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Table S1. Genes and Assays Selected for Reverse Transcription Quantitative PCR, Including Ratio Between Mean Relative Expression of Marsh 3 Biopsies

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Table S1. Genes and Assays Selected for Reverse Transcription Quantitative PCR, Including Ratio Between Mean Relative Expression of Marsh 3 Biopsies Bragde et al. – Supplemental Material Table S1. Genes and assays selected for reverse transcription quantitative PCR, including ratio between mean relative expression of Marsh 3 biopsies (n=10) and reference population (n=4), and results from Mann-whitney comparing the same two groups. Official symbol Gene name Gene Expression assay** Relative expression‡ P-value§ Reference genes HPRT1 hypoxanthine phosphoribosyltransferase 1 Hs99999909_m1 PGK1 phosphoglycerate kinase 1 Hs99999906_m1 Villi genes ACSL5 (1) acyl-CoA synthetase long-chain family member 5 Hs00212106_m1 0.77 0.054 ADA* (2) adenosine deaminase Hs01110949_m1 0.52 0.008 ALPI* (3) alkaline phosphatase, intestinal Hs00357578_m1 0.46 0.014 APOA1* (4, 5) apolipoprotein A-I Hs00985000_g1 0.05 0.002 APOA4* (5) apolipoprotein A-IV Hs01573751_g1 0.16 0.002 APOB* (5) apolipoprotein B Hs01071209_m1 0.13 0.002 APOC3* (1) apolipoprotein C-III Hs00163644_m1 0.11 0.002 CYP3A4* (6) cytochrome P450, family 3, subfamily A, polypeptide 4 Hs00430021_m1 0.04 0.002 DPP4* (1) dipeptidyl-peptidase 4 Hs00175210_m1 0.33 0.004 ENPP3* (1) ectonucleotide pyrophosphatase/phosphodiesterase 3 Hs01038411_m1 0.11 0.002 FABP1 (7) fatty acid binding protein 1, liver Hs00155026_m1 0.85 0.454 FABP2* (7) fatty acid binding protein 2, intestinal Hs01573162_m1 0.53 0.008 LCT* (2) lactase Hs00158722_m1 0.09 0.002 VIL1 (2) villin 1 Hs00200229_m1 0.74 0.106 Crypt genes ABCC1 (8) ATP-binding cassette, sub-family C (CFTR/MRP), member 1 Hs00219905_m1 1.19 0.188 APOA2 (2) apolipoprotein A-II Hs00155788_m1 0.78 0.076 BTC (2) betacellulin Hs01101204_m1 0.90 0.454 CDK1* (1) cyclin-dependent kinase 1 Hs00364293_m1 1.58 0.004 CDK2* (9) cyclin-dependent kinase 2 Hs01548894_m1 1.45 0.024 CDK4 (9) cyclin-dependent kinase 4 Hs00175935_m1 1.23 0.188 CLU (2) clusterin Hs00156548_m1 0.93 0.454 DMBT1 (1) deleted in malignant brain tumors 1 Hs00244838_m1 0.69 0.054 GLUL (2) glutamate-ammonia ligase (glutamine synthetase) Hs00365928_g1 1.15 0.374 HES1 (10) Hairy and enhancer of split 1 Hs00172878_m1 0.92 0.839 1 Bragde et al. – Supplemental Material KRT19 (2) keratin 19 Hs01051611_gH 1.49 0.454 MAD2L1* (1) MAD2 mitotic arrest deficient-like 1 (yeast) Hs01554513_g1 1.53 0.004 MKI67* (1) antigen identified by monoclonal antibody Ki-67 Hs00606991_m1 1.93 0.002 MYC (9) v-myc myelocytomatosis viral oncogene homolog (avian) Hs99999003_m1 0.65 0.188 OLFM4 (1) olfactomedin 4 Hs00910490_m1 0.65 0.054 PCNA* (9) proliferating cell nuclear antigen Hs00952870_g1 1.56 0.004 REG3A (11) regenerating islet-derived 3 alpha Hs00170171_m1 0.77 0.240 RRM2* (1) ribonucleotide reductase M2 Hs01072069_g1 2.23 0.004 SEMA3F* (11) sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F Hs01030912_m1 0.55 0.004 TOP2A* (2) topoisomerase (DNA) II alpha 170kDa Hs00172214_m1 1.51 0.004 Epithelial permeability genes CDH1* (12) cadherin 1, type 1, E-cadherin (epithelial) Hs00170423_m1 0.75 0.024 CLDN1 (12) claudin 1 Hs00221623_m1 1.67 0.076 CLDN2 (12) claudin 2 Hs00252666_s1 1.54 0.374 CLDN3 (12) claudin 3 Hs00265816_s1 0.95 0.454 CLDN4 (12) claudin 4 Hs00976831_s1 0.86 0.304 CLDN5 (12) claudin 5 Hs00533949_s1 1.23 0.454 CLDN8 (12) claudin 8 Hs00273282_s1 n.d.¶ CLDN15* (13) claudin 15 Hs00204982_m1 0.43 0.004 CTNNB1 (12) catenin (cadherin-associated protein), beta 1, 88kDa Hs00170025_m1 0.93 0.106 F11R* (12) F11 receptor Hs00375889_m1 0.75 0.014 JAM2 (12) junctional adhesion molecule 2 Hs01022007_m1 0.88 0.142 JAM3* (12) junctional adhesion molecule 3 Hs01113227_m1 0.79 0.036 MAGI2 (14) membrane associated guanylate kinase, WW and PDZ domain containing 2 Hs00202321_m1 1.02 1.000 OCLN* (12) occludin Hs00170162_m1 0.51 0.002 PARD3 (14) par-3 partitioning defective 3 homolog (C. elegans) Hs00969067_m1 0.68 0.014 TJP1* (12) tight junction protein 1 (zona occludens 1) Hs00268480_m1 0.59 0.002 TJP2* (12) tight junction protein 2 (zona occludens 2) Hs00910543_m1 0.79 0.036 TJP3* (12) tight junction protein 3 (zona occludens 3) Hs00274276_m1 0.70 0.004 Immune response related genes CCR9 (15) chemokine (C-C motif) receptor 9 Hs01890924_s1 0.98 0.945 CD28 (16) CD28 molecule Hs01007419_m1 1.12 0.839 CSF2 (17) colony stimulating factor 2 (granulocyte-macrophage) Hs00171266_m1 1.16 0.454 2 Bragde et al. – Supplemental Material CSF3 (17) colony stimulating factor 3 (granulocyte) Hs99999083_m1 10.60 0.733 CTLA4* (18) cytotoxic T-lymphocyte-associated protein 4 (soluble isoform) Hs03044419_m1 2.46 0.002 CTLA4* (18) cytotoxic T-lymphocyte-associated protein 4 (membrane bound isoform) Hs01011591_m1 2.41 0.002 CXCL11* (17) chemokine (C-X-C motif) ligand 11 Hs00171138_m1 12.55 0.002 FGF7* (15) fibroblast growth factor 7 (keratinocyte growth factor) Hs00940253_m1 2.13 0.024 GZMA (19) granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3) Hs00196206_m1 1.04 0.839 GZMB* (20) granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1) Hs00188051_m1 6.38 0.002 ICOS (17) inducible T-cell co-stimulator Hs00359999_m1 1.39 0.304 IFNA1 (21) interferon, alpha 1 Hs03044218_g1 0.31 0.240 IFNG*† interferon, gamma Hs00174143_m1 21.72 0.002 IL1A† interleukin 1, alpha Hs00174092_m1 2.46 0.304 IL1B† interleukin 1, beta Hs00174097_m1 4.23 0.106 IL2*† interleukin 2 Hs00174114_m1 0.31 0.014 IL4† Interleukin 4 Hs99999030_m1 1.30 0.635 IL6* (17) interleukin 6 (interferon, beta 2) Hs00985639_m1 2.25 0.036 IL8*† interleukin 8 Hs00174103_m1 7.63 0.002 IL10*† interleukin 10 Hs00174086_m1 2.23 0.008 IL11 (22) interleukin 11 Hs00174148_m1 3.44 0.106 IL12A*† interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35) Hs00168405_m1 2.61 0.002 IL12B† interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40) Hs01011516_g1 1.26 0.839 IL13 (23) interleukin 13 Hs00174379_m1 n.d.¶ IL15† interleukin 15 Hs01003716_m1 0.90 0.454 IL17A* (24) interleukin 17A Hs00174383_m1 14.44 0.002 IL17B (25) interleukin 17B Hs00975262_m1 0.55 0.188 IL18* (17) interleukin 18 (interferon-gamma-inducing factor) Hs00155517_m1 0.49 0.036 IL21 (26) interleukin 21 Hs00222327_m1 2.47 0.142 ITGAX (27) integrin, alpha X (complement component 3 receptor 4 subunit) Hs01015064_m1 1.66 0.054 KLRK1 (28) killer cell lectin-like receptor subfamily K, member 1 Hs00183683_m1 1.05 0.839 LTA (17) lymphotoxin alpha (TNF superfamily, member 1) Hs00236874_m1 1.35 0.142 MICA (28) MHC class I polypeptide-related sequence A Hs00792195_m1 1.38 0.240 MICB (21) MHC class I polypeptide-related sequence B Hs00792952_m1 1.31 0.054 RGS1 (29) regulator of G-protein signaling 1 Hs00175260_m1 1.67 0.539 TBX21 (17) T-box 21 Hs00203436_m1 1.46 0.240 3 Bragde et al. – Supplemental Material TGFB1 (30) transforming growth factor, beta 1 Hs00171257_m1 1.20 0.374 TLR3* (31) toll-like receptor 3 Hs01551078_m1 0.38 0.004 TNF† tumor necrosis factor (TNF superfamily, member 2) Hs00174128_m1 0.92 0.839 TNFRSF4 (27) tumor necrosis factor receptor superfamily, member 4 Hs00533968_m1 1.79 0.142 TNFRSF9* (27) tumor necrosis factor receptor superfamily, member 9 Hs00155512_m1 4.31 0.002 TNFRSF18 (17) tumor necrosis factor receptor superfamily, member 18 Hs02572926_s1 1.46 0.635 TYROBP (32) TYRO protein tyrosine kinase binding protein Hs00182426_m1 0.72 0.106 Other potential marker genes ARG1 (33) arginase, liver Hs00968979_m1 1.91 0.539 ARG2 (33) arginase, type II Hs00982833_m1 0.94 0.539 CYP4F2* (17) cytochrome P450, family 4, subfamily F, polypeptide 2 Hs02557757_s1 0.16 0.002 CYP4F3 (17) cytochrome P450, family 4, subfamily F, polypeptide 3 Hs00168521_m1 1.12 0.945 E2F4 (34) E2F transcription factor 4, p107/p130-binding Hs01053570_m1 0.84 0.142 ECE1* (17) endothelin converting enzyme 1 Hs01043741_m1 0.59 0.008 EDN1* (17) endothelin 1 Hs01116576_g1 0.15 0.002 MYO9B (35) myosin IXB Hs00994622_m1 1.11 0.635 NOS2* (17, 33) nitric oxide synthase 2, inducible Hs00167257_m1 3.06 0.008 SELE* (17) selectin E Hs00174057_m1 10.24 0.036 SMAD3* (17) SMAD family member 3 Hs00232219_m1 0.48 0.004 SMAD7* (17) SMAD family member 7 Hs00178696_m1 0.44 0.002 TAGAP* (29) T-cell activation RhoGTPase activating protein Hs01097871_m1 1.60 0.036 TM4SF4* (36) transmembrane 4 L six family member 4 Hs00270335_m1 0.08 0.002 * Selected for further analyses. † Gene present on Taqman cytokine gene expression plate I (Applied Biosystems). ** Final concentrations of primers and probe 900 nM and 250 nM, respectively. Minor groove binding Taqman probes, fluorescently labelled in the 5’ end with FAM and in the 3’ end with a non- fluorescent quencher. ‡ Ratio between mean relative expression of Marsh 3 biopsies (n=10) and the reference population (n=4). § P-value based on expression in Marsh 3 biopsies (n=10) compared to the reference population (n=4) (Mann-Whitney). ¶ Not detected. 4 Bragde et al. – Supplemental Material Table S1: References 1. Gassler N, Newrzella D, Bohm C, Lyer S, Li L, Sorgenfrei O, van Laer L, Sido B, Mollenhauer J, Poustka A, Schirmacher P, Gretz N 2006 Molecular characterisation of non-absorptive and absorptive enterocytes in human small intestine. Gut 55:1084-1089. 2. Olsen L, Hansen M, Ekstrom CT, Troelsen JT, Olsen J 2004 CVD: the intestinal crypt/villus in situ hybridization database. Bioinformatics 20:1327-1328. 3. Prasad KK, Thapa BR, Nain CK, Sharma AK, Singh K 2008 Brush border enzyme activities in relation to histological lesion in pediatric celiac disease. J Gastroenterol Hepatol 23:e348-352. 4. Floren CH, Alm P 1988 Defective synthesis of apolipoprotein A-I in jejunal mucosa in coeliac disease. Scand J Gastroenterol 23:856-860.
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