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Cell Research

Springer Science and Business Media LLC

Preprints posted in the last 30 days, ranked by how well they match Cell Research's content profile, based on 51 papers previously published here. The average preprint has a 0.05% match score for this journal, so anything above that is already an above-average fit.

1
Avs2 drives non-canonical tetrameric assembly of trypsin-like domain for anti-phage defense

Guo, L.; Huang, P.; Liu, W.; Liu, J.; Xu, D.; Yu, S.; Wang, Z.; Zhang, L.; Li, Z.; Cao, X.; Yang, Q.; Cheng, M.; Wu, N.; Lu, M.; Qi, L.-W.; Xiao, Y.; Chen, M.

2026-08-26 microbiology 10.64898/2026.08.25.746987 medRxiv
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Bacteria have evolved diverse anti-phage defense systems, with the antiviral STAND family (Avs) representing one of the most diverse and widespread, encompassing at least 90 distinct families, yet only Avs3, Avs4, Avs5 and Avs7 have been well characterized. Here, we elucidated the molecular mechanism of Avs2-trypsin-MBL system, where phage terminase recognition by Avs2 triggers coupled activation of the protease and nuclease activities of trypsin-MBL. Cryo-EM structure of Avs2-trypsin-terminase and biochemical analysis reveal that the binding of terminase ATPase domain triggers the assembly of Avs2 into tetramer, with two unique ATP molecules bridging ATPase active-site recognition by TPR domain. This tetramerization drives the fused trypsin into an active C4-symmetric assembly, an architecture distinct from the conventional non-defense trypsin. Our study unravels the activation mechanism of Avs2-trypsin-MBL system, expanding our understanding on commonality and diversity of widespread Avs-mediated anti-phage immunity, alongside the structural and functional adaption of trypsin.

2
Consensus native-like hepatitis C virus E1E2 engages broadly neutralizing antibody precursors

Mulder, F.; Cannac, F.; Capella-Pujol, J.; Peters, S.; Poniman, M.; Olijhoek, W.; Granger, L.; Briones-Orta, M.; Paschos, K.; van der Pol, S.; Walen, R.; Newby, M. L.; Lee, W.-H.; Radic, L.; Zon, I.; Weber, T.; Crispin, M.; Klein, F.; Shattock, R. J.; Sanders, R. W.; Ward, A.; Schinkel, j.; Sliepen, K.

2026-08-26 immunology 10.64898/2026.08.25.746952 medRxiv
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A major goal for hepatitis C virus (HCV) vaccine development is to elicit broadly neutralizing antibodies (bNAbs) against the E1E2 glycoprotein complex located on the viral surface. Inducing HCV bNAbs requires engagement of their germline B cell precursors. HCV glycoproteins usually do not bind and activate inferred germline precursors of bNAbs (igl-bNAbs), possibly because most circulating strains contain non-conserved isolate-specific residues, even in bNAb epitopes. Here, we generated stabilized native-like soluble E1E2 (sE1E2) antigens based on a consensus sequence of HCV (HepCon) to limit the exposure of antigenically rare residues. The antigenicity and glycosylation profiles show that HepCon sE1E2 resembles a native-like E1E2 heterodimer. HepCon sE1E2 induced cross-reactive neutralizing antibody responses as a soluble protein immunogen and as membrane-anchored mRNA-delivered immunogen in animals. Importantly, HepCon sE1E2 engages multiple igl-bNAbs against two major epitopes: antigenic region 3 (AR3), which is targeted by igl-bNAbs derived from the widely expressed human VH1-69 B cell gene, and antigenic region 4 (AR4), which is only present on native-like E1E2. Nanoparticles with HepCon sE1E2 efficiently activated B cell lines expressing AR3 and AR4 igl-bNAb B cell receptors in vitro. Finally, using HepCon sE1E2 we elucidated the atomic contacts of an AR3 igl-bNAb by cryo-electron microscopy. Thus, HepCon sE1E2 is a promising candidate for germline-targeting vaccination strategies.

3
TM6SF2 binds cholesterol, interacts with apolipoprotein B, and promotes hepatic lipid secretion

Hong, S.; Wang, J.; Mitsche, M. A.; Cohen, J. C.; Li, X.; Hobbs, H. H.

2026-08-21 cell biology 10.64898/2026.08.17.745233 medRxiv
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A missense variant in TM6SF2 (transmembrane 6 superfamily member 2, TM6SF2E167K) is a major risk factor for steatotic liver disease1, while protecting against coronary artery disease2. TM6SF2 is a polytopic resident protein of the smooth endoplasmic reticulum (ER) and ER-Golgi intermediate compartment that promotes lipidation of hepatic ApoB-containing lipoproteins before secretion into the circulation. Here, we used cryo-electron microscopy (cryo-EM) to determine the structures of TM6SF2 and TM6SF2E167K at 3.64 [A] and 3.58 [A] resolution, respectively. TM6SF2 comprises 10 transmembrane helices that bind a single cholesterol molecule within a transmembrane cavity. The protein assembles into homodimers and homotetramers that interact with ApoB. Structural and biochemical analyses show that the E167K substitution reduces cholesterol binding and ApoB interaction without disrupting overall protein structure. Expression of wild-type, but not mutant, TM6SF2 restores hepatic triglyceride secretion in TM6SF2-deficient hepatocytes. Together, these findings establish the first structural framework for the bulk lipidation step in hepatic lipoprotein biogenesis, the principal pathway for hepatic triglyceride and cholesterol export into the circulation.

4
Rapid and efficient generation of human 8-cell-like cells for embryo modelling

Odabas, A.; Unlu, S.; Ozturk, E.; Karasurmeli, N.; Hu, K.; Leleu, M.; Aztekin, C.; Onder, T. T.

2026-08-19 developmental biology 10.64898/2026.08.18.745473 medRxiv
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8-cell blastomeres of human embryos possess broad lineage potential and undergo major zygotic genome activation (ZGA), yet experimental access to this transient cell state remains limited. Rare 8-cell-like cells (8CLCs) arise spontaneously in naive pluripotent stem cell cultures, but their low abundance has constrained mechanistic and functional studies. Here, we develop a chemically defined strategy for rapid and robust induction of 8CLCs. Through sequential small-molecule screens focused on chromatin regulators, we identify five compounds acting through distinct pathways that generate up to 40% 8CLCs within 48 hours. The resulting cells, which we term rapidly induced 8CLCs (ri8CLCs), recapitulate key molecular features of 8-cell blastomeres, including induction of ZGA-associated genes, cleavage-stage transposable elements, and 8-cell-stage transcriptional signatures in bulk and single-cell transcriptomic analyses. Functionally, ri8CLCs exhibit enhanced developmental competence, acquiring the ability for spontaneous extraembryonic differentiation and assembly into well-cavitated blastoids on an accelerated 72-hour timeline. Notably, ri8CLC induction enables blastoid formation even in the absence of MEK inhibition, TGF-{beta}/Activin/Nodal inhibition and exogenous LIF, revealing a developmental competence consistent with an early embryonic state. Together, these findings establish a rapid, defined, and highly efficient platform for generating human ri8CLCs and provide a tractable model for studying early human embryogenesis.

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Decoding Humoral Immunity During Acute MPXV Infection via Comprehensive Serological Analysis and Antigen-agnostic Monoclonal Antibody Profiling

Zhang, Y.; Fan, J.; Wang, J.; Jiang, N.; Wan, Y.; Meng, L.; Qi, W.; Cheng, X.; Luo, K.; Zhang, T.; Li, R.; Chen, H.; Zhao, R.; Ren, Y.; Zhang, W.; Zhu, Z.

2026-08-31 public and global health 10.64898/2026.08.21.26360138 medRxiv
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Dissecting the complexity of antibody responses in orthopoxvirus (OPXV) infected individuals is essential for elucidating protective mechanisms and identifying candidate protective immunogens. Here, we profiled the acute humoral response in 51 mpox cases, showing distinct IgG trajectories among multiple antigens alongside the rise of plasma neutralizing activities to plateau within 6 weeks after symptom onset. Utilizing a single-cell transcriptomic and BCR sequencing based antigen-agnostic mAb isolation workflow, we further generated monoclonal antibodies (mAbs) from 254 expanded peripheral B cell clones of 3 patients. We discerned 97 specific mAbs recognizing at least 12 different OPXV proteins via integrated screening approaches, which comprised neutralizing antibodies binding unconventional viral targets and antibodies exhibiting extraordinary in vitro and in vivo anti-OPXV effects. The number of OPXV-specific mAbs recovered per donor reflected the percentage of expanded clones among circulating B cells. More interestingly, we demonstrated that the inferred unmutated common ancestors (UCAs) of neutralizing antibody clones did not necessarily react with OPXV, implying that OPXV neutralizing antibodies might frequently originate from B cells previously activated by unknown antigens. Our work establishes an efficient workflow for antigen-agnostic isolation of pathogen specific mAbs and reveals previously unclarified features of antibody responses induced by acute MPXV infection.

6
Protective pan-betacoronavirus neutralizing antibodies by vaccination

Zhou, P.; Feng, Z.; He, W.-t.; Zhu, Y.; Yuan, M.; Li, X.; Zhang, Y.; Vo, L.; Capozzola, T.; Callaghan, S.; Mishra, N.; Avillion, G.; Dueker, K.; Liang, B.; Roy Chowdhury, R.; Nedellec, R.; Lee, W.-H.; Allen, J. D.; Walsh, A.; Melo, M.; McAnarney, E. T.; Kumar, N. A.; Rinaldi, W.; Ferguson, M.; Crispin, M. M.; Ward, A. B.; Irvine, D. J.; Alameh, M.-G.; Weissman, D.; Baric, R.; Gralinski, L. E.; Wilson, I.; Burton, D. R.; Andrabi, R.

2026-08-07 immunology 10.64898/2026.08.06.743418 medRxiv
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The continued emergence of betacoronaviruses underscores the urgent need for vaccines that provide broadly protective immunity. Here, we present an epitope-focused vaccine strategy targeting the conserved S2 stem-helix region of the spike fusion machinery, a broadly neutralizing antibody-(bnAb) epitope shared across betacoronaviruses yet partially occluded on the native spike. Immunization of non-human primates with engineered S2 stem-helix nanoparticle immunogens, alone or followed by a SARS-CoV-2 BA.1 spike mRNA boost, elicited broadly cross-reactive antibody responses against sarbecoviruses, merbecoviruses, and embecoviruses and neutralized SARS-CoV-2, multiple variants, other sarbecoviruses, and MERS-CoV. Vaccine-elicited monoclonal antibodies displayed broad in-vitro neutralizing activity and protected against both SARS-CoV-2 and MERS-CoV in-vivo. Structural analyses revealed conserved features between rhesus and human stem-helix bnAbs, supporting the translational potential. Overall, our findings provide proof-of-concept that epitope-focused nanoparticle immunogens can target partially occluded, immunoquiescent bnAb epitopes, laying the groundwork for pan-betacoronavirus vaccines that provide broad protection and strengthen pandemic preparedness. ONE SENTENCE SUMMARYEpitope-focused S2 stem-helix nanoparticle immunogens elicit protective broadly neutralizing antibodies (bnAbs) against diverse betacoronaviruses in non-human primates, establishing a framework for development of pan-betacoronavirus vaccines.

7
Structural and mutational analyses define distinct molecular routes to broad SARS-CoV-2 receptor-binding domain recognition

Abernathy, M. E.; Foreman, W. B.; Lopez, J. A.; Baharani, V. A.; Vahdat, D.; Lee, Y. E.; Eso, M. R.; Wang, Z.; Bieniasz, P. D.; Nussenzweig, M. C.; Starr, T. N.; Barnes, C. O.

2026-08-21 biophysics 10.64898/2026.08.17.745277 medRxiv
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Broadly reactive antibodies elicited by SARS-CoV-2 infection or vaccination can reveal conserved viral vulnerabilities and inform vaccines with broad coronavirus coverage. Here, we characterize two human-derived monoclonal antibodies, B2014 and C5078, that recognize conserved epitopes on the SARS-CoV-2 RBD and retain activity across antigenically distinct variants. Notably, C5078 also recognizes diverse sarbecoviruses and remains active against currently circulating variants, including XFG and NB.1.8.1. Cryo-EM structures reveal that B2014 recognizes an epitope adjacent to the class 3 antibody site, whereas C5078 targets the highly conserved, cryptic site V epitope. Structural analysis defines how C5078 uses affinity-matured interactions to engage conserved RBD residues, providing a molecular basis for its exceptional breadth. Deep mutational scanning across multiple SARS-CoV-2 variant backgrounds further defines potential pathways of antibody escape, explaining the loss of B2014 activity against antigenically evolved variants while revealing a high barrier to escape from C5078. Together, these findings define distinct structural solutions for broad RBD recognition and highlight conserved, mutationally constrained epitopes that may serve as targets for vaccines designed to elicit antibody responses resilient to ongoing SARS-CoV-2 evolution and future sarbecovirus emergence.

8
Dissociation kinetics and avidity gate SARS-CoV-2 neutralization by HR2 stem helix antibodies

Crivelli, V.; Guerra, C.; Abernathy, M. E.; Sgrignani, J.; Zoppi, G.; Greeson, M. L.; Sanga, A.; Locatelli, P.; Cantergiani, J.; Cena, B.; Cervantes Rincon, T.; Lee, Y. E.; Eso, M.; Jarrossay, D.; Biggiogero, M.; Calvaruso, V.; Franzetti Pellanda, A.; Garzoni, C.; Tamagnini, E.; Lestani, S.; Varani, L.; Sommer, S.; Fernandez, D.; Barba Spaeth, G.; Niejadlik, E. G.; Bournazos, S.; Robbiani, D. F.; Barnes, C. O.; Cavalli, A.

2026-08-18 immunology 10.64898/2026.08.17.745160 medRxiv
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SARS-CoV-2 evolution has reduced the efficacy of clinical monoclonal antibodies, underscoring the need for therapeutics targeting conserved viral regions. The Spike (S) heptad repeat 2 (HR2) stem helix is highly conserved across SARS-CoV-2 variants and related betacoronaviruses. Although antibodies to this region can neutralize infection, their natural occurrence and evolution remain poorly understood. We previously identified human neutralizing antibodies to a conserved peptide within this region (HR2 coldspot). Here, we show that plasma IgG reactivity to this region remains rare, even after repeated antigen exposure. Longitudinal analysis over 30 months revealed continued somatic hypermutation of HR2-specific antibodies, yet none surpassed the potency or breadth of hr2.016, which emerged shortly after primary infection. Crystal structures of four HR2 stem helix antibodies revealed convergent recognition across distinct antibody lineages. Comparison of hr2.016 with its non-neutralizing clonal relative hr2.086 showed that structural convergence masks distinct binding kinetics. Surface plasmon resonance and molecular dynamics simulations revealed a more stable interaction network for hr2.016, with slower dissociation and prolonged S residence time. Neutralization required the IgG format, supporting an avidity-driven mechanism. Together, these findings define kinetic and avidity constraints governing neutralization at the HR2 stem helix and position hr2.016 as a resilient therapeutic candidate.

9
Inflammatory restraint and membrane lipid integrity protect hematopoietic stem cells under stress

Nakamura-Ishizu, A.; Yahagi, A.; Okabe-Kitajima, H.; Mochizuki-Kashio, M.; Komai, K.; Matsumura, T.; Umemoto, T.; Nawa, M.; Nakamura, F.; Yoshimoto, T.; Kanekura, K.; Xie, S. Z.; Takubo, K.; Suda, T.

2026-08-25 cell biology 10.64898/2026.08.24.746871 medRxiv
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Life-long production of blood requires the preservation of hematopoietic stem cell (HSCs) regenerative capacity during inflammation. The cytokine, Thrombopoietin (THPO), is essential for HSC maintenance yet its role during inflammatory stress remains incompletely understood. Long-term repopulating potential was rapidly depleted in THPO-deficient HSCs upon poly(I:C) administration through inflammatory pyroptosis. Transcriptomic and chromatin accessibility analyses revealed constitutive interferon (IFN) pathway activation in THPO-deficient HSCs, characterized by enhanced STAT1 signaling, increased accessibility of STAT and IRF motifs, and elevated expression of IFN-stimulated genes. Lipidomic profiling further identified selective shifts in sphingomyelin (SM) species and enrichment of features associated with increased bilayer rigidity. THPO-deficient HSCs displayed elevated membrane SM incorporation, impaired membrane fluidity and altered membrane ultrastructure. Genetic ablation of Stat1 normalized membrane lipid abnormalities and reduced pyroptotic activation and restored HSC survival and regenerative function under inflammatory stress. Together, these findings identify a STAT1 and SM metabolism as critical THPO downstream to protect HSCs from inflammatory pyroptosis. Our results reveal membrane lipid homeostasis as a fundamental mechanism through which cytokine signaling safeguards HSC function during stress.

10
CRISPR-FOIL: A Programmable CRISPR Tool to Engineer and Illuminate Chromatin Folding in Live Human Cells

Chung, Y.-C.; Willey, S.; He, S.-L.; Wise, N.; Tu, L.-C.

2026-08-11 cell biology 10.64898/2026.08.09.743771 medRxiv
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Chromatin organization plays a critical role in regulating gene expression. Chromatin compaction represses gene expression by physically restricting the access of the transcriptional machinery to DNA, while spatial proximity between enhancers and promoters, often mediated by chromatin loops, is essential for gene activation. To investigate the regulatory mechanisms underlying loop formation and chromatin compaction, as well as their effects on gene expression, we developed CRISPR-FOIL (utilizing CRISPR to FOld and ILluminate chromosomal DNA), a novel programmable platform for engineering chromatin loops and inducing chromatin compaction in live cells. CRISPR-FOIL anchors pairs of genomic loci in proximity by engineered single-guide RNAs (sgRNAs), resulting in an artificial chromatin loop. The fused two CRISPR-Sirius gRNAs enable genomic loci to be visualized through fluorescent RNA coat proteins in various colors. In addition, multiple CRISPR-FOIL complexes can act cooperatively to drive chromatin compaction. These results establish CRISPR-FOIL as a powerful tool for engineering chromatin organization in live cells and highlight its potential as a therapeutic platform for gene regulation and disease control.

11
Tumor-tropic E. coli engineered as living T and NK cell engagers

Yang, S.; Bader, A. C.; Sendker, S.; Hu, A.; Chen, D. C.; Nath, H.; Chen, A.; Bobilev, E.; Sheffer, M.; Hui, V. W.; Kochs, T. E.; Maia, A.; Tang, J.; Liu, F.; Deng, X.; Nguyen, M.; Stanojevic, M.; Tarannum, M.; Albert, C. L.; Ali, A. K.; Shapiro, R.; Wei, Y.; Zhang, K.; Wang, Z.; Chung, Y. R.; Parry, E.; Campisi, M.; Barbie, D.; Lane, A. A.; Li, H.; Ligon, K. L.; Huang, K.; Wucherpfennig, K. W.; Chugh, S.; Ullrich, E.; Einsele, H.; Chen, J.; Koreth, J.; Silveira, V. S.; Soiffer, R.; Little, J. S.; Wu, C. J.; Ritz, J.; Li, J.; Aguirre, A. J.; Romee, R.

2026-08-20 bioengineering 10.64898/2026.08.18.745642 medRxiv
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Despite advances in immunotherapy, most solid tumors remain resistant to treatment. Immune cell engagers redirect cytotoxic lymphocytes against cancer, but limited tumor access, immunosuppressive microenvironments and systemic immune activation limit efficacy. Here we develop live immune modulating engagers (LIME), a modular platform where non-pathogenic, tumor-tropic Escherichia coli display tandem single-chain variable fragments targeting a tumor-associated antigen and an activating receptor on T or natural killer cells. LIME bridged effector and tumor cells, induced transcriptional programs of T cell activation, metabolism and proliferation, and enhanced cytotoxicity across cancer cell lines and patient-derived organoids. In mouse models, LIME safely accumulated in tumors, outperformed tarlatamab in small cell lung cancer, and induced durable immunity in lymphoma. RAS inhibition and PD-L1 blockade enhanced LIME activity in pancreatic cancer and induced humoral responses. Multi-lineage immune modulation remained tumor-confined, without organ toxicity. These findings establish LIME as a versatile living therapeutic platform for programmable, tumor-restricted immune orchestration.

12
In vivo gene disruption and homology-directed repair in muscles and muscle stem cells using CRISPR/Cas9

Peacker, B. L.; Lin, K.-H.; Lam, A.; Rios, C. L.; Zhu, K.; Goldstein, J. M.; Messemer, K.; Ellis, R.; Florea, M.; Kletzien, H.; Horwitz, N.; Bratti, A. D.; Paul, U. S.; Maier, M.; KC, M.; Liu, T.; Kakhki, S. A.; Xiao, R.; Vandenberghe, L.; Wagers, A. J.

2026-08-17 cell biology 10.64898/2026.06.30.735705 medRxiv
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Programmable endonucleases such as CRISPR/Cas9 provide powerful tools to edit mammalian genomes by engaging cellular mechanisms of DNA double-strand break (DSB) repair. CRISPR-catalysed homology-directed repair (CRISPR-HDR), though generally less efficient than other modes of DNA repair, holds particular promise to enable precise sequence replacement by targeted insertion of a homologous DNA template1,2. While recent studies have reported appreciable levels of HDR in cardiomyocytes in vivo3, skeletal muscle myofibres have historically been considered refractory to HDR-mediated genome editing4. Furthermore, how repair outcomes differ across tissues after systemic delivery of CRISPR/Cas9 editors, whether precise HDR editing can be achieved in regenerative tissue stem cells, and how developmental timing influences accessibility to CRISPR-induced repair remain unclear. Here, we use an adeno-associated virus (AAV)-delivered in vivo GFP-to-BFP colour-switching reporter system (AAV-GFP-to-BFP) to examine in vivo CRISPR-HDR with cellular- and tissue-level resolution. We find that postnatal cardiac muscle, skeletal muscle, and muscle stem cells undergo templated HDR at different rates across discrete developmental stages in mice. While HDR-edited muscle stem cells and myofibres were readily detectable after in vivo editing in juvenile mice, editing in neonatal mice yielded more efficient HDR in cardiac tissue. Based on these results, we adapted the CRISPR-HDR approach to rescue the therapeutically relevant Dmd mutation in mdx mice, demonstrating recoding to the wild-type protein sequence in both skeletal and cardiac muscles. These results provide a framework for advancing donor-templated DNA repair in living postnatal animals, and reveal unexpected cellular, developmental, and disease-related constraints on precise, therapeutic in vivo gene correction.

13
Dll4 and Jag1a signalling act sequentially and cooperatively to drive hematopoietic stem cell fate specification

Wu, D.; Edginton-White, B.; Bornhorst, D.; Hejjaji, A. V.; Gunawan, F.; Monteiro, R.

2026-08-20 developmental biology 10.64898/2026.08.17.745164 medRxiv
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Hematopoietic stem and progenitor cells (HSPCs) arise from a specialized subset of arterial endothelial cells, the hemogenic endothelium (HE), during embryonic development and sustain blood production throughout life. Notch signalling is a key regulator of this process: its ligand Jag1 promotes HSPC formation, whereas Dll4 promotes arterial identity. However, how the activities of these ligands are temporally coordinated during HSPC emergence remains unresolved. Here we demonstrate that Dll4 is required prior to circulation onset, acting by dampening MAPK signalling to drive the transition from pre-HE to HE fate and enabling HE differentiation towards HSPCs. Subsequently, after circulation starts, Jag1a acts to maintain gene expression in HE and support transition to HSPC fate. Jag1a activity depends on blood flow-induced shear stress and rescues HSPC loss caused by impaired flow. Thus, rather than playing opposing roles, Dll4 and Jag1a act sequentially and coordinately to drive the endothelial-to-hematopoietic transition and promote HSPC emergence.

14
Structural and functional basis of the non-canonical human Dicer-tRNA complex

Di Fazio, A.; Hirschi, S.; Battistini, F.; Santos, N.; Boot, J.; Ajit, K.; Abdullah, A.; Alagia, A.; Orozco, M.; Gullerova, M.

2026-08-13 molecular biology 10.64898/2026.08.12.744379 medRxiv
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Human Dicer (hDicer) is a key enzyme in the RNA interference (RNAi) pathway that generates [~]21-22 nt micro-RNA (miRNAs) and small interfering RNAs (siRNAs). We have previously shown that hDicer also generates tRNA-derived small RNAs (tsRNAs), which mediate nuclear gene silencing and regulate hundreds of disease-associated genes. As powerful and evolutionarily conserved cellular regulators, tsRNAs emerged as an important class of small RNAs. Therefore, it is essential to understand their biogenesis. However, the molecular and structural basis of tRNA cleavage by hDicer, as well as the role of chemical modifications such as 5-methylcytosine (m5C), in this process, remain unknown. Here, we present the first structural insights into hDicer in complex with tRNA, obtained by cryo-electron microscopy (cryo-EM), selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) and molecular dynamics (MD) simulations. Our results reveal that tRNAs adopt alternative conformations that are recognized and processed by hDicer. Furthermore, we show that tRNA cleavage by hDicer is facilitated by the m5C modification deposited by Nop2/SUN RNA methyltransferase 2 (NSUN2). Collectively, our findings redefine tRNAs as bona fide hDicer substrates and uncover a modification-dependent biogenetic pathway that reshapes the current understanding of the origins and regulation of human small RNAs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/744379v1_ufig1.gif" ALT="Figure 1000"> View larger version (24K): org.highwire.dtl.DTLVardef@ad78aborg.highwire.dtl.DTLVardef@cd3a7dorg.highwire.dtl.DTLVardef@1bb2594org.highwire.dtl.DTLVardef@1a0427e_HPS_FORMAT_FIGEXP M_FIG C_FIG

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A shark variable new antigen receptor recognizes an occluded epitope of fibroblast activation protein

Broadberry, R.; Ott, K.; Lake, E.; Ravi, T.; Hemme, C.; Chi, S.; West, J.; Gunaratne, G.; Ong, I. M.; LeBeau, A.; Grant, T.

2026-08-12 biochemistry 10.64898/2026.08.11.744296 medRxiv
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Variable new antigen receptors (VNARs) are the smallest naturally occurring antibody binding domains. Their size allows VNARs to access sterically restricted epitopes that are inaccessible to conventional antibodies. We recently identified a suite of VNARs that target fibroblast activation protein (FAP), a stromal serine protease indicative of extracellular matrix remodeling. The presence of FAP on the surface of cancer-associated fibroblasts (CAFs) that promote immunosuppression has made FAP a compelling therapeutic target for cancer therapy. Although antibodies targeting FAP have been developed, there is a paucity of information on how biologics engage FAP. Here, we used single-particle cryogenic electron microscopy (cryo-EM) to compare FAP recognition of three antibody architectures: a shark-derived VNAR, variable heavy (VH) and light domains (VL) of a humanized Immunoglobulin G (IgG), and a camelid-derived VHH. The humanized VH-VL domains and camelid VHH both target a solvent-exposed {beta}-propeller domain, whereas the VNAR binds a highly conserved, topologically recessed epitope at the FAP dimer interface. Radical-footprinting mass spectrometry (MS) further mapped two additional immune-derived VNARs to distinct FAP surfaces outside the shared {beta}-propeller epitope. These findings demonstrate how unique VNAR architecture can expand access to underexplored FAP surfaces and establish a structural framework for rational multiepitope targeting strategies.

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Reprogramming VHL with molecular glues enables selective degradation of caspase-2

Hu, J.; Deng, W.; Ou, S.-C.; Golkar, A.; Inglis, A.; Smither, K.; Li, S.; Chen, K.; Bae, S. J.; Zech, S.; Choi, K.; den Besten, W.; Voss, S.; Bedel, O.; Zhou, B.; Potts, P. R.; Sadok, A.; Min, J.

2026-08-13 biochemistry 10.64898/2026.08.12.744529 medRxiv
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Molecular glue degraders (MGDs) reprogram E3 ligases to eliminate neosubstrates, yet their application has largely been confined to CRBN. Here, we identify caspase-2 as a new neosubstrate for von Hippel-Lindau (VHL), expanding the scope of VHL-based MGDs. Guided by a focused VHL ligand library design, we employed TurboID-based proximity labeling to discover stereoisomeric compounds (dCASP2-1 and dCASP2-2) that selectively recruit caspase-2 to VHL and promote its ubiquitin-proteasome system-dependent degradation. Further structure-activity relationship (SAR) studies yielded dCASP2-3 and dCASP2-4, which enhanced degradation potency (by 622-fold relative to dCASP2-1) and abolished enantioselectivity. Mechanistic mapping localized the degrader-induced interface to a two-helix region of the caspase-2 CARD domain, with residues H33, P34, and D100 essential for VHL engagement. Degron-guided computational modeling of the VHL/MGD/caspase-2 ternary complex provided structural insight into neosubstrate recognition. Together, we report the development of VHL molecular glues that selectively and potently degrade caspase-2, offering chemical probes to interrogate its functions in apoptosis and stress responses, while broadening the substrate landscape of VHL-based MGDs.

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Structure-aware deep learning predicts influenza antigenicity and guides vaccine strain recommendation

Li, X.; Zhou, C.; Xiao, K.; Xu, J.; Jia, X.; Zhao, D.; Chen, L.; Li, Y.; Peng, J.; Zhu, J.; Liu, Y.; Shang, X.; Kong, H.

2026-08-07 bioinformatics 10.64898/2026.08.02.742372 medRxiv
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The continuous accumulation of genetic mutations in influenza A viruses (IAVs) drives antigenic drift, necessitating precise antigenic prediction for optimal vaccine strain selection. While sequence-based methods have advanced antigenic surveillance, they neglect the three-dimensional structural context that fundamentally dictates viral antigenicity. Here, we introduce Vir3D, which leverages ESMFold-derived structural information from amino acid sequences to precisely predict viral antigenicity and guide vaccine strain selection. Across both human H3 and highly pathogenic avian H5 subtypes, Vir3D not only accurately discriminates antigenic variants and infers pairwise antigenic distances, but also mechanistically delineates key structural residues driving viral immune evasion. In a decade-long retrospective analysis, Vir3D-prioritized vaccines consistently achieve broader antigenic coverage of circulating strains than World Health Organization (WHO) recommendations. Crucially, Vir3D successfully predicts that the emerging U.S. dairy cattle H5N1 virus (TX/24) remains antigenically stable relative to clade 2.3.4.4b vaccine strains, and subsequent wet-laboratory validation of hemagglutination inhibition (HI) assays definitively corroborates this finding. Overall, Vir3D establishes a powerful, structure-driven framework for proactive influenza surveillance and pandemic preparedness.

18
Structure of a dodecameric double-ferritin-fold protein from an Asgard archaeon

Remeeva, A.; Anuchina, A.; Dashevskii, D.; Kurkin, T.; Semenov, O.; Mishin, A.; Osipov, S.; Li, G.; Shishkin, P.; Shuvaev, Y.; Mikhailov, A.; Kuznetsova, E.; Natarov, I.; Nikolaev, A.; Sudarev, V.; Vlasov, A.; Borshchevskiy, V.; Rogachev, A.; Gushchin, I.

2026-08-26 biophysics 10.64898/2026.08.25.747088 medRxiv
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Ferritins are ubiquitous iron homeostasis proteins found across the tree of life that form conserved 24-subunit cages with octahedral (4-3-2) symmetry. New types of ferritins and ferritin-like proteins are being continuously discovered, such as mini-bacterioferritins, which form smaller shells of 12 subunits, and double-ferritin-fold proteins, which act as ferroxidases but do not form shells. Here, we describe double-ferritin-fold proteins from Asgard archaea, dubbed dFTNs, and determine Cryo-EM structure of a representative from Candidatus Heimdallarchaeum endolithica. The protein forms a dodecameric shell with tetrahedral (2-3) symmetry. N-terminal (NTD) and C-terminal (CTD) domains are bridged by an ordered linker and are related by two-fold rotational pseudosymmetry. C-terminal -helix (helix E) that forms the four-fold channel in classic ferritins is repositioned to be the helix 2 out of 5 ferritin domain -helices in dFTN, with two such helices from NTD and two helices from CTD forming a pseudo-four-fold symmetry structural element. Four three-fold channels are formed by NTDs, and four other such channels are formed by CTDs. The overall arrangement of dFTN ferritin domains is similar to that of protomers in classic ferritin shells. Altogether, our findings expand the range of known ferritin family proteins and provide insight into Asgard archaea iron metabolism.

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Cryo-EM Structure of Duck Secretory IgM Reveals a Conserved Pentameric Assembly with Avian-Specific Features at Molecular Interfaces

Schneider, R. M.; Liu, Q.; Stadtmueller, B. M.

2026-08-30 immunology 10.64898/2026.08.26.747385 medRxiv
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IgM is the most ancient antibody isotype, playing an important role in both circulatory and mucosal immune responses across vertebrates, yet structural characterization of its polymeric forms is limited outside of mammals. Here, we report the cryo-electron microscopy structure of mallard duck secretory (S) IgM at 3.37-[A] resolution. The structure revealed a pentameric core globally similar to human SIgM, supporting the view that pentameric IgM is subject to strong evolutionary constraints. However, compared to mammalian structures, we observed species-specific differences at molecular interfaces. Surface plasmon resonance binding assays characterizing secretory component (SC)-IgM interactions supported structural observations and, when compared to IgA binding, revealed isotype-specific contributions from the avian SC N-terminal extension. Together, these findings establish a comparative structural framework for polymeric IgM across vertebrates and provide insight into how avian SIgM-specific features may support mucosal immunity in birds.

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An Exact-Residue Atlas of Opioid Receptor Wiring and Rewiring across Ligand and Transducer Contexts

Nael, M.; Alakonda, L.; Elokely, K.

2026-08-19 bioinformatics 10.64898/2026.08.14.744957 medRxiv
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Opioid-receptor structures span four human receptor subtypes, diverse ligands, signaling partners, and experimental constructs. We curated 86 human opioid-receptor structures representing 84 independent experimental maps, with one unique experimental data set counted once for structure-level inference, and analyzed them using our in-house StrucMind platform. StrucMind constructs exact Ballesteros-Weinstein (BW) contact graphs, meaning residue-contact networks restricted to unambiguous generic BW positions. Relative to active transducer-bound structures, structures classified as inactive showed 2.49% lower mean contact similarity and 34.84% more rewired contacts, where rewiring is the static set of contacts gained or lost between two structures. Among 77 maps with a resolved selected-ligand site, changed contacts were 15.28% direct to the site, 40.13% adjacent at one graph edge, and 44.59% connected-distal at a finite graph distance greater than one. The deposited-water analysis identified 137 receptor-proximal waters. Sixty-one contacted at least two protein residues, including 38 that bridged at least two exact-BW residues; a separate ligand-contact branch contained 10 waters contacting both selected ligand and receptor, only 3 of which belonged to the 38-water set. None of 32 component-association tests survived global correction. For peptide versus small molecule, the smallest nominal p value among four outcomes corresponded to 6.18% lower shared-contact distance root-mean-square deviation (p=0.00989; q=0.3165, where q is the adjusted p value). The atlas supports bounded, testable hypotheses, not causal component, hydration, or efficacy mechanisms.