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      Indirubin attenuates mouse psoriasis-like skin lesion in a CD274-dependent manner: an achievement of RNA sequencing

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          Abstract

          It was previously reported that the expression of CD274 was down-regulated in psoriatic epidermis, leading to immune disorders of psoriasis. However, the regulatory mechanisms of CD274 were rarely elucidated. We aimed to explore the regulatory mechanisms of CD274. Skin samples were collected from 18 patients with psoriasis vulgaris and 9 healthy participants for RNA sequencing. Candidate genes were chosen based on degree and k-core difference of genes in the co-expression network. The relations between candidate genes and CD274 were validated by flow cytometry and real-time PCR in primary human epidermal keratinocytes. The therapeutic effect of indirubin was assessed in an imiquimod-treated mouse model. Interferon-γ (IFN-γ), cyclin-dependent kinase (CDK) 1, Toll-like receptor 3 (TLR3), TLR4 and interleukin (IL)-17A were considered as candidate genes. In primary human epidermal keratinocytes, the level of CD274 was obviously increased under the stimulation of IFN-γ and CDK1 inhibitor (indirubin), independent of TLR4, TLR3 or IL-17A. Indirubin alleviated the severity of psoriatic mice in a CD274-dependent manner. Co-expression network analysis served as an effective method for the exploration of molecular mechanisms. We demonstrated for the first time that CD274 was the regulator of indirubin-mediated effect on mouse psoriasis-like skin lesion based on co-expression network analysis, contributing to the alleviation of mouse psoriasis-like skin lesion.

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Hierarchical organization of modularity in metabolic networks

            Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated biochemical networks lacks quantitative support. Here we show that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, their number and degree of clustering following a power law. Within Escherichia coli the uncovered hierarchical modularity closely overlaps with known metabolic functions. The identified network architecture may be generic to system-level cellular organization.
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              Quantifying tumor-infiltrating immune cells from transcriptomics data

              By exerting pro- and anti-tumorigenic actions, tumor-infiltrating immune cells can profoundly influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the quantification of tumor-infiltrating immune cells holds the promise to unveil the multi-faceted role of the immune system in human cancers and its involvement in tumor escape mechanisms and response to therapy. Tumor-infiltrating immune cells can be quantified from RNA sequencing data of human tumors using bioinformatics approaches. In this review, we describe state-of-the-art computational methods for the quantification of immune cells from transcriptomics data and discuss the open challenges that must be addressed to accurately quantify immune infiltrates from RNA sequencing data of human bulk tumors. Electronic supplementary material The online version of this article (10.1007/s00262-018-2150-z) contains supplementary material, which is available to authorized users.
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                Author and article information

                Journal
                Biosci Rep
                Biosci. Rep
                ppbioscirep
                BSR
                Bioscience Reports
                Portland Press Ltd.
                0144-8463
                1573-4935
                19 October 2018
                21 December 2018
                23 November 2018
                : 38
                : 6
                : BSR20180958
                Affiliations
                [1 ]Department of Pharmacy, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
                [2 ]Department of Pharmacy, the 85th Hospital of PLA, Shanghai 200052, China
                [3 ]Department of Dermatology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
                [4 ]Department of Plastic Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
                [5 ]Department of Pharmacy, Wuxi Maternal and Child Health-Care Hospital, Wuxi 214000, China
                [6 ]Department of Pharmacy, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
                Author notes
                Correspondence: Jinhong Hu ( jinhonghu2018@ 123456163.com )
                [*]

                These authors contributed equally to this work.

                Author information
                http://orcid.org/0000-0002-9218-4673
                Article
                10.1042/BSR20180958
                6250808
                30341238
                fabdf4a7-ebb3-4eaa-9ee4-e027dda91e4a
                © 2018 The Author(s).

                This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY).

                History
                : 19 June 2018
                : 10 October 2018
                : 11 October 2018
                Page count
                Pages: 14
                Categories
                Research Articles
                Research Article
                49
                45
                13
                17
                48

                Life sciences
                differentially expressed genes,indirubin,ifn-γ,psoriasis,pd-l1,rna sequencing
                Life sciences
                differentially expressed genes, indirubin, ifn-γ, psoriasis, pd-l1, rna sequencing

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