Genomics Meets Glycomics—The First GWAS Study of Human N-Glycome Identifies HNF1α as a Master Regulator of Plasma Protein Fucosylation
Over half of all proteins are glycosylated, and alterations in glycosylation have been observed in numerous physiological and pathological processes. Attached glycans significantly affect protein function; but, contrary to polypeptides, they are not directly encoded by genes, and the complex processes that regulate their assembly are poorly understood. A novel approach combining genome-wide association and high-throughput glycomics analysis of 2,705 individuals in three population cohorts showed that common variants in the Hepatocyte Nuclear Factor 1α (HNF1α) and fucosyltransferase genes FUT6 and FUT8 influence N-glycan levels in human plasma. We show that HNF1α and its downstream target HNF4α regulate the expression of key fucosyltransferase and fucose biosynthesis genes. Moreover, we show that HNF1α is both necessary and sufficient to drive the expression of these genes in hepatic cells. These results reveal a new role for HNF1α as a master transcriptional regulator of multiple stages in the fucosylation process. This mechanism has implications for the regulation of immunity, embryonic development, and protein folding, as well as for our understanding of the molecular mechanisms underlying cancer, coronary heart disease, and metabolic and inflammatory disorders.
Vyšlo v časopise:
Genomics Meets Glycomics—The First GWAS Study of Human N-Glycome Identifies HNF1α as a Master Regulator of Plasma Protein Fucosylation. PLoS Genet 6(12): e32767. doi:10.1371/journal.pgen.1001256
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1001256
Souhrn
Over half of all proteins are glycosylated, and alterations in glycosylation have been observed in numerous physiological and pathological processes. Attached glycans significantly affect protein function; but, contrary to polypeptides, they are not directly encoded by genes, and the complex processes that regulate their assembly are poorly understood. A novel approach combining genome-wide association and high-throughput glycomics analysis of 2,705 individuals in three population cohorts showed that common variants in the Hepatocyte Nuclear Factor 1α (HNF1α) and fucosyltransferase genes FUT6 and FUT8 influence N-glycan levels in human plasma. We show that HNF1α and its downstream target HNF4α regulate the expression of key fucosyltransferase and fucose biosynthesis genes. Moreover, we show that HNF1α is both necessary and sufficient to drive the expression of these genes in hepatic cells. These results reveal a new role for HNF1α as a master transcriptional regulator of multiple stages in the fucosylation process. This mechanism has implications for the regulation of immunity, embryonic development, and protein folding, as well as for our understanding of the molecular mechanisms underlying cancer, coronary heart disease, and metabolic and inflammatory disorders.
Zdroje
1. MarthJD
GrewalPK
2008 Mammalian glycosylation in immunity. Nature Reviews Immunology 8 874 887
2. DennisJW
LauKS
DemetriouM
NabiIR
2009 Adaptive Regulation at the Cell Surface by N-Glycosylation. Traffic 10 1569 1578
3. OhtsuboK
MarthJD
2006 Glycosylation in cellular mechanisms of health and disease. Cell 126 855 867
4. ApweilerR
HermjakobH
SharonN
1999 On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochimica et Biophysica Acta 1473 4 8
5. SkropetaD
2009 The effect of individual N-glycans on enzyme activity. Bioorganic & Medicinal Chemistry 17 2645 2653
6. HartGW
HousleyMP
SlawsonC
2007 Cycling of O-linked beta-N-acetylglucosamine on nucleocytoplasmic proteins. Nature 446 1017 1022
7. CrockerPR
PaulsonJC
VarkiA
2007 Siglecs and their roles in the immune system. Nature Reviews Immunology 7 255 266
8. BrownJR
CrawfordBE
EskoJD
2007 Glycan antagonists and inhibitors: a fount for drug discovery. Critical reviews in biochemistry and molecular biology 42 481 515
9. JaekenJ
2003 Komrower Lecture. Congenital disorders of glycosylation (CDG): it's all in it! J Inherit Metab Dis 26 99 118
10. FreezeHH
2006 Genetic defects in the human glycome. Nature Reviews Genetics 7 537 551
11. FreezeHH
2002 Human disorders in N-glycosylation and animal models. Biochimica et Biophysica Acta 1573 388 393
12. LaucG
RudanI
CampbellH
RuddPM
2010 Complex Genetic Regulation of Protein Glycosylation. Molecular Biosystems 6 329 335
13. RoyleL
CampbellMP
RadcliffeCM
WhiteDM
HarveyDJ
2008 HPLC-based analysis of serum N-glycans on a 96-well plate platform with dedicated database software. Analytical Biochemistry 376 1 12
14. RuddPM
RudanI
WrightAF
2009 High-Throughput Glycome Analysis Is Set To Join High-Throughput Genomics. Journal of Proteome Research 8 1105 1105
15. KneževićA
PolašekO
GornikO
RudanI
CampbellH
2009 Variability, Heritability and Environmental Determinants of Human Plasma N-Glycome. Journal of Proteome Research 8 694 701
16. GornikO
WagnerJ
PučićM
KneževićA
RedžićI
2009 Stability of N-glycan profiles in human plasma. Glycobiology 19 1547 1553
17. KneževićA
GornikO
PolašekO
PučićM
NovokmetM
2010 Effects of aging, body mass index, plasma lipid profiles, and smoking on human plasma N-glycans. Glycobiology 20 959 969
18. PučićM
PintoS
NovokmetM
KneževićA
GornikO
2010 Common aberrations from normal human N-glycan plasma profile. Glycobiology 20 970 975
19. BeckerDJ
LoweJB
2003 Fucose: biosynthesis and biological function in mammals. Glycobiology 13 41R 53R
20. TonettiM
SturlaL
BissoA
BenattiU
De FloraA
1996 Synthesis of GDP-L-fucose by the human FX protein. Journal of Biological Chemistry 271 27274 27279
21. JavaudC
DupuyF
MaftahA
JulienR
PetitJM
2003 The fucosyltransferase gene family: an amazing summary of the underlying mechanisms of gene evolution. Genetica 118 157 170
22. GornikO
LaucG
2008 Glycosylation of serum proteins in inflammatory diseases. Disease Markers 25 267 278
23. MiyoshiE
MoriwakiK
NakagawaT
2008 Biological function of fucosylation in cancer biology. Journal of Biochemistry 143 725 729
24. OdomDT
ZizlspergerN
GordonDB
BellGW
RinaldiNJ
2004 Control of pancreas and liver gene expression by HNF transcription factors. Science 303 1378 1381
25. YamagataK
FurutaH
OdaN
KaisakiPJ
MenzelS
1996 Mutations in the hepatocyte nuclear factor-4alpha gene in maturity-onset diabetes of the young (MODY1). Nature 384 458 460
26. YamagataK
OdaN
KaisakiPJ
MenzelS
FurutaH
1996 Mutations in the hepatocyte nuclear factor-1alpha gene in maturity-onset diabetes of the young (MODY3). Nature 384 455 458
27. ElliottP
ChambersJC
ZhangW
ClarkeR
HopewellJC
2009 Genetic Loci associated with C-reactive protein levels and risk of coronary heart disease. JAMA 302 37 48
28. YuanX
WaterworthD
PerryJR
LimN
SongK
2008 Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes. American Journal of Human Genetics 83 520 528
29. ReinerAP
GrossMD
CarlsonCS
BielinskiSJ
LangeLA
2009 Common coding variants of the HNF1A gene are associated with multiple cardiovascular risk phenotypes in community-based samples of younger and older European-American adults: the Coronary Artery Risk Development in Young Adults Study and The Cardiovascular Health Study. Circ Cardiovasc Genet 2 244 254
30. BarrettJC
LeeJC
LeesCW
PrescottNJ
AndersonCA
2009 Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. Nature Genetics 41 1330 1334
31. KathiresanS
WillerCJ
PelosoGM
DemissieS
MusunuruK
2009 Common variants at 30 loci contribute to polygenic dyslipidemia. Nature Genetics 41 56 65
32. VitartV
RudanI
HaywardC
GrayNK
FloydJ
2008 SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout. Nature Genetics 40 437 442
33. TaniguchiN
HonkeK
FukudaM
2002 Handbook of glycosyltransferases and related genes. Tokyo Springer Verlag
34. Brinkman-Van der LindenEC
MolliconeR
OriolR
LarsonG
Van den EijndenDH
1996 A missense mutation in the FUT6 gene results in total absence of alpha3-fucosylation of human alpha1-acid glycoprotein. J Biol Chem 271 14492 14495
35. MaB
Simala-GrantJL
TaylorDE
2006 Fucosylation in prokaryotes and eukaryotes. Glycobiology 16 158R 184R
36. HigaiK
MiyazakiN
AzumaY
MatsumotoK
2008 Transcriptional regulation of the fucosyltransferase VI gene in hepatocellular carcinoma cells. Glycoconjugate Journal 25 225 235
37. ServitjaJM
PignatelliM
MaestroMA
CardaldaC
BojSF
2009 Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver. Molecular & Cellular Biology 29 2945 2959
38. BojSF
PetrovD
FerrerJ
2010 Epistasis of transcriptomes reveals synergism between transcriptional activators Hnf1alpha and Hnf4alpha. PLoS Genet 6 e1000970 doi:10.1371/journal.pgen.1000970
39. BejeranoG
SiepelAC
KentWJ
HausslerD
2005 Computational screening of conserved genomic DNA in search of functional noncoding elements. Nature Methods 2 535 545
40. OdomDT
DowellRD
JacobsenES
GordonW
DanfordTW
2007 Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 39 730 732
41. LootsG
OvcharenkoI
2007 ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. Bioinformatics 23 122 124
42. BoydM
BressendorffS
MollerJ
OlsenJ
TroelsenJT
2009 Mapping of HNF4alpha target genes in intestinal epithelial cells. BMC Gastroenterol 9 68
43. BenkoS
FantesJA
AmielJ
KleinjanDJ
ThomasS
2009 Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet 41 359 364
44. EssafiA
Fernandez de MattosS
HassenYA
SoeiroI
MuftiGJ
2005 Direct transcriptional regulation of Bim by FoxO3a mediates STI571-induced apoptosis in Bcr-Abl-expressing cells. Oncogene 24 2317 2329
45. WithersDA
HakomoriSI
2000 Human alpha (1,3)-fucosyltransferase IV (FUTIV) gene expression is regulated by elk-1 in the U937 cell line. Journal of Biological Chemistry 275 40588 40593
46. ErdmannJ
GrosshennigA
BraundPS
KonigIR
HengstenbergC
2009 New susceptibility locus for coronary artery disease on chromosome 3q22.3. Nature Genetics 41 280 282
47. KelAE
NiehofM
MatysV
ZemlinR
BorlakJ
2008 Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context. Genome Biol 9 R36
48. BrandleyBK
KisoM
AbbasS
NikradP
SrivasatavaO
1993 Structure-function studies on selectin carbohydrate ligands. Modifications to fucose, sialic acid and sulphate as a sialic acid replacement. Glycobiology 3 633 641
49. LuhnK
MarquardtT
HarmsE
VestweberD
2001 Discontinuation of fucose therapy in LADII causes rapid loss of selectin ligands and rise of leukocyte counts. Blood 97 330 332
50. KleinA
2008 Human total serum N-glycome. Advances in Clinical Chemistry 46 51 85
51. RoyleL
RadcliffeCM
DwekRA
RuddPM
2006 Detailed structural analysis of N-glycans released from glycoproteins in SDS-PAGE gel bands using HPLC combined with exoglycosidase array digestions. Methods Mol Biol 347 125 143
52. CampbellMP
RoyleL
RadcliffeCM
DwekRA
RuddPM
2008 GlycoBase and autoGU: tools for HPLC-based glycan analysis. Bioinformatics 24 1214 1216
53. AulchenkoYS
RipkeS
IsaacsA
van DuijnCM
2007 GenABEL: an R library for genome-wide association analysis. Bioinformatics 23 1294 1296
54. ChenWM
AbecasisGR
2007 Family-based association tests for genomewide association scans. Am J Hum Genet 81 913 926
55. BarrettJC
FryB
MallerJ
DalyMJ
2005 Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21 263 265
56. JohnsonAD
HandsakerRE
PulitSL
NizzariMM
O'DonnellCJ
2008 SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics 24 2938 2939
57. SchaidDJ
RowlandCM
TinesDE
JacobsonRM
PolandGA
2002 Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70 425 434
58. AkaikeH
1974 New Look at Statistical-Model Identification. Ieee Transactions on Automatic Control AC19 716 723
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Genetika Reprodukčná medicínaČlánok vyšiel v časopise
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