Publications of the IBD-BIOM
Research Programme

Highlighted Publications:

Nature Communications
2016 Nov 25;7:13507. doi: 10.1038/ncomms13507. Epub 25 November 2016
Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease. Ventham NT et al.

Inflammatory Bowel Diseases
2015 Jun;21(6):1237-47. doi: 10.1097/MIB.0000000000000372. Epub 17 April 2015
Inflammatory Bowel Disease Associates with Proinflammatory Potential of the Immunoglobulin G Glycome. Trbojević Akmačić I, Ventham NT, Theodoratou E, Vučković F, Kennedy NA, Krištić J, Nimmo ER, Kalla R, Drummond H, Štambuk J, Dunlop MG, Novokmet M, Aulchenko Y, Gornik O, Campbell H, Pučić Baković M, Satsangi J, Lauc G, IBD-BIOM Consortium

Nature Reviews Gastroenterology & Hepatology
2014 Oct;11(10):588-600. doi:10.1038/nrgastro.2014.78. Epub 2014 Jun 10
The role of glycosylation in IBD. Theodoratou E, Campbell H, Ventham NT, Kolarich D3, Pučić-Baković M, Zoldoš V, Fernandes D, Pemberton IK, Rudan I, Kennedy NA, Wuhrer M, Nimmo E, Annese V, McGovern DP, Satsangi J, Lauc G

Nucleic Acids Research
2016 Jul 8;44(12):5615-28. doi: 10.1093/nar/gkw159. Epub 2016 Mar 11
Repurposing the CRISPR-Cas9 system for targeted DNA methylation Vojta A, Dobrinić P, Tadić V, Bočkor L, Korać P, Julg B, Klasić M, Zoldoš V

Journal of Crohn's and Colitis
2016 Mar;10(3):363-70. doi: 10.1093/ecco-jcc/jjv237. Epub 2016 Jan 7
How to Apply for and Secure EU Funding for Collaborative IBD Research Projects Satsangi J, Kitten O, Chavez M, Kalla R, Prel N, Meuwis MA, Scott S, Bonetti I, Ventham NT, Louis E

Gastroenterology
2013 Aug;145(2):293-308. doi: 10.1053/j.gastro.2013.05.050. Epub 2013 Jun 8
Beyond gene discovery in inflammatory bowel disease: the emerging role of epigenetics. Ventham NT, Kennedy NA, Nimmo ER, Satsangi J

PLoS One
2013 Dec 6;8(12):e82558. doi: 10.1371/journal.pone.0082558. eCollection 2013
Glycosylation of immunoglobulin g: role of genetic and epigenetic influences. Menni C, Keser T, Mangino M, Bell JT, Erte I, Akmačić I, Vučković F, Pučić Baković M, Gornik O, McCarthy MI, Zoldoš V, Spector TD, Lauc G, Valdes AM

The Lancet
2016 Jan 9;387(10014):156-67. doi: 10.1016/S0140-6736(15)00465-1. Epub 2015 Oct 18
Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study Cleynen I et al.

Gut
2015 March;64:504-513. doi: 10.1136/gutjnl-2014-307891. Epub 2014 Dec 4
MicroRNAs: new players in IBD. Kalla R, Ventham NT, Kennedy NA, Quintana JF, Nimmo ER, Buck AH, Satsangi J

2016:

Methods in Molecular Biology
2017;1503:131-145. doi: 10.1007/978-1-4939-6493-2_11. Epub 2016 October 15
N- and O-Glycomics from Minor Amounts of Formalin-Fixed, Paraffin-Embedded Tissue Samples Hinneburg H, Schirmeister F, Korać P, Kolarich D

Gastroenterology
2016 Oct;151(4):724-32. doi: 10.1053/j.gastro.2016.06.051. Epub 2016 Aug 1
A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn's Disease and Human Gut Microbiome Composition Li D et al.

Gastroenterology
2016 Oct;151(4):710-723.e2. doi: 10.1053/j.gastro.2016.06.045. Epub 2016 Jul 1
A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF Chuang LS et al.

Inflammatory Bowel Diseases
2016 Oct;22(10):2311-6. doi: 10.1097/MIB.0000000000000913
Genetic Predictors of Benign Course of Ulcerative Colitis-A North American Inflammatory Bowel Disease Genetics Consortium Study Kopylov U, Boucher G, Waterman M, Rivers CR, Patel M, Cho JH, Colombel JF, Duerr RH, Binion D, McGovern DP, Schumm PP, Brant SR, Silverberg MS, Rioux JD, Bitton A

Current Medical Research and Opinion
2016 Aug 22:1-5. [Epub ahead of print]. doi: 10.1080/03007995.2016.1221802
Early remission status predicts long-term outcomes in patients with Crohn's disease treated with certolizumab pegol Melmed GY, McGovern D, Schreiber S, Kosutic G, Spearman M, Coarse J, Sandborn WJ

Analytical Chemistry
2016 Sep 6;88(17):8562-9. doi: 10.1021/acs.analchem.6b01639. Epub 2016 Aug 15
Automated High-Throughput Permethylation for Glycosylation Analysis of Biologics Using MALDI-TOF-MS Shubhakar A, Kozak RP, Reiding KR, Royle L, Spencer DI, Fernandes DL, Wuhrer M

Inflammatory Bowel Diseases
2016 Sep;22(9):2058-62. doi: 10.1097/MIB.0000000000000872
Increased Prevalence of Inflammatory Bowel Disease in Patients with Mutations in Genes Encoding the Receptor Subunits for TGFβ Guerrerio AL, Frischmeyer-Guerrerio PA, Huang C, Wu Y, Haritunians T, McGovern DP, MacCarrick GL, Brant SR, Dietz HC

Gastroenterology
2016 Aug 26. pii: S0016-5085(16)34967-8. doi: 10.1053/j.gastro.2016.08.025
Identification of Loci at 1q21 and 16q23 That Affect Susceptibility to Inflammatory Bowel Disease in Koreans Yang SK et al.

Nature Communications
2016 Aug 9;7:12342. doi: 10.1038/ncomms12342
A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis Rivas MA et al.

Scientific Reports
2016 Aug 9;6:31234. doi: 10.1038/srep31234.
Changes in total plasma and serum N-glycome composition and patient-controlled analgesia after major abdominal surgery Gudelj I, Baciarello M, Ugrina I, De Gregori M, Napolioni V, Ingelmo PM, Bugada D, De Gregori S, Đerek L, Pučić-Baković M, Novokmet M, Gornik O, Saccani Jotti G, Meschi T, Lauc G, Allegri M

BBA General Subjects
2016 Aug;1860(8):1574-82. doi: 10.1016/j.bbagen.2015.10.016. Epub 2015 Oct 21
Mechanisms of disease: The human N-glycome Lauc G, Pezer M, Rudan I, Campbell H

European Journal of Immunology
2016 Aug;46(8):1912-25. doi: 10.1002/eji.201546237. Epub 2016 Jun 1
Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses Simon JM, Davis JP, Lee SE, Schaner MR, Gipson GR, Weiser M, Sartor RB, Herfarth HH, Rahbar R, Sadiq TS, Koruda MJ, McGovern DP, Lieb JD, Mohlke KL, Furey TS, Sheikh SZ

Glycoconjugate Journal
2016 Jun;33(3):405-15. doi: 10.1007/s10719-015-9625-3. Epub 2015 Oct 28
Comparison of analytical methods for profiling N- and O-linked glycans from cultured cell lines: HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study Ito H et al.

Scientific Reports
2016 Jun 15;6:28098. doi: 10.1038/srep28098.
Glycosylation of plasma IgG in colorectal cancer prognosis Theodoratou E, Thaçi K, Agakov F, Timofeeva MN, Štambuk J, Pučić-Baković M, Vučković F, Orchard P, Agakova A, Din FV, Brown E, Rudd PM, Farrington SM, Dunlop MG, Campbell H, Lauc G

Clinical Cancer Research
2016 Jun 15;22(12):3078-86. doi: 10.1158/1078-0432.CCR-15-1867. Epub 2016 Feb 1
IgG Glycome in Colorectal Cancer Vučković F, Theodoratou E, Thaçi K, Timofeeva M, Vojta A, Štambuk J, Pučić-Baković M, Rudd PM, Đerek L, Servis D, Wennerström A, Farrington SM, Perola M, Aulchenko Y, Dunlop MG, Campbell H, Lauc G

Journal of Proteome Research
2016;15(7):2198–2210. doi: 10.1021/acs.jproteome.6b00171. Epub 2016 June 7
LaCyTools: A Targeted Liquid Chromatography–Mass Spectrometry Data Processing Package for Relative Quantitation of Glycopeptides Jansen B.C, Falck D, de Haan N, Hipgrave Ederveen A.L, Razdorov G, Lauc G, Wuhrer M

Inflammatory Bowel Diseases
2016 Jun;22(6):1346-52. doi: 10.1097/MIB.0000000000000771
TNFRSF1B Is Associated with ANCA in IBD Li D, Silverberg MS, Haritunians T, Dubinsky MC, Landers C, Stempak JM, Milgrom R, Guo X, Chen YD, Rotter JI, Taylor KD, McGovern DP, Targan SR

Science
2016 May 27;352(6289):1116-20. doi: 10.1126/science.aad9948. Epub 2016 May 5
Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease Chu H, Khosravi A, Kusumawardhani IP, Kwon AH, Vasconcelos AC, Cunha LD, Mayer AE, Shen Y, Wu WL, Kambal A, Targan SR, Xavier RJ, Ernst PB, Green DR, McGovern DP, Virgin HW, Mazmanian SK

Journal of Proteome Research
2016;15(6):1853–1861. doi: 10.1021/acs.jproteome.6b00038. Epub 2016 May 10
Changes in Healthy Human IgG Fc-Glycosylation after Birth and during Early Childhood de Haan N, Reiding K.R, Driessen G, van der Burg M, Wuhrer M

Analytical Chemistry
2016;88(11):5904-5913. doi: 10.1021/acs.analchem.6b00819. Epub 2016 May 4
Linkage-Specific in Situ Sialic Acid Derivatization for N-Glycan Mass Spectrometry Imaging of Formalin-Fixed Paraffin-Embedded Tissues Holst S, Heijs B, de Haan N, van Zeijl R.J.M, Briaire-de Bruijn I.H, van Pelt G.W, Mehta A.S, Angel P.M, Mesker W.E, Tollenaar R.A, Drake R.R, Bovée J.V.M.G, McDonnell L.A, Wuhrer M

Nature Genetics
2016 May;48(5):510-8. doi: 10.1038/ng.3528. Epub 2016 Mar 14
Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci Ellinghaus D

Scientific Reports
2016 Apr 13;6:24363. doi: 10.1038/srep24363
DNA hypomethylation upregulates expression of the MGAT3 gene in HepG2 cells and leads to changes in N-glycosylation of secreted glycoproteins Klasić M, Krištić J, Korać P, Horvat T, Markulin D, Vojta A, Reiding KR, Wuhrer M, Lauc G, Zoldoš V

Inflammatory Bowel Diseases
2016 Apr;22(4):862-9. doi: 10.1097/MIB.0000000000000705
Perianal Crohn's Disease is Associated with Distal Colonic Disease, Stricturing Disease Behavior, IBD-Associated Serologies and Genetic Variation in the JAK-STAT Pathway Kaur M, Panikkath D, Yan X, Liu Z, Berel D, Li D, Vasiliauskas EA, Ippoliti A, Dubinsky M, Shih DQ, Melmed GY, Haritunians T, Fleshner P, Targan SR, McGovern DP

Chemical Communications
2016 Mar 21;52(23):4381-4. doi: 10.1039/c6cc01114d
Distinguishing N-acetylneuraminic acid linkage isomers on glycopeptides by ion mobility-mass spectrometry. Hinneburg H, Hofmann J, Struwe WB, Thader A, Altmann F, Varón Silva D, Seeberger PH, Pagel K, Kolarich D

Journal of the American Society for Mass Spectrometry
2016 Mar;27(3):507-19. doi: 10.1007/s13361-015-1308-6. Epub 2016 Jan 4
The Art of Destruction: Optimizing Collision Energies in Quadrupole-Time of Flight (Q-TOF) Instruments for Glycopeptide-Based Glycoproteomics Hinneburg H, Stavenhagen K, Schweiger-Hufnagel U, Pengelley S, Jabs W, Seeberger PH, Silva DV, Wuhrer M, Kolarich D

Glycobiology
2016 Jan;26(1):74-87. doi: 10.1093/glycob/cwv087. Epub 2015 Sep 24
Flagellin glycosylation in Paenibacillus alvei CCM 2051T Janesch B, Schirmeister F, Maresch D, Altmann F, Messner P, Kolarich D, Schäffer C

2015:

Arthritis and Rheumatism
2015 Nov;67(11):2978–2989. doi: 10.1002/art.39273. Epub 2015 Oct 28
Systemic lupus erythematosus associates with the decreased immunosuppressive potential of the IgG glycome. Vučković F et al.

Analytical Chemistry
2015 Aug;87(16):8284–8291. doi: 10.1021/acs.analchem.5b02426. Epub 2015 July 20
Linkage-Specific Sialic Acid Derivatization for MALDI-TOF-MS Profiling of IgG Glycopeptides. Haan N, Reiding KR, Haberger M, Reusch D, Falck D, Wuhrer M

Journal of the American Society of Nephrology : JASN
2015 July;27. doi: 10.1681/ASN.2015010109. Epub 2015 July 20
Glycosylation Profile of IgG in Moderate Kidney Dysfunction. Barrios C, Zierer J, Gudelj I, Stambuk J, Ugrina I, Rodriguez E, Soler MJ, Pavi T, Simurina M, Keser T, Pucic-Bakovic M, Mangino M, Pascual J, Spector TD, Lauc G, Menni C

Biochemistry (Moscow)
2015 Jul;80(7):934-42. doi: 10.1134/S0006297915070123.
High-throughput glycomics: optimization of sample preparation Trbojević Akmačić I, Ugrina I, Štambuk J, Gudelj I, Vučković F, Lauc G, Pučić-Baković M

International Journal of Epidemiology
2015 June;44(3). doi: 10.1093/ije/dyv088. Epub 2015 June 4
Cohort Profile: The Inflammatory Bowel Disease South Limburg Cohort (IBDSL). van den Heuvel TR, Jonkers DM, Jeuring SF, Romberg-Camps MJ, Oostenbrug LE, Zeegers MP, Masclee AA, Pierik MJ

Expert Review of Gastroenterology and Hepatology
2015 April;9(4):405-415. doi: 10.1586/17474124.2015.992880. Epub 2014 Dec 15
Predicting outcomes in acute severe ulcerative colitis. Ventham NT, Kalla R, Kennedy NA, Satsangi J, Arnott ID

PLoS One
2015 April;10(4):e0123028. doi:10.1371/journal.pone.0123028. Epub 1 April 2015
Changes to Serum Sample Tube and Processing Methodology Does Not Cause Inter-Individual Variation in Automated Whole Serum N-Glycan Profiling in Health and Disease. Ventham NT, Gardner RA, Kennedy NA, Shubhakar A, Kalla R, Nimmo ER, IBD-BIOM consortium, Fernandes DL, Satsangi J, Specer DI

Chromatographia
2015 March;78(5):307-320. doi: 10.1007/s10337-014-2813-7. Epub 2014 Dec 9
Clinical Glycomics Employing Graphitized Carbon Liquid Chromatography–Mass Spectrometry. Stavenhagen K, Kolarich D, Wuhrer M

Annals of Surgery
2015 March;261(3):487–496. doi: 10.1097/sla.0000000000000757. Epub 2015
The Impact of Preoperative Serum Anti-TNFα Therapy Levels on Early Postoperative Outcomes in Inflammatory Bowel Disease Surgery. Lau C, Dubinsky M, Melmed G, Vasiliauskas E, Berel D, McGovern D, Ippoliti A, Shih D, Targan S, Fleshner P

2014:

Bioinformatics
2014 November;31(7):1067-1074. doi: 10.1093/bioinformatics/btu778. Epub 2014 Nov 20
Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data. Liu Z, Sun F, Braun J, McGovern DP, Piantadosi S

BMJ Open
2014 November;349:g6670. doi: 10.1136/bmj.g6670. Epub 2014 Nov 19
Crohn's disease. Kalla R, Ventham NT, Satsangi J, Arnott IDR

Inflammatory Bowel Diseases
2014 October;20(10):1784–1793. doi: 10.1097/MIB.0000000000000179
Two-stage Genome-wide Methylation Profiling in Childhood-onset Crohn’s Disease Implicates Epigenetic Alterations at the VMP1/MIR21 and HLA Loci. Adams AT et al.

Journal of Crohn's and Colitis
2014 Sept;pii:S1873-9946(14)00267-0. doi: 10.1016/j.crohns.2014.09.002. Epub ahead of print
Nationwide linkage analysis in Scotland: Has mortality following hospital admission for Crohn's disease changed in the early 21st century? Ventham NT, Kennedy NA, Duffy A, Clark DN, Crowe AM, Knight AD, Nicholls RJ, Satsangi J

PLoS One
2014 Sept;9(9):e108204. doi: 10.1371/journal.pone.0108204. Epub 2014 Sept 26
Association of NOD2 and IL23R with Inflammatory Bowel Disease in Puerto Rico. Ballester V, Guo X, Vendrell R, Haritunians T, Klomhaus AM, Li D, McGovern DP, Rotter JI, Torres EA, Taylor KD

Antimicrobial Agents and Chemotherapy
2014 Sept;58(9):5054-5059. doi: 10.1128/AAC.02606-13. Epub 2014 June 9
Antibiotics for Treatment of Clostridium difficile Infection in Hospitalized Patients with Inflammatory Bowel Disease. Horton HA et al.

Seminars in Immunopathology
2014 Sept;36(5):541-551. doi: 10.1007/s00281-014-0444-6. Epub 2014 Sept 12
Use of animal models in elucidating disease pathogenesis in IBD. Khanna PV, Shih DQ, Haritunians T, McGovern DP, Targan S

Nature Genetics
2014 August;46:1017–1020. doi: 10.1038/ng.3060. Epub 2014 Aug 10
A common missense variant in NUDT15 confers susceptibility to thiopurine-induced leukopenia. Yang SK et al.

PLoS One
2014 August;9(8):e103954. doi: 10.1371/journal.pone.0103954. Epub 2014 Aug 5
Inhibition of DNA Methylation Alters Chromatin Organization, Nuclear Positioning and Activity of 45S rDNA Loci in Cycling Cells of Q. robur. Bočkor VV, Barišić D, Horvat T, Maglica Ž, Vojta A, Zoldoš V

Journal of Immunology
2014 July;193(2):940-949. doi: 10.4049/jimmunol.1400093. Epub 2014 June 16
Human NK Cells Licensed by Killer Ig Receptor Genes Have an Altered Cytokine Program That Modifies CD4+ T Cell Function. Lin L, Ma C, Wei B, Aziz N, Rajalingam R, Yusung S, Erlich HA, Trachtenberg EA, Targan SR, McGovern DP, Heath JR, Braun J

Nature Reviews Gastroenterology and Hepatology
2014 Oct;11(10):588-600. doi: 10.1038/nrgastro.2014.78. Epub 2014 June 10
The role of glycosylation in IBD. Theodoratou E, Campbell H, Ventham NT, Kolarich D, Pučić-Baković M, Zoldoš V, Fernandes D, Pemberton IK, Rudan I, Kennedy NA, Wuhrer M, Nimmo E, Annese V, McGovern DP, Satsangi J, Lauc G

Frontiers in Genetics
2014 May;5:145. doi: 10.3389/fgene.2014.00145. Epub 23 May 2014
Glycans - the third revolution in evolution. Lauc G, Krištić J, Zoldoš V

Alimentary Pharmacology and Therapeutics
2014 June;39(12):1387–1397. doi: 10.1111/apt.12750. Epub 2014 Apr 20
Comparison of mortality following hospitalisation for ulcerative colitis in Scotland between 1998-2000 and 2007-2009. Ventham NT, Kennedy NA, Duffy A, Clark DN, Crowe AM, Knight AD, Nicholls RJ, Satsangi J

Molecular and Cellular Proteomics
2014 Jun;13(6):1598-610. doi: 10.1074/mcp.M113.037465. Epub 2014 Apr 9
Comparative Performance of Four Methods for High-throughput Glycosylation Analysis of Immunoglobulin G in Genetic and Epidemiological Research. Huffman JE, Pučić-Baković M, Klarić L, Hennig R, Selman MH, Vučković F, Novokmet M, Krištić J, Borowiak M, Muth T, Polašek O, Razdorov G, Gornik O, Plomp R, Theodoratou E, Wright AF, Rudan I, Hayward C, Campbell H, Deelder AM, Reichl U, Aulchenko YS, Rapp E, Wuhrer M, Lauc G

Nature Scientific Reports Vol 4
2014; 4: 4347. Published online Mar 11, 2014. doi: 10.1038/srep04347
Changes in IgG and total plasma protein glycomes in acute systemic inflammation. Novokmet M, Lukić E, , Vučković F, Željko –Durić, Keser T, Rajšl K, Remondini D, Castellani G, Gašparović H, Gornik O, Lauc G

Gastroenterology
2014 April;146(4):1028–1039. doi: 10.1053/j.gastro.2014.01.015. Epub 2014 Jan 13
Mutations in Tetratricopeptide Repeat Domain 7A Result in a Severe Form of Very Early Onset Inflammatory Bowel Disease. Avitzur Y et al.

Inflammatory Bowel Diseases
2014 April;20(4):646–651. doi: 10.1097/01.MIB.0000442838.21040.d7
Spatial and Temporal Stability of Paneth Cell Phenotypes in Crohn’s Disease: Implications for Prognostic Cellular Biomarker Development. Liu TC, Gao F, McGovern DP, Stappenbeck TS

Nature Reviews Gastroenterology & Hepatology
2014 Jan;11:287-299. doi:10.1038/nrgastro.2013.242. Epub 17 December 2013
Towards personalized care in IBD. Gerich M, McGovern D

2013:

Journals of Gerontology - Series A Biological Sciences and Medical Sciences
2014 Jul;69(7):779-89. doi: 10.1093/gerona/glt190. Epub 2013 Dec 10
Glycans Are a Novel Biomarker of Chronological and Biological Ages. Krištić J, Vučković F, Menni C, Klarić L, Keser T, Beceheli I, Pučić-Baković M, Novokmet M, Mangino M, Thaqi K, Rudan P, Novokmet N, Šarac J, Missoni S, Kolčić I, Polašek O, Rudan I, Campbell H, Hayward C, Aulchenko Y, Valdes A, Wilson JF, Gornik O, Primorac D, Zoldoš V, Spector T and Lauc G

Current Opinion in Chemical Biology
2013 February;17(1):34–40. doi: 10.1016/j.cbpa.2012.12.007. Epub 2013 Jan 1
Glycomics meets genomics, epigemonics and other high throughput omics for system biology studies. Zoldoš V, Horvat T, Lauc G