Biology subjects

Lilly, M.

Publications and source records attributed to Lilly, M..

12 recordsLinked to original sources

bioRxiv2026

Structural Adaptability in HIV-2 Vif Drives Broad Antagonism of APOBEC3G

APOBEC3G (A3G), a restriction factor, is a barrier for zoonosis and targeted for degradation by the lentiviral protein Vif. Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2 arose from transmissions of lentiviruses from Old World monkeys to hominid primates. While HIV-1 Vif needed to adapt to specific residues in the arms race interface with A3G, HIV-2 Vif has greater tolerance for diversity there. Here, our cryo-EM structure of HIV-2 Vif and human A3G allows us to explore the mechanism underlying HIV-2 Vif broad specificity. While HIV-2 Vif does bind the arms race interface on A3G, HIV-2 Vif encodes tryptophans with low backbone stability to engage another interface on A3G. We propose a model where flexible loops in HIV-2 Vif undergo conformational selection to recognize diverse A3Gs, whereas the equivalent loops in HIV-1 Vif are preorganized to bind hA3G.

biophysics↗

bioRxiv2026

GATOR2 regulates the nutrient-dependent recruitment of GATOR1 to lysosomes

TORC1 is a central regulator of cellular metabolism. TORC1 activation depends on its recruitment to the lysosome, a process mediated by the Rag GTPases and their upstream regulator, the GATOR complex. GATOR consists of two subcomplexes: GATOR1, which converts the Rag GTPases into an inactive form during nutrient starvation by acting as a GAP towards RagA, and GATOR2, which counteracts GATOR1 through an unknown mechanism. Here we dissect the GATOR-Rag GTPases network at the cellular and subcellular level in Drosophila using genomically tagged proteins. We find that GATOR2 maintains GATOR1 in the GAP-inactive state under nutrient-replete conditions. Moreover, using fluorescent recovery after photobleaching we show that while GATOR1 and GATOR2 are recruited to lysosomes as a supercomplex in fed conditions, their recruitment becomes decoupled during starvation. Taken together, our findings support a model in which GATOR1 forms an inactive supercomplex with GATOR2 under nutrient-rich conditions. However, upon nutrient starvation, this supercomplex dissociates, enabling GATOR1 to adopt a GAP-active state and inhibit the Rag GTPases, thereby preventing the recruitment and activation of TORC1 on lysosomes. Finally, our data identify Wdr59 as a critical regulator of this nutrient-dependent remodeling that is required to relieve GATOR2-mediated inhibition of GATOR1.

cell biology↗

bioRxiv2026

Genomes of Betacoronavirus gravedinis from white-footed mice in New York City and a phylogenetically weighted model of its probable distribution in North America

Rodents are an important reservoir of zoonotic viruses and are ubiquitously present in densely populated urban areas. Betacoronaviruses in the Embecovirus lineage are well known to infect both humans and animals and have established rodent reservoirs. Here three Betacoronavirus gravedinis genomes were sequenced and characterized in white footed mice (Peromyscus leucopus, commonly white footed mice) collected in New York City, the second most populous city in North America. The genomes were distinct from mouse hepatitis virus (MHV), the prototype mouse betacoronavirus, and highly similar and identical in one case to previously characterized B. gravedinis sequences from white footed mice in Connecticut. Codon aware evolutionary models were used to identify specific sites under positive selection within the spike protein of B. gravedinis. A novel method was developed to predict the probable geographic distribution of the virus using publicly available data from the Global Biodiversity Information Facility to generate a weighted distribution map highlighting overlapping potential host ranges based on the evolutionary distance using a high resolution cytocrome B (CYTB) phylogeny of rodent species with potentially overlapping ranges. Our models predict three current hotspots of circulation in North America under different possible transmission regimes, and an additional fourth hotspot was predicted to arise in a warming future. This study highlights the continued need for biodiversity-informed surveillance of potential zoonotic pathogens in rodents.

microbiology↗

bioRxiv2025

Fitness Landscapes of APOBEC3G Antagonism by HIV-1 Vif proteins

Host immune factors shape viral evolution. The HIV-1 Vif protein counteracts host APOBEC3G (A3G) to ensure productive infection. Using deep mutational scanning (DMS) across two divergent HIV-1 Vif proteins, we systematically mapped and compared the mutational landscapes governing Vif antagonism of A3G. These high-resolution fitness maps reveal core principles of host-virus coevolution. Most missense mutations were strongly deleterious, reflecting pervasive purifying selection. Yet several highly conserved Vif residues at binding interfaces with A3G, RNA, and CBF{beta} exhibited unexpected mutational tolerance, indicating structural flexibility at these sites. Comparative analysis revealed that strain-specific epistasis dictates Vif-A3G interactions, including adaptive changes at the Vif-A3G interface. Further analysis uncovered striking temporal epistasis, whereby initially adaptive Vif mutations critical for antagonizing hominoid A3G subsequently exhibited reduced fitness. Thus, structural robustness permits adaptation, while epistasis imposes constraints on Vifs ability to maintain A3G antagonism while remaining responsive to new evolutionary pressures. TeaserMapping how HIV-1 evolves to outsmart a key human antiviral protein reveals both unexpected flexibility and evolutionary constraints in viral adaptation.

microbiology↗

bioRxiv2025

Re-infection with SARS-CoV-2 is associated with increased antibody breadth and potency against diverse sarbecovirus strains

The ease with which emerging SARS-CoV-2 variants escape neutralizing antibodies limits protection afforded by a prior exposure, be it infection or vaccination. While rare, broadly neutralizing antibodies with activity towards diverse sarbecoviruses have been detected in convalescent serum. Motivated by findings that plasma responses show increased neutralization breadth and potency with continued antigen exposure, we isolated monoclonal antibodies (mAbs) after a SARS-CoV-2 re-infection and compared them to those isolated one year prior, after the first breakthrough infection. Among clonal lineage members identified at both time points, mAbs from the later time point showed improved neutralization potency and breadth. One mAb isolated after re-infection, C68.490, targets a conserved region in the receptor binding domain core and shows remarkable activity not only against SARS-CoV-2 variants, but also diverse sarbecoviruses from more distant clades present in animal reservoirs. These findings suggest that a focus on individuals with diverse and repeated antigen exposure could lead to identification of antibodies with therapeutic utility not just towards current and future SARS-CoV-2 variants, but also distant sarbecoviruses in the event of a future spillover.

immunology↗

bioRxiv2025

Determinants of Natural Killer Cell-Mediated Antibody Dependent Cellular Cytotoxicity in SARS-CoV-2 Antibodies

A growing body of evidence underscores the role of antibody-dependent cellular cytotoxicity (ADCC) in antiviral immunity. Yet, the mechanisms underlying the ability of certain antibodies (Abs) to mediate potent ADCC activity remain poorly characterized - in particular the contribution of features within the antigen binding Fab region remain largely unexplored. In this study, we leveraged a collection of 142 SARS-CoV2 monoclonal Abs to systematically dissect the determinants of ADCC activity. We analyzed their epitope domain target, binding characteristics, neutralization potency, somatic hypermutation (SHM) and CDR3 length to determine the contribution of these features to ADCC activity. We found that ADCC activity is primarily shaped by epitope target-particularly targeting of the S2 domain of the Spike glycoprotein. ADCC potency was not associated with the degree of SHM or neutralization. Notably, ADCC activity was not correlated with binding affinity and moderate binding to antigen was sufficient for ADCC activity. By integrating these analyses, we provide a comprehensive framework for understanding the molecular and functional determinants of ADCC. Together, these findings offer novel insights into the mechanisms that underpin ADCC functions, with implications for vaccine design and therapeutic Abs development. Author SummaryWhile antibodies are best known for stopping viruses from entering cells, they also activate other arms of the immune system. One important function is their ability to signal immune cells to destroy virus-infected targets, a process called antibody-dependent cellular cytotoxicity (ADCC). In this study, we examined 142 antibodies directed against the spike protein of the virus that causes COVID-19. We compared their binding patterns, neutralizing ability, level of maturation, and other features to determine what drives their capacity to trigger ADCC. We found that the region of the spike protein targeted by the antibody was the main factor shaping this activity, with antibodies that recognized the S2 region being particularly effective. In contrast, the amount of antibody maturation, the strength of binding, or the ability to neutralize the virus did not predict immune cell activation. Our findings show that antibodies can contribute to antiviral defense through distinct mechanisms and provide new insights for guiding vaccine and antibody therapy design.

immunology↗

bioRxiv2024

Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses

The recurring spillover of pathogenic coronaviruses and demonstrated capacity of sarbecoviruses, such SARS-CoV-2, to rapidly evolve in humans underscores the need to better understand immune responses to this virus family. For this purpose, we characterized the functional breadth and potency of antibodies targeting the receptor binding domain (RBD) of the spike glycoprotein that exhibited cross-reactivity against SARS-CoV-2 variants, SARS-CoV-1 and sarbecoviruses from diverse clades and animal origins with spillover potential. One neutralizing antibody, C68.61, showed remarkable neutralization breadth against both SARS-CoV-2 variants and viruses from different sarbecovirus clades. C68.61, which targets a conserved RBD class 5 epitope, did not select for escape variants of SARS-CoV-2 or SARS-CoV-1 in culture nor have predicted escape variants among circulating SARS-CoV-2 strains, suggesting this epitope is functionally constrained. We identified 11 additional SARS-CoV-2/SARS-CoV-1 cross-reactive antibodies that target the more sequence conserved class 4 and class 5 epitopes within RBD that show activity against a subset of diverse sarbecoviruses with one antibody binding every single sarbecovirus RBD tested. A subset of these antibodies exhibited Fc-mediated effector functions as potent as antibodies that impact infection outcome in animal models. Thus, our study identified antibodies targeting conserved regions across SARS-CoV-2 variants and sarbecoviruses that may serve as therapeutics for pandemic preparedness as well as blueprints for the design of immunogens capable of eliciting cross-neutralizing responses. AUTHOR SUMMARYThere is a large collection of sarbecoviruses related to SARS-CoV-2 circulating in animal reservoirs with the potential to spillover into humans. Neutralizing antibodies have the potential to protect against infection, although viral escape is common. In this study, we isolated several monoclonal antibodies that show broad activity against different sarbecoviruses. The antibodies target epitopes in the core of the receptor binding domain that are highly conserved in sequence across sarbecoviruses and emerging SARS-CoV-2 variants. One antibody showed remarkable breadth against both SARS-CoV-1 variants as well as diverse sarbecoviruses. The results of deep mutational scanning suggest that mutations at these predicted sites of escape may functionally constrain viral fitness. Our functional profiling of cross-reactive antibodies highlights vulnerable sites of sarbecoviruses, with some antibodies poised as broadly neutralizing candidates for therapeutic use against future sarbecovirus emergence.

immunology↗

bioRxiv2024

The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2

The SARS-CoV-2 virus responsible for the COVID-19 global pandemic has exhibited a striking capacity for viral evolution that drives continued evasion from vaccine and infection-induced immune responses. Mutations in the receptor binding domain of the S1 subunit of the spike glycoprotein have led to considerable escape from antibody responses, reducing the efficacy of vaccines and monoclonal antibody (mAb) therapies. Therefore, there is a need to interrogate more constrained regions of Spike, such as the S2 subdomain. Here, we describe a collection of S2 mAbs from two SARS-CoV-2 convalescent individuals that target multiple regions in the S2 subdomain and can be grouped into at least five epitope classes. Most did not neutralize SARS-CoV-2 with the exception of C20.119, which bound to a highly conserved epitope in the fusion peptide and showed broad binding and neutralization activity across SARS-CoV-2, SARS-CoV-1, and closely related zoonotic sarbecoviruses. Several of the S2 mAbs tested mediated antibody-dependent cellular cytotoxicity (ADCC) at levels similar to the S1 mAb S309 that was previously authorized for treatment of SARS-CoV-2 infections. Three of the mAbs with ADCC function also bound to spike trimers from HCoVs, such as MERS-CoV and HCoV-HKU1. Our findings suggest there are diverse epitopes in S2, including functional S2 mAbs with HCoV and sarbecovirus breadth that likely target functionally constrained regions of spike. These mAbs could be developed for potential future pandemics, while also providing insight into ideal epitopes for eliciting a broad HCoV response. AUTHOR SUMMARYThe early successes of vaccines and antibody therapies against SARS-CoV-2, the virus responsible for the COVID-19 global pandemic, leveraged the considerable antibody response to the viral entry protein, spike, after vaccination or infection. These initial interventions were highly effective at protecting from infection and reducing severe disease or death. However, SARS-CoV-2 has shown no sign of abating, with the continued rise of new variants that have escaped some of the antibody defense due to distinct alterations most significantly in regions of the spike protein that elicit most of the anti-viral, functional antibody response. These findings suggest a critical need to identify vaccine approaches and therapies that provide the broadest possible antibody responses, focused on regions of spike critical for SARS-CoV-2 infection and, therefore, do not undergo changes that could lead to immune evasion. Our study describes a panel of functional antibodies, from individuals after SARS-CoV-2 infection, that recognize the S2 spike subdomain that is responsible for carrying out viral fusion with host cells. These regions in S2 are generally well conserved across SARS-CoV-2 variants and other closely related viruses and thus, could guide more effective vaccine design in the face of continued viral evolution.

immunology↗

bioRxiv2022

Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection

The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs through BA.4/BA.5 in both pseudovirus-based and authentic virus assays. Three mAbs also retain potency to recently circulating VOCs XBB.1.5 and BQ.1.1 and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are novel in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1. Significance StatementSARS-CoV-2 infections can result in diverse clinical outcomes, including severe disease. Monoclonal antibodies (mAbs) have been used therapeutically to treat infection, but the emergence of variants has compromised their efficacy. Thus, identifying mAbs that are more durable in the face of SARS-CoV-2 evolution is a pressing need. Here, we describe four new mAbs isolated from a Delta-breakthrough infection, that can potently neutralize diverse variants, including multiple Omicron variants. In addition, one mAb shows broader activity against coronaviruses. The breadth of these mAbs is due to their focus on highly conserved regions of the viral protein antigen, including regions that are required for the virus to enter the cell. These properties make them promising candidates for therapeutic use.

immunology↗

bioRxiv2022

Mechanical activation of mitochondrial energy metabolism during cell differentiation

In multicellular lives, differentiation of many types of stem and progenitor cells is often accompanied by a metabolic transition from glycolysis to mitochondrial oxidative phosphorylation. The mechanisms driving this metabolic transition in vivo are largely unknown. Here, we show that, during differentiation of the Drosophila female germline cyst, the surrounding somatic cells compress the cyst and increase the tension of cyst cells membranes. Transmembrane channel-like, an evolutionarily conserved ion channel involved in mechanosensation, maintains cytosolic Ca2+ levels in compressed differentiating cysts. Cytosolic Ca2+ induces transcriptional activation of oxidative phosphorylation through a CaMKI-Fray-JNK signaling relay. Our findings demonstrate a molecular link between cell mechanics and mitochondrial energy metabolism, with implications in other developmentally orchestrated metabolic transitions in mammals. One-Sentence SummaryMechanical forces from the surrounding tissue activate mitochondrial energy metabolism in differentiating cells in vivo.

cell biology↗

bioRxiv2021

Modeling ex vivo tumor-infiltrating lymphocyte expansion from established solid malignancies

Adoptive transfer of tumor-infiltrating lymphocytes (TIL) elicits the regression of metastatic malignancies, yet a low proportion of patients achieve complete durable responses. The high incidence of relapse in these patients highlights the need to better understand mechanisms of tumor escape from T cell control. While melanoma has provided the foundation for developing TIL therapy, much less is known about TIL efficacy and relapse in other malignancies. We sought to investigate TIL characteristics in mouse tumors which have not been studied in this setting. Here, we expanded murine TIL ex vivo in IL-2 from fragments of multiple tumor models, including oral cavity cancer models of varying immunogenicity. Additionally, TIL was expanded from pmel-1 mice bearing B16 melanoma, yielding an enriched population of tumor-infiltrating TCR transgenic T cells. Murine TILs are similar to human TIL in that they express high levels of inhibitory receptors (PD-1, Tim-3, etc.) and can be expanded ex vivo in IL-2 extensively. Of clinical relevance, we draw parallels between murine and patient TIL, evaluating relationships between PD-1, Lag-3, and Tim-3 on TILs from a cohort of oral cavity cancer patients. This platform can be used by labs even in the absence of clinical specimens or clean cell facilities and will be important to more broadly understand TIL phenotypes across many different malignancies.

immunology↗

bioRxiv2018

The GATOR complex regulates an essential response to meiotic double-stranded breaks in Drosophila

The TORC1 inhibitor GATOR1/SEACIT controls meiotic entry and early meiotic events in yeast. However, how metabolic pathways influence meiotic progression in metazoans remains poorly understood. Here we report that the TORC1 regulators GATOR1 and GATOR2 mediate a response to meiotic double-stranded breaks (DSBs) during Drosophila oogenesis. We find that meiotic DSBs trigger the activation of a GATOR1 dependent pathway that downregulates TORC1 activity in the female germline. In GATOR1 mutants, high TORC1 activity results in the delayed repair of meiotic DSBs and the hyperactivation of p53. Conversely, the GATOR2 component Mio is required to attenuate GATOR1 activity, to ensure that meiotic DSBs do not trigger a permanent growth arrest. Unexpectedly, we found that GATOR1 inhibits retrotransposon expression in the presence of meiotic DSBs in a pathway that functions in parallel to p53. Our studies have revealed a link between the GATOR complex, the repair of meiotic DSBs and retrotransposon expression

developmental biology↗