Papers of the Month
By Anika Dzierlenga, Mahita Kadmiel, Cody Nichols, Simone Otto, and Qing Xu
Personal care product use and health outcomes in the NIEHS Sister Study
Scientists from the National Toxicology Program, NIEHS, and the University of North Carolina at Chapel Hill report that women with the highest use of personal care products in the Sister Study were more likely to have used hormone medications in the form of hormonal therapy or contraceptives. The Sister Study, composed of 50,884 women with a sister who had breast cancer, is a nationwide effort to identify environmental and genetic risk factors for breast cancer. The researchers hope to better understand the relationship between product use and health outcomes.
A statistical method called latent class analysis was used to divide the subjects into classes based on product type — beauty, skincare, or hair — and frequency of use. Personal identifiers for the population studied included race — non-Hispanic black and non-Hispanic white — age, menopausal status, education, and geography.
The team found that moderate lotion use was the most common product usage grouping among both black and white women. They also noted that race was a distinguishing factor in generating the subgroups across personal care product classes. Within subgroups, the highest correlation was between infrequent users of beauty products and infrequent users of skincare products. Exogenous hormonal exposures were strongly associated with higher levels of beauty and skincare product use. (AD)
Taylor KW, Baird DD, Herring AH, Engel LS, Nichols HB, Sandler DP, Troester MA. 2017. Associations among personal care product use patterns and exogenous hormone use in the NIEHS Sister Study. J Expo Sci Environ Epidemiol; doi:10.1038/jes.2016.82 [Online 25 January 2017].
Oxidized nucleotides block DNA repair
NIEHS researchers have revealed that oxidized nucleotides, which are DNA precursors modified by oxidative stress, can impede DNA repair mediated by polymerase beta (pol beta) and induce cytotoxicity. Oxidative stress occurs when reactive oxygen species are overproduced in cells due to various environmental factors. The findings shed light on the role of pol beta in genome maintenance following oxidative damage.
Because oxidized nucleotides incorporated in the genome could trigger DNA damage, they are either removed from the cellular nucleotide pool by the sanitizing enzyme MTH1, or corrected in DNA by the pol beta-dependent repair pathway, base excision repair (BER). The researchers in this study dissected the effect of oxidized nucleotides on DNA ligation, the final step of BER.
They found that insertion of oxidized nucleotides by pol beta led to ligation failure and cell cytotoxicity. In cells treated with the oxidizing agent, deletion of pol beta reduced cytotoxicity and DNA strand breaks, whereas MTH1 deficiency increased cell sensitivity to the oxidative stress. In addition, the type of oxidized nucleotides and template bases had an influence on the ligation. These results suggested that oxidized nucleotides could block pol beta-mediated DNA repair and lead to the DNA mutation and cell death involved in many oxidative stress-induced diseases. (QX)
Caglayan M, Horton JK, Dai DP, Stefanick DF, Wilson SH. 2017. Oxidized nucleotide insertion by pol beta confounds ligation during base excision repair. Nat Commun 8:14045. Story
DNA polymerase beta contains a nuclear localization signal
NIEHS scientists demonstrated that the repair enzyme DNA polymerase beta (pol beta) contains an N-terminal motif crucial to binding the import protein, Importin.
The scientists explained in the paper that DNA repair proteins must enter the nucleus to function, and that most of these proteins contain a nuclear localization signal (NLS) that binds to nuclear transport proteins. However, it was widely believed that pol beta lacked such a signal. Examination of the unstructured N-terminus suggested it might contain an NLS, and this fact was confirmed using nuclear magnetic resonance and fluorescence polarization studies. The pol beta NLS binds to Importin alpha, a nuclear import protein, supporting nuclear import.
Due to its small size, some pol beta is able to diffuse into and out of the nucleus through the large nuclear pore; however, development of a nuclear and cytosolic concentration gradient requires NLS-dependent transport. By manipulating the N-terminal sequence of pol beta in cellular models, the authors tested how the interaction of the sequence with import proteins affected cellular localization. Mutating the localization sequence reduced nuclear accumulation of the enzyme. The authors suggested this sequence could be used as a tool to alter the nuclear and cytosolic distribution of pol beta. (CN)
Kirby TW, Gassman NR, Smith CE, Zhao ML, Horton JK, Wilson SH, London RE. 2016. DNA polymerase beta contains a functional nuclear localization signal at its N-terminus. Nucleic Acids Res; doi:10.1093/nar/gkw1257 [Online 11 December 2016].
NIEHS clinical researcher helps find cause of rare congenital malformation
Working with an international team of doctors and scientists, Natalie Shaw, M.D., an NIEHS clinical investigator and pediatric endocrinologist, discovered the first genetic cause of human arhinia, or the complete absence of a nose. Mutations in this gene, called SMCHD1, were already known to cause a rare form of muscular dystrophy, but had never been linked to facial development.
SMCHD1 is an epigenetic repressor, or a protein that turns other genes off. Many of the patients in this study were not only born without a nose, they were also blind and did not go through puberty, suggesting that SMCHD1 may fine tune the expression of many genes during development.
In this study, the authors performed DNA sequencing in 40 patients with arhinia and found that 86 percent had a missense mutation in SMCHD1. Suppressing SMCHD1 function in zebrafish embryos produced abnormalities in the facial cartilage, smaller eyes, and changes to the central nervous system. Similar knockdown studies in mice did not cause morphological abnormalities, suggesting that SMCHD1 may not be working alone. That is, arhinia might only occur when the mutant SMCHD1 protein interacts with other proteins that are encoded by humans, but not by the mouse genome. (MK)
Shaw ND, Brand H, Kupchinsky ZA, Bengani H, Plummer L, Jones TI, Erdin S, Williamson KA, Rainger J, Stortchevoi A, Samocha K, Currall BB, Dunican DS, Collins RL, Willer JR, Lek A, Lek M, Nassan M, Pereira S, Kammin T, Lucente D, Silva A, Seabra CM, Chiang C, An Y, Ansari M, Rainger JK, Joss S, Smith JC, Lippincott MF, Singh SS, Patel N, Jing JW, Law JR, Ferraro N, Verloes A, Rauch A, Steindl K, Zweier M, Scheer I, Sato D, Okamoto N, Jacobsen C, Tryggestad J, Chernausek S, Schimmenti LA, Brasseur B, Cesaretti C, Garcia-Ortiz JE, Beitrago TP, Silva OP, Hoffman JD, Muhlbauer W, Ruprecht KW, Loeys BL, Shino M, Kaindl AM, Cho CH, Morton CC, Meehan RR, van Heyningen V, Liao EC, Balasubramanian R, Hall JE, Seminara SB, Macarthur D, Moore SA, Yoshiura KI, Gusella JF, Marsh JA, Graham JM Jr, Lin AE, Katsanis N, Jones PL, Crowley WF Jr, Davis EE, Fitzpatrick DR, Talkowski ME. 2017. SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome. Nat Genet 49:238–248. Story
Zinc finger domain critical to DNA repair
NIEHS scientists and their collaborators have discovered a novel DNA binding domain in the apurinic/apyrimidinic endonuclease 2 (APE2) that is critical for activating DNA damage response pathways following oxidative stress. The domain, Zf-GRF, is a highly conserved and widely distributed zinc finger module that activates APE2 to degrade DNA damage at single strand breaks. This work adds to the growing body of knowledge about how the body deals with the genomic instability that occurs with oxidative stress and its possible links to human disease.
To determine how the structure of APE2 informs its function, the team used a variety of techniques, including nuclear magnetic resonance, small angle X-ray scattering, X-ray crystallography, and functional studies in Xenopus extracts. The scientists found that APE2 has a Zf-GRF domain at the C-terminus of its amino acid chain, which is flexibly linked to the catalytic domain of APE2. The Zf-GRF specifically recognizes and binds the structure of single-stranded DNA (ssDNA), tethering APE2 to its DNA substrate.
APE2 is active in proliferating cells and is closely associated with proliferating cell nuclear antigen. When this complex attaches to DNA damage, it acts to generate ssDNA. The authors determined this process is critical for activation of the cellular DNA damage checkpoint, an alarm that is signaled in response to DNA damage caused by oxidative stress. (SO)
Wallace BD, Berman Z, Mueller GA, Lin Y, Chang T, Andres SN, Wojtaszek JL, DeRose EF, Appel CD, London RE, Yan S, Williams RS. 2017. APE2 Zf-GRF facilitates 3’-5’ resection of DNA damage following oxidative stress. Proc Natl Acad Sci U S A 114(2):304–309.