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Xu C, Suo Y, Wang X, Qin JG, Chen L, Li E. Recovery from Hypersaline-Stress-Induced Immunity Damage and Intestinal-Microbiota Changes through Dietary β-glucan Supplementation in Nile tilapia ( Oreochromis niloticus). Animals (Basel) 2020; 10:ani10122243. [PMID: 33265935 PMCID: PMC7761230 DOI: 10.3390/ani10122243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Long-term hypersaline stress can induce coagulation disorders and splenomegaly and down-regulate the complement pathway in tilapia, which can increase risk in healthy breeding. As a prebiotic, β-glucan dietary supplementation can significantly reduce enlarged spleen resulting from hypersaline stress. The hematological aspects of the red blood cell count, hematocrit, red cell distribution width, platelet count, and plateletcrit were also decreased by supplementation with dietary β-glucan. In the spleen and intestine, β-glucan intake significantly decreased the high expression of immune-related genes due to hypersaline stress resulting from β-glucan intake in tilapia. β-glucan supplementation also significantly increased the abundance of beneficial microbiota such as Lactobacillus, Phycicoccus, and Rikenellaceae in the intestine. In summary, β-glucan intake can relieve tissue damage and optimize the intestinal microbiota of tilapia in brackish water and improve fish health. Abstract Long-term exposure to hyperosmotic environments can induce severe immune damage and increase risk in tilapia breeding. As an effective immunoregulator, β-glucan has attracted extensive attention in nutritional research and given rise to high expectations of improving health status and alleviating organismal damage in tilapia, Oreochromis niloticus, in brackish water. In this study, an 8-week cultivation experiment was conducted on tilapia fed a basal diet or diets with β-glucan supplementation in freshwater (control) and brackish water. Growth performance, hematological aspects, immune cytokine expression, and the intestinal microbiota of tilapia were analyzed. The results indicated that supplementation with β-glucan significantly reduced the enlarged spleen of tilapia resulting from hypersaline stress. Tilapia fed β-glucan showed significantly-greater decreases in the red blood cell count, hematocrit, red cell distribution width, platelet count, and plateletcrit than those fed the basal diet. β-glucan significantly decreased the high expression of immune-related genes in the spleen induced by hyperosmotic stress. In the intestine, the high migration inhibitory factor-2 (MIF-2) and IL-1β gene expression induced by hypersaline stress was significantly reduced. β-glucan supplementation also significantly increased the abundance of beneficial microbiota such as Lactobacillus, Phycicoccus, and Rikenellaceae. Therefore, dietary β-glucan supplementation can significantly reduce spleen enlargement and improve immune function in tilapia in brackish water. β-glucan intake can also optimize the intestinal microbiota of tilapia in brackish water and improve fish health.
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Affiliation(s)
- Chang Xu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou 570228, China;
- School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.S.); (X.W.); (L.C.)
| | - Yantong Suo
- School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.S.); (X.W.); (L.C.)
| | - Xiaodan Wang
- School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.S.); (X.W.); (L.C.)
| | - Jian G Qin
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia;
| | - Liqiao Chen
- School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.S.); (X.W.); (L.C.)
| | - Erchao Li
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou 570228, China;
- School of Life Sciences, East China Normal University, Shanghai 200241, China; (Y.S.); (X.W.); (L.C.)
- Correspondence:
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Anti-Inflammatory Effects of a Stauntonia hexaphylla Fruit Extract in Lipopolysaccharide-Activated RAW-264.7 Macrophages and Rats by Carrageenan-Induced Hind Paw Swelling. Nutrients 2018; 10:nu10010110. [PMID: 29361789 PMCID: PMC5793338 DOI: 10.3390/nu10010110] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/12/2018] [Accepted: 01/16/2018] [Indexed: 01/17/2023] Open
Abstract
The fruit of Stauntonia hexaphylla is commonly used as a traditional anthelmintic in Korea, Japan, and China. However, its anti-inflammatory activity and the underlying mechanisms have not been studied systematically. In the present study, we examined the anti-inflammatory activities of an aqueous extract of S. hexaphylla fruit (SHF) in lipopolysaccharide (LPS)-activated RAW 264.7 cells. The SHF extract contained anti-inflammatory compounds, such as neochlorogenic acid, chlorogenic acid, and cryptochlorogenic acid. The extract inhibited protein levels of inducible nitric oxide synthase and the activity of cyclooxygenase enzyme, with concomitant reductions in the production of nitric oxide and prostaglandin E2 in LPS-activated RAW 264.7 cells. Additionally, the SHF extract reduced the production of pro-inflammatory cytokines, including tumor necrosis factor-α, interleukin (IL)-1β, and IL-6. The SHF extract attenuated LPS-induced nuclear factor-κB (NF-κB) activation by decreasing the phosphorylation of its inhibitor, IκBα. Furthermore, the SHF extract showed a significant anti-inflammatory effect in vivo by reducing the volume of carrageenan-induced paw edema in rats. Our results suggest that the SHF extract exerts potential anti-inflammatory properties against LPS-activated RAW 254.7 cells, and in an animal model of inflammation.
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Williams SB, Kamat AM, Mmeje C, Ye Y, Huang M, Chang DW, Dinney CP, Wu X. Genetic variants in the inflammation pathway as predictors of recurrence and progression in non-muscle invasive bladder cancer treated with Bacillus Calmette-Guérin. Oncotarget 2017; 8:88782-88791. [PMID: 29179475 PMCID: PMC5687645 DOI: 10.18632/oncotarget.21222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/02/2017] [Indexed: 01/17/2023] Open
Abstract
Inflammation plays a critical role in the etiology of several cancers and may affect their clinical outcome. Our objective was to assess the association of genetic variants within the inflammation pathway with recurrence and progression among non-muscle invasive bladder cancer (NMIBC) patients with or without Bacillus Calmette–Guérin (BCG) treatment. We genotyped 372 single nucleotide polymorphisms (SNPs) in 27 selected genes within the inflammation pathway in 349 patients diagnosed with NMIBC, followed by internal validation in 322 additional patients. We used Cox proportional hazards regression analyses to identify SNPs as predictors for recurrence and progression. In the discovery phase, we identified 20 variants that were significantly associated with recurrence outcomes and 15 SNPs significantly associated with progression in patients treated with BCG but not in the transurethral resection (TUR)-only group. In BCG treated patients, rs7089861 was the only SNP significantly associated with risk of progression in both the discovery phase (Hazard Ratio [HR]=3.15, 95% Confidence Interval [CI]: 1.38-7.22, P<0.01) and validation phase (HR=3.84, 95% CI: 1.64-9.0, P=0.002; meta-analysis HR=3.47, 95% CI: 1.92-6.28, P<0.001). Two variants, rs1800686 and rs2071081, had probable association with HRs of the same trend in the discovery and validation groups (meta-analysis P=0.002). These findings supported the notion that genetic variation of inflammation pathway may impact clinical outcome of NMIBC patients treated with BCG immunotherapy. Further validation of these results in order to improve risk stratification to identify patients most likely to benefit from BCG treatment versus upfront radical cystectomy and future development of potential targeted therapies are warranted.
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Affiliation(s)
- Stephen B Williams
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Division of Urology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Ashish M Kamat
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chinedu Mmeje
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuanquing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David W Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Colin P Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Dai X, Dong M, Yu H, Xie Y, Yu Y, Cao Y, Kong Z, Zhou B, Xu Y, Yang T, Li K. Knockdown of TCTN1 Strongly Decreases Growth of Human Colon Cancer Cells. Med Sci Monit 2017; 23:452-461. [PMID: 28123172 PMCID: PMC5291083 DOI: 10.12659/msm.899595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background Tectonic family member 1 (TCTN1), a member of the tectonic family, is involved in several developmental processes and is aberrantly expressed in multiple solid tumors. However, the expression and regulation of TCTN1 in human colorectal cancer (CRC) is still not clear. Material/Methods The expression of TCTN1 mRNA was first explored by using Oncomine microarray datasets. TCTN1 expression was silenced in human CRC cell lines HCT116 and SW1116 via RNA interference (RNAi). Furthermore, we investigated the effect of TCTN1 depletion on CRC cell growth by MTT, colony formation, and flow cytometry in vitro. Results In this study, meta-analysis showed that the expressions of TCTN1 mRNA in CRC specimens were significantly higher than that in normal specimens. Knockdown of TCTN1 expression potently inhibited the abilities of cell proliferation and colony formation as determined. Flow cytometry analysis showed that depletion of TCTN1 could cause cell cycle arrest at the G2/M phase. In addition, Annexin V/7-AAD double-staining indicated that TCTN1 silencing promoted cell apoptosis through down-regulation of caspase 3 and Bcl-2 and upregulation of cleaved caspase 3 and PARP. Conclusions Our results indicate that TCTN1 may be crucial for CRC cell growth, providing a novel alternative to target therapies of CRC. Further research on this topic is warranted.
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Affiliation(s)
- Xiaoyu Dai
- Department of Anorectal Surgery, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
| | - Mingjun Dong
- Department of Anorectal Surgery, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
| | - Hua Yu
- Department of Anorectal Surgery, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
| | - Yangyang Xie
- Department of Anorectal Surgery, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
| | - Yongming Yu
- Department of Anorectal Surgery, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
| | - Yisheng Cao
- Department of Anorectal Surgery, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
| | - Zhenfang Kong
- Department of Anorectal Surgery, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
| | - Baofeng Zhou
- Department of Anorectal Surgery, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
| | - Yidong Xu
- Department of Anorectal Surgery, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
| | - Tong Yang
- Department of Anorectal Surgery, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
| | - Keqiang Li
- Clinical Research Center, Ningbo Second Hospital, Ningbo, Zhejiang, China (mainland)
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The Role of Alternative Splicing in the Control of Immune Homeostasis and Cellular Differentiation. Int J Mol Sci 2015; 17:ijms17010003. [PMID: 26703587 PMCID: PMC4730250 DOI: 10.3390/ijms17010003] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing of pre-mRNA helps to enhance the genetic diversity within mammalian cells by increasing the number of protein isoforms that can be generated from one gene product. This provides a great deal of flexibility to the host cell to alter protein function, but when dysregulation in splicing occurs this can have important impact on health and disease. Alternative splicing is widely used in the mammalian immune system to control the development and function of antigen specific lymphocytes. In this review we will examine the splicing of pre-mRNAs yielding key proteins in the immune system that regulate apoptosis, lymphocyte differentiation, activation and homeostasis, and discuss how defects in splicing can contribute to diseases. We will describe how disruption to trans-acting factors, such as heterogeneous nuclear ribonucleoproteins (hnRNPs), can impact on cell survival and differentiation in the immune system.
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Rao S, Liu X, Freedman BD, Behrens EM. Spleen tyrosine kinase (Syk)-dependent calcium signals mediate efficient CpG-induced exocytosis of tumor necrosis factor α (TNFα) in innate immune cells. J Biol Chem 2013; 288:12448-58. [PMID: 23515313 DOI: 10.1074/jbc.m113.454405] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pattern recognition receptors expressed by cells of the innate immune system initiate the immune response upon recognition of microbial products. Activation of pattern recognition receptors result in the production and release of proinflammatory cytokines, including TNFα and IL-6. Because these cytokines promote disparate effector cell responses, understanding the signaling pathways involved in their regulation is critical for directing the immune response. Using macrophages and dendritic cells deficient in spleen tyrosine kinase (Syk), we identified a novel pathway by which TNFα trafficking and secretion are regulated by Syk following stimulation with CpG DNA. In the absence of PLCγ2, a Syk substrate, or the calcium-responsive kinase calcium calmodulin kinase II, CpG-induced TNFα secretion was impaired. Forced calcium mobilization rescued the TNFα secretion defect in Syk-deficient cells. In contrast to its effect on TNFα, Syk deficiency did not affect IL-6 secretion, suggesting that Syk-dependent signals participate in differential sorting of cytokines, thus tailoring the cytokine response. Our data report a novel pathway for TNFα regulation and provide insight into non-transcriptional mechanisms for shaping cytokine responses.
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Affiliation(s)
- Sheila Rao
- Division of Pediatric Rheumatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
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Huo M, Cui X, Xue J, Chi G, Gao R, Deng X, Guan S, Wei J, Soromou LW, Feng H, Wang D. Anti-inflammatory effects of linalool in RAW 264.7 macrophages and lipopolysaccharide-induced lung injury model. J Surg Res 2013; 180:e47-54. [DOI: 10.1016/j.jss.2012.10.050] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 09/22/2012] [Accepted: 10/26/2012] [Indexed: 11/24/2022]
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Moshkani S, Kuzin II, Adewale F, Jansson J, Sanz I, Schwarz EM, Bottaro A. CD23+ CD21(high) CD1d(high) B cells in inflamed lymph nodes are a locally differentiated population with increased antigen capture and activation potential. THE JOURNAL OF IMMUNOLOGY 2012; 188:5944-53. [PMID: 22593620 DOI: 10.4049/jimmunol.1103071] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CD23(+)CD21(high)CD1d(high) B cells in inflamed nodes (Bin cells) accumulate in the lymph nodes (LNs) draining inflamed joints of the TNF-α-transgenic mouse model of rheumatoid arthritis and are primarily involved in the significant histological and functional LN alterations that accompany disease exacerbation in this strain. In this study, we investigate the origin and function of Bin cells. We show that adoptively transferred GFP(+) sorted mature follicular B (FoB) cells home preferentially to inflamed LNs of TNF-α-transgenic mice where they rapidly differentiate into Bin cells, with a close correlation with the endogenous Bin fraction. Bin cells are also induced in wild-type LNs after immunization with T-dependent Ags and display a germinal center phenotype at higher rates compared with FoB cells. Furthermore, we show that Bin cells can capture and process Ag-immune complexes in a CD21-dependent manner more efficiently than can FoB cells, and they express greater levels of MHC class II and costimulatory Ags CD80 and CD86. We propose that Bin cells are a previously unrecognized inflammation-induced B cell population with increased Ag capture and activation potential, which may facilitate normal immune responses but may contribute to autoimmunity when chronic inflammation causes their accumulation and persistence in affected LNs.
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Affiliation(s)
- Safiehkhatoon Moshkani
- Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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Abstract
Tumor necrosis factor-α (TNFα) was cloned over 2 decades ago and its identification in part led to the discovery of a super family of tumor necrosis factors (TNFs) and their receptors. TNFα signals through two transmembrane receptors, TNFR1 and TNFR2, and regulates a number of critical cell functions including cell proliferation, survival, differentiation, and apoptosis. Macrophages are the major producers of TNFα and interestingly are also highly responsive to TNFα. Aberrant TNFα production and TNF receptor signaling have been associated with the pathogenesis of several diseases, including rheumatoid arthritis, Crohn's disease, atherosclerosis, psoriasis, sepsis, diabetes, and obesity. TNFα has been shown to play a pivotal role in orchestrating the cytokine cascade in many inflammatory diseases and because of this role as a "master-regulator" of inflammatory cytokine production, it has been proposed as a therapeutic target for a number of diseases. Indeed anti-TNFα drugs are now licensed for treating certain inflammatory diseases including rheumatoid arthritis and inflammatory bowel disease. In this review we discuss the discovery of TNFα and its actions especially in regulating macrophage biology. Given its importance in several human diseases, we also briefly discuss the role of anti-TNFα therapeutics in the treatment of inflammatory diseases.
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Affiliation(s)
- Narayanan Parameswaran
- Department of Physiology and Division of Pathology, Michigan State University, East Lansing, MI 48824, USA.
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Wilson HM, Chettibi S, Jobin C, Walbaum D, Rees AJ, Kluth DC. Inhibition of macrophage nuclear factor-kappaB leads to a dominant anti-inflammatory phenotype that attenuates glomerular inflammation in vivo. THE AMERICAN JOURNAL OF PATHOLOGY 2005; 167:27-37. [PMID: 15972949 PMCID: PMC1603438 DOI: 10.1016/s0002-9440(10)62950-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Infiltrating macrophages (mphi) can cause injury or facilitate repair, depending on how they are activated by the microenvironment. Studies in vitro have defined the roles of individual cytokines and signaling pathways in activation, but little is known about how macrophages integrate the multiple signals they receive in vivo. We inhibited nuclear factor-kappaB in bone marrow-derived macrophages (BMDMs) by using a recombinant adenovirus expressing dominant-negative IkappaB (Ad-IkappaB). This re-orientated macrophage activation so they became profoundly anti-inflammatory in settings where they would normally be classically activated. In vitro, the lipopolysaccharide-induced nitric oxide, interleukin-12, and tumor necrosis factor-alpha synthesis was abrogated while interleukin-10 synthesis increased. In vivo, fluorescently labeled BMDMs transduced with Ad-IkappaB and injected into the renal artery significantly reduced inducible nitric oxide synthase and MHC class II expression when activated naturally in glomeruli of rats with nephrotoxic nephritis. Furthermore, although they only comprised 15% of glomerular macrophages, their presence significantly reduced glomerular infiltration and activation of host macrophages. Injury in nephrotoxic nephritis was also decreased when assessed morphologically and by severity of albuminuria. The results demonstrate the power of Ad-IkappaB-transduced BMDMs to inhibit injury when activated by acute immune-mediated inflammation within the glomerulus.
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Affiliation(s)
- Heather M Wilson
- Department of Medicine and Therapeutics, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK.
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Knobler H, Zhornicky T, Sandler A, Haran N, Ashur Y, Schattner A. Tumor necrosis factor-alpha-induced insulin resistance may mediate the hepatitis C virus-diabetes association. Am J Gastroenterol 2003; 98:2751-6. [PMID: 14687828 DOI: 10.1111/j.1572-0241.2003.08728.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Among patients infected with hepatitis C virus (HCV), 13-33% develop type 2 diabetes mellitus (DM). The mechanism for this remains unclear. Because tumor necrosis factor-alpha (TNF-alpha) has been identified as a mediator of insulin resistance and is induced by HCV, we examined TNF-alpha and proinflammatory cytokines in noncirrhotic patients with chronic hepatitis C, both with and without diabetes. METHODS HCV-infected patients with type 2 DM (n = 23) were compared with age- and sex-matched patients with chronic hepatitis C and without DM (n = 28), patients with DM and without HCV (n = 31), and healthy controls (n = 21). Serum levels of TNF-alpha, interleukin-1beta (IL-1beta), interleukin-6 (IL-6), and soluble TNF receptors (sTNFR) 1 (p55) and 2 (p75) were determined by ELISA. RESULTS Detectable serum TNF was found in 74% of the HCV/DM patients, versus 64% of the nondiabetic HCV group and < or =10% in the other groups. Mean sTNFR1 in the HCV/DM group was 1931 pg/ml (95% CI = 1449-2413), compared with 1289 pg/ml (95% CI = 1101-1476) in nondiabetic HCV patients, with similar values in the other two groups (p = 0.001). The mean sTNFR2 level in the HCV/DM patients was 3326 pg/ml (95% CI = 2924-3727) compared with 2367 pg/ml (95% CI = 1951-2784) in the nondiabetic HCV patients, and similar results in the other groups (p < 0.0001). Serum IL-1beta, IL-6, and C-reactive protein were not significantly different between HCV patients with or without DM. CONCLUSIONS Excessive TNF-alpha response characterizes HCV-infected patients who develop DM. STNFR may be a marker for the development of DM in chronic hepatitis C.
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Affiliation(s)
- Hilla Knobler
- Hebrew University and Hadassah Medical School, Department of Medicine, Kaplan Medical Center, Rehovot 76100, Israel
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Clark HF, Gurney AL, Abaya E, Baker K, Baldwin D, Brush J, Chen J, Chow B, Chui C, Crowley C, Currell B, Deuel B, Dowd P, Eaton D, Foster J, Grimaldi C, Gu Q, Hass PE, Heldens S, Huang A, Kim HS, Klimowski L, Jin Y, Johnson S, Lee J, Lewis L, Liao D, Mark M, Robbie E, Sanchez C, Schoenfeld J, Seshagiri S, Simmons L, Singh J, Smith V, Stinson J, Vagts A, Vandlen R, Watanabe C, Wieand D, Woods K, Xie MH, Yansura D, Yi S, Yu G, Yuan J, Zhang M, Zhang Z, Goddard A, Wood WI, Godowski P, Gray A. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Genome Res 2003; 13:2265-70. [PMID: 12975309 PMCID: PMC403697 DOI: 10.1101/gr.1293003] [Citation(s) in RCA: 259] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2003] [Accepted: 07/28/2003] [Indexed: 11/24/2022]
Abstract
A large-scale effort, termed the Secreted Protein Discovery Initiative (SPDI), was undertaken to identify novel secreted and transmembrane proteins. In the first of several approaches, a biological signal sequence trap in yeast cells was utilized to identify cDNA clones encoding putative secreted proteins. A second strategy utilized various algorithms that recognize features such as the hydrophobic properties of signal sequences to identify putative proteins encoded by expressed sequence tags (ESTs) from human cDNA libraries. A third approach surveyed ESTs for protein sequence similarity to a set of known receptors and their ligands with the BLAST algorithm. Finally, both signal-sequence prediction algorithms and BLAST were used to identify single exons of potential genes from within human genomic sequence. The isolation of full-length cDNA clones for each of these candidate genes resulted in the identification of >1000 novel proteins. A total of 256 of these cDNAs are still novel, including variants and novel genes, per the most recent GenBank release version. The success of this large-scale effort was assessed by a bioinformatics analysis of the proteins through predictions of protein domains, subcellular localizations, and possible functional roles. The SPDI collection should facilitate efforts to better understand intercellular communication, may lead to new understandings of human diseases, and provides potential opportunities for the development of therapeutics.
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Affiliation(s)
- Hilary F Clark
- Departments of Bioinformatics, Molecular Biology and Protein Chemistry, Genentech, Inc, South San Francisco, California 94080, USA.
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