling paired with single-cell chimerism analysis provided an in-depth characterization of these bona fide skin resident T cells. Their phenotype, functions and regulatory checkpoints may serve therapeutic strategies for the treatment of autoimmune diseases and chronic infections, where their specific depletion versus maintenance, respectively, will have to be harnessed pharmaceutically.

immunology↗

bioRxiv2018

Sodium chloride is an ionic checkpoint for human Th2 cell responses and shapes the atopic skin microenvironment

One sentence summarySodium is an ionic checkpoint for the induction and amplification of human Th2 cell responses and shapes the atopic skin microenvironment, where it could serve as a novel therapeutic target for Th2 mediated diseases.\n\nAbstractThere has been a strong increase in the incidence of allergic diseases over the last 50 years. Environmental factors most likely account for this phenomenon. However, the nature of these factors and the mode of action by which they induce the type 2 immune deviation, which is characteristic of atopic diseases, remains unclear. It has previously been reported that dietary sodium chloride promotes the polarization of Th17 cells with implications for autoimmune diseases such as multiple sclerosis. Here, we demonstrate that sodium chloride also potently promotes Th2 cell responses on multiple regulatory levels. Sodium chloride enhanced IL-4 and IL-13 production while suppressing IFN-{gamma} production in effector T cells. It diverted alternative T cell fates into the Th2 cell phenotype and also induced de novo Th2 cell polarization from naive T cell precursors. Mechanistically, it exerted its effects via the osmosensitive transcription factor NFAT-5 and the kinase SGK-1, which regulated Th2 signature cytokines and master transcription factors in hyperosmolar salt conditions. The skin of patients suffering from atopic dermatitis contained highly elevated amounts of sodium compared to non-lesional atopic and healthy skin. This demonstrates that sodium chloride represents a so far overlooked cutaneous microenvironmental factor in atopic dermatitis that can induce Th2 cell responses, the orchestrators of allergic diseases. Together, our data propose ionic signaling through sodium chloride as a novel checkpoint and potential therapeutic target for type 2 immunity and its associated allergic diseases.

immunology↗