COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas.

A dysfunctional immune response in coronavirus disease 2019 (COVID-19) patients is a recurrent theme impacting symptoms and mortality, yet a detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 196 COVID-19 patients and controls and created a comprehensive immune landscape with 1.46 million cells. The large dataset enabled us to identify that different peripheral immune subtype changes are associated with distinct clinical features, including age, sex, severity, and disease stages of COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was found in diverse epithelial and immune cell types, accompanied by dramatic transcriptomic changes within virus-positive cells. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis of and developing effective therapeutic strategies for COVID-19.

Publisher Correction: The immune cell landscape in kidneys of patients with lupus nephritis.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry.

To define the cell populations that drive joint inflammation in rheumatoid arthritis (RA), we applied single-cell RNA sequencing (scRNA-seq), mass cytometry, bulk RNA sequencing (RNA-seq) and flow cytometry to T cells, B cells, monocytes, and fibroblasts from 51 samples of synovial tissue from patients with RA or osteoarthritis (OA). Utilizing an integrated strategy based on canonical correlation analysis of 5,265 scRNA-seq profiles, we identified 18 unique cell populations. Combining mass cytometry and transcriptomics revealed cell states expanded in RA synovia: THY1(CD90)+HLA-DRAhi sublining fibroblasts, IL1B+ pro-inflammatory monocytes, ITGAX+TBX21+ autoimmune-associated B cells and PDCD1+ peripheral helper T (TPH) cells and follicular helper T (TFH) cells. We defined distinct subsets of CD8+ T cells characterized by GZMK+, GZMB+, and GNLY+ phenotypes. We mapped inflammatory mediators to their source cell populations; for example, we attributed IL6 expression to THY1+HLA-DRAhi fibroblasts and IL1B production to pro-inflammatory monocytes. These populations are potentially key mediators of RA pathogenesis.

The immune cell landscape in kidneys of patients with lupus nephritis.

Lupus nephritis is a potentially fatal autoimmune disease for which the current treatment is ineffective and often toxic. To develop mechanistic hypotheses of disease, we analyzed kidney samples from patients with lupus nephritis and from healthy control subjects using single-cell RNA sequencing. Our analysis revealed 21 subsets of leukocytes active in disease, including multiple populations of myeloid cells, T cells, natural killer cells and B cells that demonstrated both pro-inflammatory responses and inflammation-resolving responses. We found evidence of local activation of B cells correlated with an age-associated B-cell signature and evidence of progressive stages of monocyte differentiation within the kidney. A clear interferon response was observed in most cells. Two chemokine receptors, CXCR4 and CX3CR1, were broadly expressed, implying a potentially central role in cell trafficking. Gene expression of immune cells in urine and kidney was highly correlated, which would suggest that urine might serve as a surrogate for kidney biopsies.

Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3'UTRs In Vivo.

To study the function of Rli1/ABCE1 in vivo, we used ribosome profiling and biochemistry to characterize its contribution to ribosome recycling. When Rli1 levels were diminished, 80S ribosomes accumulated both at stop codons and in the adjoining 3'UTRs of most mRNAs. Frequently, these ribosomes reinitiated translation without the need for a canonical start codon, as small peptide products predicted by 3'UTR ribosome occupancy in all three reading frames were confirmed by western analysis and mass spectrometry. Eliminating the ribosome-rescue factor Dom34 dramatically increased 3'UTR ribosome occupancy in Rli1 depleted cells, indicating that Dom34 clears the bulk of unrecycled ribosomes. Thus, Rli1 is crucial for ribosome recycling in vivo and controls ribosome homeostasis. 3'UTR translation occurs in wild-type cells as well, and observations of elevated 3'UTR ribosomes during stress suggest that modulating recycling and reinitiation is involved in responding to environmental changes.

Tuning commensurability in twisted van der Waals bilayers.

Moiré superlattices based on van der Waals bilayers1-4 created at small twist angles lead to a long wavelength pattern with approximate translational symmetry. At large twist angles (θt), moiré patterns are, in general, incommensurate except for a few discrete angles. Here we show that large-angle twisted bilayers offer distinctly different platforms. More specifically, by using twisted tungsten diselenide bilayers, we create the incommensurate dodecagon quasicrystals at θt = 30° and the commensurate moiré crystals at θt = 21.8° and 38.2°. Valley-resolved scanning tunnelling spectroscopy shows disparate behaviours between moiré crystals (with translational symmetry) and quasicrystals (with broken translational symmetry). In particular, the K valley shows rich electronic structures exemplified by the formation of mini-gaps near the valence band maximum. These discoveries demonstrate that bilayers with large twist angles offer a design platform to explore moiré physics beyond those formed with small twist angles.

Cholesterol inhibits TCR signaling by directly restricting TCR-CD3 core tunnel motility.

Cholesterol molecules specifically bind to the resting αßTCR to inhibit cytoplasmic CD3ζ ITAM phosphorylation through sequestering the TCR-CD3 complex in an inactive conformation. The mechanisms of cholesterol-mediated inhibition of TCR-CD3 and its activation remain unclear. Here, we present cryoelectron microscopy structures of cholesterol- and cholesterol sulfate (CS)-inhibited TCR-CD3 complexes and an auto-active TCR-CD3 variant. The structures reveal that cholesterol molecules act like a latch to lock CD3ζ into an inactive conformation in the membrane. Mutations impairing binding of cholesterol molecules to the tunnel result in the movement of the proximal C terminus of the CD3ζ transmembrane helix, thereby activating the TCR-CD3 complex in human cells. Together, our data reveal the structural basis of TCR inhibition by cholesterol, illustrate how the cholesterol-binding tunnel is allosterically coupled to TCR triggering, and lay a foundation for the development of immunotherapies through directly targeting the TCR-CD3 complex.

The HP1 homolog rhino anchors a nuclear complex that suppresses piRNA precursor splicing.

piRNAs guide an adaptive genome defense system that silences transposons during germline development. The Drosophila HP1 homolog Rhino is required for germline piRNA production. We show that Rhino binds specifically to the heterochromatic clusters that produce piRNA precursors, and that binding directly correlates with piRNA production. Rhino colocalizes to germline nuclear foci with Rai1/DXO-related protein Cuff and the DEAD box protein UAP56, which are also required for germline piRNA production. RNA sequencing indicates that most cluster transcripts are not spliced and that rhino, cuff, and uap56 mutations increase expression of spliced cluster transcripts over 100-fold. LacI::Rhino fusion protein binding suppresses splicing of a reporter transgene and is sufficient to trigger piRNA production from a trans combination of sense and antisense reporters. We therefore propose that Rhino anchors a nuclear complex that suppresses cluster transcript splicing and speculate that stalled splicing differentiates piRNA precursors from mRNAs.

Evidence for Dirac flat band superconductivity enabled by quantum geometry.

In a flat band superconductor, the charge carriers' group velocity vF is extremely slow. Superconductivity therein is particularly intriguing, being related to the long-standing mysteries of high-temperature superconductors1 and heavy-fermion systems2. Yet the emergence of superconductivity in flat bands would appear paradoxical, as a small vF in the conventional Bardeen-Cooper-Schrieffer theory implies vanishing coherence length, superfluid stiffness and critical current. Here, using twisted bilayer graphene3-7, we explore the profound effect of vanishingly small velocity in a superconducting Dirac flat band system8-13. Using Schwinger-limited non-linear transport studies14,15, we demonstrate an extremely slow normal state drift velocity vn ≈ 1,000 m s-1 for filling fraction ν between -1/2 and -3/4 of the moiré superlattice. In the superconducting state, the same velocity limit constitutes a new limiting mechanism for the critical current, analogous to a relativistic superfluid16. Importantly, our measurement of superfluid stiffness, which controls the superconductor's electrodynamic response, shows that it is not dominated by the kinetic energy but instead by the interaction-driven superconducting gap, consistent with recent theories on a quantum geometric contribution8-12. We find evidence for small Cooper pairs, characteristic of the Bardeen-Cooper-Schrieffer to Bose-Einstein condensation crossover17-19, with an unprecedented ratio of the superconducting transition temperature to the Fermi temperature exceeding unity and discuss how this arises for ultra-strong coupling superconductivity in ultra-flat Dirac bands.

Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes.

Rheumatoid arthritis is a prototypical autoimmune disease that causes joint inflammation and destruction1. There is currently no cure for rheumatoid arthritis, and the effectiveness of treatments varies across patients, suggesting an undefined pathogenic diversity1,2. Here, to deconstruct the cell states and pathways that characterize this pathogenic heterogeneity, we profiled the full spectrum of cells in inflamed synovium from patients with rheumatoid arthritis. We used multi-modal single-cell RNA-sequencing and surface protein data coupled with histology of synovial tissue from 79 donors to build single-cell atlas of rheumatoid arthritis synovial tissue that includes more than 314,000 cells. We stratified tissues into six groups, referred to as cell-type abundance phenotypes (CTAPs), each characterized by selectively enriched cell states. These CTAPs demonstrate the diversity of synovial inflammation in rheumatoid arthritis, ranging from samples enriched for T and B cells to those largely lacking lymphocytes. Disease-relevant cell states, cytokines, risk genes, histology and serology metrics are associated with particular CTAPs. CTAPs are dynamic and can predict treatment response, highlighting the clinical utility of classifying rheumatoid arthritis synovial phenotypes. This comprehensive atlas and molecular, tissue-based stratification of rheumatoid arthritis synovial tissue reveal new insights into rheumatoid arthritis pathology and heterogeneity that could inform novel targeted treatments.

Structural Basis for the Modulation of Human KCNQ4 by Small-Molecule Drugs.

Among the five KCNQ channels, also known as the Kv7 voltage-gated potassium (Kv) channels, KCNQ2-KCNQ5 control neuronal excitability. Dysfunctions of KCNQ2-KCNQ5 are associated with neurological disorders such as epilepsy, deafness, and neuropathic pain. Here, we report the cryoelectron microscopy (cryo-EM) structures of human KCNQ4 and its complexes with the opener retigabine or the blocker linopirdine at overall resolutions of 2.5, 3.1, and 3.3 Å, respectively. In all structures, a phosphatidylinositol 4,5-bisphosphate (PIP2) molecule inserts its head group into a cavity within each voltage-sensing domain (VSD), revealing an unobserved binding mode for PIP2. Retigabine nestles in each fenestration, inducing local shifts. Instead of staying within the central pore, linopirdine resides in a cytosolic cavity underneath the inner gate. Electrophysiological analyses of various mutants corroborated the structural observations. Our studies reveal the molecular basis for the modulatory mechanism of neuronal KCNQ channels and provide a framework for structure-facilitated drug discovery targeting these important channels.

Intelligent infrared sensing enabled by tunable moiré quantum geometry.

Quantum geometric properties of Bloch wave functions in solids, that is, Berry curvature and the quantum metric, are known to significantly influence the ground- and excited-state behaviour of electrons1-5. The bulk photovoltaic effect (BPVE), a nonlinear phenomenon depending on the polarization of excitation light, is largely governed by the quantum geometric properties in optical transitions6-10. Infrared BPVE has yet to be observed in graphene or moiré systems, although exciting strongly correlated phenomena related to quantum geometry have been reported in this emergent platform11-14. Here we report the observation of tunable mid-infrared BPVE at 5 µm and 7.7 µm in twisted double bilayer graphene (TDBG), arising from the moiré-induced strong symmetry breaking and quantum geometric contribution. The photoresponse depends substantially on the polarization state of the excitation light and is highly tunable by external electric fields. This wide tunability in quantum geometric properties enables us to use a convolutional neural network15,16 to achieve full-Stokes polarimetry together with wavelength detection simultaneously, using only one single TDBG device with a subwavelength footprint of merely 3 × 3 µm2. Our work not only reveals the unique role of moiré engineered quantum geometry in tunable nonlinear light-matter interactions but also identifies a pathway for future intelligent sensing technologies in an extremely compact, on-chip manner.

Reproducibility in the fabrication and physics of moiré materials.

Overlaying two atomic layers with a slight lattice mismatch or at a small rotation angle creates a moiré superlattice, which has properties that are markedly modified from (and at times entirely absent in) the 'parent' materials. Such moiré materials have progressed the study and engineering of strongly correlated phenomena and topological systems in reduced dimensions. The fundamental understanding of the electronic phases, such as superconductivity, requires a precise control of the challenging fabrication process, involving the rotational alignment of two atomically thin layers with an angular precision below 0.1 degrees. Here we review the essential properties of moiré materials and discuss their fabrication and physics from a reproducibility perspective.

Quantum cascade of correlated phases in trigonally warped bilayer graphene.

Divergent density of states offers an opportunity to explore a wide variety of correlated electron physics. In the thinnest limit, this has been predicted and verified in the ultraflat bands of magic-angle twisted bilayer graphene1-5, the band touching points of few-layer rhombohedral graphite6-8 and the lightly doped rhombohedral trilayer graphene9-11. The simpler and seemingly better understood Bernal bilayer graphene is also susceptible to orbital magnetism at charge neutrality7 leading to layer antiferromagnetic states12 or quantum anomalous Hall states13. Here we report the observation of a cascade of correlated phases in the vicinity of electric-field-controlled Lifshitz transitions14,15 and van Hove singularities16 in Bernal bilayer graphene. We provide evidence for the observation of Stoner ferromagnets in the form of half and quarter metals10,11. Furthermore, we identify signatures consistent with a topologically non-trivial Wigner-Hall crystal17 at zero magnetic field and its transition to a trivial Wigner crystal, as well as two correlated metals whose behaviour deviates from that of standard Fermi liquids. Our results in this reproducible, tunable, simple system open up new horizons for studying strongly correlated electrons.

UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery.

piRNAs silence transposons during germline development. In Drosophila, transcripts from heterochromatic clusters are processed into primary piRNAs in the perinuclear nuage. The nuclear DEAD box protein UAP56 has been previously implicated in mRNA splicing and export, whereas the DEAD box protein Vasa has an established role in piRNA production and localizes to nuage with the piRNA binding PIWI proteins Ago3 and Aub. We show that UAP56 colocalizes with the cluster-associated HP1 variant Rhino, that nuage granules containing Vasa localize directly across the nuclear envelope from cluster foci containing UAP56 and Rhino, and that cluster transcripts immunoprecipitate with both Vasa and UAP56. Significantly, a charge-substitution mutation that alters a conserved surface residue in UAP56 disrupts colocalization with Rhino, germline piRNA production, transposon silencing, and perinuclear localization of Vasa. We therefore propose that UAP56 and Vasa function in a piRNA-processing compartment that spans the nuclear envelope.

Quantum anomalous Hall octet driven by orbital magnetism in bilayer graphene.

The quantum anomalous Hall (QAH) effect-a macroscopic manifestation of chiral band topology at zero magnetic field-has been experimentally realized only by the magnetic doping of topological insulators1-3 and the delicate design of moiré heterostructures4-8. However, the seemingly simple bilayer graphene without magnetic doping or moiré engineering has long been predicted to host competing ordered states with QAH effects9-11. Here we explore states in bilayer graphene with a conductance of 2 e2 h-1 (where e is the electronic charge and h is Planck's constant) that not only survive down to anomalously small magnetic fields and up to temperatures of five kelvin but also exhibit magnetic hysteresis. Together, the experimental signatures provide compelling evidence for orbital-magnetism-driven QAH behaviour that is tunable via electric and magnetic fields as well as carrier sign. The observed octet of QAH phases is distinct from previous observations owing to its peculiar ferrimagnetic and ferrielectric order that is characterized by quantized anomalous charge, spin, valley and spin-valley Hall behaviour9.

The genomic origins of the Bronze Age Tarim Basin mummies.

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000-2800 BC from the Dzungarian Basin and 13 individuals dating to around 2100-1700 BC from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early-Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo1,2 or to have originated among the Bactria-Margiana Archaeological Complex3 or Inner Asian Mountain Corridor cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.

Triangulation supports agricultural spread of the Transeurasian languages.

The origin and early dispersal of speakers of Transeurasian languages-that is, Japanese, Korean, Tungusic, Mongolic and Turkic-is among the most disputed issues of Eurasian population history1-3. A key problem is the relationship between linguistic dispersals, agricultural expansions and population movements4,5. Here we address this question by 'triangulating' genetics, archaeology and linguistics in a unified perspective. We report wide-ranging datasets from these disciplines, including a comprehensive Transeurasian agropastoral and basic vocabulary; an archaeological database of 255 Neolithic-Bronze Age sites from Northeast Asia; and a collection of ancient genomes from Korea, the Ryukyu islands and early cereal farmers in Japan, complementing previously published genomes from East Asia. Challenging the traditional 'pastoralist hypothesis'6-8, we show that the common ancestry and primary dispersals of Transeurasian languages can be traced back to the first farmers moving across Northeast Asia from the Early Neolithic onwards, but that this shared heritage has been masked by extensive cultural interaction since the Bronze Age. As well as marking considerable progress in the three individual disciplines, by combining their converging evidence we show that the early spread of Transeurasian speakers was driven by agriculture.

PINK1 Inhibits Local Protein Synthesis to Limit Transmission of Deleterious Mitochondrial DNA Mutations.

We have previously proposed that selective inheritance, the limited transmission of damaging mtDNA mutations from mother to offspring, is based on replication competition in Drosophila melanogaster. This model, which stems from our observation that wild-type mitochondria propagate much more vigorously in the fly ovary than mitochondria carrying fitness-impairing mutations, implies that germ cells recognize the fitness of individual mitochondria and selectively boost the propagation of healthy ones. Here, we demonstrate that the protein kinase PINK1 preferentially accumulates on mitochondria enriched for a deleterious mtDNA mutation. PINK1 phosphorylates Larp to inhibit protein synthesis on the mitochondrial outer membrane. Impaired local translation on defective mitochondria in turn limits the replication of their mtDNA and hence the transmission of deleterious mutations to the offspring. Our work confirms that selective inheritance occurs at the organelle level during Drosophila oogenesis and provides molecular entry points to test this model in other systems.