Search

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.

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.

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.

Both environmental factors and genetic factors influence human immunity. Albert and colleagues leverage data from the Milieu Intérieur Consortium to comprehensively describe the effects of lifestyle, environment and genetics on human innate and adaptive immunity.

A pangenome of oat, assembled from 33 wild and domesticated oat lines, sheds light on the evolution and genetic diversity of this cereal crop and will aid genomics-assisted breeding to improve productivity and sustainability.

Here the authors provide an explanation for 95% of examined predicted loss of function variants found in disease-associated haploinsufficient genes in the Genome Aggregation Database (gnomAD), underscoring the power of the presented analysis to minimize false assignments of disease risk.

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.

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.

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.

Wastewater-based surveillance tends to focus on specific pathogens. Here, the authors mapped the wastewater virome from 62 cities worldwide to identify over 2,500 viruses, revealing city-specific virome fingerprints and showing that wastewater metagenomics enables early detection of emerging viruses.

A large genome-wide association study of more than 5 million individuals reveals that 12,111 single-nucleotide polymorphisms account for nearly all the heritability of height attributable to common genetic variants.

Kitaev interactions on a honeycomb lattice can potentially lead to a quantum spin liquid state. Unfortunately, materials hosting Kitaev interactions also host Heisenberg interactions favouring long range order. Here, Sakrikar, Shen, Poldi and coauthors find that the relative strength of the Heisenberg and Kitaev interactions can be tuned by pressure in Ag₃LiRh₂O₆.

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.

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 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.

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.

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

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.

A general stereospecific glycosylation is developed that is applicable across a range of monosaccharides. A directing-group-on-leaving-group strategy allows mild donor activation and enables the complete inversion of anomeric configuration with excellent yields. This method can be applied in multistep oligosaccharide syntheses and automated glycan assembly.

Superconducting qubits are sensitive to multiple noise sources that compromise their coherence. Here the authors report a piezoelectric effect in aluminum-silicon junctions, revealing a previously unexplored mechanism that may limit superconducting quantum processor performance.

Cells rely on diversification and redundancy of protein chaperones to maintain proteostasis. Here, the authors show that two C. elegans orthologs of a chaperone have distinct roles in stress resistance, aging, and autophagy through an ER-phagy receptor-dependent pathway.

VCPIP1 is a deubiquitylase that binds the essential protein VCP/p97. Here, the authors present cryo-EM structures of VCPIP1 bound to VCP and the VCP-VCPIP1-p47 ternary complex along with biochemical and cellular data highlighting the functional importance of VCPIP1 domains in Golgi maintenance.

XRISM observations show the presence of odd-numbered elements chlorine and potassium in Cas A. These findings suggest that stellar activity plays an important role in cosmic chemical evolution, enriching space with elements vital for planets and life.

A neuron-specific isoform of PGC-1α is regulated independently from other isoforms and is repressed with age. Here, the authors show PGC-1α is central in a growth and metabolism networks directly relevant to brain aging.

The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

Insights into active sites on cathode surfaces are important in developing lithium–oxygen batteries. Here, Lu et al.present a cathode architecture deposited with precisely controlled small metal clusters, and report a cluster size-dependence of the battery discharge product morphology.

Non-equilibrium intercalation reactions may determine the performance of lithium-ion battery materials undergoing lithiation, but it is difficult to probe in real time. Here, the authors use in situelectron microscopy to identify kinetically-driven phase evolution in magnetite single nanoparticles.

Federated learning (FL) algorithms have emerged as a promising solution to train models for healthcare imaging across institutions while preserving privacy. Here, the authors describe the Federated Tumor Segmentation (FeTS) challenge for the decentralised benchmarking of FL algorithms and evaluation of Healthcare AI algorithm generalizability in real-world cancer imaging datasets.

Thermal transistors can enable game changing applications in energy harvesting and heat routing. Here, the authors demonstrate reversible thermal modulation of nearly 10 times by ion intercalation in MoS₂ nanofilms. A new thermal microscopy technique allows operando imaging of Li ion segregation.

The renal epithelium is sensitive to changes in blood K⁺. Here, Zhang et al. identify low K⁺ as a potent activator of proximal tubule mTOR/AKT signaling, which occurs through the K⁺ channel, Kir4.2 to modulate epithelial cell growth and Na⁺ transport.

Lo and colleagues report that double-positive thymocytes from neonates express less Zap70 and show reduced Ca^2⁺/NFAT signaling compared to double-positive thymocytes from older thymi. This diminished Ca^2⁺ signaling alters negative selection for self-reactive TCRs, resulting in a cell-intrinsic temporal window for regulatory T versus conventional T cell development in the thymus.

Whether electron–phonon coupling is a generic feature in FeSe/SrTiO₃ to enhance superconductivity remains unclear. Here, Zhang et al. report replica bands in FeSe/SrTiO₃(110), suggesting a common mechanism in FeSe on SrTiO₃with different surface terminations.

Extending the interval between doses of mRNA Covid-19 vaccines has been linked with a reduced risk of myocarditis in children and adolescents, but impacts on vaccine effectiveness are not known. Here, the authors perform a nested case-control study using data from Hong Kong and find evidence of reduced risk of infection following a longer dosing interval.

This global study shows that short-term exposure to landscape fire sourced PM_2.5 increases hospital admissions for multiple diseases in children, especially those aged 5-9 years and in low-SES areas, highlighting the need for targeted protection.

Oat is an important food crop, but the genetic diversity within the gene pool remains unclear. Here, the authors report the analyses of worldwide diversity and population structure of hexaploid oat, and identify signatures of structural rearrangements within the germplasm collection.

Using well-calibrated statistical methods the authors jointly analyze Undiagnosed Diseases Network genomes, identifying known and novel disease genes. Software is publicly available to support future cross-cohort rare disease discovery efforts.