Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome

Journal of Translational Medicine

Volumn 13, Issue 1, 2015, Pages

  Johar, Angad S ^a   Mastronardi, Claudio ^a   Rojas Villarraga, Adriana ^b   Patel, Hardip R ^a   Chuah, Aaron ^a   Peng, Kaiman ^a   Higgins, Angela ^a   Milburn, Peter ^a   Palmer, Stephanie ^a   Silva Lara, Maria Fernanda ^a   Velez, Jorge I ^a   Andrews, Dan ^a   Field, Matthew ^a   Huttley, Gavin ^a   Goodnow, Chris ^a   Anaya, Juan Manuel ^b   Arcos Burgos, Mauricio ^a  

^a Australian National University   (Australia)

^b UNIVERSIDAD DEL ROSARIO   (Colombia)

Author keywords

Autoimmune diseases; Extreme phenotypes; Genetics; Multiple autoimmune syndrome; Polyautoimmunity; Sj gren's syndrome; Whole exome sequencing

Indexed keywords

DNA; HLA B ANTIGEN; INTERLEUKIN 10; LIPOPOLYSACCHARIDE; PHOSPHOLIPASE A2; STAT6 PROTEIN;

AIRE GENE; ANKLE1 GENE; APOPTOSIS; ARTICLE; AUTOIMMUNE DISEASE; AUTOIMMUNITY; BIOINFORMATICS; CELA1 GENE; CLINICAL ARTICLE; DNA DETERMINATION; DUSP12 GENE; ENZYME REGULATION; EXOME; FKRP GENE; GENE; GENE IDENTIFICATION; GENE MUTATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME; GRIN3B GENE; HETEROZYGOTE; HLA B GENE; HOMOZYGOTE; HUMAN; ICA1 GENE; IL10 GENE; IRF5 GENE; KIAA0754 GENE; LRP1 GENE; MACF1 GENE; MULTIPLE AUTOIMMUNE SYNDROME; PHAGOCYTOSIS; SJOEGREN SYNDROME; TMEM161A GENE; WHOLE EXOME SEQUENCING; ADULT; AGED; CASE CONTROL STUDY; CONNECTOME; FEMALE; GENE REGULATORY NETWORK; GENETIC PREDISPOSITION; GENETICS; HUMAN GENOME; MIDDLE AGED; MUTATION; NUCLEOTIDE SEQUENCE; PHENOTYPE;

ADULT; AGED; AUTOIMMUNITY; BASE SEQUENCE; CASE-CONTROL STUDIES; CONNECTOME; FEMALE; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; HUMANS; MIDDLE AGED; MUTATION; PHENOTYPE; SJOGREN'S SYNDROME;

EID: 84930643679     PISSN: None     EISSN: 14795876     Source Type: Journal    
DOI: 10.1186/s12967-015-0525-x     Document Type: Article

References (46)

1. Paz-Filho G, Boguszewski MC, Mastronardi CA, Patel HR, Johar AS, Chuah A et al (2014) Whole exome sequencing of extreme morbid obesity patients: translational implications for obesity and related disorders. Genes 5:709-725
2. Cirulli ET, Goldstein DB (2010) Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nature Rev Genet 11:415-425
3. Anaya JM (2014) The diagnosis and clinical significance of polyautoimmunity. Autoimmun Rev 13:423-426
4. Anaya JM, Castiblanco J, Rojas-Villaraga A, Pineda-Tamayo R, Levy RA, Gomez-Puerta J et al (2012) The multiple autoimmune syndromes. A clue for the autoimmune tautology. Clin Rev Allergy Immunol 43:256-264
5. Johar AS, Anaya JM, Andrews D, Patel HR, Field M, Goodnow C et al (2015) Candidate gene discovery in autoimmunity by using extreme phenotypes, next generation sequencing and whole exome capture. Autoimmun Rev 14:204-209
6. Anaya JM (2012) Common mechanisms of autoimmune diseases (the autoimmune tautology). Autoimmun Rev 11:781-784
7. Amador-Patarroyo MJ, Arbelaez JG, Mantilla RD, Rodriguez-Rodriguez A, Cárdenas-Roldán J, Pineda-Tamayo R et al (2012) Sjögren's syndrome at the crossroad of polyautoimmunity. J Autoimmun 39:199-205
8. Anaya JM, Tobon GJ, Vega P, Castiblanco J (2006) Autoimmune disease aggregation in families with primary Sjögren's syndrome. J Rheumatol 33:2227-2234
9. Bozeman MT (2014) SNP and variation suite (Version 7.7.6) [Software]. Golden Helix, Inc. http://www.goldenhelix.com . Accessed 20 Apr 2015
10. Bozeman MT (2015) Variant classification. In: SNP and Variation Suite Manual version 8.3.1, Copyright 2014. Accessed 11 Feb 2015
11. Sheth N, Roca X, Hastings ML, Roeder T, Krainer AR, Sachidanandam R (2006) Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res 34:3955-3967
12. Desmet FO, Hamroun D, Lalande M, Collod-Beroud G, Claustres M, Beroud C (2009) Human splicing finder: an online tool to predict bioinformatic signals. Nucleic Acids Res 37:e67
13. Zhang C, Li WH, Krainer AR, Zhang MQ (2008) RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci USA 105:5797-5802
14. Itan Y, Zhang SY, Vogt G, Abhyankar A, Herman M, Nitschke P et al (2013) The human gene connectome as a map of short cuts for morbid allele discovery. Proc Natl Acad Sci USA 110:5558-5563
15. Itan Y, Mazel M, Mazel B, Abhyankar A, Nitschke P, Quintana-Murci L et al (2014) HGCS: an online tool for prioritizing disease-causing gene variants by biological distance. BMC Genom 15:256
16. Yu W, Wulf A, Liu T, Khoury MJ, Gwinn M (2008) Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases. BMC Bioinform 9:528
17. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a powerful and practical approach to multiple testing. J R Statist Soc B 57:289-300
18. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904-909
19. Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative genomics viewer (IGV): high performance genomics data visualisation and exploration. Brief Bioinform 14:178-192
20. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G et al (2011) Integrative genomics viewer. Nat Biotechnol 29:24-26
21. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D (2010) MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 7:575-576
22. Schwarz JM, Cooper DN, Schuelke M, Seelow D (2014) MutationTaster2: mutation prediction for the deep sequencing age. Nat Methods 11:361-362
23. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM et al (2002) The human genome browser at UCSC. Genome Res 12:996-1006
24. Kraja AT, Chasman DI, North KP, Reiner AP, Yanek LR, Kiplelainen TO et al (2014) Pleiotropic genes for metabolic syndrome and inflammation. Mol Genet Metab 112:317-338
25. Shibata M, Yamada S, Kumar SR, Calero M, Bading J, Frangione B et al (2000) Clearance of Alzheimer's amyloid-ss(1-40) peptide from brain by LDL receptor-related protein-1 at the blood-brain barrier. J Clin Invest 106:1489-1499
26. Zurhove K, Nakajima C, Herz J, Bock HH, May P (2008) Gamma-secretase limits the inflammatory response through the processing of LRP1. Sci Signal 1:ra15
27. Nilsson A, Vesterlund L, Oldenborg PA (2012) Macrophage expression of LRP1, a receptor for apoptotic cells and unopsonized erythrocytes, can be regulated by glucocorticoids. Biochem Biophys Res Commun 417:1304-1309
28. Fernandez-Castaneda A, Arandjelovic S, Stiles TL, Schlobach RK, Mowen KA, Gonias SL et al (2013) Identification of the low density lipoprotein (LDL) receptor-related protein-1 interactome in central nervous system myelin suggests a role in the clearance of necrotic cell debris. J Biol Chem 288:4538-4548
29. Dalli J, Norling LV, Montero-Melendez T, Federici Canova D, Lashin H, Pavlov AM et al (2014) Microparticle alpha-2-macroglobulin enhances pro-resolving responses and promotes survival in sepsis. EMBO Mol Med 6:27-42
30. Mandrekar S, Jiang Q, Lee CY, Koenigsknecht-Talboo J, Holtzman DM, Landreth GE (2009) Microglia mediate the clearance of soluble Abeta through fluid phase macropinocytosis. J Neurosci 29:4252-4262
31. Biermann MH, Veissi S, Maueröder C, Chaurio R, Berens C, Herrmann M et al (2014) The role of dead cell clearance in the etiology and pathogenesis of systemic lupus erythematosus: dendritic cells as potential targets. Expert Rev Clin Immunol 10:1151-1164
32. Poon IK, Lucas CD, Rossi AG, Ravichandran KS (2014) Apoptotic cell clearance: basic biology and therapeutic potential. Nat Rev Immunol 14:166-180
33. Cush JJ, Splawski JB, Thomas R, McFarlin JE, Schulze-Koops H, Davis LS et al (1995) Elevated interleukin-10 levels in patients with rheumatoid arthritis. Arthritis Rheum 38:96-104
34. Anaya JM, Correa PA, Herrera M, Eskdale J, Gallagher G (2002) Interleukin 10 (IL-10) influences autoimmune response in primary Sjögren's syndrome and is linked to IL-10 gene polymorphism. J Rheumatol 29:1874-1876
35. Gomez LM, Anaya JM, Gonzalez CI, Pineda-Tamayo R, Otero W, Arango A et al (2005) PTPN22 C1858T polymorphism in Colombian patients with autoimmune diseases. Genes Immun 6:628-631
36. Anaya JM, Gómez L, Castiblanco J (2006) Is there a common genetic basis for autoimmune diseases? Clin Dev Immunol 13:185-195
37. Bonner SM, Pietropaolo SL, Fan Y, Chang Y, Sethupathy P, Morran MP et al (2012) Sequence variation in promoter of Ica1 gene, which encodes protein implicated in type 1 diabetes, causes transcription factor autoimmune regulator (AIRE) to increase its binding and down-regulate expression. J Biol Chem 287:17882-17893
38. Reksten TR, Johnsen SJ, Jonsson MV, Omdal R, Brun JG, Theander E et al (2014) Genetic associations to germinal centre formation in primary Sjögren's syndrome. Ann Rheum Dis 73:1253-1258
39. Villarino AV, Kanno Y, Ferdinand JR, O'Shea JJ (2015) Mechanisms of Jak/STAT signaling in immunity and disease. J Immunol 194:21-27
40. Wang Z, Burge CB (2008) Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14:802-813
41. Pietropaolo M, Castaño L, Babu S, Buelow R, Kuo YS, Martin S et al (1993) Molecular cloning and characterization of a novel diabetes-associated autoantigen. J Clin Invest 92:359-371
42. Fan Y, Gaultierroti G, Tajima A, Grupillo M, Coppola A, He J (2014) Compromised central tolerance of ICA69 induces multiple organ autoimmunity. J Autoimmun 53:10-25
43. Pérez P, Anaya JM, Aguilera S, Urzúa U, Munroe D, Molina C et al (2009) Gene expression and chromosomal location for susceptibility to Sjögren's syndrome. J Autoimmun 33:99-108
44. Gordon TP, Cavill D, Neufing P, Zhang YJ, Pietropaolo M (2004) ICA69 autoantibodies in primary Sjögren's syndrome. Lupus 13:483-484
45. Gerli R, Bartoloni Bocci E, Vaudo G, Marchesi S, Vitali C, Shoenfeld Y (2006) Traditional cardiovascular risk factors in primary Sjögren's syndrome-role of dyslipidaemia. Rheumatology (Oxford) 45:1580-1581
46. Cárdenas-Roldán J, Rojas-Villarraga A, Anaya JM (2013) How do autoimmune diseases cluster in families? A systematic review and meta-analysis. BMC Med 11:73