Papers of the Month
By Douglas Ganini da Silva, Katie Glenn, Ketrell McWhorter, Rajneesh Pathania, and Qing Xu
NTP identifies new candidate markers of liver toxicity
National Toxicology Program (NTP) scientists and their collaborators used an animal model to identify new genetic markers that predict liver cancer before tumors form. The authors evaluated novel liver RNAs in rats fed low levels of the fungal toxin aflatoxin B1, a known animal and human liver carcinogen. The newly identified genetic RNA markers could lead to sensitive and early diagnosis of liver cancer in humans.
The new genetic markers were a type of RNA molecule that does not contain the code for protein, also known as long noncoding RNA. The researchers named these newly discovered long noncoding RNAs hepatic aflatoxin transcripts (HAfTs). Of the 28 HAfTs that were initially detected, the identity, presence, and levels of 17 were confirmed by Sanger sequencing or polymerase chain reaction. The others were identified bioinformatically.
Because long noncoding RNAs can act as modulators of gene expression, the authors hypothesized that detection of the newly identified HAfTs might reflect a liver stress response to continued aflatoxin exposure in the animal model. Interestingly, many of the HAfTs identified in rats were also predicted to occur in mice and humans, including some novel forms in all three species. The scientists affirmed that HAfTs could be important for understanding human liver toxicity and the development of hepatic cancer. (DGS)
Citation: Merrick BA, Chang JS, Phadke DP, Bostrom MA, Shah RR, Wang X, Gordon O, Wright GM. 2018. HAfTs are novel IncRNA transcripts from aflatoxin exposure. PLoS One 13(1):e0190992.
Structural insights on DNA repair protein complexes
Research from NIEHS scientists suggests that the direct interaction of two scaffold proteins, XRCCI and APLF, forms a complex that optimizes repair of DNA double-strand breaks (DSBs). DSBs represent an extremely serious threat to the cell, and when they occur, a range of repair proteins is immediately recruited to the two DNA ends. In general, most of these first responder proteins are not the optimal repair proteins. Consequently, the second step of DSB repair involves a competition in which proteins supporting alternate DNA repair pathways compete to fix the damage. Initial recruitment of XRCC1 to a DSB is generally not an optimal response, and the interaction of APLF with XRCC1 may provide a rescue pathway that facilitates more optimal repair.
The investigators used various structural approaches to study the interactions between the APLF forkhead associated (FHA) domain and a phosphorylated FHA domain binding motif (FBM) on XRCC1. They found that the XRCC1-APLF binding affinity was greatly affected by nonspecific electrostatic interactions, with residues flanking the defined FBM of XRCC1. The study provides further understanding of the role of the XRCCI-APLF complex in DNA repair, a process that underpins the survival of all living organisms. (KG)
Citation: Kim K, Pedersen LC, Kirby TW, DeRose EF, London RE. 2017. Characterization of the APLF FHA-XRCC1 phosphopeptide interaction and its structural and functional implications. Nucleic Acids Res 45(21):12374–12387.
Brain receptors are required for generation of brain theta waves
NIEHS researchers revealed that two neurotransmitter receptors, the cholinergic receptor and the N-methyl-D-aspartate (NMDA) receptor, are essential for generation of theta rhythms, a state of brain waves involved in memory and spatial navigation. The findings shed new light on molecular mechanisms that control generation of theta waves and formation of spatial memory.
Brain cells transmit signals by passing neurotransmitters that bind to receptors on receiving neurons. The neurotransmission systems have been implicated in generation of theta waves, which are divided into two types, based on animal mobility. Type I occurs during active exploration and Type II occurs during immobility. In this study, researchers investigated how two memory-related receptors, cholinergic and NMDA, mediated the generation of type I theta waves in different brain regions.
After infusing freely moving mice with inhibitors of cholinergic or NMDA receptors in either the hippocampus or entorhinal cortex (EC), the scientists recorded theta waves from the hippocampus. They found that cholinergic receptors in the hippocampus and NMDA receptors in the EC were indispensable for theta generation. Inhibition of the receptors also impaired the ability of mice to memorize and recall locations. The results suggested both receptors play important roles in theta generation and associated behavioral performance. (QX)
Citation: Gu Z, Alexander GM, Dudek SM, Yakel JL. 2017. Hippocampus and entorhinal cortex recruit cholinergic and NMDA receptors separately to generate hippocampal theta oscillations. Cell Rep 21(12):3585–3595.
Defense against environmental stressors shortens life
NIEHS scientists and their collaborators used fruit flies to demonstrate that inflammatory responses to environmental stressors can reduce lifespan. The authors studied the stress-protecting roles of a molecule known as growth-blocking peptide (GBP) and discovered GBP’s binding partner, Methuselah-like receptor-10 (Mthl10). Working together, GBP and Mthl10 regulate processes that can either shorten or extend lifespan.
The scientists discovered Mthl10, which appears on the surface of cells, by screening more than 1,700 fruit fly proteins. They determined that GBP and Mthl10 bind together to promote inflammation, but in turn, shorten the lives of the fruit flies. When Mthl10 was removed from the fruit flies, GBP could not bind to the cells. These flies exhibited lower amounts of inflammation and lived longer. However, they succumbed to stressors in the environment and died faster than wild-type fruit flies. The scientists also showed that reducing dietary calories could reduce inflammation and extend lifespan.
The work supports a theory of aging that suggests more inflammation accelerates aging, leading to an earlier demise, and less inflammation extends life. The scientists propose that genes that are functionally equivalent to GBP and Mthl10 are present in humans. (RP)
Citation: Sung EJ, Ryuda M, Matsumoto H, Uryu O, Ochiai M, Cook ME, Yi NY, Wang H, Putney JW, Bird GS, Shears SB, Hayakawa Y. 2017. Cytokine signaling through Drosophila Mthl10 ties lifespan to environmental stress. Proc Natl Acad Sci U S A 114(52):13786–13791. (Story)
Diet and the microbiome lead to cancer-related changes
Using a mouse model of diet-induced obesity, NIEHS scientists found that the combination of diet and the microbiome can affect gene expression in the colonic epithelium. The findings, which suggest these changes may lead to obesity, obesity-related diseases, and colon cancer, provide important insight into the relationship between the microbiome and host disease risk.
Male and female mice were fed a high-fat diet (HFD), or a low-fat control diet for 20 weeks. After sequencing 16S rDNA from fecal samples, the scientists found the HFD led to an altered microbiome before the development of obesity, which altered bacterial metabolite production and potentially worsened obesity. The researchers also observed changes in histone methylation and acetylation at genomic loci associated with signaling pathways that were integral to the development of colon cancer.
Using germ-free mice, the research team found that transplantation of HFD-conditioned microbiota, combined with an obesogenic diet, recapitulated features of the long-term diet regimen. The diet and microbiome-dependent changes were reflected in both the composition of the recipient animals' microbiomes and in the set of transcription factor motifs identified at diet-influenced enhancers. Finally, they identified the signal-responsive nuclear receptor HNF4a as a putative target of bacterial metabolites that exerts regulatory effects on host gene expression. (KM)
Citation: Qin Y, Roberts JD, Grimm SA, Lih FB, Deterding LJ, Li R, Chrysovergis K, Wade PA. 2018. An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression. Genome Biol 19(1):7.
(Douglas Ganini da Silva, Ph.D., is a research fellow in the NIEHS Free Radical Metabolism Group. Katie Glenn, Ph.D., is an Intramural Research Training Award (IRTA) fellow in the NIEHS Mechanisms of Mutation Group. Ketrell McWhorter, Ph.D., is an IRTA fellow in the NIEHS Social and Environmental Determinants of Health Equity Group. Rajneesh Pathania, Ph.D., is a research fellow in the Systems Biology Group. Qing Xu is a biologist in the NIEHS Metabolism, Genes, and Environment Group.)