DOCSLIB.ORG

Importance of NUDT15 Polymorphisms in Thiopurine Treatments

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Importance of NUDT15 Polymorphisms in Thiopurine Treatments Journal of Personalized Medicine Review Importance of NUDT15 Polymorphisms in Thiopurine Treatments Yoichi Tanaka * and Yoshiro Saito Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki City 210-9501, Kanagawa, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-44-270-6600 Abstract: Thiopurines, mercaptopurine, and azathioprine are used as immunosuppressants in the treatments of inflammatory bowel disease, rheumatoid arthritis, and organ transplantation and as chemotherapeutic drugs for the treatment of acute leukemia and chronic myeloid leukemia. This drug class sometimes causes severe adverse reactions, including bone marrow suppression and hair loss. Genetic polymorphisms of the metabolizing enzyme thiopurine S-methyltransferase have been used for predicting these reactions in Caucasians, but these allele frequencies are less frequently observed in Asian populations. Recently, nudix hydrolase 15 (NUDT15) polymorphisms have been shown to play an important role in thiopurine-induced adverse reactions in Asians. In this review, we summarize the NUDT15 studies, mainly in Asian countries, and their implementation in several countries. Keywords: NUDT15; thiopurine; mercaptopurine; azathioprine; Asian; adverse effect; implementation 1. Introduction Thiopurines, 6-mercaptopurine (6-MP) and azathioprine (AZA) are used as immuno- Citation: Tanaka, Y.; Saito, Y. suppressive and cytotoxic agents. AZA is used to maintain remission of inflammatory Importance of NUDT15 bowel disease (IBD) [1,2] and rheumatoid arthritis [3] and to inhibit immunological rejection Polymorphisms in Thiopurine of transplanted organs [4]. In hematological malignancies, 6-MP is used as maintenance Treatments. J. Pers. Med. 2021, 11, 778. therapy for 2–3 years [5]. Although thiopurine is the main component of these therapies, https://doi.org/10.3390/jpm11080778 severe adverse effects of grade 3 or higher frequently occur. The typical adverse effects of thiopurines include myelosuppression, hair loss, hepatotoxicity, and pancreatitis. Academic Editor: Su-Jun Lee To date, many studies have used a genetic approach to predict thiopurine-induced severe toxicities, especially myelosuppression. Thiopurine S-methyltransferase (TPMT) is Received: 5 July 2021 an enzyme involved in thiopurine metabolism (Figure1), and its genetic polymorphisms Accepted: 8 August 2021 are known to be risk factors for intolerance to thiopurines [6]. The TPMT variants of Published: 10 August 2021 c.238G>C, c.460G>A, and c.719G>A induce protein instability and decrease the TPMT enzyme activity [7]. A low TPMT activity results in the accumulation of active metabolites, Publisher’s Note: MDPI stays neutral thiopurine nucleosides, in the cells, leading to cytotoxicity. The frequencies of variants with regard to jurisdictional claims in with low TPMT activity differ among ethnic groups [6]. Caucasians and Africans have a published maps and institutional affil- high frequency of these polymorphisms, but Asians have lower frequencies of these TPMT iations. nonfunctional variants; nonetheless, the frequencies of severe toxicities are similar among these races. In addition to TPMT polymorphisms, nudix hydrolase 15 (NUDT15) c.415C>T (p.R139C) was associated with thiopurine intolerance in Asian populations, as reported in a previous Copyright: © 2021 by the authors. genome-wide association study (GWAS) [8,9]. To date, NUDT15 is known to have 26 alleles, Licensee MDPI, Basel, Switzerland. and NUDT15 *2 (p.V18_V19insGV and c.415C>T), *3 (c.415C>T), and *9 (c.50delGAGTCG) This article is an open access article are recognized as loss-of-function variants (Table1)[ 10,11]; however, other variants have distributed under the terms and been uncertain about the functional significance, referring to the Pharmacogene Variation conditions of the Creative Commons Consortium (PharmVar, www.pharmvar.org). The NUDT15 enzyme dephosphorylates Attribution (CC BY) license (https:// thiopurine triphosphate, which is the active metabolite incorporated into the DNA, to its creativecommons.org/licenses/by/ monophosphate (Figure1). The NUDT15 loss-of-function variants induce the increased 4.0/). J. Pers. Med. 2021, 11, 778. https://doi.org/10.3390/jpm11080778 https://www.mdpi.com/journal/jpm J. Pers. Med. 2021, 11, x FOR PEER REVIEW 2 of 11 other variants have been uncertain about the functional significance, referring to the Phar- J. Pers. Med. 2021, 11, 778 macogene Variation Consortium (PharmVar, www.pharmvar.org). The NUDT15 enzyme2 of 10 dephosphorylates thiopurine triphosphate, which is the active metabolite incorporated into the DNA, to its monophosphate (Figure 1). The NUDT15 loss-of-function variants induce the increased levels of thiopurine triphosphate and thus higher incorporation of levelsthioguanine of thiopurine nucleotides triphosphate into the DNA and thus and RNA. higher As incorporation a result, patients of thioguaninewho inherited nucleotides these intovariants the DNA experienced and RNA. severe As thiopurine-induced a result, patients whocytotoxicities, inherited such these as myelosuppression variants experienced severeand alopecia. thiopurine-induced NUDT15 c.415C>T cytotoxicities, (p.R139C) such is commonly as myelosuppression detected in Asians and alopecia. but is rarelyNUDT15 c.415C>Tfound in (p.R139C) Caucasians is and commonly Africans, detected with allele in Asiansfrequencies but isof rarely0.12 and found <0.01, in respectively Caucasians and Africans,[6]. In this with review, allele we frequencies aimed to provide of 0.12 anda summary <0.01, respectively of the associations [6]. In of this NUDT15 review, alleles we aimed toand provide their aclinical summary significance, of the associations mainly in Asians, of NUDT15 as well asalleles their andimplementation their clinical in significance,several countries. mainly in Asians, as well as their implementation in several countries. FigureFigure 1. Thiopurine 1. Thiopurine metabolism metabolism pathway. pathway. ABCC,ABCC, ATP-binding ca cassette,ssette, subfamily subfamily C; C;GDP, GDP, guanosine guanosine diphosphate; diphosphate; GMP,GMP, guanosine guanosine monophosphate; monophosphate; GMPS, GMPS, guanine guanine monophosphatemonophosphate synthetase; synthetase; GTP, GTP, guanos guanosineine triphosphate; triphosphate; HGPRT, HGPRT, hypoxanthine guanine phosphoribosyltransferase; IMP, inosine monophosphate; ITP, inosine triphosphate; IMPDH, ino- hypoxanthinesine monophosphate guanine phosphoribosyltransferase; dehydrogenase; NUDT15, nudix IMP, inosinehydrolase monophosphate; 15; TPMT, thiopurine ITP, inosine S-methyltransferase. triphosphate; IMPDH, inosine monophosphate dehydrogenase; NUDT15, nudix hydrolase 15; TPMT, thiopurine S-methyltransferase. Table 1. Clinical impact of NUDT15 alleles in Asians. Table 1. Clinical impact of NUDT15 alleles in Asians. Estimated Allele Variation Amino Acid Disease Clinical Impact Reference EnzymeEstimated Activity Allele Variation Amino Acid Disease Clinical Impact Reference Enzyme Activity AZA dose reduction [12] 55_56insGAGTCG V18_V19insGV IBD LeukopeniaAZA dose and reduction hair loss [12] *2 55_56insGAGTCG V18_V19insGV Low IBD [13] *2 415C>T R139C Low ALL Leukopenia,Leukopenia 6-MP and hairdose loss reduc- [13] 415C>T R139C ALL [14,15] tionLeukopenia, 6-MP dose reduction [14,15] AZAAZA dose dose reduction reduction [12] [12] IBDIBD *3 *3 415C>T415C>T R139CR139C LowLow LeukopeniaLeukopenia and and hair hair loss loss [13] [13] ALLALL Leukopenia,Leukopenia, dose dose reduction reduction [10,14,16][10,14 ,16] *4 *4 416G>A416G>A R139HR139H IntermediateIntermediate IBD IBD Leukopenia Leukopenia and and hair hair loss loss (homo) (homo) [13,17] [13 ,17] IBDIBD LeukopeniaLeukopenia [13] [13] *5 *5 52G>A52G>A V18IV18I IntermediateIntermediate ALLALL 6-MP6-MP dose dose reduction reduction (homo) (homo) [14] [14] *6 55_56insGAGTCG V18_V19insGV Intermediate *7 101G>C R34T Low ALL Dose reduction [11] *8 103A>G K35E Intermediate ALL Dose reduction (patient with *2/*8) [11] *9 50delGAGTCG del17_18GV Low IBD, inflammatory bowel disease; ALL, acute lymphoblastic leukemia; AZA, azathioprine; 6-MP, 6-mercaptopurine. J. Pers. Med. 2021, 11, 778 3 of 10 2. NUDT15 Variants and Toxicities in Thiopurine Metabolism 2.1. Thiopurine for Inflammatory Bowel Disease Thiopurine is administered for maintenance of remission and is used as a steroid- sparing treatment for IBD. Approximately 25% of patients experience thiopurine-induced toxicities, especially myelosuppression [18]. The first study that reported the association between NUDT15 polymorphisms and 6-MP-induced toxicities was the GWAS conducted in Korean patients with Crohn’s disease. Genotyping was performed in 978 patients us- ing the immunochip array, while genotype imputation was carried out using the Asian reference panel. This study identified that the NUDT15 c.415C>T (p.R139C) variant was strongly associated with thiopurine-induced early leukopenia (white blood cell [WBC] count <3000/mm3) (odds ratio [OR] = 35.6; P [combined] = 4.88 × 10−94)[8]. The associa- tion between the c.415C>T variant and with early leukopenia was replicated, and severe hair loss occurred within 8 weeks in 142 Japanese IBD patients with homozygous T variants treated with thiopurine [19]. The NUDT15 enzyme with 139C showed deficient activity and was significantly associated with thiopurine-induced leukopenia and alopecia. Some Asian study groups have validated the association between p.R139C or other variants of NUDT15 and thiopurine-induced
Load more

Recommended publications
  • NUDT15 Hydrolyzes 6-Thio-Deoxygtp to Mediate the Anticancer Efficacy of 6-Thioguanine Nicholas C.K
    Published OnlineFirst August 16, 2016; DOI: 10.1158/0008-5472.CAN-16-0584 Cancer Therapeutics, Targets, and Chemical Biology Research NUDT15 Hydrolyzes 6-Thio-DeoxyGTP to Mediate the Anticancer Efficacy of 6-Thioguanine Nicholas C.K. Valerie1, Anna Hagenkort1, Brent D.G. Page1, Geoffrey Masuyer2, Daniel Rehling2, Megan Carter2, Luka Bevc1, Patrick Herr1, Evert Homan1, Nina G. Sheppard1, Pa l Stenmark2, Ann-Sofie Jemth1, and Thomas Helleday1 Abstract Thiopurines are a standard treatment for childhood leuke- for NUDT15, a finding supported by a crystallographic deter- mia, but like all chemotherapeutics, their use is limited by mination of NUDT15 in complex with 6-thio-GMP. We found inherent or acquired resistance in patients. Recently, the nucle- that NUDT15 R139C mutation did not affect enzymatic activity oside diphosphate hydrolase NUDT15 has received attention on but instead negatively influenced protein stability, likely due to the basis of its ability to hydrolyze the thiopurine effector a loss of supportive intramolecular bonds that caused rapid metabolites 6-thio-deoxyGTP (6-thio-dGTP) and 6-thio-GTP, proteasomal degradation in cells. Mechanistic investigations in thereby limiting the efficacy of thiopurines. In particular, cells indicated that NUDT15 ablation potentiated induction of increasing evidence suggests an association between the the DNA damage checkpoint and cancer cell death by 6-thio- NUDT15 missense variant, R139C, and thiopurine sensitivity. guanine. Taken together, our results defined how NUDT15 In this study, we elucidated the role of NUDT15 and NUDT15 limits thiopurine efficacy and how genetic ablation via the R139C in thiopurine metabolism. In vitro and cellular results R139C missense mutation confers sensitivity to thiopurine argued that 6-thio-dGTP and 6-thio-GTP are favored substrates treatment in patients.
    [Show full text]
  • Homozygous Mutation in NUDT15 in Childhood Acute Lymphoblastic Leukemia with Increased Susceptibility to Mercaptopurine Toxicity: a Case Report
    EXPERIMENTAL AND THERAPEUTIC MEDICINE 17: 4285-4288, 2019 Homozygous mutation in NUDT15 in childhood acute lymphoblastic leukemia with increased susceptibility to mercaptopurine toxicity: A case report JUAN CHENG1*, HAO ZHANG1*, HAI-ZHEN MA1 and JUAN LI2 Departments of 1Hematology and 2Central Laboratory, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China Received April 11, 2018; Accepted March 13, 2019 DOI: 10.3892/etm.2019.7434 Abstract. As an essential component of consolidation and of induction therapy, and the different expression of minimal maintenance therapy for acute lymphoblastic leukemia (ALL), residual disease (MRD) (3,4). Newly diagnosed patients mercaptopurine (6-MP) causes critical myelosuppression. The with ALL require a rigorous, standardized and long‑course current study aimed to clarify the reasons for severe myelosup- chemotherapy treatment strategy, which includes induction, pression and significant hyperpigmentationin a patient with ALL consolidation, intensification and maintenance therapy (5). that received consolidation therapy. The present study performed Additionally, stratification of treatment intensity is based on patient NUDT15 testing with fluorescence in situ hybridization the risk stratification of leukemic blasts identified in ALL (4). and whole‑exome sequencing. The results revealed that the The disease-free survival and the curative rate have greatly patient was a homozygous carrier (415C>T, TT) for rs116855232 improved with improved diagnosis and treatment regi- (NUDT15). The dose of 6‑MP was adjusted down from 30%, mens (6). However, treatment interruption or discontinuation with the patient receiving maintenance therapy at 8% of the due to hematopoietic toxicity is a common adverse event and recommended dose. The homozygous mutant (TT genotype) results in a higher risk of relapse (7).
    [Show full text]
  • Cardiovascular & Hematological Agents Inmedicinal Chemistry
    Send Orders for Reprints to [email protected] 23 Cardiovascular & Hematological Agents in Medicinal Chemistry, 2017, 15, 23-30 REVIEW ARTICLE ISSN: 1871-5257 eISSN: 1875-6182 Cardiovascular & Hematological Agents Thiopurine S-Methyltransferase as a Pharmacogenetic Biomarker: Signif- icance of Testing and Review of Major Methods The journal for current and in-depth reviews on Cardiovascular & Hematological Agents Chingiz Asadov*, Gunay Aliyeva and Kamala Mustafayeva Department of Hematopoietic Pathologies, Institute of Hematology and Blood Transfusion, Baku, Azerbaijan Abstract: Background: Thiopurine S-methyltransferase (TPMT) enzyme metabolizes thiopurine drugs which are widely used in various disciplines as well as in leukemias. Individual enzyme activity varies depending on the genetic polymorphisms of TPMT gene located at chromosome 6. Up to 14% of population is known to have a decreased enzyme activity, and if treated with standard doses of thiopurines, these individuals are at a high risk of severe Adverse Drug Reactions (ADR) as myelosuppression, gastrointestinal intolerance, pancreati- A R T I C L E H I S T O R Y tis and hypersensitivity. However, TPMT-deficient patients can successfully be treated with decreased thiopu- Received: November 30, 2016 rine doses if enzyme status is identified by a prior testing. TPMT status identification is a pioneering experience Revised: February 25, 2017 Accepted: March 21, 2017 in application of pharmacogenetic testing in clinical settings. 4 TPMT (*2, *3A, *3B, *3C) alleles are known to account for 80-95% of a decreased enzyme activity, and therefore, identifying the presence of these alleles sup- DOI: 10.2174/1871525715666170529091921 ported by phenotypic measurement of the enzyme activity can reveal patient’s TPMT status.
    [Show full text]
  • Massively Parallel Variant Characterization Identifies NUDT15 Alleles Associated with Thiopurine Toxicity
    Massively parallel variant characterization identifies NUDT15 alleles associated with thiopurine toxicity Chase C. Suitera, Takaya Moriyamaa, Kenneth A. Matreyekb, Wentao Yanga, Emma Rose Scalettic,d, Rina Nishiia, Wenjian Yanga, Keito Hoshitsukia, Minu Singhe, Amita Trehane, Chris Parisha, Colton Smitha, Lie Lia, Deepa Bhojwanif, Liz Y. P. Yueng, Chi-kong Lih, Chak-ho Lii, Yung-li Yangj, Gareth J. Walkerk,l, James R. Goodhandk,l, Nicholas A. Kennedyk,l, Federico Antillon Klussmannm,n, Smita Bhatiao, Mary V. Rellinga, Motohiro Katop, Hiroki Horiq, Prateek Bhatiae, Tariq Ahmadk,l, Allen E. J. Yeohr,s, Pål Stenmarkc,d, Douglas M. Fowlerb,t,u, and Jun J. Yanga,1 aDepartment of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105; bDepartment of Genome Sciences, University of Washington, Seattle, WA 98195; cDepartment of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden; dDepartment of Experimental Medical Science,Lund University, 221 00 Lund, Sweden; eDepartment of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education & Research, 160012 Chandigarh, India; fDepartment of Pediatrics, Children’s Hospital of Los Angeles, Los Angeles, CA 90027; gDepartment of Pathology, Hong Kong Children’s Hospital, Hong Kong; hDepartment of Paediatrics, The Chinese University of Hong Kong, Hong Kong; iDepartment of Paediatrics and Adolescent Medicine, Tuen Mun Hospital, Hong Kong; jDepartment of Laboratory Medicine and Pediatrics,
    [Show full text]
  • Association of Genetic Variants in NUDT15 with Thiopurine-Induced
    Research JAMA | Original Investigation AssociationofGeneticVariantsinNUDT15WithThiopurine-Induced Myelosuppression in Patients With Inflammatory Bowel Disease Gareth J. Walker, MBBS; James W. Harrison, PhD; Graham A. Heap, PhD; Michiel D. Voskuil, MD; Vibeke Andersen, MD; Carl A. Anderson, PhD; Ashwin N. Ananthakrishnan, MD; Jeffrey C. Barrett, PhD; Laurent Beaugerie, PhD; Claire M. Bewshea, MSc; Andy T. Cole, DM; Fraser R. Cummings, DPhil; Mark J. Daly, PhD; Pierre Ellul, PhD; Richard N. Fedorak, MD; Eleonora A. M. Festen, MD; Timothy H. Florin, MBBS; Daniel R. Gaya, DM; Jonas Halfvarson, MD; Ailsa L. Hart, PhD; Neel M. Heerasing, MBBS; Peter Hendy, MBBS; Peter M. Irving, MD; Samuel E. Jones, PhD; Jukka Koskela, MD; James O. Lindsay, PhD; John C. Mansfield, MD; Dermot McGovern, DPhil; Miles Parkes, DM; Richard C. G. Pollok, PhD; Subramaniam Ramakrishnan, MD; David S. Rampton, DPhil; Manuel A. Rivas, DPhil; Richard K. Russell, PhD; Michael Schultz, PhD; Shaji Sebastian, MD; Philippe Seksik, PhD; Abhey Singh, MBBS; Kenji So, MBBS; Harry Sokol, PhD; Kavitha Subramaniam, MBBS; Anthony Todd, MBChB; Vito Annese, MD; Rinse K. Weersma, MD; Ramnik Xavier, MD; Rebecca Ward, MSc; Michael N. Weedon, PhD; James R. Goodhand, MBBS; Nicholas A. Kennedy, MBBS; Tariq Ahmad, DPhil; for the IBD Pharmacogenetics Study Group Supplemental content IMPORTANCE Use of thiopurines may be limited by myelosuppression. TPMT pharmacogenetic testing identifies only 25% of at-risk patients of European ancestry. Among patients of East Asian ancestry, NUDT15 variants are associated with thiopurine-induced myelosuppression (TIM). OBJECTIVE To identify genetic variants associated with TIM among patients of European ancestry with inflammatory bowel disease (IBD). DESIGN, SETTING, AND PARTICIPANTS Case-control study of 491 patients affected by TIM and 679 thiopurine-tolerant unaffected patients who were recruited from 89 international sites between March 2012 and November 2015.
    [Show full text]
  • Genome-Wide Analyses of XRN1-Sensitive Targets in Osteosarcoma Cells Identifies Disease-Relevant 2 Transcripts Containing G-Rich Motifs
    Downloaded from rnajournal.cshlp.org on October 11, 2021 - Published by Cold Spring Harbor Laboratory Press 1 Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identifies disease-relevant 2 transcripts containing G-rich motifs. 3 Amy L. Pashler, Benjamin P. Towler+, Christopher I. Jones, Hope J. Haime, Tom Burgess, and Sarah F. 4 Newbury1+ 5 6 Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, UK 7 8 +Corresponding author: Prof Sarah Newbury, Medical Research Building, Brighton and Sussex 9 Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK. 10 Tel: +44(0)1273 877874 11 [email protected] 12 13 +Co-corresponding author: Dr Ben Towler, Medical Research Building, Brighton and Sussex Medical 14 School, University of Sussex, Falmer, Brighton BN1 9PS, UK. 15 Tel: +44(0)1273 877876 16 [email protected] 17 18 Running title: Genome-wide analyses of XRN1 targets in OS cells 19 20 Key words: XRN1, RNA-seq, Ewing sarcoma, lncRNAs, RNA degradation 21 22 23 24 25 26 27 28 29 30 31 32 33 Pashler et al 1 Downloaded from rnajournal.cshlp.org on October 11, 2021 - Published by Cold Spring Harbor Laboratory Press 34 35 ABSTRACT 36 XRN1 is a highly conserved exoribonuclease which degrades uncapped RNAs in a 5’-3’ direction. 37 Degradation of RNAs by XRN1 is important in many cellular and developmental processes and is 38 relevant to human disease. Studies in D. melanogaster demonstrate that XRN1 can target specific 39 RNAs, which have important consequences for developmental pathways.
    [Show full text]
  • IMURAN ® (Azathioprine)
    IMURAN ® (azathioprine) 50-mg Scored Tablets PRODUCT INFORMATION Rx only WARNING - MALIGNANCY Chronic immunosuppression with IMURAN, a purine antimetabolite increases risk of malignancy in humans. Reports of malignancy include post-transplant lymphoma and hepatosplenic T-cell lymphoma (HSTCL) in patients with inflammatory bowel disease. Physicians using this drug should be very familiar with this risk as well as with the mutagenic potential to both men and women and with possible hematologic toxicities. Physicians should inform patients of the risk of malignancy with IMURAN. See WARNINGS. DESCRIPTION: IMURAN (azathioprine), an immunosuppressive antimetabolite, is available in tablet form for oral administration. Each scored tablet contains 50 mg azathioprine and the inactive ingredients lactose, magnesium stearate, potato starch, povidone, and stearic acid. Azathioprine is chemically 6-[(1-methyl-4-nitro-1 H-imidazol-5-yl)thio]-1 H-purine. The structural formula of azathioprine is: It is an imidazolyl derivative of 6-mercaptopurine and many of its biological effects are similar to those of the parent compound. Azathioprine is insoluble in water, but may be dissolved with addition of one molar equivalent of alkali. Azathioprine is stable in solution at neutral or acid pH but hydrolysis to mercaptopurine occurs in excess sodium hydroxide (0.1N), especially on warming. Conversion to mercaptopurine also occurs in the presence of sulfhydryl compounds such as cysteine, glutathione, and hydrogen sulfide. CLINICAL PHARMACOLOGY: Azathioprine is well absorbed following oral administration. Maximum serum radioactivity occurs at 1 to 2 hours after oral 35S- azathioprine and decays with a half-life of 5 hours. This is not an estimate of the half-life of azathioprine itself, but is the decay rate for all 35S-containing metabolites of the drug.
    [Show full text]
  • Pharmacogene Variation Consortium Gene Introduction: NUDT15 Jun J
    DEVELOPMENT Pharmacogene Variation Consortium Gene Introduction: NUDT15 Jun J. Yang1, Michelle Whirl-Carrillo2, Stuart A. Scott3,4 , Amy J. Turner5,6, Matthias Schwab7,8 , Yoichi Tanaka9, Guilherme Suarez-Kurtz10, Elke Schaeffeler6,11, Teri E. Klein2, Neil A. Miller12,13 and Andrea Gaedigk13,14 The Pharmacogene Variation (PharmVar) Consortium is the guideline on TPMT- guided thiopurine dosing recommendation successor of the Human Cytochrome P450 (CYP) Allele that includes NUDT15 in addition to TPMT.3 Nomenclature website that served the pharmacogenetics commu- The initial genome- wide studies associated only a single nity by designating CYP star (*) alleles. The aim of PharmVar is to nonsynonymous single- nucleotide polymorphism in exon 3 of continue the mission of serving as an official allele designation au- NUDT15 with thiopurine toxicity.4 There is, however, growing thority for the global pharmacogenetics community.1 Herein, we evidence that additional functional variants exist. A total of 16 describe the introduction of the first non-CYP gene to PharmVar. coding region variants have been reported to date (Figure 1), Pharmacogenetic variation of NUDT15 plays a significant role in most of which affect function and/or thermal stability of the thiopurine response variability and toxicity. NUDT15 protein. On the basis of NUDT15 pyrophosphatase activity with thioguanosine triphosphate as the substrate, hap- THE NUDT15 GENE lotypes containing p.R139C (c.414C>T, rs116855232) or the NUDT15 is a member of a large phosphatase protein family that p.G17_V18del (c.55_56insGAGTCG, rs869320766) variant shares a common NUDIX catalytic domain and metabolizes a showed a severe decrease in activity2 and were thus classified as wide range of nucleotide substrates (Table 1).
    [Show full text]
  • Four Novel NUDT15 Haplotypes Relevant for Treatment of Acute Lymphoblastic Leukemia
    Four Novel NUDT15 Haplotypes Relevant for Treatment of Acute Lymphoblastic Leukemia (ALL) Amy Turner1, Praful Aggarwal1, Gunter Scharer1, and Ulrich Broeckel1 1RPRD Diagnostics LLC, Wauwatosa, WI 53226 Introduction Methodology Results Thiopurines, including azathioprine and mercaptopurine, Figure 4. Testing methodology. Figure 5. Novel NUDT15 Haplotypes Azathioprine are used clinically in the treatment of acute lymphoblastic leukemia (ALL)1. Genetic variation in two genes (TPMT and NUDT15 ) can lead to reduced or loss Day 0-Sample Collection Saliva gDNA 6-Mercaptopurine of enzyme activity, which can impact the Blood TPMT pharmacokinetics of thiopurine metabolism. If these variants are present, changes in drug dosing may be necessary to prevent severe myelosuppression1-4. Figure 1 highlights the gDNA Day 1-Lab Receives samples 6-TU 6-TIMP 6-MeMP steps in metabolism that are impacted by Extraction and extracts gDNA if needed. TPMT and NUDT15. TPMT Day 1/2-NGS library preparation: NGS library Coriell ID Ethnicity NUDT15 Amino Minor Allele protein modeling Figure 1. Metabolism of Multiplexed PCR is performed Acid Change Frequency Predict impact Azathioprine and Mercaptopurine. preparation meTIMP 6-TU: Thiouric Acid; TIMP: using targeted amplification. 6-TGMP 6-TGDP 6-TGTP NA20845; GUJARATI INDIAN, p.Pro12Leu 0.01 to 0.20 deleterious to Thioinosine monophosphate; 6- HG03673 USA; Sri Lankan enzyme activity MeMP: 6-methyl mercaptopurine; Day 2/3-NGS sequencing Tamil, UK NUDT15 6-MeTIMP: 6-Methyl thioinosine NGS TPMT NUDT15 monophosphate; 6-TGMP: Sequencing performed on Illumina iSeq. HG02840 LUHGAMBIA, p.Gly13Ala 0.0008-0.08 No impact to GAMBIA enzyme activity 6-Thioguanine Monophosphate; 6-TGDP:6-thioguanine-diphosphate; 6- MeTGMP meTGNs TGTP: 6-thioguanine-triphosphate; MeTGMP: methylthioguanosine NA19403 LUHYA, KENYA p.Lys33Asn 0.003 to 0.08 deleterious to monophosphate; meTGNs: methyl 6-thioguanosine mono-, di-, or enzyme activity triphosphates.
    [Show full text]
  • Downloaded Per Proteome Cohort Via the Web- Site Links of Table 1, Also Providing Information on the Deposited Spectral Datasets
    www.nature.com/scientificreports OPEN Assessment of a complete and classifed platelet proteome from genome‑wide transcripts of human platelets and megakaryocytes covering platelet functions Jingnan Huang1,2*, Frauke Swieringa1,2,9, Fiorella A. Solari2,9, Isabella Provenzale1, Luigi Grassi3, Ilaria De Simone1, Constance C. F. M. J. Baaten1,4, Rachel Cavill5, Albert Sickmann2,6,7,9, Mattia Frontini3,8,9 & Johan W. M. Heemskerk1,9* Novel platelet and megakaryocyte transcriptome analysis allows prediction of the full or theoretical proteome of a representative human platelet. Here, we integrated the established platelet proteomes from six cohorts of healthy subjects, encompassing 5.2 k proteins, with two novel genome‑wide transcriptomes (57.8 k mRNAs). For 14.8 k protein‑coding transcripts, we assigned the proteins to 21 UniProt‑based classes, based on their preferential intracellular localization and presumed function. This classifed transcriptome‑proteome profle of platelets revealed: (i) Absence of 37.2 k genome‑ wide transcripts. (ii) High quantitative similarity of platelet and megakaryocyte transcriptomes (R = 0.75) for 14.8 k protein‑coding genes, but not for 3.8 k RNA genes or 1.9 k pseudogenes (R = 0.43–0.54), suggesting redistribution of mRNAs upon platelet shedding from megakaryocytes. (iii) Copy numbers of 3.5 k proteins that were restricted in size by the corresponding transcript levels (iv) Near complete coverage of identifed proteins in the relevant transcriptome (log2fpkm > 0.20) except for plasma‑derived secretory proteins, pointing to adhesion and uptake of such proteins. (v) Underrepresentation in the identifed proteome of nuclear‑related, membrane and signaling proteins, as well proteins with low‑level transcripts.
    [Show full text]
  • PGX NUDT15 Genotyping for Detection of NUDT15 Variants Affecting Drug Metabolism
    PGX NUDT15 Genotyping For detection of NUDT15 variants affecting drug metabolism Clinical Background • NUDT15 is a negative regulator of thiopurine activation and toxicity. NUDT15 affects thiopurine drugs such as azathioprine, 6-mercaptopurine and 6-thioguanine. • NUDT15 catalyzes the conversion of cytotoxic thioguanine triphosphate (TGTP) metabolites to the less toxic thioguanine monophosphate. • Metabolizer phenotypes can be predicted by the NUDT15 genotype. • The clinical impact of the NUDT15 genotype is influenced by involvement of other metabolic pathways and other non-genetic factors. Epidemiology • NUDT15 variant frequency is ethnicity dependent. NUDT15*3 is present in approximately 7% of individuals of south/central Asian descent. NUDT15*5 is present in approximately 1% of individuals of East Asian descent. • The poor metabolizer phenotype is caused by two non-functional NUDT15 alleles. Genetics • The NUDT15 gene has three exons and is located on chromosome 13q14.2. • Inheritance is autosomal recessive. • Penetrance is drug-dependent. Indications for Ordering • Pre-therapeutic testing to identify individuals who should avoid, or may require unconventional doses of medications metabolized by NUDT15. Interpretation • If no NUDT15 variants are detected, this suggests *1 allele and normal enzymatic activity. • If one decreased functional or non-functional NUDT15 variant is detected, intermediate-to- normal NUDT15 enzymatic activity is predicted. Indiana University School of Medicine Genetics Testing Laboratories 975 W. Walnut St., IB350 Indianapolis, IN. 46202 Tel. 317-274-7597 • If two non-functional variants are present on opposite alleles, this predicts low NUDT15 enzymatic activity and a poor metabolizer phenotype. • Genotype results should be interpreted in the context of the individual clinical situation. Consultation with a clinical pharmacy professional is recommended.
    [Show full text]
  • PGX TPMT and NUDT15 Genotyping for Detection of TPMT and NUDT15 Variants Affecting Drug Metabolism
    PGX TPMT and NUDT15 Genotyping For detection of TPMT and NUDT15 variants affecting drug metabolism Clinical Background • NUDT15 is a negative regulator of thiopurine activation and toxicity. • TPMT and NUDT15 affect thiopurine drugs such as azathioprine, 6-mercaptopurine or 6- thioguanine. • Defects in the TPMT gene lead to decreased methylation and decreased inactivation of 6MP, which enhances bone marrow toxicity and may cause myelosuppression, anemia, bleeding tendency, leukopenia and infection. • NUDT15 catalyzes the conversion of cytotoxic thioguanine triphosphate (TGTP) metabolites to the less toxic thioguanine monophosphate. • Metabolizer phenotypes can be predicted by the TPMT and NUDT15 genotypes. • The clinical impact of the TPMT and NUDT15 genotype is influenced by involvement of other metabolic pathways and other non-genetic factors. Epidemiology • TPMT variant frequency is ethnicity dependent. TPMT*3A is present in approximately 3% of Caucasians, Mediterranean descent, South Americans; 5% Mexican descent and 1% Middle Eastern descent. TMPT*3C is present in approximately 5% of individuals of African descent. • NUDT15 variant frequency is ethnicity dependent. NUDT15*3 is present in approximately 7% of individuals of south/central Asian descent. NUDT15*5 is present in approximately 1% of individuals of East Asian descent. • The poor metabolizer phenotype is caused by two non-functional alleles. Genetics • The TPMT gene has nine exons and is located on chromosome 6p22.3. • The NUDT15 gene has three exons and is located on chromosome 13q14.2. • Inheritance is autosomal recessive. • Penetrance is drug-dependent. Indications for Ordering Indiana University School of Medicine Genetics Testing Laboratories 975 W. Walnut St., IB350 Indianapolis, IN. 46202 Tel. 317-274-7597 • Pre-therapeutic testing to identify individuals who should avoid, or may require unconventional doses of medications metabolized by TPMT and NUDT15.
    [Show full text]