Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly.

Ebola virus nucleoprotein (eNP) assembles into higher-ordered structures that form the viral nucleocapsid (NC) and serve as the scaffold for viral RNA synthesis. However, molecular insights into the NC assembly process are lacking. Using a hybrid approach, we characterized the NC-like assembly of eNP, identified novel regulatory elements, and described how these elements impact function. We generated a three-dimensional structure of the eNP NC-like assembly at 5.8 Å using electron cryo-microscopy and identified a new regulatory role for eNP helices α22-α23. Biochemical, biophysical, and mutational analyses revealed that inter-eNP contacts within α22-α23 are critical for viral NC assembly and regulate viral RNA synthesis. These observations suggest that the N terminus and α22-α23 of eNP function as context-dependent regulatory modules (CDRMs). Our current study provides a framework for a structural mechanism for NC-like assembly and a new therapeutic target.

Human IFIT3 Modulates IFIT1 RNA Binding Specificity and Protein Stability.

Although interferon-induced proteins with tetratricopeptide repeats (IFIT proteins) inhibit infection of many viruses by recognizing their RNA, the regulatory mechanisms involved remain unclear. Here we report a crystal structure of cap 0 (m7GpppN) RNA bound to human IFIT1 in complex with the C-terminal domain of human IFIT3. Structural, biochemical, and genetic studies suggest that IFIT3 binding to IFIT1 has dual regulatory functions: (1) extending the half-life of IFIT1 and thereby increasing its steady-state amounts in cells; and (2) allosterically regulating the IFIT1 RNA-binding channel, thereby enhancing the specificity of recognition for cap 0 but not cap 1 (m7GpppNm) or 5'-ppp RNA. Mouse Ifit3 lacks this key C-terminal domain and does not bind mouse Ifit1. The IFIT3 interaction with IFIT1 is important for restricting infection of viruses lacking 2'-O methylation in their RNA cap structures. Our experiments establish differences in the regulation of IFIT1 orthologs and define targets for modulation of human IFIT protein activity.

MRI Is a DNA Damage Response Adaptor during Classical Non-homologous End Joining.

The modulator of retrovirus infection (MRI or CYREN) is a 30-kDa protein with a conserved N-terminal Ku-binding motif (KBM) and a C-terminal XLF-like motif (XLM). We show that MRI is intrinsically disordered and interacts with many DNA damage response (DDR) proteins, including the kinases ataxia telangiectasia mutated (ATM) and DNA-PKcs and the classical non-homologous end joining (cNHEJ) factors Ku70, Ku80, XRCC4, XLF, PAXX, and XRCC4. MRI forms large multimeric complexes that depend on its N and C termini and localizes to DNA double-strand breaks (DSBs), where it promotes the retention of DDR factors. Mice deficient in MRI and XLF exhibit embryonic lethality at a stage similar to those deficient in the core cNHEJ factors XRCC4 or DNA ligase IV. Moreover, MRI is required for cNHEJ-mediated DSB repair in XLF-deficient lymphocytes. We propose that MRI is an adaptor that, through multivalent interactions, increases the avidity of DDR factors to DSB-associated chromatin to promote cNHEJ.

Electrophilic properties of itaconate and derivatives regulate the IκBζ-ATF3 inflammatory axis.

Metabolic regulation has been recognized as a powerful principle guiding immune responses. Inflammatory macrophages undergo extensive metabolic rewiring 1 marked by the production of substantial amounts of itaconate, which has recently been described as an immunoregulatory metabolite 2 . Itaconate and its membrane-permeable derivative dimethyl itaconate (DI) selectively inhibit a subset of cytokines 2 , including IL-6 and IL-12 but not TNF. The major effects of itaconate on cellular metabolism during macrophage activation have been attributed to the inhibition of succinate dehydrogenase2,3, yet this inhibition alone is not sufficient to account for the pronounced immunoregulatory effects observed in the case of DI. Furthermore, the regulatory pathway responsible for such selective effects of itaconate and DI on the inflammatory program has not been defined. Here we show that itaconate and DI induce electrophilic stress, react with glutathione and subsequently induce both Nrf2 (also known as NFE2L2)-dependent and -independent responses. We find that electrophilic stress can selectively regulate secondary, but not primary, transcriptional responses to toll-like receptor stimulation via inhibition of IκBζ protein induction. The regulation of IκBζ is independent of Nrf2, and we identify ATF3 as its key mediator. The inhibitory effect is conserved across species and cell types, and the in vivo administration of DI can ameliorate IL-17-IκBζ-driven skin pathology in a mouse model of psoriasis, highlighting the therapeutic potential of this regulatory pathway. Our results demonstrate that targeting the DI-IκBζ regulatory axis could be an important new strategy for the treatment of IL-17-IκBζ-mediated autoimmune diseases.

An Interactive Modeling Tool for Projecting the Health and Direct Medical Cost Impact of Changes in the Sexually Transmitted Diseases Prevention Program Budgets.

CONTEXT: Estimating the return on investment for public health services, tailored to the state level, is critical for demonstrating their value and making resource allocation decisions. However, many health departments have limited staff capacity and expertise to conduct economic analyses in-house. PROGRAM: We developed a user-friendly, interactive Excel-based spreadsheet model that health departments can use to estimate the impact of increases or decreases in sexually transmitted infection (STI) prevention funding on the incidence and direct medical costs of chlamydia, gonorrhea, syphilis, and STI-attributable HIV infections. Users tailor results to their jurisdictions by entering the size of their population served; the number of annual STI diagnoses; their prior annual funding amount; and their anticipated new funding amount. The interface was developed using human-centered design principles, including focus groups with 15 model users to collect feedback on an earlier model version and a usability study on the prototype with 6 model users to finalize the interface. IMPLEMENTATION: The STI Prevention Allocation Consequences Estimator ("SPACE Monkey 2.0") model will be publicly available as a free downloadable tool. EVALUATION: In the usability testing of the prototype, participants provided overall positive feedback. They appreciated the clear interpretations, outcomes expressed as direct medical costs, functionalities to interact with the output and copy charts into external applications, visualization designs, and accessible information about the model's assumptions and limitations. Participants provided positive responses to a 10-item usability evaluation survey regarding their experiences with the prototype. DISCUSSION: Modeling tools that synthesize literature-based estimates and are developed with human-centered design principles have the potential to make evidence-based estimates of budget changes widely accessible to health departments.

Delivering Partner Services to Reduce Transmission and Promote Linkage to Care: Process Outcomes Varied for Chlamydial Infection, Gonorrhea, HIV, and Syphilis Cases.

CONTEXT: Partner services for HIV and sexually transmitted diseases, a public health intervention activity recommended by the Centers for Disease Control and Prevention, includes counseling, partner notification, linkage to care, and referral to other services. OBJECTIVE: A time study of partner services case investigations documented differences in times to process HIV/sexually transmitted disease cases. SETTING: Cases were from 9 local and regional sites in New York. PARTICIPANTS: Fifty-two partner services disease investigators documented 542 randomly selected cases (271 chlamydial infections, 162 gonorrhea, 48 HIV, and 61 syphilis cases) assigned between June and September 2014. Cases were the unit of the analysis and represented 6.9% of all partner services investigations in 2014. DESIGN: Cases were selected via stratified random sampling of infections assigned to staff. For each case, disease investigators completed a standard time study form to document the time spent on specific tasks and other outcomes. Kruskal-Wallis tests for continuous variables and χ tests for categorical variables assessed variation in outcomes across infection type. MAIN OUTCOME MEASURES: Outcomes included minutes spent on specific tasks (such as medical provider and index case outreach, travel, and partner notification), days the case remained open, disposition codes, and number of partners reached. RESULTS: Case processing times varied, with HIV and syphilis tasks taking more minutes (P < .001) and cases staying open for more days (P < .001). Partners were notified in 33% of cases overall, with more notifications in syphilis (44%). Most time (median = 77%) was spent on index cases and 2% (median) on partner notification, with a wide range across cases. CONCLUSIONS: Given their chronic resource constraints, public health agencies must identify efficient methods to allocate resources, including which infections to prioritize. Documenting how workers allocate time across cases is essential to improving the effectiveness and efficiency of this program and generating the data to model return on investment.

Improving Retention in HIV Care Through New York's Expanded Partner Services Data-to-Care Pilot.

CONTEXT: Data to Care (DTC) represents a public health strategy using HIV surveillance data to link persons living with diagnosed HIV infection (PLWDHI) to HIV-related medical care. OBJECTIVE: To investigate the feasibility of the DTC approach applied to a Partner Services program serving a geographically diffuse area of New York State. DESIGN: Disease intervention specialists received training to function as Expanded Partner Services (ExPS) advocates. HIV surveillance data identified PLWDHI presumed to be out of care (OOC). ExPS advocates attempted to locate and reengage OOC individuals in HIV-related care. The pilot ran from September 1, 2013, to August 31, 2014. SETTING: Four upstate New York counties, home to one-third of all PLWDHI in upstate New York. PARTICIPANTS: A total of 1155 PLWDHI presumed to be OOC. MAIN OUTCOME MEASURES: Linked to HIV medical care-cases verified as attending 1 or more HIV medical appointments subsequent to case assignment; reengaging in HIV care-any HIV laboratory test in the 6 months following case closure; and retention in HIV care-2 or more HIV laboratory tests in the 6 months following case closure. RESULTS: The majority of assigned cases (85.3%) were located; 23.7% (n = 233) of located cases confirmed as OOC; and 71.2% of OOC cases (n = 166) were successfully relinked into care. Relinkage success did not differ by gender, transmission risk, or major race/ethnicity categories; however, there was a direct relationship between age and successful relinkage (P < .001). Ninety-five percent of relinked cases reengaged in medical care, and 63.3% were retained in care. Individuals relinked by ExPS advocates were more likely to reengage in care (95%) than individuals interviewed but not relinked to care by advocates (53.7%) and individuals ineligible for the ExPS intervention (34.2%). CONCLUSION: DTC can be effective when conducted outside large metropolitan areas and/or closed health care systems. It can also be effectively incorporated into existing Partner Services programs; however, the relative priority of DTC work must be established in this context.

Preparation, crystallization, and preliminary crystallographic analysis of wild-type and mutant human TREM-2 ectodomains linked to neurodegenerative and inflammatory diseases.

TREM-2 (triggering receptor expressed on myeloid cells-2) is an innate immune receptor expressed on dendritic cells, macrophages, osteoclasts, and microglia. Recent genetic studies have reported the occurrence of point mutations in TREM-2 that correlate with a dramatically increased risk for the development of neurodegenerative diseases, including Alzheimer's disease, frontotemporal dementia, and Parkinson's disease. Structural and biophysical studies of wild-type and mutant TREM-2 ectodomains are required to understand the functional consequences of these mutations. In order to facilitate these studies, we undertook the production and crystallization of these proteins. Here we demonstrate that, unlike many single Ig domain proteins, TREM-2 could not be readily refolded from bacterially-expressed inclusion bodies. Instead, we developed a mammalian-cell based expression system for the successful production of wild-type and mutant TREM-2 proteins in milligram quantities and a single-chromatography-step purification scheme that produced diffraction-quality crystals. These crystals diffract to a resolution of 3.3 Å and produce data sufficient for structure determination. We describe herein the procedures to produce wild-type and mutant human TREM-2 Ig domains in sufficient quantities for structural and biophysical studies. Such studies are crucial to understand the functional consequences of TREM-2 point mutations linked to the development of neurodegenerative diseases and, ultimately, to develop patient-specific molecular therapies to treat them.

Structure-dependent lipid peroxidation by photoirradiation of pyrene and its mono-substituted derivatives.

Pyrene, one of the most studied polycyclic aromatic hydrocarbons, can damage biological macromolecules and cause toxicity when irradiated by light. The effect of substituents, 1-amino, 1-hydroxy, 1-nitro, and 1-bromo, on light-induced lipid peroxidation is studied. Degradation kinetics and photoproduct analyses were conducted to test how these substituents affect the photoreaction. All five compounds have widely different photodegradation rates, with degradation half-lives, ranging from 8 min to 495 min. These rates parallel their light absorptivity. Four out of the five compounds induce lipid peroxidation when irradiated with UVA light, whereas 1-aminopyrene causes minimum or no lipid peroxidation. The relative amount of lipid peroxidation caused is: 1-bromopyrene > pyrene > 1-nitropyrene ≈ 1-hydroxypyrene > 1-aminopyrene. This relative lipid peroxidation is dependent on the substituent due to the following factors: light absorptivity, relative rates of the competing processes in the excited states, nature of the photoreaction, and nature of the photoproducts.

Small Molecule Compounds That Inhibit Antioxidant Response Gene Expression in an Inducer-Dependent Manner.

Marburg virus (MARV) causes severe disease in humans and is known to activate nuclear factor erythroid 2-related factor 2 (Nrf2), the major transcription factor of the antioxidant response. Canonical activation of Nrf2 involves oxidative or electrophilic stress that prevents Kelch-like ECH-associated protein 1 (Keap1) targeted degradation of Nrf2, leading to Nrf2 stabilization and activation of the antioxidant response. MARV activation of Nrf2 is noncanonical with the MARV VP24 protein (mVP24) interacting with Keap1, freeing Nrf2 from degradation. A high-throughput screening (HTS) assay was developed to identify inhibitors of mVP24-induced Nrf2 activity and used to screen more than 55,000 compounds. Hit compounds were further screened against secondary HTS assays for the inhibition of antioxidant activity induced by additional canonical and noncanonical mechanisms. This pipeline identified 14 compounds that suppress the response, dependent on the inducer, with 50% inhibitory concentrations below 5 µM and selectivity index values greater than 10. Notably, several of the identified compounds specifically inhibit mVP24-induced Nrf2 activity.

A novel mode of capping protein-regulation by twinfilin.

Cellular actin assembly is controlled at the barbed ends of actin filaments, where capping protein (CP) limits polymerization. Twinfilin is a conserved in vivo binding partner of CP, yet the significance of this interaction has remained a mystery. Here, we discover that the C-terminal tail of Twinfilin harbors a CP-interacting (CPI) motif, identifying it as a novel CPI-motif protein. Twinfilin and the CPI-motif protein CARMIL have overlapping binding sites on CP. Further, Twinfilin binds competitively with CARMIL to CP, protecting CP from barbed-end displacement by CARMIL. Twinfilin also accelerates dissociation of the CP inhibitor V-1, restoring CP to an active capping state. Knockdowns of Twinfilin and CP each cause similar defects in cell morphology, and elevated Twinfilin expression rescues defects caused by CARMIL hyperactivity. Together, these observations define Twinfilin as the first 'pro-capping' ligand of CP and lead us to propose important revisions to our understanding of the CP regulatory cycle.

Allosteric Coupling of CARMIL and V-1 Binding to Capping Protein Revealed by Hydrogen-Deuterium Exchange.

Actin assembly is important for cell motility. The ability of actin subunits to join or leave filaments via the barbed end is critical to actin dynamics. Capping protein (CP) binds to barbed ends to prevent subunit gain and loss and is regulated by proteins that include V-1 and CARMIL. V-1 inhibits CP by sterically blocking one binding site for actin. CARMILs bind at a distal site and decrease the affinity of CP for actin, suggested to be caused by conformational changes. We used hydrogen-deuterium exchange with mass spectrometry (HDX-MS) to probe changes in structural dynamics induced by V-1 and CARMIL binding to CP. V-1 and CARMIL induce changes in both proteins' binding sites on the surface of CP, along with a set of internal residues. Both also affect the conformation of CP's ßß subunit "tentacle," a second distal actin-binding site. Concerted regulation of actin assembly by CP occurs through allosteric couplings between CP modulator and actin binding sites.

Cost Analysis and Performance Assessment of Partner Services for Human Immunodeficiency Virus and Sexually Transmitted Diseases, New York State, 2014.

OBJECTIVE: To estimate the programmatic costs of partner services for HIV, syphilis, gonorrhea, and chlamydial infection. STUDY SETTING: New York State and local health departments conducting partner services activities in 2014. STUDY DESIGN: A cost analysis estimated, from the state perspective, total program costs and cost per case assignment, patient interview, partner notification, and disease-specific key performance indicator. DATA COLLECTION: Data came from contracts, a time study of staff effort, and statewide surveillance systems. PRINCIPAL FINDINGS: Disease-specific costs per case assignment (mean: $580; range: $502-$1,111), patient interview ($703; $608-$1,609), partner notification ($1,169; $950-$1,936), and key performance indicator ($2,697; $1,666-$20,255) varied across diseases. Most costs (79 percent) were devoted to gonorrhea and chlamydial infection investigations. CONCLUSIONS: Cost analysis complements cost-effectiveness analysis in evaluating program performance and guiding improvements.

A Sensitive in Vitro High-Throughput Screen To Identify Pan-filoviral Replication Inhibitors Targeting the VP35-NP Interface.

The 2014 Ebola outbreak in West Africa, the largest outbreak on record, highlighted the need for novel approaches to therapeutics targeting Ebola virus (EBOV). Within the EBOV replication complex, the interaction between polymerase cofactor, viral protein 35 (VP35), and nucleoprotein (NP) is critical for viral RNA synthesis. We recently identified a peptide at the N-terminus of VP35 (termed NPBP) that is sufficient for interaction with NP and suppresses EBOV replication, suggesting that the NPBP binding pocket can serve as a potential drug target. Here we describe the development and validation of a sensitive high-throughput screen (HTS) using a fluorescence polarization assay. Initial hits from this HTS include the FDA-approved compound tolcapone, whose potency against EBOV infection was validated in a nonfluorescent secondary assay. High conservation of the NP-VP35 interface among filoviruses suggests that this assay has the capacity to identify pan-filoviral inhibitors for development as antivirals.

Dimerization Controls Marburg Virus VP24-dependent Modulation of Host Antioxidative Stress Responses.

Marburg virus (MARV), a member of the Filoviridae family that also includes Ebola virus (EBOV), causes lethal hemorrhagic fever with case fatality rates that have exceeded 50% in some outbreaks. Within an infected cell, there are numerous host-viral interactions that contribute to the outcome of infection. Recent studies identified MARV protein 24 (mVP24) as a modulator of the host antioxidative responses, but the molecular mechanism remains unclear. Using a combination of biochemical and mass spectrometry studies, we show that mVP24 is a dimer in solution that directly binds to the Kelch domain of Kelch-like ECH-associated protein 1 (Keap1) to regulate nuclear factor (erythroid-derived 2)-like 2 (Nrf2). This interaction between Keap1 and mVP24 occurs through the Kelch interaction loop (K-Loop) of mVP24 leading to upregulation of antioxidant response element transcription, which is distinct from other Kelch binders that regulate Nrf2 activity. N-terminal truncations disrupt mVP24 dimerization, allowing monomeric mVP24 to bind Kelch with higher affinity and stimulate higher antioxidative stress response element (ARE) reporter activity. Mass spectrometry-based mapping of the interface revealed overlapping binding sites on Kelch for mVP24 and the Nrf2 proteins. Substitution of conserved cysteines, C209 and C210, to alanine in the mVP24 K-Loop abrogates Kelch binding and ARE activation. Our studies identify a shift in the monomer-dimer equilibrium of MARV VP24, driven by its interaction with Keap1 Kelch domain, as a critical determinant that modulates host responses to pathogenic Marburg viral infections.

The Marburg virus VP24 protein interacts with Keap1 to activate the cytoprotective antioxidant response pathway.

Kelch-like ECH-associated protein 1 (Keap1) is a ubiquitin E3 ligase specificity factor that targets transcription factor nuclear factor (erythroid-derived 2)-like 2 (Nrf2) for ubiquitination and degradation. Disrupting Keap1-Nrf2 interaction stabilizes Nrf2, resulting in Nrf2 nuclear accumulation, binding to antioxidant response elements (AREs), and transcription of cytoprotective genes. Marburg virus (MARV) is a zoonotic pathogen that likely uses bats as reservoir hosts. We demonstrate that MARV protein VP24 (mVP24) binds the Kelch domain of either human or bat Keap1. This binding is of high affinity and 1:1 stoichiometry and activates Nrf2. Modeling based on the Zaire ebolavirus (EBOV) VP24 (eVP24) structure identified in mVP24 an acidic loop (K-loop) critical for Keap1 interaction. Transfer of the K-loop to eVP24, which otherwise does not bind Keap1, confers Keap1 binding and Nrf2 activation, and infection by MARV, but not EBOV, activates ARE gene expression. Therefore, MARV targets Keap1 to activate Nrf2-induced cytoprotective responses during infection.