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The meningeal compartment communicates with the brain to modulate homeostatic functions. Here, the authors demonstrate that natural killer (NK) cells and innate lymphoid cells (ILC) 1 shape synaptic neuronal transmission and affect mouse behavior.

A method to coherently manipulate excitons and perform all-optical logic operations using the valley degree of freedom in monolayer WS₂ is discussed.

RNA modifications influence gene regulation, but global mapping was limited. Here, the authors introduce ORCA, a deep learning framework using nanopore RNA sequencing to detect multiple modification types, revealing isoform-specific patterns and regulatory interactions.

A complementary analysis of DESI DR2 distance measurements along with supernova and CMB data shows consistent, moderate evidence that dark energy changes over time rather than behaving as a simple cosmological constant.

The CMS Collaboration reports the measurement of the spin, parity, and charge conjugation properties of all-charm tetraquarks, exotic fleeting particles formed in proton–proton collisions at the Large Hadron Collider.

Asymmetric cell division often requires alignment of the mitotic spindle to cortical polarity cues. Here the authors show that cortical Wnt signaling induces formation of a complex between NuMA/dynein microtubule motors, LRP6 and β-catenin that promotes asymmetric division.

The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitating the discovery of potential effects of genetic variants, including variants associated with disease, on genome structure and function.

The authors optimize an in vitro human epiblast model, which they utilize to show that early TGFβ family inhibition prevents epithelial identity, whereas it is dispensable after epithelium formation. These phenomena are conserved in mice.

The quark structure of the f₀(980) hadron is still unknown after 50 years of its discovery. Here, the CMS Collaboration reports a measurement of the elliptic flow of the f₀(980) state in proton-lead collisions at a nucleon-nucleon centre-of-mass energy of 8.16 TeV, providing strong evidence that the state is an ordinary meson.

A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

The authors found, after analyzing 10,960 individuals from 9 multiancestry biobanks across 6 countries, that genetic factors previously associated with BMI have limited impact on GLP-1 receptor agonist-induced weight loss.

Experiments under upper-tropospheric conditions map the chemical formation of isoprene oxygenated organic molecules (important molecules for new particle formation) and reveal that relative radical ratios control their composition

A genome-wide study by the Long COVID Host Genetics Initiative identifies an association between the FOXP4 locus and long COVID, implicating altered lung function in its pathophysiology.

Strontium isotope analysis can be applied to animal and plant tissues to help determine their provenance. Here, the authors generate a strontium isoscape of sub-Saharan Africa using data from 2266 environmental samples and demonstrate its efficacy by tracing the African roots of individuals from historic slavery contexts.

In this Review, Galli and colleagues discuss the mechanisms and associated biomarkers of traditional and emerging factors responsible for the residual risk of recurrent adverse cardiovascular events in patients with coronary artery disease, with a focus on new pathophysiological insights and the therapeutic implications.

Prostate cancer (PCa) evaluation remains challenging due to its heterogenous and multifocal nature. Here, the authors reconstruct the nuclear chromatin compartmentalization of PCa patients-derived biopsies distinguishing two epigenetic subtypes and deriving an 18-gene signature with prognostic value on TCGA samples that is further validated with multiple independent PCa cohorts.

Light-sensitive azobenzene compounds can be engineered to stably partition into the plasma membrane, thus causing its thinning in the dark and relaxation upon light stimulation. In neurons, the resulting light-dependent change in membrane capacitance induces a transient hyperpolarization followed by rebound depolarization and action potential firing.

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.

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.

Tumor-associated macrophages are pivotal in control over solid tumors. Here the authors show that these macrophages express chemosensors that detect lipid variants in the tumor microenvironment that can regulate the function of these cells.

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.

Whole-genome sequencing and phenotype data sharing are introduced in a national health system to streamline diagnosis and to discover coding and non-coding variants that cause rare diseases.

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

Dengue and chikungunya are an increasing public health concern in Europe, and Italy is particularly affected. Here, the authors analyse travel-related cases and outbreaks in Italy from 2006 to 2023 and assess current transmission risks.

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.

Understanding species’ spatiotemporal dynamics is key to predicting their responses to climate change. Here, the authors combine landscape genomics, demographic reconstructions, and species distribution models to assess lineage-specific responses to past and future climate in a migratory raptor.

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.

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.

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.

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.

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.

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.

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 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.

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.

Observations of SN 2021yfj reveal that its progenitor is a massive star stripped down to its O/Si/S core, which remarkably continued to expel vast quantities of silicon-, sulfur-, and argon-rich material before the explosion, informing us that current theories for how stars evolve are too narrow.

The clinical implications of molecular heterogeneity in HER2-positive breast cancer remain to be explored. Here, the authors investigate the transcriptomic landscape of HER2-positive breast cancer patients receiving adjuvant trastuzumab in the ALTTO clinical trial and identify five distinct molecular subtypes.

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.

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.

The viability of Antarctic ice shelves under low rates and high rates of global warming is modelled to estimate when it will become unfeasible for the ice shelves to maintain their present-day shape.

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.

Genomic surveillance has been important for tracking the evolution and spread of SARS-CoV-2. Here, the authors analyse ~300,000 SARS-CoV-2 genomes from two years of sequencing in the Latin America and Caribbean regions and describe the emergence and spread of different lineages over time.

Survey data collected across ten low-income and middle-income countries (LMICs) in Asia, Africa and South America compared with surveys from Russia and the United States reveal heterogeneity in vaccine confidence in LMICs, with healthcare providers being trusted sources of information, as well as greater levels of vaccine acceptance in these countries than in Russia and the United States.