A MEDLINE literature search for pharmacogenetic studies was conducted independently by the two authors from database inception up to 12 August 2020, by using a predefined search algorithm (see electronic supplementary material [ESM] Methods: Search strategy). We did not apply any restrictions or filters. Out of the 2663 identified articles, 37 duplicates were removed and titles and abstracts of the remaining 2626 publications were scanned. To identify further relevant articles, we also screened the reference lists of included articles. Finally, 12 published studies on DPP-4i, six on GLP-1 RA and four on SGLT2i were included. The characteristics and main results of these pharmacogenetic studies are summarised in Tables 1, 2 and 3.
In the following text, we, describe which genes have been associated with therapeutic responses to each of the three newest glucose-lowering drugs. Then, after summarising the main findings we highlight important limitations of the currently available studies.
The GLP1R gene encodes the receptor for glucagon-like peptide-1 (GLP-1), a peptide hormone expressed in pancreatic beta cells . Activation of the GLP-1 receptor facilitates a glucose-stimulated insulin secretion . It has been hypothesised that genetic alterations of the GLP-1 receptor may change the therapeutic response to DPP-4i. In fact, a variant in the GLP1R gene (rs6923761; p.Gly168Ser) was found to be associated with a smaller reduction in HbA1c (by 3.0 mmol/mol [0.27%] per A allele) in individuals with type 2 diabetes treated with sitagliptin, vildagliptin or linagliptin for 6 months . This study confirmed an earlier report that this particular gene variant was related to a smaller HbA1c reduction during 6 months of gliptin treatment . Another variant in the GLP1R gene (rs3765467; p.Arg131Gln) was reported to be linked to an insulinotropic effect . People with type 2 diabetes with the A allele (GA/AA vs GG) responded better to therapy with DPP-4i (>10% relative HbA1c reduction) and showed a greater HbA1c decrease after 24 weeks of therapy (1.3 ± 1.1 vs 0.9 ± 1.2%; p = 0.02) .
Potassium channel gene family
Potassium voltage-gated KQT-like (KCNQ1) channels play a role in the intestinal secretion of GLP-1 and glucose-dependent insulinotropic polypeptide (GIP), and polymorphisms in the gene coding for these channels have been linked to type 2 diabetes through a role in insulin release . A variant in KCNQ1 (rs163184) was found to be associated with a smaller reduction in HbA1c after 6 months of newly onset DPP-4i therapy in type 2 diabetes patients (0.3% reduction in response per each G allele) . This study indicated a clinically relevant pharmacogenetic effect, although persistence of the effect was not assessed due to lack of a longer follow-up of HbA1c values.
The KCNJ11 gene regulates one of the pancreatic beta cell ATP-sensitive potassium channels, that play a role in insulin secretion . After sitagliptin, vildagliptin or linagliptin therapy (≥3 months), individuals with type 2 diabetes and who carried the KCNJ11 rs2285676 CC alleles had a twofold higher odds of responding to DPP-4i, defined as HbA1c ≤53.0 mmol/mol (7.0%), than other individuals .
A SNP (rs7202877) that is located near genes that encode chymotrypsinogen B1 and B2 (CTRB1/CTRB2), with no known functional effect, is related to GLP-1-stimulated insulin secretion . The rs7202877 GG and GT genotypes were associated with a 5.5 mmol/mol (0.5%) smaller reduction in HbA1c compared with the TT genotype after 3 months of gliptin therapy . The genetic variant was shown to be associated with GLP-1-induced insulin secretion. CTRB1/2 encodes chymotrypsin, and the G allele was also associated with increased chymotrypsin levels in the pancreas and faeces . Thus, chymotrypsin may be important for the response to DPP-4i treatment.
The serine/threonine protein kinase D1 enzyme, encoded by PRKD1, plays a role in various processes such as the regulation of cell proliferation, differentiation and apoptosis, immune reactions, cardiac contraction, angiogenesis and cancer development. Furthermore, the enzyme has been shown to contribute to insulin secretion . A genome-wide association study (GWAS) found that in people with type 2 diabetes treated with sitagliptin, saxagliptin, vildagliptin or linagliptin, a polymorphism in PRKD1 (rs57803087; intron variant) was associated with a greater response to the DPP-4i . In a replication cohort, rs57803087 remained significantly associated with a better DPP-4i response after controlling for BMI . However, the results of this small GWAS (n = 171) need to be replicated in a larger sample and the lacking information on the association of specific risk alleles should be provided.
GWAS revealed relationships between several SNPs in CDKAL1, encoding cyclin-dependent kinase 5 regulatory subunit associated protein 1-like 1 (CDKAL1), and type 2 diabetes risk . Cyclin-dependent kinase 5, which shares similarities with CDKAL1, is a serine/threonine protein kinase, which contributes to the glucose-dependent regulation of insulin secretion . In individuals with type 2 diabetes treated with DPP-4i, the HbA1c reduction after 6 months varied according to two CDKAL1 SNPs (rs7754840, G>C, intron variant; rs756992, A>G) . The HbA1c decrease was greater in people who carried at least one variant allele in comparison with two copies of the common allele (for rs7754840, GG 4.4 mmol/mol [0.4%], CG 5.5 mmol/mol [0.5%] and CC 8.7 mmol/mol [0.8%], p = 0.02; for rs7756992, AA 4.4 mmol/mol [0.4%], AG 5.5 mmol/mol [0.5%] and GG 8.7 mmol/mol [0.8%], p = 0.01) . The differences persisted after adjusting for age, sex, BMI, diabetes duration, baseline HbA1c and the number of concomitant glucose-lowering drugs in a linear regression analysis . Thus, people with CDKAL1 type 2 diabetes risk variants showed a better glycaemic response to DPP-4i.
IL6 promoter region
IL-6, derived from muscle cells during exercise, was shown to enhance intestinal GLP-1 secretion in animal models . It has been hypothesised that genetic variants that upregulate IL6 transcription might also increase GLP-1 synthesis and secretion in humans . In people with type 2 diabetes, DPP-4i treatment response (3 months) was defined as a ≥2.2 mmol/mol (0.2%) HbA1c decrease (about 70% responders) . Two IL6 SNPs were then analysed (rs1800796, intron variant; rs2097677) and multivariate analysis showed that the adjusted OR for DPP-4i non-response of the two SNPs combined (rs1800796 G* and rs2097677 A* vs CC-GG) was 0.45 (p = 0.07). After stratifying the population into low (n = 149) and moderate/high (n = 167) levels of physical activity, the OR for each group was 1.58 (p = 0.62) and 0.15 (p < 0.01), respectively . These data suggest that IL6 variants might contribute to an improved DPP-4i response in people who are more physically active.
Variation in the TCF7L2 gene has been associated with an increased risk of type 2 diabetes . There are several hypotheses as to how the TCF7L2 gene product, transcription factor 7-like 2, exerts its effects on the gut, liver or pancreatic beta cells . TCF7L2 variant alleles impact GLP-1-induced insulin secretion, suggesting a functional defect in pancreatic GLP-1 signalling . After genotyping TCF7L2 variants in participants with type 2 diabetes undergoing phase 3 trials with 24 weeks of treatment with linagliptin, a smaller decrease in HbA1c was observed in individuals with the rs7903146 TT genotype (6.2 mmol/mol [0.57%]) compared with other genotypes (9.0 mmol/mol [0.82%] for CC; 8.4 mmol/mol [0.77%] for CT; p = 0.02 for TT vs CC genotypes) . Thus, the TCF7L2 SNP rs7903146 may be associated with lower response to incretins.
DPP-4i bind to the dipeptidyl peptidase-4 (DPP-4) enzyme to enhance GLP-1 activity . The efficacy of DPP-4i could be affected by DPP4 gene variants . This hypothesis was investigated in a small study comparing people with type 2 diabetes receiving treatment with sitagliptin (100 mg/day or 200 mg/day) with healthy control individuals . In regression analysis, DPP4 genotype rs2909451 (intron variant) TT was associated with increased short-term DPP-4 enzyme activity during sitagliptin treatment in the whole sample (standardised regression coefficient, 0.19 nmol ml−1 min−1; p = 0.04) .
Variants in the PNPLA3 gene, encoding patatin-like phospholipase 3 (PNPLA3), are related to increased plasma levels of hepatic NEFA and triacylglycerols [33, 34]. A genetic variant (rs738409) of PNPLA3 was associated with non-alcoholic fatty liver disease (NAFLD) and its histological severity in GWAS . In a small study of people with biopsy-proven NAFLD and type 2 diabetes treated with alogliptin (25 mg/day; median follow-up 33 months), participants with the rs738409 G allele showed a positive correlation between temporal changes in HbA1c and aminotransferase levels (CG/GG and alanine aminotransferase: r = 0.52; p = 0.001) . In addition, in participants who lost weight, those with CG and GG genotypes showed greater improvements in total cholesterol and triacylglycerols, and similar improvement in HbA1c . Thus, the effects of alogliptin (and possibly other DPP4i) on liver function in type 2 diabetes and NAFLD may differ by PNPLA3 genotypes.
SNPs around the exon region of the GLP1R gene were genotyped in a small sample of people with poorly controlled type 2 diabetes, who received exenatide for 3 days (5 μg twice daily) and were also treated with a continuous subcutaneous insulin infusion . The CT/TT genotypes of rs761386 (intron variant) were related to higher glucose levels at 120 min of a 75 g OGTT (p = 0.032). Insulin and C-peptide throughout the OGTT were not significantly different between the genotypes. Unfortunately, data on the long-term effects, in particular on HbA1c, are lacking.
Two further studies from Spain  and China  explored the relationship between GLP1R variants and weight loss in type 2 diabetes. The study from Spain included individuals with poorly controlled type 2 diabetes and who were overweight, who began liraglutide treatment up to 1.8 mg/day for 14 weeks . The GLP1R rs6923761 (non-coding) A allele (GA/AA vs GG) was associated with a 2.9 kg larger weight reduction after liraglutide treatment in multivariable analysis . The decreases in basal glucose levels, HOMA-IR and HbA1c were similar in both groups. In a hospital-based Chinese study including obese individuals with poorly controlled type 2 diabetes, the variant T allele of GLP1R rs10305420 (amino acid change: Pro to Leu) was associated with a smaller reduction in HbA1c (4.4 mmol/mol [0.4%]) and body weight (−1.3 kg) after 6 months of exenatide treatment . It is unclear whether these genetic associations would be of the same magnitude in people with type 2 diabetes who were of normal body weight.
The endocannabinoid system plays a role in appetite and body-weight regulation . The cannabinoid type 1 receptor, encoded by the CNR1 gene, is located in adipose tissue and in several brain areas . In obese people with type 2 diabetes stratified by CNR1 genotypes (GA and AA genotypes vs GG genotypes), glucose, HbA1c, insulin sensitivity, BMI, body weight, waist circumference and fat mass were measured before and after 14 weeks of liraglutide treatment . Among metabolic markers, insulin resistance was found to decrease in individuals carrying the variant CNR1 A allele. However, liraglutide therapy resulted in comparable improvements of anthropometric measures and glycaemic markers in all CNR1 genotypes .
In a small pharmacogenetic study, individuals with type 2 diabetes and the TCF7L2 rs7903146 CC genotype were matched with individuals with CT and TT genotypes and similar diabetes duration and BMI . Participants received a 500 kcal (2092 kJ) mixed-meal test and treatment with exenatide for 8 weeks . The rs7903146 (intron variant) T allele was associated with higher secretion of insulin, proinsulin and C-peptide in response to the mixed meal . After exenatide treatment, T allele carriers showed lower postprandial plasma insulin and C-peptide levels compared with non-carriers. The data suggest that use of GLP-1 RA could play a role in beta cell function in individuals with the rs7903146 CT and TT genotypes. However, no difference between genotype was observed for plasma glucose values during the meal tests after exenatide treatment; the same was true for HbA1c and body-weight reduction .
Sortilin related VPS10 domain containing receptor 1 (SORCS1) is expressed in the brain, heart, kidney and pancreatic islets, and in beta cell lines . SORCS1 belongs to the sortilin family of vacuolar protein sorting-10 domain-containing proteins and has been genetically linked to Alzheimer’s disease . SORCS1 haplotypes were associated with higher fasting insulin levels and insulin secretion in non-diabetic obese women but not in men or lean individuals . In persons with newly diagnosed type 2 diabetes treated with exenatide for 48 weeks, stratifying for SORCS1 rs1416406 genotypes, revealed differences in HbA1c, glucose values and beta cell function between the genotype groups (GG, GA, AA) following treatment . However, only the proinsulin/insulin ratio (PIR) showed a greater reduction in people with the GG genotype vs other genotypes and this difference persisted after adjusting for age, sex and BMI in regression analysis . The reduced PIR suggests that people with newly diagnosed type 2 diabetes and the rs1416406 GG genotype might benefit from exenatide treatment.
The sodium–glucose cotransporter 2 (SGLT2) protein, which contributes to renal glucose reabsorption, is encoded by the SLC5A2 gene . Several rare mutations of this gene result in familial renal glucosuria . Therefore, variants in the SLC5A2 pose a promising target for pharmacogenetic research. So far, only one study has investigated the association between SLC5A2 gene variants (intron variants) and the glycaemic effects of SGLT2i therapy . Between five common gene variants, no clinically relevant differences in response to empagliflozin treatment after 24 weeks were observed in type 2 diabetes . Moreover, these variants were not associated with diabetes-related metabolic traits in people at increased risk of type 2 diabetes .
PNPLA3 is expressed in liver and adipose tissue and mediates triacylglycerol hydrolysis . A PNPLA3 variant has been identified as a risk factor for steatohepatitis . A 12 week randomised clinical trial investigated the effects of a combination of dapagliflozin and n-3 carboxylic acids on the hepatic proton density fat fraction (PDFF) in people with type 2 diabetes and NAFLD . Baseline liver PDFF was lower in individuals with the PNPLA3 rs738409 (p.Ile148Met) CC genotype (median 17%) than in those with the CG and GG genotype (20%). In response to the combination therapy, the relative PDFF reduction was greater in individuals with the CG and GG genotypes (relative change, −25%) than in those with the CC genotype (−16%). The relative change in PDFF observed following dapagliflozin monotherapy differed from that seen with the combination therapy (CG and GG, +7%; CC, −22%) .
Canagliflozin is mainly metabolised by uridine diphosphate-glucuronosyltransferase (UGT) 1A9 and UGT2B4 into inactive glucuronides . In vitro studies suggested that UGT1A9 gene variants result in an alteration of UGT enzymatic activity . Therefore, variants in the UGT genes could potentially influence the pharmacokinetics of canagliflozin or other SGLT2i [47, 48]. A pharmacokinetic model of canagliflozin based on data from 14 clinical trials showed that carriers of the rare UGT1A9*3 allele showed 26% higher median dose-normalised AUC values for canagliflozin, indicating a better drug availability . A smaller study based on phase 1 clinical trials confirmed the role of UGT genes in canagliflozin metabolism, with higher plasma canagliflozin levels being observed in carriers of the UGT2B4*2 genotype compared with non-carriers . However, because of the small number of individuals with this gene variant in those with diabetes these findings may not be clinically relevant.
Summary of studies, and limitations
The small number of studies, thus far, that report associations between genetic variants and response to novel glucose-lowering drug treatment have focused on glycaemic response (e.g. HbA1c) and changes in body weight. With respect to DPP-4i and GLP-1 RA, most studies of gene variants have focused on the drug’s metabolic pathways (e.g. variants of GLP1R) and variants of genes involved in intestinal GLP-1 secretion (e.g. KCNQ1). The few studies on GLP1R variants indicated a reduced glycaemic response to treatment with both DPP-4i and GLP-1 RA. Conflicting results for GLP1R gene variants were found for body weight changes under GLP-1 RA therapy. Other studies have examined SNPs in genes that are implicated in the development of diabetes by affecting pathophysiological defects such as beta cell failure (e.g. TCF7L2 and CDKAL1). For these genes, reductions in HbA1c in response to DPP-4i therapy have been reported to be greater for CDKAL1 variants and smaller for TCF7L2 variants.
SGLT2i reduce blood glucose concentrations via inhibition of renal glucose reabsorption, a mechanism that is not related to type 2 diabetes aetiology. Therefore, genetic variants related to the development of diabetes are not likely to affect the response to SGLT2i therapy. Most studies have focused on examining genes affecting renal glucose reabsorption (e.g. SLC5A2). However, the few data available indicate no clinically relevant differences between SLC5A2 variants in response to SGLT2i treatment. In addition, variants of genes potentially involved in the pharmacokinetics of SGLT2i were found to have no clinically relevant effects on therapeutic response.
The relevance of the currently available pharmacogenetic studies is largely hampered by small genetic effects, low sample sizes, limited statistical power, often inadequate statistics (e.g. lack of gene–drug interactions in models), inadequate account of confounders and effects modifiers (e.g. obesity, comorbidity), limited comparability due to different study designs, study populations and definitions of study outcomes, and a lack of replication studies. Therefore, more well-designed studies with a sufficiently large sample size and well-characterised diabetes phenotypes are required to investigate and replicate the effect of genetic variants on the metabolic response to novel glucose-lowering drugs. A major limitation of the current studies is that most findings have not been replicated. Currently, the replication of results for relevant gene variants is more important than producing new findings. When possible, meta-analysis across studies should be undertaken to provide robust evidence for associations.
This review also indicates that genetic studies on drug response to DPP-4i, GLP-1 RA and SGLT2i in type 2 diabetes have been mainly based on candidate genes, derived from aetiological processes or drug pathways. Overall, the degree of insight provided by these studies is rather limited. GWAS, on the other hand, have the potential to provide novel insights, as these studies make no assumptions about drug mechanisms or underlying disease processes . Only GWAS of metformin have been reported to date [2, 49].
In conclusion, the amount and level of evidence of the current research results are not sufficient to guide stratified prescription use of novel glucose-lowering drugs in type 2 diabetes.