Cross-talk between Lysine-Modifying Enzymes Controls Site-Specific DNA Amplifications.

Acquired chromosomal DNA amplifications are features of many tumors. Although overexpression and stabilization of the histone H3 lysine 9/36 (H3K9/36) tri-demethylase KDM4A generates transient site-specific copy number gains (TSSGs), additional mechanisms directly controlling site-specific DNA copy gains are not well defined. In this study, we uncover a collection of H3K4-modifying chromatin regulators that function with H3K9 and H3K36 regulators to orchestrate TSSGs. Specifically, the H3K4 tri-demethylase KDM5A and specific COMPASS/KMT2 H3K4 methyltransferases modulate different TSSG loci through H3K4 methylation states and KDM4A recruitment. Furthermore, a distinct chromatin modifier network, MLL1-KDM4B-KDM5B, controls copy number regulation at a specific genomic locus in a KDM4A-independent manner. These pathways comprise an epigenetic addressing system for defining site-specific DNA rereplication and amplifications.

Resveratrol: Friend or Foe?

In this issue of Molecular Cell, Benslimane et al. (2020) perform a CRISPR-Cas9 chemogenomic screen, identifying a network of DNA replication and genome integrity genes with the nutraceutical compound Resveratrol and its analog Pterostilbene, linking these compounds to the induction of DNA replication stress in mammalian cells.

PRMT5-Dependent Methylation of the TIP60 Coactivator RUVBL1 Is a Key Regulator of Homologous Recombination.

Protein post-translation modification plays an important role in regulating DNA repair; however, the role of arginine methylation in this process is poorly understood. Here we identify the arginine methyltransferase PRMT5 as a key regulator of homologous recombination (HR)-mediated double-strand break (DSB) repair, which is mediated through its ability to methylate RUVBL1, a cofactor of the TIP60 complex. We show that PRMT5 targets RUVBL1 for methylation at position R205, which facilitates TIP60-dependent mobilization of 53BP1 from DNA breaks, promoting HR. Mechanistically, we demonstrate that PRMT5-directed methylation of RUVBL1 is critically required for the acetyltransferase activity of TIP60, promoting histone H4K16 acetylation, which facilities 53BP1 displacement from DSBs. Interestingly, RUVBL1 methylation did not affect the ability of TIP60 to facilitate ATM activation. Taken together, our findings reveal the importance of PRMT5-mediated arginine methylation during DSB repair pathway choice through its ability to regulate acetylation-dependent control of 53BP1 localization.

Zinc finger proteins: guardians of genome stability.

Zinc finger proteins (ZNF), a unique yet diverse group of proteins, play pivotal roles in fundamental cellular mechanisms including transcription regulation, chromatin remodeling, protein/RNA homeostasis, and DNA repair. Consequently, the mis regulation of ZNF proteins can result in a variety of human diseases, ranging from neurodevelopmental disorders to several cancers. Considering the promising results of DNA damage repair (DDR) inhibition in the clinic, as a therapeutic strategy for patients with homologous recombination (HR) deficiency, identifying other potential targetable DDR proteins as emerged vulnerabilities in resistant tumor cells is essential, especially when considering the burden of acquired drug resistance. Importantly, there are a growing number of studies identifying new ZNFs and revealing their significance in several DDR pathways, highlighting their great potential as new targets for DDR-inhibition therapy. Although, there are still many uncharacterized ZNF-containing proteins with unknown biological function. In this review, we highlight the major classes and observed biological functions of ZNF proteins in mammalian cells. We briefly introduce well-known and newly discovered ZNFs and describe their molecular roles and contributions to human health and disease, especially cancer. Finally, we discuss the significance of ZNFs in DNA repair mechanisms, their potential in cancer therapy and advances in exploiting ZNF proteins as future therapeutic targets for human disease.

DNA repair as a shared hallmark in cancer and ageing.

Increasing evidence demonstrates that DNA damage and genome instability play a crucial role in ageing. Mammalian cells have developed a wide range of complex and well-orchestrated DNA repair pathways to respond to and resolve many different types of DNA lesions that occur from exogenous and endogenous sources. Defects in these repair pathways lead to accelerated or premature ageing syndromes and increase the likelihood of cancer development. Understanding the fundamental mechanisms of DNA repair will help develop novel strategies to treat ageing-related diseases. Here, we revisit the processes involved in DNA damage repair and how these can contribute to diseases, including ageing and cancer. We also review recent mechanistic insights into DNA repair and discuss how these insights are being used to develop novel therapeutic strategies for treating human disease. We discuss the use of PARP inhibitors in the clinic for the treatment of breast and ovarian cancer and the challenges associated with acquired drug resistance. Finally, we discuss how DNA repair pathway-targeted therapeutics are moving beyond PARP inhibition in the search for ever more innovative and efficacious cancer therapies.

Assessing kinetics and recruitment of DNA repair factors using high content screens.

Repair of genetic damage is coordinated in the context of chromatin, so cells dynamically modulate accessibility at DNA breaks for the recruitment of DNA damage response (DDR) factors. The identification of chromatin factors with roles in DDR has mostly relied on loss-of-function screens while lacking robust high-throughput systems to study DNA repair. In this study, we have developed two high-throughput systems that allow the study of DNA repair kinetics and the recruitment of factors to double-strand breaks in a 384-well plate format. Using a customized gain-of-function open-reading frame library ("ChromORFeome" library), we identify chromatin factors with putative roles in the DDR. Among these, we find the PHF20 factor is excluded from DNA breaks, affecting DNA repair by competing with 53BP1 recruitment. Adaptable for genetic perturbations, small-molecule screens, and large-scale analysis of DNA repair, these resources can aid our understanding and manipulation of DNA repair.

Histone Lysine Methylation Dynamics Control EGFR DNA Copy-Number Amplification.

Acquired chromosomal DNA copy gains are a feature of many tumors; however, the mechanisms that underpin oncogene amplification are poorly understood. Recent studies have begun to uncover the importance of epigenetic states and histone lysine methyltransferases (KMT) and demethylases (KDM) in regulating transient site-specific DNA copy-number gains (TSSG). In this study, we reveal a critical interplay between a myriad of lysine methyltransferases and demethylases in modulating H3K4/9/27 methylation balance to control extrachromosomal amplification of the EGFR oncogene. This study further establishes that cellular signals (hypoxia and EGF) are able to directly promote EGFR amplification through modulation of the enzymes controlling EGFR copy gains. Moreover, we demonstrate that chemical inhibitors targeting specific KMTs and KDMs are able to promote or block extrachromosomal EGFR amplification, which identifies potential therapeutic strategies for controlling EGFR copy-number heterogeneity in cancer, and, in turn, drug response. SIGNIFICANCE: This study identifies a network of epigenetic factors and cellular signals that directly control EGFR DNA amplification. We demonstrate that chemical inhibitors targeting enzymes controlling this amplification can be used to rheostat EGFR copy number, which uncovers therapeutic opportunities for controlling EGFR DNA amplification heterogeneity and the associated drug response.This article is highlighted in the In This Issue feature, p. 161.

PRMT5 Is a Critical Regulator of Breast Cancer Stem Cell Function via Histone Methylation and FOXP1 Expression.

Breast cancer progression, treatment resistance, and relapse are thought to originate from a small population of tumor cells, breast cancer stem cells (BCSCs). Identification of factors critical for BCSC function is therefore vital for the development of therapies. Here, we identify the arginine methyltransferase PRMT5 as a key in vitro and in vivo regulator of BCSC proliferation and self-renewal and establish FOXP1, a winged helix/forkhead transcription factor, as a critical effector of PRMT5-induced BCSC function. Mechanistically, PRMT5 recruitment to the FOXP1 promoter facilitates H3R2me2s, SET1 recruitment, H3K4me3, and gene expression. Our findings are clinically significant, as PRMT5 depletion within established tumor xenografts or treatment of patient-derived BCSCs with a pre-clinical PRMT5 inhibitor substantially reduces BCSC numbers. Together, our findings highlight the importance of PRMT5 in BCSC maintenance and suggest that small-molecule inhibitors of PRMT5 or downstream targets could be an effective strategy eliminating this cancer-causing population.

Responding to a bioterrorism attack--one scenario: part 1.

This article continues the discussions introduced in an earlier article submitted to The Health Care Manager entitled "Epidemic Simulation for Syndromic Surveillance," wherein a format for analysis of the incidence of a bioterrorist attack was presented. This article outlines a simulation conducted as part of a federal grant award administered through the Center for Biological Defense at the University of South Florida. The disease entity simulated was an attack of anthrax introduced into the Central Florida region. The spread, effects, and eventual control of the disease entity are highlighted.

Responding to a bioterrorism attack-one scenario: part 2.

This article continues the discussions introduced in the earlier article submitted to The Health Care Manager that is titled Epidemic Simulation for Syndromic Surveillance, where a format for analysis of the incidence of a bioterrorist attack was presented. Part 2 of this series provides a discussion of the observed outcomes from the simulation techniques. This simulation was conducted as part of a federal grant award administered through the Center for Biological Defense at the University of South Florida. The disease entity simulated was an attack of anthrax introduced into the Central Florida region. The spread, effects, and eventual control of the disease entity are highlighted.

Epidemic simulation for syndromic surveillance.

This article reports on a project to develop a simulation-based test bed for the BioDefend Syndromic Surveillance System. BioDefend is a system that data mines syndrome reports from emergency rooms and so forth to produce early alerts of epidemic onset. An existing large-scale epidemic simulation will be adapted to provide synthetic reports of syndromes associated with extremely rare events such as pandemics and bioterrorism. The Spatiotemporal Epidemiological Modeler will be used as the basis of the test bed. Results from the much simpler Spatiotemporal Epidemiological Modeler simulation will be validated by comparison against results from the more complex Epidemiological Simulation System. These synthesized reports will be used to test BioDefend's ability to detect epidemic outbreaks and to evaluate its data-mining algorithm. The development of an optimal algorithm for processing syndrome reports to provide reliable epidemic early warnings is a difficult research problem that the test bed should help address.

Condom acquisition and preferences within a sample of sexually active gay and bisexual men in the southern United States.

Health departments, community-based organizations (CBOs), and AIDS service organizations (ASOs) in the United States and abroad distribute large quantities of free condoms to sexually active individuals; however, little is known about where individuals who use condoms actually acquire them. This community-based participatory research (CBPR) study was designed to identify factors associated with the use of free condoms during most recent anal intercourse among self-identifying gay and bisexual men who reported condom use. Data were collected using targeted intercept interviewing during North Carolina Pride Festival events in Fall 2006, using the North Carolina Condom Acquisition and Preferences Assessment (NC-CAPA). Of the 606 participants who completed the assessment, 285 met the inclusion criteria. Mean age of participants was 33 (+/-10.8) years. The sample was predominantly white (80%), 50% reported being single or not dating anyone special, and 38% reported the use of free condoms during most recent anal intercourse. In multivariable analysis, participants who reported using free condoms during most recent anal sex were more likely to report increased age; dating someone special or being partnered; and having multiple male sexual partners in the past 3 months. These participants were less likely to report ever having had a sexually transmitted disease. Despite being in the third decade of the HIV epidemic, little is known about condom acquisition among, and condom preferences of, gay and bisexual men who use condoms. Although more research is needed, our findings illustrate the importance of free condom distribution.