HIV

HIV-1 Matrix and Envelope Protein Interactions

It is important to characterize how HIV-1 proteins fulfill their functions in order to develop new approaches for curtailing the AIDS epidemic. One of the remaining frontiers of HIV-1 research concerns the mechanisms by which the HIV-1 matrix (MA) and envelope (Env) proteins collaborate with each other to ensure the assembly of infectious viruses. The HIV-1 MA protein directs the delivery of precursor Gag (PrGag) proteins to the plasma membranes (PMs) of infected cells, and drives the formation of lipid raft-like, liquid ordered (Lo) membrane domains. This membrane reorganization attracts a number of proteins that favor lipid raft-type microdomains. Such proteins appear to assemble into virus particles as innocent bystanders, and this appears to be how Env proteins that carry cytoplasmic tail deletions (CT) can be incorporated into virions. In contrast, wild type (WT) Env proteins additionally require an interaction with MA proteins to assemble into viruses. This is most easily understood in the context of the lattice that MA proteins construct at the PMs of infected cells. In particular, multiple lines of evidence imply that the CTs of WT Env proteins are trapped by MA lattices in immature, assembling virus particles, and then are released after assembled viruses are processed into their mature forms. Despite a seeming consensus on the MA-Env interaction steps, there are a number of very significant unknowns. Using our recent and preliminary results as a foundation, and taking advantage of the unique expertise of our collaborators, we propose the characterization of WT and mutant MA lattices, and of interactions of MA and Env with each other, and with membrane lipids. Our results will help clarify how MA and Env cooperate; they will illuminate aspects of host cell protein-membrane interactions; and they will foster the development of new approaches to intefere with HIV-1 replication.

Mentoring investigators in patient-oriented research on HIV and public health

PROJECT SUMMARY/ABSTRACT Despite marked progress in treatment and prevention, HIV remains a significant public health threat in the US and globally. Innovative strategies are needed to effectively deploy interventions and reduce HIV incidence, which requires a sustained and committed workforce. Dr. Dennis is an infectious disease physician and researcher at the University of North Carolina (UNC) at Chapel Hill, Division of Infectious Diseases. She seeks the protected time of the K24 award to ensure adequate time and effort to provide mentorship in patient- oriented HIV research focused on applied public health strategies. Dr. Dennis has a track record of performing high-quality patient-oriented research supported by independent funding. Her research bridges basic, clinical, and epidemiologic science by using HIV-1 molecular epidemiology and phylogenetics to understand HIV transmission at the population level and to use this information to direct prevention. She has expanded this work to optimize strategies to detect and respond to HIV networks using mixed-methods approaches. The overall goal of this work is to uncover the links between these sub-epidemics - which are overlapping sub- epidemics defined by risk groups, geography, social interaction - to facilitate the design of timely, effective interventions. The research specific aims are 1) Investigate HIV transmission networks using molecular epidemiology and phylodynamics (R01AI135970), 2) Evaluate uptake of HIV treatment and prevention services in public health with social network approaches (supported by R01AI169602), and 3) Pilot a network-based characterization of early syphilis infections to inform strategies to increase the uptake of injectable antiretrovirals for HIV treatment and prevention (supported by K24). With the support of the K24, she will leverage resources at UNC to support mentorship and professional development to strengthen new directions (implementation science, community-engaged research). Dr. Dennis is deeply committed to expanding her mentorship and dedicated to fostering diverse mentees with lived experiences that are critical for sustaining the HIV workforce. Dr. Dennis is Co-Director of the UNC Center for AIDS Research (CFAR) Scientific Working Group which focuses on Ending the HIV Epidemic efforts in North and South Carolina. She has strong institutional support and a multidisciplinary team of advisors, including the UNC CFAR, and is an advisor on the UNC T32 HIV/STI institutional training program. She has collaborated for the past 10 years with NC Division of Public Health and with multiple investigators and trainees at the UNC Gillings School of Public Health. She is active in the UNC Infectious Diseases Fellowship program, providing clinical and research mentorship to numerous ID fellows. Her clinical activity provides practical grounding and relevance in patient-oriented research. The K24 will provide 50% of Dr. Dennis’ salary and additional funds to support mentees’ research. The proposed research is timely and aligned with the National HIV/AIDS Strategy and will support the protected time needed to mentor the next-generation of investigators in HIV patient-oriented research.

Research on End-user Acceptability.and Long-term Impacts of HIV Cure Strategies (REALISE)

ABSTRACT Despite remarkable advances in HIV cure science, emerging cure candidates will likely involve trade-offs (e.g., incomplete eradication, monitoring burdens) and must compete with increasingly convenient long-acting ART; without early implementation guidance, even efficacious products may see limited uptake, particularly among the ~30–40% of people with HIV (PWH) in the U.S. who are not durably suppressed. We propose REALISE, a multidisciplinary program to define plausible cure profiles, quantify end-user preferences, and project population-level impact to inform product design and policy before market entry. Aim 1 conducts qualitative interviews with ~30 researchers and developers to delineate credible 10–20-year cure and long-acting treatment scenarios (eradication vs functional control, safety, monitoring, durability), yielding bounded “target product profiles.” Aim 2 elicits patient-centered preferences through a two-stage study: formative interviews (n=60; ≥50% not virally suppressed) to identify salient attributes; best-worst scaling (n=360 across Missouri, Georgia, and San Francisco) to prioritize attributes; and a discrete choice experiment (n=360) to quantify trade-offs versus alternative therapies, with latent class analysis to identify preference segments and estimate potential reach. Aim 3 integrates preference-based uptake from Aim 2 with Aim 1 efficacy and cost inputs in a mathematical model to estimate health impact, QALYs, net QALYs, and incremental cost-effectiveness across heterogeneous populations and Ending the HIV Epidemic jurisdictions. Innovation lies in linking cure R&D horizons to end-user preferences and transmission-dynamic outcomes, an approach that anticipates real-world use rather than retrofitting after approval. Deliverables include ranked cure attributes for product optimization, uptake projections including among unsuppressed PWH, and jurisdiction-specific value assessments to guide public health investment. By aligning cure design with what patients will accept and systems can sustain, REALISE will accelerate effective deployment of future cure strategies and maximize their contribution to Ending the HIV Epidemic. In doing so, this study advances NIH's priorities by connecting implementation science with prevention, treatment, and cure research. Using a multidisciplinary strategy to refine and extend `target product profiles,' REALISE will ensure cure development reflects patient needs and accelerate translation into real-world benefit.

Behavioral, Implementation & Community Sciences Core

PROJECT SUMMARY: BEHAVIORAL, IMPLEMENTATION, AND COMMUNITY SCIENCES (BICS) CORE Like many US jurisdictions, New York City (NYC) is not on track to achieve 2030 End the Epidemic (EHE) 95- 95-95 goals. By the end of 2023, 95% of people with HIV (PWH) in NYC had been diagnosed with HIV, but only 88% of those were in HIV care, and of those, only 80% were virally suppressed. Further, in 2022, only 40% of individuals estimated to need PrEP were prescribed it. Highly efficacious biomedical HIV treatment and prevention interventions have the potential to end the HIV epidemic, but only if they are accessed and used. Yet, behavioral, social, and structural determinants of real-world adoption as well as population-level impact of HIV prevention, care, and treatment innovations have not been addressed adequately for individuals or communities. Meeting EHE goals will depend on behavioral, implementation, and community sciences research that identifies factors contributing to these outcomes, informs interventions to address them, and ensures that communities affected by HIV are engaged throughout the research process. The Behavioral, Implementation, and Community Sciences (BICS) Core will facilitate such rigorous, innovative research by Columbia University (CU) and Weill Cornell Medicine (WCM) investigators – particularly early career investigators (ECIs) and those new to HIV research – to help achieve EHE 2030 goals. The BICS Core will support the use of relevant theories, methods, and analytic approaches to advance the integration of context-specific behavioral, implementation, and community sciences perspectives across the research continuum – from basic research through scale-up and sustainment of evidence-based interventions. The Core has three Aims: (1) Behavioral science: To support CFAR users in developing, selecting, and integrating behavioral science methodologies across the research continuum; (2) Implementation science: To support CFAR users in designing and conducting implementation studies and related health services research and (3) Community science: To facilitate rigorous community-based participatory research across the research continuum to strengthen and sustain stakeholder engagement that will optimize research translation and impact. Led by Core Co-Directors Robert Remien and Bruce Schackman and Core Associate Directors Delivette Castor, Shashi Kapadia, and Justin Knox, the BICS Core will use multiple approaches to achieve each of these aims, including substantive scientific consultations on proposed or ongoing research; access to resources and tools; and seminars and educational activities that promote integration of these methods into EHE research. The Core, thus, will support CU-WCM CFAR investigators and outside collaborators – including ECIs and investigators new to HIV research – to advance local and national EHE goals.

ATPase Chromatin Remodeling Complexes as Modulators of HIV-1 Latency and Therapeutic Targets

Abstract Significance: HIV persists in long-lived CD4⁺ T cell reservoirs despite suppressive ART, as integrated proviruses remain poised for reactivation. Chromatin remodeling is a central barrier to durable silencing, yet most studies have focused on SWI/SNF family members. The roles of non- SWI/SNF remodelers remain poorly defined, limiting our ability to rationally design host-directed “block-and-lock” cure strategies. Our unbiased shRNA screen of all 16 human remodeler ATPases identified EP400, CHD1, and CHD9 as repressors and INO80A, SMARCA5, and CHD2 as activators, establishing chromatin remodeling as a key determinant of HIV latency. Innovation: Our prior studies revealed that the p400 complex regulates HIV transcription through dual mechanisms: directly, by engaging Tat via the DMAP1 subunit to block Tat-TAR RNA interactions and restrict p-TEFb recruitment; and indirectly, by altering host transcriptional programs that control T cell activation states. Building on this mechanistic precedent and methodological platform, we now focus on INO80A, SMARCA5, CHD1, and CHD2, remodelers from distinct ATPase families that govern Tat-independent checkpoints at initiation, pause release, and elongation. Methodologically, we will apply TurboID-ChAP-MS (locus-specific proteomics), BEM-seq (single-nucleosome mapping), and degron-mediated acute depletion with ATPase-dead rescue to interrogate remodeler function with unprecedented resolution. Approach: Aim 1 will define the ATPase requirement and transcriptional checkpoints regulated by INO80A, SMARCA5, CHD1, and CHD2 using degron/CRISPR perturbations, ChIP-seq, nascent RNA profiling, and nucleosome mapping. Aim 2 will characterize remodeler-specific complexes and Tat dependence at the HIV promoter via TurboID proximity labeling integrated with chromatin affinity purification-mass spectrometry. Aim 3 will test combinatorial perturbations in Jurkat and primary CD4⁺ T cell latency models, including ART-suppressed donor cells, to identify synergistic “block-and-lock” strategies that enforce durable proviral silencing. Impact: By defining remodeler-specific mechanisms at discrete transcriptional checkpoints and leveraging their enzymatic, druggable activities, this work will establish chromatin remodeling as a therapeutic axis for durable HIV suppression and functional cure.

TAR RNA binding to INI1/SMARCB1 and its role in HIV-1 transcription and latency reactivation

Abstract The goal of this application is to study the role of interplay between the components of chromatin remodeling SWI/SNF (BAF complex) and HIV-1 transcription machinery, focusing on the interaction of a BAF component, INI1 (Integrase Interactor 1) with TAR RNA. HIV-1 reservoirs are a mixture of latent cells harboring proviruses silenced at transcriptional level. Cure strategies need a deeper understanding of HIV-1 transcriptional regulation. HIV-1 transcription, initiated by RNA Pol II, pauses producing short TAR transcripts. pTEFb recruitment to TAR by Tat overcomes this transcriptional pause, facilitating elongation. Beyond Tat, the action of chromatin remodeling complexes (CRCs) is required to facilitate elongation. The BAF complexes CBAF and PBAF play distinct roles. While CBAF represses proviral transcription by maintaining nucleosomes in an unfavorable state, PBAF remodels nucleosomes to facilitate elongation. INI1 is a component of both CBAF and PBAF, and its role in transcription is not fully understood. INI1 was identified as a binding partner for HIV-1 integrase (IN) and exerts multifacted roles in virus assembly, production and morphogenesis. INI1 has multiple functional domains. IN binding Rpt1 domain structurally mimics TAR RNA & is necessary for late events. We have made a novel observation that another domain of INI1, the N-terminal Winged Helix DNA binding domain (WHD) specifically binds to TAR RNA and that this interaction is necessary for mediating HIV-1 transcriptional elongation. These exciting results suggest that different functional domains of INI1(Rpt1 and WHD) involved in “TAR RNA mimicry” or “TAR RNA binding” regulate distinct stages of replication. We hypothesize that INI1 WHD domain-TAR interaction is necessary for recruitment of PBAF to HIV-1 LTR for transcriptional elongation and latency reactivation. Disrupting this interaction results in transcriptional repression. We will investigate the role of this novel INI1:TAR RNA interaction in HIV-1 transcription and latency reactivation. This is a multi-PI application involving Drs. Kalpana (HIV-1 virologist), Heng (NMR biophysicist) and Zou (computational biologist/protein-RNA structure). In Aim 1, we will characterize INI1-WHD:TAR interaction in vitro and in vivo via molecular/genetic analyses (Kalpana/Heng). We will employ alanine scanning mutagenesis based on WHD NMR structure to test WHD:TAR interaction. We will use biophysical & biochemical approaches to probe TAR structural elements required for this interaction. In Aim 2, we will employ computational modeling and NMR to determine the structure of INI1- WHD:TAR RNA complex (Zou/Heng). In Aim 3, we will determine the role of INI1:TAR interactions in HIV-1 transcription, latency reactivation and mechanism of action (Kalpana). We will analyze the effect of TAR- Interaction-Defective (TID) INI1 mutants on transcription of LTR-reporters and full-length HIV in INI1-/- cells. Latent cells in which TID-INI1 mutants are knocked in (KI) will be used to assess effect on reactivation via RNA-FISH and qRT-PCR assays. Our studies will establish INI1:TAR interaction as a drug target. Inhibiting this interaction could block latency reactivation promoting deep latency and advancing cure strategies.

From Evidence to Scale: Implementation Science and Simulation Modeling to Transform HIV-Hypertension Care Integration

Project Summary As HIV programs mature, cardiovascular disease (CVD) is becoming a leading contributor to morbidity and mortality. Integration of HIV and CVD prevention, with a focus on hypertension–the most prevalent and impactful modifiable CVD risk factor, presents an opportunity to build more robust primary health systems that improve health outcomes and advance health system sustainability–a key priority for the U.S. PEPFAR program. Using an expanded version of the HIV Synthesis microsimulation model—which incorporates hypertension and CVD outcomes—and data from the NHLBI-funded HLB-SIMPLe consortium’s cluster randomized trials in six African countries, we will evaluate the health effects, cost-effectiveness, and scalability of implementation strategies to promote HIV-hypertension integration to improve health outcomes for people with and without HIV under a range of health system constraints. Our first aim is to develop and validate an additional layer to HIV Synthesis model that accounts for health system constraints and implementation strategies for integration of HIV and hypertension care. This will include parameterization using data from the WHO Health System Building Blocks framework and empiric data from trials in the HLB-SIMPLe consortium. Our second aim is to evaluate the health effects and cost-effectiveness of implementation strategies for HIV-hypertension integration to identify the most effective and scalable approaches for settings with varying health system constraints representative of conditions in west, east, and southern Africa. Analyses will include scenarios targeting people with HIV and scaling up to the broader population. Our third aim focuses on engaging policymakers and program managers to promote uptake of findings through dissemination workshops and interactive modeling tools, with tailored model outputs to specific health system contexts. Using qualitative interviews with policymakers, we will use the Weiss schema for conceptualizing research utilization to assess model impact on decision-making. We will use the Translational Science Benefits Model, to capture, classify and conceptualize the clinical, policy, economic, and operational impacts and identify barriers and facilitators to use in country programs focused on HIV, hypertension, and related NCDs. The overarching project goal is to inform evidence-based, cost-effective implementation strategies for integrating NCD care into HIV platforms, improving population health outcomes in Africa and advancing implementation science through generalizable knowledge about the intersection of implementation strategies, health system strength, and service integration.

SUPPORT SERVICES FOR THE PREVENTION AND TREATMENT THROUGH A COMPREHENSIVE CARE CONTINUUM FOR HIV-AFFECTED ADOLESCENTS IN RESOURCE CONSTRAINED SETTINGS IMPLEMENTATION SCIENCE NETWORK

Support Services for the Prevention and Treatment through a Comprehensive Care Continuum for HIV-affected Adolescents in Resource Constrained Settings Implementation Science Network (PATC3H-IN) (UG1/UM2) Program The Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) requires support for logistical and operational coordination, website and communication management, analytic and data management, infrastructure for emerging research, regulatory, and monitoring of research activities for the Prevention and Treatment through a Comprehensive Care Continuum for HIV-affected Adolescents in Resource Constrained Settings Implementation Science Network (PATC3H-IN) (UG1/UM2) Program. The NICHD and partner NIH Institutes anticipate funding 8 PATC3H-IN UG1 awards in Asia and throughout sub-Saharan Africa in 2023 through a cooperative agreement mechanism for interventions of high public health significance: The prevention of new HIV infections among adolescents at risk, and the identification of, linkage to and retention in care of, and long-term viral suppression among youth living with HIV in low-to-middle income countries with high HIV burden. The PATC3H-IN network will expand and/or improve on successes achieved by its predecessor, PATC3H, to new geographic settings and/or risk populations and stimulate much needed implementation science (IS) research in the prevention of new HIV infections among adolescents at risk and the identification of, and linkage and retention to care of and long-term viral suppression among youth living with HIV in low-to-middle income countries (LMICs). PATC3H-IN will establish a network of investigators with multidisciplinary expertise on the youth-specific PHCC and in IS research, whose mission will be to evaluate promising prevention innovations contextually and developmentally tailored for HIV uninfected at-risk youth, and treatment and care interventions for youth living with HIV which have demonstrated efficacy and/or effectiveness in adolescent or adult populations and to translate them into public health practices. The structure of PATC3H-IN will consist of multiple interdependent functional components: (1) Five Clinical Research Centers (CRC) awarded through the UG1 grant mechanism; (2) one Implementation Science Coordinating Center (ISCC) to be awarded through a UM2 grant mechanism in 2024; and (3) a Scientific Leadership Committee (SLC). The CRCs will conduct clinical research and clinical trials, including implementation, effectiveness, and hybrid implementation-effectiveness studies at their 8-or more participating Clinical Research Performance Sites (CRPS). The ISCC will establish infrastructure to support research education and capacity building across PATC3H-IN, as well as infrastructure for stakeholder engagement in and dissemination of findings from PATC3H-IN and advanced statistical modeling support across PATC3H-IN. The ISCC will also provide infrastructure for conducting foundational research to support the work of clinical sites, including possible modeling studies and translation projects, as well as national surveys, and/or systematic collection and analysis of relevant policies and laws. Lastly, the SLC will be responsible for PATC3H-IN governance, oversight, and coordination, and will develop and implement the network research agenda, convening working groups as needed, prioritizing emerging research projects, efficiently managing the development of clinical protocols, implementing and completing clinical trials, and ensuring timely publication and communication of results.

Understanding antiretroviral phosphorylation and dephosphorylation using mass spectrometry imaging-based enzyme histochemistry

PROJECT SUMMARY Our overall goal is to understand the mechanistic differences in the activation and deactivation of two widely used first-line antiretroviral drugs: tenofovir (TFV) and emtricitabine (FTC) in colonic tissues. HIV is a global health problem and roughly 1.3 million people became newly infected with HIV globally in 2022. Pre-exposure prophylaxis (PrEP) is an HIV prevention strategy where HIV-negative individuals use antiretrovirals to reduce the risk of HIV infection. Specifically, oral fixed-dose combinations of two antiretrovirals, namely, TFV (TFV; prescribed as TFV disoproxil fumarate or TFV alafenamide prodrugs) and FTC are FDA-approved for HIV PrEP. The pharmacologically active forms of TFV and FTC are TFV-diphosphate (TFV-DP) and FTC-triphosphate (FTC-TP), respectively, and these phosphorylated metabolites are found in cells. Unfortunately, high variability in the responses of TFV and FTC can lead to poor clinical outcomes, including therapeutic failure. However, the molecular mechanisms responsible for the observed variability in TFV and FTC responses are poorly understood. Although the observed variability in TFV and FTC drug responses is likely to be multifactorial, alterations in drug activation and deactivation can contribute to the observed variability in drug responses. Phosphorylation of TFV is known and recent studies suggest that nucleotidases may involve in the dephosphorylation of TFV metabolites. Although the kinases that phosphorylate FTC in peripheral blood mononuclear cells are known, the kinases that are responsible for the phosphorylation of FTC in putative sites of HIV infection such as colonic tissues are yet to be determined. Notably, unprotected receptive anal intercourse has a 20-fold higher risk of HIV transmission than vaginal intercourse. Thus, understanding the biotransformation of TFV and FTC in colonic tissue is important since it is a susceptible tissue to HIV infection. Recently, we have reported the enzymatic activities of nucleotidases toward the pharmacologically active metabolites of TFV and FTC in vitro. However, the mechanistic details of the biotransformation of the above drugs in HIV susceptible tissues such as colonic tissues are yet to be elucidated. Gaining a mechanistic understanding of the biotransformation of TFV and FTC in putative sites of HIV infection is important to improve their therapeutic efficacy. As such, in this application, we propose an innovative mass spectrometry imaging-based interdisciplinary approach to understand the biotransformation of TFV and FTC in the colon. Aim 1 will establish the role of nucleotide kinases and nucleotidases in regulating TFV and FTC metabolites in colonic cells mechanistically. Aim 2 will characterize the region- and cell-type-specific expression patterns, as well as enzymatic activities of nucleotide kinases and nucleotidases in situ. The proposed project will provide novel understandings of TFV and FTC activating and deactivating mechanisms that can be leveraged to optimize the therapeutic efficacy of the above drugs.

Structure-Based Development of Nucleotide-Competing Inhibitors Against HIV-1 and LINE-1 Reverse Transcriptases

PROJECT SUMMARY Reverse transcriptases (RTs) from retroviruses and endogenous retroelements are essential polymerases that catalyze RNA- and DNA-dependent DNA synthesis. Nucleoside inhibitors (NIs) remain central to HIV-1 therapy and are also used against other viral infections and in cancer, but toxicity, limited selectivity, pharmacokinetic (PK) liabilities, and the emergence of drug resistance highlight the need for alternative RT inhibitor mechanisms. In contrast to NIs, nucleotide-competing inhibitors (NCIs) block the polymerase active site without requiring incorporation into nucleic acids. Structural studies by PI Ruiz have defined the NCI mechanism of action for HIV- 1 RT and revealed conserved binding modules shared across multiple polymerase families. These advances now enable rational discovery of improved NCIs. LINE-1 (L1) ORF2 RT is an emerging therapeutic target in cancer, autoimmunity, and aging, yet NIs are the only inhibitors known to act against L1 RT. Notably, the NCI-binding region is structurally similar between HIV-1 RT and L1 RT, suggesting that NCI recognition principles may extend across these two biologically distinct polymerases. This R21 seeks to establish proof-of-concept for NCI development against both enzymes. Aim 1 will discover and structurally optimize NCIs targeting HIV-1 RT by combining binding modules from known NCI chemotypes and determining their biochemical activity and co-crystal structures. Aim 2 will determine whether HIV-1 RT NCI principles translate to L1 RT by solving L1 RT/nucleic acid/NCI structures, evaluating enzymatic inhibition, and applying AI-based structure prediction and generative design to propose L1-specific NCI candidates. Cellular retrotransposition assays will test mechanism of action. Aim 3 will develop a fragment library tailored to protein–nucleic acid interfaces and perform fragment screening of HIV-1 and L1 RT/nucleic acid complexes to identify additional chemotypes that engage the NCI binding region. Successful completion will yield NCI scaffolds and mechanistic insights applicable to HIV-1 RT and L1 RT, define structural principles governing NCI recognition across two evolutionarily related polymerases, and establish new avenues for RT inhibitor development. The PI is highly qualified to lead this work, with extensive expertise in RT structural biology, drug design, and fragment-based discovery.

Neutralizing persistent IFN-I to improve HIV-specific CAR T cell therapy

PROJECT SUMMARY A critical hurdle to further improving the quality of life for people living with HIV (PLWH) is the need to resolve the residual immune activation and inflammation that persists even in those taking effective antiretroviral therapy (ART), which suppresses HIV replication. This unresolved and persistent immune activation is associated with increased type-I interferon (IFN-I) signaling, and increased incidence of comorbidities. Encouragingly, reports demonstrate that blocking IFN-I signaling in animal models of HIV infection can reduce HIV reservoirs and restore T cell immune function. We hypothesize that blocking IFN-I would likewise augment engineered T cell-based therapies against HIV, such as chimeric antigen receptor (CAR) T cells. Our prior work has demonstrated that when engineered to express both the 4-1BB and CD28 costimulatory domains and protected from HIV infection, HIV-specific CD4 ectodomain CAR T cells can reduce acute viremia, prevent CD4+ T cell loss, and reduce viral burden in the tissues of HIV-infected humanized mice. However, the reduction of plasma viral loads was ultimately transient, suggesting that the potency of HIV-specific CAR T cells should be further optimized for clinical translation. Our preliminary data highlights interferon-beta (IFNb) as a key immunosuppressive IFN-I negatively regulating CAR T cell proliferation, and we demonstrate that neutralizing IFNb in vivo enhanced the engraftment and persistence of HIV-specific CAR T cells adoptively transferred into HIV-infected ART- suppressed humanized mice. This proposal will interrogate whether IFNb neutralization augments CAR T cell therapy through 1) identifying the mechanism(s) by which chronic IFNb exposure mediates HIV-specific CAR T cell dysfunction, and 2) determining the effect of neutralizing IFNb on CAR T cell function and persistence in HIV infection in vivo. The proposed aims seek to develop the neutralization of IFNb as a novel immunotherapy approach to maximize the potency of HIV-specific CAR T cells aimed at achieving a functional HIV cure.

Continued HIV Production From Infected Macrophage In People On ART

PROJECT ABSTRACT After a few weeks of antiretroviral therapy (ART), HIV-1 RNA often decays to undetectable levels in blood. The initial decay is typically rapid due to the loss of short-lived, HIV-infected CD4+ T cells, but despite being adherent to ART, some people experience a subsequent period of slower decay and may require months to years to reach virologic suppression. The clinical significance of ‘slow decay’ of HIV-1 RNA after starting ART is currently unknown. Assessing the clinical significance of ‘slow decay virus’ requires identify the mechanisms generating it and exploring whether there is ongoing inflammation and neuronal damage in these people. There are three potential mechanisms that may generate ‘slow decay virus’ and they may have very different clinical implications. (1) Continued HIV-1 replication due to ineffective ART, poor ART adherence or drug- resistance. (2) Alternatively, ART could stop HIV-1 replication, but HIV-1 virions may continue to be produced by HIV-infected CD4+ T cells or (3) macrophage. Virus production without replication that emerges at the time of ART initiation is called primary nonsuppresible viremia (NSV) and is mechanistically distinct from secondary NSV observed in people who were previously suppressed. We recently examined four people who required approximately a year to become suppressed and found that ART stopped HIV-1 replication, but HIV-infected macrophage continued to produce substantial amounts of virus. These preliminary results are consistent with the long-held belief that after starting ART there is a period of rapid viral decay due to loss of HIV-infected CD4+ T cells, but some people have a subsequent period of slower decay due to continued virus production from long- lived, HIV-infected macrophage. The proposed work will expand on these observations and examine the mechanisms generating ‘slow decay virus’ in a much larger cohort of people on ART and explore the clinical implications of having ‘slow decay virus’ after starting ART (i.e. primary NSV). We will use existing, archived, longitudinal blood samples from 99 people in the MACS/WIHS Combined Cohort Study (MWCCS) who did not suppress HIV-1 RNA to undetectable levels by 6 months on ART (i.e. people with ‘slow decay virus’) and samples from 30 people who suppressed virus with typical, rapid kinetics. The proposed experiments will identify the mechanisms generating ‘slow decay virus’ during ART and the clinical implications of ‘slow decay virus’ (Aim 1). In our previous study, we also observed that ‘slow decay virus’ produced by macrophage often had nonsense/frameshift mutations in the HIV-1 vpr gene that may have promoted continued HIV-1 production from macrophage during ART. Specifically, we will explore whether ‘slow decay virus’ populations produced by macrophage have mutations in vpr or other genes that impact macrophage survival and/or HIV-1 production from infected macrophage (Aim 2). We will accomplish these aims using cutting-edge, but highly rigorous approaches. Accomplishing these aims will address clinical concerns about ‘slow decay virus’, the source of ‘slow decay virus’ as well as the role that Vpr plays in HIV-1 persistence and expression in macrophage during ART.

Directing the Evolution of Common Human Precursors into HIV-1 Broadly Neutralizing Antibodies

Project Summary An effective HIV vaccine will likely elicit broadly neutralizing antibodies (bnAbs). Doing so, however, remains a major challenge because bnAbs usually require multiple rare and unusual changes that emerge after years of active infection. It is not clear that a practical number of immunizations can consistently recapitulate this process. Although investigators have successfully expanded defined precursors of known bnAbs, they have not moved these diversified precursors to a specific target in humans. Importantly here, the severity of this problem increases rapidly with the number changes needed. The problem further deepens if the required changes are in slow-to-mutate antibody framework regions or require specific indels. The need to move from precursor to bnAb in the fewest steps motivates our focus on the V2 apex epitope of the HIV-1 envelope glycoprotein (Env). Apex bnAbs are qualitatively different from other bnAb classes. They require far fewer mutations, located in their rapidly evolving heavy-chain CDR3 (HCDR3) regions. These HCDR3s are unusually important to their ability to neutralize virus. For example, we have shown that a diverse repertoire of mouse B cell receptors can be modified with apex bnAb HCDR3s, and the resulting mouse B cells generated potent neutralizing sera. Thus, apex precursors can largely be defined by their HCDR3s alone and are far more common than other defined bnAb precursors. Interestingly, these HCDR3 are very similar to those of another class of antibodies that recognize the CD4-induced co-receptor-binding site (CoRBS). Both antibody classes have unusually long HCDR3s with sulfated tyrosines at their tips. Unlike apex bnAbs, these non-neutralizing CoRBS antibodies are readily elicited through vaccination. We have recently shown that apex precursors also bind the CoRBS, suggesting that some apex bnAbs emerge from CoRBS antibodies. Thus, the first step of sequential vaccine strategies, expanding and diversifying a defined precursor pool, is straightforward. Here we divide the remaining goals into two: moving from a precursor that does not bind Env to one that does so and then broaden it to recognize the majority of circulating isolates. We have already made significant progress in the first step: we have shown in our original mouse vaccine model that we can generate potent apex- specific neutralizing antisera. However the breadth of this sera remains limited. Building on these studies, we will pursue three goals: (1) Define the essential mutations that transform a CoRBS antibody into one that binds the Env apex and then generate antigens that select for these mutations. (2) Define mutations and generate antigens that expand the breadth of these antibodies, transforming them to bnAbs, and (3) Evaluate these antigens in a novel system that models key features of the human apex response in mice, and iteratively refine this process using antibodies and HCDR3s drawn from a wide panel of HIV-naïve persons. In short, these studies develop original concepts and tools that can accelerate development of an HIV-1 vaccine and deepen our understanding of the antibody response to vaccines and pathogens.

Glycoengineering core a(1,3)-fucose motifs to enhance HIV-1 envelope vaccine immunogenicity

Project Summary The HIV-1 envelope glycoprotein (Env) is the sole target of neutralizing antibodies (NAbs). We previously developed a vaccine platform integrating three innovations: (1) the uncleaved prefusion-optimized (UFO) trimer design to stabilize Env; (2) multilayered single-component self-assembling protein nanoparticles (1c-SApNPs) for multivalent trimer display; and (3) enzymatic trimming of oligomannose glycans on CHO cell-produced Env immunogens. Glycan trimming substantially improved Env immunogenicity by enhancing tier 2 NAb elicitation, reducing off-target responses to immunodominant glycan sites, and increasing responder rates. These vaccine candidates are now in phase 1 clinical trials (NCT06541093; NCT06905275). Building on this foundation, we propose a novel strategy to enhance immunogenicity by incorporating core α(1,3)-fucose into HIV-1 Env. Core α(1,3)-fucose, a key allergenic epitope in many plant and insect glycoproteins, is highly immunogenic in humans and other mammals. Our central hypothesis is that the targeted introduction of core α(1,3)-fucose will convert the glycan shield from an immune-evasive barrier into an immunogenic trigger that promotes NAb induction. Glycoengineered cell lines expressing α(1,3)-fucose will enable production of highly immunogenic Env vaccines suitable for preclinical and clinical testing. Importantly, particulate display of these Env trimers on 1c-SApNPs can suppress IgE-mediated allergic pathways by inducing high-affinity protective IgGs, ensuring vaccine safety. Aim 1 will focus on producing core α(1,3)-fucosylated HIV-1 Env immunogens. We will begin by developing a transient insect cell expression system using BTI-TN-5B1-4 (“High Five” or Hi5) cells to produce Env with short paucimannose glycans bearing native α(1,3)-fucose. To further enhance α(1,3)-fucosylation, we will co-express exogenous core α(1,3)-fucosyltransferases in insect and CHO cells. We will validate glycan profiles and characterize the biochemical, biophysical, structural, and antigenic properties of the resulting immunogens. Aim 2 will assess the immunogenicity of these glycoengineered HIV-1 Env immunogens. Using our previously established glycan-trimmed Env immunogens as benchmarks, we will immunize mice, rabbits, and nonhuman primates (NHPs). Mice will be used for early-stage immunogen and adjuvant screening; rabbits to evaluate glycan hole-targeting NAb responses; and key vaccine formulations will advance to NHP studies. We will assess autologous and heterologous tier 2 NAb responses and vaccine responder rates. Aim 3 will elucidate the functional, structural, repertoire, and mechanistic basis of vaccine-induced immunity. We will isolate NAbs via Env-specific single-cell sorting and antibody cloning, map epitopes by electron microscopy (EM) and X-ray crystallography, perform next-generation sequencing (NGS) of B-cell repertoires, and trace NAb lineages. Finally, we will investigate antigen trafficking, retention, presentation, and germinal center (GC) reactions in lymph nodes. Together, these studies will define a new class of glycoengineered HIV-1 vaccines and establish core α(1,3)-fucose as a novel immunomodulatory tool to overcome glycan shield-mediated immune evasion.

Cell-type specific genomics and transcriptomics of HIV in the brain

Exploration of genome organization and function in the HIV infected brain is critical to aid in the understanding and development of treatments for HIV-associated neurocognitive disorder (HAND). Here, we applied a multiomic approach, including single nuclei transcriptomics, cell-type specific Hi-C 3D genome mapping, and viral integration site sequencing (IS-seq) to frontal lobe tissue from HIV-infected individuals with encephalitis (HIVE) and without encephalitis (HIV+). We observed reorganization of open/repressive (A/B) compartment structures in HIVE microglia encompassing 6.4% of the genome with enrichment for regions containing interferon (IFN) pathway genes. 3D genome remodeling was associated with transcriptomic reprogramming, including down-regulation of cell adhesion and synapse-related functions and robust activation of IFN signaling and cell migratory pathways, and was recapitulated by IFN-g stimulation of cultured microglial cells. Microglia from HIV+ brains showed, to a lesser extent, similar transcriptional alterations. IS-seq recovered 1,221 integration sites in the brain that were enriched for chromosomal domains newly mobilized into a permissive chromatin environment in HIVE microglia. Viral transcription, which was detected in 0.003% of all nuclei in HIVE brain, occurred in a subset of highly activated microglia that drove differential expression in HIVE. Thus, we observed a dynamic interrelationship of interferon-associated 3D genome and transcriptome remodeling with HIV integration and transcription in the brain.

Emerging Treatment Options in Psychiatry

The World Health Organization (WHO) estimates that untreated mental disorders accountfor 13% of the total global burden of disease, and by 2030, depression alone will be the leadingcause of disability around the world – outpacing heart disease, cancer, and HIV. This grim pictureis further compounded by the mental health burden delivered by the coronavirus pandemic.The lack of novel treatment options in psychiatry is restricted by a limited understanding in theneuroscience basis of mental disorders, availability of relevant biomarkers, poor predictability inanimal models, and high failure rates in psychiatric drug development. However, theannouncement in 2019 from the Federal Drug Administration (FDA) for approvals of newinterventions for treatment-resistant depression (intranasal esketamine) and postpartumdepression (i.v. brexanolone), demand critical attention. Novel public-private partnerships indrug discovery, new translational data on co-morbid biology, in particular the ascendance ofpsycho-immunology, have highlighted the arrival of a new frontier in biological psychiatryresearch for depressive disorders.

The circadian clock and neural circuits maintaining body fluid homeostasis

Neurons in the suprachiasmatic nucleus (SCN, the brain’s master circadian clock) display a 24 hour cycle in the their rate of action potential discharge whereby firing rates are high during the light phase and lower during the dark phase. Although it is generally agreed that this cycle of activity is a key mediator of the clock’s neural and humoral output, surprisingly little is known about how changes in clock electrical activity can mediate scheduled physiological changes at different times of day. Using opto- and chemogenetic approaches in mice we have shown that the onset of electrical activity in vasopressin releasing SCN neurons near Zeitgeber time 22 (ZT22) activates glutamatergic thirst-promoting neurons in the OVLT (organum vasculosum lamina terminalis) to promote water intake prior to sleep. This effect is mediated by activity-dependent release of vasopressin from the axon terminals of SCN neurons which acts as a neurotransmitter on OVLT neurons. More recently we found that the clock receives excitatory input from a different subset of sodium sensing neurons in the OVLT. Activation of these neurons by a systemic salt load delivered at ZT19 stimulated the electrical activity of SCN neurons which are normally silent at this time. Remarkably, this effect induced an acute reduction in non-shivering thermogenesis and body temperature, which is an adaptive response to the salt load. These findings provide information regarding the mechanisms by which the SCN promotes scheduled physiological rhythms and indicates that the clock’s output circuitry can also be recruited to mediate an unscheduled homeostatic response.

Sympathetic nerve remodeling in adipose tissue

Sympathetic nerve activation of adrenergic receptors on fat is the major pathway the brain uses to drive non-shivering thermogenesis in brown adipose tissue and lipolysis in white fat. There is accumulating evidence that the peripheral nerve architecture inside of organs is plastic (can be remodeled) but the factors and conditions that regulate or result in remodeling are largely unknown. Particularly for fat, it remains unclear if nerves in fat can be remodeled in step with hyperplasia/trophy of adipose tissue as result of a prolonged energy surfeit. This talk will discuss our recent work identifying the sympathetic nerve architecture in adipose tissue as highly plastic in response to the adipose hormone leptin, the brain circuitry leptin acts on to regulate this and the physiological effects remodeling of innervation has on fat tissue function.

Retroviruses and retrotransposons interacting with the 3D genome in mouse and human brain

Repeat-rich sequence blocks are considered major determinants for 3D folding and structural genome organization in the cell nucleus in all higher eukaryotes. Here, we discuss how megabase-scale chromatin domain and chromosomal compartment organization in adult mouse cerebral cortex is linked, in highly cell type-specific fashion, to multiple retrotransposon superfamilies which comprise the vast majority of mobile DNA elements in the murine genome. We show that neuronal megadomain architectures include an evolutionarily adaptive heterochromatic organization which, upon perturbation, unleashes proviruses from the Long Terminal Repeat (LTR) Endogenous Retrovirus family that exhibit strong tropism in mature neurons. Furthermore, we mapped, in the human brain, cell type-specific genomic integration patterns of the human pathogen and exogenous retrovirus, HIV, together with changes in genome organization and function of the HIV infected brain. Our work highlights the critical importance of chromosomal conformations and the ‘spatial genome’ for neuron- and glia-specific regulatory mechanisms and defenses aimed at exogenous and endogenous retrotransposons in the brain

Towards a neurally mechanistic understanding of visual cognition

I am interested in developing a neurally mechanistic understanding of how primate brains represent the world through its visual system and how such representations enable a remarkable set of intelligent behaviors. In this talk, I will primarily highlight aspects of my current research that focuses on dissecting the brain circuits that support core object recognition behavior (primates’ ability to categorize objects within hundreds of milliseconds) in non-human primates. On the one hand, my work empirically examines how well computational models of the primate ventral visual pathways embed knowledge of the visual brain function (e.g., Bashivan*, Kar*, DiCarlo, Science, 2019). On the other hand, my work has led to various functional and architectural insights that help improve such brain models. For instance, we have exposed the necessity of recurrent computations in primate core object recognition (Kar et al., Nature Neuroscience, 2019), one that is strikingly missing from most feedforward artificial neural network models. Specifically, we have observed that the primate ventral stream requires fast recurrent processing via ventrolateral PFC for robust core object recognition (Kar and DiCarlo, Neuron, 2021). In addition, I have been currently developing various chemogenetic strategies to causally target specific bidirectional neural circuits in the macaque brain during multiple object recognition tasks to further probe their relevance during this behavior. I plan to transform these data and insights into tangible progress in neuroscience via my collaboration with various computational groups and building improved brain models of object recognition. I hope to end the talk with a brief glimpse of some of my planned future work!

Collective Ecophysiology and Physics of Social Insects

Collective behavior of organisms creates environmental micro-niches that buffer them from environmental fluctuations e.g., temperature, humidity, mechanical perturbations, etc., thus coupling organismal physiology, environmental physics, and population ecology. This talk will focus on a combination of biological experiments, theory, and computation to understand how a collective of bees can integrate physical and behavioral cues to attain a non-equilibrium steady state that allows them to resist and respond to environmental fluctuations of forces and flows. We analyze how bee clusters change their shape and connectivity and gain stability by spread-eagling themselves in response to mechanical perturbations. Similarly, we study how bees in a colony respond to environmental thermal perturbations by deploying a fanning strategy at the entrance that they use to create a forced ventilation stream that allows the bees to collectively maintain a constant hive temperature. When combined with quantitative analysis and computations in both systems, we integrate the sensing of the environmental cues (acceleration, temperature, flow) and convert them to behavioral outputs that allow the swarms to achieve a dynamic homeostasis.

Virus-like intercellular communication in the nervous system

The neuronal gene Arc is essential for long-lasting information storage in the mammalian brain and mediates various forms of synaptic plasticity. We recently discovered that Arc self-assembles into virus-like capsids that encapsulate RNA. Endogenous Arc protein is released from neurons in extracellular vesicles that mediate the transfer of Arc mRNA into new target cells. Evolutionary analysis indicates that Arc is derived from a vertebrate lineage of Ty3/gypsy retrotransposons, which are also ancestral to retroviruses such as HIV. These findings suggest that Gag retroelements have been repurposed during evolution to mediate intercellular communication in the nervous system that may underlie cognition and memory.

Affordable Robots/Computer Systems to Identify, Assess, and Treat Impairment After Brain Injury

Non-traumatic brain injury due to stroke, cerebral palsy and HIV often result in serious long-term disability worldwide, affecting more than 150 million persons globally; with the majority of persons living in low and middle income countries. These diseases often result in varying levels of motor and cognitive impairment due to brain injury which then affects the person’s ability to complete activities of daily living and fully participate in society. Increasingly advanced technologies are being used to support identification, diagnosis, assessment, and therapy for patients with brain injury. Specifically, robot and mechatronic systems can provide patients, physicians and rehabilitation clinical providers with additional support to care for and improve the quality of life of children and adults with motor and cognitive impairment. This talk will provide a brief introduction to the area of rehabilitation robotics and, via case studies, illustrate how computer/technology-assisted rehabilitation systems can be developed and used to assess motor and cognitive impairment, detect early evidence of functional impairment, and augment therapy in high and low-resource settings.

Targeting the Endocannabinoid System for Management of Chemotherapy, HIV and Antiretroviral-Induced Neuropathic Pain

Chemotherapeutic drugs (used for treating cancer), HIV infection and antiretroviral therapy (ART) can independently cause difficult-to-manage painful neuropathy. Paclitaxel, a chemotherapeutic drug, for example is associated with high incidence of peripheral neuropathy, around 71% of the patients of which 27% of these develop neuropathic pain. Use of cannabis or phytocannabinoids has been reported to improve pain measures in patients with neuropathic pain, including painful HIV-associated sensory neuropathy and cancer pain. Phytocannabinoids and endocannabinoids, such as anandamide and 2-arachidonoylglycerol (2-AG), produce their effects via cannabinoid (CB) receptors, which are present both in the periphery and central nervous system. Endocannabinoids are synthesized in an “on demand” fashion and are degraded by various enzymes such as fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MGL). Various studies, including those from our group, suggest that there are changes in gene and protein expression of endocannabinoid molecules during chemotherapy-induced neuropathic pain (CINP), HIV and antiretroviral-induced neuropathic pain. Analysis of endocannabinoid molecule expression in the brain, spinal cord and paw skin using LC-MS/MS show that there is a specific deficiency of the endocannabinoids 2-AG and/or anandamide in the periphery during CINP. Various drugs including endocannabinoids, cannabidiol, inhibitors of FAAH and MGL, CB receptor agonists, desipramine and coadministered indomethacin plus minocycline have been found to either prevent the development and/or attenuate established CINP, HIV and antiretroviral-induced neuropathic pain in a CB receptor-dependent manner. The results available suggest that targeting the endocannabinoid system for prevention and treatment of CINP, HIV-associated neuropathic pain and antiretroviral-induced neuropathic pain is a plausible therapeutic option.

Who can turn faster? Comparison of the head direction circuit of two species

Ants, bees and other insects have the ability to return to their nest or hive using a navigation strategy known as path integration. Similarly, fruit flies employ path integration to return to a previously visited food source. An important component of path integration is the ability of the insect to keep track of its heading relative to salient visual cues. A highly conserved brain region known as the central complex has been identified as being of key importance for the computations required for an insect to keep track of its heading. However, the similarities or differences of the underlying heading tracking circuit between species are not well understood. We sought to address this shortcoming by using reverse engineering techniques to derive the effective underlying neural circuits of two evolutionary distant species, the fruit fly and the locust. Our analysis revealed that regardless of the anatomical differences between the two species the essential circuit structure has not changed. Both effective neural circuits have the structural topology of a ring attractor with an eight-fold radial symmetry (Fig. 1). However, despite the strong similarities between the two ring attractors, there remain differences. Using computational modelling we found that two apparently small anatomical differences have significant functional effect on the ability of the two circuits to track fast rotational movements and to maintain a stable heading signal. In particular, the fruit fly circuit responds faster to abrupt heading changes of the animal while the locust circuit maintains a heading signal that is more robust to inhomogeneities in cell membrane properties and synaptic weights. We suggest that the effects of these differences are consistent with the behavioural ecology of the two species. On the one hand, the faster response of the ring attractor circuit in the fruit fly accommodates the fast body saccades that fruit flies are known to perform. On the other hand, the locust is a migratory species, so its behaviour demands maintenance of a defined heading for a long period of time. Our results highlight that even seemingly small differences in the distribution of dendritic fibres can have a significant effect on the dynamics of the effective ring attractor circuit with consequences for the behavioural capabilities of each species. These differences, emerging from morphologically distinct single neurons highlight the importance of a comparative approach to neuroscience.

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