Radiation-related genomic profile of papillary thyroid carcinoma after the Chernobyl accident

Lindsay M. Morton1, Danielle M. Karyadi2, Chip Stewart3, Bogdanova Ti4, Eric T. Dawson2,5, Mia Steinberg6, Jieqiong Dai6, Stephen W. Hartley2, Sara J. Schonfeld1, Joshua N. Sampson7, Yosef E. Maruvka3, Vidushi Kapoor6, Dale A. Ramsden8, Juan Carvajal-Garcia9, Charles M. Perou10,11, Joel S. Parker10, Marko Krznarić12, Meredith Yeager6, Joseph F. Boland6, Amy Hutchinson6, Belynda Hicks6, Casey Dagnall6, Julie M. Gastier‐Foster13, Jay Bowen14, Olivia W. Lee2, Mitchell J. Machiela15, Elizabeth K. Cahoon1, Alina V. Brenner16, Kiyóhiko Mabuchi1, Vladimir Drozdovitch1, Sergii Masiuk17, Mykola Chepurny17, Liudmyla Zurnadzhy4, Maureen Hatch1, Amy Berrington de González1, Gerry Thomas12, М.D. Тronko18, Gad Getz3,19,20, Stephen J. Chanock2
1Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
2Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
3Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
4Laboratory of Morphology of the Endocrine System, V. P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv 04114, Ukraine.
5NVIDIA Corporation, Santa Clara, CA 95051, USA
6Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA.
7Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
8Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
9Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
10Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA.
11Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
12Department of Surgery and Cancer, Imperial College London, Charing Cross Hospital, London W6 8RF, UK.
13Departments of Pathology and Pediatrics, Ohio State University College of Medicine, Columbus, OH 43210, USA.
14Nationwide Children’s Hospital, Biospecimen Core Resource, Columbus, OH 43205, USA.
15Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
16Radiation Effects Research Foundation, Hiroshima 732-0815, Japan.
17Radiological Protection Laboratory, Institute of Radiation Hygiene and Epidemiology, National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv 04050, Ukraine.
18Department of Fundamental and Applied Problems of Endocrinology, V. P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv 04114, Ukraine.
19Center for Cancer Research and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.
20Harvard Medical School Boston, MA 02115 USA

Tóm tắt

Genomics of radiation-induced damage The potential adverse effects of exposures to radioactivity from nuclear accidents can include acute consequences such as radiation sickness, as well as long-term sequelae such as increased risk of cancer. There have been a few studies examining transgenerational risks of radiation exposure but the results have been inconclusive. Morton et al. analyzed papillary thyroid tumors, normal thyroid tissue, and blood from hundreds of survivors of the Chernobyl nuclear accident and compared them against those of unexposed patients. The findings offer insight into the process of radiation-induced carcinogenesis and characteristic patterns of DNA damage associated with environmental radiation exposure. In a separate study, Yeager et al. analyzed the genomes of 130 children and parents from families in which one or both parents had experienced gonadal radiation exposure related to the Chernobyl accident and the children were conceived between 1987 and 2002. Reassuringly, the authors did not find an increase in new germline mutations in this population. Science , this issue p. eabg2538 , p. 725

Từ khóa


Tài liệu tham khảo

United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) Sources and Effects of Ionizing Radiation: UNSCEAR 2008 Report to the General Assembly with Scientific Annexes (2010).

10.1002/ijc.30857

10.1002/ijc.27749

10.1667/RR14213.1

International Agency for Research on Cancer IARC Monographs on the Evaluation of Carcinogenic Risks to Humans vol. 100D: Radiation (2012).

10.1080/09553002.2019.1664788

10.1016/j.mrgentox.2013.07.016

10.1038/ncomms12605

10.1093/jnci/djx209

10.1016/j.cell.2014.09.050

10.1088/0952-4746/32/1/N77

10.1126/science.289.5488.2283a

10.1097/HP.0b013e31829f3096

10.1093/rpd/nct096

10.1097/HP.0b013e3181ff391a

10.2307/3579003

10.1093/jncimonographs/lgaa009

10.1093/jncimonographs/lgaa010

10.1038/s41586-020-1943-3

10.1038/nbt.3966

10.1016/j.celrep.2012.12.008

10.1038/s41586-020-1969-6

10.1016/j.ccell.2018.06.013

10.1016/j.ccell.2018.07.002

10.1093/nar/25.5.955

10.1093/bioinformatics/btq466

10.1073/pnas.1017137108

10.1038/onc.2014.311

10.1093/carcin/bgv043

10.1073/pnas.0506580102

10.1038/ncomms14517

10.1038/nrm.2017.48

10.1073/pnas.1921791117

10.1038/s41580-020-00297-8

10.1038/s41523-020-0161-3

10.1016/j.radmp.2020.01.005

10.1186/gb-2013-14-10-r115

10.1016/j.molcel.2012.10.016

10.1097/MD.0b013e31826a9c71

10.1002/path.5005

10.1007/s00439-002-0892-2

10.1016/j.molcel.2012.03.030

10.1038/s41568-018-0007-6

10.1126/science.aao3130

10.1016/j.clon.2011.01.160

10.1089/thy.2020.0308

10.1038/sj.bjc.6601860

10.1097/01.HP.0000291191.49583.f7

Interactive RadioEpidemiological Program Information Version 5.7 (2020); https://radiationcalculators.cancer.gov/irep/.

National Research Council Health Risks from Exposure to Low Levels of Ionizing Radiation: BEIR VII Phase 2 (National Academies Press 2006).

10.1186/2041-9414-4-1

10.1038/s41574-020-00448-z

10.1667/3148

10.1210/jc.2018-00847

H. Li Aligning sequence reads clone sequences and assembly contigs with BWA-MEM. arXiv 1303.3997v2 [q-bio.GN] (26 May 2013).

G. A. Van der Auwera et al . From FastQ data to high confidence variant calls: The Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinformatics 43 11 10 11–11 10 33 (2013).

J. Dai NCI-CGR/ChernobylThyroidCancer-RNAseq v1.0.1 (2021); DOI: 10.5281/zenodo.4543812.

J. Dai NCI-CGR/ChernobylThyroidCancer-miRNAseq v1.0.1 (2021); DOI: 10.5281/zenodo.4543818.

10.1186/s13059-014-0503-2

10.1093/nar/30.10.e47

10.1016/j.bbmt.2016.09.012

C. Birger . FireCloud a scalable cloud-based platform for collaborative genome analysis: Strategies for reducing and controlling costs. bioRxiv [preprint]. 3 November 2017.209494

10.1038/nbt.2514

D. Benjamin . Calling Somatic SNVs and Indels with Mutect2. bioRxiv [preprint]. 2 December 2019.861054

10.1093/bioinformatics/bts271

10.1038/s41592-018-0051-x

10.1101/gr.221028.117

10.1093/bioinformatics/btr446

10.1093/bioinformatics/btr330

10.1002/humu.22771

10.1158/0008-5472.CAN-17-0337

A. Smit R. Hubley P. Green RepeatMasker Open-4.0 (2013–2015); www.repeatmasker.org.

10.1093/nar/gks1443

10.1038/nature15395

10.1016/j.cels.2018.03.002

10.1038/s41586-020-1965-x

10.1101/gr.229202

10.1038/s41592-018-0036-9

10.1101/gr.141382.112

10.1038/s41586-019-1913-9

10.1093/bioinformatics/btv710

C. Stewart getzlab/REBC_tools: v1.1.0 (2021); DOI: 10.5281/zenodo.4558189.

10.1038/nbt.2203

S. W. Hartley REBC SCNA utils (2021); DOI: 10.5281/zenodo.4535549.

10.1038/nature12912

10.1186/gb-2011-12-4-r41

E. T. Dawson edawson/presig: Presig - REBC (2021); DOI: 10.5281/zenodo.4539528.

E. T. Dawson edawson/SigProfilerHelper: SigProfilerHelper - REBC (2021); DOI: 10.5281/zenodo.4539568.

E. T. Dawson edawson/tidysig: tidysig (REBC) (2021); DOI: 10.5281/zenodo.4539636.

10.1038/ng.3557

10.1038/ng.723

10.1126/science.296.5566.261b

10.1534/g3.118.200925

10.1038/ng1847

10.1038/ng1847

10.1038/nature19057

10.1038/nature15393

10.4161/fly.19695

10.1093/nar/gkt1113

10.1073/pnas.1919976117

10.1093/bioinformatics/btr467

10.1093/bioinformatics/bts617

B. J. Haas . STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. bioRxiv [preprint]. 24 March 2017.120295

10.1093/nar/gkq622

10.1038/srep21597

10.1093/nar/gkv1234

M. K. Steinberg NCI-CGR/ChernobylThyroidCancer-RNAFusionCalling v1.0.1 (2021); DOI: 10.5281/zenodo.4544030.

10.1093/nar/gkw227

M. K. Steinberg NCI-CGR/ChernobylThyroidCancer-RNAVariantCalling v1.0.1 (2021); DOI: 10.5281/zenodo.4544031.

J. Dai NCI-CGR/ChernobylThyroidCancer-Clustering v1.0.1 (2021); DOI: 10.5281/zenodo.4543808.

J. Dai NCI-CGR/ChernobylThyroidCancer-Methylation v1.0.1 (2021); DOI: 10.5281/zenodo.4543824.

10.1111/j.2517-6161.1995.tb02031.x

10.1093/bioinformatics/btu049

10.1093/bioinformatics/btx513

10.1073/pnas.0900780106

J. Dai NCI-CGR/ChernobylThyroidCancer-Scores v1.0.1 (2021); DOI: 10.5281/zenodo.4543809.

10.1038/s41586-020-1970-0

10.1186/1471-2105-14-7

10.1016/j.cell.2016.12.025

10.1073/pnas.1614265114

UNSCEAR Effects of Ionizing Radiation: United Nations Scientific Committee on the Effects of Atomic Radiation - UNSCEAR 2006 Report Volume 1 - Report to the General Assembly with Scientific Annexes A and B (2008).

D. Preston J. Lubin D. Pierce M. McConney N. Shilnikova Epicure Risk Regression and Person-Year Computation Software: Command Summary and User Guide (Risk Sciences International Ottawa 2015).