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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.

Skutterudites are a family of materials whose properties make them appealing for studying thermoelectric, magnetic, heavy-fermion and superconducting effects, among many others. Through a combination of theoretical and experimental approaches, this study identifies 43 new skutterudite compounds.

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.

Several multi-cancer GWAS loci within the region encoding telomerase reverse transcriptase (TERT) have been identified. Here, the authors explore the locus within TERT intron 4, link it with a variable number tandem repeat (VNTR), and investigate its biological significance and role in cancer.

Passive immunisation for respiratory syncytial virus for infants is recommended by the World Health Organization but products currently available have limited duration of protection. Here, the authors investigate the age distribution of infant hospitalisation for respiratory syncytial virus to inform optimal timing of immunisation.

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.

The host factors that drive adaptive substitutions in the influenza virus remain poorly understood. Here, Zou et al. identify GGCX as a key determinant for the adaption of Eurasian avian-like H1N1 swine influenza virus to receptor binding.

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.

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.

This study reveals that the varying responses of plant biomass to phosphorus addition across plant functional groups align with the leaf economics spectrum, with plants characterized by more acquisitive traits exhibiting stronger responses to phosphorus addition.

Recent evidence has questioned the dogma of strict maternal transmission of mitochondrial DNA (mtDNA) in humans. Wei et al. saw no evidence of paternal transmission of mtDNA in 11,035 human trios, and show that nuclear-mitochondrial segments (NUMTs) can give the impression of paternal mtDNA transmission, but are actually inherited through the nuclear genome.

The study of lattice vibrations coupled to electronic excitations may provide an avenue for exploring exotic physical phenomena. Here, Xuet al. observe a Fano resonance in the Weyl semimetal TaAs, revealing evidence for a strong coupling between phonons and Weyl fermions.

Schmid and colleagues show that pancreatic cancer cell colonization of the liver is accompanied by low-grade tissue injury and efferocytosis, which promotes reprogramming of macrophages and upregulation of arginase.

Analyses of five treponemal genomes representing ancient relatives of Treponema pallidum suggest that this pathogen originated in the Americas.

Zinc deficiency is a global health issue, particularly in populations consuming wheat with low Zn concentration. This meta-analysis finds that foliar and combined soil+foliar Zn applications significantly increase wheat grain Zn levels, proposing optimized fertilization methods to meet nutritional targets.

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.

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.

Exploring the diversity of the wild progenitor of the wheat D subgenome allows for rapid trait discovery.

Measurements of solid stresses in breast tumours by means of intravital microscopy of tumour-embedded hydrogel beads shows that the transmission of solid stresses depends on length scale and on the tumour microenvironment.

Non-enterotoxigenic Bacteroides fragilis (NTBF) is abundant in colorectal cancer (CRC) patients and in a high-fat diet (HFD)-induced CRC model. Here the authors show that bile salt hydrolase-expressing NTBF is enriched in CRC patients with overweight and promotes tumor growth in an HFD-induced CRC mouse model.

How LGR4 impacts nutrition absorption and energy homeostasis is unknown. Here, the authors show that LGR4 loss in the intestinal epithelium decreases the proportion of enterocytes selective for long-chain fatty acid absorption, reducing lipid absorption and improving lipid and glucose metabolism.

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.

Analyses of genome and exome sequencing data identify rare coding and structural variants associated with atrial fibrillation and highlight genetic links between atrial fibrillation and cardiomyopathies.

Adaptive tactile interactions transfer across users, space, and time, via embroidered smart gloves is reported by the authors. The scalable fabrication and adaptive computation pipeline enable tactile occlusion alleviation, human skills transfer, and interactive teleoperation.

Harnessing single-nucleus RNA sequencing and spatial profiling, this work dissects unanticipated aspects of human liver regeneration to uncover a novel migratory hepatocyte subpopulation mediating wound closure following acute liver injury.

Despite their discovery in the 19th century, the islands of Calleja, clusters of densely packed granule cells in the ventral striatum, remain enigmatic. This study reveals that islands of Calleja neurons are critical for grooming control in mice.

With impressive electronic transport properties, wide bandgap perovskite oxides are promising transparent conductors. Prakashet al. report n-type BaSnO₃ films with room temperature conductivity exceeding 10⁴ S cm⁻¹and investigate factors limiting carrier mobility.

The sequencing and assembly of the highly polymorphic oyster genome through a combination of short reads and fosmid pooling, complemented with extensive transcriptome analysis of development and stress response and proteome analysis of the shell, provides new insight into oyster biology and adaptation to a highly changeable environment.

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.

A study uses Amethyst, a comprehensive single-cell methylation analysis tool, to resolve distinct non-CG methylation patterns in human astrocytes and oligodendrocytes. Findings challenge historically neuron-centric perspectives on noncanonical methylation.

The authors observe a coherent Kondo lattice in a monolayer of VSe₂ grown on a superconducting 2H-NbSe₂ substrate. Superconductivity is established in the Kondo lattice through proximity effect from the substrate.

Acetylcholine–α9 nAChR signaling regulates thymic negative selection.

Using data from a single time point, passenger-approximated clonal expansion rate (PACER) estimates the fitness of common driver mutations that lead to clonal haematopoiesis and identifies TCL1A activation as a mediator of clonal expansion.

Plants regulate chlorophyll levels to optimise photosynthesis. Here Wang et al. describe two paralogous thylakoid proteins, BCM1 and BCM2, which stimulate chlorophyll biosynthesis and attenuate chlorophyll degradation respectively through interaction with the Mg-chelatase-stimulating factor GUN4 and Mg-dechelatase isoform SGR1.

Together with an accompanying paper presenting a transcriptomic atlas of the mouse lemur, interrogation of the atlas provides a rich body of data to support the use of the organism as a model for primate biology and health.

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.

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.

The involvement of nuclear pore proteins in cellular mechanosensing and metastasis is unclear. Here the authors identify that nuclear pore protein NUP210 promotes metastasis through the interaction with mechanotransducer LINC complex protein and chromatin to regulate mechanosensitive genes.

A globally chiral atomic superfluid is induced by time-reversal symmetry breaking in an optical lattice and exhibits global angular momentum, which is expected to lead to topological excitations and the demonstration of a topological superfluid.

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.

Here, English et al. show that after expanding in lymphoid tissues, CD4⁺ and CD8⁺ T cells recognising hepatic antigens migrate into specialised vascular liver areas where CD4⁺ T cells locally license hepatic dendritic cells and further expand CD8⁺ T cell numbers.

Multidimensional coherent spectroscopy measurements in iron-based superconductors demonstrate how the coupling between a superconductor and strong light pulses can drive the transition into a non-equilibrium superconducting state with distinct collective modes.

Applying the concept of ecosystem energetics to a grassland biodiversity experiment, the authors show that the storage and flow of energy across the whole trophic network, both above- and belowground, becomes more efficient as plant diversity increases.

A deep learning and data-driven modelling study finds that microbial carbon use efficiency is a major determinant of soil organic carbon storage and its spatial variation across the globe.