Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.

Many growth factors and cytokines signal by binding to the extracellular domains of their receptors and driving association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affect signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo-designed fibroblast growth factor receptor (FGFR)-binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and mitogen-activated protein kinase (MAPK) pathway activation. The high specificity of the designed agonists reveals distinct roles for two FGFR splice variants in driving arterial endothelium and perivascular cell fates during early vascular development. Our designed modular assemblies should be broadly useful for unraveling the complexities of signaling in key developmental transitions and for developing future therapeutic applications.

Inadequate DNA Damage Repair Promotes Mammary Transdifferentiation, Leading to BRCA1 Breast Cancer.

Loss of BRCA1 p220 function often results in basal-like breast cancer (BLBC), but the underlying disease mechanism is largely opaque. In mammary epithelial cells (MECs), BRCA1 interacts with multiple proteins, including NUMB and HES1, to form complexes that participate in interstrand crosslink (ICL) DNA repair and MEC differentiation control. Unrepaired ICL damage results in aberrant transdifferentiation to a mesenchymal state of cultured, human basal-like MECs and to a basal/mesenchymal state in primary mouse luminal MECs. Loss of BRCA1, NUMB, or HES1 or chemically induced ICL damage in primary murine luminal MECs results in persistent DNA damage that triggers luminal to basal/mesenchymal transdifferentiation. In vivo single-cell analysis revealed a time-dependent evolution from normal luminal MECs to luminal progenitor-like tumor cells with basal/mesenchymal transdifferentiation during murine BRCA1 BLBC development. Growing DNA damage accompanied this malignant transformation.

Affinity-independent memory B cell origin of the early antibody-secreting cell response in naive individuals upon SARS-CoV-2 vaccination.

Memory B cells (MBCs) formed over the individual's lifetime constitute nearly half of the circulating B cell repertoire in humans. These pre-existing MBCs dominate recall responses to their cognate antigens, but how they respond to recognition of novel antigens is not well understood. Here, we tracked the origin and followed the differentiation paths of MBCs in the early anti-spike (S) response to mRNA vaccination in SARS-CoV-2-naive individuals on single-cell and monoclonal antibody levels. Pre-existing, highly mutated MBCs showed no signs of germinal center re-entry and rapidly developed into mature antibody-secreting cells (ASCs). By contrast, and despite similar levels of S reactivity, naive B cells showed strong signs of antibody affinity maturation before differentiating into MBCs and ASCs. Thus, pre-existing human MBCs differentiate into ASCs in response to novel antigens, but the quality of the humoral and cellular anti-S response improved through the clonal selection and affinity maturation of naive precursors.

Blueprinting extendable nanomaterials with standardized protein blocks.

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures1. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight 'train track' assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to 'back of an envelope' architectural blueprints.

A LaCl3-based lithium superionic conductor compatible with lithium metal.

Inorganic superionic conductors possess high ionic conductivity and excellent thermal stability but their poor interfacial compatibility with lithium metal electrodes precludes application in all-solid-state lithium metal batteries1,2. Here we report a LaCl3-based lithium superionic conductor possessing excellent interfacial compatibility with lithium metal electrodes. In contrast to a Li3MCl6 (M = Y, In, Sc and Ho) electrolyte lattice3-6, the UCl3-type LaCl3 lattice has large, one-dimensional channels for rapid Li+ conduction, interconnected by La vacancies via Ta doping and resulting in a three-dimensional Li+ migration network. The optimized Li0.388Ta0.238La0.475Cl3 electrolyte exhibits Li+ conductivity of 3.02 mS cm-1 at 30 °C and a low activation energy of 0.197 eV. It also generates a gradient interfacial passivation layer to stabilize the Li metal electrode for long-term cycling of a Li-Li symmetric cell (1 mAh cm-2) for more than 5,000 h. When directly coupled with an uncoated LiNi0.5Co0.2Mn0.3O2 cathode and bare Li metal anode, the Li0.388Ta0.238La0.475Cl3 electrolyte enables a solid battery to run for more than 100 cycles with a cutoff voltage of 4.35 V and areal capacity of more than 1 mAh cm-2. We also demonstrate rapid Li+ conduction in lanthanide metal chlorides (LnCl3; Ln = La, Ce, Nd, Sm and Gd), suggesting that the LnCl3 solid electrolyte system could provide further developments in conductivity and utility.

Mouse circulating extracellular vesicles contain virus-derived siRNAs active in antiviral immunity.

Induction and suppression of antiviral RNA interference (RNAi) has been observed in mammals during infection with at least seven distinct RNA viruses, including some that are pathogenic in humans. However, while the cell-autonomous immune response mediated by antiviral RNAi is gradually being recognized, little is known about systemic antiviral RNAi in mammals. Furthermore, extracellular vesicles (EVs) also function in viral signal spreading and host immunity. Here, we show that upon antiviral RNAi activation, virus-derived small-interfering RNAs (vsiRNAs) from Nodamura virus (NoV), Sindbis virus (SINV), and Zika virus (ZIKV) enter the murine bloodstream via EVs for systemic circulation. vsiRNAs in the EVs are biologically active, since they confer RNA-RNA homology-dependent antiviral activity in both cultured cells and infant mice. Moreover, we demonstrate that vaccination with a live-attenuated virus, rendered deficient in RNAi suppression, induces production of stably maintained vsiRNAs and confers protective immunity against virus infection in mice. This suggests that vaccination with live-attenuated VSR (viral suppressor of RNAi)-deficient mutant viruses could be a new strategy to induce immunity.

An RNA-informed dosage sensitivity map reflects the intrinsic functional nature of genes.

Understanding dosage sensitivity or why Mendelian diseases have dominant vs. recessive modes of inheritance is crucial for uncovering the etiology of human disease. Previous knowledge of dosage sensitivity is mainly based on observations of rare loss-of-function mutations or copy number changes, which are underpowered due to ultra rareness of such variants. Thus, the functional underpinnings of dosage constraint remain elusive. In this study, we aim to systematically quantify dosage perturbations from cis-regulatory variants in the general population to yield a tissue-specific dosage constraint map of genes and further explore their underlying functional logic. We reveal an inherent divergence of dosage constraints in genes by functional categories with signaling genes (transcription factors, protein kinases, ion channels, and cellular machinery) being dosage sensitive, while effector genes (transporters, metabolic enzymes, cytokines, and receptors) are generally dosage resilient. Instead of being a metric of functional dispensability, we show that dosage constraint reflects underlying homeostatic constraints arising from negative feedback. Finally, we employ machine learning to integrate DNA and RNA metrics to generate a comprehensive, tissue-specific map of dosage sensitivity (MoDs) for autosomal genes.

Tumor-repopulating cells evade ferroptosis via PCK2-dependent phospholipid remodeling.

Whether stem-cell-like cancer cells avert ferroptosis to mediate therapy resistance remains unclear. In this study, using a soft fibrin gel culture system, we found that tumor-repopulating cells (TRCs) with stem-cell-like cancer cell characteristics resist chemotherapy and radiotherapy by decreasing ferroptosis sensitivity. Mechanistically, through quantitative mass spectrometry and lipidomic analysis, we determined that mitochondria metabolic kinase PCK2 phosphorylates and activates ACSL4 to drive ferroptosis-associated phospholipid remodeling. TRCs downregulate the PCK2 expression to confer themselves on a structural ferroptosis-resistant state. Notably, in addition to confirming the role of PCK2-pACSL4(T679) in multiple preclinical models, we discovered that higher PCK2 and pACSL4(T679) levels are correlated with better response to chemotherapy and radiotherapy as well as lower distant metastasis in nasopharyngeal carcinoma cohorts.

Targeted inhibition of Wnt signaling with a Clostridioides difficile toxin B fragment suppresses breast cancer tumor growth.

Wnt signaling pathways are transmitted via 10 homologous frizzled receptors (FZD1-10) in humans. Reagents broadly inhibiting Wnt signaling pathways reduce growth and metastasis of many tumors, but their therapeutic development has been hampered by the side effect. Inhibitors targeting specific Wnt-FZD pair(s) enriched in cancer cells may reduce side effect, but the therapeutic effect of narrow-spectrum Wnt-FZD inhibitors remains to be established in vivo. Here, we developed a fragment of C. difficile toxin B (TcdBFBD), which recognizes and inhibits a subclass of FZDs, FZD1/2/7, and examined whether targeting this FZD subgroup may offer therapeutic benefits for treating breast cancer models in mice. Utilizing 2 basal-like and 1 luminal-like breast cancer models, we found that TcdBFBD reduces tumor-initiating cells and attenuates growth of basal-like mammary tumor organoids and xenografted tumors, without damaging Wnt-sensitive tissues such as bones in vivo. Furthermore, FZD1/2/7-positive cells are enriched in chemotherapy-resistant cells in both basal-like and luminal mammary tumors treated with cisplatin, and TcdBFBD synergizes strongly with cisplatin in inhibiting both tumor types. These data demonstrate the therapeutic value of narrow-spectrum Wnt signaling inhibitor in treating breast cancers.

Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis.

Chromosomal rearrangements resulting in the fusion of TMPRSS2, an androgen-regulated gene, and the ETS family transcription factor ERG occur in over half of prostate cancers. However, the mechanism by which ERG promotes oncogenic gene expression and proliferation remains incompletely understood. Here, we identify a binding interaction between ERG and the mammalian SWI/SNF (BAF) ATP-dependent chromatin remodeling complex, which is conserved among other oncogenic ETS factors, including ETV1, ETV4, and ETV5. We find that ERG drives genome-wide retargeting of BAF complexes in a manner dependent on binding of ERG to the ETS DNA motif. Moreover, ERG requires intact BAF complexes for chromatin occupancy and BAF complex ATPase activity for target gene regulation. In a prostate organoid model, BAF complexes are required for ERG-mediated basal-to-luminal transition, a hallmark of ERG activity in prostate cancer. These observations suggest a fundamental interdependence between ETS transcription factors and BAF chromatin remodeling complexes in cancer.

HetDDI: a pre-trained heterogeneous graph neural network model for drug-drug interaction prediction.

The simultaneous use of two or more drugs due to multi-disease comorbidity continues to increase, which may cause adverse reactions between drugs that seriously threaten public health. Therefore, the prediction of drug-drug interaction (DDI) has become a hot topic not only in clinics but also in bioinformatics. In this study, we propose a novel pre-trained heterogeneous graph neural network (HGNN) model named HetDDI, which aggregates the structural information in drug molecule graphs and rich semantic information in biomedical knowledge graph to predict DDIs. In HetDDI, we first initialize the parameters of the model with different pre-training methods. Then we apply the pre-trained HGNN to learn the feature representation of drugs from multi-source heterogeneous information, which can more effectively utilize drugs' internal structure and abundant external biomedical knowledge, thus leading to better DDI prediction. We evaluate our model on three DDI prediction tasks (binary-class, multi-class and multi-label) with three datasets and further assess its performance on three scenarios (S1, S2 and S3). The results show that the accuracy of HetDDI can achieve 98.82% in the binary-class task, 98.13% in the multi-class task and 96.66% in the multi-label one on S1, which outperforms the state-of-the-art methods by at least 2%. On S2 and S3, our method also achieves exciting performance. Furthermore, the case studies confirm that our model performs well in predicting unknown DDIs. Source codes are available at https://github.com/LinsLab/HetDDI.

3D-SMGE: a pipeline for scaffold-based molecular generation and evaluation.

In the process of drug discovery, one of the key problems is how to improve the biological activity and ADMET properties starting from a specific structure, which is also called structural optimization. Based on a starting scaffold, the use of deep generative model to generate molecules with desired drug-like properties will provide a powerful tool to accelerate the structural optimization process. However, the existing generative models remain challenging in extracting molecular features efficiently in 3D space to generate drug-like 3D molecules. Moreover, most of the existing ADMET prediction models made predictions of different properties through a single model, which can result in reduced prediction accuracy on some datasets. To effectively generate molecules from a specific scaffold and provide basis for the structural optimization, the 3D-SMGE (3-Dimensional Scaffold-based Molecular Generation and Evaluation) work consisting of molecular generation and prediction of ADMET properties is presented. For the molecular generation, we proposed 3D-SMG, a novel deep generative model for the end-to-end design of 3D molecules. In the 3D-SMG model, we designed the cross-aggregated continuous-filter convolution (ca-cfconv), which is used to achieve efficient and low-cost 3D spatial feature extraction while ensuring the invariance of atomic space rotation. 3D-SMG was proved to generate valid, unique and novel molecules with high drug-likeness. Besides, the proposed data-adaptive multi-model ADMET prediction method outperformed or maintained the best evaluation metrics on 24 out of 27 ADMET benchmark datasets. 3D-SMGE is anticipated to emerge as a powerful tool for hit-to-lead structural optimizations and accelerate the drug discovery process.

Engineering allorejection-resistant CAR-NKT cells from hematopoietic stem cells for off-the-shelf cancer immunotherapy.

The clinical potential of current FDA-approved chimeric antigen receptor (CAR)-engineered T (CAR-T) cell therapy is encumbered by its autologous nature, which presents notable challenges related to manufacturing complexities, heightened costs, and limitations in patient selection. Therefore, there is a growing demand for off-the-shelf universal cell therapies. In this study, we have generated universal CAR-engineered NKT (UCAR-NKT) cells by integrating iNKT TCR engineering and HLA gene editing on hematopoietic stem cells (HSCs), along with an ex vivo, feeder-free HSC differentiation culture. The UCAR-NKT cells are produced with high yield, purity, and robustness, and they display a stable HLA-ablated phenotype that enables resistance to host cell-mediated allorejection. These UCAR-NKT cells exhibit potent antitumor efficacy to blood cancers and solid tumors, both in vitro and in vivo, employing a multifaceted array of tumor-targeting mechanisms. These cells are further capable of altering the tumor microenvironment by selectively depleting immunosuppressive tumor-associated macrophages and myeloid-derived suppressor cells. In addition, UCAR-NKT cells demonstrate a favorable safety profile with low risks of graft-versus-host disease and cytokine release syndrome. Collectively, these preclinical studies underscore the feasibility and significant therapeutic potential of UCAR-NKT cell products and lay a foundation for their translational and clinical development.

On-Chip Meta-Optics for Engineering Arbitrary Trajectories with Longitudinal Polarization Variation.

On-chip integrated meta-optics promise to achieve high-performance and compact integrated photonic devices. To arbitrarily engineer the optical trajectory along the propagation path in an on-chip integrated scheme is of significance in fundamental physics and various emerging applications. Here, we experimentally demonstrate an on-chip metasurface integrated on a waveguide to enable predefined arbitrary optical trajectories in the visible regime. By transformation of the transverse phase to generate longitudinal mapping, the guided waves are extracted and molded into any different optical trajectories (parabola, hyperbola, and cosine). More intriguingly, predefined polarization states with longitudinal variation are also successfully imparted along the trajectory. Owing to the on-chip propagation scheme, the trajectories are uniquely free from zero-order diffraction interference, naturally having a higher signal-to-noise ratio beyond conventional free-space forms. Overall, such on-chip optical trajectory engineering allows for miniaturized integration and can find paths in potential applications of complex optical manipulation, advanced laser fabrication, and microscopic imaging.

A New Strategy for the Design of Triple-Phase Eutectic High-Entropy Alloys Based on Infinite Solid Solution and Pseudo-Ternary Method.

Eutectic high-entropy alloys (EHEAs) have combined both high-entropy alloys and eutectic alloy contributions, with excellent castability and high-temperature application potential. Yet, multielement/triple-phase eutectic high-entropy alloy (TEHEA) designs remain puzzling. This work proposed a new strategy based on an infinite solid solution and pseudo-ternary model to reveal the puzzle of TEHEAs. The designed triple-phase eutectic high-entropy alloys (TEHEAs) with more than seven elements were identified as face-centered cubic (FCC), ordered body-centered cubic (B2), and Laves phase structures. In this work, the alloy C showcases outstanding comprehensive mechanical properties, offering a novel avenue for the design of high-performance EHEAs.

Interfacial Passivation Engineering for Highly Efficient Quantum Dot Light-Emitting Diodes via Aromatic Amine-Functionalized Dipole Molecules.

Blue quantum dot (QD) light-emitting diodes (QLEDs) exhibit unsatisfactory operational stability and electroluminescence (EL) properties due to severe nonradiative recombination induced by large numbers of dangling bond defects and charge imbalance in QD. Herein, dipolar aromatic amine-functionalized molecules with different molecular polarities are employed to regulate charge transport and passivate interfacial defects between QD and the electron transfer layer (ETL). The results show that the stronger the molecular polarity, especially with the -CF3 groups possessing a strong electron-withdrawing capacity, the more effective the defect passivation of S and Zn dangling bonds at the QD surface. Moreover, the dipole interlayer can effectively reduce electron injection into QD at high current density, enhancing charge balance and mitigating Joule heat. Finally, blue QLEDs exhibit a peak external quantum efficiency (EQE) of 21.02% with an operational lifetime (T50 at 100 cd m-2) exceeding 4000 h.

Organic Ligand Engineering for Tailoring Electron-Phonon Coupling in 2D Hybrid Perovskites.

In the emerging two-dimensional organic-inorganic hybrid perovskites, the electronic structures and carrier behaviors are strongly impacted by intrinsic electron-phonon interactions, which have received inadequate attention. In this study, we report an intriguing phenomenon of negative carrier diffusion induced by electron-phonon coupling in (2T)2PbI4. Theoretical calculations reveal that the electron-phonon coupling drives the band alignment in (2T)2PbI4 to alternate between type I and type II heterostructures. As a consequence, photoexcited holes undergo transitions between the organic ligands and inorganic layers, resulting in abnormal carrier transport behavior compared to other two-dimensional hybrid perovskites. These findings provide valuable insights into the role of electron-phonon coupling in shaping the band alignments and carrier behaviors in two-dimensional hybrid perovskites. They also open up exciting avenues for designing and fabricating functional semiconductor heterostructures with tailored properties.

Layered Ferromagnetic Structure Caused by the Proximity Effect and Interlayer Charge Transfer for LaNiO3/LaMnO3 Superlattices.

Magnetic proximity-induced magnetism in paramagnetic LaNiO3 (LNO) has spurred intensive investigations in the past decade. However, no consensus has been reached so far regarding the magnetic order in LNO layers in relevant heterostructures. This paper reports a layered ferromagnetic structure for the (111)-oriented LNO/LaMnO3 (LMO) superlattices. It is found that each period of the superlattice consisted of an insulating LNO-interfacial phase (five unit cells in thickness, ∼1.1 nm), a metallic LNO-inner phase, a poorly conductive LMO-interfacial phase (three unit cells in thickness, ∼0.7 nm), and an insulating LMO-inner phase. All four of these phases are ferromagnetic, showing different magnetizations. The Mn-to-Ni interlayer charge transfer is responsible for the emergence of a layered magnetic structure, which may cause magnetic interaction across the LNO/LMO interface and double exchange within the LMO-interfacial layer. This work indicates that the proximity effect is an effective means of manipulating the magnetic state and associated properties of complex oxides.

Charge Carrier Regulation for Efficient Blue Quantum-Dot Light-Emitting Diodes Via a High-Mobility Coplanar Cyclopentane[b]thiopyran Derivative.

The performance of blue quantum dot light-emitting diodes (QLEDs) is limited by unbalanced charge injection, resulting from insufficient holes caused by low mobility or significant energy barriers. Here, we introduce an angular-shaped heteroarene based on cyclopentane[b]thiopyran (C8-SS) to modify the hole transport layer poly-N-vinylcarbazole (PVK), in blue QLEDs. C8-SS exhibits high hole mobility and conductivity due to the π···π and S···π interactions. Introducing C8-SS to PVK significantly enhanced hole mobility, increasing it by 2 orders of magnitude from 2.44 × 10-6 to 1.73 × 10-4 cm2 V-1 s-1. Benefiting from high mobility and conductivity, PVK:C8-SS-based QLEDs exhibit a low turn-on voltage (Von) of 3.2 V. More importantly, the optimized QLEDs achieve a high peak power efficiency (PE) of 7.13 lm/W, which is 2.65 times that of the control QLEDs. The as-proposed interface engineering provides a novel and effective strategy for achieving high-performance blue QLEDs in low-energy consumption lighting applications.

Dimensional and Doping Engineering of Chiral Perovskites with Enhanced Spin Selectivity for Green Emissive Spin Light-Emitting Diodes.

Chiral perovskites play a pivotal role in spintronics and optoelectronic systems attributed to their chiral-induced spin selectivity (CISS) effect. Specifically, they allow for spin-polarized charge transport in spin light-emitting diodes (LEDs), yielding circularly polarized electroluminescence at room temperature without external magnetic fields. However, chiral lead bromide-based perovskites have yet to achieve high-performance green emissive spin-LEDs, owing to limited CISS effects and charge transport. Herein, we employ dimensional regulation and Sn2+-doping to optimize chiral bromide-based perovskite architecture for green emissive spin-LEDs. The optimized (PEA)x(S/R-PRDA)2-xSn0.1Pb0.9Br4 chiral perovskite film exhibits an enhanced CISS effect, higher hole mobility, and better energy level alignment with the emissive layer. These improvements allow us to fabricate green emissive spin-LEDs with an external quantum efficiency (EQE) of 5.7% and an asymmetry factor |gCP-EL| of 1.1 × 10-3. This work highlights the importance of tailored perovskite architectures and doping strategies in advancing spintronics for optoelectronic applications.