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UBERON-AE

{"project":"UBERON-AE","denotations":[{"id":"T17435","span":{"begin":15259,"end":15264},"obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"T17434","span":{"begin":15694,"end":15700},"obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"T17433","span":{"begin":15218,"end":15224},"obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"T15483","span":{"begin":11605,"end":11616},"obj":"http://purl.obolibrary.org/obo/UBERON_2000106"},{"id":"T12641","span":{"begin":8252,"end":8258},"obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"T12640","span":{"begin":8067,"end":8072},"obj":"http://purl.obolibrary.org/obo/UBERON_0002107"},{"id":"T9641","span":{"begin":5064,"end":5069},"obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"T9640","span":{"begin":5333,"end":5339},"obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"T9639","span":{"begin":4610,"end":4616},"obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"T9638","span":{"begin":3816,"end":3826},"obj":"http://purl.obolibrary.org/obo/UBERON_0000483"},{"id":"T9637","span":{"begin":3805,"end":3826},"obj":"http://purl.obolibrary.org/obo/UBERON_0001277"},{"id":"T9636","span":{"begin":3696,"end":3717},"obj":"http://purl.obolibrary.org/obo/UBERON_0001277"},{"id":"T9635","span":{"begin":3574,"end":3595},"obj":"http://purl.obolibrary.org/obo/UBERON_0001277"},{"id":"T9634","span":{"begin":3805,"end":3815},"obj":"http://purl.obolibrary.org/obo/UBERON_0000160"},{"id":"T9633","span":{"begin":3696,"end":3706},"obj":"http://purl.obolibrary.org/obo/UBERON_0000160"},{"id":"T9632","span":{"begin":3574,"end":3584},"obj":"http://purl.obolibrary.org/obo/UBERON_0000160"}],"text":"Negative regulation of NF-κB signalling in RA\nSince NF-κB activation is so crucial to many cellular processes, a tight regulation of the NF-κB signalling pathway and the genes it induces is an absolute requirement to fine-tune the inflammatory response. Moreover, terminating an NF-κB response is essential to prevent persistent NF-κB activation that may lead to chronic inflammation and/or tumorigenesis. To achieve this, cells employ different mechanisms, including the expression of inhibitory proteins that downregulate NF-κB signalling [32]. Below we give an overview of a number of proteins that are involved in the dampening or termination of the NF-κB response, some of them under the control of NF-κB itself and thus acting in a negative feedback loop. In addition, we discuss the potential role of these NF-κB inhibitory factors in the immunopathology of RA. Several other proteins involved in the negative regulation of NF-κB-dependent inflammatory responses, such as MyD88s, IRAK-M, and TOLLIP, have been described (reviewed in [33]). These proteins are not discussed here, since a link with RA pathology has not yet been reported.\nAlthough IKK1 is a critical component of the non-canonical NF-κB pathway, it should be mentioned that this kinase also plays a prominent role in the negative regulation of both canonical and noncanonical NF-κB pathways. Macrophages from IKK1-deficient mice or knockin mice expressing inactive IKK1 show increased production of proinflammatory cytokines as a result of enhanced IKK2 activation and IκBα degradation [34]. IKK1 has also been shown to inhibit nuclear NF-κB and to downregulate proinflammatory signalling by phosphorylating STAT1 [35]. Interestingly, a recent study has demonstrated that IKK1 phosphorylates NIK in negative feedback regulation of the noncanonical NF-κB pathway [36], supporting the idea that IKK1 plays important roles in terminating both canonical and noncanonical NF-κB pathways with possible implications for chronic inflammatory diseases like RA.\n\nA20 protein\nA20 (also known as TNFAIP3) is a ubiquitin-editing protein that negatively regulates NF-κB-dependent gene expression in response to different immune-activating stimuli, including TNF, IL-1 and antigens, and the triggering of TLRs and the nucleotide-binding oligomerisation domain-containing 2 receptor (reviewed in [37]). A20 is believed to inhibit NF-κB function by deubiquitinating specific NF-κB signalling molecules, such as RIP1, RIP2, TRAF6 and MALT1, which disrupts specific protein-protein interactions [38-41] (Figure 1). Recently, the disruption of interactions between E2 ubiquitin conjugating enzymes (Ubc13 and Ubc5hc) and E3 ubiquitin ligases (TRAF6, TRAF2 and cIAP1/2) were described as another important mechanism used by A20 to downregulate NF-κB signalling [42]. The association of A20 with its targets requires specific ubiquitin-binding adaptor proteins, including A20-binding inhibitor of NF-κB (ABIN) 1 and Tax1-binding protein 1 [43-46].\nNext to its role in suppressing NF-κB activation, A20 is also a strong inhibitor of apoptosis, at least in some cell types. The mechanisms by which A20 regulates apoptotic signalling, however, are still elusive. A20-deficient mice spontaneously develop multiorgan inflammation and cachexia and die within 2 weeks of birth, illustrating the potent anti-inflammatory function of this molecule [46]. A20-deficient cells are also more susceptible to TNF-mediated apoptosis, confirming its role as an antiapoptotic protein. We recently showed that mice specifically lacking A20 in intestinal epithelial cells exhibit increased susceptibility to experimental colitis due to the hypersensitivity of their intestinal epithelial cells to TNF-induced apoptosis, confirming A20 as a major antiapoptotic protein in the intestinal epithelium [47]. Two independent studies showed that mice lacking A20 in B cells develop autoimmunity due to hyperactive NF-κB responses in B cells leading to unrestricted B-cell survival [48,49].\nA20 expression has been observed in several cell types that play important roles in the pathophysiology of RA, such as fibroblasts, synoviocytes and lymphocytes. Interestingly, A20 expression is itself regulated by NF-κB [50], implicating A20 in the negative feedback regulation of NF-κB signalling. Recently, intra-articular injection of an A20-expressing adenovirus was shown to reduce the severity of synovial inflammation and joint destruction in a mouse model of collagen-induced arthritis, even in untreated joints, in both a prophylactic and therapeutic setting. A20 expression in synovial tissue was associated with inhibition of NF-κB activity and decreased levels of TNF, IL-1β, IL-6, soluble RANKL, monocyte chemo-attractant protein 1, and IL-17, suggesting that A20 induces a protective effect in collagen-induced arthritis mice through suppression of NF-κB activation and NF- κB-dependent gene expression [51]. Because TNF and IL-1β are known to mediate synovitis, pannus formation, and erosion of cartilage and bone in RA, the decreased serum levels of TNF and IL-1β in A20-transduced mice might explain the beneficial effects in the clinical, pathological, and radiological findings. This study also demonstrated that A20 overexpression leads to a decrease in the number of activated osteoclasts in joint tissue. A20 might therefore minimise joint destruction through decreasing the osteoclast number and activity. It will be interesting to analyse in future the susceptibility of conditional knockout mice that lack A20 in specific cell types such as synovial fibroblasts, macrophages, dendritic cells, B cells or T cells.\nImportantly, several SNPs in the human A20 locus have been associated with increased susceptibility to development of autoimmune pathologies (reviewed in [52]). Several genome-wide association studies also revealed a clear association between mutations in the A20 locus in the 6q23 chromosome and susceptibility to RA [52]. Although the identified variants are not located in a gene, they are thought to influence A20 as its nearest gene (~150 kb downstream of A20), probably by the presence of potential regulatory DNA elements in this region. As A20 is required for termination of TNF-induced signals, and TNF is the primary inflammatory cytokine in RA, these findings reveal A20 as a candidate susceptibility locus for RA. How these variants affect normal A20 activity and how they cause RA, however, remain unclear. Recently, Elsby and colleagues functionally evaluated in vitro the regulatory ability of RA-associated SNP variants on A20 promoter activity, and could show repressed A20 transcription for some of the SNPs investigated [53]. It will be of interest to identify the actual causal variants and to elucidate the functional consequences of these variants. In this context, knockin mice for the corresponding A20 SNPs, combined with mouse models for RA, will be very valuable tools.\n\nA20-binding inhibitors of NF-κB\nABIN-1, ABIN-2 and ABIN-3 (also known as TNIP-1, TNIP-2, and TNIP-3) were identified as ubiquitously expressed A20 interacting proteins and were shown to inhibit NF-κB activation by TNF and several other inflammatory stimuli upon overexpression. Because ABINs contain a specific ubiquitin-binding motif, they have been proposed to target A20 to polyubiquitinated substrates [43,44]. Similar to A20, ABIN-1 and ABIN-3 expression is NF-κB dependent, implicating a potential role for the A20/ABIN complex in the negative feedback regulation of NF-κB activation (reviewed in [54]). Unexpectedly, both ABIN-1-deficient and ABIN-2-deficient mice exhibit only slightly increased or normal NF-κB responses, respectively, possibly reflecting redundant NF-κB inhibitory activities of multiple ABINs [55,56]. Functional ABIN-3 is expressed in humans, but mice only express a truncated and inactive form lacking the crucial ubiquitin-binding domain [57]. As for A20, ABIN-1 also strongly inhibits TNF-induced apoptosis [58], and ABIN-1 deficient mice die embryonically due to TNF-dependent foetal liver apoptosis [56].\nUsing oligonucleotide microarray analysis, ABIN-1 was identified among TNF-induced genes in human synoviocytes, and high levels of ABIN-1 mRNA were detected in RA tissue biopsies, indicating a potential role for ABIN-1, together with A20, in the negative feedback regulation of NF-κB signalling and the pathogenesis of RA [59]. In a recent study, inhibition of TLR responses by immunoreceptor tyrosine-based activation motif (ITAM)-coupled receptors was shown to depend on the expression of the NF-κB inhibitory proteins ABIN-3 and A20. Moreover, this protective effect of the ITAM was strongly suppressed in inflammatory arthritis synovial macrophages [60]. Interestingly, ABIN-1 polymorphisms have been associated with psoriasis and systemic lupus erythematosus in humans [61,62]. A high degree of overlap between systemic lupus erythematosus and RA susceptibility loci might be expected as the two diseases show some clinical overlap in joint involvement, autoantibody production, systemic features and response to treatments such as B-cell depletion (rituximab). It will therefore be interesting to investigate whether SNPs that have been reported to be associated with systemic lupus erythematosus are also associated with RA.\n\nCylindromatosis protein\nCylindromatosis (CYLD) protein was originally identified as a tumour suppressor involved in familial cylindromatosis [63]. CYLD is also involved, however, in diverse physiological processes ranging from immunity and inflammation to cell cycle progression, spermatogenesis, and osteoclastogenesis (reviewed in [64]). CYLD is a deubiquitinating enzyme that negatively regulates NF-κB signalling initiated by TNFR, RANK and T-cell receptor stimulation (reviewed in [64]) (Figure 1), by deubiquitina-ting several NF-κB signalling proteins including NEMO, TRAF2, TRAF6, TRAF7, RIP1 and TAK1. Many of these are also targeted by A20 and it is still not clear why the cell needs A20 as well as CYLD to control NF-κB activation. As A20 is only expressed in many cell types upon stimulation, it has been suggested that this protein mainly regulates later phases of NF-κB signalling, whereas CYLD would regulate constitutive and early signalling. In addition, their relative activity might also be cell-type dependent [64].\nInterestingly, CYLD has been shown to negatively regulate RANK signalling and osteoclastogenesis in mice [65]. Mice with a genetic deficiency of CYLD have aberrant osteoclast differentiation and develop severe osteoporosis. Osteoclast precursors of these mice are hyper-responsive to RANKL-induced differentiation and produce more and larger osteoclasts. CYLD expression is markedly upregulated under conditions of RANKL-induced osteoclastogenesis and is recruited to ubiquitinated TRAF6 via the ubiquitin-binding adaptor protein p62 (also known as sequestosome 1) [65], followed by the CYLD-mediated deubiquitination of TRAF6. In this context, it is worth mentioning that transgenic mice expressing a mutated form of p62 also display abnormal osteoclastogenesis and develop progressive bone loss [66]. These findings suggest that CYLD-mediated inhibi-tion of RANK-induced NF-κB signalling plays a key role in the negative regulation of osteoclastogenesis and indicate CYLD as a potential genetic factor involved in the pathology of bone disorders such as RA.\n\nSingle-immunoglobulin IL-1 receptor-related protein\nSingle-immunoglobulin IL-1 receptor-related (SIGIRR) protein, also known as TIR-8, is a member of the TLR/IL-1R family that has been extensively characterised as an inhibitor of IL-1R and TLR signalling, probably through direct interaction with these receptors, MyD88, IRAK1 or TRAF6 [67] (Figure 1). Given the important role of IL-1R and TLR signalling in the chronic inflammation observed in RA [68], a regulatory role for SIGIRR in RA is not unlikely. SIGIRR has a very restricted expression pattern, being expressed in epithelial cells, monocytes and immature dendritic cells, but not in mature macro-phages [69,70]. Recently, SIGIRR overexpression was shown to inhibit the spontaneous release of inflammatory cytokines by human RA synovial cells. This inhibitory function of SIGIRR was further confirmed in vivo, since SIGIRR-deficient mice developed a more severe disease in zymosan-induced arthritis, as well as collagen-induced arthritis mouse models [70]. It will be interesting to compare the expression of SIGIRR in RA patients with its expression in control patients, or to investigate whether the function of SIGIRR is compromised in RA patients. Because of its restricted expression pattern, SIGIRR may also be an interesting therapeutic target in RA.\n\nTNF receptor-associated factor 1\nTRAF1 is a unique member of the TRAF protein family because it lacks a RING finger domain and therefore lacks ubiquitin ligase activity. Accumulating data support a role for TRAF1 as both a negative and a positive modulator of NF-κB signalling by certain TNF family receptors, possibly in a cell-type-dependent manner [71,72]. Expression of TRAF1 is inducible by TNF and overexpression of TRAF1 inhibits TNF-induced NF-κB activation. TRAF1-deficient T cells are hyper-responsive to TNF, with enhanced proliferation and activation of the NF-κB signalling pathway. TRAF1 also functions as a negative regulator of CD40-induced NF-κB activation. TRAF1-deficient dendritic cells, however, show attenuated responses to secondary stimulation by TRAF2-dependent factors, suggesting a positive regulatory role in these cells. The mechanism by which TRAF1 modulates NF- κB activation is still unclear. Most probably, TRAF1 competes with TRAF family members for binding to the receptor or other signalling proteins. Alternatively, TRAF1 might recruit A20 with which it can physically interact [73]. A genome-wide association study examining more than 300,000 SNPs among approximately 1,500 autoantibody-positive RA cases and 1,800 controls identified a genetic variation at the TRAF1-complement component 5 locus as an important RA risk locus [74]. Subsequent work indicates that TRAF1 is more likely to be the causative locus [75]. Recent work in a Korean population also demonstrates genetic association of the TRAF1 region with RA [76].\n\nmicroRNAs\nmiRNAs are recently discovered regulators of gene expression and represent a class of noncoding RNA molecules essential in many cellular and developmental processes, including immune responses and inflammation. They bind the 3'-UTR of target mRNAs leading to the repression of protein expression and the promotion of target mRNA degradation [77].\nmiR-146a/b and miR-155 are of particular interest for inflammatory signalling to NF-κB, since these miRNAs can be induced by inflammatory stimuli such as IL-1β, TNF and TLRs [78,79]. In addition, miR-146a is an NF-κB-dependent gene, and the NF-κB signalling molecules IRAK1 and TRAF6 were identified as target genes of miR-146a [78] (Figure 1). Similarly, miR-155 was shown to target transcripts for the NF-κB signalling molecules IKKε and RIP1 [79,80]. Notably, both miR-146 and miR-155 are expressed at higher levels in RA synovial fibroblasts and synovial tissue [81,82], as well as in peripheral blood mononuclear cells of RA patients [83]. miR-146a is also overexpressed in CD4+ and IL-17-producing T cells from RA patients [84,85]. Interestingly, a polymorphism in the 3'-UTR of the miR-146a target gene was recently shown to be associated with RA susceptibility [86]. miR-155 overexpression in synovial fibroblasts was able to prevent the TLR and cytokine-inducible expression of specific matrix metalloproteinases that mediate tissue destruction in RA [81]. Moreover, miR-155 was shown to promote TNF production, a key process in the pathogenesis of RA [87]. miR-146 and miR-155 may therefore be important negative regulators of inflammation in RA and their potential for the development of new treatments is substantial. In addition, their increased expression in RA patients is potentially useful as a marker for disease diagnosis, progression, or treatment efficacy [88], but this will require confirmation using a large and well-defined cohort.\nBesides miR-146 and miR-155, a number of other miRNAs with a potential role in the control of NF-κB-dependent inflammatory responses in RA pathology were recently identified. In this context, miR-124a - a key regulator of the chemokine monocyte chemoattractant protein 1 - was shown to be decreased in synoviocytes from RA patients [89]. Similarly, elevated levels of miR-203 - leading to increased secretion of matrix metalloproteinase-1 and IL-6 - were detected in RA synovial fibroblasts [90]. Finally, miR-16, miR-132, and miR-223 were also shown to have an altered expression in RA patients, indicating their potential as diagnostic biomarkers for pathogenesis [83,88,91]."}

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bionlp-st-ge-2016-test-ihmc

bionlp-st-ge-2016-test-tees

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PMC:3218875 / 15916-32809 JSONTXT

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PMC:3218875 / 15916-32809 JSON TXT