New bioinformatics approach to analyze gene expressions and signaling pathways reveals unique purine gene dysregulation profiles that distinguish between CD and UC.
BACKGROUND
Expression of purine genes is modulated by inflammation or experimental colitis and altered expression leads to disrupted gut function. We studied purine gene dysregulation profiles in inflammatory bowel disease (IBD) and determined whether they can distinguish between Crohn's disease (CD) and ulcerative colitis (UC) using Pathway Analysis and a new Comparative Analysis of Gene Expression and Selection (CAGES) method.


METHODS
Raw datasets for 22 purine genes and 36 probe-sets from National Center for Biotechnology Information (NCBI) GEO (Gene Expression Omnibus) (http://www.ncbi.nlm.nih.gov/projects/geo/) were analyzed by National Cancer Institute (NCI) Biological Resources Branch (BRB) array tools for random-variance of multiple/36 t-tests in colonic mucosal biopsies or peripheral blood mononuclear cells (PBMCs) of CD, UC or control subjects. Dysregulation occurs in 59% of purine genes in IBD including ADORA3, CD73, ADORA2A, ADORA2B, ADAR, AMPD2, AMPD3, DPP4, P2RY5, P2RY6, P2RY13, P2RY14, and P2RX5.


RESULTS
In CD biopsies, expression of ADORA3, AMPD3, P2RY13, and P2RY5 were negatively correlated with acute inflammatory score, Crohn's Disease Activity Index (CDAI) or disease chronicity; P2RY14 was positively correlated in UC. In mucosal biopsies or PBMCs, CD and UC were distinguished by unique patterns of dysregulation (up- or downregulation) in purine genes. Purine gene dysregulation differs between PBMCs and biopsies and possibly between sexes for each disease. Ingenuity Pathway Analysis (IPA) revealed significant associations between alterations in the expression of CD73 (upregulation) or ADORA3 (downregulation) and inflammatory or purine genes (<or=10% of 57 genes) as well as G-protein coupled receptors, cAMP-dependent, and inflammatory pathways; IPA distinguishes CD from UC.


CONCLUSIONS
CAGES and Pathway Analysis provided novel evidence that UC and CD have distinct purine gene dysregulation signatures in association with inflammation, cAMP, or other signaling pathways. Disease-specific purine gene signature profiles and pathway associations may be of therapeutic, diagnostic, and functional relevance.
Rybaczyk
Leszek
L
Department of Bioinformatics, Ohio State University, Columbus, Ohio 43210, USA.
Rozmiarek
Andrew
A
Circle
Kristin
K
Grants
Iveta
I
Needleman
Bradley
B
Wunderlich
Jacqueline E
JE
Huang
Kun
K
Christofi
Fievos L
FL
D001706:Biopsy; D002908:Chronic Disease; D003093:Colitis, Ulcerative / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D019295:Computational Biology; D003424:Crohn Disease / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D011687:Purines / Q000378:metabolism*; D043684:Receptor, Adenosine A3 / Q000235:genetics / Q000378:metabolism; D043683:Receptors, Adenosine A2 / Q000235:genetics / Q000378:metabolism; D018048:Receptors, Purinergic P2 / Q000235:genetics / Q000378:metabolism; D012720:Severity of Illness Index; D015398:Signal Transduction / Q000235:genetics*
D011687:Purines; D043684:Receptor, Adenosine A3; D043683:Receptors, Adenosine A2; D018048:Receptors, Purinergic P2; C030985:purine