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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.

A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

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.

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.

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.

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.

The REX element is associated with long-range enhancer–promoter interactions.

Study of human heart failure is limited by access to human tissue. Here, the authors apply multi-omic screening in human ischaemic and dilated myocardial tissue and matched controls to determine molecular changes common and unique to each aetiology and to reveal differences between male and female hearts.

Subduction of oceanic crust and sediments contributes to heterogeneities in the mantle, which are sampled by mantle plumes. Here, the authors find that extreme isotopic heterogeneity in Samoan clinopyroxenes can help constrain the composition of mantle sources containing sediment recycled into the Earth’s mantle.

Benjamin P Cohen, Carson C Chow, and Shashaank Vattikuti show that dynamical mutual inhibition models can explain variability during neuronal competition at two scales: neuronal spiking activity and perceptual rivalry variability. These models make predictions for how spiking and perceptual variability will change with stimulus conditions.

White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.

mRNA vaccines have been successfully developed, but a better understanding of in vivo distribution of the encoded antigen may aid further improvements. Here the authors use PET imaging and demonstrate transient expression of the vaccine antigen in the injection site and draining lymph nodes in mice and non-human primates.

CARD9 and CARD11 propagate signaling by nucleating Bcl10 polymerization in immune cells and are both held in an autoinhibited state prior to activation. Here, the authors combine structural, biochemical, and cell-based approaches to reveal the structural basis for CARD9/11 autoinhibition and show that the two proteins are activated through similar but distinct mechanisms.

A pan-cancer epigenetic and transcriptomic atlas identifies epigenetic drivers associated with cancer transitions.

Large genome-wide meta-analysis of clinically diagnosed late-onset Alzheimer’s disease (LOAD) from 94,437 individuals identifies new LOAD risk loci and implicates Aβ formation, tau protein binding, immune response and lipid metabolism.

Oncologic tumour resection is not fully accurate. Here the authors report a label-free virtual histological imaging method based on a non-contact, reflection-mode ultraviolet photoacoustic remote sensing and scattering microscope, combined with unsupervised deep learning using a cycle-consistent GAN.

Global aquatic foods are a key source of nutrition, but how their production is influenced by anthropogenic environmental changes is not well known. The vulnerability of global blue food systems to main environmental stressors and the related spatial impacts across blue food nations are now quantified.

Ochre, a strain of Escherichia coli engineered to have a single stop codon, enables reassignment of four codons for non-degenerate functions, such as incorporation of non-standard amino acids into proteins.

Tumour heterogeneity in clear cell renal cell carcinoma (ccRCC) remains to be investigated. Here, the integration of spatial omics, transcriptional and chromatin accessibility profiling at the single-nucleus level and bulk proteogenomics data reveal markers and pathways important for ccRCC.

The efficiency with which melts disaggregate and entrain macrocrysts from crystal mushes varies on inter-eruption timescales at ocean-island volcanoes, according to a study combining thin-section scale chemical mapping, in situ geochemistry, and modelling.

Polygenic risk scores for Alzheimer’s disease derived from individuals of European ancestry can show improved performance in multiancestry settings after incorporating genome-wide association summary statistics from diverse populations.

A microfluidic bronchial-airway-on-a-chip lined by human bronchial-airway epithelium and pulmonary endothelium can be used to rapidly identify antiviral therapeutics and prophylactics with repurposing potential.

The photoinduced hidden metallic state in 1T-TaS₂ has so far been stabilized only at cryogenic temperatures. Now it is shown that accessing an additional mixed-phase long-lived metastable state can stabilize the hidden phase at higher temperatures.

Determining the origins of life on Earth is confounded by the fact that the sources of nutrients necessary to create early life forms remain mysterious. Here the authors show that lightning strikes could have supplied a major source of essential phosphorus on early Earth.

Comparing the eyes of crane-fly fossils with those of extant species demonstrates that they contain eumelanic screening pigments and that the lenses are calcified during fossilization, with implications for interpreting optical systems in other extinct arthropods such as trilobites.

Patient-derived xenograft models (PDX) have been extensively used to study the molecular and clinical features of cancers. Here the authors present a cohort of 536 PDX models from 25 cancers, as well as their genomic and evolutionary profiles and their suitability for clinical trials.

An improved, fully re-annotated Aedes aegypti genome assembly (AaegL5) provides insights into the sex-determining M locus, chemosensory systems that help mosquitoes to hunt humans and loci involved in insecticide resistance and will help to generate intervention strategies to fight this deadly disease vector.

Serpentine subducted below the Lesser Antilles volcanic arc supplies water to the arc, controlling the location of seismicity, volcanic productivity and thickness of crust.

Two waves of glucose metabolism provide distinct ERK-mediated cellular signals during gastrulation, which regulate cell fate and specialized cellular functions that are necessary for development.

A transparent electronic skin, composed of an elastomer and an ionic liquid, can autonomously self-heal in both dry and wet conditions due to ion–dipole interactions.

Clay minerals played a vital role in the delivery of phosphorus (P) to shallow Neoproterozoic post-Snowball glaciation marine waters. The resulting increase in P bioavailability by at least 20-fold coincided with seawater oxygenation.

Sinclair et al. explore the contribution of chronic inflammation to cardiovascular symptoms associated with post-acute sequelae of SARS-CoV-2 infection (PASC-CVS). The authors identify trace levels of inflammatory cytokines in individuals with PASC-CVS that impair the function of cardiomyocytes derived from induced pluripotent stem cells.

Antibody mediated immunity to SARS-CoV-2 will affect future transmission and disease severity. This systematic review on antibody response to coronaviruses, including SARS-CoV-2, SARS-CoV, MERS-CoV and endemic coronaviruses provides insights into kinetics, correlates of protection, and association with disease severity.

A study proposes four ways in which foods sourced in aquatic environments can contribute to healthier, more environmentally sustainable and equitable food systems, and examines the relevance of these ambitions to nations.

Cryo-electron microscopy structures reveal the mechanisms underlying multiple-substrate specificity, coupling of epoxidation with carboxylation and allosteric motions during VKGC catalysis, offering potential strategies for targeting haemostatic and non-haemostatic disorders associated with defects in γ-carboxylation.

Aged hematopoietic stem cells (HSC) are characterised by reduced regenerative potential and a loss of quiescence. Here, the authors show nicotinamide riboside treatment shrinks the age-enlarged stem cell pool and shifts aged HSC functionally, metabolically and molecularly towards the young state.

The study of human microglia function in health and disease is limited by the availability of sound models. Here, the authors develop a method to generate functional microglia in human cortical organoids and investigate the role of human microglia during amyloid beta1-42- induced inflammation.

Here the authors screen a saturation mutagenesis library of the disordered N-terminal tail of the actin severing protein cofilin. Their results reveal how a key phosphorylation site can balance competing sequence constraints on function and regulation.

Meta-analysis of genome-wide association studies on Alzheimer’s disease and related dementias identifies new loci and enables generation of a new genetic risk score associated with the risk of future Alzheimer’s disease and dementia.

While recognized as the first effective immunotherapy for human cancer, IL-2 based immunotherapy still encounters several limitations in the clinic. Here, the authors design a cytokine receptor-masked IL-2 mutein prodrug that is selectively activated by matrix metalloproteinases in the tumor microenvironment, promoting anti-tumor immune response while minimizing systemic toxicity.

Imbalance and loss of cell types is a hallmark in many diseases. Still, quantifying compositional changes in scRNAseq data remains challenging. Here the authors present scCODA, a Bayesian model to assess cell type compositions in scRNA-seq data.

Materials exhibiting room temperature phosphorescence (RTP) with short afterglow are desirable for bio-medical applications. Here the authors synthesise a library of compounds with tunable RTP properties, embedding carbon nanodots in non-toxic alkaline-earth carbonate, sulphate and oxalate hosts.

The EMDataResource Ligand Model Challenge aimed at assessing the reliability and reproducibility of modeling ligands bound to protein and protein–nucleic acid complexes in cryo-EM maps determined at near-atomic resolution. This analysis presents the results and recommends best practices for assessing cryo-EM structures of liganded macromolecules.