In-utero exposure to zidovudine-containing antiretroviral therapy and clonal hematopoiesis in HIV-exposed uninfected newborns

Shu-Hong Lin, Youjin Wang, Stephen W Hartley, Danielle M Karyadi, Olivia W Lee, Bin Zhu, Weiyin Zhou, Derek W Brown, Erin Beilstein-Wedel, Rohan Hazra, Deborah Kacanek, Ellen G Chadwick, Carmen J Marsit, Miriam C Poirier, Sean S Brummel, Stephen J Chanock, Eric A Engels, Mitchell J Machiela, Pediatric HIV/AIDS Cohort Study, Shu-Hong Lin, Youjin Wang, Stephen W Hartley, Danielle M Karyadi, Olivia W Lee, Bin Zhu, Weiyin Zhou, Derek W Brown, Erin Beilstein-Wedel, Rohan Hazra, Deborah Kacanek, Ellen G Chadwick, Carmen J Marsit, Miriam C Poirier, Sean S Brummel, Stephen J Chanock, Eric A Engels, Mitchell J Machiela, Pediatric HIV/AIDS Cohort Study

Abstract

Objective: Zidovudine (ZDV) has been extensively used in pregnant women to prevent vertical transmission of HIV but few studies have evaluated potential mutagenic effects of ZDV during fetal development.

Design: Our study investigated clonal hematopoiesis in HIV-exposed uninfected (HEU) newborns, 94 of whom were ZDV-exposed and 91 antiretroviral therapy (ART)-unexposed and matched for potential confounding factors.

Methods: Utilizing high depth sequencing and genotyping arrays, we comprehensively examined blood samples collected during the first week after birth for potential clonal hematopoiesis associated with fetal ZDV exposure, including clonal single nucleotide variants (SNVs), small insertions and deletions (indels), and large structural copy number or copy neutral alterations.

Results: We observed no statistically significant difference in the number of SNVs and indels per person in ZDV-exposed children (adjusted ratio [95% confidence interval, CI] for expected number of mutations = 0.79 [0.50--1.22], P = 0.3), and no difference in the number of large structural alterations. Mutations in common clonal hematopoiesis driver genes were not found in the study population. Mutational signature analyses on SNVs detected no novel signatures unique to the ZDV-exposed children and the mutational profiles were similar between the two groups.

Conclusion: Our results suggest that clonal hematopoiesis at levels detectable in our study is not strongly influenced by in-utero ZDV exposure; however, additional follow-up studies are needed to further evaluate the safety and potential long-term impacts of in-utero ZDV exposure in HEU children as well as better investigate genomic aberrations occurring late in pregnancy.

Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.

Figures

Figure 1.
Figure 1.
Number of somatic SNVs and indels combined in peripheral blood mononuclear cell derived DNA. Dotted lines indicate median for each group.
Figure 2.
Figure 2.
Mutation count by base context for somatic SNVs detected by deep coverage whole exome sequencing. Top panel: 94 ZDV-exposed infants. Lower panel: 91 ART-unexposed infants. Footnote: *: Base mutations are displayed in the reference>alternate format (e.g., C>A represents a C to A mutation). The X axis shows base context in which the base pair before and after the mutation are displayed. The Y axis represents the total number of mutations detected from each base context.
Figure 3.
Figure 3.
Log intensity ratio (LRR) and B-allele frequency (BAF) of detected SCNA by SNP arrays. (a) Detected mosaic SCNA on chromosome 6 from one participant. (b) Detected SCNA on chromosome X from another participant. Footnote: *: Black dots denote LRR of each SNP with scale on the left (Y1 axis), and red dots denote BAF of each SNP with scale on the right (Y2 axis). Three red bands represent BAF of SNPs with homozygous major alleles (bottom), heterozygous alleles (middle), and homozygous minor alleles (top). (a) Vertical grey lines and the horizontal blue line indicate the region with detected SCNA event (from 9,661,265 to 39,016,096). The two panels to the right are the probability density of BAF (red) and LRR (black) in normal (norm) and SCNA (Seg1) regions. The two black lines are the modes of two potentially overlapping BAF distributions, and the green shaded area shows the 95% confidence interval for the predicted mode. Based on the mode of BAF, about 5% of the cells carry this SCNA. (b) Both LRR and BAF suggested the event covered the whole chromosome. The decreased intensity in LRR suggested copy number loss, and the modes of BAF indicated that 62% of sampled cells carried this event.

References

    1. Connor EM, Sperling RS, Gelber R, Kiselev P, Scott G, O’Sullivan MJ, et al. Reduction of maternal-infant transmission of human immunodeficiency virus type 1 with zidovudine treatment. Pediatric AIDS Clinical Trials Group Protocol 076 Study Group. N Engl J Med 1994; 331:1173–1180.
    1. Little KM, Taylor AW, Borkowf CB, Mendoza MCB, Lampe MA, Weidle PJ, et al. Perinatal Antiretroviral Exposure and Prevented Mother-to-child HIV Infections in the Era of Antiretroviral Prophylaxis in the United States, 1994–2010. Pediatr Infect Dis J 2017; 36:66–71.
    1. Balzarini J, Naesens L, De Clercq E. New antivirals - mechanism of action and resistance development. Curr Opin Microbiol 1998; 1:535–546.
    1. Poirier MC, Olivero OA, Walker DM, Walker VE. Perinatal genotoxicity and carcinogenicity of anti-retroviral nucleoside analog drugs. Toxicol Appl Pharmacol 2004; 199:151–161.
    1. Le Chenadec J, Mayaux M-J, Guihenneuc-Jouyaux C, Blanche S, Enquête Périnatale Française Study Group. Perinatal antiretroviral treatment and hematopoiesis in HIV-uninfected infants. AIDS 2003; 17:2053–2061.
    1. European Collaborative Study. Levels and patterns of neutrophil cell counts over the first 8 years of life in children of HIV-1-infected mothers. AIDS 2004; 18:2009–2017.
    1. Pacheco SE, McIntosh K, Lu M, Mofenson LM, Diaz C, Foca M, et al. Effect of perinatal antiretroviral drug exposure on hematologic values in HIV-uninfected children: An analysis of the women and infants transmission study. J Infect Dis 2006; 194:1089–1097.
    1. Sussman HE, Olivero OA, Meng Q, Pietras SM, Poirier MC, O’Neill JP, et al. Genotoxicity of 3’-azido-3’-deoxythymidine in the human lymphoblastoid cell line, TK6: relationships between DNA incorporation, mutant frequency, and spectrum of deletion mutations in HPRT. Mutat Res 1999; 429:249–259.
    1. Meng Q, Walker DM, Olivero OA, Shi X, Antiochos BB, Poirier MC, et al. Zidovudine-didanosine coexposure potentiates DNA incorporation of zidovudine and mutagenesis in human cells. Proc Natl Acad Sci USA 2000; 97:12667–12671.
    1. Olivero OA, Anderson LM, Diwan BA, Haines DC, Harbaugh SW, Moskal TJ, et al. Transplacental effects of 3’-azido-2’,3’-dideoxythymidine (AZT): tumorigenicity in mice and genotoxicity in mice and monkeys. J Natl Cancer Inst 1997; 89:1602–1608.
    1. Walker DM, Malarkey DE, Seilkop SK, Ruecker FA, Funk KA, Wolfe MJ, et al. Transplacental carcinogenicity of 3’-azido-3’-deoxythymidine in B6C3F1 mice and F344 rats. Environ Mol Mutagen 2007; 48:283–298.
    1. Olivero OA, Torres LR, Gorjifard S, Momot D, Marrogi E, Divi RL, et al. Perinatal exposure of patas monkeys to antiretroviral nucleoside reverse-transcriptase inhibitors induces genotoxicity persistent for up to 3 years of age. J Infect Dis 2013; 208:244–248.
    1. Vivanti A, Soheili TS, Cuccuini W, Luce S, Mandelbrot L, Lechenadec J, et al. Comparing genotoxic signatures in cord blood cells from neonates exposed in utero to zidovudine or tenofovir. AIDS 2015; 29:1319–1324.
    1. André-Schmutz I, Dal-Cortivo L, Six E, Kaltenbach S, Cocchiarella F, Le Chenadec J, et al. Genotoxic signature in cord blood cells of newborns exposed in utero to a Zidovudine-based antiretroviral combination. J Infect Dis 2013; 208:235–243.
    1. IARC. Some Antiviral and Antineoplastic Drugs, and Other Pharmaceutical Agents. International Agency for Research on Cancer; 2000.
    1. Zink F, Stacey SN, Norddahl GL, Frigge ML, Magnusson OT, Jonsdottir I, et al. Clonal hematopoiesis, with and without candidate driver mutations, is common in the elderly. Blood 2017; 130:742–752.
    1. Desai P, Roboz GJ. Clonal Hematopoiesis and therapy related MDS/AML. Best Pract Res Clin Haematol 2019; 32:13–23.
    1. Desai P, Hassane D, Roboz GJ. Clonal Hematopoiesis and risk of Acute Myeloid Leukemia. Best Pract Res Clin Haematol 2019; 32:177–185.
    1. Jaiswal S, Natarajan P, Silver AJ, Gibson CJ, Bick AG, Shvartz E, et al. Clonal Hematopoiesis and Risk of Atherosclerotic Cardiovascular Disease. N Engl J Med 2017; 377:111–121.
    1. Dumanski JP, Lambert J-C, Rasi C, Giedraitis V, Davies H, Grenier-Boley B, et al. Mosaic Loss of Chromosome Y in Blood Is Associated with Alzheimer Disease. Am J Hum Genet 2016; 98:1208–1219.
    1. Loftfield E, Zhou W, Yeager M, Chanock SJ, Freedman ND, Machiela MJ. Mosaic Y Loss Is Moderately Associated with Solid Tumor Risk. Cancer Res 2019; 79:461–466.
    1. Genovese G, Kähler AK, Handsaker RE, Lindberg J, Rose SA, Bakhoum SF, et al. Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N Engl J Med 2014; 371:2477–2487.
    1. Coombs CC, Zehir A, Devlin SM, Kishtagari A, Syed A, Jonsson P, et al. Therapy-Related Clonal Hematopoiesis in Patients with Non-hematologic Cancers Is Common and Associated with Adverse Clinical Outcomes. Cell Stem Cell 2017; 21:374–382.e4.
    1. Hsu JI, Dayaram T, Tovy A, De Braekeleer E, Jeong M, Wang F, et al. PPM1D Mutations Drive Clonal Hematopoiesis in Response to Cytotoxic Chemotherapy. Cell Stem Cell 2018; 23:700–713.e6.
    1. Dumanski JP, Rasi C, Lönn M, Davies H, Ingelsson M, Giedraitis V, et al. Mutagenesis. Smoking is associated with mosaic loss of chromosome Y. Science 2015; 347:81–83.
    1. Wong JYY, Margolis HG, Machiela M, Zhou W, Odden MC, Psaty BM, et al. Outdoor air pollution and mosaic loss of chromosome Y in older men from the Cardiovascular Health Study. Environ Int 2018; 116:239–247.
    1. Williams PL, Seage GR, Van Dyke RB, Siberry GK, Griner R, Tassiopoulos K, et al. A trigger-based design for evaluating the safety of in utero antiretroviral exposure in uninfected children of human immunodeficiency virus-infected mothers. Am J Epidemiol 2012; 175:950–961.
    1. Williams PL, Crain MJ, Yildirim C, Hazra R, Van Dyke RB, Rich K, et al. Congenital anomalies and in utero antiretroviral exposure in human immunodeficiency virus-exposed uninfected infants. JAMA Pediatr 2015; 169:48–55.
    1. Rodriguez EM, Mendez H, Rich K, Sheon A, Fox H, Green K, et al. Maternal drug use in perinatal HIV studies. The Women and Infants Transmission Study. Ann N Y Acad Sci 1993; 693:245–248.
    1. Wang Y, Brummel SS, Beilstein-Wedel E, Dagnall CL, Hazra R, Kacanek D, et al. Association between zidovudine-containing antiretroviral therapy exposure in utero and leukocyte telomere length at birth. AIDS 2019; 33:2091–2096.
    1. Shi J, Yang XR, Ballew B, Rotunno M, Calista D, Fargnoli MC, et al. Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma. Nat Genet 2014; 46:482–486.
    1. Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, et al. The UCSC Genome Browser database: 2019 update. Nucleic Acids Res 2019; 47:D853–D858.
    1. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120.
    1. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011; 43:491–498.
    1. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv:12073907 [q-bio] Published Online First: 20 July 2012. (accessed 4 Mar2020).
    1. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012; 6:80–92.
    1. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 2016; 536:285–291.
    1. Auer PL, Reiner AP, Wang G, Kang HM, Abecasis GR, Altshuler D, et al. Guidelines for Large-Scale Sequence-Based Complex Trait Association Studies: Lessons Learned from the NHLBI Exome Sequencing Project. Am J Hum Genet 2016; 99:791–801.
    1. 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, et al. A global reference for human genetic variation. Nature 2015; 526:68–74.
    1. Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, et al. Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. bioRxiv 2019; :531210.
    1. Genovese G, Handsaker RE, Li H, Kenny EE, McCarroll SA. Mapping the Human Reference Genome’s Missing Sequence by Three-Way Admixture in Latino Genomes. Am J Hum Genet 2013; 93:411–421.
    1. Li H Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics 2014; 30:2843–2851.
    1. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, et al. Recent segmental duplications in the human genome. Science 2002; 297:1003–1007.
    1. Bergstrom EN, Huang MN, Mahto U, Barnes M, Stratton MR, Rozen SG, et al. SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. BMC Genomics 2019; 20:685.
    1. Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res 2019; 47:D941–D947.
    1. Dawson ET. edawson/tidysig.; 2020. (accessed 2 Jun2020).
    1. Rosales R, Drummond R, Valieris R, Silva IT da. signeR: Empirical Bayesian approach to mutational signature discovery. Bioconductor version: Release (3.11); 2020. doi:10.18129/B9.bioc.signeR
    1. Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, et al. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res 2006; 16:1136–1148.
    1. Jacobs KB, Yeager M, Zhou W, Wacholder S, Wang Z, Rodriguez-Santiago B, et al. Detectable clonal mosaicism and its relationship to aging and cancer. Nat Genet 2012; 44:651–658.
    1. Loh P-R, Genovese G, Handsaker RE, Finucane HK, Reshef YA, Palamara PF, et al. Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations. Nature 2018; 559:350–355.
    1. Hwang JTG, Yang M-C. AN OPTIMALITY THEORY FOR MID p–VALUES IN 2 × 2 CONTINGENCY TABLES. Statistica Sinica 2001; 11:807–826.
    1. R Core Team. R: A language and environment for statistical computing. Vienna, Austria:; 2014.
    1. Dorsheimer L, Assmus B, Rasper T, Ortmann CA, Ecke A, Abou-El-Ardat K, et al. Association of Mutations Contributing to Clonal Hematopoiesis With Prognosis in Chronic Ischemic Heart Failure. JAMA Cardiol 2019; 4:25–33.
    1. Haybar H, Shahrabi S, Ghanavat M, Khodadi E. Clonal hematopoiesis: Genes and underlying mechanisms in cardiovascular disease development. J Cell Physiol 2019; 234:8396–8401.
    1. Fuster JJ, Walsh K. Somatic Mutations and Clonal Hematopoiesis: Unexpected Potential New Drivers of Age-Related Cardiovascular Disease. Circ Res 2018; 122:523–532.
    1. Alexandrov LB, Jones PH, Wedge DC, Sale JE, Campbell PJ, Nik-Zainal S, et al. Clock-like mutational processes in human somatic cells. Nat Genet 2015; 47:1402–1407.
    1. Hagenkord JM, Parwani AV, Lyons-Weiler MA, Alvarez K, Amato R, Gatalica Z, et al. Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors. Diagn Pathol 2008; 3:44.
    1. Hleyhel M, Goujon S, Sibiude J, Tubiana R, Dollfus C, Faye A, et al. Risk of cancer in children exposed to antiretroviral nucleoside analogues in utero: The french experience. Environmental and Molecular Mutagenesis 2019; 60:404–409.

Source: PubMed

Patrocinadores y Colaboradores

Condiciones médicas

Intervenciones de drogas

3
Suscribir