Table 2.
Summary of candidate genes linked to GI diseases.
| GI disease | Candidate genes | Potential mechanism of action | References |
|---|---|---|---|
| TB | ASAP1 | Cytoskeleton remodeling | (Curtis et al., 2015) |
| CD209, TLR1,2,4,8,10 | Pathogen recognition | (Bulat-Kardum et al., 2015; Salie et al., 2015; Yi L. et al., 2015; Zhao et al., 2015; Jafari et al., 2016) | |
| IRGM | Autophagy | (Yuan et al., 2016) | |
| AGMO, FOXP1 | Macrophage function | (Grant et al., 2016) | |
| TOX, DUSP14, CCL2, CCL5, CCL13 | Monocyte and T cell function | (Thuong et al., 2008; Grant et al., 2013; Hijikata et al., 2016; Kouhpayeh et al., 2016; Nonghanphithak et al., 2016) | |
| SP110, IFNA1, IFITM3, TYK2 | Interferon signaling | (Bhanothu et al., 2015; Naderi et al., 2016; Zhang et al., 2017; Boisson-Dupuis et al., 2018) | |
| IL17A, IL17F, IL27, IL8 | Immunoregulation | (Braun et al., 2015; Du et al., 2015; Hu et al., 2020; Li et al., 2020) | |
| CTSZ | Protein localization and activity | (Adams et al., 2011) | |
| HLA-DQA1, HLA-DRB1, MR1 | Guiding antigen specific T cell immune response | (Sveinbjornsson et al., 2016; Seshadri et al., 2017) | |
| MAFB | Regulation of lineage-specific hematopoiesis | (Mahasirimongkol et al., 2012) | |
| TNF, NOTCH4 | Apoptosis, differentiation and proliferation | (Yi Y.X. et al., 2015; Zhang et al., 2020) | |
| MC3R | Regulation of energy homeostasis | (Adams et al., 2011) | |
| UBE3A, | Ubiquitin protein degradation | (Cervino et al., 2002) | |
| NCF2, CYBA | Oxidation | (Liu et al., 2016; Jiao et al., 2020) | |
| CYP7A1, VDR, VDBP, ITPA | Metabolism | (Qrafli et al., 2014; Lee et al., 2016; Nakauchi et al., 2016) | |
| HSPEP1, UBLCP1, SIGLEC15 | Unknown | (Mahasirimongkol et al., 2012; Sobota et al., 2016; Bhattacharyya et al., 2019) | |
| leprosy | CUBN, NRAMP1/SLC11A1, VDR | Vitamin and iron metabolism | (Hatta et al., 2010; Grant et al., 2014; Neela et al., 2015) |
| LACC1/C13orf31, SOD2, | Cellular ROS production | (Ramos et al., 2016; Lahiri et al., 2017) | |
| NOD2, TLR1, NLRP1 | Pathogen recognition | (Schuring et al., 2009; Zhang et al., 2009; Berrington et al., 2010; Marques Cde et al., 2013; Pontillo et al., 2013) | |
| HLA-C, HLA-DQA1, HLA-DRB1, HLA-DQB1 | Guiding antigen specific T cell immune response | (Geluk and Ottenhoff, 2006; Alter et al., 2011; Jarduli et al., 2013; Zhang et al., 2019) | |
| LTA, TNF, TNFSF15 | Apoptosis and inflammation | (Zhang et al., 2009; Cardoso et al., 2011) | |
| IL23R, GATA3, IL10, RIPK2 | Immunoregulation | (Zhang et al., 2009; Zhang et al., 2011; Medeiros et al., 2016) | |
| LRRK2/RIPK7, RAB32, PARK2/PRKN, MRC1 | Autophagy | (Mira et al., 2004; Zhang et al., 2009; Alter et al., 2010; Zhang et al., 2011) | |
| NEBL | Focal adhesion | (Grant et al., 2014) | |
| PACRG | Protein degradation | (Mira et al., 2004) | |
| HIF1A | Apoptosis and metabolism | (Wang et al., 2018) | |
| TYK2 | Interferon signaling | (Liu et al., 2017) | |
| CCDC122 | Unknown | (Zhang et al., 2009) | |
| CD | ATG16L1, IRGM, LRRK2, MUC19, PTPN2, PTPN22 | Capture bacteria, autophagy | (Barrett et al., 2008; Cadwell et al., 2010; Tong et al., 2010; Spalinger et al., 2018) |
| Annexin A11 | Apoptosis, proliferation | (Reischl et al., 2020) | |
| LACC1/C13orf31, DUOX2, NOX2/CYBB, CYBA, NCF1, NCF2, NCF4 | Oxidation | (Cleynen et al., 2013; Denson et al., 2018) | |
| HLA-A2,HLA-DR1, HLA-DQw5 | Guiding antigen specific T cell immune response | (Orchard et al., 2000; Orchard et al., 2002) | |
| IL-23R, IL10, IL6, JAK2, STAT3, CCR6, ICOSLG, PUS10, SLC22A23 | Immunoregulation and iron metabolism | (Yamamoto et al., 2000; Petit-Bertron et al., 2005; Van Limbergen et al., 2009; Festen et al., 2011; Cleynen et al., 2013; Xu et al., 2015) | |
| NOD2, NLRP3, NLRP6, CARD9, TLR1,2,4,6, | Pathogen recognition | (Ogura et al., 2001; Van Limbergen et al., 2009; Villani et al., 2009; Kordjazy et al., 2018) | |
| TNFSF15, TAB2, PRDM1 | Apoptosis, inflammation and immunoregulation | (Barrett et al., 2008; Cleynen et al., 2013) | |
| C10orf6 | Unknown | (Franke et al., 2008) | |
| Sarcoidosis | Annexin A11, XAF1 | Apoptosis and proliferation | (Li et al., 2010; Levin et al., 2014) |
| BTNL2, NOTCH4, CCDC88B, ZNF592 | T cell response | (Valentonyte et al., 2005; Adrianto et al., 2012; Fischer et al., 2012; Lareau et al., 2015) | |
| COX2, NOX2/CYBB | Oxidation | (Christophi et al., 2014; Werner et al., 2017) | |
| HLA-DRB1, DPB1, DQB1, TAP2 | Guiding antigen specific T cell immune response | (Design of a Case Control Etiologic Study of Sarcoidosis (ACCESS). ACCESS Research Group, 1999; Hulpke et al., 2012; Malkova et al., 2020) | |
| IL23R, IL12B | Immunoregulation | (Kim et al., 2011; Fischer et al., 2015) | |
| NOD2, TLR2, | Pathogen recognition | (Kanazawa et al., 2005; Chen et al., 2010) | |
| SH2B3 | Negative regulator of TNF signaling | (Fischer et al., 2015) | |
| RAB23 | Autophagy | (Davoudi et al., 2018) | |
| TNF, LTA | Apoptosis and inflammation | (Mcdougal et al., 2009; Song et al., 2014) | |
| MAGI1 | Epithelial and endothelial cell-cell contacts | (Garman et al., 2020) | |
| BU | ATG16L1, PARK2/PRKN | Autophagy | (Capela et al., 2016) |
| IFNG | Interferon signaling | (Bibert et al., 2017) | |
| NOS2 | Immunoregulation | (Bibert et al., 2017) | |
| NOD2 | Pathogen recognition | (Capela et al., 2016) | |
| NRAMP1/SLC11A1 | Iron metabolism | (Stienstra et al., 2006) | |
| CGD | NOX2/CYBB, CYBA, NCF1, NCF2, NCF4 | Oxidation | (Idh et al., 2017) |
| OFG | HLA-A3, B7, DR2, HLA-B16, HLA-CW3 | Guiding antigen specific T cell immune response | (Gibson and Wray, 2000) |
| GPA | SERPINA1 | Protein activity | (Lyons et al., 2012) |
| HLA-DOA, DP, DPA1, DPB1, DPB2, DQ, DRB1 | Guiding antigen specific T cell immune response | (Cao et al., 2011; Lyons et al., 2012; Xie et al., 2013) | |
| TLR9 | Pathogen recognition | (Husmann et al., 2014) | |
| PTPN22, CTLA4, FCGR3B, IL2RA MOSPD2 | Immune response and T cell function | (Jagiello et al., 2005; Willcocks et al., 2008; Carr et al., 2009; Lyons et al., 2012) | |
| DCTD, GHSR, HSD17B8, LEPR, RING1, RXRB | Metabolism | (Wieczorek et al., 2010; Xie et al., 2013) | |
| COL11A2 | Extracellular matrix | (Lyons et al., 2012) | |
| COBL, ARHGAP18, SEMA6A | Cell shape and cytoskeleton | (Lyons et al., 2012; Xie et al., 2013) | |
| CD226, PRTN3 | Cellular adhesion, cell-cell contacts | (Wieczorek et al., 2009; Lyons et al., 2012) | |
| IRF5 | Interferon signaling | (Wieczorek et al., 2010) | |
| CCDC86, WSCD1 | Unknown | (Xie et al., 2013) |
TB, tuberculosis; CD, Crohn’s disease; BU, Buruli ulcer; CGD, chronic granulomatous disease; GPA, Wegener’s granulomatosis; OFG, orofacial granulomatosis; ROS, reactive oxygen species.