Determination of NUDT15 variants by targeted sequencing can identify compound heterozygosity in pediatric acute lymphoblastic leukemia patients

Yu, Chih-Hsiang; Chang, Ya‐Hsuan; Wang, Der-Shiun; Jou, Shiann-Tarng; Lin, Chien‐Yu; Lin, Kai‐Hsin; Lu, Meng‐Yao; Raghav, Lovely; Chang, Hong-Yeh; Wu, Kang‐Hsi; Chou, Shu‐Wei; Ni, Yu-Ling; Lin, Dong‐Tsamn; Lin, Shu‐Wha; Chen, Hsuan‐Yu; Yang, Yung‐Li

doi:10.1038/s41598-020-71468-y

Cited by 10 publications

(18 citation statements)

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“…Pediatric leukemia studies have revealed that patients with this variant can tolerate only 8% of the usual PA dose and account for approximately 22% of PA intolerance cases. [ 14 , 15 ] In vivo and in vitro studies of NUDT15 *3 have revealed that this variant does not affect enzyme activity; instead, it causes instability in NUDT15 protein structure, leading to early protein degradation in cells. Physiologically, diplotype *2/*3 makes enzyme NUDT15 no function at all.…”

Section: Discussionmentioning

confidence: 99%

Alopecia and colon ulcers following azathioprine use in a patient with myasthenia gravis: A case report

et al. 2022

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Rationale: Azathioprine is a purine analog (PA) used to treat myasthenia gravis (MG). However, some patients are sensitive to azathioprine and develop severe side effects, such as leukopenia, alopecia, and diarrhea soon after using the medication. Pharmacogenetics plays a crucial role in such intolerance. Patient concerns: A 16-year-old woman with MG developed hair loss, pancytopenia, bloody diarrhea, and fever shortly after azathioprine treatment. Diagnosis: Pharmacogenetic analysis revealed compound heterozygosity of the nudix hydrolase 15 (NUDT15) gene, which led to suppressed NUDT15 function. Colonoscopy revealed large ulcers with polypoid lesions in the terminal ileum, cecum, ascending colon, and rectum. These are the characteristics of inflammatory bowel disease (IBD). Interventions: Sanger sequencing of NUDT15 gene and colonoscopy for bloody stool evaluation. Outcomes: The patient recovered completely from this acute episode after discontinuation of azathioprine treatment. Her hemogram turned back to normal range. There was also no blood in stool during follow-up. Lessons: Pharmacogenetic effects should be considered when prescribing PA medication. The possibility of secondary or concomitant autoimmune diseases must always be considered in patients with MG.

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Section: Discussionmentioning

confidence: 99%

Alopecia and colon ulcers following azathioprine use in a patient with myasthenia gravis: A case report

et al. 2022

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“…Recent advances in sequencing technologies using next-generation sequencing (NGS) approaches allow allelic phasing based on mapping of paired-end sequencing reads, enabling the differentiation between NUDT15 *1/*2 and NUDT15 *3/*6 diplotypes. Yu et al developed a method using NGS to sequence messenger RNA (mRNA)-derived complementary DNA to determine NUDT15 haplotypes [ 21 ], which was able to differentiate between NUDT15 *1/*2 and NUDT15 *3/*6 diplotypes. This method detects NUDT15 variants on expressed transcripts, and serves as an “indirect” method for studying the genomic sequence of NUDT15 .…”

Section: Discussionmentioning

confidence: 99%

A direct sequencing assay for pharmacogenetic testing of thiopurine-intolerant NUDT15 alleles in an Asian population

et al. 2022

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Objective The nucleoside diphosphate linked moiety X (Nudix)-Type motif 15 (NUDT15) enzyme is involved in thiopurine metabolism. Genetic variants in the NUDT15 gene result in decreased NUDT15 activity, which in addition to decreased thiopurine S-methyltransferase (TPMT) activity, contributes to thiopurine toxicity. Current standard approaches of NUDT15 genetic analysis have mainly been targeting several common variants. We aimed to develop a clinical-grade DNA-based assay for genetic analysis of the NUDT15 gene using Sanger di-deoxy sequencing. Results Sanger sequencing results were fully concordant with the expected NUDT15 genotype in all 17 cell line samples with known NUDT15 variants (accuracy = 100%; 95% CI 80.49 to 100.00%). Precision studies showed 100% intra-run repeatability and 100% inter-run reproducibility, respectively. Genetic analysis of the NUDT15 gene was performed for 80 patients of Asian ethnicity with wildtype TPMT. 76% (N = 61) of the studied individuals had NUDT15 *1/*1 diplotype. 25% (N = 14) of Chinese and 36% (N = 5) of Malays were found to carry at least 1 non-functional NUDT15 allele. Our study confirmed a high frequency of NUDT15 c.415C>T and c.55_56insGAGTCG variants in the Chinese and Malay ethnic groups in Singapore, highlighting the importance of determining NUDT15 genotype prior to thiopurine dosing.

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“…Apart from the NUDT15*3 , we failed to identify additional polymorphisms in NUDT15 exon 1 that has been reported to play role in 6-MP intolerance. 28 , 29 It is possible that additional confounding genetic/non-genetic factors could also contribute to increased tolerance, especially in patients homozygous for NUDT15 c.415C>T polymorphism in the Indian population compared to other ethnicities, which needs to be further evaluated.…”

Section: Discussionmentioning

confidence: 99%

NUDT15 c.415C>T Polymorphism Predicts 6-MP Induced Early Myelotoxicity in Patients with Acute Lymphoblastic Leukemia Undergoing Maintenance Therapy

Pai¹,

Mohan²,

Benjamin³

et al. 2021

PGPM

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Purpose Severe myelosuppression in patients with acute lymphoblastic leukemia (ALL) undergoing 6-MP-based maintenance therapy is attributed to TPMT gene polymorphisms, which is rare in Asian populations. This study aims to evaluate the role of selected polymorphisms in NUDT15, ITPA , and MRP4 genes in addition to TPMT in predicting 6-MP intolerance during ALL maintenance therapy. Patients and Methods We screened for the presence of NUDT15*3 (c.415 C>T, rs116855232); MRP4 c.2269 C>T (rs3765534), ITPA c.94 C>A (rs1127354) polymorphisms in addition to TPMT *2 (rs1800462), *3A (*3B and *3C; rs1800460 and rs1142345) in ALL patients with documented severe neutropenia (cohort-1; n=42). These polymorphisms were then screened in a prospective cohort of ALL patients (cohort-2; n=133) and compared with 6-MP dose reduction, early/late myelotoxicity. Results Nineteen (45%) patients in cohort-1 and 18 (14%) in cohort-2 had NUDT15 c.415 C>T variant while 4 (3%) patients in cohort-2 had TPMT*3C variant. Five (12%) in cohort-1 and 30 (24%) in cohort-2 had ITPA c.94 C>A variant while 9 (22%) and 15 (12%) had MRP4 c.2269 C>T variant in cohorts-1 and 2, respectively. All in cohort-1 and 36 (27%) in cohort-2 had severe myelotoxicity. Twenty-eight patients (66.6%) in cohort-1 and 40 (30%) patients in cohort-2 had significant 6-MP dose reduction. NUDT15 c.415 C>T variant explained severe myelotoxicity in 63% and 33% in cohort 1 and 2. TPMT *3C and ITPA c.94 C>A variants also explained myelotoxicity in cohort-2 (Median ANC: 376 vs 1014 mm 3 ; p=0.04 and 776 vs 1023 mm 3 ; p=0.04 respectively). NUDT15 c.415 C>T polymorphism explained significant myelotoxicity (507 vs 1298 mm 3 ; p<0.0001) in the multivariate analysis as well (β=−0.314, p<0.0001). Conclusion NUDT15 c.415 C>T (15*3), TPMT*3C, as well as ITPA c.94 C>A and MRP4 c.2269 C>T polymorphisms explain hematotoxicities. Preemptive genotype-based ( NUDT15*3, TPMT, ITPA c.94 C>A) 6-MP dosing could improve the outcome after maintenance therapy.

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Determination of NUDT15 variants by targeted sequencing can identify compound heterozygosity in pediatric acute lymphoblastic leukemia patients

Cited by 10 publications

References 45 publications

Alopecia and colon ulcers following azathioprine use in a patient with myasthenia gravis: A case report

Alopecia and colon ulcers following azathioprine use in a patient with myasthenia gravis: A case report

A direct sequencing assay for pharmacogenetic testing of thiopurine-intolerant NUDT15 alleles in an Asian population

NUDT15 c.415C>T Polymorphism Predicts 6-MP Induced Early Myelotoxicity in Patients with Acute Lymphoblastic Leukemia Undergoing Maintenance Therapy

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