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The mechanisms by which tillandsioids adapt to elevated aerial habitats remain largely unexplored. Here, the authors report their evolution and link life history, diversification, comparative genomic, and functional changes to processes underlying the unique biology of air plants.

Comprehensive analyses of Cas9 proteins shed light on the evolution of the CRISPR–Cas9 system, and identify a pro-CRISPR accessory protein in bacteria that boosts CRISPR-mediated immunity by enhancing the DNA binding and cleavage activity of Cas9.

Current strategies to boost anti-tumor immune response include the use of immune checkpoint inhibitors and bispecific T cell-engaging antibodies. Here the authors describe a versatile antibody immobilization nanoplatform that can be used to deliver different combinations of immunotherapeutics, showing therapeutic superiority in pre-clinical models.

Spatial cell distribution within a tissue microenvironment is a rapidly advancing field. Here, authors assess three commercially available single-cell resolution spatial transcriptomics approaches (CosMx, MERFISH, and Xenium) to inform which technology outperforms for immune profiling of solid tumors using patient samples.

Harsh reaction pathways make transition metal nitride (TMN) grains susceptible to sintering. Here, the authors report a general route to synthesize multilayered TMN hollow spheres with high specific surface area from a single-source precursor.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer.

Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

Some cancer patients first present with metastases where the location of the primary is unidentified; these are difficult to treat. In this study, using machine learning, the authors develop a method to determine the tissue of origin of a cancer based on whole sequencing data.

The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

Both dietary and microbial factors influence the composition of the gut bile acid pool, which in turn modulates the frequencies and functionalities of RORγ-expressing colonic FOXP3⁺ regulatory T cells, contributing to protection from inflammatory colitis.

Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

The characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.

In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.

Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

Cross-linked polymers with covalent adaptable networks are reprocessed under external stimuli at high temperatures which might deteriorate their performance. Here, the authors introduce carbon dioxide responsive ionic clusters into covalent adaptable polymer networks to facilitate the exchange of dynamic bonds providing materials with a rapid recycling and good mechanical performance.

How aging induces aortic aneurysm and dissection (AAD) remains unclear. Here, the authors show that aging induces miR-1204 to inhibit MYLK, promoting vascular smooth muscle cells to acquire senescence-associated secretory phenotype, resulting in vascular inflammation, and the aggravation of AAD formation.

The distinction of liver lesions is critical for the accurate diagnosis and treatment of liver cancer. Here, the authors develop LiLNet, a deep learning-based system to identify focal liver lesions as well as benign and malignant liver tumours from CT images with high accuracy across multiple patient cohorts.

Alpine plants exhibit phenological adaptations to germinate and complete their reproductive cycles during the most favorable growing seasons. Here, the authors show that allelic variation in the GA20ox3 gene is crucial for the adaptability of fruit length and seed germination timing in high-altitude ecotypes of A. thaliana.

Ubiquitination and deubiquitination processes regulate the stability of PD-1, affecting T cell biology. Here the authors identify the ubiquitin-specific protease 5 (USP5) as a deubiquitinase for PD-1 and show that USP5 inhibition in combination with a MEK inhibitor or anti-CTLA-4 could promote anti-tumor immune responses in preclinical models.

Designing catalysts with uniform, site-specific selectivity and activity is a significant challenge. This study introduces design principles for topological-single-atom catalysts that utilize electronic shielding to protect surfaces and control reaction pathways, achieving high selectivity without compromising activity.

Aberrant protein O-GlcNAcylation has been linked with endometrial cancer (EC). Here the authors report that cellular O-GlcNAcylation level is positively correlated with EC histologic grade, and FBXO31 regulates O-GlcNAcylation homeostasis in EC by ubiquitinating the O-GlcNAc transferase OGT.

UDA-seq incorporates a post-indexing step to enhance the throughput of droplet-based single-cell multimodal sequencing, enabling efficient large-scale single-cell analysis.

Ostwald ripening is thermodynamically favoured in many liquid and gas systems, where small particles tend to dissolve into large ones. Against this effect, Huanget al. use patterned microstructures to guide the evolution of two-dimensional liquid foams as a platform for the assembly of nanoparticles.

All-solid-state batteries with silicon anodes have high capacities but low initial coulombic efficiencies (ICEs) because of first cycle irreversible capacity loss. Here, the authors report a prelithiation strategy to improve ICEs and reversibility.

The reasons for why hepatocellular carcinoma (HCC) is unresponsive to anti-PD-1 inhibition in some patients is not fully understood. Here the authors use human samples and mice tumour models to implicate serum amyloid A and STAT3 signalling involvement in the resistance to anti-PD1 immunotherapy in HCC.

Catalytic syngas conversion is an essential part of sustainable chemical production but is hindered by the trade-off between conversion activity and product selectivity. Here the authors address this challenge by developing a catalytic shunt strategy.

Enzymes installing an intact hydropersulfide (-SSH) group into natural products have so far not been identified. Here, the authors report the characterization of an S-adenosyl methionine-dependent hydropersulfide methyltransferase (GnmP) for guangnanmycin biosynthesis, and identification of three SH domains within several NRPS-PKS assembly lines as thiocysteine lyases.

A large number of cell disease models with pathogenic SNVs are needed. Here the authors report an automated high-throughput platform to perform the genome editing process from gRNA design to the analysis of the editing results; they characterise in situ base editing outcomes.

The molecular classification and tumour microenvironment in intrahepatic cholangiocarcinoma (iCCA) need further characterisation. Here, the authors perform single cell RNA-sequencing from 14 pairs of iCCA tumours and non-tumour liver tissues and propose S100P and SPP1 as markers for patient classification.

Multi-omics characterization of ZIKA virus–infected mouse brains reveals metabolic reprogramming events, including dysregulation of NAD⁺ metabolism, the correction of which is shown to alleviate ZIKA virus–induced microcephaly.

A 2.5-billion-year record of oxygen isotopes in sedimentary sulfate reveals the transitional oxygenation of the Earth’s surface and provides constraints on the dynamic, lengthy co-oxygenation of Earth’s atmosphere and oceans.

Slow growth rate of synthetic methylotrophs affects methanol valorization. Here, the strains self-adjust expression of topoisomerase I inhibitor to alleviate transcription-replication conflicts in synthetic methylotrophic E. coli and reduce its doubling time to that of natural methylotrophs.

The study explores the possibility of using electrical impedance tomography (EIT) as an early screening method to identify lung function impairment in participants with normal spirometry results. It identifies EIT-based regional τ values can be a promising tool for early screening of lung function impairment.

Quantum entanglement contains important information about quantum systems, but its calculation is challenging. Here the authors develop a quantum Monte Carlo technique for full tomography on microscopic subregions of a system, enabling extraction of multipartite quantum entanglement in large scale models.

The histone deacetylase HDAC6 is a sensor of valine levels, and the abundance of valine in cells regulates DNA damage and cell homeostasis functions.