Gene hunting in autoinflammation

Clinical and Translational Allergy

Paul Brogan¹  Ebun Omoyinmi¹  Ariane Standing¹ 

[1] Institute of Child Health, UCL, 30 Guilford Street, London WC1N 1EH, UK

关键词: CANDLE;    NGS;    CAPS;    Autoinflammatory diseases;    Genetic mapping;   

Others  :  794188
DOI  :  10.1186/2045-7022-3-32

 received in 2013-08-06, accepted in 2013-09-23,  发布年份 2013

【 摘 要 】

Steady progress in our understanding of the genetic basis of autoinflammatory diseases has been made over the past 16 years. Since the discovery of the familial Mediterranean fever gene MEFV (also known as marenostrin) in 1997, 18 other genes responsible for monogenic autoinflammatory diseases have been identified to date. The discovery of these genes was made through the utilisation of many genetic mapping techniques, including next generation sequencing platforms. This review article clearly describes the gene hunting approaches, methods of data analysis and the technological platforms used, which has relevance to all those working within the field of gene discovery for Mendelian disorders.

【 授权许可】

   
2013 Standing et al.; licensee BioMed Central Ltd.

【 参考文献 】

• [1]McDermott MF, Aksentijevich I, Galon J, McDermott EM, Ogunkolade BW, Centola M, Mansfield E, Gadina M, Karenko L, Pettersson T, McCarthy J, Frucht DM, Aringer M, Torosyan Y, Teppo A-M, Wilson M, Karaarslan HM, Wan Y, Todd I, Wood G, Schlimgen R, Kumarajeewa TR, Cooper SM, Vella JP, Amos CI, Mulley J, Quane KA, Molloy MG, Ranki A, Powell RJ, et al.: Germline mutations in the extracellular domains of the 55 kDa TNF receptor, TNFR1, define a family of dominantly inherited autoinflammatory syndromes. Cell 1999, 97:133-144.
• [2]Kastner DL, Aksentijevich I, Goldbach-Mansky R: Autoinflammatory disease reloaded: a clinical perspective. Cell 2010, 140:784-790.
• [3]de Sarrauste Menthiere C, Terrierre S, Pugnere D, Ruiz M, Demaille J, Touitou I: INFEVERS: the registry for FMF and hereditary inflammatory disorders mutations. Nucleic Acids Res 2003, 31:282-285.
• [4]Dickie LJ, Savic S, Aziz A, Sprakes M, McDermott MF: Periodic fever syndrome and autoinflammatory diseases. F1000 med reports 2010, 2:3.
• [5]French F.M.F.Consortium: Localization of the familial mediterranean fever gene to a 250-kb interval in non Ashkenazi Jewish founder haplotypes. Am J Hum Genet 1996, 59:603-612.
• [6]French F.M.F.Consortium: A candidate gene for familial Mediterranean fever. Nat gene 1997, 17:25-31.
• [7]Mulley J, Saar K, Hewitt G, Ruschendorf F, Phillips H, Colley A, Sillence D, Reis A, Wilson M: Gene localization for an autosomal dominant familial periodic fever to 12p13. Am J Human Gene 1998, 62:884-889.
• [8]Drenth JPH, Cuisset L, Grateau G, Vasseur C, van de Velde-Visser SD, de Jong JGN, Beckmann JS, van der Meer JWM, Delpech M: Mutations in the gene encoding mevalonate kinase cause hyper-IgD and periodic fever syndrome. Nature genetics 1999, 22:178-181.
• [9]Cuisset L, Drenth JPH, Berthelot JM, Meyrier A, Vaudour G, Watts RA, Scott DGI, Nicholls A, Pavek S, Vasseur C, Beckmann JS, Delpech M, Grateau G: Genetic Linkage of the Muckle-Wells Syndrome to Chromosome 1q44. Am J Hum Genet 1999, 65:1054-1059.
• [10]Hoffman HM, Wright FA, Broide DH, Wanderer AA, Kolodner RD: Identification of a Locus on Chromosome 1q44 for Familial Cold Urticaria. Am J Hum Genet 2000, 66:1693-1698.
• [11]Feldmann J, Prieur AM, Quartier P, Berquin P, Certain S, Cortis E, Teillac-Hamel D, Fischer A, Basile GS: Chronic infantile neurological cutaneous and articular syndrome is caused by mutations in CIAS1, a gene highly expressed in polymorphonuclear cells and chondrocytes. Am J Human Gene 2002, 71:198-203.
• [12]Tromp G, Kuivaniemi H, Raphael S, Ala-Kokko L, Christiano A, Considine E, Dhulipala R, Hyland J, Jokinen A, Kivirikko S: Genetic linkage of familial granulomatous inflammatory arthritis, skin rash, and uveitis to chromosome 16. Am J Hum Genet 1996, 59:1097.
• [13]Miceli-Richard C, Lesage S, Rybojad M, Prieur AM, Manouvrier-Hanu S, Häfner R, Chamaillard M, Zouali H, Thomas G, Hugot JP: CARD15 mutations in Blau syndrome. Nat Genet 2001, 29:19-20.
• [14]Ueki Y, Tiziani V, Santanna C, Fukai N, Maulik C, Garfinkle J, Ninomiya C, DoAmaral C, Peters H, Habal M, Rhee-Morris L, Doss JB, Kreiborg S, Olsen BR, Reichenberger E: Mutations in the gene encoding c-Abl-binding protein SH3BP2 cause cherubism. Nat Genet 2001, 28:125-126.
• [15]Tiziani V, Reichenberger E, Buzzo CL, Niazi S, Fukai N, Stiller M, Peters H, Salzano FM, Amaral CM R d, Olsen BR: The gene for Cherubism maps to chromosome 4p16. Am J Hum Genet 1999, 65:158-166.
• [16]Mangion J, Rahman N, Edkins S, Barfoot R, Nguyen T, Sigurdsson A, Townend JV, Fitzpatrick DR, Flanagan AM, Stratton MR: The gene for Cherubism maps to chromosome 4p16.3. Am J Hum Genet 1999, 65:151-157.
• [17]Wise CA, Gillum JD, Seidman CE, Lindor NM, Veile R, Bashiardes S, Lovett M: Mutations in CD2BP1 disrupt binding to PTP PEST and are responsible for PAPA syndrome, an autoinflammatory disorder. Hum Mol Genet 2002, 11:961-969.
• [18]Wise CA, Bennett LB, Pascual V, Gillum JD, Bowcock AM: Localization of a gene for familial recurrent arthritis. Arthritis Rheum 2000, 43:2041-2045.
• [19]Yeon HB, Lindor NM, Seidman JG, Seidman CE: Pyogenic Arthritis, Pyoderma Gangrenosum, and Acne Syndrome Maps to Chromosome 15q. Am J Human Gene 2000, 66:1443-1448.
• [20]Kanazawa N, Okafuji I, Kambe N, Nishikomori R, Nakata-Hizume M, Nagai S, Fuji A, Yuasa T, Manki A, Sakurai Y, Nakajima M, Kobayashi H, Fujiwara I, Tsutsumi H, Utani A, Nishigori C, Heike T, Nakahata T, Miyachi Y: Early-onset sarcoidosis and CARD15 mutations with constitutive nuclear factor-kappa B activation: common genetic etiology with Blau syndrome. Blood 2005, 105:1195-1197.
• [21]Kanazawa N, Matsushima S, Kambe N, Tachibana T, Nagai S, Miyachi Y: Presence of a sporadic case of systemic granulomatosis syndrome with a CARD15 mutation. J Invest Dermatol 2004, 122:851-852.
• [22]Ferguson PJ, Chen S, Tayeh MK, Ochoa L, Leal SM, Pelet A, Munnich A, Lyonnet S, Majeed HA, El-Shanti H: Homozygous mutations in LPIN2 are responsible for the syndrome of chronic recurrent multifocal osteomyelitis and congenital dyserythropoietic anaemia (Majeed syndrome). J Med Genet 2005, 42:551-557.
• [23]Moglabey YB, Kircheisen R, Seoud M, El Mogharbel N, Van den Veyver I, Slim R: Genetic Mapping of a Maternal Locus Responsible for Familial Hydatidiform Moles. Hum Mol Genet 1999, 8:667.
• [24]Murdoch S, Djuric U, Mazhar B, Seoud M, Khan R, Kuick R, Bagga R, Kircheisen R, Ao A, Ratti B: Mutations in NALP7 cause recurrent hydatidiform moles and reproductive wastage in humans. Nat Genet 2006, 38:300-302.
• [25]Jeru I, Duquesnoy P, Fernandes-Alnemri T, Cochet E, Yu JW, Lackmy-Port-Lis M, Grimprel E, Landman-Parker J, Hentgen V, Marlin S, McElreavey K, Sarkisian T, Grateau G, Alnemri ES, Amselem S: Mutations in NALP12 cause hereditary periodic fever syndromes. Proc Natl Acad Sci 2008, 105:1614-1619.
• [26]Aksentijevich I, Masters SL, Ferguson PJ, Dancey P, Frenkel J, van Royen-Kerkhoff A, Laxer R, Tedgard U, Cowen EW, Pham TH, Booty M, Estes JD, Sandler NG, Plass N, Stone DL, Turner ML, Hill S, Butman JA, Schneider R, Babyn P, El-Shanti HI, Pope E, Barron K, Bing X, Laurence A, Lee CC, Chapelle D, Clarke GI, Ohson K, Nicholson M, et al.: An autoinflammatory disease with deficiency of the interleukin-1-receptor antagonist. N Engl J Med 2009, 360:2426-2437.
• [27]Glocker EO, Kotlarz D, Boztug K, Gertz EM, Schaffer AA, Noyan F, Perro M, Diestelhorst J, Allroth A, Murugan D, Hatscher N, Pfeifer D, Sykora KW, Sauer M, Kreipe H, Lacher M, Nustede R, Woellner C, Baumann U, Salzer U, Koletzko S, Shah N, Segal AW, Sauerbrey A, Buderus S, Snapper SB, Grimbacher B, Klein C: Inflammatory Bowel Disease and Mutations Affecting the Interleukin-10 Receptor. N Engl J Med 2009, 361:2033-2045.
• [28]Glocker EO, Frede N, Perro M, Sebire N, Elawad M, Shah N, Grimbacher B: Infant colitis it's in the genes. The Lancet 2009, 376:1272.
• [29]Agarwal AK, Xing C, DeMartino GN, Mizrachi D, Hernandez MD, Sousa AB, Martinez De Villarreal L, Dos Santos HG, Garg A: PSMB8 encoding the B5i proteasome subunit is mutated in joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy syndrome. Am J Hum Genet 2010, 87:866-872.
• [30]Arima K, Kinoshita A, Mishima H, Kanazawa N, Kaneko T, Mizushima T, Ichinose K, Nakamura H, Tsujino A, Kawakami A, Matsunaka M, Kasagi S, Kawano S, Kumagai S, Ohmura K, Mimori T, Hirano M, Ueno S, Tanaka K, Tanaka M, Toyoshima I, Sugino H, Yamakawa A, Tanaka K, Niikawa N, Furukawa F, Murata S, Eguchi K, Ida H, Yoshiura K: Proteasome assembly defect due to a proteasome subunit beta type 8 (PSMB8) mutation causes the autoinflammatory disorder, Nakajo-Nishimura syndrome. Proc Natl Acad Sci 2011, 108:14914-14919.
• [31]Kitamura A, Maekawa Y, Uehara H, Izumi K, Kawachi I, Nishizawa M, Toyoshima Y, Takahashi H, Standley DM, Tanaka K, Hamazaki J, Murata S, Obara K, Toyoshima I, Yasutomo K: A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans. J Clin Invest 2011, 121:4150-4160.
• [32]Liu Y, Ramot Y, Torrelo A, Paller AS, Si N, Babay S, Kim PW, Sheikh A, Lee CCR, Chen Y, Vera A, Zhang X, Goldbach-Mansky R, Zlotogorski A: Mutations in PSMB8 cause CANDLE syndrome with evidence of genetic and phenotypic heterogeneity. Arthritis Rheum 2011, 64:895-907.
• [33]Marrakchi S, Guigue P, Renshaw BR, Puel A, Pei XY, Fraitag S, Zribi J, Bal E, Cluzeau C, Chrabieh M, Towne JE, Douangpanya J, Pons C, Mansour S, Serre V, Makni H, Mahfoudh N, Fakhfakh F, Bodemer C, Feingold J, Hadj-Rabia S, Favre M, Genin E, Sahbatou M, Munnich A, Casanova JL, Sims JE, Turki H, Bachelez H, Smahi A: Interleukin-36 Receptor Antagonist Deficiency and Generalized Pustular Psoriasis. N Engl J Med 2011, 365:620-628.
• [34]Onoufriadis A, Simpson M, Pink A, Di-áMeglio P, Smith C, Pullabhatla V, Knight J, Spain S, Nestle F, Burden A, Capon F, Trembath R, Barker J: Mutations in IL36RN/IL1F5 Are Associated with the Severe Episodic Inflammatory Skin Disease Known as Generalized Pustular Psoriasis. Am J Hum Genet 2011, 89:432-437.
• [35]Zhou Q, Lee GS, Brady J, Datta S, Katan M, Sheikh A, Martins M, Bunney T, Santich B, Moir S, Kuhns D, Priel D, Ombrello A, Stone D, Ombrello MJ, Khan J, Milner JD, Kastner D, Aksentijevich I: A hypermorphic missense mutation in PLCG2, encoding phospholipase C gamma 2, causes a dominantly inherited autoinflammatory disease with immunodeficiency. Am J Hum Genet 2012, 91:713-720.
• [36]Boisson B, Laplantine E, Prando C, Giliani S, Israelsson E, Xu Z, Abhyankar A, Israel L, Trevejo-Nunez G, Bogunovic D: Immunodeficiency, autoinflammation and amylopectinosis in humans with inherited HOIL-1 and LUBAC deficiency. Nat Immunol 2012, 13:1178-1186.
• [37]Fuchs-Telem D, Sarig O, Van-áSteensel M, Isakov O, Israeli S, Nousbeck J, Richard K, Winnepenninckx V, Vernooij M, Shomron N, Uitto J, Fleckman P, Richard G, Sprecher E: Familial Pityriasis Rubra Pilaris is caused by mutations in CARD14. Am J Hum Genet 2012, 91:163-170.
• [38]Jordan CT, Cao L, Roberson E, Pierson K, Yang CF, Joyce C, Ryan C, Duan S, Helms C, Liu Y, Chen Y, McBride A, Hwu WL, Wu JY, Chen YT, Menter A, Goldbach-Mansky R, Lowes M, Bowcock A: PSORS2 is due to mutations in CARD14. Am J Hum Genet 2012, 90:784-795.
• [39]Pras E, Aksentijevich I, Gruberg L, Balow JE, Prosen L, Dean M, Steinberg AD, Pras M, Kastner DL: Mapping of a gene causing Familial Mediterranean Fever to the short arm of chromosome 16. N Engl J Med 1992, 326:1509-1513.
• [40]Pras E, Aksentijevich I, Levy E, Gruberg L, Prosen L, Dean M, Pras M, Kastner D: The gene causing familial mediterranean fever maps to the short arm of chromosome 16 in Druze and Moslem Arab families. Hum Genet 1994, 94:576-577.
• [41]Gruberg L, Aksentijevich I, Pras E, Kastner DL, Pras M: Mapping of the familial Mediterranean fever gene to chromosome 16. Am J Reprod Immunol 1992, 28:241.
• [42]Shohat M, Bu X, Shohat T, Fischel-Ghodsian N, Magal N, Nakamura Y, Schwabe AD, Schlezinger M, Danon Y, Rotter JI: The gene for familial Mediterranean fever in both Armenians and non-Ashkenazi Jews is linked to the alpha-globin complex on 16p: evidence for locus homogeneity. Am J Hum Genet 1992, 51:1349.
• [43]The International F.M.F.Consortium: Ancient missense mutations in a new member of the RoRet gene family are likely to cause familial Mediterranean fever. Cell 1997, 90:797-807.
• [44]McDermott MF, Ogunkolade BW, McDermott EM, Jones LC, Wan Y, Quane KA, McCarthy J, Phelan M, Molloy MG, Powell RJ, Amos CI, Hitman GA: Linkage of Familial Hibernian Fever to Chromosome 12p13. Am J Hum Genet 1998, 62:1446-1451.
• [45]Gul A: Genome-wide association studies in Behcet's disease: expectations and promises. Clin Exp Rheumatol 2011, 29:S3-S5.
• [46]Lee JC, Parkes M: Genome-wide association studies and Crohns disease. Brief Funct Genomics 2011, 10:71-76.
• [47]Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR: A method and server for predicting damaging missense mutations. Nat Methods 2010, 7:248-249.
• [48]Schwarz JM, Rodelsperger C, Schuelke M, Seelow D: MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 2010, 7:575-576.
• [49]Su SY, Kasberger J, Baranzini S, Byerley W, Liao W, Oksenberg J, Sherr E, Jorgenson E: Detection of identity by descent using next-generation whole genome sequencing data. BMC Bioinformatics 2012, 13:121. BioMed Central Full Text
• [50]Casals F, Idaghdour Y, Hussin J, Awadalla P: Next-generation sequencing approaches for genetic mapping of complex diseases. J Neuroimmunol 2012, 248:10-22.
• [51]Ellinghaus D, Zhang H, Zeissig S, Lipinski S, Till A, Jiang T, Stade B, Bromberg Y, Ellinghaus E, Keller A, Rivas MA, Skieceviciene J, Doncheva NT, Liu X, Liu Q, Jiang F, Forster M, Mayr G, Albrecht M, Hasler R, Boehm BO, Goodall J, Berzuini CR, Lee J, Andersen V, Vogel U, Kupcinskas L, Kayser M, Krawczak M, Nikolaus S, et al.: Association between variants of PRDM1 and NDP52 and Crohns disease, based on exome sequencing and functional studies. Gastroenterology 2013, 145:339-347.
• [52]Tanaka N, Izawa K, Saito MK, Sakuma M, Oshima K, Ohara O, Nishikomori R, Morimoto T, Kambe N, Goldbach-Mansky R: High incidence of NLRP3 somatic mosaicism in patients with chronic infantile neurologic, cutaneous, articular syndrome: results of an International Multicenter Collaborative Study. Arthritis Rheum 2011, 63:3625-3632.
• [53]Ku C-S, Cooper DN, Polychronakos C, Naidoo N, Wu M, Soong R: Exome sequencing: dual role as a discovery and diagnostic tool. Ann Neurol 2012, 71:5-14.
• [54]Evans JP, Rothschild BB: Return of results: not that complicated? Genet Med 2012, 14:358-360.