Acquired Human Immunodeficiency Virus Type 1 Drug Resistance in Rhode Island, USA, 2004-2021.

BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) acquired drug resistance (ADR) compromises antiretroviral therapy (ART). METHODS: We aggregated all HIV-1 protease-reverse transcriptase-integrase sequences over 2004-2021 at the largest HIV center in Rhode Island and evaluated ADR extent, trends, and impact using Stanford Database tools. Trends were measured with Mann-Kendall statistic, and multivariable regressions evaluated resistance predictors. RESULTS: Sequences were available for 914 ART-experienced persons. Overall ADR to any drug decreased from 77% to 49% (-0.66 Mann-Kendall statistic); nucleoside reverse transcriptase inhibitors 65% to 32%, nonnucleoside reverse transcriptase inhibitors 53% to 43%, and protease inhibitors 28% to 7% (2004-2021), and integrase strand transfer inhibitors 16% to 13% (2017-2021). Multiclass resistance decreased from 44% to 12% (2-class) and 12% to 6% (3-class). In 2021, 94% had at least one 3-drug or 2-drug one-pill-once-daily (OPOD) option. Males and those exposed to more ART regimens were more likely to have ≥2-class resistance, and higher regimen exposure was also associated with fewer OPOD options. CONCLUSIONS: Comprehensive analyses within a densely-sampled HIV epidemic over 2004-2021 demonstrated decreasing ADR. Continued ADR monitoring is important to maintain ART success, particularly with rising INSTI use in all lines of therapy and 2-drug and long-acting formulations.

Considerations for STI Clinics During the COVID-19 Pandemic.

Coronavirus disease (COVID-19) is responsible for a global pandemic. It is important to balance the need for access to healthcare services, including testing and treatment for sexually transmitted infections. Sexually transmitted infection programs must consider how to use limited resources and implement novel approaches to provide continued access to care.

The Cost and Cost-utility of Three Public Health HIV Case-finding Strategies: Evidence from Rhode Island, 2012-2014.

To evaluate three testing strategies to identify new HIV diagnoses in Rhode Island (RI). RI deployed three testing strategies, by using rapid HIV tests at clinical settings, community-based organization (CBO) settings, and the Partner Notification Services (PNS) program from 2012 to 2014. We reviewed the rapid HIV test results and confirmatory test results to identify new diagnoses, and conducted a cost-utility analysis. The average cost per new diagnosis was $33,015 at CBO settings, $5446 at clinical settings, and $33,818 at the PNS program. The cost-utility analysis showed the state-wide program was cost-saving; testing was cost-saving at clinical settings, and cost-effective at CBO settings and the PNS program. Further analyses showed that cost-effectiveness varied widely across CBOs. The HIV testing expansion program in RI was cost-saving overall. The heterogeneity of cost-effectiveness across settings should provide guidance to officials for allocation of future resources to HIV testing.

Public health opportunities and challenges in the provision of partner notification services: the New England experience.

BACKGROUND: Partner notification services (PNS) are recommended by the Centers for Disease Control and Prevention as a public health intervention for addressing the spread of HIV and other sexually transmitted diseases (STDs). Barriers and facilitators to the partner notification process from a public health perspective have not been well described. METHODS: In 2015, a coalition of New England public health STD directors and investigators formed to address the increasing STD prevalence across the region (Connecticut, Maine, Massachusetts, New Hampshire, Rhode Island, and Vermont) and to promote communication between state STD programs. To evaluate barriers and facilitators of PNS programs, a survey was administered to representatives from each state to describe PNS processes and approaches. RESULTS: Of the six PNS programs, Connecticut, Maine, Massachusetts, Vermont, and New Hampshire had combined HIV and STD PNS programs; Rhode Island's programs were integrated but employed separate disease intervention specialists (DIS). All states performed PNS for HIV and syphilis. Maine, New Hampshire and Vermont performed services for all gonorrhea cases. Rhode Island, Connecticut, and Massachusetts performed limited partner notification for gonorrhea due to lack of resources. None of the six states routinely provided services for chlamydia, though Maine and Vermont did so for high-priority populations such as HIV co-infected or pregnant individuals. Across all programs, clients received risk reduction counseling and general STD education as a component of PNS, in addition to referrals for HIV/STD care at locations ranging from Planned Parenthood to community- or hospital-based clinics. Notable barriers to successful partner notification across all states included anonymous partners and index cases who did not feel comfortable sharing partners' names with DIS. Other common barriers included insufficient staff, inability of DIS to identify and contact partners, and index cases declining to speak with DIS staff. CONCLUSIONS: In New England, state health departments use different strategies to implement PNS programs and referral to STD care. Despite this, similar challenges exist across settings, including difficulty with anonymous partners and limited state resources.

Insurance Coverage and Utilization at a Sexually Transmitted Disease Clinic in a Medicaid Expansion State.

BACKGROUND: In Rhode Island, the Patient Protection and Affordable Care Act has led to over 95% of the state's population being insured. We evaluated insurance coverage and barriers to insurance use among patients presenting for services at the Rhode Island sexually transmitted disease (STD) clinic. METHODS: We analyzed factors associated with insurance coverage and utilization among patients presenting for STD services between July and December 2015. RESULTS: A total of 692 patients had insurance information available; of those, 40% were uninsured. Patients without insurance were more likely than those with insurance to be nonwhite (50% among uninsured, compared with 40% among insured; P = 0.014) and Hispanic or Latino/a (25%, compared with 16%; P = 0.006), and less likely to be men who have sex with men (27%, compared with 39%; P = 0.001). Of those with health insurance, 26% obtained coverage as a result of the Affordable Care Act, and 56% of those were previously uninsured. Among uninsured individuals, barriers to obtaining health insurance included cost and unemployment. Among those with insurance, 43% reported willingness to use insurance for STD services. Barriers to insurance use included concerns about anonymity and out-of-pocket costs. CONCLUSIONS: Despite expanded insurance access, many individuals presenting to the Rhode Island STD Clinic were uninsured. Among those who were insured, significant barriers still existed to using insurance. STD clinics continue to play an important role in providing safety-net STD services in states with low uninsured rates. Both public and private insurers are needed to address financial barriers and optimize payment structures for services.

A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy.

Vps34 is a phosphoinositide 3-kinase (PI3K) class III isoform that has attracted major attention over the recent years because of its role in autophagy. Herein we describe the biological characterization of SAR405, which is a low-molecular-mass kinase inhibitor of Vps34 (KD 1.5 nM). This compound has an exquisite protein and lipid kinase selectivity profile that is explained by its unique binding mode and molecular interactions within the ATP binding cleft of human Vps34. To the best of our knowledge, this is the first potent and specific Vps34 inhibitor described so far. Our results demonstrate that inhibition of Vps34 kinase activity by SAR405 affects both late endosome-lysosome compartments and prevents autophagy. Moreover, we show that the concomitant inhibition of Vps34 and mTOR, with SAR405 and the US Food and Drug Administration-approved mTOR inhibitor everolimus, results in synergistic antiproliferative activity in renal tumor cell lines, indicating a potential clinical application in cancer.

Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications.

Phosphoinositide 3-kinases (PI3Ks) are involved in important cellular functions and represent desirable targets for drug discovery efforts, especially related to oncology; however, the four PI3K subtypes (α, ß, γ, and δ) have highly similar binding sites, making the design of selective inhibitors challenging. A series of inhibitors with selectivity toward the ß subtype over δ resulted in compound 3(S), which has entered a phase I/Ib clinical trial for patients with advanced PTEN-deficient cancer. Interestingly, X-ray crystallography revealed that the modifications making inhibitor 3(S) and related compounds selective toward the ß-isoform do not interact directly with either PI3Kß or PI3Kδ, thereby confounding rationalization of the SAR. Here, we apply explicit solvent molecular dynamics and solvent thermodynamic analysis using WaterMap in an effort to understand the unusual affinity and selectivity trends. We find that differences in solvent energetics and water networks, which are modulated upon binding of different ligands, explain the experimental affinity and selectivity trends. This study highlights the critical role of water molecules in molecular recognition and the importance of considering water networks in drug discovery efforts to rationalize and improve selectivity.

Structural insights into epitope-paratope interactions of a monoclonal antibody targeting CEACAM5-expressing tumors.

Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) are overexpressed in some tumor types. The antibody-drug conjugate tusamitamab ravtansine specifically recognizes the A3-B3 domains of human CEACAM5 (hCEACAM5). To understand this specificity, here we map the epitope-paratope interface between the A3-B3 domains of hCEACAM5 (hCEACAM5A3-B3) and the antigen-binding fragment of tusamitamab (tusa Fab). We use hydrogen/deuterium exchange mass spectrometry to identify the tusa Fab paratope, which involves heavy chain (HC) residues 101-109 and light chain residues 48-54 and 88-104. Using surface plasmon resonance, we demonstrate that alanine variants of HC residues 96-108 abolish binding to hCEACAM5, suggesting that these residues are critical for tusa-Fab-antigen complex formation. The cryogenic electron microscopy structure of the hCEACAM5A3-B3- tusa Fab complex (3.11 Å overall resolution) reveals a discontinuous epitope involving residues in the A3-B3 domains and an N-linked mannose at residue Asn612. Conformational constraints on the epitope-paratope interface enable tusamitamab to target hCEACAM5A3-B3 and distinguish CEACAM5 from other CEACAMs.

Integration of Partner Notification Services at a Sexually Transmitted Infections Clinic.

OBJECTIVES: PNS is critical to prevent the spread of STIs. We evaluated the feasibility of integrating PNS into an STI clinic focused on MSM. DESIGN/METHODS: The RI STI Clinic, in partnership with the RIDOH, implemented a PNS program in 2019. Interviews with patients diagnosed with gonorrhea/ syphilis were conducted. RIDOH attempted outreach to partners identified. We utilized interview data among MSM diagnosed with gonorrhea/syphilis in clinic from 1/1/19-12/31/2021. Bivariate analyses/multivariable logistic regression were conducted. RESULTS: 341 MSM were diagnosed with gonorrhea/syphilis during the three-year period, and 233 (68%) interviews were completed. Partner information was provided in 173 (74%) interviews. At least one workable partner was provided in 110 (47%) interviews. No statistically significant associations between provision of workable partners and index patient age/race/ethnicity were found. CONCLUSIONS: PNS at an STI clinic was successful, but challenges led to suboptimal information. Research is needed to identify barriers to integrate/optimize PNS in STI clinics.

Integrating HIV Cluster Analysis in Everyday Public Health Practice: Lessons Learned From a Public Health--Academic Partnership.

BACKGROUND: The use of molecular HIV cluster analysis to supplement public health contact tracing has shown promise in addressing HIV outbreaks. However, the potential of HIV cluster analysis as an adjunct to daily, person-by-person HIV prevention efforts remains unknown. We documented lessons learned within a unique public health-academic partnership while guiding workaday HIV prevention efforts with near-real-time molecular cluster analysis. SETTING: A public health-academic partnership in the State of Rhode Island, the United States. METHODS: We recorded perceptions of our team of academicians and public health practitioners that were encountered in an 18-month study evaluating the integration of molecular cluster analysis with HIV contact tracing for public health benefit. The focus was on monthly conferences where molecular clustering of each new statewide diagnosis was discussed to facilitate targeted interventions and on attempted reinterviews of all newly HIV-diagnosed persons statewide whose HIV sequences clustered to increase partner naming. RESULTS: Three main themes emerged: First, multidisciplinary conferences are substantially beneficial for gleaning actionable inferences from integrating molecular cluster analysis and public health data. Second, universal reinterviews were perceived to potentially have negative consequences but may be selectively beneficial. Third, the translation of cluster analysis into public health action is hampered by jurisdictional surveillance boundaries and within-jurisdictional data silos, across which data sharing is problematic. CONCLUSIONS: Insights from a statewide public health-academic partnership support integration of molecular HIV cluster analyses with public health efforts, which can guide public health activities to prevent transmission while identifying substantial barriers to integration, informing continued research.

Pre-Exposure Prophylaxis Care Cascade Among Men Who Have Sex with Men Engaging in Partner Notification Services at a Sexually Transmitted Infections Clinic.

Partner notification services (PNS) offers opportunities to discuss HIV pre-exposure prophylaxis (PrEP) and provide referrals. We evaluated the PrEP care cascade among men who have sex with men (MSM) engaging in PNS within a sexually transmitted infections clinic. Among 121 MSM eligible for PrEP during PNS, 21% subsequently initiated PrEP.

Prospective Evaluation of Routine Statewide Integration of Molecular Epidemiology and Contact Tracing to Disrupt Human Immunodeficiency Virus Transmission.

Background: Human immunodeficiency virus (HIV) remains a global challenge and novel measures for transmission disruption are needed. Contact tracing is limited by reluctance or inability of newly diagnosed individuals to name at-risk contacts. Molecular cluster analysis is mostly used for outbreak investigations, and its role in routine public health activities remains uncertain. Methods: We conducted a 2-year prospective statewide study in Rhode Island to evaluate integration of HIV cluster analyses into routine contact tracing, by attempting to reinterview all new diagnoses who clustered, notifying them of clustering, and evaluating benefits of this strategy. Clustering was compared between a phylogenetic ensemble versus distance-based HIV-TRACE. Results: Of 100 new diagnoses during 2021-2022, 52 individuals clustered, of whom only 31% were reinterviewed. Reinterviewing did not improve contact tracing beyond initial interviews, and the study was stopped early for futility. Clustering concordance within the phylogenetic ensemble was high (88%-89%), but lower (74%) for HIV-TRACE. Despite hypothesis rejection, we established a public health-academic partnership, developed a bioinformatics pipeline enabling near real-time cluster analysis, and identified gaps and unique opportunities for intervention. Conclusions: Attempting to reinterview all statewide new HIV diagnoses in molecular clusters showed no evidence of improving contact tracing. However, a strong academic-public health partnership enabled near real-time, longitudinal integration of molecular cluster analysis into routine public health activities, and identified barriers and opportunities tailoring data-driven approaches to unique individual and community characteristics, guiding future work on optimal use of molecular epidemiology to disrupt HIV transmission.

GluN2D subunit-containing NMDA receptors control tissue plasminogen activator-mediated spatial memory.

Tissue plasminogen activator (tPA) is a serine protease with pleiotropic actions in the CNS, such as synaptic plasticity and neuronal death. Some effects of tPA require its interaction with the GluN1 subunit of the NMDA receptor (NMDAR), leading to a potentiation of NMDAR signaling. We have reported previously that the pro-neurotoxic effect of tPA is mediated through GluN2D subunit-containing NMDARs. Thus, the aim of the present study was to determine whether GluN2D subunit-containing NMDARs drive tPA-mediated cognitive functions. To address this issue, a strategy of immunization designed to prevent the in vivo interaction of tPA with NMDARs and GluN2D-deficient mice were used in a set of behavioral tasks. Altogether, our data provide the first evidence that tPA influences spatial memory through its preferential interaction with GluN2D subunit-containing NMDARs.

Not all clusters are equal: dynamics of molecular HIV-1 clusters in a statewide Rhode Island epidemic.

OBJECTIVES: Molecular epidemiology is a powerful tool to characterize HIV epidemics and prioritize public health interventions. Typically, HIV clusters are assumed to have uniform patterns over time. We hypothesized that assessment of cluster evolution would reveal distinct cluster behavior, possibly improving molecular epidemic characterization, towards disrupting HIV transmission. DESIGN: Retrospective cohort. METHODS: Annual phylogenies were inferred by cumulative aggregation of all available HIV-1 pol sequences of individuals with HIV-1 in Rhode Island (RI) between 1990 and 2020, representing a statewide epidemic. Molecular clusters were detected in annual phylogenies by strict and relaxed cluster definition criteria, and the impact of annual newly-diagnosed HIV-1 cases to the structure of individual clusters was examined over time. RESULTS: Of 2153 individuals, 31% (strict criteria) - 47% (relaxed criteria) clustered. Longitudinal tracking of individual clusters identified three cluster types: normal, semi-normal and abnormal. Normal clusters (83-87% of all identified clusters) showed predicted growing/plateauing dynamics, with approximately three-fold higher growth rates in large (15-18%) vs. small (∼5%) clusters. Semi-normal clusters (1-2% of all clusters) temporarily fluctuated in size and composition. Abnormal clusters (11-16% of all clusters) demonstrated collapses and re-arrangements over time. Borderline values of cluster-defining parameters explained dynamics of non-normal clusters. CONCLUSIONS: Comprehensive tracing of molecular HIV clusters over time in a statewide epidemic identified distinct cluster types, likely missed in cross-sectional analyses, demonstrating that not all clusters are equal. This knowledge challenges current perceptions of consistent cluster behavior over time and could improve molecular surveillance of local HIV epidemics to better inform public health strategies.

An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic.

Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting. We integrated heterogeneous data sources across systems and developed an open-source, automatic bioinformatics pipeline that provides molecular HIV cluster data to inform public health responses to new statewide HIV-1 diagnoses, overcoming data management, computational, and analytical challenges. We demonstrate implementation of this pipeline in a statewide HIV epidemic and use it to compare the impact of specific phylogenetic and distance-only methods and datasets on molecular HIV cluster analyses. The pipeline was applied to 18 monthly datasets generated between January 2020 and June 2022 in Rhode Island, USA, that provide statewide molecular HIV data to support routine public health case management by a multi-disciplinary team. The resulting cluster analyses and near-real-time reporting guided public health actions in 37 phylogenetically clustered cases out of 57 new HIV-1 diagnoses. Of the 37, only 21 (57%) clustered by distance-only methods. Through a unique academic-public health partnership, an automated open-source pipeline was developed and applied to prospective, routine analysis of statewide molecular HIV data in near-real-time. This collaboration informed public health actions to optimize disruption of HIV transmission.

Patient and physician preferences for non-invasive diagnostic cardiovascular imaging technologies: a discrete choice experiment.

PURPOSE: Diagnostic imaging techniques have to be selected for their accuracy, efficiency, cost-efficiency, and impact on outcome. But beyond that, the choice of non-invasive cardiovascular imaging tests for diagnosing coronary artery disease also has to respect patient safety and comfort. In this study, we investigated patient and physician preference in relation to the choice of cardiovascular imaging tests. RESULTS: A total of 211 subjects (148 cardiac patients and 63 physicians) were enrolled and completed a discrete choice experiment. Tests and modalities were deconstructed into 6 attributes (risks and side effects, diagnostic accuracy, patient out-of-pocket cost, type of procedure, type of scanner and test duration). A Sawtooth software choice-based conjoint analysis with hierarchical Bayes estimation was performed and showed the risks and side effects attribute was assigned the most relative importance (30%) when considering patients' preference. Patients gave notably high value to tests with milder side effects, while preferring to avoid exposure to ionizing radiation and risks associated the use of pharmacological agents inducing direct coronary arteriolar vasodilation. Physicians allocated more importance to the patient out-of-pocket cost attribute (29%). Both patients and physicians valued tests' risks and side effects, diagnostic accuracy, patient out-of-pocket cost as the three most important attributes, but in diverging order. A market simulation comparing current cardiovascular imaging tests revealed breathing maneuver-enhanced cardiac magnetic resonance had the highest shares of preference in both patients (59.6%) and physicians (32.7%). CONCLUSION: A patients' preference for a particular cardiovascular imaging test was most determined by the risks and side effects, while physicians prioritized less costly tests for their patients. In shared decision-making with patients, physicians should therefore focus on a balanced discussion of risks and side effects associated with cardiovascular imaging tests. Both, patients and physicians would prefer a cardiovascular MR imaging test using a vasoactive breathing maneuver instead of currently used alternatives that require intravenous contrast agents, pharmacological stress, or radiation.

Statewide Longitudinal Trends in Transmitted HIV-1 Drug Resistance in Rhode Island, USA.

BACKGROUND: HIV-1 transmitted drug resistance (TDR) remains a global challenge that can impact care, yet its comprehensive assessment is limited and heterogenous. We longitudinally characterized statewide TDR in Rhode Island. METHODS: Demographic and clinical data from treatment-naïve individuals were linked to protease, reverse transcriptase, and integrase sequences routinely obtained over 2004-2020. TDR extent, trends, impact on first-line regimens, and association with transmission networks were assessed using the Stanford Database, Mann-Kendall statistic, and phylogenetic tools. RESULTS: In 1123 individuals, TDR to any antiretroviral increased from 8% (2004) to 26% (2020), driven by non-nucleotide reverse transcriptase inhibitor (NNRTI; 5%-18%) and, to a lesser extent, nucleotide reverse transcriptase inhibitor (NRTI; 2%-8%) TDR. Dual- and triple-class TDR rates were low, and major integrase strand transfer inhibitor resistance was absent. Predicted intermediate to high resistance was in 77% of those with TDR, with differential suppression patterns. Among all individuals, 34% were in molecular clusters, some only with members with TDR who shared mutations. Among clustered individuals, people with TDR were more likely in small clusters. CONCLUSIONS: In a unique (statewide) assessment over 2004-2020, TDR increased; this was primarily, but not solely, driven by NNRTIs, impacting antiretroviral regimens. Limited TDR to multiclass regimens and pre-exposure prophylaxis are encouraging; however, surveillance and its integration with molecular epidemiology should continue in order to potentially improve care and prevention interventions.

KRAS G12C fragment screening renders new binding pockets.

KRAS genes belong to the most frequently mutated family of oncogenes in cancer. The G12C mutation, found in a third of lung, half of colorectal and pancreatic cancer cases, is believed to be responsible for a substantial number of cancer deaths. For 30 years, KRAS has been the subject of extensive drug-targeting efforts aimed at targeting KRAS protein itself, but also its post-translational modifications, membrane localization, protein-protein interactions and downstream signalling pathways. So far, most KRAS targeting strategies have failed, and there are no KRAS-specific drugs available. However, clinical candidates targeting the KRAS G12C protein have recently been developed. MRTX849 and recently approved Sotorasib are covalent binders targeting the mutated cysteine 12, occupying Switch II pocket.Herein, we describe two fragment screening drug discovery campaigns that led to the identification of binding pockets on the KRAS G12C surface that have not previously been described. One screen focused on non-covalent binders to KRAS G12C, the other on covalent binders.

Beyond HIV outbreaks: protocol, rationale and implementation of a prospective study quantifying the benefit of incorporating viral sequence clustering analysis into routine public health interventions.

INTRODUCTION: HIV continues to have great impact on millions of lives. Novel methods are needed to disrupt HIV transmission networks. In the USA, public health departments routinely conduct contact tracing and partner services and interview newly HIV-diagnosed index cases to obtain information on social networks and guide prevention interventions. Sequence clustering methods able to infer HIV networks have been used to investigate and halt outbreaks. Incorporation of such methods into routine, not only outbreak-driven, contact tracing and partner services holds promise for further disruption of HIV transmissions. METHODS AND ANALYSIS: Building on a strong academic-public health collaboration in Rhode Island, we designed and have implemented a state-wide prospective study to evaluate an intervention that incorporates real-time HIV molecular clustering information with routine contact tracing and partner services. We present the rationale and study design of our approach to integrate sequence clustering methods into routine public health interventions as well as related important ethical considerations. This prospective study addresses key questions about the benefit of incorporating a clustering analysis triggered intervention into the routine workflow of public health departments, going beyond outbreak-only circumstances. By developing an intervention triggered by, and incorporating information from, viral sequence clustering analysis, and evaluating it with a novel design that avoids randomisation while allowing for methods comparison, we are confident that this study will inform how viral sequence clustering analysis can be routinely integrated into public health to support the ending of the HIV pandemic in the USA and beyond. ETHICS AND DISSEMINATION: The study was approved by both the Lifespan and Rhode Island Department of Health Human Subjects Research Institutional Review Boards and study results will be published in peer-reviewed journals.