We present SCENIC, a computational method for simultaneous gene regulatory network reconstruction and cell-state identification from single-cell RNA-seq data (http://scenicaertslaborg) On a compendium of single-cell data from tumors and brain, we demonstrate that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states SCENIC provides critical biological insights into the mechanisms driving cellular heterogeneity

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SCENIC: single-cell regulatory network inference and clustering.

Transforming growth factor-beta (TGF-β)/bone morphogenic protein (BMP) signaling is involved in a vast majority of cellular processes and is fundamentally important throughout life. TGF-β/BMPs have widely recognized roles in bone formation during mammalian development and exhibit versatile regulatory functions in the body. Signaling transduction by TGF-β/BMPs is specifically through both canonical Smad-dependent pathways (TGF-β/BMP ligands, receptors and Smads) and non-canonical Smad-independent signaling pathway (e.g. p38 mitogen-activated protein kinase pathway, MAPK). Following TGF-β/BMP induction, both the Smad and p38 MAPK pathways converge at the Runx2 gene to control mesenchymal precursor cell differentiation. The coordinated activity of Runx2 and TGF-β/BMP-activated Smads is critical for formation of the skeleton. Recent advances in molecular and genetic studies using gene targeting in mice enable a better understanding of TGF-β/BMP signaling in bone and in the signaling networks underlying osteoblast differentiation and bone formation. This review summarizes the recent advances in our understanding of TGF-β/BMP signaling in bone from studies of genetic mouse models and human diseases caused by the disruption of TGF-β/BMP signaling. This review also highlights the different modes of cross-talk between TGF-β/BMP signaling and the signaling pathways of MAPK, Wnt, Hedgehog, Notch, and FGF in osteoblast differentiation and bone formation.

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TGF-β and BMP Signaling in Osteoblast Differentiation and Bone Formation

Single-cell RNA-seq allows building cell atlases of any given tissue and infer the dynamics of cellular state transitions during developmental or disease trajectories. Both the maintenance and transitions of cell states are encoded by regulatory programs in the genome sequence. However, this regulatory code has not yet been exploited to guide the identification of cellular states from single-cell RNA-seq data. Here we describe a computational resource, called SCENIC (Single Cell rEgulatory Network Inference and Clustering), for the simultaneous reconstruction of gene regulatory networks (GRNs) and the identification of stable cell states, using single-cell RNA-seq data. SCENIC outperforms existing approaches at the level of cell clustering and transcription factor identification. Importantly, we show that cell state identification based on GRNs is robust towards batch-effects and technical-biases. We applied SCENIC to a compendium of single-cell data from the mouse and human brain and demonstrate that the proper combinations of transcription factors, target genes, enhancers, and cell types can be identified. Moreover, we used SCENIC to map the cell state landscape in melanoma and identified a gene regulatory network underlying a proliferative melanoma state driven by MITF and STAT and a contrasting network controlling an invasive state governed by NFATC2 and NFIB. We further validated these predictions by showing that two transcription factors are predominantly expressed in early metastatic sentinel lymph nodes. In summary, SCENIC is the first method to analyze scRNA-seq data using a network-centric, rather than cell-centric approach. SCENIC is generic, easy to use, and flexible, and allows for the simultaneous tracing of genomic regulatory programs and the mapping of cellular identities emerging from these programs. Availability: SCENIC is available as an R workflow based on three new R/Bioconductor packages: GENIE3, RcisTarget and AUCell. As scalable alternative to GENIE3, we also provide GRNboost, paving the way towards the network analysis across millions of single cells.

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SCENIC: Single-Cell Regulatory Network Inference And Clustering

Polymorphisms in the gene encoding the transcription factor IRF5 that lead to higher mRNA expression are associated with many autoimmune diseases. Here we show that IRF5 expression in macrophages was reversibly induced by inflammatory stimuli and contributed to the plasticity of macrophage polarization. High expression of IRF5 was characteristic of M1 macrophages, in which it directly activated transcription of the genes encoding interleukin 12 subunit p40 (IL-12p40), IL-12p35 and IL-23p19 and repressed the gene encoding IL-10. Consequently, those macrophages set up the environment for a potent T helper type 1 (TH1)-TH17 response. Global gene expression analysis demonstrated that exogenous IRF5 upregulated or downregulated expression of established phenotypic markers of M1 or M2 macrophages, respectively. Our data suggest a critical role for IRF5 in M1 macrophage polarization and define a previously unknown function for IRF5 as a transcriptional repressor.

Irf5 promotes inflammatory macrophage polarization and th1/th17 response

Saponins are a diverse group of compounds widely distributed in the plant kingdom, which are characterized by their structure containing a triterpene or steroid aglycone and one or more sugar chains. Consumer demand for natural products coupled with their physicochemical (surfactant) properties and mounting evidence on their biological activity (such as anticancer and anticholesterol activity) has led to the emergence of saponins as commercially significant compounds with expanding applications in food, cosmetics, and pharmaceutical sectors. The realization of their full commercial potential requires development of new processes/processing strategies to address the processing challenges posed by their complex nature. This review provides an update on the sources, properties, and applications of saponins with special focus on their extraction and purification. Also reviewed is the recent literature on the effect of processing on saponin structure/properties and the extraction and purification of sapogenins.

Saponins: Properties, Applications and Processing

When ginsenoside Rg3 was anaerobically incubated with human fecal microflora, all specimens metabolized ginsenoside Rg3 to ginsenoside Rh2 and protopanaxadiol. The main metabolite was ginsenoside Rh2. 20(S)-ginsenoside Rg3 was quickly transformed to 20(S)-ginsenoside Rh2 or 20(S)-protopanaxadiol in an amount 19-fold that compared with the transformation of 20(R)-ginsenoside Rg3 to 20(R)-ginsenoside Rh2 or 20(R)-protopanaxadiol. Among the bacteria isolated from human fecal microflora, Bacteroides sp., Eubacterium sp., and Bifidobacterium sp. metabolized ginsenoside Rg3 to protopanaxadiol via ginsenoside Rh2. However, Fusobacterium sp. metabolized ginsenoside Rg3 to ginsenoside Rh2 alone. Among ginsenoside Rg3 and its metabolites, 20(S)-protopanaxadiol and 20(S)-ginsenoside Rh2 exhibited the most potent cytotoxicity against tumor cell lines, 20(S)- and 20(R)-protopanaxadiols potently inhibited the growth of Helicobacter pylori, and 20(S)-ginsenoside Rh2 inhibited H+/K+ ATPase of rat stomach.

https://www.jstage.jst.go.jp/article/bpb/25/1/25_1_58/_pdf

Metabolism of 20(S)- and 20(R)-Ginsenoside Rg3 by Human Intestinal Bacteria and Its Relation to in Vitro Biological Activities

Background: Ginseng (the root of Panax ginseng C.A. Meyer, Araliaceae) has been reported to possess various biological activities, including anti-inflammatory and

Ginsenoside Rh1 possesses antiallergic and anti-inflammatory activities.

When ginsenoside R(c) was anaerobically incubated with human fecal microflora, all specimens metabolized ginsenoside R(c) to compound K and protopanaxadiol. The main metabolite was compound K. Among the bacteria isolated from human fecal microflora, most bacteria, such as Bacteroides sp., Eubacterium sp., and Bifidobacterium sp. potently transformed ginsenoside R(c) to compound K. Bifidobacterium K-103 and Eubacterium A-44 transformed it to compound K via ginsenoside R(d) and Bacteroides HJ-15 and Bifidobacterium K-506 metabolized to compound K via ginsenoside Mb, which was isolated as a new metabolite (M.W. 940[+Na]). Among ginsenoside R(c) and its metabolites, compound K exhibited the most potent antiallergic activity on the IgE-induced RBL cell line as well as potent cytotoxic activity against tumor cell lines.

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Metabolism of ginsenoside Rc by human intestinal bacteria and its related antiallergic activity

Vanillin suppresses in vitro invasion and in vivo metastasis of mouse breast cancer cells

In this study, we measured the antiallergic activities of ginsenosides isolated from the root of Panax ginseng ( Araliaceae), and of their metabolites, as produced by human intestinal bacteria. Compound K, which was identified as a main metabolite, had the most potent inhibitory activity on beta-hexosaminidase release from RBL-2H3 cells and on the PCA reaction. The inhibitory activity of compound K was more potent than that of disodium cromoglycate, one of the commercial anti-allergic drugs. This compound demonstrated a membrane stabilizing action on differential scanning calorimetry. However, compound K did not inhibit the activation of hyaluronidase and did not scavenge active oxygen. These results suggest that the antiallergic action of compound K originates from its cell membrane stabilizing activity and that the ginsenosides of ginseng are prodrugs with extensive antiallergic properties. Abbreviations. compound K:20- O-beta- D-glucopyranosyl-20( S)-protopanaxadiol DNP:dinitrophenol DSCG:disodium cromoglycate DPPC:dipalmitoylphosphatidylcholine DPPH:1,1-diphenyl-2-picrylhydrazyl HSA:human serum albumin IC 50 :50% inhibitory concentration EC 50 :50% effective concentration XOD:xanthine oxidase ICR:Institute of Cancer Research PBS:phosphate buffered saline PCA:passive cutaneous anaphylaxis RAW264.7:mouse monocyte leukemiaRBL-2H3: rat basophil leukemia SD:Sprague-Dawley

Min-Kyung Choo

Papers

Metabolism of 20(S)- and 20(R)-Ginsenoside Rg3 by Human Intestinal Bacteria and Its Relation to in Vitro Biological Activities

Ginsenoside Rh1 possesses antiallergic and anti-inflammatory activities.

Metabolism of ginsenoside Rc by human intestinal bacteria and its related antiallergic activity

Vanillin suppresses in vitro invasion and in vivo metastasis of mouse breast cancer cells

Antiallergic activity of ginseng and its ginsenosides.