Top

Journal of Inflammation

Published in:

Open Access 01-12-2010 | Research

TNFRSF11B computational development network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients

Authors: Ju X Huang, L Wang, Ming H Jiang

Published in: Journal of Inflammation | Issue 1/2010

Abstract

Background

TNFRSF11B computational development network construction and analysis of frontal cortex of HIV encephalitis (HIVE) is very useful to identify novel markers and potential targets for prognosis and therapy.

Methods

By integration of gene regulatory network infer (GRNInfer) and the database for annotation, visualization and integrated discovery (DAVID) we identified and constructed significant molecule TNFRSF11B development network from 12 frontal cortex of HIVE-control patients and 16 HIVE in the same GEO Dataset GDS1726.

Results

Our result verified TNFRSF11B developmental process only in the downstream of frontal cortex of HIVE-control patients (BST2, DGKG, GAS1, PDCD4, TGFBR3, VEZF1 inhibition), whereas in the upstream of frontal cortex of HIVE (DGKG, PDCD4 activation) and downstream (CFDP1, DGKG, GAS1, PAX6 activation; BST2, PDCD4, TGFBR3, VEZF1 inhibition). Importantly, we datamined that TNFRSF11B development cluster of HIVE is involved in T-cell mediated immunity, cell projection organization and cell motion (only in HIVE terms) without apoptosis, plasma membrane and kinase activity (only in HIVE-control patients terms), the condition is vital to inflammation, brain morphology and cognition impairment of HIVE. Our result demonstrated that common terms in both HIVE-control patients and HIVE include developmental process, signal transduction, negative regulation of cell proliferation, RNA-binding, zinc-finger, cell development, positive regulation of biological process and cell differentiation.

Conclusions

We deduced the stronger TNFRSF11B development network in HIVE consistent with our number computation. It would be necessary of the stronger TNFRSF11B development function to inflammation, brain morphology and cognition of HIVE.

Available only for authorised users

Masliah E, Roberts ES, Langford D, Everall I, Crews L, Adame A, Rockenstein E, Fox HS: Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. J Neuroimmunol. 2004, 157: 163-175. 10.1016/j.jneuroim.2004.08.026.PubMedCrossRef

Chang L, Wang GJ, Volkow ND, Ernst T, Telang F, Logan J, Fowler JS: Decreased brain dopamine transporters are related to cognitive deficits in HIV patients with or without cocaine abuse. Neuroimage. 2008, 42: 869-878. 10.1016/j.neuroimage.2008.05.011.PubMedPubMedCentralCrossRef

Descamps M, Hyare H, Stebbing J, Winston A: Magnetic resonance imaging and spectroscopy of the brain in HIV disease. J HIV Ther. 2008, 13: 55-58.PubMed

Georgiou MF, Gonenc A, Waldrop-Valverde D, Kuker RA, Ezuddin SH, Sfakianakis GN, Kumar M: Analysis of the effects of injecting drug use and HIV-1 infection on 18F-FDG PET brain metabolism. J Nucl Med. 2008, 49: 1999-2005. 10.2967/jnumed.108.052688.PubMedCrossRef

Beyens G, Daroszewska A, de Freitas F, Fransen E, Vanhoenacker F, Verbruggen L, Zmierczak HG, Westhovens R, Van Offel J, Ralston SH: Identification of sex-specific associations between polymorphisms of the osteoprotegerin gene, TNFRSF11B, and Paget's disease of bone. J Bone Miner Res. 2007, 22: 1062-1071. 10.1359/jbmr.070333.PubMedCrossRef

Chong B, Hegde M, Fawkner M, Simonet S, Cassinelli H, Coker M, Kanis J, Seidel J, Tau C, Tuysuz B: Idiopathic hyperphosphatasia and TNFRSF11B mutations: relationships between phenotype and genotype. J Bone Miner Res. 2003, 18: 2095-2104. 10.1359/jbmr.2003.18.12.2095.PubMedCrossRef

Cundy T, Hegde M, Naot D, Chong B, King A, Wallace R, Mulley J, Love DR, Seidel J, Fawkner M: A mutation in the gene TNFRSF11B encoding osteoprotegerin causes an idiopathic hyperphosphatasia phenotype. Hum Mol Genet. 2002, 11: 2119-2127. 10.1093/hmg/11.18.2119.PubMedCrossRef

Janssens K, de Vernejoul MC, de Freitas F, Vanhoenacker F, Van Hul W: An intermediate form of juvenile Paget's disease caused by a truncating TNFRSF11B mutation. Bone. 2005, 36: 542-548. 10.1016/j.bone.2004.12.004.PubMedCrossRef

Vidal C, Brincat M, Xuereb Anastasi A: TNFRSF11B gene variants and bone mineral density in postmenopausal women in Malta. Maturitas. 2006, 53: 386-395. 10.1016/j.maturitas.2005.11.003.PubMedCrossRef

10.

Whyte MP, Singhellakis PN, Petersen MB, Davies M, Totty WG, Mumm S: Juvenile Paget's disease: the second reported, oldest patient is homozygous for the TNFRSF11B "Balkan" mutation (966_969delTGACinsCTT), which elevates circulating immunoreactive osteoprotegerin levels. J Bone Miner Res. 2007, 22: 938-946. 10.1359/jbmr.070307.PubMedCrossRef

11.

Storey. JD: A direct approach to false discovery rates. J Roy Stat Soc, Ser B. 2002, 64: 479-498. 10.1111/1467-9868.00346.CrossRef

12.

Wang Y, Joshi T, Zhang XS, Xu D, Chen L: Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics. 2006, 22: 2413-2420. 10.1093/bioinformatics/btl396.PubMedCrossRef

13.

Huang da W, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA: The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 2007, 8: R183-10.1186/gb-2007-8-9-r183.PubMedPubMedCentralCrossRef

14.

Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA: DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003, 4: P3-10.1186/gb-2003-4-5-p3.PubMedCrossRef

15.

Sun Y, Wang L, Jiang M, Huang J, Liu Z, Wolfl S: Secreted Phosphoprotein 1 Upstream Invasive Network Construction and Analysis of Lung Adenocarcinoma Compared with Human Normal Adjacent Tissues by Integrative Biocomputation. Cell Biochem Biophys. 2009, ISSN: 1085-9195 (Print) 1559-0283 (Online)

16.

Sun Y, Wang L, Lui L: Integrative decomposition procedure and Kappa statistics set up ATF2 ion binding module in Malignant Pleural Mesothelioma (MPM). Frontiers of Electrical and Electronic Engineering in China. 2008, 3: 381-387. 10.1007/s11460-008-0086-3.CrossRef

17.

Wang L, Huang J, Jiang M, Zheng X: AFP computational secreted network construction and analysis between human hepatocellular carcinoma (HCC) and no-tumor hepatitis/cirrhotic liver tissues. Tumour Biol.

18.

Wang L, Sun Y, Jiang M, Zhang S, Wolfl S: FOS proliferating network construction in early colorectal cancer (CRC) based on integrative significant function cluster and inferring analysis. Cancer Invest. 2009, 27: 816-824. 10.1080/07357900802672753.PubMedCrossRef

19.

Wang L, Sun Y, Jiang M, Zheng X: Integrative decomposition procedure and Kappa statistics for the distinguished single molecular network construction and analysis. J Biomed Biotechnol. 2009, 726728-

20.

Rath MF, Bailey MJ, Kim JS, Coon SL, Klein DC, Moller M: Developmental and daily expression of the Pax4 and Pax6 homeobox genes in the rat retina: localization of Pax4 in photoreceptor cells. J Neurochem. 2008

21.

Sjodal M, Gunhaga L: Expression patterns of Shh, Ptc2, Raldh3, Pitx2, Isl1, Lim3 and Pax6 in the developing chick hypophyseal placode and Rathke's pouch. Gene Expr Patterns. 2008, 8: 481-485. 10.1016/j.gep.2008.06.007.PubMedCrossRef

22.

Suter DM, Tirefort D, Julien S, Krause KH: A Sox1 to Pax6 switch drives neuroectoderm to radial glia progression during differentiation of mouse embryonic stem cells. Stem Cells. 2008

23.

Tuoc TC, Stoykova A: Trim11 modulates the function of neurogenic transcription factor Pax6 through ubiquitin-proteosome system. Genes Dev. 2008, 22: 1972-1986. 10.1101/gad.471708.PubMedPubMedCentralCrossRef

24.

Villarroel CE, Villanueva-Mendoza C, Orozco L, Alcantara-Ortigoza MA, Jimenez DF, Ordaz JC, Gonzalez-del Angel A: Molecular analysis of the PAX6 gene in Mexican patients with congenital aniridia: report of four novel mutations. Mol Vis. 2008, 14: 1650-1658.PubMedPubMedCentral

25.

Wen JH, Chen YY, Song SJ, Ding J, Gao Y, Hu QK, Feng RP, Liu YZ, Ren GC, Zhang CY: Paired box 6 (PAX6) regulates glucose metabolism via proinsulin processing mediated by prohormone convertase 1/3 (PC1/3). Diabetologia. 2008

26.

Hozumi Y, Fukaya M, Adachi N, Saito N, Otani K, Kondo H, Watanabe M, Goto K: Diacylglycerol kinase beta accumulates on the perisynaptic site of medium spiny neurons in the striatum. Eur J Neurosci. 2008, 28: 2409-2422. 10.1111/j.1460-9568.2008.06547.x.PubMedCrossRef

27.

Hozumi Y, Watanabe M, Otani K, Goto K: Diacylglycerol kinase beta promotes dendritic outgrowth and spine maturation in developing hippocampal neurons. BMC Neurosci. 2009, 10: 99-10.1186/1471-2202-10-99.PubMedPubMedCentralCrossRef

28.

Nakano T, Hozumi Y, Ali H, Saino-Saito S, Kamii H, Sato S, Kayama T, Watanabe M, Kondo H, Goto K: Diacylglycerol kinase zeta is involved in the process of cerebral infarction. Eur J Neurosci. 2006, 23: 1427-1435. 10.1111/j.1460-9568.2006.04685.x.PubMedCrossRef

29.

Nakano T, Iseki K, Hozumi Y, Kawamae K, Wakabayashi I, Goto K: Brain trauma induces expression of diacylglycerol kinase zeta in microglia. Neurosci Lett. 2009, 461: 110-115. 10.1016/j.neulet.2009.06.001.PubMedCrossRef

30.

Gobeil S, Zhu X, Doillon CJ, Green MR: A genome-wide shRNA screen identifies GAS1 as a novel melanoma metastasis suppressor gene. Genes Dev. 2008, 22: 2932-2940. 10.1101/gad.1714608.PubMedPubMedCentralCrossRef

31.

Hirayama H, Fujita M, Yoko-o T, Jigami Y: O-mannosylation is required for degradation of the endoplasmic reticulum-associated degradation substrate Gas1*p via the ubiquitin/proteasome pathway in Saccharomyces cerevisiae. J Biochem. 2008, 143: 555-567. 10.1093/jb/mvm249.PubMedCrossRef

32.

Lopez-Ramirez MA, Dominguez-Monzon G, Vergara P, Segovia J: Gas1 reduces Ret tyrosine 1062 phosphorylation and alters GDNF-mediated intracellular signaling. Int J Dev Neurosci. 2008, 26: 497-503. 10.1016/j.ijdevneu.2008.02.006.PubMedCrossRef

33.

Seppala M, Depew MJ, Martinelli DC, Fan CM, Sharpe PT, Cobourne MT: Gas1 is a modifier for holoprosencephaly and genetically interacts with sonic hedgehog. J Clin Invest. 2007, 117: 1575-1584. 10.1172/JCI32032.PubMedPubMedCentralCrossRef

34.

Lankat-Buttgereit B, Muller S, Schmidt H, Parhofer KG, Gress TM, Goke R: Knockdown of Pdcd4 results in induction of proprotein convertase 1/3 and potent secretion of chromogranin A and secretogranin II in a neuroendocrine cell line. Biol Cell. 2008, 100: 703-715. 10.1042/BC20080052.PubMedCrossRef

35.

Schmid T, Jansen AP, Baker AR, Hegamyer G, Hagan JP, Colburn NH: Translation inhibitor Pdcd4 is targeted for degradation during tumor promotion. Cancer Res. 2008, 68: 1254-1260. 10.1158/0008-5472.CAN-07-1719.PubMedCrossRef

36.

Suzuki C, Garces RG, Edmonds KA, Hiller S, Hyberts SG, Marintchev A, Wagner G: PDCD4 inhibits translation initiation by binding to eIF4A using both its MA3 domains. Proc Natl Acad Sci USA. 2008, 105: 3274-3279. 10.1073/pnas.0712235105.PubMedPubMedCentralCrossRef

37.

Talotta F, Cimmino A, Matarazzo MR, Casalino L, De Vita G, D'Esposito M, Di Lauro R, Verde P: An autoregulatory loop mediated by miR-21 and PDCD4 controls the AP-1 activity in RAS transformation. Oncogene. 2008

38.

Wang Q, Sun Z, Yang HS: Downregulation of tumor suppressor Pdcd4 promotes invasion and activates both beta-catenin/Tcf and AP-1-dependent transcription in colon carcinoma cells. Oncogene. 2008, 27: 1527-1535. 10.1038/sj.onc.1210793.PubMedCrossRef

39.

Wang X, Wei Z, Gao F, Zhang X, Zhou C, Zhu F, Wang Q, Gao Q, Ma C, Sun W: Expression and prognostic significance of PDCD4 in human epithelial ovarian carcinoma. Anticancer Res. 2008, 28: 2991-2996.PubMed

40.

Diekwisch TG, Luan X: CP27 function is necessary for cell survival and differentiation during tooth morphogenesis in organ culture. Gene. 2002, 287: 141-147. 10.1016/S0378-1119(01)00868-X.PubMedCrossRef

41.

Diekwisch TG, Luan X, McIntosh JE: CP27 localization in the dental lamina basement membrane and in the stellate reticulum of developing teeth. J Histochem Cytochem. 2002, 50: 583-586.PubMedCrossRef

42.

Iwashita S, Itoh T, Takeda H, Sugimoto Y, Takahashi I, Nobukuni T, Sezaki M, Masui T, Hashimoto K: Gene organization of bovine BCNT that contains a portion corresponding to an endonuclease domain derived from an RTE-1 (Bov-B LINE), non-LTR retrotransposable element: duplication of an intramolecular repeat unit downstream of the truncated RTE-1. Gene. 2001, 268: 59-66. 10.1016/S0378-1119(01)00422-X.PubMedCrossRef

43.

Iwashita S, Osada N, Itoh T, Sezaki M, Oshima K, Hashimoto E, Kitagawa-Arita Y, Takahashi I, Masui T, Hashimoto K, Makalowski W: A transposable element-mediated gene divergence that directly produces a novel type bovine Bcnt protein including the endonuclease domain of RTE-1. Mol Biol Evol. 2003, 20: 1556-1563. 10.1093/molbev/msg168.PubMedCrossRef

44.

Luan X, Diekwisch TG: CP27 affects viability, proliferation, attachment and gene expression in embryonic fibroblasts. Cell Prolif. 2002, 35: 207-219. 10.1046/j.1365-2184.2002.00238.x.PubMedCrossRef

45.

Lanzrein AS, Johnston CM, Perry VH, Jobst KA, King EM, Smith AD: Longitudinal study of inflammatory factors in serum, cerebrospinal fluid, and brain tissue in Alzheimer disease: interleukin-1beta, interleukin-6, interleukin-1 receptor antagonist, tumor necrosis factor-alpha, the soluble tumor necrosis factor receptors I and II, and alpha1-antichymotrypsin. Alzheimer Dis Assoc Disord. 1998, 12: 215-227. 10.1097/00002093-199809000-00016.PubMedCrossRef

46.

Wassink TH, Crowe RR, Andreasen NC: Tumor necrosis factor receptor-II: heritability and effect on brain morphology in schizophrenia. Mol Psychiatry. 2000, 5: 678-682. 10.1038/sj.mp.4000807.PubMedCrossRef

Title: TNFRSF11B computational development network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients
Authors: Ju X Huang
L Wang
Ming H Jiang
Publication date: 01-12-2010
Publisher: BioMed Central
Published in: Journal of Inflammation / Issue 1/2010
Electronic ISSN: 1476-9255
DOI: https://doi.org/10.1186/1476-9255-7-50

ACC 2024 Congress Coverage

Heart Failure Video

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

TNFRSF11B computational development network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients

Abstract

Background

Methods

Results

Conclusions

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Abstract

Background

Methods

Results

Conclusions

Please log in to get access to this content

Other articles of this Issue 1/2010

The anti-inflammatory effects of the tellurium redox modulating compound, AS101, are associated with regulation of NFκB signaling pathway and nitric oxide induction in macrophages

Differential splicing of the apoptosis-associated speck like protein containing a caspase recruitment domain (ASC) regulates inflammasomes

The role of toll-like receptors in acute and chronic lung inflammation

The inflammatory response seen when human omental adipose tissue explants are incubated in primary culture is not dependent upon albumin and is primarily in the nonfat cells

Histone deacetylase inhibitors induce apoptosis in human eosinophils and neutrophils

Simvastatin protects bladder and renal functions following spinal cord injury in rats

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page