Abstract
In unstimulated cells, NF-κB dimers usually exist as latent complexes in the cytoplasm with the IκB (inhibitor of NF-κB) proteins or IκB-like protein p100, the precursor of NF-κB2 mature form p52. Accordingly, there are two major mechanisms leading to NF-κB activation: inducible degradation of IκBs and processing of p100 to generate p52 (selective degradation of the C-terminal IκB-like sequence of p100), which are termed the canonical and noncanonical NF-κB pathways, respectively. While activation of the canonical NF-κB pathway plays critical roles in a wide range of biological processes, the noncanonical NF-κB pathway has important but more restricted roles in both normal and pathological processes. Systematic detection of the noncanonical NF-κB pathway activation is very important for understanding the physiological role of this pathway in biological processes, and for the diagnosis, prevention, and treatment of related diseases. We describe here the methods we employ to detect noncanonical NF-κB activation in cells and tissues. These methods are immunoblotting, co-immunoprecipitation, immunofluorescence, immunohistochemistry, chromatin immunoprecipitation (ChIP) analysis, and electrophoretic mobility shift assay (EMSA). Noncanonical NF-κB-induced gene expression changes can be determined by gene array analysis and quantitative real-time PCR.
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Xiao G, Fu J (2011) NF-kappaB and cancer: a paradigm of Yin-Yang. Am J Cancer Res 1(2):192–221
Xiao G et al (2006) Alternative pathways of NF-kappaB activation: a double-edged sword in health and disease. Cytokine Growth Factor Rev 17(4):281–293
Claudio E et al (2002) BAFF-induced NEMO-independent processing of NF-kappa B2 in maturing B cells. Nat Immunol 3(10):958–965
Coope HJ et al (2002) CD40 regulates the processing of NF-kappaB2 p100 to p52. EMBO J 21(20):5375–5385
Dejardin E et al (2002) The lymphotoxin-beta receptor induces different patterns of gene expression via two NF-kappaB pathways. Immunity 17(4):525–535
Novack DV et al (2003) The IkappaB function of NF-kappaB2 p100 controls stimulated osteoclastogenesis. J Exp Med 198(5):771–781
Saitoh T et al (2003) TWEAK induces NF-kappaB2 p100 processing and long lasting NF-kappaB activation. J Biol Chem 278(38):36005–36012
Xiao G, Harhaj EW, Sun SC (2001) NF-kappaB-inducing kinase regulates the processing of NF-kappaB2 p100. Mol Cell 7(2):401–409
Qing G, Qu Z, Xiao G (2005) Stabilization of basally translated NF-kappaB-inducing kinase (NIK) protein functions as a molecular switch of processing of NF-kappaB2 p100. J Biol Chem 280(49):40578–40582
Liao G et al (2004) Regulation of the NF-kappaB-inducing kinase by tumor necrosis factor receptor-associated factor 3-induced degradation. J Biol Chem 279(25):26243–26250
Grech AP et al (2004) TRAF2 differentially regulates the canonical and noncanonical pathways of NF-kappaB activation in mature B cells. Immunity 21(5):629–642
Senftleben U et al (2001) Activation by IKKalpha of a second, evolutionary conserved, NF-kappa B signaling pathway. Science 293(5534):1495–1499
Vallabhapurapu S et al (2008) Nonredundant and complementary functions of TRAF2 and TRAF3 in a ubiquitination cascade that activates NIK-dependent alternative NF-kappaB signaling. Nat Immunol 9(12):1364–1370
Zarnegar BJ et al (2008) Noncanonical NF-kappaB activation requires coordinated assembly of a regulatory complex of the adaptors cIAP1, cIAP2, TRAF2 and TRAF3 and the kinase NIK. Nat Immunol 9(12):1371–1378
Fong A, Sun SC (2002) Genetic evidence for the essential role of beta-transducin repeat-containing protein in the inducible processing of NF-kappa B2/p100. J Biol Chem 277(25):22111–22114
Xiao G, Fong A, Sun SC (2004) Induction of p100 processing by NF-kappaB-inducing kinase involves docking IkappaB kinase alpha (IKKalpha) to p100 and IKKalpha-mediated phosphorylation. J Biol Chem 279(29):30099–30105
Ling L, Cao Z, Goeddel DV (1998) NF-kappaB-inducing kinase activates IKK-alpha by phosphorylation of Ser-176. Proc Natl Acad Sci U S A 95(7):3792–3797
Franzoso G et al (1998) Mice deficient in nuclear factor (NF)-kappa B/p52 present with defects in humoral responses, germinal center reactions, and splenic microarchitecture. J Exp Med 187(2):147–159
Caamano JH et al (1998) Nuclear factor (NF)-kappa B2 (p100/p52) is required for normal splenic microarchitecture and B cell-mediated immune responses. J Exp Med 187(2):185–196
Yin L et al (2001) Defective lymphotoxin-beta receptor-induced NF-kappaB transcriptional activity in NIK-deficient mice. Science 291(5511):2162–2165
Shinkura R et al (1999) Alymphoplasia is caused by a point mutation in the mouse gene encoding Nf-kappa b-inducing kinase. Nat Genet 22(1):74–77
Miyawaki S et al (1994) A new mutation, aly, that induces a generalized lack of lymph nodes accompanied by immunodeficiency in mice. Eur J Immunol 24(2):429–434
Futterer A et al (1998) The lymphotoxin beta receptor controls organogenesis and affinity maturation in peripheral lymphoid tissues. Immunity 9(1):59–70
Thompson JS et al (2001) BAFF-R, a newly identified TNF receptor that specifically interacts with BAFF. Science 293(5537):2108–2111
Shulga-Morskaya S et al (2004) B cell-activating factor belonging to the TNF family acts through separate receptors to support B cell survival and T cell-independent antibody formation. J Immunol 173(4):2331–2341
Sasaki Y et al (2004) TNF family member B cell-activating factor (BAFF) receptor-dependent and -independent roles for BAFF in B cell physiology. J Immunol 173(4):2245–2252
Kawabe T et al (1994) The immune responses in CD40-deficient mice: impaired immunoglobulin class switching and germinal center formation. Immunity 1(3):167–178
Dougall WC et al (1999) RANK is essential for osteoclast and lymph node development. Genes Dev 13(18):2412–2424
Ishikawa H et al (1997) Gastric hyperplasia and increased proliferative responses of lymphocytes in mice lacking the COOH-terminal ankyrin domain of NF-kappaB2. J Exp Med 186(7):999–1014
Mackay F et al (1999) Mice transgenic for BAFF develop lymphocytic disorders along with autoimmune manifestations. J Exp Med 190(11):1697–1710
Khare SD et al (2000) Severe B cell hyperplasia and autoimmune disease in TALL-1 transgenic mice. Proc Natl Acad Sci U S A 97(7):3370–3375
Moore CR et al (2012) Specific deletion of TRAF3 in B lymphocytes leads to B-lymphoma development in mice. Leukemia 26(5):1122–1127
Rosebeck S et al (2011) Cleavage of NIK by the API2-MALT1 fusion oncoprotein leads to noncanonical NF-kappaB activation. Science 331(6016):468–472
Rosebeck S, Lucas PC, McAllister-Lucas LM (2011) Protease activity of the API2-MALT1 fusion oncoprotein in MALT lymphoma development and treatment. Future Oncol 7(5):613–617
Pham LV et al (2011) Constitutive BR3 receptor signaling in diffuse, large B-cell lymphomas stabilizes nuclear factor-kappaB-inducing kinase while activating both canonical and alternative nuclear factor-kappaB pathways. Blood 117(1):200–210
Demchenko YN et al (2010) Classical and/or alternative NF-kappaB pathway activation in multiple myeloma. Blood 115(17):3541–3552
Compagno M et al (2009) Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature 459(7247):717–721
Keats JJ et al (2007) Promiscuous mutations activate the noncanonical NF-kappaB pathway in multiple myeloma. Cancer Cell 12(2):131–144
Annunziata CM et al (2007) Frequent engagement of the classical and alternative NF-kappaB pathways by diverse genetic abnormalities in multiple myeloma. Cancer Cell 12(2):115–130
Nagel I et al (2009) Biallelic inactivation of TRAF3 in a subset of B-cell lymphomas with interstitial del(14)(q24.1q32.33). Leukemia 23(11):2153–2155
Braggio E et al (2009) Identification of copy number abnormalities and inactivating mutations in two negative regulators of nuclear factor-kappaB signaling pathways in Waldenstrom’s macroglobulinemia. Cancer Res 69(8):3579–3588
Rayet B, Gelinas C (1999) Aberrant rel/nfkb genes and activity in human cancer. Oncogene 18(49):6938–6947
Sun SC, Xiao G (2003) Deregulation of NF-kappaB and its upstream kinases in cancer. Cancer Metastasis Rev 22(4):405–422
Qing G, Qu Z, Xiao G (2007) Endoproteolytic processing of C-terminally truncated NF-kappaB2 precursors at kappaB-containing promoters. Proc Natl Acad Sci U S A 104(13):5324–5329
Qu Z, Xiao G (2011) Human T-cell lymphotropic virus: a model of NF-kappaB-associated tumorigenesis. Viruses 3(6):714–749
Xiao G, Sun SC (2000) Activation of IKKalpha and IKKbeta through their fusion with HTLV-I tax protein. Oncogene 19(45):5198–5203
Xiao G et al (2001) Retroviral oncoprotein Tax induces processing of NF-kappaB2/p100 in T cells: evidence for the involvement of IKKalpha. EMBO J 20(23):6805–6815
Qu Z et al (2004) Tax deregulation of NF-kappaB2 p100 processing involves both beta-TrCP-dependent and -independent mechanisms. J Biol Chem 279(43):44563–44572
Fu J et al (2011) The tumor suppressor gene WWOX links the canonical and noncanonical NF-kappaB pathways in HTLV-I Tax-mediated tumorigenesis. Blood 117(5):1652–1661
de Oliveira DE, Ballon G, Cesarman E (2010) NF-kappaB signaling modulation by EBV and KSHV. Trends Microbiol 18(6):248–257
Wu JT, Kral JG (2005) The NF-kappaB/IkappaB signaling system: a molecular target in breast cancer therapy. J Surg Res 123(1):158–169
Storz P (2013) Targeting the alternative NF-kappaB pathway in pancreatic cancer: a new direction for therapy? Expert Rev Anticancer Ther 13(5):501–504
Ueda Y, Richmond A (2006) NF-kappaB activation in melanoma. Pigment Cell Res 19(2):112–124
Groom J et al (2002) Association of BAFF/BLyS overexpression and altered B cell differentiation with Sjogren’s syndrome. J Clin Invest 109(1):59–68
Zhang J et al (2001) Cutting edge: a role for B lymphocyte stimulator in systemic lupus erythematosus. J Immunol 166(1):6–10
Cheema GS et al (2001) Elevated serum B lymphocyte stimulator levels in patients with systemic immune-based rheumatic diseases. Arthritis Rheum 44(6):1313–1319
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Qu, Z., Xiao, G. (2015). Systematic Detection of Noncanonical NF-κB Activation. In: May, M. (eds) NF-kappa B. Methods in Molecular Biology, vol 1280. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2422-6_8
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DOI: https://doi.org/10.1007/978-1-4939-2422-6_8
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