Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

The angiogenic factors angiopoietin (Ang)-1 and -2 contribute to inflammation and are differentially expressed in synovial tissue of patients with rheumatoid arthritis (RA) and psoriatic arthritis (PsA). The underlying mechanisms for promoting differential expression are unknown. Here, we identified which cells express Ang-1 and Ang-2 in synovial tissue, transcription factors (TFs) predicted to regulate Ang-1 and Ang-2 transcription, and examined expression of these TFs in RA and PsA synovial tissue. Immunofluorescent double stainings of RA and PsA synovial tissue were performed with CD68, CD163, CD3, CD22 and vWF markers, in combination with antibodies against Ang-1 and Ang-2, using confocal imaging. In silico analysis was conducted to identify TF binding sites in the Ang-1 and Ang-2 promoters, using four different TF binding site prediction programs. RA synovial expression of TFs, Ang-1 and Ang-2 was examined in publicly available gene expression data sets. Candidate TFs were characterized by real-time PCR (qPCR). Ang-1 production was detected in CD68 and CD163 –positive macrophage, CD3-positive T lymphocytes, and CD22-positive B cells, while Ang-2 expression was restricted to vWF- positive endothelial cells, as well as macrophages. In silico studies identified 34 TFs that were predicted to regulate Ang-1 expression and 22 TFs which are involved in Ang-2 expression and are upregulated in RA synovial tissue (P< 0.05). Expression of these TF was readily detected by qPCR in RA and PsA synovial tissue biopsies. Our studies suggest that expression of Ang-1 and Ang-2 by different cell types could additional underlie the previously observed specific Ang-1 high signature in RA, compared to PsA. Enhanced expression of Ang-1 and Ang-2 in RA and PsA is strongly associated with expression of specific TFs, and understanding the mechanisms leading to the differential expression of these TFs may give insight into the etiology of RA and PsA.

Macrophages play a crucial role in eliminating respiratory pathogens. Both pulmonary resident alveolar macrophages (AMs) and recruited macrophages contribute to detecting, responding to, and resolving infections in the lungs. Despite their distinct functions, it remains unclear how these macrophage subsets regulate their responses to infection, including how activation by the cytokine IFN-γ is regulated. This shortcoming prevents the development of therapeutics that effectively target distinct lung macrophage populations without exacerbating inflammation. We aimed to better understand the transcriptional regulation of resting and IFN-γ-activated cells using a new ex vivo model of AMs from mice, fetal liver-derived alveolar-like macrophages (FLAMs), and immortalized bone marrow-derived macrophages. Our findings reveal that IFN-γ robustly activates both macrophage types; however, the profile of activated IFN-γ-stimulated genes varies greatly between these cell types. Notably, FLAMs show limited expression of costimulatory markers essential for T cell activation upon stimulation with only IFN-γ. To understand cell type-specific differences, we examined how the inhibition of the regulatory kinases GSK3α/β alters the IFN-γ response. GSK3α/β controlled distinct IFN-γ responses, and in AM-like cells, we found that GSK3α/β restrained the induction of type I IFN and TNF, thus preventing the robust expression of costimulatory molecules and limiting CD4+ T cell activation. Together, these data suggest that the capacity of AMs to respond to IFN-γ is restricted in a GSK3α/β-dependent manner and that IFN-γ responses differ across distinct macrophage populations. These findings lay the groundwork to identify new therapeutic targets that activate protective pulmonary responses without driving deleterious inflammation.

Heterogeneity of Embryonic and Adult Stem Cells

Breast cancer is the leading cause of cancer death among women worldwide being distant metastases the main cause of disease. Patients with triple negative breast cancer tumors develop distant metastases earlier compared to luminal tumors. Epithelial-mesenchymal transition (EMT) induced by TGFβ signaling pathways, is the main mechanism to promote metastasis through the expression of the transcription factors TWIST, SNAIL, SLUG and ZEB1. Expression of EMT transcription factors has been studied in cancer cell lines however studies in breast cancer tumors with different subtype have not been reported. In addition, the molecular mechanism that induce EMT program is not known yet. In this study we evaluated the expression of the four transcription factors as well as the state of TGFβ/SMAD, ERK/MAPK and PI3K/AKT pathways in breast cancer cell lines HCC1937 (triple negative) and T47D (luminal) after TGFβ treatment. The same analysis was done by immunohistochemistry in 100 breast cancer tumors with different subtype. After TGFβ treatment T47D showed activation of ERK/MAPK and PI3K/AKT pathways and expression of only two transcription factors: SNAIL and SLUG. HCC1937 cells showed activation of TGFβ/SMAD and ERK/MAPK pathways and expression of TWIST, SLUG and ZEB1 but not SNAIL. Similar results were observed in breast cancer tumors, being TGFβ/SMAD pathway active in the majority of triple negative tumors, whereas an active state of PI3K/AKT was observed in luminal tumors. Active ERK/MAPK pathway was observed in both triple negative and luminal tumors. In relation to expression of transcription factors triple negative tumors with an active state of the TGFβ/SMAD pathway showed expression of transcription factors TWIST, SNAIL and SLUG, whereas those tumors with an active state of ERK/MAPK pathway showed only ZEB1 expression. Luminal tumors with an active PI3K/AKT pathway frequently showed ZEB1 expression. Our results showed that expression of a specific EMT transcription factor induced by TGFβ is related to the tumor subtype and depends on the activated signaling pathway. These results suggest different mechanisms of EMT induction by TGFβ in relation to breast cancer tumor subtype. Citation Format: Victoria Ortega-Hernández, Wanda Fernandez, Pilar Carvallo. Alternative activation of TGFβ signaling pathways in breast cancer tumors with different subtype is related to a differential expression of transcription factors that induce EMT [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2036.

During ontogeny, cells progress through multiple alternate differentiation states by activating distinct gene regulatory networks. In this review, we highlight the important role of chromatin priming in facilitating gene activation during lineage specification and in maintaining an epigenetic memory of previous gene activation. We show that chromatin priming is part of a hugely diverse repertoire of regulatory mechanisms that genes use to ensure that they are expressed at the correct time, in the correct cell type, and at the correct level, but also that they react to signals. We also emphasize how increasing our knowledge of these principles could inform our understanding of developmental failure and disease.

Emerging role of neuregulin-1beta1 in pathogenesis and progression of multiple sclerosis

In the vertebrate retina, amacrine and ganglion cells represent the most diverse cell classes. They can be classified into different cell types by several features, such as morphology, light responses, and gene expression profile. Although birds possess high visual acuity (similar to primates that we used here for comparison) and tetrachromatic color vision, data on the expression of transcription factors in retinal ganglion cells of birds are largely missing. In this study, we tested various transcription factors, known to label subpopulations of cells in mammalian retinae, in two avian species: the common buzzard (Buteo buteo), a raptor with exceptional acuity, and the domestic pigeon (Columba livia domestica), a good navigator and widely used model for visual cognition. Staining for the transcription factors Foxp2, Satb1 and Satb2 labeled most ganglion cells in the avian ganglion cell layer. CtBP2 was established as marker for displaced amacrine cells, which allowed us to reliably distinguish ganglion cells from displaced amacrine cells and assess their densities in buzzard and pigeon. When we additionally compared the temporal and central fovea of the buzzard with the fovea of primates, we found that the cellular organization in the pits was different in primates and raptors. In summary, we demonstrate that the expression of transcription factors is a defining feature of cell types not only in the retina of mammals but also in the retina of birds. The markers, which we have established, may provide useful tools for more detailed studies on the retinal circuitry of these highly visual animals.

Inbred mouse strains display significant differences in their levels of brain alpha7 nicotinic acetylcholine receptor (alpha7 nAChR) expression, as measured by binding of the alpha7-selective antagonist alpha-bungarotoxin. Variations in alpha-bungarotoxin binding have been shown to correlate with an animal's sensitivity to nicotine-induced seizures and sensory gating. In two inbred mouse strains, C3H/2Ibg (C3H) and DBA/2Ibg (DBA/2), the inter-strain binding differences are linked to a restriction length polymorphism in the alpha7 nAChR gene, Chrna7. Despite this finding, the molecular mechanism(s) through which genetic variability in Chrna7 may contribute to alpha7 nAChR expression differences remains unknown. However, studies of the human alpha7 nAChR gene (CHRNA7) previously have demonstrated that CHRNA7 promoter polymorphisms are associated with differences in promoter activity as well as differences in sensory processing. In the present study, a 947-base pair region of the Chrna7 promoter was cloned from both the C3H and DBA/2 inbred mouse strains in an attempt to identify polymorphisms that may underlie alpha7 nAChR differential expression. Sequence analysis of these fragments identified 14 single nucleotide polymorphisms (SNPs). A combination of two of these SNPs affects promoter activity in an in vitro luciferase reporter assay. These results suggest a mechanism through which the Chrna7 promoter genotype may influence interstrain variations in alpha7 nAChR expression.

Beyond PROX1: transcriptional, epigenetic, and noncoding RNA regulation of lymphatic identity and function.

Planarian stem cells specify fate yet retain potency during the cell cycle.

Cryptotanshinone and tanshinone IIA enhance IL-15-induced natural killer cell differentiation

Pancreatic ductal adenocarcinoma (PDA) is accompanied by reprogramming of the local microenvironment, but changes at distal sites are poorly understood. We implanted biomaterial scaffolds, which act as an artificial premetastatic niche, into immunocompetent tumor-bearing and control mice, and identified a unique tumor-specific gene expression signature that includes high expression of C1qa, C1qb, Trem2, and Chil3 Single-cell RNA sequencing mapped these genes to two distinct macrophage populations in the scaffolds, one marked by elevated C1qa, C1qb, and Trem2, the other with high Chil3, Ly6c2 and Plac8 In mice, expression of these genes in the corresponding populations was elevated in tumor-associated macrophages compared with macrophages in the normal pancreas. We then analyzed single-cell RNA sequencing from patient samples, and determined expression of C1QA, C1QB, and TREM2 is elevated in human macrophages in primary tumors and liver metastases. Single-cell sequencing analysis of patient blood revealed a substantial enrichment of the same gene signature in monocytes. Taken together, our study identifies two distinct tumor-associated macrophage and monocyte populations that reflects systemic immune changes in pancreatic ductal adenocarcinoma patients.

Introduction: The first aim of this study was to isolate the dental tissue-derived stem cells from the dental follicle (DF), dental pulp (DP) , and root apical papilla (RAP) of the extracted wisdom teeth. Second was to evaluate their characterization with the expressions of trans cription factors and cell surface markers. Finally, their ability of the in vitro multi-lineage differentiations into osteogenic and adipogenic cells were compared, respectively. Materials and Methods: Dental tissues, including dental follicle, dental pulp, and root apical papilla, were separated in the extracted wisdom teeth. These three dental tissues were cultured in Dulbecco' s modified Eagle' s medium (DMEM) with supplements, respectively. After passage 3, the homogeneous shaped dental tissue-derived cells were analyzed the expression of transcription factors (Oct-4, Nanog and Sox-2) a nd cell surface mark- ers (CD44, CD90 and CD105) with reverse transcription polymerase chain reaction (RT-PCR) and fluorescence-activated cell sortin g (FACS) analy- sis. In order to evaluate in vitro multi-lineage differentiations, the culture media were changed to the osteogenic and adipogenic induction mediums when the dental tissue-derived cells reached to passage 3. The characteristics of these three dental tissue-derived cells were compared with immuno- histochemistry. Results: During primary culture, heterogenous and colony formatted dental tissue-derived cells were observed in the culture plates. Afte r passage 2 or 3, homogenous spindle-like cells were observed in all culture plates. Transcription factors and mesenchymal stem cell marker s were positively observed in all three types of dental tissue-derived cells. However, the quantity of expressed transcription factors was most l arge in RAP-derived cells. In all three types of dental tissue-derived cells, osteogenic and adipogenic differentiations were observed after treatment of specific induction media. In vitro adipogenic differentiation was similar among these three types of cells. In vitro osteogenic differentiation was most strongly and frequently observed in the RAP-derived cells, whereas rarely osteogenic differentiation was observed in the DP-derived cells. Conclusion: These findings suggest that three types of human dental tissue-derived cells from extracted wisdom teeth were multipotent mesen chy- mal stem cells, have the properties of multi-lineage differentiations. Especially, stem cells from root apical papilla (SCAP) h ave much advantage in osteogenic differentiation, whereas dental follicle cells (DFCs) have a characteristic of easy adipogenic differentiation.

CD4+ T cells can be subdivided from a functional point of view into two main subsets: effector cells, which provide protection against exogenous offending agents, and regulatory T (Treg) cells whose function is to avoid autoimmune reactions and to stop the effector response against exogenous antigens, when the response itself becomes dangerous for the host. Human effector CD4+ T lymphocytes can be additionally classified into lineages based mainly on their immunological functions that are supported by distinct profile of cytokine, transcription factor, and homing receptors expression. In the last years, beyond the well known populations of human T helper (Th) lymphocytes, Th1 and Th2 cells, other populations have been discovered and phenotypically characterized. These include the Th17 subset, which is certainly the most intensively studied, but also Th22, Th9, and T follicular helper (Tfh) lymphocytes. In addition to their protective functions, these T helper populations are also involved in the pathogenesis of several inflammatory immune-mediated disorders. Th1 and Th17 cells are involved in the pathogenesis of organ-specific autoimmune diseases and other chronic inflammatory disorders, whereas allergen-specific Th2 lymphocytes play a crucial role in allergy. Although classically viewed as distinct lineages, recent evidence indicate that CD4+ T cells, particularly the Th17 subset, are more plastic than previously thought. It is not fully understood how often such plasticity occurs in the course of physiologic responses to pathogens and what its importance is in protective immunity, but in inflammatory conditions Th17 lymphocytes that have shifted towards a Th1 or Th2 phenotype, acquiring the ability to produce IFN-γ or IL-4, and seem to be particularly aggressive and more pathogenic than the unshifted cells. In this context, the possibility to interfere with this modulation of phenotype can be considered a possible target for developing novel therapeutic strategies in the above mentioned diseases.

Single-cell multiomics reveals the gene regulatory networks and enhancer logic underlying two distinct wound response cell states in the Drosophila wing imaginal disc and finds similarities with cell states observed in the Ras-scrib tumor model.