Papers of the Month
By Aidin Alejo Abdala, Melissa Li, Victoria Placentra, Payel Sil, and Dahea You
NTP identifies differential molecular changes in rodent liver tumors
Using a mouse model, scientists at the National Toxicology Program (NTP) have demonstrated that in a type of liver cancer called hepatocellular carcinoma (HCC), methylation and gene expression profiles differ between HCCs that arise spontaneously and those due to chronic exposure to gingko biloba extract (GBE). A commonly used botanical supplement in the U.S., GBE is marketed as an anticancer and antioxidant agent. Previous NTP studies showed that in rodents, exposure to GBE for 2 years results in HCCs, but the mechanisms behind that cancer development are not fully understood.
Epigenetic modifications, such as methylation, can alter gene expression and play an important role in cancer development. The NTP researchers evaluated the global methylation profiles and the corresponding gene expression profiles in mice with HCCs arising either spontaneously or due to GBE exposure. Although these tumors are morphologically indistinguishable, the methylation and gene expression profiles are very different. For example, the researchers were able to validate that the promoter of oncogene c-myc¬ had less methylation in GBE-induced tumors compared to spontaneous tumors. Consistent with the decrease in methylation, c-myc gene expression was upregulated in GBE-induced tumors.
As more chemicals make their way into the environment, studies like this one potentially allow scientists to differentiate between chemically-induced and spontaneous cancers. (ML)
Citation: Kovi RC, Bhusari S, Mav D, Shah RR, Ton TV, Hoenerhoff MJ, Sills RC, Pandiri AR. 2019. Genome-wide promoter DNA methylation profiling of hepatocellular carcinomas arising either spontaneously or due to chronic exposure to Ginkgo biloba extract (GBE) in B6C3F1/N mice. Arch Toxicol; doi:10.1007/s00204-019-02505-7 [Online 5 July 2019].
Beta-arrestin-1 is a critical regulator of glucocorticoid signaling
NIEHS researchers have identified a novel interaction between the glucocorticoid receptor (GR) and beta-arrestin-1, a protein involved in a process called G protein-coupled receptor signaling. Beta-arrestin-1 binds to GR in the cytoplasm and stabilizes GR protein expression. The finding may reveal the mechanisms that contribute to the cell type-specific activities of glucocorticoids, which are molecules that can help stop inflammation.
The scientists explained that beta-arrestin-1 protects GR by binding to it. The resulting protein complex translocates to the nucleus to engage in various regulatory activities, such as binding to DNA or tethering other transcription factors.
During the study, the authors silenced the expression of the beta-arrestin-1 gene, known as ARRB1, in adenocarcinomic human alveolar basal epithelial cells. The resulting reduction of GR half-life led them to uncover the role of a protein known as E3 ubiquitin ligase pellino-1 (PELI1) in marking GR for proteosomal degradation. The results indicated that ARRB1 protected GR by tempering the transcription of PELI1 and preventing the binding of PELI1 to GR. ARRB1 and related genes are known to modulate the function of beta-2 adrenergic receptors involved in vital biological functions. Therefore, this work provides an opportunity to explore their role in other cellular functions. (PS)
Citation: Petrillo MG, Oakley RH, Cidlowski JA. 2019. Beta-arrestin-1 inhibits glucocorticoid receptor turnover and alters glucocorticoid signaling. J Biol Chem 294(29):11225–11239.
NF-Y protein key for proper transcription initiation
An international research team led by NIEHS scientists showed that a protein called NF-Y plays a crucial role in transcription. Transcription, the process of copying or transcribing a gene’s DNA sequence into messenger RNA, is the first step in making a protein. The researchers determined that NF-Y maintains the nucleosome-depleted region (NDR) at gene promoters while ensuring transcription begins at the right place. NDR maintenance — a previously unknown role for NF-Y — is essential for the proper binding of transcription factors at the appropriate transcription start site (TSS). Nucleosomes are formed when DNA wraps around histone proteins, like thread wrapped around a spool.
Using mouse embryonic stem cells (ESCs), the researchers compared ChIP-Seq and MNase-Seq data to demonstrate that when NF-Y was bound at the promoters, NDR was maintained and transcription started at the correct TSS. However, when NF-Y was removed from mouse ESCs, NDR was not maintained and transcription began at an incorrect TSS. The research indicates that NF-Y is necessary to prevent the mutant proteins that would result from incorrect transcription initiation, which can have detrimental effects on cell function. (VP)
Citation: Oldfield AJ, Henriques T, Kumar D, Burkholder AB, Cinghu S, Paulet D, Bennett BD, Yang P, Scruggs BS, Lavender CA, Rivals E, Adelman K, Jothi R. 2019. NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region. Nat Commun 10(1):3072. (Story)
Compound treats corticosteroid-resistant form of asthma
Scientists at NIEHS report that VTP-938, a new, orally-available drug that selectively opposes the action of the nuclear receptor known as retinoic acid-related orphan receptor gamma-t (RORgamma-t), might be a novel therapeutic approach for treating neutrophilic asthma. That form of asthma can be particularly severe and responds poorly to the standard asthma therapy of corticosteroids. It is thought that neutrophilic asthma is driven by a T-cell type known as T-helper 17 (Th17) cells, which are in turn controlled by the master transcription factor, RORgamma-t.
Because other inhibitors of this transcription factor previously had been shown to alleviate different types of Th17-associated inflammatory diseases, the researchers tested whether VTP-938 could prevent or reduce the severity of neutrophilic asthma. When administered to mice before allergic sensitization, the compound suppressed the development of allergen-specific Th17 cells, thus largely preventing the neutrophilic inflammation and allergic responses seen upon subsequent exposure to inhaled allergen. Importantly, VTP-938 also diminished established airway hyperresponsiveness, a hallmark clinical presentation of asthma, which developed after exposure to house dust extracts. These results suggest that VTP-938 may be an innovative, orally-administered treatment for patients with this steroid-resistant form of asthma. (DY)
Citation: Whitehead GS, Kang HS, Thomas SY, Medvedev A, Karcz TP, Izumi G, Nakano K, Makarov SS, Nakano H, Jetten AM, Cook DN. 2019. Therapeutic suppression of pulmonary neutrophilia and allergic airway hyperresponsiveness by a RORgamma-t inverse agonist. JCI Insight; doi:10.1172/jci.insight.125528 [Online 11 June 2019].
Crystal structure shows RNA-binding domains collaborate within protein
After obtaining crystal structures for RNA bound to the Pumilio-homology domain (PUM-HD) of PUF protein Puf1, NIEHS researchers and their collaborators demonstrated that two domains in the same protein work together to create a unique RNA-binding specificity. PUF proteins are a family of RNA-binding proteins that are conserved among eukaryotes. These molecules are key for the lifecycle of mRNAs, and their dysfunction is associated with neurological disorders and cancer in humans. Specifically, Puf1 and Puf2 differ from other PUF proteins because they have two RNA-binding domains: a PUM-HD and an RNA recognition motif (RRM).
The crystal structure shows two Puf1 proteins from Schizosaccharomyces pombe bound to one RNA molecule, which contains two binding motifs (UAAU). It represents a new stoichiometry for RNA binding in PUF proteins. Using other molecular biology assays, the authors determined the collaboration between the PUM-HD and RRM domains. Though the RRM domain does not directly bind RNA, it influences PUM-HD to favor dual UAAU motif binding and dimerization. This paper showed a new mechanism of RNA binding in which cooperation between different modules within a single protein alters target specificity. These insights advance the understanding of RNA regulation and can serve to propel genomic studies forward. (AAA)
Citation: Qiu C, Dutcher RC, Porter DF, Arava Y, Wickens M, Hall TMT. 2019. Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity. Nucleic Acids Res; doi:10.1093/nar/gkz583 [Online 11 July 2019].
(Aidin Alejo Abdala is an Intramural Research Training Award [IRTA] postbaccalaureate fellow in the NIEHS Clinical Investigation of Host Defense Group. Melissa Li, Ph.D., is an IRTA fellow in the NIEHS Biostatistics and Computational Biology Branch. Victoria Placentra is an IRTA postbaccalaureate fellow in the NIEHS Mutagenesis and DNA Repair Regulation Group. Payel Sil, Ph.D., is an IRTA fellow in the NIEHS Inflammation and Autoimmunity Group. Dahea You, Pharm.D., Ph.D., is an IRTA postdoctoral fellow in the Biomolecular Screening Branch of NTP.)