Cell surface RNAs control neutrophil recruitment.

RNAs localizing to the outer cell surface have been recently identified in mammalian cells, including RNAs with glycan modifications known as glycoRNAs. However, the functional significance of cell surface RNAs and their production are poorly known. We report that cell surface RNAs are critical for neutrophil recruitment and that the mammalian homologs of the sid-1 RNA transporter are required for glycoRNA expression. Cell surface RNAs can be readily detected in murine neutrophils, the elimination of which substantially impairs neutrophil recruitment to inflammatory sites in vivo and reduces neutrophils' adhesion to and migration through endothelial cells. Neutrophil glycoRNAs are predominantly on cell surface, important for neutrophil-endothelial interactions, and can be recognized by P-selectin (Selp). Knockdown of the murine Sidt genes abolishes neutrophil glycoRNAs and functionally mimics the loss of cell surface RNAs. Our data demonstrate the biological importance of cell surface glycoRNAs and highlight a noncanonical dimension of RNA-mediated cellular functions.

Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues.

The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding in tissue (Patho-DBiT) by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for 5 years. Furthermore, genome-wide single-nucleotide RNA variants can be captured to distinguish malignant subclones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis. Single-cell level Patho-DBiT dissects the spatiotemporal cellular dynamics driving tumor clonal architecture and progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to aid in clinical pathology evaluation.

Nano-achiral complex composites for extreme polarization optics.

Composites from 2D nanomaterials show uniquely high electrical, thermal and mechanical properties1,2. Pairing their robustness with polarization rotation is needed for hyperspectral optics in extreme conditions3,4. However, the rigid nanoplatelets have randomized achiral shapes, which scramble the circular polarization of photons with comparable wavelengths. Here we show that multilayer nanocomposites from 2D nanomaterials with complex textured surfaces strongly and controllably rotate light polarization, despite being nano-achiral and partially disordered. The intense circular dichroism (CD) in nanocomposite films originates from the diagonal patterns of wrinkles, grooves or ridges, leading to an angular offset between axes of linear birefringence (LB) and linear dichroism (LD). Stratification of the layer-by-layer (LBL) assembled nanocomposites affords precise engineering of the polarization-active materials from imprecise nanoplatelets with an optical asymmetry g-factor of 1.0, exceeding those of typical nanomaterials by about 500 times. High thermal resilience of the composite optics enables operating temperature as high as 250 °C and imaging of hot emitters in the near-infrared (NIR) part of the spectrum. Combining LBL engineered nanocomposites with achiral dyes results in anisotropic factors for circularly polarized emission approaching the theoretical limit. The generality of the observed phenomena is demonstrated by nanocomposite polarizers from molybdenum sulfide (MoS2), MXene and graphene oxide (GO) and by two manufacturing methods. A large family of LBL optical nanocomponents can be computationally designed and additively engineered for ruggedized optics.

A rechargeable calcium-oxygen battery that operates at room temperature.

Calcium-oxygen (Ca-O2) batteries can theoretically afford high capacity by the reduction of O2 to calcium oxide compounds (CaOx) at low cost1-5. Yet, a rechargeable Ca-O2 battery that operates at room temperature has not been achieved because the CaOx/O2 chemistry typically involves inert discharge products and few electrolytes can accommodate both a highly reductive Ca metal anode and O2. Here we report a Ca-O2 battery that is rechargeable for 700 cycles at room temperature. Our battery relies on a highly reversible two-electron redox to form chemically reactive calcium peroxide (CaO2) as the discharge product. Using a durable ionic liquid-based electrolyte, this two-electron reaction is enabled by the facilitated Ca plating-stripping in the Ca metal anode at room temperature and improved CaO2/O2 redox in the air cathode. We show the proposed Ca-O2 battery is stable in air and can be made into flexible fibres that are weaved into textile batteries for next-generation wearable systems.

The microRNA miR-31 inhibits CD8+ T cell function in chronic viral infection.

During infection, antigen-specific T cells undergo tightly regulated developmental transitions controlled by transcriptional and post-transcriptional regulation of gene expression. We found that the microRNA miR-31 was strongly induced by activation of the T cell antigen receptor (TCR) in a pathway involving calcium and activation of the transcription factor NFAT. During chronic infection with lymphocytic choriomeningitis virus (LCMV) clone 13, miR-31-deficent mice recovered from clinical disease, while wild-type mice continued to show signs of disease. This disease phenotype was explained by the presence of larger numbers of cytokine-secreting LCMV-specific CD8+ T cells in miR-31-deficent mice than in wild-type mice. Mechanistically, miR-31 increased the sensitivity of T cells to type I interferons, which interfered with effector T cell function and increased the expression of several proteins related to T cell dysfunction during chronic infection. These studies identify miR-31 as an important regulator of T cell exhaustion in chronic infection.

Nonstochastic reprogramming from a privileged somatic cell state.

Reprogramming somatic cells to induced pluripotency by Yamanaka factors is usually slow and inefficient and is thought to be a stochastic process. We identified a privileged somatic cell state, from which acquisition of pluripotency could occur in a nonstochastic manner. Subsets of murine hematopoietic progenitors are privileged whose progeny cells predominantly adopt the pluripotent fate with activation of endogenous Oct4 locus after four to five divisions in reprogramming conditions. Privileged cells display an ultrafast cell cycle of ∼8 hr. In fibroblasts, a subpopulation cycling at a similar ultrafast speed is observed after 6 days of factor expression and is increased by p53 knockdown. This ultrafast cycling population accounts for >99% of the bulk reprogramming activity in wild-type or p53 knockdown fibroblasts. Our data demonstrate that the stochastic nature of reprogramming can be overcome in a privileged somatic cell state and suggest that cell-cycle acceleration toward a critical threshold is an important bottleneck for reprogramming. PAPERCLIP:

The microRNA miR-148a functions as a critical regulator of B cell tolerance and autoimmunity.

Autoreactive B cells have critical roles in a large diversity of autoimmune diseases, but the molecular pathways that control these cells remain poorly understood. We performed an in vivo functional screen of a lymphocyte-expressed microRNA library and identified miR-148a as a potent regulator of B cell tolerance. Elevated miR-148a expression impaired B cell tolerance by promoting the survival of immature B cells after engagement of the B cell antigen receptor by suppressing the expression of the autoimmune suppressor Gadd45α, the tumor suppressor PTEN and the pro-apoptotic protein Bim. Furthermore, increased expression of miR-148a, which occurs frequently in patients with lupus and lupus-prone mice, facilitated the development of lethal autoimmune disease in a mouse model of lupus. Our studies demonstrate a function for miR-148a as a regulator of B cell tolerance and autoimmunity.

Molecular structure of ß-amyloid fibrils in Alzheimer's disease brain tissue.

In vitro, ß-amyloid (Aß) peptides form polymorphic fibrils, with molecular structures that depend on growth conditions, plus various oligomeric and protofibrillar aggregates. Here, we investigate structures of human brain-derived Aß fibrils, using seeded fibril growth from brain extract and data from solid-state nuclear magnetic resonance and electron microscopy. Experiments on tissue from two Alzheimer's disease (AD) patients with distinct clinical histories showed a single predominant 40 residue Aß (Aß40) fibril structure in each patient; however, the structures were different from one another. A molecular structural model developed for Aß40 fibrils from one patient reveals features that distinguish in-vivo- from in-vitro-produced fibrils. The data suggest that fibrils in the brain may spread from a single nucleation site, that structural variations may correlate with variations in AD, and that structure-specific amyloid imaging agents may be an important future goal.

Strain-retardant coherent perovskite phase stabilized Ni-rich cathode.

The use of state-of-the-art Ni-rich layered oxides (LiNixCoyMn1-x-yO2, x > 0.5) as the cathode material for lithium-ion batteries can push the energy and power density to a higher level than is currently available1,2. However, volume variation associated with anisotropic lattice strain and stress that is being developed during lithium (de)intercalation induces severe structural instability and electrochemical decay of the cathode materials, which is amplified further when the battery is operating at a high voltage (above 4.5 V), which is essential for unlocking its high energy3-6. Even after much effort by the research community, an intrinsic strain-retardant method for directly alleviating the continuous accumulation of lattice strain remains elusive. Here, by introducing a coherent perovskite phase into the layered structure functioning as a 'rivet', we significantly mitigate the pernicious structural evolutions by a pinning effect. The lattice strain evolution in every single cycle is markedly reduced by nearly 70% when compared with conventional materials, which significantly enhances morphological integrity leading to a notable improvement in battery cyclability. This strain-retardant approach broadens the perspective for lattice engineering to release the strain raised from lithium (de)intercalation and paves the way for the development of high-energy-density cathodes with long durability.

Chiral assemblies of pinwheel superlattices on substrates.

The unique topology and physics of chiral superlattices make their self-assembly from nanoparticles highly sought after yet challenging in regard to (meta)materials1-3. Here we show that tetrahedral gold nanoparticles can transform from a perovskite-like, low-density phase with corner-to-corner connections into pinwheel assemblies with corner-to-edge connections and denser packing. Whereas corner-sharing assemblies are achiral, pinwheel superlattices become strongly mirror asymmetric on solid substrates as demonstrated by chirality measures. Liquid-phase transmission electron microscopy and computational models show that van der Waals and electrostatic interactions between nanoparticles control thermodynamic equilibrium. Variable corner-to-edge connections among tetrahedra enable fine-tuning of chirality. The domains of the bilayer superlattices show strong chiroptical activity as identified by photon-induced near-field electron microscopy and finite-difference time-domain simulations. The simplicity and versatility of substrate-supported chiral superlattices facilitate the manufacture of metastructured coatings with unusual optical, mechanical and electronic characteristics.

Origin of structural degradation in Li-rich layered oxide cathode.

Li- and Mn-rich (LMR) cathode materials that utilize both cation and anion redox can yield substantial increases in battery energy density1-3. However, although voltage decay issues cause continuous energy loss and impede commercialization, the prerequisite driving force for this phenomenon remains a mystery3-6 Here, with in situ nanoscale sensitive coherent X-ray diffraction imaging techniques, we reveal that nanostrain and lattice displacement accumulate continuously during operation of the cell. Evidence shows that this effect is the driving force for both structure degradation and oxygen loss, which trigger the well-known rapid voltage decay in LMR cathodes. By carrying out micro- to macro-length characterizations that span atomic structure, the primary particle, multiparticle and electrode levels, we demonstrate that the heterogeneous nature of LMR cathodes inevitably causes pernicious phase displacement/strain, which cannot be eliminated by conventional doping or coating methods. We therefore propose mesostructural design as a strategy to mitigate lattice displacement and inhomogeneous electrochemical/structural evolutions, thereby achieving stable voltage and capacity profiles. These findings highlight the significance of lattice strain/displacement in causing voltage decay and will inspire a wave of efforts to unlock the potential of the broad-scale commercialization of LMR cathode materials.

Anti-hsa-miR-59 alleviates premature senescence associated with Hutchinson-Gilford progeria syndrome in mice.

Hutchinson-Gilford progeria syndrome (HGPS) is a lethal premature aging disorder without an effective therapeutic regimen. Because of their targetability and influence on gene expression, microRNAs (miRNAs) are attractive therapeutic tools to treat diseases. Here we identified that hsa-miR-59 (miR-59) was markedly upregulated in HGPS patient cells and in multiple tissues of an HGPS mouse model (LmnaG609G/G609G ), which disturbed the interaction between RNAPII and TFIIH, resulting in abnormal expression of cell cycle genes by targeting high-mobility group A family HMGA1 and HMGA2. Functional inhibition of miR-59 alleviated the cellular senescence phenotype of HGPS cells. Treatment with AAV9-mediated anti-miR-59 reduced fibrosis in the quadriceps muscle, heart, and aorta, suppressed epidermal thinning and dermal fat loss, and yielded a 25.5% increase in longevity of LmnaG609G/G609G mice. These results identify a new strategy for the treatment of HGPS and provide insight into the etiology of HGPS disease.

The calcium-dependent protein kinase CPK16 regulates hypoxia-induced ROS production by phosphorylating the NADPH oxidase RBOHD in Arabidopsis.

Reactive oxygen species (ROS) production is a key event in modulating plant responses to hypoxia and post-hypoxia reoxygenation. However, the molecular mechanism by which hypoxia-associated ROS homeostasis is controlled remains largely unknown. Here, we showed that the calcium-dependent protein kinase CPK16 regulates plant hypoxia tolerance by phosphorylating the plasma membrane-anchored NADPH oxidase respiratory burst oxidase homolog D (RBOHD) to regulate ROS production in Arabidopsis (Arabidopsis thaliana). In response to hypoxia or reoxygenation, CPK16 was activated through phosphorylation of its Ser274 residue. The cpk16 knockout mutant displayed enhanced hypoxia tolerance, whereas CPK16-overexpressing (CPK16-OE) lines showed increased sensitivity to hypoxic stress. In agreement with these observations, hypoxia and reoxygenation both induced ROS accumulation in the rosettes of CPK16-OEs more strongly than in the rosettes of the cpk16-1 mutant or the wild type. Moreover, CPK16 interacted with and phosphorylated the N-terminus of RBOHD at 4 serine residues (Ser133, Ser148, Ser163, and Ser347) that were necessary for hypoxia- and reoxygenation-induced ROS accumulation. Furthermore, the hypoxia-tolerant phenotype of cpk16-1 was fully abolished in the cpk16 rbohd double mutant. Thus, we have uncovered a regulatory mechanism by which the CPK16-RBOHD module shapes the ROS production during hypoxia and reoxygenation in Arabidopsis.

Design principles of heterointerfacial redox chemistry for highly reversible lithium metal anode.

High electrochemical reversibility is required for the application of high-energy-density lithium (Li) metal batteries; however, inactive Li formation and SEI (solid electrolyte interface)-instability-induced electrolyte consumption cause low Coulombic efficiency (CE). The prior interfacial chemical designs in terms of alloying kinetics have been used to enhance the CE of Li metal anode; however, the role of its redox chemistry at heterointerfaces remains a mystery. Herein, the relationship between heterointerfacial redox chemistry and electrochemical transformation reversibility is investigated. It is demonstrated that the lower redox potential at heterointerface contributes to higher CE, and this enhancement in CE is primarily due to the regulation of redox chemistry to Li deposition behavior rather than the formation of SEI films. Low oxidation potential facilitates the formation of the surface with the highly electrochemical binding feature after Li stripping, and low reduction potential can maintain binding ability well during subsequent Li plating, both of which homogenize Li deposition and thus optimize CE. In particular, Mg hetero-metal with ultra-low redox potential enables Li metal anode with significantly improved CE (99.6%) and stable cycle life for 700 cycles at 3.0 mA cm-2. This work provides insight into the heterointerfacial design principle of next-generation negative electrodes for highly reversible metal batteries.

TRIM21 induces selective autophagic degradation of c-Myc and sensitizes regorafenib therapy in colorectal cancer.

Kirsten rat sarcoma virus (KRAS) mutation is associated with malignant tumor transformation and drug resistance. However, the development of clinically effective targeted therapies for KRAS-mutant cancer has proven to be a formidable challenge. Here, we report that tripartite motif-containing protein 21 (TRIM21) functions as a target of extracellular signal-regulated kinase 2 (ERK2) in KRAS-mutant colorectal cancer (CRC), contributing to regorafenib therapy resistance. Mechanistically, TRIM21 directly interacts with and ubiquitinates v-myc avian myelocytomatosis viral oncogene homolog (c-Myc) at lysine 148 (K148) via K63-linkage, enabling c-Myc to be targeted to the autophagy machinery for degradation, ultimately resulting in the downregulation of enolase 2 expression and inhibition of glycolysis. However, mutant KRAS (KRAS/MT)-driven mitogen-activated protein kinase (MAPK) signaling leads to the phosphorylation of TRIM21 (p-TRIM21) at Threonine 396 (T396) by ERK2, disrupting the interaction between TRIM21 and c-Myc and thereby preventing c-Myc from targeting autophagy for degradation. This enhances glycolysis and contributes to regorafenib resistance. Clinically, high p-TRIM21 (T396) is associated with an unfavorable prognosis. Targeting TRIM21 to disrupt KRAS/MT-driven phosphorylation using the antidepressant vilazodone shows potential for enhancing the efficacy of regorafenib in treating KRAS-mutant CRC in preclinical models. These findings are instrumental for KRAS-mutant CRC treatment aiming at activating TRIM21-mediated selective autophagic degradation of c-Myc.

Dynamic chromatin accessibility tuning by the long noncoding RNA ELDR accelerates chondrocyte senescence and osteoarthritis.

Epigenetic reprogramming plays a critical role in chondrocyte senescence during osteoarthritis (OA) pathology, but the underlying molecular mechanisms remain to be elucidated. Here, using large-scale individual datasets and genetically engineered (Col2a1-CreERT2;Eldrflox/flox and Col2a1-CreERT2;ROSA26-LSL-Eldr+/+ knockin) mouse models, we show that a novel transcript of long noncoding RNA ELDR is essential for the development of chondrocyte senescence. ELDR is highly expressed in chondrocytes and cartilage tissues of OA. Mechanistically, exon 4 of ELDR physically mediates a complex consisting of hnRNPL and KAT6A to regulate histone modifications of the promoter region of IHH, thereby activating hedgehog signaling and promoting chondrocyte senescence. Therapeutically, GapmeR-mediated silencing of ELDR in the OA model substantially attenuates chondrocyte senescence and cartilage degradation. Clinically, ELDR knockdown in cartilage explants from OA-affected individuals decreased the expression of senescence markers and catabolic mediators. Taken together, these findings uncover an lncRNA-dependent epigenetic driver in chondrocyte senescence, highlighting that ELDR could be a promising therapeutic avenue for OA.

scGIR: deciphering cellular heterogeneity via gene ranking in single-cell weighted gene correlation networks.

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular heterogeneity through high-throughput analysis of individual cells. Nevertheless, challenges arise from prevalent sequencing dropout events and noise effects, impacting subsequent analyses. Here, we introduce a novel algorithm, Single-cell Gene Importance Ranking (scGIR), which utilizes a single-cell gene correlation network to evaluate gene importance. The algorithm transforms single-cell sequencing data into a robust gene correlation network through statistical independence, with correlation edges weighted by gene expression levels. We then constructed a random walk model on the resulting weighted gene correlation network to rank the importance of genes. Our analysis of gene importance using PageRank algorithm across nine authentic scRNA-seq datasets indicates that scGIR can effectively surmount technical noise, enabling the identification of cell types and inference of developmental trajectories. We demonstrated that the edges of gene correlation, weighted by expression, play a critical role in enhancing the algorithm's performance. Our findings emphasize that scGIR outperforms in enhancing the clustering of cell subtypes, reverse identifying differentially expressed marker genes, and uncovering genes with potential differential importance. Overall, we proposed a promising method capable of extracting more information from single-cell RNA sequencing datasets, potentially shedding new lights on cellular processes and disease mechanisms.

The DNA Methylcytosine Dioxygenase Tet2 Sustains Immunosuppressive Function of Tumor-Infiltrating Myeloid Cells to Promote Melanoma Progression.

Ten-Eleven-Translocation-2 (Tet2) is a DNA methylcytosine dioxygenase that functions as a tumor suppressor in hematopoietic malignancies. We examined the role of Tet2 in tumor-tissue myeloid cells and found that Tet2 sustains the immunosuppressive function of these cells. We found that Tet2 expression is increased in intratumoral myeloid cells both in mouse models of melanoma and in melanoma patients and that this increased expression is dependent on an IL-1R-MyD88 pathway. Ablation of Tet2 in myeloid cells suppressed melanoma growth in vivo and shifted the immunosuppressive gene expression program in tumor-associated macrophages to a proinflammatory one, with a concomitant reduction of the immunosuppressive function. This resulted in increased numbers of effector T cells in the tumor, and T cell depletion abolished the reduced tumor growth observed upon myeloid-specific deletion of Tet2. Our findings reveal a non-cell-intrinsic, tumor-promoting function for Tet2 and suggest that Tet2 may present a therapeutic target for the treatment of non-hematologic malignancies.

A disordered rock salt anode for fast-charging lithium-ion batteries.

Rechargeable lithium-ion batteries with high energy density that can be safely charged and discharged at high rates are desirable for electrified transportation and other applications1-3. However, the sub-optimal intercalation potentials of current anodes result in a trade-off between energy density, power and safety. Here we report that disordered rock salt4,5 Li3+xV2O5 can be used as a fast-charging anode that can reversibly cycle two lithium ions at an average voltage of about 0.6 volts versus a Li/Li+ reference electrode. The increased potential compared to graphite6,7 reduces the likelihood of lithium metal plating if proper charging controls are used, alleviating a major safety concern (short-circuiting related to Li dendrite growth). In addition, a lithium-ion battery with a disordered rock salt Li3V2O5 anode yields a cell voltage much higher than does a battery using a commercial fast-charging lithium titanate anode or other intercalation anode candidates (Li3VO4 and LiV0.5Ti0.5S2)8,9. Further, disordered rock salt Li3V2O5 can perform over 1,000 charge-discharge cycles with negligible capacity decay and exhibits exceptional rate capability, delivering over 40 per cent of its capacity in 20 seconds. We attribute the low voltage and high rate capability of disordered rock salt Li3V2O5 to a redistributive lithium intercalation mechanism with low energy barriers revealed via ab initio calculations. This low-potential, high-rate intercalation reaction can be used to identify other metal oxide anodes for fast-charging, long-life lithium-ion batteries.

Dynamic phase evolution of MoS3 accompanied by organodiselenide mediation enables enhanced performance rechargeable lithium battery.

Considerable efforts have been devoted to Li-S batteries, typically the soluble polysulfides shuttling effect. As a typical transition metal sulfide, MoS2 is a magic bullet for addressing the issues of Li-S batteries, drawing increasing attention. In this study, we introduce amorphous MoS3 as analogous sulfur cathode material and elucidate the dynamic phase evolution in the electrochemical reaction. The metallic 1T phase incorporated 2H phase MoS2 with sulfur vacancies (SVs-1T/2H-MoS2) decomposed from amorphous MoS3 achieves refined mixing with the "newborn" sulfur at the molecular level and supplies continuous conduction pathways and controllable physical confinement. Meanwhile, the in situ-generated SVs-1T/2H-MoS2 allows lithium intercalation in advance at high discharge voltage (≥1.8 V) and enables fast electron transfer. Moreover, aiming at the unbonded sulfur, diphenyl diselenide (PDSe), as a model redox mediator is applied, which can covalently bond sulfur atoms to form conversion-type organoselenosulfides, changing the original redox pathway of "newborn" sulfur in MoS3, and suppressing the polysulfides shuttling effect. It also significantly lowers the activation energy and thus accelerates the sulfur reduction kinetics. Thus, the in situ-formed intercalation-conversion hybrid electrode of SVs-1T/2H-MoS2 and organoselenosulfides realizes enhanced rate capability and superior cycling stability. This work provides a novel concept for designing high-energy-density electrode materials.