TPMT and NUDT15: two critical PGx genes to guide thiopurines dosing and reduce adverse reactions
Background
Thiopurines are a class of immunosuppression drugs that include azathioprine, mercaptopurine and thioguanine. They are frequently prescribed to treat a variety of conditions, such as acute lymphoblastic leukemia (ALL), myeloid leukemia, autoimmune diseases (e.g. inflammatory bowel disease (IBD) or Crohn’s disease), or to prevent rejection after organ transplant. Thiopurines can cause severe and life-threatening toxicity, such as myelosuppression in some patients.
Thiopurines are activated by multiple enzymes to 6-thioguanine nucleotide (6-TGN), which is the main source of cytotoxicity of thiopurine drugs. Thiopurine methytransferase (TPMT) catabolizes thiopurines to an inactive form, resulting in less 6-TGN. Therefore, individuals carrying loss-of-function TPMT alleles are at high risk for life-threatening myelosuppression, due to high level of 6-TGN1.
The Nudix hydrolase (NUDT15) enzyme is another critical determinant of thiopurines metabolisms. It catalyzes the conversion of cytotoxic thioguanine triphosphate (TGTP) to the less toxic thioguanine monophosphate (TGMP). Therefore, defect in NUDT15 activity results in higher risk of toxicity. NUDT15 variants have been identified that strongly associate with thiopurine-induced myelosuppression in patients with ALL and IBD1. NUDT15 variants most frequently occur among East Asians (23%), followed by South Asians (14%), and Latinos (10%)2. A recent study in patients with European ancestry also show among individuals who developed toxicity within 3 months of treatment, 13% were found to be carriers of NUDT15 variants. The authors argue that NUDT15 and TPMT genetics explains 50% of severe thiopurine-induced toxicity, providing a compelling rationale for preemptive testing of both NUDT15 and TPMT, not only in Asians, but also in Europeans3.
Individuals with variants in both TPMT and NUDT15 are significantly more sensitive to thiopurines than individuals with variants in only one gene4. Therefore, investigating both TPMT and NUDT15 allows for more accurate prediction of thiopurine-related toxicity risk to guide dosing, particularly among patients from diverse population.
Webinar recording: Using TPMT and NUDT15 PGx to reduce adverse drug reactions
RPRD’s comprehensive NT (NUDT15 and TPMT) Panel investigates all clinically relevant variants of both NUDT15 (9 alleles) and TPMT genes (10 alleles), in a single test.
Compared to testing only a limited number of common variants, the NT Panel yields thorough dosing guideline for thiopurines with high accuracy.
Clinical Pharmacogenetics Implementation Consortium (CPIC) provides thiopurines dosing guideline based on genotypes of TPMT and NUDT15. Click here for details.
Learn more about the NT (NUDT15 and TPMT) Test
NUDT15
Alleles Detected
Normal function allele: *1
No function allele: *2, *3
Uncertain function allele: *4, *5, *6, *7, *8, *9
In Vitro Function/Predicted Activity for Alleles with CPIC Function Assignment of “Uncertain”
*4, *5, *7, *8, *9: Severely decreased activity with TGTP or TdTP as substrate
*6: Significantly decreased function with TGTP; decrease more pronounced with TdTP as substrate
Phenotype Categories
Normal Metabolizer: This phenotype indicates the presence of two copies of a normal function allele in the NUDT15 gene.
Diplotype: *1/*1
Intermediate Metabolizer: Presence of one copy of a normal function allele and one copy of a no function allele in the NUDT15 gene. This is consistent with intermediate activity of NUDT15. Such patients are at risk for myelosuppression with normal doses of drugs in the thiopurine class.
Diplotypes: *1/*2 or *1/*3*
Poor Metabolizer: This phenotype indicates low or absent activity of NUDT15. This phenotype includes individuals with two copies of no function alleles (i.e., *2, *3) in the NUDT15 gene. This is consistent with low or absent activity of NUDT15. These patients are at high risk for toxicity with normal doses of drugs in the thiopurine class.
Diplotypes: *2/*2, *2/*3, *3/*3
Possible Intermediate Metabolizer: Presence of one copy of a normal function allele and one copy of an uncertain function allele in the NUDT15 gene (alleles that have not yet been assigned a CPIC function but have predicted low or deficient activity of NUDT15 (in vitro function/predicted activity) based on the current literature4). Such patients may be at risk for myelosuppression with normal doses of drugs in the thiopurine class.
Diplotypes: *1/*4, *1/*5, *1/*6, *1/*7, *1/*8, *1/*9
Possible Poor Metabolizer: This phenotype indicates the presence of two copies of uncertain function alleles (alleles that have not yet been assigned a CPIC function but have predicted low or deficient activity of NUDT15 (in vitro function/predicted activity) based on the current literature4) or the presence of one copy of an uncertain function allele and one no function allele in the NUDT15 gene. These patients may be at high risk for toxicity with normal doses of drugs in the thiopurine class.
Diplotypes: *2/*4, *2/*5, *2/*6, *2/*7, *2/*8, *2/*9
*3/*3, *3/*4, *3/*5, *3/*6, *3/*7, *3/*8, *3/9
*4/*4, *4/*5, *4/*6, *4/*7, *4/*8, *4/*9
*5/*5, *5/*6, *5/*7, *5/*8, *5/*9
*6/*6, *6/*7, *6/*8, *6/*9
*7/*7, *7/*8, *7/*9
*8/*8,*8/*9
*9/*9
Indeterminate-Phasing Positive: This phenotype represents the detection of an uncharacterized allele composition. If rs116855232 and rs147390019 variants are detected on the same allele, then this genotype has currently not been characterized, and thus the function of this allele is unknown.
NUDT15 Phenotype Frequencies in Multiple Race/Ethnic Groups1
| African | African American | Caucasian | Middle Eastern | East Asian | South/Central Asian | Americas | Oceanian | |
|---|---|---|---|---|---|---|---|---|
| NUDT15 Normal Metablizer | 99.38% | NA | 98.63% | NA | 77.26% | 86.49% | 87.68% | NA |
| NUDT15 Intermediate Metabolizer | 0.27% | NA | 0.76% | NA | 16.79% | 12.55% | 8.29% | NA |
| NUDT15 Possible Intermediate Metabolizer | 0.00% | NA | 0.00% | NA | 0.49% | 0.03% | 0.17% | NA |
| NUDT15 Poor Metabolizer | 0.00% | NA | 0.00% | NA | 0.91% | 0.46% | 0.20% | NA |
| Indeterminate | 0.35% | NA | 0.60% | NA | 4.55% | 0.46% | 3.66% | NA |
TPMT
Alleles Detected
Normal function allele: *1
Unknown function allele: *3D, *24
Probable reduced function allele: *8
No function alleles: *2, *3A, *3B, *3C, *4
Phenotype Categories
Normal Metabolizer: Presence of two copies of a normal activity allele in the TPMT gene.
Diplotypes: *1/*1
Intermediate Metabolizer: Presence of one copy of a normal function allele and one copy of a no function allele in the TPMT gene. This is consistent with intermediate activity of TPMT. Such patients are at risk for myelosuppression with normal doses of drugs in the thiopurine class.
Diplotypes: *1/*2, *1/*3A, *1/*3B, *1/*3C, *1/*4
Poor Metabolizer: Presence of two copies of a no function allele in the TPMT gene. This can be observed as either compound heterozygous or homozygous variant alleles. This is consistent with low or deficient activity of TPMT. These patients are at high risk for life-threatening myelosuppression with normal doses of drugs in the thiopurine class.
Diplotypes: *2/*2, *2/*3A, *2/*3B, *2/*3C, *2/*4,
*3A/*3A, *3A/*3B, *3A/*3C, *3A/*4, *3B/*3B, *3B/*3C, *3B/*4, *3C/*3C, *3C/*4, *4/*4
Indeterminate activity – CPIC: Presence of either one or two copies of an unknown allele in the TPMT gene, including the probable function alleles. At the time of this publication, it is not possible to predict the actual activity of TPMT, and hence the expected phenotype for this patient cannot be determined by genotyping alone.
Diplotypes: *1/*3D, *1/*24, *2/*3D, *2/*24,
*3A/*3D, *3A/*24, *3B/*3D, *3B/*24, *3C/*3D, *3C/*24, *3D/*3D, *3D/*4, 3D/*24,
*4/*24, *1/*8, *1S/*8, *2/*8, *3A/*8, *3B/*8, *3C/*8, *3D/*8, *4/*8, *8/*8, *8/*24,
*24/*24
TPMT Phenotype Frequencies in Multiple Race/Ethnic Groups1
| African | African American | Caucasian | Middle Eastern | East Asian | South/Central Asian | Americas | Oceanian | |
|---|---|---|---|---|---|---|---|---|
| TPMT Normal Metablizer | 80.22% | 76.68% | 87.37% | 92.44% | 95.89% | 98.04% | 87.22% | 96.04% |
| TPMT Intermediate Metabolizer | 9.72% | 14.90% | 11.72% | 7.41% | 3.40% | 1.72% | 11.76% | 3.79% |
| TPMT Possible Intermediate Metabolizer | 0.54% | 0.67% | 0.03% | 0.00% | 0.01% | 0.00% | 0.04% | 0.00% |
| TPMT Poor Metabolizer | 0.29% | 0.73% | 0.44% | 0.17% | 0.03% | 0.01% | 0.43% | 0.04% |
| Indeterminate | 9.23% | 7.03% | 0.48% | 0.00% | 0.67% | 0.24% | 0.58% | 0.12% |
Methodology
Real-time polymerase chain reaction (PCR) with fluorescence detection.
Turnaround Time
3-5 days from receipt of samples that meet specified requirements. Test results are reported Monday through Friday.
Ordering
Click here to download the Test Requisition Form.
| Test Name | CNT or NT Panel |
| CPT Code | 81355, 81306 |
| Collection | Whole blood (3-5mL peripheral whole blood in ETDA tube) or Saliva in Oragene Dx, Part # OGD-500 |
| Labeling | Must label with patient name plus one additional identifier: date of birth, medical record number, or date of collection |
| Stability | Samples must be received by RPRD within 7 days of collection. Ambient or refrigerated storage is acceptable. |
| Shipping | Ambient temperature. Ship for RPRD receipt on Monday through Friday only. |
| Rejection | Blood sample may be rejected if frozen, hemolyzed, or clotted |
Limitations
The presence of other variants of TPMT and NUDT15 that are not detected in this assay may influence drug metabolism. Additional variants that are not detected but located proximally to variants interrogated may affect the assay’s ability to detect the above listed alleles.
Please consider all relevant patient information (including but not limited to additional medications, gender, weight, etc.) when making any dosing decisions.
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Disclaimer
“RPRD Insights” pages are an educational tool to provide additional information on pharmacogenetic relevant topics. Always consult a medical professional before making any healthcare-related decisions.
References
- Relling MV, et al. CPIC Guideline for Thiopurines and TPMT and NUDT15. Clin Pharmacol Ther. 2019 May;105(5):1095-1105.
- Moriyama T, et al. NUDT15 Polymorphisms Alter Thiopurine Metabolism and Hematopoietic Toxicity. Nat Genet. 2016 Apr;48(4):367-73.
- Schaeffeler, E. et al. Impact of NUDT15 Genetics on Severe Thiopurine-related Hematotoxicity in Patients with European Ancestry. Genetics in Medicine. Feb 2019. [Ahead of ePub].
- Yang, JJ. et al. Inherited NUDT15 Variant is a Genetic Determinant of Mercaptopurine Intolerance in Children with Acute Lymphoblastic Leukemia. J Clin Oncol. 2015 Apr; 33(11): 1235-42