Curr Diab Rep (2015) 15:97 DOI 10.1007/s11892-015-0655-9
PATHOGENESIS OF TYPE 1 DIABETES (A PUGLIESE, SECTION EDITOR)
Genes Affecting β-Cell Function in Type 1 Diabetes Tina Fløyel 1 & Simranjeet Kaur 1 & Flemming Pociot 1
# Springer Science+Business Media New York 2015
Abstract Type 1 diabetes (T1D) is a multifactorial disease resulting from an immune-mediated destruction of the insulin-producing pancreatic β cells. Several environmental and genetic risk factors predispose to the disease. Genomewide association studies (GWAS) have identified around 50 genetic regions that affect the risk of developing T1D, but the disease-causing variants and genes are still largely unknown. In this review, we discuss the current status of T1D susceptibility loci and candidate genes with focus on the β cell. At least 40 % of the genes in the T1D susceptibility loci are expressed in human islets and β cells, where they according to recent studies modulate the β-cell response to the immune system. As most of the risk variants map to noncoding regions of the genome, i.e., promoters, enhancers, intergenic regions, and noncoding genes, their possible involvement in T1D pathogenesis as gene regulators will also be addressed.
Keywords T1D . GWAS . Candidate genes . Pancreatic islets . Noncoding RNA . CTSH
This article is part of the Topical Collection on Pathogenesis of Type 1 Diabetes * Flemming Pociot
[email protected] Tina Fløyel
[email protected] Simranjeet Kaur
[email protected] 1
Copenhagen Diabetes Research Center, Department of Pediatrics, Herlev and Gentofte Hospital, Herlev Ringvej 75, DK-2730 Herlev, Denmark
Introduction In type 1 diabetes (T1D), the pancreatic β cells in the islets of Langerhans are selectively destroyed by the immune system resulting in absolute insulin deficiency. It is a multifactorial disease where environmental risk factors may trigger an immune-mediated process leading to β-cell destruction and overt T1D in genetically susceptible individuals. Approximately 70 % of children with recent-onset T1D display a mild inflammatory infiltration of the pancreatic islets, referred to as insulitis, which is often absent in adults [1, 2]. The invading immune cells contribute to β-cell dysfunction and death through contact mediators, such as Fas-FasL, and release of pro-inflammatory cytokines, including interleukin (IL)-1β, interferon (IFN)-γ, and tumor necrosis factor (TNF)-α [3, 4]. Accumulating data indicate that many patients with T1D have a substantial residual β-cell mass at clinical onset— much higher than the 10–20 % as previously assumed. This is evident from studies of patients with long-standing T1D, who even after disease durations of more than 50 years still demonstrate a residual endogenous insulin production [5, 6], and in some patients with long-standing T1D insulin-positive cells are present even without detectable C-peptide levels [2, 7]. Furthermore, a recent study showed that islets isolated from pancreatic biopsies of live patients at T1D onset in some cases can recover their insulin secretion after in vitro culture in a nondiabetogenic environment [8•]. This indicates that the loss of β-cell function in T1D is not only due to a decreased number of β cells but also a result of β-cell dysfunction, which lends hope to the possibility of preserving or enhancing the residual β-cell function in T1D. The variations in residual β-cell function among patients with T1D may also reflect individual differences in β-cell mass at birth and variability in the tempo of β-cell destruction resulting in different rates of disease progression [9, 10•]; two factors influenced by genetic
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predisposition. Thus, identifying the genes and mechanisms that are involved in the loss of β-cell function is crucial for the development of therapeutic strategies aimed at improving βcell function in patients with recent-onset T1D and avoiding β-cell dysfunction and destruction in at-risk individuals.
coding genes, noncoding RNAs, pseudogenes, etc.) almost 40 % of the genes were expressed in human islets [24] (Table 1). Thus, accumulating evidence supports the concept that genetic susceptibility to T1D affects both the immune system and the β-cell function.
Candidate Genes for T1D Are Expressed in Pancreatic β Cells
Candidate Genes Affecting β-Cell Functions
In recent years, genome-wide association studies (GWAS) have added significantly to the number of established loci known to contribute to T1D susceptibility. GWAS metaanalyses have identified around 50 T1D susceptibility loci [11–13, 14••] (Table 1). Together, these loci explain around 80 % of the heritability of T1D [15–17], which is considerably higher than for any other complex disease [18]. Many of the T1D susceptibility loci harbor several genes (Table 1), and for most of the loci the causal variant(s) and gene(s) are still unknown. Noteworthy, the recent ImmunoChip study provided fine-mapping of the T1D loci, which for many of the loci led to identification of novel more strongly associated risk variants than the ones previously identified [14]. Genetic variation in specific genes may cause differential expression patterns—often referred to as expression quantitative traits (eQTLs). Gene expression may also be regulated indirectly by genetic variations in regulatory elements or by epigenetics changes. Genetic variation can also result in amino acid substitution, thereby having a structural and/or functional effect on the encoded protein. Because T1D is an immune-mediated disease, it has been speculated that the T1D risk variants affect genes with functions in the immune system and thereby modulate immune responses. In support of this, several susceptibility loci are shared between different autoimmune diseases and a number of T1D candidate genes have documented functions in the immune system, e.g., HLA, INS, CTLA4, PTPN22, SH2B3, BACH2, and IL2RA [19, 20•, 21]. However, recent studies have demonstrated that many of the genes in the susceptibility loci are also expressed in the pancreatic islets and β cells, where they are likely to have a major impact on the triggering and development of T1D by modulating the function and survival of the β cells when exposed to the immune system [22••, 23••]. Using RNA sequencing, Eizirik and colleagues identified transcripts expressed in human islets under control conditions and following exposure to pro-inflammatory cytokines [23••]. They examined the expression of the pin-pointed candidate genes in each of the known susceptibility loci and demonstrated that 60 % of the genes were expressed in human islets, and several of these were differentially regulated in response to cytokines [23••]. Furthermore, when all the genes in the susceptibility loci were taken into account (protein-
To identify the causal variants and genes important for β-cell function, a combination of genetic fine-mapping, genotypephenotype correlation studies, and functional investigations in experimental models, e.g., knockdown and overexpression studies, is necessary. Furthermore, studies on knock-in and knock-out mice will aid in the understanding of how the candidate genes affect the disease pathogenesis and contribute to the risk of T1D. This field is in its early stages, but recent studies [21, 22••, 23••, 24, 25, 26•, 27, 28••, 29, 30••, 31, 32•, 33] have identified candidate genes that affect β-cell function or survival in T1D settings (Fig. 1a). Molecular mechanistic studies have also demonstrated that several T1D candidate genes undergo alternative splicing following cytokine exposure [23••, 28••] suggesting that different transcripts may have different functions under such conditions. INS Although INS is the only Bβ-cell-specific^ susceptibility gene, its major function in T1D pathogenesis is ascribed to its role as an autoantigen [34, 35]. The genetic INS susceptibility to T1D maps to a polymorphic repeat sequence (VNTR), where VNTR class I alleles predispose to and class III alleles significantly protect from T1D [36]. Today, more than 50 INS mutations causing monogenic diabetes have been identified [37]. Diabetogenic INS mutations have a broad spectrum of clinical presentations ranging from severe insulin deficient diabetes with neonatal onset to late-onset mild diabetes, indicating that the different mutant alleles utilize distinct mechanisms to cause diabetes. Though intriguingly, there is currently no evidence that mutations in the INS gene will confer susceptibility to T1D through β-cell dysfunction. IFIH1 Genetic variants in IFIH1 have been associated with protection from T1D through reduced expression of the encoded protein MDA5, a cytoplasmic sensor of viral double stranded RNA (dsRNA) that activates a cascade of antiviral responses [38, 39]. IFIH1 is expressed in human islets and β cells and upregulated, e.g., by enterovirus infection or exposure to synthetic dsRNA (polyinosinic:polycytidylic acid, poly(I:C)) [25, 40]. IFIH1 knockdown (KD) in INS-1E cells and primary rat β cells diminishes poly(I:C)-induced cytokine and chemokine
Curr Diab Rep (2015) 15:97 Table 1
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Islet-expressed genes in the T1D susceptibility loci
Locus
Pin-pointed candidate gene
No. of genes (coding/noncoding)
Genes expressed in human islets
1p13.2
PTPN22
9/7
1q32.1 1q32.1 2p23.3 2q13 2q24.2 2q33.2 3p21.31 4p15.2
None IL10 None None IFIH1 CTLA4 CCR5 None
5/2 4/1 6/8 6/16 5/3 2/4 11/6 0/1
8 (AP4B1, BCL2L15c, DCLRE1B, HIPK1, MAGI3, OLFML3c, PHTF1, RSBN1) 3 (C1orf106, CAMSAP2, DDX59) 1 (MAPKAPK2) 6 (ADCY3c, CENPO, DNAJC27, DNMT3A, EFR3B, POMC) 3 (LIMS3, PGPD6, LINC00116a) 4 (FAP, GCA, GCG, IFIH1) 0 2 (FYCO1, LTF) 0
4q27 4q32.3 5p13.2 6p21.32 6q15 6q22.32 6q27 7p12.1 7p12.2 7p15.2 9p24.2 10p15.1 10p15.1 10q23.31 11p15.5 12p13.31 12q13.2
IL2-IL21 None IL7R HLA BACH2 CENPW/Corf173 None COBL IKZF1 SKAP2 GLIS3 PRKCQ IL2RA RNLS/C10orf59 INS CD69 ERBB3, IKZF4
4/3 0/1 5/4 157/169 1/2 1/8 0/0 1/4 4/2 10/16 1/1 1/0 3/3 1/1 4/4 4/17 27/15
12q24.12
SH2B3
17/30
13q22.2 13q32.3 14q24.1 14q32.2 15q14 15q25.1 16p11.2
LMO7 GPR183 ZFP36L1, C14orf181 None RASGRP1 CTSH IL27
1/0 4/5 1/6 0/5 2/2 5/6 24/30
16p13.13 16q23.1 17q12
CLEC16A, DEXI CTRB1, BCAR1 ORMDL3, IKZF3, GSDMB
10/15 7/10 22/15
17q21.2 18p11.21 18q22.2
SMARCE1, CCR7 PTPN2 CD226
5/5 1/6 2/0
1 (KIAA1109) 0 1 (IL7R) 135b 1 (BACH2) 1 (CENPWc) 0 2 (COBL, SNORA4a) 3 (DDC, FIGNL1, GRB10) 1 (SKAP2) 1 (GLIS3) 1 (PRKCQc) 1 (RBM17) 1 (RNLS) 5 (INS, IGF2, INS-IGF2, AC132217.4a, IGF2-ASa) 1 (CLEC2D) 26 (ANKRD52, CDK2, CNPY2, COQ10Ac, CS, ERBB3, ESYT1c, IKZF4, IL23A, MYL6, MYL6Bc, PA2G4, PAN2, PMEL, RAB5B, RNF41, RP11-603J24.9, RP11-977G19.10, RP11-977G19.5a, RPL41, RPS26, SLC39A5, SMARCC2, STAT2, SUOX, ZC3H10) 15 (ACAD10, ALDH2, ATXN2, BRAP, ERP29, FAM109A, MAPKAPK5, NAA25, PTPN11, RP11-162P23.2, RPH3A, RPL6, SH2B3, TMEM116, TRAFD1) 1 (LMO7) 3 (GPR183, TM9SF2, UBAC2) 1 (ZFP36L1) 2 (MEG3a, RP11-123M6.2a) 1 (RASGRP1c) 4 (ADAMTS7, CTSH, MORF4L1, RASGRF1) 16 (APOBR, ATXN2L, CCDC101, CLN3, EIF3C, EIF3CL, LAT, NFATC2IP, NUPR1, RABEP2, SBK1, SH2B1, SPNS1, SULT1A1, SULT1A2, TUFM) 3 (CIITA, CLEC16A, DEXI) 7 (BCAR1, CFDP1, CHST6, CTRB1, CTRB2, RP11-331F4.4a, TMEM170A) 16 (CDK12, CSF3, ERBB2c, FBXL20, GRB7, GSDMB, MED1, MED24, MIEN1, ORMDL3, PGAP3c, PPP1R1Bc, PSMD3, SNORD124a, STARD3, THRA) 3 (CCR7, KRT222, SMARCE1) 1 (PTPN2) 1 (DOK6)
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Table 1 (continued) Locus
Pin-pointed candidate gene
No. of genes (coding/noncoding)
Genes expressed in human islets
19p13.2
TYK2
14/5
19q13.32 19q13.33
PRKD2 FUT2
6/8 14/2
20p13 21q22.3 22q12.2 22q12.3 Xq28
SIRPG UBASH3A HORMAD2 C1QTNF6, RAC2 GAB3
4/8 2/1 9/15 4/2 21/21
13 (CDC37, FDX1L, ICAM1, ICAM3, ICAM4, ICAM5, KEAP1, MIR1181a, PDE4A, RAVER1c, S1PR5, TYK2, ZGLP1) 4 (FKRP, PRKD2, SLC1A5, STRN4) 10 (CA11c, DBP, FAM83E, FUT1c, FUT2, NTN5, RASIP1, RPL18, SPHK2, SULT2B1) 1 (SIRPB1) 1 (TMPRSS3) 8 (ASCC2, CABP7c, LIFc, MTMR3, NF2, OSM, UQCR10, ZMAT5) 3 (C1QTNF6, RAC2, SSTR3) 15 (ATP6AP1, DKC1, F8A1, FAM3A, FAM50A, FUNDC2, G6PD, GDI1, IKBKG, LAGE3, MPP1, PLXNA3, SLC10A3, SNORA56a, UBL4A)
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