Virology Research Techniques

A new study from Northwestern Medicine, published in Nature Communications, uncovers a previously unrecognized way #HIV evades the #immunesystem and points to a promising new therapeutic strategy. ▪️ Led by Dr. Mohamed Abdel-Mohsen, PhD, Margaret Gray Morton Professor of Medicine in the Division of Infectious Diseases at Northwestern University, the research shows that HIV-infected cells reprogram their surface sugars (sialoglycans) to engage inhibitory Siglec receptors (including Siglec-3, -7, -9, and -10) on #immunecells. These act as “glyco-immune checkpoints,” effectively cloaking infected cells from immune attack. 🔬 What this study adds to what we know: While #antiretroviraltherapy (#ART) suppresses viral replication, HIV persists because infected cells escape #immune surveillance. This study provides mechanistic insight into how that escape happens - identifying sugar–Siglec interactions as a key immune evasion pathway. The team also demonstrates a novel therapeutic concept: an engineered HIV-targeting antibody linked to sialidase, designed to strip away the protective sugars and restore immune-mediated killing. In cell models and mice, this approach enhanced immune clearance, reduced viral load, and lowered #inflammation. 🌍 Why it matters: Beyond HIV, this work highlights a broader #immunology principle: sugar-based immune evasion mechanisms seen in viral #infection mirror those described in #cancer, opening new avenues for cross-disciplinary therapeutic strategies. The team’s next step is to test this approach in ART-treated models, moving closer to the goal of a functional cure - sustained HIV remission without lifelong therapy. Dr. Abdel-Mohsen is also a member of the ROBERT H. LURIE COMPREHENSIVE CANCER CENTER OF NORTHWESTERN UNIVERSITY. 🗃️ See comments for reference.

SARS-CoV-2 may evade immune responses by inducing unproductive antiviral response proteins In a paper published today, we collaborated with Gloria Franco's lab to demonstrate that the interferon-stimulated genes activated during viral infection most likely do not produce functional proteins. This also applies to class I MHC genes, which encode proteins essential for alerting the immune system to virally infected cells. Consequently, antiviral responses are likely to be impaired at the translational level. We propose that SARS-CoV-2 employs a previously unreported strategy of manipulating the host's splicing machinery to enhance viral replication and evade the immune response. This is achieved by selectively upregulating unproductive splicing isoforms of genes involved in antigen presentation and antiviral defense. Congrats: Gloria Franco Thomaz Lüscher Dias, PhD Izabela Mamede Ícaro Castro Rafael Polidoro

The Lineage IV Lassa virus glycoprotein, particularly the Josiah strain, plays a critical role in the virus's ability to infect host cells and initiate disease. Structurally, the glycoprotein complex (GPC) is synthesized as a single polypeptide precursor (pre-GP), which undergoes post-translational cleavage by host proteases. The primary function of the Lassa virus glycoprotein is to mediate viral entry into host cells, which involves two critical steps: receptor binding and membrane fusion. GP1 is responsible for the initial binding to the host cell receptor, α-DG. However, this interaction is complex and heavily influenced by the glycosylation pattern of the host receptor. Once the virus attaches to the host cell, it is endocytosed into the host cell via clathrin-mediated endocytosis. Upon acidification within the endosome, the GP2 subunit undergoes a conformational change, exposing its hydrophobic fusion peptide. This conformational change allows the GP2 fusion peptide to insert into the host cell membrane, facilitating the merging of the viral and host membranes. The Lassa virus glycoprotein also plays a significant role in immune evasion. The extensive glycan shield on the glycoprotein surface masks critical antigenic sites, reducing the efficacy of host antibodies in recognizing and neutralizing the virus. Understanding the structural and functional nuances of the glycoprotein offers valuable insights for therapeutic interventions, including vaccine development and the design of neutralizing antibodies Here you can see a cryoEM structure of the lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody (GPC-C epitope) (PDB code: 8VCV) #molecularart #virus #lassa #membrane #glycoprotein #entry #immuneresponse #cryoem Structure rendered with 3D Protein Imaging, post-processed with Dzine (formerly Stylar AI) and depicted with @corelphotopaint

RNA N-glycosylation enables immune evasion and homeostatic efferocytosis by chemically caging acp3U. Excited to report this work lead by Vincent Graziano and in collaboration with Vijay Rathinam in Nature Magazine  https://lnkd.in/erHGJ_iN We found that de-N-glycosylation of purified small RNA using PNGaseF causes the RNA to be immunostimulatory to both mouse and human macrophages. This effect was also true on the surface of apoptotic material which is normally cleared via efferocytosis in an immune silent process. Loss of N-glycans on this material triggers innate immune cells. We defined the chemical moiety causing this stimulation to be the core RNA modification of acp3U, which we had previously found to be a covalent linker between RNA and N-glycans (Xie et al. Cell 2024). We confirmed this with chemical synthesis RNAs containing only 1 acp3U. Finally, we found that the de-N-glycosylated RNA is sensed through both TLR3 and TLR7 which could suggest that encoding both ssRNA and dsRNA motifs with acp3U and thus dual engagement of TLR3 and TLR7 provides sufficient signal threshold. The work brought together a lot of expertise from labs including Penghua Wang Michael Wilson Sivapriya Kailasan Vanaja, Beiyan Zhou Franck Barrat Thomas Carell - and we were critically supported by grants from NIH (NIGMS, NIAID, NIDDK) and Scleroderma Research Foundation

🚀 Breaking Down Viral Defenses: A New Frontier in Antibody Therapy & Vaccine Design 🦠💡 Neutralizing antibodies (NAbs)  play a critical role in combating viral infections, guiding both therapeutic strategies and vaccine development. However, viral evolution and immune evasion present ongoing challenges, necessitating a deeper understanding of antibody mechanisms. A groundbreaking study from Yang Huang and colleagues at Xiamen University reveals how a powerful antibody, 7H13, neutralizes #rotavirus (#RV) by exploiting a hidden vulnerability in its VP4 “#spike” protein—a discovery with far-reaching implications for combating viral evolution and designing universal vaccines! Utilizing advanced cryo-electron microscopy (#cryoEM) and cryo-electron tomography (#cryoET), scientists revealed how 7H13 induces irreversible damage to the viral VP4 protein, effectively blocking the virus's adsorption process. Read the full study to dive deeper into this! 🔗 https://lnkd.in/dWv7e4N5 🔑 Insights: 🔍 Broad-Spectrum Power: 7H13 targets a conserved epitope on VP4, enabling neutralization across diverse RV genotypes and protecting mice from infection. 🔍  Essential Structural Insights: Structure-guided mutations confirmed the crucial role of the 7H13 heavy chain I54 in activating the 'molecular switch' of F418 and initiating VP4 disruption. This destabilizes the spike’s meta-stable structure, irreversibly disabling the virus. Cryo-EM’s Crucial Role: 📌 By employing a low-temperature, time-resolved cryo-EM technique, scientists captured a series of intermediate states of viral immune complexes and elucidated the high-resolution structure of the VP4:7H13 complex. 📌 Time-resolved cryo-EM unveiled dynamic, asymmetric antibody binding and intermediate states of viral disruption—a feat impossible with traditional methods. This highlights cryo-EM’s critical role in resolving complex biological mechanisms at near-atomic resolution. 💥 Why This Matters: Viruses like RV rely on dynamic, unstable proteins to invade host cells. By targeting these structural Achilles’ heels, antibodies like 7H13 offer escape-resistant therapies and blueprints for broad-spectrum vaccines and therapeutics against rotaviruses. 🌍 The Bigger Picture: As viral evolution outpaces conventional therapies, understanding how antibodies dismantle pathogens is critical. This work not only expands our toolkit against RV but also sets a paradigm for tackling other viruses—from influenza to coronaviruses—by targeting conserved, conformationally fragile sites. #AntiviralResearch #CryoEM #BroadlyNeutralizingAntibodies #Rotavirus #VaccineDevelopment #StructuralBiology #Biotechnology #HealthcareInnovation

You’re ready for more? #ItsNotACold Summary by Zdenek Vrozina: ”A new review breaks down what SARS-CoV-2 ORF/accessory proteins actually do - from interferon suppression to mitochondrial disruption. Here are the key points, followed by how some of these mechanisms compare to those used by HIV. This new review makes something very clear. SARS-CoV-2 doesn’t rely only on spike. It uses a broad arsenal of accessory proteins (APs) that shape how severe the acute phase becomes, which organs are affected, and the biological conditions that make long-term sequelae more likely. These proteins aren’t side notes - they’re central modules of pathogenesis. The review goes protein by protein and shows a pattern we haven’t had clearly assembled before. SARS-CoV-2 runs a multi-layer immune-evasion network. Total interferon shutdown, secondary inflammatory escalation, mitochondrial disruption, antigen-presentation interference, and the capacity to persist inside tissue compartments. Each layer has a defined mechanism. Interferon is shut down at every critical node. The virus doesn’t use one trick - it uses all of them. ORF3a - suppresses STAT1 phosphorylation ORF3c / ORF10 - degrade MAVS ORF6 - blocks IRF3/STAT1/STAT2 from entering the nucleus ORF7a/7b - disrupt downstream IFN signaling ORF8 - interferes with ER chaperones ORF9b - blocks TOM70 - TBK1 never activates Result: early immune paralysis. After IFN collapse, the viral proteins flip the switch to inflammation Several APs ignite strong inflammatory pathways. ORF3a - NF-κB + NLRP3 inflammasome ORF7a - IL-6, IL-1β, TNF ORF8 - IL-17-like activation ORF9b - inflammasome activation in specific cells The classic COVID pattern. Silent phase - inflammatory explosion. Mitochondria are a primary battlefield. Arguably the strongest piece of the review. ORF3a - loss of cristae, ROS burst, HIF-1α stabilization, autophagy block ORF3c - shift to fatty acid oxidation + lysosomal dysfunction ORF9b/9c/10 - collapse of OXPHOS with no compensatory pathway This is the mechanical foundation for systemic symptoms and LC - COVID as a mitochondria targeting disease. APs can persist inside tissues. According to the review, accessory proteins may remain in the ER, mitochondria, autophagic vesicles, even after viral RNA is no longer detectable. They can maintain low-grade inflammation, HIF-1α activation, metabolic dysfunction. A mechanistic bridge between acute COVID and Long COVID. Omicron may have become milder because key accessory proteins mutated - not because of spike alone. ORF6 D61L - weaker IFN blockade ORF3a T223I - reduced replication ORF9b mutations - less effective IFN antagonism ORF7b changes - impaired oligomerization Accessory proteins act as the gearbox of virulence.” (Cont’d in comments) #SARSCoV2 #ImmunityTheft #ImmuneDysregulation #mitochondria #coronavirus #PublicHealth #Covid19 #LongCovid #postcovid #pandemic https://lnkd.in/dSB5pAFn

Paper of the day, from Science Magazine How many hidden tools do viruses have to deactivate our immune system, and could we find them all at once instead of one at a time? Great work by Caleb Glassman and Steve Elledge's group at Harvard Medical School! The authors applied a library of roughly 10,000 viral open reading frames to hunt for enzymes called ubiquitin ligases, molecular machines viruses use to degrade host proteins and evade immune recognition. They found these viral ligases fall into three distinct strategies: canonical ligases that mimic host E3s, hijackers that redirect host E3s, and non-canonical ligases that rewire Cullin-RING ligase machinery. Strikingly, these diverse strategies converge on immune-related substrates, including JAK1 and CUL1. This work departs from a one-at-a-time approach to identifying viral degradation factors, instead deploying a virome-wide library coupled with targeted CRISPR screens and proteomics to discover viral ubiquitin ligases and map their mechanisms and host substrates. The study offers both a functional classification of these viral effectors and a set of immune-related targets. What I find interesting is how different viruses converge on the same immune-related substrates through different tools and can AI foundation models eventually map these non-canonical protein-protein interactions directly from viral sequences, allowing us to predict immune chokepoints for novel viruses before we ever have to run a physical screen? Paper: https://lnkd.in/ggDvpd2d #CRISPR #Virology #Immunology #ProteinDegradation #Genomics #Biotech #Virus #Biology #Foundationmodels #AI #Virus #Genetics #LifeSciences

Our immune system relies on specialized defenders called T cells to hunt down and destroy microscopic threats. However, aggressive cancers and severe viruses often manage to survive by hiding in plain sight. Scientists have recently uncovered exactly how these diseases evade detection, discovering a molecular off-switch that effectively shuts down our natural biological defenses. A breakthrough study published in the Journal of Clinical Investigation identifies a specific protein known as TRAILshort. While researchers previously noticed the presence of this protein in HIV and certain tumors, its exact function remained elusive. The new research reveals that diseased cells use TRAILshort to actively disrupt the internal communication of our T cells. When a T cell approaches a diseased cell, TRAILshort triggers a molecular brake within the immune cell. This prematurely stops the T cell from launching an attack, neutralizing the threat response before it even begins. By using this protein to suppress the local immune environment, cancer cells and viruses can multiply completely unchecked by the body's natural security system. Understanding this evasion tactic fundamentally changes our approach to treating severe illnesses. Now that researchers know how tumors use TRAILshort as a biological shield, they can focus on developing targeted medications to block it. Neutralizing this protein has the potential to strip away the camouflage used by cancers, restore the immune system's fighting power, and significantly boost the effectiveness of modern immunotherapies. Journal of Clinical Investigation (2026). DOI: 10.1172/jci194449. Cancer doesn't hide — it hits the off-switch. New JCI 2026 study: tumors & HIV use protein TRAILshort to brake T cells and stop the attack before it starts. Blocking it could restore immune killing and boost immunotherapy. Jalali et al., JCI 2026. DOI: 10.1172/jci194449

🟥 Engineered Viral Vectors with Reduced Immunogenicity and Enhanced Targeting Viral vectors remain one of the most effective methods for in vivo gene delivery, but their clinical application is often limited by immune responses, toxicity, and off-target effects. To overcome these challenges, researchers are developing engineered viral vectors with reduced immunogenicity and enhanced targeting to improve the safety and efficacy of gene therapies. One major advance is the modification of adeno-associated viruses (AAV) and lentiviral vectors (LV) to minimize immune recognition. AI-driven capsid engineering enables the creation of stealth viral vectors that evade neutralizing antibodies, enabling repeated dosing and prolonged therapeutic effects. In addition, genetic modification of viral proteins can reduce activation of innate and adaptive immune responses, preventing rapid clearance from the blood. Another breakthrough is the development of tissue-specific viral vectors with enhanced tropism. By engineering viral surface proteins, researchers can redirect viral vectors to specific organs, improving target cell transduction while minimizing off-target effects. For example, AAVs targeting the brain have been optimized to cross the blood-brain barrier (BBB), enabling gene therapy for neurodegenerative diseases. Similarly, tumor-homing viral vectors are being developed for cancer gene therapy to deliver therapeutic genes directly into solid tumors with greater precision. In addition, hybrid viral-nanoparticle systems are emerging that combine the efficiency of viral vectors with the biocompatibility of lipid nanoparticles (LNPs) to enhance gene delivery control and immune evasion. These engineered viral vectors pave the way for safer, more efficient, and highly targeted gene therapies, accelerating the development of next-generation precision medicine. References [1] Jiang-Hui Wang et al., Signal Transduction and Targeted Therapy 2024 (https://lnkd.in/duHNMwkf) [2] David Schaffer et al., Annu Rev Biomed Eng 2009 (doi: 10.1146/annurev.bioeng.10.061807.160514) #GeneTherapy #ViralVectors #AAV #Lentivirus #CapsidEngineering #SyntheticBiology #PrecisionMedicine #BiotechInnovation #Immunotherapy #GeneticMedicine #CSTEAMBiotech

"In this study, we demonstrate a “trade-off” strategy in SARS-CoV-2 Omicron JN.1 in which the reduced infectivity caused by spike mutation is compensated by non-spike mutations.". Taken from the Importance section of the following article... Evolution of BA.2.86 to JN.1 reveals that functional changes in non-structural viral proteins are required for fitness of SARS-CoV-2. ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is still circulating among humans, leading to the continuous evolution. SARS-CoV-2 Omicron JN.1 evolved from a distinct SARS-CoV-2 lineage, BA.2.86, and spread rapidly worldwide. It is unclear why BA.2.86 did not become dominant and was quickly replaced by JN.1, which possesses one amino acid substitution in the spike protein (S:L455S) and two in the non-spike proteins NSP6 and ORF7b (NSP6:R252K and ORF7b:F19L) compared to BA.2.86. Here, we utilized recombinant viruses to elucidate the impact of these mutations on the virological characteristics of JN.1. We found that the mutation in the spike attenuated viral replication, while the non-spike mutations acted synergistically to enhance replication. This suggests that the mutations in the non-spike proteins compensate for the one in the spike, improving viral fitness, as the mutations in the spike contribute to further immune evasion. Our findings suggest that functional changes in both the spike and non-spike proteins are necessary for the evolution of SARS-CoV-2, enabling evasion of adaptive immunity within the human population while sustaining replication. https://lnkd.in/eWpCP7Jp