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Table S1 : Upregulated Intragraft Gene Transcripts in Only Graft Loss Group

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Table S1 : Upregulated intragraft gene transcripts in only graft loss group (Table S1a), in only functioning allograft group (Table S1b) and in both groups (Table S1c) compared to normal transplant kidney biopsies Table S1a: Transcript Gene Name Adjusted Cluster ID P value 7898793 Complement component 1, q subcomponent, A chain 0.0176 (C1QA),mRNA 7898799 Complement component 1, q subcomponent, C chain (C1QC), 0.0325 transcript variant 1, mRNA 7899394 Chromosome 1 open reading frame 38 (C1orf38), transcript 0.004 variant 3, mRNA 7906435 Duffy blood group, chemokine receptor (DARC), transcript 0.0007 variant 2, mRNA 7906486 SLAM family member 8 (SLAMF8), mRNA 0.0154 7906757 Fc fragment of IgG, low affinity IIa, receptor (CD32) 0.0062 (FCGR2A), transcript variant 1, mRNA 7912145 Tumor necrosis factor receptor superfamily, member 9 0.0128 (TNFRSF9), mRNA 7922773 Neutrophil cytosolic factor 2 (NCF2), transcript variant 1, 0.004 mRNA 7923043 Potassium channel, subfamily T, member 2 (KCNT2), mRNA 0.002 7926410 Mannose receptor, C type 1 (MRC1), mRNA 0.002 7926451 Mannose receptor, C type 1 (MRC1), mRNA 0.002 7934979 Ankyrin repeat domain 1 (cardiac muscle) (ANKRD1), mRNA 0.008 7943749 Layilin (LAYN), mRNA 0.001 7943998 Nicotinamide N-methyltransferase (NNMT), mRNA 0.005 7948455 Membrane-spanning 4-domains, subfamily A, member 6A 0.006 (MS4A6A), transcript variant 1, mRNA 7951217 Matrix metallopeptidase 7 (matrilysin, uterine) (MMP7), 0.029 mRNA 7953200 Cyclin D2 (CCND2), mRNA 0.01 7953901 C-type lectin domain family 12, member A (CLEC12A), 0.004 transcript variant 1, mRNA 7954527 Aryl hydrocarbon receptor nuclear translocator-like 2 0.0006 (ARNTL2), mRNA 7956878 Interleukin-1 receptor-associated kinase 3 (IRAK3), transcript 0.001 variant 1, mRNA 7960464 Von Willebrand factor (VWF), mRNA 0.005 7960874 Complement component 3a receptor 1 (C3AR1), mRNA 0.021 7973101 Ribonuclease, RNase A family, k6 (RNASE6), mRNA 0.006 7983910 Aquaporin 9 (AQP9), mRNA 0.004 7994769 Coronin, actin binding protein, 1A (CORO1A), transcript 0.013 variant 1, mRNA 7995128 Integrin, alpha X (complement component 3 receptor 4 0.01 subunit) (ITGAX), mRNA 7997712 Interferon regulatory factor 8 (IRF8), mRNA 0.004 8006608 Chemokine (C-C motif) ligand 4-like 1 (CCL4L1), mRNA 0.006 8008885 MicroRNA 21 (MIR21), microRNA 0.001 8025601 Intercellular adhesion molecule 1 (ICAM1), mRNA 0.004 8028104 Hematopoietic cell signal transducer (HCST), transcript 0.006 variant 1, mRNA 8031293 Killer cell immunoglobulin-like receptor, two domains, long 0.009 cytoplasmic tail, 3 (KIR2DL3), mRNA 8034873 EGF-like module containing, mucin-like, hormone receptor- 0.005 like 2 (EMR2), transcript variant 1, mRNA 8036224 TYRO protein tyrosine kinase binding protein (TYROBP), 0.003 transcript variant 1, mRNA 8039212 Leukocyte immunoglobulin-like receptor, subfamily B (with 0.001 TM and ITIM domains), member 2 (LILRB2), transcript variant 1, mRNA 8043236 Granulysin (GNLY), transcript variant 519, mRNA 0.002 8044049 Interleukin 18 receptor accessory protein (IL18RAP), mRNA 0.0006 8045688 Tumor necrosis factor, alpha-induced protein 6 (TNFAIP6), 0.046 mRNA 8050427 Family with sequence similarity 49, member A (FAM49A), 0.002 mRNA 8054722 Interleukin 1, beta (IL1B), mRNA 0.003 8061668 Hemopoietic cell kinase (HCK), transcript variant 1, mRNA 0.001 8066117 SAM domain and HD domain 1 (SAMHD1), mRNA 0.008 8068697 Myxovirus (influenza virus) resistance 2 (mouse) (MX2), 0.009 mRNA 8072798 Cytohesin 4 (CYTH4), mRNA 0.005 8073056 Apolipoprotein B mRNA editing enzyme, catalytic polypeptide- 0.005 like 3A (APOBEC3A), transcript variant 1, mRNA 8075886 Interleukin 2 receptor, beta (IL2RB), mRNA 0.019 8081386 Nuclear factor of kappa light polypeptide gene enhancer in B- 0.0006 cells inhibitor, zeta (NFKBIZ), transcript variant 1, mRNA 8081890 Phospholipase A1 member A (PLA1A), mRNA 0.006 8089911 Hematopoietic cell-specific Lyn substrate 1 (HCLS1), mRNA 0.001 8091511 Purinergic receptor P2Y, G-protein coupled, 14 (P2RY14), 0.001 transcript variant 2, mRNA 8091723 Retinoic acid receptor responder (tazarotene induced) 1 0.005 (RARRES1), transcript variant 1, mRNA 8098146 Neuropeptide Y receptor Y5 (NPY5R), mRNA 0.0005 8101780 Hematopoietic prostaglandin D synthase (HPGDS), mRNA 0.002 8103508 Membrane-associated ring finger (C3HC4) 1 (MARCH1), 0.003 transcript variant 2, mRNA 8105040 Oncostatin M receptor (OSMR), transcript variant 1, mRNA 0.005 8114010 Interferon regulatory factor 1 (IRF1), mRNA 0.012 8115076 Colony stimulating factor 1 receptor (CSF1R), mRNA 0.003 8118149 Leukocyte specific transcript 1 (LST1), transcript variant 2, 0.0006 mRNA 8118324 Complement component 2 (C2), transcript variant 1, mRNA 0.025 8118345 Complement factor B (CFB), mRNA 0.007 8118556 Major histocompatibility complex, class II, DQ alpha 1 (HLA- 0.042 DQA1), mRNA 8118594 Major histocompatibility complex, class II, DP beta 1 (HLA- 0.003 DPB1), mRNA 8122265 Tumor necrosis factor, alpha-induced protein 3 (TNFAIP3), 0.002 mRNA 8124650 Ubiquitin D (UBD), mRNA 0.012 8129573 Monooxygenase, DBH-like 1 (MOXD1), transcript variant 2, 0.01 mRNA 8134420 Tachykinin, precursor 1 (TAC1), transcript variant beta, 0.015 mRNA 8135069 Serpin peptidase inhibitor, clade E (nexin, plasminogen 0.007 activator inhibitor type 1), member 1 (SERPINE1), transcript variant 1, mRNA 8138381 Anterior gradient homolog 2 (Xenopus laevis) (AGR2), mRNA 0.028 8139207 Inhibin, beta A (INHBA), mRNA 0.002 8140556 Hepatocyte growth factor (hepapoietin A; scatter factor) 0.002 (HGF), transcript variant 1, mRNA 8151101 V-myb myeloblastosis viral oncogene homolog (avian)-like 1 0.001 (MYBL1), transcript variant 1, mRNA 8157487 Pregnancy-associated plasma protein A, pappalysin 1 0.002 (PAPPA), mRNA 8161444 ncrna:misc_RNA 0.049 chromosome:GRCh37:20:29543691:29543802:-1 gene:ENSG00000200325 8165011 Ficolin (collagen/fibrinogen domain containing) 1 (FCN1), 0.049 mRNA 8166065 Toll-like receptor 8 (TLR8), mRNA 0.002 8167560 G antigen 12J (GAGE12J), mRNA 0.025 8167971 MicroRNA 223 (MIR223), microRNA 0.0005 8174051 Bruton agammaglobulinemia tyrosine kinase (BTK), mRNA 0.007 8177988 Leukocyte specific transcript 1 (LST1), transcript variant 2, 0.0006 mRNA 8178095 Complement component 2 (C2), transcript variant 1, mRNA 0.023 8178115 Complement factor B (CFB), mRNA 0.006 8178220 Major histocompatibility complex, class II, DP beta 1 (HLA- 0.002 DPB1), mRNA 8178295 Ubiquitin D (UBD), mRNA 0.01 8179268 Leukocyte specific transcript 1 (LST1), transcript variant 2, 0.0006 mRNA 8179331 Complement component 2 (C2), transcript variant 1, mRNA 0.023 8179519 Major histocompatibility complex, class II, DP beta 1 (HLA- 0.003 DPB1), mRNA Table S1b Transcript cluster ID Gene name Adjusted p value 7918657 Protein tyrosine phosphatase, non-receptor type 22 (lymphoid) 0.003 (PTPN22), transcript variant 1, mRNA 7918794 Adenosine monophosphate deaminase 1 (AMPD1), transcript 0.009 variant 1, mRNA. 7920333 ncrna:misc_RNA 0.003 chromosome:GRCh37:1:153698728:153698829:-1 gene:ENSG00000199565 7921625 SLAM family member 6 (SLAMF6), transcript variant 1, 0.012 mRNA 7940287 Membrane-spanning 4-domains, subfamily A, member 1 0.012 (MS4A1), transcript variant 1, mRNA 7940287 Membrane-spanning 4-domains, subfamily A, member 1 0.001 (MS4A1), transcript variant 1, mRNA 7944179 CD3e molecule, epsilon (CD3-TCR complex) (CD3E), mRNA 0.003 7944185 CD3g molecule, gamma (CD3-TCR complex) (CD3G), mRNA 0.011 7952056 CD3d molecule, delta (CD3-TCR complex) (CD3D), transcript 0.001 variant 1, mRNA 7956046 Diacylglycerol kinase, alpha 80kDa (DGKA), transcript variant 0.00005 1, mRNA 7957962 Spi-C transcription factor (Spi-1/PU.1 related) (SPIC), mRNA 0.005 7961151 Killer cell lectin-like receptor subfamily K, member 1 (KLRK1), 0.005 mRNA 7969050 Cysteinyl leukotriene receptor 2 (CYSLTR2), mRNA 0.003 7981601 mRNA; cDNA DKFZp686C02218 (from clone 0.001 DKFZp686C02218); complete cds 7981718 Immunoglobulin heavy constant mu, mRNA (cDNA clone 0.01 IMAGE:4309253) 7981726 cdna:pseudogene 0.0003 chromosome:GRCh37:14:106974509:106974954:-1 gene:ENSG00000229092 7981732 13 kDa protein gene:ENSG00000224373 0.011 7986637 cdna:Genscan chromosome:GRCh37:15:22448372:22448819:-1 0.001 7986639 cdna:known chromosome:GRCh37:15:22472918:22473353:-1 0.018 gene:ENSG00000189039 8014891 IKAROS family zinc finger 3 (Aiolos) (IKZF3), transcript 0.004 variant 1, mRNA 8016980 MicroRNA 142 (MIR142), microRNA 0.001 8029136 CD79a molecule, immunoglobulin-associated alpha (CD79A), 0.022 transcript variant 1, mRNA 8042986 Regenerating islet-derived 1 alpha (REG1A), mRNA 0.031 8043360 Immunoglobulin kappa locus, mRNA (cDNA clone MGC:22645 0.005 IMAGE:4700961), complete cds 8043436 Immunoglobulin kappa constant, mRNA (cDNA clone 0.0008 IMAGE:6282376) 8043441 cdna:pseudogene chromosome:GRCh37:2:90007677:90008145:1 0.001 gene:ENSG00000224607 8043443 13 kDa protein gene:ENSG00000241294 0.0003 8043446 12 kDa protein gene:ENSG00000211611 0.043 8043449 Immunoglobulin kappa locus, mRNA (cDNA clone MGC:22645 0.01 IMAGE:4700961), complete cds 8043456 cdna:pseudogene chromosome:GRCh37:2:90091427:90092218:1 0.0005 gene:ENSG00000254220 8043465 Immunoglobulin kappa constant, mRNA (cDNA clone 0.009 IMAGE:4692138) 8043468 9F11 monoclonal IgM antibody light chain mRNA, complete cds 0.002 8043470 Human Ig germline kappa-chain gene Vk3 region, 13k11 and 0.026 13k12, complete cds 8043476 Similar to pre-B lymphocyte gene 1 gene:ENSG00000241755 0.008 8053690 Immunoglobulin kappa locus, mRNA (cDNA clone MGC:40426 0.005 IMAGE:5178085), complete cds 8053715 cdna:pseudogene chromosome:GRCh37:2:90091427:90092218:1
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    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,
  • Review Article Complement System and Age-Related Macular Degeneration: Implications of Gene-Environment Interaction for Preventive and Personalized Medicine

    Review Article Complement System and Age-Related Macular Degeneration: Implications of Gene-Environment Interaction for Preventive and Personalized Medicine

    Hindawi BioMed Research International Volume 2018, Article ID 7532507, 13 pages https://doi.org/10.1155/2018/7532507 Review Article Complement System and Age-Related Macular Degeneration: Implications of Gene-Environment Interaction for Preventive and Personalized Medicine Andrea Maugeri ,1 Martina Barchitta ,1 Maria Grazia Mazzone,2 Francesco Giuliano,2 and Antonella Agodi 1 1 Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Via S. Sofa 87, 95123 Catania, Italy 2SIFI SpA, Research and Development Department, Via Ercole Patti 36, 95025 Catania, Italy Correspondence should be addressed to Antonella Agodi; [email protected] Received 18 May 2018; Accepted 18 July 2018; Published 26 August 2018 Academic Editor: Sajib Chakraborty Copyright © 2018 Andrea Maugeri et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Age-related macular degeneration (AMD) is the most common cause of visual loss in developed countries, with a signifcant economic and social burden on public health. Although genome-wide and gene-candidate studies have been enabled to identify genetic variants in the complement system associated with AMD pathogenesis, the efect of gene-environment interaction is still under debate. In this review we provide an overview of the role of complement system and its genetic variants in AMD, summarizing the consequences of the interaction between genetic and environmental risk factors on AMD onset, progression, and therapeutic response. Finally, we discuss the perspectives of current evidence in the feld of genomics driven personalized medicine and public health.