Biology subjects

Korkmaz, A.

Publications and source records attributed to Korkmaz, A..

5 recordsLinked to original sources

bioRxiv2025

Single-Cell Roadmap of Early Hemato-Endothelial Development: Functions of Atf3, Zfp711 and Bcl6b

Hematopoiesis is the process of producing blood cells. In mammalian embryos, hematopoiesis occurs in three consecutive overlapping waves (Neo et al. 2021; Dzierzak and Bigas 2018) that are regulated by transcription factors (TFs) and signaling proteins. We investigated the functions of three relatively poorly studied TFs in early embryonic hematopoietic development at single-cell resolution: Activating transcription factor 3 (Atf3), Zinc finger protein 711 (Zfp711), and B cell CLL/lymphoma 6, member B (Bcl6b). These TFs are upregulated early in development when hematopoietic and endothelial lineages separate from cardiac and other mesodermal lineages. We combined multiplexed single-cell RNA sequencing (scRNA-seq) and cell identity analysis using Flow Cytometric Analysis (FCA) with TF knockouts (KO) in in-vitro differentiating mouse embryonic stem cells (mESCs) to dissect the function of these TFs in lineage induction, specification, and separation. The Atf3-KO showed an increase of distinct mesodermal subpopulations, but a decrease of endothelial and erythro-myeloid progenitors (EMPs) by downregulation of important genes (i.e. Runx1, Mafb, Egr1, Jun, Jund, Fos, Batf3, and Zf608) that likely explains the effects on EMPs and the increased expression of interferon-related genes. In Zfp711-KO cells, the number of blood progenitor cells and erythroid cells increased, while the number of endothelial cells decreased. Furthermore, Hoxa expressing mesoderm decreased, while Hoxb expressing mesoderm increased. In contrast, the Bcl6b-KO had no observable effects on early hematopoiesis. In conclusion, we report the function of these three TFs function at different stages of hemato-endothelial lineage specification. HIGHLIGHTSO_LICombined scRNA-seq and FCA on KO mESCs in vitro differentiation enabled unbiased identification of the respective TF functions during specific stages of hematoendothelial lineage specification. C_LIO_LIAtf3-KO: Increased abundance of mesodermal lineages and decreased endothelial lineages and EMPs. - Downregulation of key TF-encoding genes (e.g., Runx1, Mafb, Egr1, Jun, Jund, Fos, Batf3, Zf608) explain the effects on EMPs. - Generation of a distinct mesodermal subpopulation with high expression of sets of interferon and antiviral-related genes. - Upregulation of interferon and anti-viral-related genes, indicating Atf3 acts as a negative regulator of these genes. C_LIO_LIZfp711-KO: Increased numbers of blood progenitor and erythroid cells. Decreased numbers of endothelial cells. - Shift in mesodermal populations: Hoxa expressing mesoderm decreased, and Hoxb expressing mesoderm increased. - Hoxa9, Hoxa10, Hoxa13, Jun, Jund and Atf3 amongst the downregulated genes. The Atf3 promoter has a potential Zfp711-binding site. - Increased expression in a given Endothelium subtype in endocardium in vivo and in vitro. C_LIO_LIBcl6b-KO: No observable impact on early hematopoiesis. C_LI

developmental biology↗

bioRxiv2024

Kabasura Kudineer Choornam, a medicinal polyherbal formulation, modulates human macrophage polarization and phagocytic function

BackgroundKabasura kudineer choornam (KKC) is a polyherbal formulation with 15 ingredients. It has been shown to have anti-inflammatory and anti-microbial properties and demonstrate efficacy in managing the symptoms of H1N1 swine flu and COVID-19. However, its mechanism of action is not fully comprehended. PurposeHerein, we examined the effect of the KKC on the polarization and function of primary human macrophages. MethodsHuman monocyte-derived macrophages (M0 macrophages) pre-treated with KKC extract were polarized into M1, M2a, or M2c subtypes. The expression of the M1/M2 polarization markers was analyzed by qPCR, flow cytometry, and ELISA, and the phagocytosis capacity of macrophages was analyzed by flow cytometry. ResultsOur data show that the KKC treatment increased the expression of the M1 markers IDO1, IL-1{beta}, IL-12a(p35), and TNF in both polarized and unpolarized macrophages at mRNA level. However, it decreased the secretion of IL-12 (p70) in M1 macrophages and increased the secretion of TNF in M0, M2a, and M2c macrophages. IL-10 secretion was increased in M0 and M2a macrophages, while it was decreased in M1 macrophages after the KKC treatment. Interestingly, all KKC-treated macrophage phenotypes displayed a downregulation in the expression of the M1/M2 surface markers CD64, CD206, CD209, and CD163, which also play a role in phagocytosis. In accordance with this result, the phagocytic capacity of both polarized and unpolarized macrophages was decreased after the KKC treatment. ConclusionIn conclusion, KKC extract modulates macrophage inflammatory response and could be a potential supplement for the treatment of infectious and inflammatory diseases.

immunology↗

bioRxiv2022

Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain

Stem cells in the adult brain are specialized astrocytes capable of generating neurons and glial cells. While neural stem cells (NSCs) and common astrocytes have clearly distinct functions, they share highly similar transcriptome profiles. How stemness is molecularly encoded is therefore unclear. Here we use single-cell NMT-seq to simultaneously characterize the transcriptome, DNA methylome and chromatin accessibility of astrocytes and the NSC lineage in the healthy and ischemic brain. Our data reveal distinct methylation profiles associated with either astrocyte or stem cell function. Stemness is conferred by methylation of astrocyte genes and demethylation of neurogenic genes that are expressed only later. Surprisingly, ischemic injury unlocks the stemness-methylome in common astrocytes enabling generation of neuroblasts. Furthermore, we show that oligodendrocytes employ Tet-mediated demethylation to regulate expression of myelin-related genes, many of which are abnormally methylated in multiple sclerosis. Overall, we show that DNA methylation is a promising target for regenerative medicine. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/499860v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@149fe11org.highwire.dtl.DTLVardef@c71902org.highwire.dtl.DTLVardef@13ae945org.highwire.dtl.DTLVardef@a8d37e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2021

The Ca2+ concentration in vitro impacts the cytokine production of mouse and human lymphoid cells and the polarization of human macrophages

Various aspects of the in vitro culture conditions can impact the functional response of immune cells. For example, it was shown that a Ca2+ concentration of at least 1.5 mM during in vitro stimulation is needed for optimal cytokine production by conventional {beta} T cells. Here we extend these findings by showing that also unconventional T cells (invariant Natural Killer T cells, mucosal-associated invariant T cells, {gamma}{delta} T cells), as well as B cells, show an increased cytokine response following in vitro stimulation in the presence of elevated Ca2+ concentrations (approx. 1.8 mM). This effect appeared more pronounced with mouse than with human lymphoid cells and did not influence their survival. A similarly increased cytokine response due to elevated Ca2+ levels was observed with primary human monocytes. In contrast, primary human monocyte-derived macrophages, either unpolarized (M0) or polarized into M1 or M2 macrophages, displayed increased cell death in the presence of elevated Ca2+ concentrations. Furthermore, elevated Ca2+ concentrations promoted phenotypic M1 differentiation by increasing M1 markers on M1 and M2 macrophages and decreasing M2 markers on M2 macrophages. However, the cytokine production of macrophages, again in contrast to the lymphoid cells, was unaltered by the Ca2+ concentration. In summary, our data demonstrate that the Ca2+ concentration during in vitro cultures is an important variable to be considered for functional experiments and that elevated Ca2+ levels can boost cytokine production by both mouse and human lymphoid cells.

immunology↗

bioRxiv2021

Effect of stimulation time on the expression of human macrophage polarization markers

Macrophages are highly plastic cells that can polarize into functionally distinct subsets in vivo and in vitro in response to environmental signals. The development of protocols to model macrophage polarization in vitro greatly contributes to our understanding of macrophage biology. Macrophages are divided into two main groups: Pro-inflammatory M1 macrophages (classically activated) and anti-inflammatory M2 macrophages (alternatively activated), based on several key surface markers and the production of inflammatory mediators. However, the expression of these common macrophage polarization markers is greatly affected by the stimulation time used. Unfortunately, there is no consensus yet regarding the optimal stimulation times for particular macrophage polarization markers in in vitro experiments. This situation is problematic, (i) as analysing a particular marker at a suboptimal time point can lead to false-negative results, and (ii) as it clearly impedes the comparison of different studies. Using human monocyte-derived macrophages (MDMs) in vitro, we analysed how the expression of the main polarization markers for M1 (CD64, CD86, CXCL9, CXCL10, HLA-DR, IDO1, IL1{beta}, IL12, TNF), M2a (CD200R, CD206, CCL17, CCL22, IL-10, TGM2), and M2c (CD163, IL-10, TGF{beta}) macrophages changes over time at mRNA and protein levels. Our data establish the most appropriate stimulation time for the analysis of the expression of human macrophage polarization markers in vitro. Providing such a reference guide will likely facilitate the investigation of macrophage polarization and its reproducibility.

immunology↗