Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers.

Defects in translation lead to changes in the expression of proteins that can serve as drivers of cancer formation. Here, we show that cytosolic NAD+ synthesis plays an essential role in ovarian cancer by regulating translation and maintaining protein homeostasis. Expression of NMNAT-2, a cytosolic NAD+ synthase, is highly upregulated in ovarian cancers. NMNAT-2 supports the catalytic activity of the mono(ADP-ribosyl) transferase (MART) PARP-16, which mono(ADP-ribosyl)ates (MARylates) ribosomal proteins. Depletion of NMNAT-2 or PARP-16 leads to inhibition of MARylation, increased polysome association and enhanced translation of specific mRNAs, aggregation of their translated protein products, and reduced growth of ovarian cancer cells. Furthermore, MARylation of the ribosomal proteins, such as RPL24 and RPS6, inhibits polysome assembly by stabilizing eIF6 binding to ribosomes. Collectively, our results demonstrate that ribosome MARylation promotes protein homeostasis in cancers by fine-tuning the levels of protein synthesis and preventing toxic protein aggregation.

Multi-organ proteomic landscape of COVID-19 autopsies.

The molecular pathology of multi-organ injuries in COVID-19 patients remains unclear, preventing effective therapeutics development. Here, we report a proteomic analysis of 144 autopsy samples from seven organs in 19 COVID-19 patients. We quantified 11,394 proteins in these samples, in which 5,336 were perturbed in the COVID-19 patients compared to controls. Our data showed that cathepsin L1, rather than ACE2, was significantly upregulated in the lung from the COVID-19 patients. Systemic hyperinflammation and dysregulation of glucose and fatty acid metabolism were detected in multiple organs. We also observed dysregulation of key factors involved in hypoxia, angiogenesis, blood coagulation, and fibrosis in multiple organs from the COVID-19 patients. Evidence for testicular injuries includes reduced Leydig cells, suppressed cholesterol biosynthesis, and sperm mobility. In summary, this study depicts a multi-organ proteomic landscape of COVID-19 autopsies that furthers our understanding of the biological basis of COVID-19 pathology.

Proteomic and Metabolomic Characterization of COVID-19 Patient Sera.

Early detection and effective treatment of severe COVID-19 patients remain major challenges. Here, we performed proteomic and metabolomic profiling of sera from 46 COVID-19 and 53 control individuals. We then trained a machine learning model using proteomic and metabolomic measurements from a training cohort of 18 non-severe and 13 severe patients. The model was validated using 10 independent patients, 7 of which were correctly classified. Targeted proteomics and metabolomics assays were employed to further validate this molecular classifier in a second test cohort of 19 COVID-19 patients, leading to 16 correct assignments. We identified molecular changes in the sera of COVID-19 patients compared to other groups implicating dysregulation of macrophage, platelet degranulation, complement system pathways, and massive metabolic suppression. This study revealed characteristic protein and metabolite changes in the sera of severe COVID-19 patients, which might be used in selection of potential blood biomarkers for severity evaluation.

Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline.

piRNAs (Piwi-interacting small RNAs) engage Piwi Argonautes to silence transposons and promote fertility in animal germlines. Genetic and computational studies have suggested that C. elegans piRNAs tolerate mismatched pairing and in principle could target every transcript. Here we employ in vivo cross-linking to identify transcriptome-wide interactions between piRNAs and target RNAs. We show that piRNAs engage all germline mRNAs and that piRNA binding follows microRNA-like pairing rules. Targeting correlates better with binding energy than with piRNA abundance, suggesting that piRNA concentration does not limit targeting. In mRNAs silenced by piRNAs, secondary small RNAs accumulate at the center and ends of piRNA binding sites. In germline-expressed mRNAs, however, targeting by the CSR-1 Argonaute correlates with reduced piRNA binding density and suppression of piRNA-associated secondary small RNAs. Our findings reveal physiologically important and nuanced regulation of individual piRNA targets and provide evidence for a comprehensive post-transcriptional regulatory step in germline gene expression.

LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade.

Chromatin regulators play a broad role in regulating gene expression and, when gone awry, can lead to cancer. Here, we demonstrate that ablation of the histone demethylase LSD1 in cancer cells increases repetitive element expression, including endogenous retroviral elements (ERVs), and decreases expression of RNA-induced silencing complex (RISC) components. Significantly, this leads to double-stranded RNA (dsRNA) stress and activation of type 1 interferon, which stimulates anti-tumor T cell immunity and restrains tumor growth. Furthermore, LSD1 depletion enhances tumor immunogenicity and T cell infiltration in poorly immunogenic tumors and elicits significant responses of checkpoint blockade-refractory mouse melanoma to anti-PD-1 therapy. Consistently, TCGA data analysis shows an inverse correlation between LSD1 expression and CD8+ T cell infiltration in various human cancers. Our study identifies LSD1 as a potent inhibitor of anti-tumor immunity and responsiveness to immunotherapy and suggests LSD1 inhibition combined with PD-(L)1 blockade as a novel cancer treatment strategy.

Primary germinal center-resident T follicular helper cells are a physiologically distinct subset of CXCR5hiPD-1hi T follicular helper cells.

T follicular helper (Tfh) cells are defined by a Bcl6+CXCR5hiPD-1hi phenotype, but only a minor fraction of these reside in germinal centers (GCs). Here, we examined whether GC-resident and -nonresident Tfh cells share a common physiology and function. Fluorescently labeled, GC-resident Tfh cells in different mouse models were distinguished by low expression of CD90. CD90neg/lo GCTfh cells required antigen-specific, MHCII+ B cells to develop and stopped proliferating soon after differentiation. In contrast, nonresident, CD90hi Tfh (GCTfh-like) cells developed normally in the absence of MHCII+ B cells and proliferated continuously during primary responses. The TCR repertoires of both Tfh subsets overlapped initially but later diverged in association with dendritic cell-dependent proliferation of CD90hi GCTfh-like cells, suggestive of TCR-dependency seen also in TCR-transgenic adoptive transfer experiments. Furthermore, the transcriptomes of CD90neg/lo and CD90hi GCTfh-like cells were enriched in different functional pathways. Thus, GC-resident and nonresident Tfh cells have distinct developmental requirements and activities, implying distinct functions.

Multiple enzymatic activities of a Sir2-HerA system cooperate for anti-phage defense.

In response to the persistent exposure to phage infection, bacteria have evolved diverse antiviral defense mechanisms. In this study, we report a bacterial two-component defense system consisting of a Sir2 NADase and a HerA helicase. Cryo-electron microscopy reveals that Sir2 and HerA assemble into a ∼1 MDa supramolecular octadecamer. Unexpectedly, this complex exhibits various enzymatic activities, including ATPase, NADase, helicase, and nuclease, which work together in a sophisticated manner to fulfill the antiphage function. Therefore, we name this defense system "Nezha" after a divine warrior in Chinese mythology who employs multiple weapons to defeat enemies. Our findings demonstrate that Nezha could sense phage infections, self-activate to arrest cell growth, eliminate phage genomes, and subsequently deactivate to allow for cell recovery. Collectively, Nezha represents a paradigm of sophisticated and multifaceted strategies bacteria use to defend against viral infections.

Glucose-induced CRL4COP1-p53 axis amplifies glycometabolism to drive tumorigenesis.

The diabetes-cancer association remains underexplained. Here, we describe a glucose-signaling axis that reinforces glucose uptake and glycolysis to consolidate the Warburg effect and overcome tumor suppression. Specifically, glucose-dependent CK2 O-GlcNAcylation impedes its phosphorylation of CSN2, a modification required for the deneddylase CSN to sequester Cullin RING ligase 4 (CRL4). Glucose, therefore, elicits CSN-CRL4 dissociation to assemble the CRL4COP1 E3 ligase, which targets p53 to derepress glycolytic enzymes. A genetic or pharmacologic disruption of the O-GlcNAc-CK2-CSN2-CRL4COP1 axis abrogates glucose-induced p53 degradation and cancer cell proliferation. Diet-induced overnutrition upregulates the CRL4COP1-p53 axis to promote PyMT-induced mammary tumorigenesis in wild type but not in mammary-gland-specific p53 knockout mice. These effects of overnutrition are reversed by P28, an investigational peptide inhibitor of COP1-p53 interaction. Thus, glycometabolism self-amplifies via a glucose-induced post-translational modification cascade culminating in CRL4COP1-mediated p53 degradation. Such mutation-independent p53 checkpoint bypass may represent the carcinogenic origin and targetable vulnerability of hyperglycemia-driven cancer.

Two-dimensional perovskitoids enhance stability in perovskite solar cells.

Two-dimensional (2D) and three-dimensional (3D) perovskite heterostructures have played a key role in advancing the performance of perovskite solar cells1,2. However, the migration of cations between 2D and 3D layers results in the disruption of octahedral networks, leading to degradation in performance over time3,4. We hypothesized that perovskitoids, with robust organic-inorganic networks enabled by edge- and face-sharing, could impede ion migration. We explored a set of perovskitoids of varying dimensionality and found that cation migration within perovskitoid-perovskite heterostructures was suppressed compared with the 2D-3D perovskite case. Increasing the dimensionality of perovskitoids improves charge transport when they are interfaced with 3D perovskite surfaces-this is the result of enhanced octahedral connectivity and out-of-plane orientation. The 2D perovskitoid (A6BfP)8Pb7I22 (A6BfP: N-aminohexyl-benz[f]-phthalimide) provides efficient passivation of perovskite surfaces and enables uniform large-area perovskite films. Devices based on perovskitoid-perovskite heterostructures achieve a certified quasi-steady-state power conversion efficiency of 24.6% for centimetre-area perovskite solar cells. We removed the fragile hole transport layers and showed stable operation of the underlying perovskitoid-perovskite heterostructure at 85 °C for 1,250 h for encapsulated large-area devices in ambient air.

Coherent growth of high-Miller-index facets enhances perovskite solar cells.

Obtaining micron-thick perovskite films of high quality is key to realizing efficient and stable positive (p)-intrinsic (i)-negative (n) perovskite solar cells1,2, but it remains a critical challenge. Here, we report an effective method for producing high-quality, micron-thick formamidinium-based perovskite films by forming coherent grain boundaries, where high-Miller-index-oriented grains grow on the low-Miller-index-oriented grains in a stabilized atmosphere. The resulting micron-thick perovskite films, with enhanced grain boundaries and grains, showed stable material properties and outstanding optoelectronic performances. The small-area solar cells achieved efficiencies of 26.1%. The 1-square-centimeter devices and 5 cm × 5 cm minimodules delivered efficiencies of 24.3% and 21.4%, respectively. The devices processed in a stabilized atmosphere presented a high reproducibility across all four seasons. The encapsulated devices exhibited superior long-term stability under both light and thermal stressors in ambient air.

Perovskite/silicon tandem solar cells with bilayer interface passivation.

Two-terminal monolithic perovskite/silicon tandem solar cells demonstrate huge advantages in power conversion efficiency compared with their respective single-junction counterparts1,2. However, suppressing interfacial recombination at the wide-bandgap perovskite/electron transport layer interface, without compromising its superior charge transport performance, remains a substantial challenge for perovskite/silicon tandem cells3,4. By exploiting the nanoscale discretely distributed lithium fluoride ultrathin layer followed by an additional deposition of diammonium diiodide molecule, we have devised a bilayer-intertwined passivation strategy that combines efficient electron extraction with further suppression of non-radiative recombination. We constructed perovskite/silicon tandem devices on a double-textured Czochralski-based silicon heterojunction cell, which featured a mildly textured front surface and a heavily textured rear surface, leading to simultaneously enhanced photocurrent and uncompromised rear passivation. The resulting perovskite/silicon tandem achieved an independently certified stabilized power conversion efficiency of 33.89%, accompanied by an impressive fill factor of 83.0% and an open-circuit voltage of nearly 1.97 V. To the best of our knowledge, this represents the first reported certified efficiency of a two-junction tandem solar cell exceeding the single-junction Shockley-Queisser limit of 33.7%.

Silicon heterojunction back contact solar cells by laser patterning.

Back contact silicon solar cells, valued for their aesthetic appeal by removing grid lines on the sunny side, find applications in buildings, vehicles and aircrafts, enabling self-power generation without compromising appearance1-3. Patterning techniques arrange contacts on the shaded side of the silicon wafer, offering benefits for light incidence as well. However, the patterning process complicates production and causes power loss. Here we employ lasers to streamline back contact solar cell fabrication and enhance power conversion efficiency. Our approach produces the first silicon solar cell to exceed 27% efficiency. Hydrogenated amorphous silicon layers are deposited on the wafer for surface passivation and collection of light-generated carriers. A dense passivating contact, diverging from conventional technology practice, is developed. Pulsed picosecond lasers at different wavelengths are used to create back contact patterns. The developed approach is a streamlined process for producing high-performance back contact silicon solar cells, with a total effective processing time of about one-third that of emerging mainstream technology. To meet terawatt demand, we develop rare indium-less cells at 26.5% efficiency and precious silver-free cells at 26.2% efficiency. The integration of solar solutions in buildings and transportation is poised to expand with these technological advancements.

Gene therapy for CNS disorders: modalities, delivery and translational challenges.

Gene therapy is emerging as a powerful tool to modulate abnormal gene expression, a hallmark of most CNS disorders. The transformative potentials of recently approved gene therapies for the treatment of spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and active cerebral adrenoleukodystrophy are encouraging further development of this approach. However, most attempts to translate gene therapy to the clinic have failed to make it to market. There is an urgent need not only to tailor the genes that are targeted to the pathology of interest but to also address delivery challenges and thereby maximize the utility of genetic tools. In this Review, we provide an overview of gene therapy modalities for CNS diseases, emphasizing the interconnectedness of different delivery strategies and routes of administration. Important gaps in understanding that could accelerate the clinical translatability of CNS genetic interventions are addressed, and we present lessons learned from failed clinical trials that may guide the future development of gene therapies for the treatment and management of CNS disorders.

Homomeric chains of intermolecular bonds scaffold octahedral germanium perovskites.

Perovskites with low ionic radii metal centres (for example, Ge perovskites) experience both geometrical constraints and a gain in electronic energy through distortion; for these reasons, synthetic attempts do not lead to octahedral [GeI6] perovskites, but rather, these crystallize into polar non-perovskite structures1-6. Here, inspired by the principles of supramolecular synthons7,8, we report the assembly of an organic scaffold within perovskite structures with the goal of influencing the geometric arrangement and electronic configuration of the crystal, resulting in the suppression of the lone pair expression of Ge and templating the symmetric octahedra. We find that, to produce extended homomeric non-covalent bonding, the organic motif needs to possess self-complementary properties implemented using distinct donor and acceptor sites. Compared with the non-perovskite structure, the resulting [GeI6]4- octahedra exhibit a direct bandgap with significant redshift (more than 0.5 eV, measured experimentally), 10 times lower octahedral distortion (inferred from measured single-crystal X-ray diffraction data) and 10 times higher electron and hole mobility (estimated by density functional theory). We show that the principle of this design is not limited to two-dimensional Ge perovskites; we implement it in the case of copper perovskite (also a low-radius metal centre), and we extend it to quasi-two-dimensional systems. We report photodiodes with Ge perovskites that outperform their non-octahedral and lead analogues. The construction of secondary sublattices that interlock with an inorganic framework within a crystal offers a new synthetic tool for templating hybrid lattices with controlled distortion and orbital arrangement, overcoming limitations in conventional perovskites.

A pangenome reference of 36 Chinese populations.

Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to a pangenome form, but populations of Asian ancestry are underrepresented. Here we present data from the first phase of the Chinese Pangenome Consortium, including a collection of 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority Chinese ethnic groups. With an average 30.65× high-fidelity long-read sequence coverage, an average contiguity N50 of more than 35.63 megabases and an average total size of 3.01 gigabases, the CPC core assemblies add 189 million base pairs of euchromatic polymorphic sequences and 1,367 protein-coding gene duplications to GRCh38. We identified 15.9 million small variants and 78,072 structural variants, of which 5.9 million small variants and 34,223 structural variants were not reported in a recently released pangenome reference1. The Chinese Pangenome Consortium data demonstrate a remarkable increase in the discovery of novel and missing sequences when individuals are included from underrepresented minority ethnic groups. The missing reference sequences were enriched with archaic-derived alleles and genes that confer essential functions related to keratinization, response to ultraviolet radiation, DNA repair, immunological responses and lifespan, implying great potential for shedding new light on human evolution and recovering missing heritability in complex disease mapping.

Regulating surface potential maximizes voltage in all-perovskite tandems.

The open-circuit voltage (VOC) deficit in perovskite solar cells is greater in wide-bandgap (over 1.7 eV) cells than in perovskites of roughly 1.5 eV (refs. 1,2). Quasi-Fermi-level-splitting measurements show VOC-limiting recombination at the electron-transport-layer contact3-5. This, we find, stems from inhomogeneous surface potential and poor perovskite-electron transport layer energetic alignment. Common monoammonium surface treatments fail to address this; as an alternative, we introduce diammonium molecules to modify perovskite surface states and achieve a more uniform spatial distribution of surface potential. Using 1,3-propane diammonium, quasi-Fermi-level splitting increases by 90 meV, enabling 1.79 eV perovskite solar cells with a certified 1.33 V VOC and over 19% power conversion efficiency (PCE). Incorporating this layer into a monolithic all-perovskite tandem, we report a record VOC of 2.19 V (89% of the detailed balance VOC limit) and over 27% PCE (26.3% certified quasi-steady state). These tandems retained more than 86% of their initial PCE after 500 h of operation.

Suppressed phase segregation for triple-junction perovskite solar cells.

The tunable bandgaps and facile fabrication of perovskites make them attractive for multi-junction photovoltaics1,2. However, light-induced phase segregation limits their efficiency and stability3-5: this occurs in wide-bandgap (>1.65 electron volts) iodide/bromide mixed perovskite absorbers, and becomes even more acute in the top cells of triple-junction solar photovoltaics that require a fully 2.0-electron-volt bandgap absorber2,6. Here we report that lattice distortion in iodide/bromide mixed perovskites is correlated with the suppression of phase segregation, generating an increased ion-migration energy barrier arising from the decreased average interatomic distance between the A-site cation and iodide. Using an approximately 2.0-electron-volt rubidium/caesium mixed-cation inorganic perovskite with large lattice distortion in the top subcell, we fabricated all-perovskite triple-junction solar cells and achieved an efficiency of 24.3 per cent (23.3 per cent certified quasi-steady-state efficiency) with an open-circuit voltage of 3.21 volts. This is, to our knowledge, the first reported certified efficiency for perovskite-based triple-junction solar cells. The triple-junction devices retain 80 per cent of their initial efficiency following 420 hours of operation at the maximum power point.

Age-Related Loss of Innate Immune Antimicrobial Function of Dermal Fat Is Mediated by Transforming Growth Factor Beta.

Dermal fibroblasts (dFBs) resist infection by locally differentiating into adipocytes and producing cathelicidin antimicrobial peptide in response to Staphylococcus aureus (S. aureus). Here, we show that neonatal skin was enriched with adipogenic dFBs and immature dermal fat that highly expressed cathelicidin. The pool of adipogenic and antimicrobial dFBs declined after birth, leading to an age-dependent loss of dermal fat and a decrease in adipogenesis and cathelidicin production in response to infection. Transforming growth factor beta (TGF-ß), which acted on uncommitted embryonic and adult dFBs and inhibited their adipogenic and antimicrobial function, was identified as a key upstream regulator of this process. Furthermore, inhibition of the TGF-ß receptor restored the adipogenic and antimicrobial function of dFBs in culture and increased resistance of adult mice to S. aureus infection. These results provide insight into changes that occur in the skin innate immune system between the perinatal and adult periods of life.

Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences.

Alternative splicing plays a crucial role in protein diversity and gene expression regulation in higher eukaryotes, and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets. However, the current methods for the quantitative prediction of splice site usage still have limited accuracy. Here, we present DeltaSplice, a deep neural network model optimized to learn the impact of mutations on quantitative changes in alternative splicing from the comparative analysis of homologous genes. The model architecture enables DeltaSplice to perform "reference-informed prediction" by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods on various prediction tasks, including evolutionary sequence divergence on lineage-specific splicing and splicing-altering mutations in human populations and neurodevelopmental disorders, and demonstrated that DeltaSplice outperformed consistently. DeltaSplice predicted ∼15% of splicing quantitative trait loci (sQTLs) in the human brain as causal splicing-altering variants. It also predicted splicing-altering de novo mutations outside the splice sites in a subset of patients affected by autism and other neurodevelopmental disorders (NDDs), including 19 genes with recurrent splicing-altering mutations. Integration of splicing-altering mutations with other types of de novo mutation burdens allowed the prediction of eight novel NDD-risk genes. Our work expanded the capacity of in silico splicing models with potential applications in genetic diagnosis and the development of splicing-based precision medicine.