Top

Published in:

01-07-2020 | Original Article

New DPYD variants causing DPD deficiency in patients treated with fluoropyrimidine

Authors: Xandra García-González, Bartosz Kaczmarczyk, Judith Abarca-Zabalía, Fabienne Thomas, Pilar García-Alfonso, Luis Robles, Vanessa Pachón, Ángeles Vaz, Sara Salvador-Martín, María Sanjurjo-Sáez, Luis A. López-Fernández

Published in: Cancer Chemotherapy and Pharmacology | Issue 1/2020

Abstract

Purpose

Several clinical guidelines recommend genetic screening of DPYD, including coverage of the variants c.1905 + 1G>A(DPYD*2A), c.1679T>G(DPYD*13), c.2846A>T, and c.1129-5923C>G, before initiating treatment with fluoropyrimidines. However, this screening is often inadequate at predicting the occurrence of severe fluoropyrimidine-induced toxicity in patients.

Methods

Using a complementary approach combining whole DPYD exome sequencing and in silico and structural analysis, as well as phenotyping of DPD by measuring uracilemia (U), dihydrouracilemia (UH₂), and the UH₂/U ratio in plasma, we were able to characterize and interpret DPYD variants in 28 patients with severe fluoropyrimidine-induced toxicity after negative screening.

Results

Twenty-five out of 28 patients (90%) had at least 1 variant in the DPYD coding sequence, and 42% of the variants (6/14) were classified as potentially deleterious by at least 2 of the following algorithms: SIFT, Poly-Phen-2, and DPYD varifier. We identified two very rare deleterious mutations, namely, c.2087G>A (p.R696H) and c.2324T>G (p.L775W). We were able to demonstrate partial DPD deficiency, as measured by the UH₂/U ratio in a patient carrying the variant p.L775W for the first time.

Conclusion

Whole exon sequencing of DPYD in patients with suspicion of partial DPD deficiency can help to identify rare or new variants that lead to enzyme inactivation. Combining different techniques can yield abundant information without increasing workload and cost burden, thus making it a useful approach for implementation in patient care.

Available only for authorised users

Brito RA, Medgyesy D, Zukowski TH et al (1999) Fluoropyrimidines: a critical evaluation. Oncology 57:2–8CrossRefPubMed

Onesti CE, Botticelli A, La TM et al (2016) 5-Fluorouracil degradation rate could predict toxicity in stages II-III colorectal cancer patients undergoing adjuvant FOLFOX. Anticancer Drugs 28:322–326. https://doi.org/10.1097/CAD.0000000000000453 CrossRef

Heggie GD, Sommadossi JP, Cross DS et al (1987) Clinical pharmacokinetics of 5-fluorouracil and its metabolites in plasma, urine, and bile. Cancer Res 47:2203–2206PubMed

Chazal M, Etienne MC, Renée N et al (1996) Link between dihydropyrimidine dehydrogenase activity in peripheral blood mononuclear cells and liver. Clin Cancer Res 2:507–510PubMed

Gamelin E, Boisdron-Celle M, Guérin-Meyer V et al (1999) Correlation between uracil and dihydrouracil plasma ratio, fluorouracil (5-FU) pharmacokinetic parameters, and tolerance in patients with advanced colorectal cancer: a potential interest for predicting 5-FU toxicity and determining optimal 5-FU dosage. J Clin Oncol 17:1105. https://doi.org/10.1200/JCO.1999.17.4.1105 CrossRefPubMed

Boisdron-Celle M, Remaud G, Traore S et al (2007) 5-Fluorouracil-related severe toxicity: a comparison of different methods for the pretherapeutic detection of dihydropyrimidine dehydrogenase deficiency. Cancer Lett 249:271–282. https://doi.org/10.1016/j.canlet.2006.09.006 CrossRefPubMed

Meulendijks D, Henricks LM, Jacobs BAW et al (2017) Pretreatment serum uracil concentration as a predictor of severe and fatal fluoropyrimidine-associated toxicity. Br J Cancer 116:1415–1424. https://doi.org/10.1038/bjc.2017.94 CrossRefPubMedPubMedCentral

Amstutz U, Froehlich TK, Largiadèr CR (2011) Dihydropyrimidine dehydrogenase gene as a major predictor of severe 5-fluorouracil toxicity. Pharmacogenomics 12:1321–1336. https://doi.org/10.2217/pgs.11.72 CrossRefPubMed

Meulendijks D, Henricks LM, Sonke GS et al (2015) Clinical relevance of DPYD variants c.1679T>G, c.1236G>A/HapB3, and c.1601G>A as predictors of severe fluoropyrimidine-associated toxicity: a systematic review and meta-analysis of individual patient data. Lancet Oncol 16:1639–1650. https://doi.org/10.1016/S1470-2045(15)00286-7 CrossRefPubMed

10.

Terrazzino S, Cargnin S, Del Re M et al (2846A) DPYD IVS14+1G>A and 2846A>T genotyping for the prediction of severe fluoropyrimidine-related toxicity: a meta-analysis. Pharmacogenomics 14:1255–1272. https://doi.org/10.2217/pgs.13.116 CrossRefPubMed

11.

Henricks LM, Opdam FL, Beijnen JH et al (2017) DPYD genotype-guided dose individualization to improve patient safety of fluoropyrimidine therapy: call for a drug label update. Ann Oncol Off J Eur Soc Med Oncol 28:2915–2922. https://doi.org/10.1093/annonc/mdx411 CrossRef

12.

Amstutz U, Henricks LM, Offer SM et al (2018) Clinical pharmacogenetics implementation consortium (CPIC) guideline for dihydropyrimidine dehydrogenase genotype and fluoropyrimidine dosing: 2017 update. Clin Pharmacol Ther 103:210–216. https://doi.org/10.1002/cpt.911 CrossRefPubMed

13.

EMA review capecitabine. https://www.ema.europa.eu/en/medicines/human/referrals/fluorouracil-fluorouracil-related-substances-capecitabine-tegafur-flucytosine-containing-medicinal. Accessed 23 Oct 2019

14.

Cortejoso L, García-González X, García MI et al (2016) Cost-effectiveness of screening for DPYD polymorphisms to prevent neutropenia in cancer patients treated with fluoropyrimidines. Pharmacogenomics 17:979–984. https://doi.org/10.2217/pgs-2016-0006 CrossRefPubMed

15.

Karczewski KJ, Francioli LC, Tiao G, et al (2019) Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. bioRxiv 531210. https://doi.org/10.1101/531210

16.

García-González X, López-Fernández LA (2017) Using pharmacogenetics to prevent severe adverse reactions to capecitabine. Pharmacogenomics 18:1199–1213. https://doi.org/10.2217/pgs-2017-0102 CrossRefPubMed

17.

Adzhubei IA, Schmidt S, Peshkin L et al (2010) A method and server for predicting damaging missense mutations. Nat Methods 7:248–249. https://doi.org/10.1038/nmeth0410-248 CrossRefPubMedPubMedCentral

18.

Kumar P, Henikoff S, Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4:1073–1081. https://doi.org/10.1038/nprot.2009.86 CrossRefPubMed

19.

Shrestha S, Zhang C, Jerde CR et al (2018) Gene-specific variant classifier (DPYD-Varifier) to identify deleterious alleles of dihydropyrimidine dehydrogenase. Clin Pharmacol Ther 104:709–718. https://doi.org/10.1002/cpt.1020 CrossRefPubMedPubMedCentral

20.

García-González X, López-Tarruella S, García MI et al (2018) Severe toxicity to capecitabine due to a new variant at a donor splicing site in the dihydropyrimidine dehydrogenase (DPYD) gene. Cancer Manag Res 10:4517–4522. https://doi.org/10.2147/CMAR.S174470 CrossRefPubMedPubMedCentral

21.

Vaser R, Adusumalli S, Leng SN et al (2016) SIFT missense predictions for genomes. Nat Protoc 11:1–9. https://doi.org/10.1038/nprot.2015.123 CrossRefPubMed

22.

Offer SM, Fossum CC, Wegner NJ et al (2014) Comparative functional analysis of DPYD variants of potential clinical relevance to dihydropyrimidine dehydrogenase activity. Cancer Res 74:2545–2554. https://doi.org/10.1158/0008-5472.CAN-13-2482 CrossRefPubMedPubMedCentral

23.

Sistonen J, Büchel B, Froehlich TK et al (2014) Predicting 5-fluorouracil toxicity: DPD genotype and 5,6-dihydrouracil:uracil ratio. Pharmacogenomics 15:1653–1666. https://doi.org/10.2217/pgs.14.126 CrossRefPubMed

24.

Offer SM, Wegner NJ, Fossum C et al (2013) Phenotypic profiling of DPYD variations relevant to 5-fluorouracil sensitivity using real-time cellular analysis and in vitro measurement of enzyme activity. Cancer Res 73:1958–1968. https://doi.org/10.1158/0008-5472.CAN-12-3858 CrossRefPubMedPubMedCentral

25.

Desmet F-O, Hamroun D, Lalande M et al (2009) Human splicing finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 37:e67. https://doi.org/10.1093/nar/gkp215 CrossRefPubMedPubMedCentral

26.

Parthiban V, Gromiha MM, Schomburg D (2006) CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Res 34:W239–W242. https://doi.org/10.1093/nar/gkl190 CrossRefPubMedPubMedCentral

27.

Huang CC, Meng EC, Morris JH et al (2014) Enhancing UCSF Chimera through web services. Nucleic Acids Res 42:W478–W484. https://doi.org/10.1093/nar/gku377 CrossRefPubMedPubMedCentral

28.

Dobritzsch D, Schneider G, Schnackerz KD, Lindqvist Y (2001) Crystal structure of dihydropyrimidine dehydrogenase, a major determinant of the pharmacokinetics of the anti-cancer drug 5-fluorouracil. EMBO J 20:650–660. https://doi.org/10.1093/emboj/20.4.650 CrossRefPubMedPubMedCentral

29.

Thomas F, Hennebelle I, Delmas C et al (2016) Genotyping of a family with a novel deleterious DPYD mutation supports the pretherapeutic screening of DPD deficiency with dihydrouracil/uracil ratio. Clin Pharmacol Ther 99:235–242. https://doi.org/10.1002/cpt.210 CrossRefPubMed

30.

Loriot M-A, Ciccolini J, Thomas F et al (2018) Dihydropyrimidine déhydrogenase (DPD) deficiency screening and securing of fluoropyrimidine-based chemotherapies: update and recommendations of the French GPCO-Unicancer and RNPGx networks. Bull Cancer 105:397–407. https://doi.org/10.1016/j.bulcan.2018.02.001 CrossRefPubMed

31.

van Kuilenburg ABP, Dobritzsch D, Meinsma R et al (2002) Novel disease-causing mutations in the dihydropyrimidine dehydrogenase gene interpreted by analysis of the three-dimensional protein structure. Biochem J 364:157–163. https://doi.org/10.1042/bj3640157 CrossRefPubMedPubMedCentral

32.

Etienne-Grimaldi MC, Boyer JC, Beroud C et al (2017) New advances in DPYD genotype and risk of severe toxicity under capecitabine. PLoS ONE 12:1–19. https://doi.org/10.1371/journal.pone.0175998 CrossRef

33.

Henricks LM, Meulendijks D, Swen JJ (2015) Translating DPYD genotype into DPD phenotype: using the DPYD gene activiy score. Pharmacogenomics 16:1275–1284CrossRef

34.

Tozer T, Heale K, Manto Chagas C et al (2019) Interdomain twists of human thymidine phosphorylase and its active-inactive conformations: binding of 5-FU and its analogues to human thymidine phosphorylase versus dihydropyrimidine dehydrogenase. Chem Biol Drug Des 94:1956–1972. https://doi.org/10.1111/cbdd.13596 CrossRefPubMed

35.

Etienne-Grimaldi M-C, Boyer J-C, Beroud C et al (2017) New advances in DPYD genotype and risk of severe toxicity under capecitabine. PLoS ONE 12:e0175998. https://doi.org/10.1371/journal.pone.0175998 CrossRefPubMedPubMedCentral

36.

Gross E, Ullrich T, Seck K et al (2003) Detailed analysis of five mutations in dihydropyrimidine dehydrogenase detected in cancer patients with 5-fluorouracil-related side effects. Hum Mutat 22:498. https://doi.org/10.1002/humu.9201 CrossRefPubMed

37.

van Kuilenburg ABP, Meijer J, Tanck MWT et al (2016) Phenotypic and clinical implications of variants in the dihydropyrimidine dehydrogenase gene. Biochim Biophys Acta Mol Basis Dis 1862:754–762. https://doi.org/10.1016/j.bbadis.2016.01.009 CrossRef

38.

Amstutz U, Farese S, Aebi S, Largiadèr CR (2009) Dihydropyrimidine dehydrogenase gene variation and severe 5-fluorouracil toxicity: a haplotype assessment. Pharmacogenomics 10:931–944. https://doi.org/10.2217/pgs.09.28 CrossRefPubMed

39.

Del Re M, Quaquarini E, Sottotetti F et al (2016) Uncommon dihydropyrimidine dehydrogenase mutations and toxicity by fluoropyrimidines: a lethal case with a new variant. Pharmacogenomics 17:5–9. https://doi.org/10.2217/pgs.15.146 CrossRefPubMed

40.

Rosmarin D, Palles C, Pagnamenta A et al (2015) A candidate gene study of capecitabine-related toxicity in colorectal cancer identifies new toxicity variants at DPYD and a putative role for ENOSF1 rather than TYMS. Gut 64:111–120. https://doi.org/10.1136/gutjnl-2013-306571 CrossRefPubMed

41.

Pellicer M, García-González X, García MI et al (2017) Use of exome sequencing to determine the full profile of genetic variants in the fluoropyrimidine pathway in colorectal cancer patients affected by severe toxicity. Pharmacogenomics 18:1215–1223. https://doi.org/10.2217/pgs-2017-0118 CrossRefPubMed

42.

Del Re M, Cinieri S, Michelucci A et al (2019) DPYD*6 plays an important role in fluoropyrimidine toxicity in addition to DPYD*2A and c.2846A>T: a comprehensive analysis in 1254 patients. Pharmacogenom J 19:556–563. https://doi.org/10.1038/s41397-019-0077-1 CrossRef

43.

Iachetta F, Romagnani A et al (2019) The clinical relevance of multiple DPYD polymorphisms on patients candidate for fluoropyrimidine based-chemotherapy. An Italian case–control Study. Br J Cancer. https://doi.org/10.1038/S41416-019-0423-8 CrossRefPubMedPubMedCentral

44.

Boige V, Vincent M, Alexandre P et al (2016) DPYD genotyping to predict adverse events following treatment with flourouracil-based adjuvant chemotherapy in patients with stage III colon cancer: a secondary analysis of the PETACC-8 randomized clinical trial. JAMA Oncol 2:655–662. https://doi.org/10.1001/jamaoncol.2015.5392 CrossRefPubMed

45.

Pellicer M, García-González X, García MI et al (2017) Identification of new SNPs associated with severe toxicity to capecitabine. Pharmacol Res 120:133–137. https://doi.org/10.1016/j.phrs.2017.03.021 CrossRefPubMed

46.

García-González X, Cortejoso L, García MI et al (2015) Variants in CDA and ABCB1 are predictors of capecitabine-related adverse reactions in colorectal cancer. Oncotarget 6:6422–6430. https://doi.org/10.18632/oncotarget.3289 CrossRefPubMedPubMedCentral

Title: New DPYD variants causing DPD deficiency in patients treated with fluoropyrimidine
Authors: Xandra García-González
Bartosz Kaczmarczyk
Judith Abarca-Zabalía
Fabienne Thomas
Pilar García-Alfonso
Luis Robles
Vanessa Pachón
Ángeles Vaz
Sara Salvador-Martín
María Sanjurjo-Sáez
Luis A. López-Fernández
Publication date: 01-07-2020
Publisher: Springer Berlin Heidelberg
Published in: Cancer Chemotherapy and Pharmacology / Issue 1/2020
Print ISSN: 0344-5704
Electronic ISSN: 1432-0843
DOI: https://doi.org/10.1007/s00280-020-04093-1

Webinar | 19-02-2024 | 17:30 (CET)

Keynote webinar | Spotlight on antibody–drug conjugates in cancer

Watch now

Antibody–drug conjugates (ADCs) are novel agents that have shown promise across multiple tumor types. Explore the current landscape of ADCs in breast and lung cancer with our experts, and gain insights into the mechanism of action, key clinical trials data, existing challenges, and future directions.

Dr. Véronique Diéras

Prof. Fabrice Barlesi

Developed by: Springer Medicine

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Abstract

Purpose

Methods

Results

Conclusion

Please log in to get access to this content

Other articles of this Issue 1/2020

A randomized phase II trial of cisplatin plus gemcitabine versus carboplatin plus gemcitabine in patients with completely resected non-small cell lung cancer: Hokkaido Lung Cancer Clinical Study Group Trial (HOT0703)

Berberine chloride suppresses non-small cell lung cancer by deregulating Sin3A/TOP2B pathway in vitro and in vivo

Assessment of effects of repeated oral doses of fedratinib on inhibition of cytochrome P450 activities in patients with solid tumors using a cocktail approach

Wide variation in tissue, systemic, and drain fluid exposure after oxaliplatin-based HIPEC: results of the GUTOX study

YLZ-F5, a novel polo-like kinase 4 inhibitor, inhibits human ovarian cancer cell growth by inducing apoptosis and mitotic defects

Comparison between single-agent and combination chemotherapy as second-line treatment for advanced non-small cell lung cancer: a multi-institutional retrospective analysis

Keynote webinar | Spotlight on antibody–drug conjugates in cancer