Identification of genetic variants associated with tacrolimus metabolism in kidney transplant recipients by extreme phenotype sampling and next generation sequencing

Abstract

An extreme phenotype sampling (EPS) model with targeted next-generation sequencing (NGS) identified genetic variants associated with tacrolimus (Tac) metabolism in subjects from the Deterioration of Kidney Allograft Function (DeKAF) Genomics cohort which included 1,442 European Americans (EA) and 345 African Americans (AA). This study included 48 subjects separated into 4 groups of 12 (AA high, AA low, EA high, EA low). Groups were selected by the extreme phenotype of dose-normalized Tac trough concentrations after adjusting for common genetic variants and clinical factors. NGS spanned >3 Mb of 28 genes and identified 18,661 genetic variants (3,961 previously unknown). A group of 125 deleterious variants, by SIFT analysis, were associated with Tac troughs in EAs (burden test, p=0.008), CYB5R2 was associated with Tac troughs in AAs (SKAT, p=0.00079). In CYB5R2, rs61733057 (increased allele frequency in AAs) was predicted to disrupt protein function by SIFT and PolyPhen2 analysis. The variants merit further validation.

Introduction

Tacrolimus (Tac), the primary immune suppressant used in >90% of solid organ transplants¹, is a substrate of cytochrome P450 (CYP) enzymes CYP3A4 and CYP3A5. Tac has a narrow therapeutic window² with blood concentrations (troughs) that are highly associated with efficacy³ and toxicity⁴. Tac troughs are routinely monitored to maintain a therapeutic range and guide dosing adjustments. Most African Americans (AAs) often have higher rates of Tac metabolism generally due to higher CYP3A5 expression. Consequently, AAs often require higher Tac doses than European Americans (EAs)⁵. High Tac clearance and low troughs in kidney transplant recipients during the first 90 days post-transplant is a risk factor for acute rejection⁶.

There is large interpatient variability⁷ in Tac metabolism which is partially due to genetic variants and clinical factors that alter clearance. Tac dosing equations including common genotypes for CYP3A single-nucleotide polymorphisms (SNPs) and clinical factors have been developed to personalize Tac dosing^{8, 9}. However, dosing equations have not allowed for low-frequency variants (<5% frequency in population) because few studies have been sufficiently powered to identify them. Thus, further understanding the genetics of Tac disposition, especially the low-frequency variants, could be translated into more precise Tac dosing strategies.

Genetic variants impact Tac troughs¹⁰ by altering CYP3A4 and CYP3A5 enzyme expression, activity¹¹, transcription factors, co-enzymes or transporters. Previously, with a diverse cohort of kidney allograft recipients and a custom SNP array, we found that 52.5% of Tac trough variation in subjects was explained by a set of common SNPs and clinical variables¹². Upon further investigation of Tac troughs using a genome-wide association study (GWAS), three loss-of-function (LoF) genetic variants, CYP3A5*3 (rs776746), CYP3A5*6 (rs10264272) and CYP3A5*7 (rs41303343), in AAs were highly associated with Tac troughs⁷; these three genetic variants and clinical factors, accounted for 53.9% of the Tac trough variability in AAs. In a cohort of EAs, CYP3A5*3 andCYP3A4*22 (rs35599367) were significantly associated with Tac troughs¹³. A limitation of GWAS SNP arrays is that the genotypes are typically restricted to known common genetic variants requiring alternative methods to identify low-frequency, and unknown, variants associated with Tac disposition.

We hypothesized that Tac trough variation between subjects is, in part, due to low-frequency genetic variants which may not be present on a GWAS SNP array. To identify low-frequency genetic variants associated with Tac metabolism, we used an extreme phenotype sampling (EPS) model and next generation sequencing (NGS). The EPS model allows increased statistical power with fewer specimens for analysis¹⁴ and can account for known clinical factors and common genotypes⁷. Our EPS model investigated subjects with either the highest or lowest dose-normalized Tac troughs in our cohort. Because AAs often have different allele frequencies than EAs, we conducted a separate analysis for EAs and AAs. After selecting the subjects with extreme dose-normalized Tac troughs, and adjusting for clinical and common genetic variants, we used targeted NGS to identify low-frequency genetic variants. The variants may be useful for improving Tac dosing and understanding Tac trough variability.

Methods

Subjects and Tacrolimus Measurements

The 48 subjects identified for EPS and NGS were selected from 345 AAs and 1,443 EAs enrolled in our multi-center prospective, observational trial Deterioration of Kidney Allograft Function (DeKAF) Genomics (clinicaltrials.gov NCT00270712). The study was approved by the Institutional Review Board and informed consent was obtained from each subject prior to entering the study. Although race status was collected by self-reporting, principal components were used to select subjects for the EPS model. GWAS was previously conducted with all subjects. Subjects in the analysis were AA or EA kidney transplant recipients, ≥18 years who received Tac maintenance immunosuppression from 7 centers: University of Minnesota, Hennepin County Medical Center, University of Alabama, Mayo Clinic-Rochester, University of Iowa, University of Manitoba and University of Alberta. Recipient characteristics, clinical outcomes, Tac troughs and doses and concomitant medications were prospectively collected. Oral Tac was initiated around time of transplant using twice daily dosing. Doses were adjusted to achieve each institution’s target trough. Tac troughs were measured at each center approximately 12-hours following the last dose, at steady state with the current dose. Generally, troughs of 8-12 ng/mL were targeted for the first 3 months and 6-10 ng/mL for 3-6 months post-transplant. Median (range) of 18 (1-24) troughs were obtained for each subject in the first 6 months post-transplant. Tac trough whole blood measurements were clinically measured at each site and analyzed in CLIA approved laboratories with >95% measured by liquid chromatography-mass spectrometry.

Genotyping of Subjects

Before this study, genotyping on all subjects was performed on recipient DNA isolated from peripheral blood with the Affymetrix Transplant GWAS array that has been previously described¹⁵. The EPS model adjusted for common SNPs and principal components data from this array to assign race.

Selection of Subjects for Extreme Phenotype Sampling (EPS)

To select subjects with the extreme phenotype of Tac troughs, 48 kidney transplant recipients with the 12 highest and 12 lowest Tac troughs from the EA or AA cohorts, after accounting for clinical factors, known common genetic variants and enrolling transplant center, were selected for this study (Figure 1). To select these individuals, linear mixed-effects models (LMMs) were used to test for associations between natural log (ln)-transformed dose-normalized Tac troughs and the LoF genotypes CYP3A5 *3 (rs776746), CYP3A5 *6 (rs10264272) and CYP3A5 *7 (rs41303343) in AAs. For EAs, we adjusted for LoF genotypes CYP3A5*3 and CYP3A4*22 (rs35599367). Log transformation was used to ensure that the outcome was normally distributed. Our prior analyses found that dose-normalized troughs initially start low, rise quickly until day 9 after transplant and then plateau in the early weeks after transplant^{12, 16}. Therefore, a simple spline method was used to model the effect of time on all trough concentrations, with the change in slope occurring at day 9. The longitudinal LMMs included a random intercept, random slopes for days after transplant, and days after post-transplant day 9. Confounding fixed clinical factors were retained in the EPS model and were selected by performing backward selection with retention p-value of 0.10. For EAs, we adjusted for factors: time post-transplant, transplant recipient age, weight, diabetes status, living vs. deceased donor, donor gender, and antibody induction type; and time-varying covariates included estimated glomerular filtration rate, steroid use, calcium channel blocker use, angiotensin-converting enzyme inhibitor use and antiviral use. For AAs, we adjusted for time post-transplant, transplant recipient age, simultaneous pancreas and kidney transplant (SPK), and antibody induction type and time-varying covariates glomerular filtration rate (GFR) and antiviral use. The multivariable models were used to determine residuals which were then used to identify the subjects with the extreme phenotypes of adjusted Tac troughs. Analyses were conducted with SAS version 9.2 software (SAS Institute, Cary, NC).

Figure 1: Extreme Phenotype Sampling (EPS) Model to Detect Genetic Variants Associated with Tacrolimus Metabolism from African American (AA) or European American (EA) Kidney Transplant Recipients.

The graphs represent the mean dose-normalized Tac troughs on the y-axis and the distribution of subjects on the x-axis. The 12 recipients with highest or lowest Tac troughs, after adjusting for clinical variables and common genetic variants, from each group were selected for targeted next generation sequencing (NGS). A. The model used to select AA kidney transplant recipients was adjusted for genetic variants CYP3A5 *3, *6, and *7. The 12 AA subjects with the highest (3.5%) or 12 with the lowest (3.5%) Tac troughs were used for NGS from a cohort of 345 total subjects. B. The model used to select EA kidney transplant recipients was adjusted for genetic variants CYP3A5 *3 and CYP3A4 *22. The 12 EA subjects with the highest (0.8%) or 12 with the lowest (0.8%) dose-normalized Tac troughs were used for NGS from a cohort of 1,443 total subjects.

Targeted Next Generation Sequencing (NGS)

Hybridization-based capture was performed with 1 μg of genomic DNA with NimbleGen SeqCap EZchoice kit (Roche, NimbleGen). Sequencing spanning the entire length of 28 genes (Table 1) was performed and extended ~20,000 base pairs upstream and downstream of these genes. Thus, the extended sequencing length included 42 partial genes adjacent to the 28 genes for a total of 70 genes (Table 2) spanning 3,123,443 base pairs. These 28 genes were selected because they were hypothesized as associated with Tac disposition. We used a custom relaxed coverage probe design (Roche NimbleGen) allowing up to 20 close matches in the genome that increased the coverage across all regions. Standard SeqCap EZ gDNA libraries were developed and hybridized with the custom EZ choice probes following standard protocols. The captured libraries were multiplexed and sequenced using MiSeq V2 chemistry (2×150 bp).

Table 1:

Full Genes Sequenced in this Study

Gene	Protein Name	Function and Relevant References Showing Association with Tac Disposition
CYP3A locus	Cytochrome P450 subfamily: CYP3A4, CYP3A5, CYP3A43, CYP3A7, CYP3A51P	Metabolism of Tac 55-58
CYP2J2	Cytochrome P450, subfamily 2J polypeptide 2	P450 enzyme expressed in intestine, heart. Drug metabolism. Metabolizes arachidonic acid promoting kidney homeostasis, Tac has inhibitory effect nephrotoxicity 59, 60
Co-enzymes
POR	cytochrome P450 oxidoreductase	P450 oxidoreductase and reduced cytochrome b5 supply electrons into the P450 cycle. Addition of cyt b5 stimulates CYP3A4 activity in vitro. Oxidoreductase responsible for electron transfer from NAD to CYP450, (POR*28 is associated with increased CYP3A activity and increase Tac clearance) 61-63
CYB5A	Cytochrome B5, TypeA	Participant in the CYP450 cycle as an electron donor for cytochrome b5. Drug metabolism
CYB5R1	NADH-Cytochrome B5 Reductase	Reduces cytochrome b5. Cytochrome b5 donates second electron in P450 cycle and enhances CYP3A activity.
CYB5R2	NADH-Cytochrome B5 Reductase-2	Bifunctional reductase that contains cytochrome b5 and reductase domains in same protein. Cytosolic enzyme. Unclear if it associated with P450.
CYB5R3	Cytochrome B5 Reductase 3	Participant in CYP450 cycle as electron donor for cytochrome b5. Drug metabolism 64, Present in endoplasmic reticulum membrane
CYB5R4	NADH-Cytochrome B5 Reductase-4	Reduces cytochrome b5. Cytochrome b5 supplies second electron in P450 cycle and stimulates CYP3A activity.
CYB5RL	NADH-Cytochrome B5 Reductase-Like	Reduces cytochrome b5
CYB5D1	Cytochrome B5 Domain-Containing Protein-1	Serves as an electron donor for cytochrome b5 and thus participates in CYP450 cycle. Thus, play a role in drug metabolism
Transporters
ABCB1	ATP-Binding Cassette, Subfamily B, member 1	Efflux transporter known as Multi Drug Resistance1 or P-glycoprotein. Tac is a substrate. Actively transports Tac into the intestinal lumen as a counter-transport pump 65-67
ABCC1	ATP-Binding Cassette, subfamily C, member 1	Efflux transporter. Also known as Multidrug resistance associated protein 1 (MRP1). Findings suggest that MDR1 polymorphisms has effect on Tac pharmacodynamics 68-70
ABCC2	ATP-Binding Cassette, subfamily C, member 2	Efflux transporter also known as Multidrug resistance associated protein 2 (MRP2) 71.
ABCG2	ATP-Binding Cassette, Subfamily G, member 2	Efflux transporter, also named Breast Cancer Resistance Protein. Tac is a inhibitor, variants in ABC transporter gene may also associate with Tac pharmacokinetics 67
ABCE1	ATP-Binding Cassette, Subfamily E, member 1	Efflux transporter also known as ribonuclease 4 inhibitor
SLCO1B3	Solute Carrier Organic anion transporter family, member 1B3	Uptake transporter for organic anions. Also known as OATP1B3.
Transcription Factors
VDR	Vitamin D Receptor	Ligand activated transcription factors) that control gene expression). Highly expressed in intestine, but not in liver. Affects intestinal expression of CYP3A 72
NR3C1(GR)	Nuclear Receptor Subfamily 3, group Member 1	Glucocorticoid Receptor. Glucocorticoid-activated transcription factor that controls gene expression (several drug metabolizing genes contain GR response elements) 73
NR1I2(PXR)	Nuclear Receptor Subfamily 1, group 1, Member 2	Pregnane X Receptor. Ligand activated transcription factors) that control gene expression Regulates expression of drug metabolizing enzymes and drug transporters in liver 62, 74, 75
NR1I3(CAR)	Nuclear Receptor Subfamily 1, group 1, Member 3	Constitutive Androstane Receptor. Ligand-activated transcription factors) that control gene expression. Alters expression of CYP3A genes. Key regulator of drug metabolizing enzymes and drug transporters 76
HNF4A	Hepatocyte Nuclear Factor-4-α	Transcription factor for hepatic gene expression regulation, Regulates PXR and CAR expression and CYP3A expression77
CEBPA	C/EBP-Alpha	Co-factor (activator) for gene regulation. Especially transporters ABBC2 and ABCB1 78, 79
CEBPB	CCAAT/Enhancer Binding Protein, Beta	Co-factor (activator) for gene regulation. Especially transporters ABBC2 and ABCB1
PPARA	Peroxisome Proliferator-Activator Receptor Alpha	Has regulatory effect on CYP3A4 expression 62, 80, 81
FOXA2	Forkhead Box protein A2	Transcription factor also named HNF3-β, has effect on hepatic CYP3A4 expression82
NCOR1	Nuclear Receptor Corepressor 1	Co-factor (repressor) for gene regulation. Associated with transporters ABBC2 and ABCB1
YY1	Transcriptional Repressor Protein	Downregulates Cytochrome c Oxidase and CYP3A4 and CYP3A5

Note: Each gene was sequenced 20 kilobases upstream and downstream of the gene.

Table 2: List of all 70 genes used in the gene based statistical test.

Since we sequenced 20 kb upstream and downstream, and spanning the entire length of 28 genes in Table 1, this led to partial sequencing of 42 genes adjacent to these 28 genes and thus 70 total genes.

ABCB1	CYB5D2	LOC401980	PPFIBP2
ABCC1	CYB5R1	LSMD1	R3HDML
ABCC2	CYB5R2	MAATS1	RIPPLY2
ABCC6	CYB5R3	MRPL37	RNU12
ABCE1	CYB5R4	NCOR1	RUNDC3B
ABCG2	CYB5RL	NDUFS2	SLC25A29
ADIPOR1	CYP2J2	NR1I2	SLCO1B3
ANAPC10	CYP3A4	NR1I3	STYXL1
ANKFY1	CYP3A43	NR3C1	TMEM120A
APOA2	CYP3A5	OR2AE1	TMEM88
CDCP2	CYP3A7-CYP3AP1	OTUD4	TOMM40L
CDPF1	FCER1G	OVCH2	TTC19
CEBPA	FOXA2	PIGL	VDR
CEBPA-AS1	GSK3B	PKD2	YY1
CEBPB	HNF4A	PKDREJ	ZSCAN25
CHD3	HOOK1	POLDIP3	ZZEF1
YB5A	KDM6B	POR
CYB5D1	LINC00261	PPARA

Bioinformatics Analysis of NGS Data

The raw Illumina sequences were evaluated for quality with FASTQC¹⁷. Sequenced reads were aligned to University of California Santa Cruz’s human reference genome (GRCH 37/hg 19) with a Burroughs-Wheeler Aligner¹⁸. Depending on the reporting group^{19, 20}, recommended sequence depth is at least 10X-30X; we targeted >20X depth for making variant calls. Genome Analysis Toolkit’s (GATK) best practices^21-26 pipeline was used to identify and call variants²⁷. The final list of variants obtained were annotated with the snpEff tool²⁸ and the Ensembl Variant Effect Predictor (VEP)²⁹. Variants were evaluated in silico by Sorting Intolerant from Tolerant (SIFT)^{30, 31} and Polymorphism Phenotyping Tool 2 (PolyPhen2)^32-34 to assess potential impact on protein.

Statistical Analysis of Extreme Phenotype Individuals

A logistic regression model was applied, as cases and controls were identified as low versus high dose-normalized Tac trough subjects respectively, in either AA or EA groups. Due to small sample size, tests for association were performed by permutation testing and p-values were calculated. A continuous trait test was performed by regressing the dose-normalized Tac troughs on the genetic variants accounting for the selection procedure. Thus, two types of analyses were performed: A) Association tests for each of the single genetic variants with both EA and AA groups to determine SNPs associated with Tac metabolism in each group. B) Gene based test on 70 genes (Table 2) with burden test (BT) (linear sum of variant scores test), sequence kernel association test (SKAT) (sum of squared variant based test), and an optimal combination of BT and SKAT (SKATO)³⁵. P-values were further Bonferroni corrected with significance level of 0.0007 for the gene-based test. Focused-SNP set analyses, with each subject group, were performed on SIFT and PolyPhen2 selected variants which were predicted to impact protein function.

Manual Curation of Genetic Variants to Identify Genetic Variants

We manually inspected variants identified by GATK analysis in the Tac related genes CYP3A4, CYP3A5, POR and CYB5A for previously unidentified genetic variants in the 5’-untranslated regions (UTR), exons and 3’-UTR regions of these genes in our EPS model cohorts.

Results

Subject characteristics are described in Table 3. The EPS model in Figure 2 shows the natural-log of dose-normalized Tac troughs from the groups over the first 6-months post-transplant. As expected, the EA high group had the highest dose-normalized Tac troughs over time. The AA high group had the next highest Tac troughs, third was the EA low group and the AA low group had lowest Tac troughs. The subjects with 2 known LoFs could have any combination of CYP3A5 *3, *6, *7 or CYP3A4 *22 alleles. After adjusting for CYP3A5 *3, *6, and *7 in the AA high group 6 subjects had 2 known LoFs, while the AA low group had 1 subject with 2 known LoFs (Table 3). After adjusting for CYP3A5 *3 and CYP3A4 *22 alleles, the EA high group had 11 subjects with 2 known LoFs and the EA low group had 10 subjects with 2 known LoFs. Since the EPS model adjusted for common LoF genetic variants, these groups may have complex genetics associated with Tac disposition.

Table 3: Clinical and Genetic Characteristics of the Extreme Phenotype Subjects in African American (AA) and European American (EA) Groups.

The High groups had the highest dose-normalized Tac troughs, while the Low groups had the lowest dose normalized Tac troughs. AA cohort N=345 and EA cohort N=1443.

Variable		Dose-Normalized Tac Trough Groups
		AAHigh	AA Low	EA High	EA Low
N		12	12	12	12
Age	18-34	2	2	1	0
	35-64	9	10	8	10
	65-84	1	0	3	2
Diabetes	yes	6	9	9	7
	no	6	3	3	5
Donor Status	Living	2	8	11	7
	Deceased	10	4	1	5
Donor Gender	Male	7	4	7	10
	Female	5	8	5	2
Number of subjects with CYP3A5*3 Allelesrs776746_G	0	5	4	0	0
	1	6	7	1	2
	2	1	1	11	10
Number of subjects with CYP3A5*6 Allelesrs10264272_T	0	10	10	12	12
	1	1	2	0	0
	2	1	0	0	0
Number of subjects with CYP3A5*7 Allelesrs41303343_TA	0	8	11	12	12
	1	3	1	0	0
	2	1	0	0	0
Number of subjects with CYP3A4*22 Allelesrs35599367_A	0	11	12	10	11
	1	1	0	2	1
	2	0	0	0	0
Number of subjects with known CYP3A Loss of Function Alleles (CYP3A5*3,*6,*7 or CYP3A4*22)	0	2	1	0	0
	1	4	10	1	2
	2	6	1	11	10
Estimated GlomerularFiltration Rate*(mL/min)	< 54.9	19.9%	9.1%	19.0%	31.6%
	54.9-67.9	11.7%	45.7%	28.8%	27.0%
	67.9-83.5	24.5%	17.8%	22.3%	20.9%
	>83.5	43.9%	27.4%	29.9%	20.5%
Weight (kg)*	< 69.4	26.5%	4.6%	56.5%	20.5%
	69.4-80.9	20.9%	12.8%	28.3%	49.3%
	80.9-94.6	32.7%	21.0%	12.0%	0.9%
	>94.6	19.9%	61.6%	3.3%	29.3%
Steroid Use in First 6 Months	Yes	11	11	12	12
	No	1	1	0	0
Simultaneous Pancreas andKidney Transplant	Yes	1	0	0	1
	No	11	12	12	11
Antibody Induction	Monoclonal	8	5	5	3
	Polyclonal	4	7	7	8
Calcium ChannelBlocker in First 6 Months	Yes	8	9	5	9
	No	4	3	7	3
ACE Inhibitor in First 6 Months	Yes	4	4	5	2
	No	8	8	7	10
Antiviral Use in First 6 Months	Yes	12	9	12	11
	No	0	3	0	1
Tac Daily Dose (mg)Median (range)		4.0(0.5 - 12.0)	14.0(1.0 - 36.0)	1.0(0.1 - 6.0)	14.0(2.0 - 36.0)
Tac Trough Concentration (ng/mL)Median (range)**		7.5(1.0 - 21)	5.1(1.0 -18)	8.9(2.4 - 26)	8.1(1.3 - 29)
Dose Normalized Tac Trough Concentration (ng/mL)Median (range)		2.4(0.3-31)	0.38(.083-1.4)	7.7(1.0-82)	0.57(0.13-4.8)

^*Estimated Glomerular Filtration Rate and Weight are for time point closest to the corresponding Tac trough measurement

^**Tac troughs, and dose normalized Tac troughs, were measured periodically for each subject, up to 24 times per subject.

Figure 2: Dose Normalized Tac Troughs of Subjects from Extreme Phenotype Sampling (EPS) Model used for Next Generation Sequencing (NGS).

The figure shows natural log transformed Tac dose-normalized troughs over time, in high and low AA or EA Tac groups. Data lines represent smoothed conditional means and gray areas represent 95% confidence intervals. The 12 EA subjects with the highest (0.8%) or 12 with the lowest (0.8%) Tac troughs were used for NGS from a cohort of 1,443 total subjects. The 12 EA subjects with the highest (3.5%) or 12 with the lowest (3.5%) Tac troughs were used for NGS from a cohort of 345 total subjects after adjustment for known genotypes and clinical factors.

Data Availability

Raw sequence data, in fastq format, are available at the United States National Center for Biotechnology Information’s (NCBI) Sequence Read Archive (SRA) with SRA accession number: SRP156752. The associated phenotype and covariate data are available at NCBI’s Database for Genotypes and Phenotypes with dbGaP accession number: phs001670.v1.p1.

Variants Identified from Sequencing

The estimated coverage of NimbleGen sequencing was 86.6% of the total bases across the entire genetic distance of 28 genes. The remaining 13.4% were not covered because of the repetitive nature of the genomic regions. The sequencing depth was 60X across these 28 genes and 42 adjacent partial genes after mapping and quality control filtering of the sequences. The sequencing of the 42 partial genes did not span the entire length of those genes. A total of 18,661 variants in 48 extreme phenotype subjects were identified and processed for quality. With the Variant Effect Predictor (VEP) tool ²⁹, out of the 18,661 total variants identified, 3,961 variants (21.2%) were unknown and 14,700 (78.8%) were previously identified. The VEP analysis of these variants, and the coding variants, based on their predicted consequences are described in Figure 3. Although many of the genetic variants had unspecified significance, we identified 15,948 variants in the AA cohort and 11,074 variants in the EA cohort that were different (alternative allele) than the reference genome GRCH 37/hg 19.

Figure 3: Variant Effect Predictor (VEP) results based on genetic variants identified.

A. Predicted consequences of the 18,661 genetic variants identified in this sequencing study. B. Predicted gene expression consequences from coding sequences in the VEP analysis.

Statistical Association of Variants Identified through Sequencing with Tac Troughs

The association testing identified 397 and 297 variants that were associated with dose-normalized Tac troughs in AA and EA, respectively, with p<0.05 by either case-control or continuous trait tests. However, 15 (Table 4) and 9 (Table 5) variants in AA or EA, respectively had a p<0.005. Variants identified in the EA cohort with p<0.005 were in ABCC1, ANAPC10, NR3C1 and OTUD4. Variants identified in the AA cohort with p<0.005 were in ADIPOR1, CYB5R2, OVCH2 and POR.

Table 4: Single Variants Associated with Dose- Normalized Tacrolimus Troughs, identified in African American Kidney Transplant Recipients (p<0.005).

The table indicates the chromosome location of the variants based on GRCH37 assembly, the variant alternate allele, the consequence effect of the variant on the Ensembl transcripts, the gene symbol, the exon number out of the total number of exon in that gene, the intron number out of the total number in that gene, Existing known variants’ rs number if available and the allele frequencies from 1000 Genomes project as given by VEP software. AF = global, AFR = African population, AMR = American population, EUR = European population, EAS = East Asian population, SAS = South Asian population, AA = Allele Frequency from in African American population from Lung and Blood Institute-Exome Sequencing Project (NHLBI-ESP), EA = Allele Frequency in European American population from NHLBI-ESP. Also shown are the related test p-values for association with Tac troughs.

Location	Allele	Consequence	Symbol	Exon	Intron	Existing_variation	Allele frequencies								Pvalb1	Pvalc2
							AF	AFR	AMR	EAS	EUR	SAS	AA	EA
7:75552252-75552252	A	intron_variant	POR	-	1/14	-	-	-	-	-	-	-	-	-	0.001	0.002
7:75558027-75558037	C	intron_variant	POR	-	1/14	rs66811056	-	-	-	-	-	-	-	-	0.001	0.002
7:75573951-75573956	GTGTTTGTT	intron_variant	POR	-	1/14	rs67675959	0.26	0.52	0.24	0.25	0.09	0.10	-	-	0.001	0.002
7:75576956-75576956	T	intron_variant	POR	-	1/14	rs239955	0.26	0.52	0.24	0.25	0.09	0.10	-	-	0.001	0.002
7:75565740-75565740	A	intron_variant	POR	-	1/14	rs239960	0.25	0.49	0.24	0.25	0.09	0.10	-	-	0.002	0.003
11:7710178-7710178	T	downstream_gene_variant	OVCH2	-	-	rs4501973	0.46	0.18	0.57	0.58	0.61	0.49	-	-	0.002	0.001
11:7711872-7711872	C	downstream_gene_variant	OVCH2	-	-	rs10839842	0.47	0.18	0.57	0.59	0.62	0.50	-	-	0.002	0.001
11:7712471-7712471	T	stop_gained	OVCH2	15/15	-	rs4509745	0.48	0.23	0.58	0.59	0.62	0.49	0.31	0.62	0.002	0.001
1:202931839-202931839	A	upstream_gene_variant	ADIPOR1	-	-	rs2232854	0.31	0.18	0.40	0.43	0.35	0.28	0.23	0.34	0.002	0.002
7:75544455-75544455	C	upstream_gene_variant	POR	-	-	rs3823884	0.48	0.94	0.42	0.27	0.27	0.35	-	-	0.002	0.004
11:7687305-7687305	T	intron_variant	CYB5R2	-	8/8	rs12794507	0.26	0.44	0.18	0.14	0.25	0.22	-	-	0.003	0.001
7:75586536-75586536	C	intron_variant	POR	-	2/14	rs4728533	0.73	0.48	0.76	0.74	0.91	0.84	-	-	0.003	0.003
7:75563682-75563682	G	intron_variant	POR	-	1/14	rs12533235	0.26	0.52	0.24	0.25	0.09	0.10	-	-	0.003	0.004
11:7687517-7687517	C	intron_variant	CYB5R2	-	8/8	rs11041523	0.49	0.30	0.49	0.68	0.51	0.53	-	-	0.004	0.004
11:7686602-7686606	TGTTTGTT	stop_retained_variant,3_prime_UTR_variant	CYB5R2	9/9	-	rs536512597,rs16411	0.47	0.26	0.49	0.64	0.51	0.53	0.28	0.51	0.004	0.004

-Tac troughs were adjusted in the extreme phenotype model for clinical variables and genotypes CYP3A5*3, CYP3A5*6, and CYP3A5*7.

¹Pvalb: Logistic regression with permutation applied to calculate p-value in the case-control trait test.

²Pvalc: Linear regression applied to obtain p-values in the continuous trait test

Table 5: Single Variants Associated with Tacrolimus Adjusted Troughs, Identified in European American Kidney Transplant Recipients of (p<0.005).

The table indicates the chromosome location of the variants based on GRCH37 assembly, the variant alternate allele, the consequence effect of the variant on the Ensembl transcripts, the gene symbol, the intron number out of the total number in the gene, Existing known variants’ rs numbers if available and the allele frequencies from 1000 Genomes project as given by VEP software. AF = global, AFR = African population, AMR = American population, EUR = European population, EAS = East Asian population, SAS = South Asian population. Also shown are the related test p-values for association with Tac troughs.

Location	Allele	Consequence	Symbol	Intron	Existing_variation	Allele frequencies						Pvalb1	Pvalc2
						AF	AFR	AMR	EAS	EUR	SAS
4:146068652-146068652	T	intron_variant	OTUD4	13/20	rs12502109	0.31	0.37	0.31	0.47	0.13	0.26	0.001	0.002
20:43074372-43074372	C	downstream_gene_variant	14kb 3’ of HNF4A	-	rs1321826	0.16	0.32	0.16	0.03	0.11	0.15	0.002	0.004
20:43075161-43075161	A	downstream_gene_variant	14kb 3’ of HNF4A	-	rs7272694	0.16	0.32	0.16	0.03	0.11	0.15	0.002	0.004
20:43075280-43075280	C	downstream_gene_variant	15kb 3’ of HNF4A	-	rs7267639	0.16	0.32	0.16	0.03	0.11	0.15	0.002	0.004
5:142803548-142803548	G	intron_variant	NR3C1	1/8	rs72802815	0.25	0.23	0.42	0.10	0.34	0.23	0.005	0.004
16:16203559-16203559	T	intron_variant	ABCC1	21/29	rs35090860	0.21	0.06	0.14	0.40	0.21	0.25	0.005	0.003
16:16208172-16208172	T	intron_variant	ABCC1	22/29	rs45443999	0.20	0.04	0.14	0.40	0.19	0.25	0.005	0.003
16:16208173-16208173	C	intron_variant	ABCC1	22/29	rs45624535	0.20	0.04	0.14	0.40	0.19	0.25	0.005	0.003
4:146001613-146001613	T	intron_variant	ANAPC10	3/4	rs35098431	0.35	0.51	0.32	0.47	0.13	0.26	0.005	0.004

-Tac troughs were adjusted in the extreme phenotype model for clinical variables and genotypes CYP3A5*3 and CYP3A4*22.

¹Pvalb: Logistic regression with permutation applied to calculate p-value in the case-control trait test.

²Pvalc: Linear regression applied to obtain p-values in the continuous trait test

SIFT and PolyPhen2 analysis of identified genetic variants

SIFT^{30, 31} analysis was conducted on all the genetic variants identified in the 48 subjects. Of the 18,661 identified genetic variants, 125 were determined to be deleterious, 22 were deleterious-low confidence while the remaining variants were tolerated.

PolyPhen2^32-34 analysis was also performed on genetic variants. Of the 18,661 genetic variants, 110 were determined to be probably damaging, 63 of the variants were determined to be possibly damaging and the remaining variants were benign.

Figure 4 shows a Venn diagram of the SIFT and PolyPhen2 results of variants predicted to impact protein function. We discovered 69 genetic variants classified as both deleterious by SIFT and probably damaging by PolyPhen2. These 69 genetic variants (Supplemental Table 1) have the highest likelihood of affecting protein function and thus may also affect Tac disposition.

Figure 4: SIFT and PolyPhen2 Results of all 18,661 variants in a Venn diagram.

SIFT and PolyPhen2 are bioinformatics analytic tools that predict the affect specific genetic variants may have on protein function. Of the 18,661 variants, 125 were deleterious and 22 were deleterious with low confidence by SIFT while the remaining variants were tolerated. Polyphen2 analysis found 110 of the variants were probably damaging, 63 were possibly damaging while the remaining variants were benign to impacting protein.

SKAT Gene Based Test Identified CYP5R2 Association with Tac Disposition in African American Cohort

By using SKAT^36-39 to test the gene-level association with the continuous trait of dose-normalized Tac troughs, the most significant gene associated with Tac troughs in AA subjects was CYB5R2 by SKAT after Bonferroni correction (p=7.9×10^-4). CYB5R2 was also significant by SKAT by case-control test (p=8.5×10^-4). None of the genes were significantly associated with the EA cohort. Of the 525 variants identified in CYB5R2 (including upstream and downstream), 4 of these variants were found within the CYB5R2 gene that were predicted to functionally impact protein function according to SIFT or PolyPhen2 (Table 6). The genetic variant identified in CYB5R2 most likely to disrupt protein function was rs61733057 (Leu163Trp) because it is predicted as deleterious by SIFT and probably damaging by PolyPhen2. As seen in Table 6, the missense A to C variant rs61733057, in CYB5R2, has a global allele frequency of 0.05, but has increased allele frequency in both Africans (0.106) and AAs (0.119) compared with EAs (0.048). Likewise, rs61733056 is more frequent in AAs. CYB5R2 is a possible co-enzyme that may supply reducing equivalents to P450, although it is generally thought that CYB5R3 functions by supplying the second electron into the P450 cycle.

Table 6: Genetic Variants in the CYB5R2 Gene Associated with Dose Normalized Tacrolimus Troughs in African American Kidney Transplant Recipients.

The table indicates the location of the variants in the CYB5R2 gene, consequences, the codon changes, rs numbers and predicted protein effect from SIFT and PolyPhen2 analysis (with prediction scores), chromosome location of the variants based on GRCH37 assembly, the variant allele used to calculate the consequence, the consequence effect of the variant on the Ensembl transcripts, the Exon number out of the total number, Existing known variant rs numbers. Also shown are the allele frequencies from 1000 Genomes project as given by VEP software. AF = global, AFR = African population, AMR = American population, EUR = European population, EAS = East Asian population, SAS = South Asian population, AA = Allele Frequency from in African American population from Lung and Blood Institute-Exome Sequencing Project (NHLBI-ESP), EA = Allele Frequency in European American population from NHLBI-ESP.

Location	Allele	Consequence	Exon	Existing_variation	SIFT	PolyPhen2	Allele Frequencies
							AF	AFR	AMR	EAS	EUR	SAS	AA	EA
11:7687146-7687146	A	missense_variant	9/9	rs67173996	deleterious(0.03)	Benign (0.019)	0.161	0.035	0.052	0.504	0.128	0.089	-	-
11:7687715-7687715	C	missense_variant	8/9	rs12801394	deleterious(0.03)	Benign (0)	-	0.853	0.679	0.817	0.763	0.766	0.852	0.771
11:7689029-7689029	C	missense_variant	7/9	rs61733057	deleterious(0)	probably_damaging (0.947)	0.050	0.106	0.043	0.002	0.060	0.016	0.119	0.048
11:7690873-7690873	T	missense_variant	4/9	rs61733056	Tolerated (0.08)	possibly_ damaging (0.875)	0.075	0.213	0.035	0.014	0.004	0.053	0.192	0.003

Focused SNP-set Analysis for Association in the EA and AA Cohorts

Genetic variants were further analyzed to detect association with dose-normalized Tac troughs within the AA or EA cohorts. The SNPs analyzed by SIFT and Polyphen2, with predicted impact on protein function, were grouped into 4 categories: 1.) Polyphen2: probably damaging (N=110) (Supplemental Table 2) 2.) PolyPhen2: possibly damaging (N=63) (Supplemental Table 3) 3.) SIFT: deleterious (N=125) (Supplemental Table 4) 4.) SIFT: deleterious-low confidence (N=22) (Supplemental Table 5). These 4 categories of variants were tested by BT, SKAT, and SKATO for association with the EA and AA cohorts, separately. The group of 125 predicted deleterious variants (Supplemental Table 4) from SIFT had significant association with the EA cohort (BT, p=0.008) by case-control test.

Variants Observed During Manual Inspection of Variants

We examined SNPs in CYP3A4, CYP3A5, POR and CYB5A genes. We found several SNPs in the 5’-UTR of CYP3A4 and CYP3A5 that could affect protein expression. Surprisingly, we identified synonymous and non-synonymous SNPs with no reported rs numbers in dbSNP database in POR. In contrast, only a single previously unreported non-synonymous variant, His44Asn in exon 2 was identified in CYB5A, along with 16 previously unreported SNPs in the first 2,300bp upstream in the 5’-UTR. These variants are shown in Supplemental Table 6 (CYP3A4), Supplemental Table 7 (CYP3A5), Supplemental Table 8 (POR) and Supplemental Table 9 (CYB5A).

Discussion

This study showed that an EPS model and NGS identified 18,661 genetic variants associated with Tac disposition in 48 extreme phenotype subjects. VEP analysis determined 3,961 variants (21.2%) were unknown and 14,700 (78.8%) were previously known. We found 125 genetic variants that were predicted as deleterious of protein function by SIFT analysis and were significantly associated with Tac disposition in the EA group (BT, p=0.008). We further found 110 genetic variants that were probably damaging to protein function by PolyPhen2. Of these variants, 69 were also deleterious according to SIFT analysis and would represent the genetic variants most likely to affect protein function, and thus Tac disposition. For our studies, individual variant analysis lacks power due to small sample size with very limited number of genotype counts. Though some individual variants in a gene have weak signals, combining them can lead to a significant result as done in SKAT. Thus, a major finding was the significant association of CYB5R2 with Tac troughs in AAs by SKAT analysis. The genetic variant, rs61733057, in the CYB5R2 gene, was identified and predicted to be deleterious by SIFT and probably damaging by PolyPhen2. Thus, we have identified variants associated with Tac troughs in kidney transplant recipients that require future in vitro assessment or validation in another cohort.

At the time of this study, it was not feasible to determine low-frequency variants, by sequencing all subjects because that required NGS of thousands of subjects. Therefore, we used an EPS approach that was successful to identify low-frequency variants in other diseases⁴⁰,⁴¹,⁴²,⁴³,⁴⁴,⁴⁵. Previous research suggests sampling from both high and low extremes is important to identify variants associated with a particular phenotype⁴⁵. This EPS approach allows for smaller sample sizes to identify low-frequency genetic variants associated with a phenotype¹⁴. Thus, our study corroborates other studies showing that the EPS approach can identify genetic variants, or genes, which are associated with a phenotype. This EPS approach can save time and money by sampling fewer subjects.

Genetic Variants associated with Tac metabolism were identified and shown in Table 4 (AA) and Table 5 (EA). Table 4 shows single genetic variants associated with Tac metabolism in AAs. Many of these variants were in POR which encodes for a coenzyme involved in cytochrome P450 metabolism. The variants in OVCH2 are upstream, and likely in the promotor, of CYB5R2. A single variant found in ADIPOR1, was likely identified since it is downstream of the gene CYB5R1. Additionally, Table 5 has genetic variants associated with Tac metabolism in EAs. The variants identified were in the genes OTUD4, NR3C1, ABCC1, upstream of HNF4A and ANAPC10. The variant in ANAPC10 was also located in the 5’-UTR of ABCE1 gene. The OTUD4 variants are located in the 3’-UTR of ABCE1. ABCE1 is an ATP-binding cassette protein but lacks the transmembrane domain needed for transporter function. ABCE1 functions as a ribonuclease L inhibitor where it associates with the ribosome and initiation factors elF3 and elF5. We speculate that this would lead to less mRNA transcription, and reduce protein expression but that may be non-specific for CYP3A4 and CYP3A5. The variant found in the glucocorticoid receptor NR3C1, a transcription factor that can influence the expression of PXR, which in turn regulates CYP3A4 and CYP3A5. The other variant found in AAs was in the ABCC1 gene which may be involved in Tac transport. In general, functional assays will be needed to validate the association of these variants with Tac metabolism.

Table 6 shows 4 variants found in CYB5R2 and indicates CYB5R2 to be associated with Tac metabolism in AAs. CYB5R2 has not previously been associated with Tac troughs, disposition or metabolism, but was unexpectedly identified in AAs with extreme Tac troughs. CYB5R2, (in chromosome 11), differs from its homolog CYB5R3 (in chromosome 22), but share high sequence identity and there is limited literature regarding CYB5R2. Both CYB5R2 and CYB5R3 can reduce cytochrome b5 and act as co-factors for cytochrome P450 function (supply electrons into the P450 cycle). While CYB5R2 is located in the nucleus, CYB5R3 is present in the endoplasmic reticulum in liver. CYB5R3 exists in two forms as a membrane-bound variant in membranes including in erythrocytes where low activity variants have been associated with methemoglobinemia and a truncated soluble cytoplasmic form containing the FAD catalytic domain. CYB5R2 has been identified as a tumor suppressor that is epigenetically regulated⁴⁶. CYB5R2 negatively regulates vascular endothelial growth factor⁴⁷ which could contribute to its tumor suppressor activity. Furthermore, CYB5R2 is epigenetically regulated through promoter methylation⁴⁸, associated with patient survival of glioblastoma, and functions in collagen maturation, immunoregulation via toll-like receptor pathways, and osmotic stress⁴⁹. The CYB5R2 variant, rs61733057, that likely impacts CYB5R2 protein function, was identified. It has elevated frequency in the AAs compared with EAs. According to 1000 genomes database (Table 6), the identified variants associated with Tac troughs in AAs rs61733057 and rs61733056 are primarily in people of African descent, which would corroborate our finding of this variant in AAs. However, with limited CYB5R2 literature it is difficult to determine its function in Tac disposition.

This study identified genetic variants in CYP3A4, CYP3A5, POR and CYB5A. Although many of these variants (Supplemental Tables 6-9) did not show significant association with Tac troughs in our analysis, numerous naturally occurring genetic variants were identified that have not been reported. Many of these variants were in the 5’ and 3’-UTR regions of CYP3A4 and CYP3A5. We identified 1 exonic SNP in CYP3A4 with gene position 1022 A>G which would lead to amino acid substitution Lys341Arg. We identified multiple non-synonymous SNPs in POR without rs numbers. More than 160 POR variants have been described to be associated with altered steroid metabolism and Antley-Bixler syndrome and disordered steroidogenesis. Five of the novel POR variants appeared only in single individuals with high Tac troughs, namely Arg186Val, Asp473Tyr, Gly589Val and Ala661Ser in the EA high group and Arg453Ser in the AA high group. If these SNPs result in lowered transfer of electrons into the P450 cycle, one would expect reduced clearance via CYP3A4 and CYP3A5.

We recently developed an in vitro method to validate the association of genetic variants with drug metabolism⁵⁰. Variants are genetically engineered into cell lines, using CRISPR/Cas9, and then the cells are assayed to determine the effect of the specific variant on drug metabolism. This method was successfully used to validate the effect of CYP3A5 *1 vs. CYP3A5 *3 (rs776746) alleles on Tac metabolism⁵⁰. This method can be used to engineer variants, identified in this study, into a hepatocyte cell lines to study Tac metabolism.

This study had limitations. Although we sequenced numerous genes expected to be associated with Tac troughs, whole genome sequencing would have been more complete. However, there were considerable cost differences between whole genome sequencing and targeted NGS. A FOXP3 genetic variant, rs3761548, was reported to be associated with Tac troughs⁵¹ and we did not sequence FOXP3. Another limitation of this study is that SIFT and PolyPhen2 are not completely accurate prediction algorithms. One study found, for missense variants in G protein couple receptor genes, that SIFT and PolyPhen2 were 83% and 85% accurate, respectively; while the LoF prediction was over 90% accurate for both, predicting non-functional variants was 54 or 57% accurate, respectively⁵². One study investigated the accuracy of SIFT and PolyPhen2 for predicting missense mutations in BRCA1, MSH2, MLH1 and TP53 genes that resulted in area under the curve of receiver operating characteristic curves for both algorithms to be between 78 and 79%⁵³. Another study has shown that SIFT, PolyPhen2 and other predictive in silico tools’ accuracy is gene dependent and also best when used in combination⁵⁴. Thus, we focused on the identified variants in this study that were identified to disrupt protein function by both SIFT and PolyPhen2. A further limitation that we did not consider was Tac adherence because adherence data was not collected. Due to the limited number of subjects in each group (N=48, 4 groups of 12), additional statistical power would be gained by sequencing more subjects. Although, there are limitations to this study, this model was effective at identifying genetic variants associated with Tac metabolism in kidney transplant recipients.

We envision expanding this study with more subjects to identify more genetic variants. We foresee these genetic variants being translated into refined Tac dosing equations^{8, 9}. Refined dosing equations could be used to reduce variability in Tac troughs while reaching optimal therapeutic Tac troughs quickly post-transplant to reduce poor outcomes.