Papers of the Month
By Robin Arnette, Douglas Ganini da Silva, Kiri Hoff, Cody Nichols, and Payel Sil
NTP-led team creates sentinel gene set for exposures studies
Researchers from the National Toxicology Program (NTP) and NIEHS partnered with members of the Tox21 project and the bioinformatics company SciOme to determine a set of genes to use to detect human responses to exposures or diseases. The authors created the S1500-plus list by applying mathematical analyses of publicly available data on nearly 78,000 samples to identify highly informative sentinel genes.
The genes in the group were first selected by their power to differentiate between control and exposed samples. They were ranked for their capacity to predict the levels of other genes. The scientists then optimized the selection for maximal representation of all major biological functions. Finally, the scientific community nominated additional genes. After the data- and knowledge-driven effort, 2,739 genes were included in the S1500-plus gene set. Although this is only 15 percent of the total number of human genes, the set accurately detects human responses to chemicals and disease processes.
The gene set allowed the authors to predict levels of unmeasured genes and biological functions with high confidence. The scientists explained that detection of the S1500-plus genes might be sufficient to understand the overall response. The lower cost of measuring only the S1500-plus genes will speed up studies using with large numbers of people or samples. (DGS)
Citation: Mav D, Shah RR, Howard BE, Auerbach SS, Bushel PR, Collins JB, Gerhold DL, Judson RS, Karmaus AL, Maull EA, Mendrick DL, Merrick BA, Sipes NS, Svoboda D, Paules RS. 2018. A hybrid gene selection approach to create the S1500-plus targeted gene sets for use in high-throughput transcriptomics. PLoS One 13(2):e0191105.
Molecular crosstalk in the ribosomal RNA processing complex
Scientists at NIEHS have characterized Grc3, a protein that is essential in the processing of ribosomal RNA. Grc3 is a polynucleotide kinase (PNK), which is a class of enzymes that targets the 5-prime end of DNA and RNA substrates to transfer a phosphate from nucleoside triphosphates to the substrate. However, Grc3 is unable to carry out its kinase function on its own and needs a binding partner, the endoribonuclease Las1. The authors had previously shown there is functional crosstalk within the Grc3 and Las1 complex, but the mechanisms behind the interaction were not fully understood.
The authors generated a series of Grc3 variants to determine the requirements for kinase activity. Through a combination of in vitro and in vivo studies, the authors established the role of the kinase motifs within Grc3 that can direct Las1 activity to carry out its nuclease function. From these experiments, the authors concluded that the complex shows metal and nucleotide selectivity similar to other members of the PNK family, but it exhibits critical differences in substrate selection. This work reveals the checks and balances necessary for ribosomal RNA processing through the Grc3-Las1 complex. (CN)
Citation: Pillon MC, Sobhany M, Stanley RE. 2018. Characterization of the molecular crosstalk within the essential Grc3-Las1 pre-rRNA processing complex. RNA; doi:10.1261/rna.065037.117 [Online 9 February 2018].
Particulates in air pollution associated with chronic bronchitis
Long-term exposure to air pollution with particulate matter less than 10 micrometers in diameter (PM10) is associated with the prevalence of chronic bronchitis, according to researchers at NIEHS and the University of Washington. Chronic bronchitis refers to chronic cough and sputum production for at least three months in two or more consecutive years. It is a common condition that affects quality of life. The scientists also found that among never-smokers, air pollution containing particulate matter less than 2.5 micrometers (PM2.5) and nitrogen dioxide (NO2) was associated with chronic bronchitis symptoms. The study is the first and largest to show an association between PM10 and chronic bronchitis.
The scientists examined these relationships in 47,357 women participating in the NIEHS Sister Study, a long-term study of U.S. women with a sister diagnosed with breast cancer. The researchers used a national land-use regression model to estimate the annual average of PM10, PM2.5, and NO2 at the home addresses of participants. The U.S. Environmental Protection Agency revoked the standard for annual PM10 due to insufficient data on health risks associated with long-term exposure to PM10 as opposed to the finer PM2.5 fraction. These results add to the limited body of evidence that relate morbidity to long-term PM10 exposure. (RA)
Citation: Hooper LG, Young MT, Keller JP, Szpiro AA, O’Brien KM, Sandler DP, Vedal S, Kaufman JD, London SJ. 2018. Ambient air pollution and chronic bronchitis in a cohort of U.S. women. Environ Health Perspect 126(2):027005.
Acetylcholine plays key role in regulating memory formation
Members of the NIEHS Neurobiology Laboratory have shown that the neurotransmitter acetylcholine (ACh) in the brain enables the formation of new temporary hippocampal memory, known as encoding, by overriding the integration of the temporary memory to the long-term storage, also known as consolidation. The scientists found that ACh suppresses the hippocampus-entorhinal cortex (EC) pathway, part of the consolidation pathway, and that this inhibition is mediated by oriens lacunosum moleculare (OLM) interneurons. The work sheds light on how hippocampus-dependent memory occurs and may provide a therapeutic target for age-related cognitive impairments.
The researchers used in vitro and in vivo laboratory techniques, as well as mouse behavior studies, to determine that cholinergic modulation of OLM neurons are necessary for memory formation. They found that ACh suppresses the consolidation pathway running between the hippocampus and the deep layers of EC, via activating OLM interneurons, which release the inhibitory neurotransmitter GABA to the circuit. Using OLM-deficient mice, the team showed these neurons are critical for formation of hippocampus-dependent memory. The evidence suggests ACh modulation of the circuit via OLM interneurons is critical for memory formation. (PS)
Citation: Haam J, Zhou J, Cui G, Yakel JL. 2018. Septal cholinergic neurons gate hippocampal output to entorhinal cortex via oriens lacunosum moleculare interneurons. Proc Natl Acad Sci U S A 115(8):E1886–E1895.
Metal change in superoxide dismutase 2 promotes oxidative stress
Researchers from NIEHS showed that replacing the typical metal cofactor manganese with iron in the mitochondrial superoxide dismutase (SOD2) turns SOD2, an enzyme, into a prooxidant peroxidase that causes oxidative stress in cells and mice. Normally, SOD2 is incorporated with manganese and the enzyme removes free radicals. The finding may provide a possible mechanism for the origin of some diseases and cancers.
Manganese-bound SOD2 converts two superoxide anion free radicals into one oxygen and one hydrogen peroxide. The researchers showed that iron-bound SOD2 (FeSOD2) does not eliminate free radicals, but instead generates them through a peroxidase activity. They demonstrated that FeSOD2 oxidizes compounds using hydrogen peroxide. Experiments with cultured cells showed that FeSOD2 led to cellular damage and increased susceptibility to oxidative stress.
The researchers altered the mouse diet to have either higher than normal iron levels or decreased manganese levels. Animals fed those diets formed FeSOD2 in the liver, showed liver dysfunction, and had higher levels of mitochondrial free radicals. The researchers suggested that supplementing the human diet with iron should be investigated for the formation of FeSOD2 in the body and for its possible effect on the susceptibility to oxidative stress and development of diseases. (KH)
Citation: Ganini D, Santos JH, Bonini MG, Mason RP. 2018. Switch of mitochondrial superoxide dismutase into a prooxidant peroxidase in manganese-deficient cells and mice. Cell Chem Biol; doi:10.1016/j.chembiol.2018.01.007 [Online 26 January 2018].
(Douglas Ganini da Silva, Ph.D., is a research fellow in the NIEHS Free Radical Metabolism Group. Kiri Hoff, Ph.D., is an Intramural Research Training Award (IRTA) fellow in the NIEHS Mitochondrial DNA Replication Group. Cody Nichols, Ph.D., is an IRTA fellow in the NIEHS Genetics, Environment, and Respiratory Disease Group. Payel Sil, Ph.D., is an IRTA fellow in the NIEHS Inflammation and Autoimmunity Group.)